maqview-0.2.5/0000755000265600020320000000000011540135531012311 5ustar tilleaadminmaqview-0.2.5/Makefile.am0000644000265600020320000000115611101246037014345 0ustar tilleaadminbin_PROGRAMS = zrio maqindex maqview maqindex_socks zlib_src = adler32.c compress.c crc32.c deflate.c gzio.c inffast.c inflate.c \ infback.c inftrees.c trees.c uncompr.c zutil.c generic_src = btree.c maqmap_index.c zrio.c stdhashc.h stdhashc.cc cns_cache.c const.c $(zlib_src) zrio_SOURCES = zrio_main.c $(generic_src) maqindex_SOURCES = maqmap_index_main.c $(generic_src) maqview_SOURCES = read_cache.c view_goto.c view_panel.c gl_gui.c MainFrame.c \ $(generic_src) maqview_LDADD = $(GLLIBS) maqindex_socks_SOURCES = read_cache.c view_goto.c socket_view.c $(generic_src) maqindex_socks_LDADD = $(GLLIBS) maqview-0.2.5/inftrees.c0000644000265600020320000003267410761137604014317 0ustar tilleaadmin/* inftrees.c -- generate Huffman trees for efficient decoding * Copyright (C) 1995-2005 Mark Adler * For conditions of distribution and use, see copyright notice in zlib.h */ #include "zutil.h" #include "inftrees.h" #define MAXBITS 15 const char inflate_copyright[] = " inflate 1.2.3 Copyright 1995-2005 Mark Adler "; /* If you use the zlib library in a product, an acknowledgment is welcome in the documentation of your product. If for some reason you cannot include such an acknowledgment, I would appreciate that you keep this copyright string in the executable of your product. */ /* Build a set of tables to decode the provided canonical Huffman code. The code lengths are lens[0..codes-1]. The result starts at *table, whose indices are 0..2^bits-1. work is a writable array of at least lens shorts, which is used as a work area. type is the type of code to be generated, CODES, LENS, or DISTS. On return, zero is success, -1 is an invalid code, and +1 means that ENOUGH isn't enough. table on return points to the next available entry's address. bits is the requested root table index bits, and on return it is the actual root table index bits. It will differ if the request is greater than the longest code or if it is less than the shortest code. */ int inflate_table(type, lens, codes, table, bits, work) codetype type; unsigned short FAR *lens; unsigned codes; code FAR * FAR *table; unsigned FAR *bits; unsigned short FAR *work; { unsigned len; /* a code's length in bits */ unsigned sym; /* index of code symbols */ unsigned min, max; /* minimum and maximum code lengths */ unsigned root; /* number of index bits for root table */ unsigned curr; /* number of index bits for current table */ unsigned drop; /* code bits to drop for sub-table */ int left; /* number of prefix codes available */ unsigned used; /* code entries in table used */ unsigned huff; /* Huffman code */ unsigned incr; /* for incrementing code, index */ unsigned fill; /* index for replicating entries */ unsigned low; /* low bits for current root entry */ unsigned mask; /* mask for low root bits */ code this; /* table entry for duplication */ code FAR *next; /* next available space in table */ const unsigned short FAR *base; /* base value table to use */ const unsigned short FAR *extra; /* extra bits table to use */ int end; /* use base and extra for symbol > end */ unsigned short count[MAXBITS+1]; /* number of codes of each length */ unsigned short offs[MAXBITS+1]; /* offsets in table for each length */ static const unsigned short lbase[31] = { /* Length codes 257..285 base */ 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 15, 17, 19, 23, 27, 31, 35, 43, 51, 59, 67, 83, 99, 115, 131, 163, 195, 227, 258, 0, 0}; static const unsigned short lext[31] = { /* Length codes 257..285 extra */ 16, 16, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 18, 18, 18, 18, 19, 19, 19, 19, 20, 20, 20, 20, 21, 21, 21, 21, 16, 201, 196}; static const unsigned short dbase[32] = { /* Distance codes 0..29 base */ 1, 2, 3, 4, 5, 7, 9, 13, 17, 25, 33, 49, 65, 97, 129, 193, 257, 385, 513, 769, 1025, 1537, 2049, 3073, 4097, 6145, 8193, 12289, 16385, 24577, 0, 0}; static const unsigned short dext[32] = { /* Distance codes 0..29 extra */ 16, 16, 16, 16, 17, 17, 18, 18, 19, 19, 20, 20, 21, 21, 22, 22, 23, 23, 24, 24, 25, 25, 26, 26, 27, 27, 28, 28, 29, 29, 64, 64}; /* Process a set of code lengths to create a canonical Huffman code. The code lengths are lens[0..codes-1]. Each length corresponds to the symbols 0..codes-1. The Huffman code is generated by first sorting the symbols by length from short to long, and retaining the symbol order for codes with equal lengths. Then the code starts with all zero bits for the first code of the shortest length, and the codes are integer increments for the same length, and zeros are appended as the length increases. For the deflate format, these bits are stored backwards from their more natural integer increment ordering, and so when the decoding tables are built in the large loop below, the integer codes are incremented backwards. This routine assumes, but does not check, that all of the entries in lens[] are in the range 0..MAXBITS. The caller must assure this. 1..MAXBITS is interpreted as that code length. zero means that that symbol does not occur in this code. The codes are sorted by computing a count of codes for each length, creating from that a table of starting indices for each length in the sorted table, and then entering the symbols in order in the sorted table. The sorted table is work[], with that space being provided by the caller. The length counts are used for other purposes as well, i.e. finding the minimum and maximum length codes, determining if there are any codes at all, checking for a valid set of lengths, and looking ahead at length counts to determine sub-table sizes when building the decoding tables. */ /* accumulate lengths for codes (assumes lens[] all in 0..MAXBITS) */ for (len = 0; len <= MAXBITS; len++) count[len] = 0; for (sym = 0; sym < codes; sym++) count[lens[sym]]++; /* bound code lengths, force root to be within code lengths */ root = *bits; for (max = MAXBITS; max >= 1; max--) if (count[max] != 0) break; if (root > max) root = max; if (max == 0) { /* no symbols to code at all */ this.op = (unsigned char)64; /* invalid code marker */ this.bits = (unsigned char)1; this.val = (unsigned short)0; *(*table)++ = this; /* make a table to force an error */ *(*table)++ = this; *bits = 1; return 0; /* no symbols, but wait for decoding to report error */ } for (min = 1; min <= MAXBITS; min++) if (count[min] != 0) break; if (root < min) root = min; /* check for an over-subscribed or incomplete set of lengths */ left = 1; for (len = 1; len <= MAXBITS; len++) { left <<= 1; left -= count[len]; if (left < 0) return -1; /* over-subscribed */ } if (left > 0 && (type == CODES || max != 1)) return -1; /* incomplete set */ /* generate offsets into symbol table for each length for sorting */ offs[1] = 0; for (len = 1; len < MAXBITS; len++) offs[len + 1] = offs[len] + count[len]; /* sort symbols by length, by symbol order within each length */ for (sym = 0; sym < codes; sym++) if (lens[sym] != 0) work[offs[lens[sym]]++] = (unsigned short)sym; /* Create and fill in decoding tables. In this loop, the table being filled is at next and has curr index bits. The code being used is huff with length len. That code is converted to an index by dropping drop bits off of the bottom. For codes where len is less than drop + curr, those top drop + curr - len bits are incremented through all values to fill the table with replicated entries. root is the number of index bits for the root table. When len exceeds root, sub-tables are created pointed to by the root entry with an index of the low root bits of huff. This is saved in low to check for when a new sub-table should be started. drop is zero when the root table is being filled, and drop is root when sub-tables are being filled. When a new sub-table is needed, it is necessary to look ahead in the code lengths to determine what size sub-table is needed. The length counts are used for this, and so count[] is decremented as codes are entered in the tables. used keeps track of how many table entries have been allocated from the provided *table space. It is checked when a LENS table is being made against the space in *table, ENOUGH, minus the maximum space needed by the worst case distance code, MAXD. This should never happen, but the sufficiency of ENOUGH has not been proven exhaustively, hence the check. This assumes that when type == LENS, bits == 9. sym increments through all symbols, and the loop terminates when all codes of length max, i.e. all codes, have been processed. This routine permits incomplete codes, so another loop after this one fills in the rest of the decoding tables with invalid code markers. */ /* set up for code type */ switch (type) { case CODES: base = extra = work; /* dummy value--not used */ end = 19; break; case LENS: base = lbase; base -= 257; extra = lext; extra -= 257; end = 256; break; default: /* DISTS */ base = dbase; extra = dext; end = -1; } /* initialize state for loop */ huff = 0; /* starting code */ sym = 0; /* starting code symbol */ len = min; /* starting code length */ next = *table; /* current table to fill in */ curr = root; /* current table index bits */ drop = 0; /* current bits to drop from code for index */ low = (unsigned)(-1); /* trigger new sub-table when len > root */ used = 1U << root; /* use root table entries */ mask = used - 1; /* mask for comparing low */ /* check available table space */ if (type == LENS && used >= ENOUGH - MAXD) return 1; /* process all codes and make table entries */ for (;;) { /* create table entry */ this.bits = (unsigned char)(len - drop); if ((int)(work[sym]) < end) { this.op = (unsigned char)0; this.val = work[sym]; } else if ((int)(work[sym]) > end) { this.op = (unsigned char)(extra[work[sym]]); this.val = base[work[sym]]; } else { this.op = (unsigned char)(32 + 64); /* end of block */ this.val = 0; } /* replicate for those indices with low len bits equal to huff */ incr = 1U << (len - drop); fill = 1U << curr; min = fill; /* save offset to next table */ do { fill -= incr; next[(huff >> drop) + fill] = this; } while (fill != 0); /* backwards increment the len-bit code huff */ incr = 1U << (len - 1); while (huff & incr) incr >>= 1; if (incr != 0) { huff &= incr - 1; huff += incr; } else huff = 0; /* go to next symbol, update count, len */ sym++; if (--(count[len]) == 0) { if (len == max) break; len = lens[work[sym]]; } /* create new sub-table if needed */ if (len > root && (huff & mask) != low) { /* if first time, transition to sub-tables */ if (drop == 0) drop = root; /* increment past last table */ next += min; /* here min is 1 << curr */ /* determine length of next table */ curr = len - drop; left = (int)(1 << curr); while (curr + drop < max) { left -= count[curr + drop]; if (left <= 0) break; curr++; left <<= 1; } /* check for enough space */ used += 1U << curr; if (type == LENS && used >= ENOUGH - MAXD) return 1; /* point entry in root table to sub-table */ low = huff & mask; (*table)[low].op = (unsigned char)curr; (*table)[low].bits = (unsigned char)root; (*table)[low].val = (unsigned short)(next - *table); } } /* Fill in rest of table for incomplete codes. This loop is similar to the loop above in incrementing huff for table indices. It is assumed that len is equal to curr + drop, so there is no loop needed to increment through high index bits. When the current sub-table is filled, the loop drops back to the root table to fill in any remaining entries there. */ this.op = (unsigned char)64; /* invalid code marker */ this.bits = (unsigned char)(len - drop); this.val = (unsigned short)0; while (huff != 0) { /* when done with sub-table, drop back to root table */ if (drop != 0 && (huff & mask) != low) { drop = 0; len = root; next = *table; this.bits = (unsigned char)len; } /* put invalid code marker in table */ next[huff >> drop] = this; /* backwards increment the len-bit code huff */ incr = 1U << (len - 1); while (huff & incr) incr >>= 1; if (incr != 0) { huff &= incr - 1; huff += incr; } else huff = 0; } /* set return parameters */ *table += used; *bits = root; return 0; } maqview-0.2.5/FUTURES0000644000265600020320000000021410761137603013374 0ustar tilleaadmin 1. Improve configure.ac. The current version is quite clumsy. 2. Improve look&feel of maqview. 3. Incorporate maq consensus into maqview.maqview-0.2.5/inffixed.h0000644000265600020320000001430710761137602014270 0ustar tilleaadmin /* inffixed.h -- table for decoding fixed codes * Generated automatically by makefixed(). */ /* WARNING: this file should *not* be used by applications. It is part of the implementation of the compression library and is subject to change. Applications should only use zlib.h. */ static const code lenfix[512] = { {96,7,0},{0,8,80},{0,8,16},{20,8,115},{18,7,31},{0,8,112},{0,8,48}, {0,9,192},{16,7,10},{0,8,96},{0,8,32},{0,9,160},{0,8,0},{0,8,128}, {0,8,64},{0,9,224},{16,7,6},{0,8,88},{0,8,24},{0,9,144},{19,7,59}, {0,8,120},{0,8,56},{0,9,208},{17,7,17},{0,8,104},{0,8,40},{0,9,176}, {0,8,8},{0,8,136},{0,8,72},{0,9,240},{16,7,4},{0,8,84},{0,8,20}, {21,8,227},{19,7,43},{0,8,116},{0,8,52},{0,9,200},{17,7,13},{0,8,100}, {0,8,36},{0,9,168},{0,8,4},{0,8,132},{0,8,68},{0,9,232},{16,7,8}, {0,8,92},{0,8,28},{0,9,152},{20,7,83},{0,8,124},{0,8,60},{0,9,216}, {18,7,23},{0,8,108},{0,8,44},{0,9,184},{0,8,12},{0,8,140},{0,8,76}, {0,9,248},{16,7,3},{0,8,82},{0,8,18},{21,8,163},{19,7,35},{0,8,114}, {0,8,50},{0,9,196},{17,7,11},{0,8,98},{0,8,34},{0,9,164},{0,8,2}, {0,8,130},{0,8,66},{0,9,228},{16,7,7},{0,8,90},{0,8,26},{0,9,148}, {20,7,67},{0,8,122},{0,8,58},{0,9,212},{18,7,19},{0,8,106},{0,8,42}, {0,9,180},{0,8,10},{0,8,138},{0,8,74},{0,9,244},{16,7,5},{0,8,86}, {0,8,22},{64,8,0},{19,7,51},{0,8,118},{0,8,54},{0,9,204},{17,7,15}, {0,8,102},{0,8,38},{0,9,172},{0,8,6},{0,8,134},{0,8,70},{0,9,236}, {16,7,9},{0,8,94},{0,8,30},{0,9,156},{20,7,99},{0,8,126},{0,8,62}, {0,9,220},{18,7,27},{0,8,110},{0,8,46},{0,9,188},{0,8,14},{0,8,142}, {0,8,78},{0,9,252},{96,7,0},{0,8,81},{0,8,17},{21,8,131},{18,7,31}, {0,8,113},{0,8,49},{0,9,194},{16,7,10},{0,8,97},{0,8,33},{0,9,162}, {0,8,1},{0,8,129},{0,8,65},{0,9,226},{16,7,6},{0,8,89},{0,8,25}, {0,9,146},{19,7,59},{0,8,121},{0,8,57},{0,9,210},{17,7,17},{0,8,105}, {0,8,41},{0,9,178},{0,8,9},{0,8,137},{0,8,73},{0,9,242},{16,7,4}, {0,8,85},{0,8,21},{16,8,258},{19,7,43},{0,8,117},{0,8,53},{0,9,202}, {17,7,13},{0,8,101},{0,8,37},{0,9,170},{0,8,5},{0,8,133},{0,8,69}, {0,9,234},{16,7,8},{0,8,93},{0,8,29},{0,9,154},{20,7,83},{0,8,125}, {0,8,61},{0,9,218},{18,7,23},{0,8,109},{0,8,45},{0,9,186},{0,8,13}, {0,8,141},{0,8,77},{0,9,250},{16,7,3},{0,8,83},{0,8,19},{21,8,195}, {19,7,35},{0,8,115},{0,8,51},{0,9,198},{17,7,11},{0,8,99},{0,8,35}, {0,9,166},{0,8,3},{0,8,131},{0,8,67},{0,9,230},{16,7,7},{0,8,91}, {0,8,27},{0,9,150},{20,7,67},{0,8,123},{0,8,59},{0,9,214},{18,7,19}, {0,8,107},{0,8,43},{0,9,182},{0,8,11},{0,8,139},{0,8,75},{0,9,246}, {16,7,5},{0,8,87},{0,8,23},{64,8,0},{19,7,51},{0,8,119},{0,8,55}, {0,9,206},{17,7,15},{0,8,103},{0,8,39},{0,9,174},{0,8,7},{0,8,135}, {0,8,71},{0,9,238},{16,7,9},{0,8,95},{0,8,31},{0,9,158},{20,7,99}, {0,8,127},{0,8,63},{0,9,222},{18,7,27},{0,8,111},{0,8,47},{0,9,190}, {0,8,15},{0,8,143},{0,8,79},{0,9,254},{96,7,0},{0,8,80},{0,8,16}, {20,8,115},{18,7,31},{0,8,112},{0,8,48},{0,9,193},{16,7,10},{0,8,96}, {0,8,32},{0,9,161},{0,8,0},{0,8,128},{0,8,64},{0,9,225},{16,7,6}, {0,8,88},{0,8,24},{0,9,145},{19,7,59},{0,8,120},{0,8,56},{0,9,209}, {17,7,17},{0,8,104},{0,8,40},{0,9,177},{0,8,8},{0,8,136},{0,8,72}, {0,9,241},{16,7,4},{0,8,84},{0,8,20},{21,8,227},{19,7,43},{0,8,116}, {0,8,52},{0,9,201},{17,7,13},{0,8,100},{0,8,36},{0,9,169},{0,8,4}, {0,8,132},{0,8,68},{0,9,233},{16,7,8},{0,8,92},{0,8,28},{0,9,153}, {20,7,83},{0,8,124},{0,8,60},{0,9,217},{18,7,23},{0,8,108},{0,8,44}, {0,9,185},{0,8,12},{0,8,140},{0,8,76},{0,9,249},{16,7,3},{0,8,82}, {0,8,18},{21,8,163},{19,7,35},{0,8,114},{0,8,50},{0,9,197},{17,7,11}, {0,8,98},{0,8,34},{0,9,165},{0,8,2},{0,8,130},{0,8,66},{0,9,229}, {16,7,7},{0,8,90},{0,8,26},{0,9,149},{20,7,67},{0,8,122},{0,8,58}, {0,9,213},{18,7,19},{0,8,106},{0,8,42},{0,9,181},{0,8,10},{0,8,138}, {0,8,74},{0,9,245},{16,7,5},{0,8,86},{0,8,22},{64,8,0},{19,7,51}, {0,8,118},{0,8,54},{0,9,205},{17,7,15},{0,8,102},{0,8,38},{0,9,173}, {0,8,6},{0,8,134},{0,8,70},{0,9,237},{16,7,9},{0,8,94},{0,8,30}, {0,9,157},{20,7,99},{0,8,126},{0,8,62},{0,9,221},{18,7,27},{0,8,110}, {0,8,46},{0,9,189},{0,8,14},{0,8,142},{0,8,78},{0,9,253},{96,7,0}, {0,8,81},{0,8,17},{21,8,131},{18,7,31},{0,8,113},{0,8,49},{0,9,195}, {16,7,10},{0,8,97},{0,8,33},{0,9,163},{0,8,1},{0,8,129},{0,8,65}, {0,9,227},{16,7,6},{0,8,89},{0,8,25},{0,9,147},{19,7,59},{0,8,121}, {0,8,57},{0,9,211},{17,7,17},{0,8,105},{0,8,41},{0,9,179},{0,8,9}, {0,8,137},{0,8,73},{0,9,243},{16,7,4},{0,8,85},{0,8,21},{16,8,258}, {19,7,43},{0,8,117},{0,8,53},{0,9,203},{17,7,13},{0,8,101},{0,8,37}, {0,9,171},{0,8,5},{0,8,133},{0,8,69},{0,9,235},{16,7,8},{0,8,93}, {0,8,29},{0,9,155},{20,7,83},{0,8,125},{0,8,61},{0,9,219},{18,7,23}, {0,8,109},{0,8,45},{0,9,187},{0,8,13},{0,8,141},{0,8,77},{0,9,251}, {16,7,3},{0,8,83},{0,8,19},{21,8,195},{19,7,35},{0,8,115},{0,8,51}, {0,9,199},{17,7,11},{0,8,99},{0,8,35},{0,9,167},{0,8,3},{0,8,131}, {0,8,67},{0,9,231},{16,7,7},{0,8,91},{0,8,27},{0,9,151},{20,7,67}, {0,8,123},{0,8,59},{0,9,215},{18,7,19},{0,8,107},{0,8,43},{0,9,183}, {0,8,11},{0,8,139},{0,8,75},{0,9,247},{16,7,5},{0,8,87},{0,8,23}, {64,8,0},{19,7,51},{0,8,119},{0,8,55},{0,9,207},{17,7,15},{0,8,103}, {0,8,39},{0,9,175},{0,8,7},{0,8,135},{0,8,71},{0,9,239},{16,7,9}, {0,8,95},{0,8,31},{0,9,159},{20,7,99},{0,8,127},{0,8,63},{0,9,223}, {18,7,27},{0,8,111},{0,8,47},{0,9,191},{0,8,15},{0,8,143},{0,8,79}, {0,9,255} }; static const code distfix[32] = { {16,5,1},{23,5,257},{19,5,17},{27,5,4097},{17,5,5},{25,5,1025}, {21,5,65},{29,5,16385},{16,5,3},{24,5,513},{20,5,33},{28,5,8193}, {18,5,9},{26,5,2049},{22,5,129},{64,5,0},{16,5,2},{23,5,385}, {19,5,25},{27,5,6145},{17,5,7},{25,5,1537},{21,5,97},{29,5,24577}, {16,5,4},{24,5,769},{20,5,49},{28,5,12289},{18,5,13},{26,5,3073}, {22,5,193},{64,5,0} }; maqview-0.2.5/stdhashc.cc0000644000265600020320000000425510761137603014435 0ustar tilleaadmin#include #include "stdhash.hh" #include "stdhashc.h" // hashci typedef hash_map_char hashci_cpp_t; hashci_t *hci_init() { hashci_t *h = (hashci_t*)malloc(sizeof(hashci_t)); h->ptr = new hashci_cpp_t; return h; } void hci_destroy(hashci_t *h) { delete (hashci_cpp_t*)h->ptr; free(h); } int hci_put(hashci_t *h, const char *key, int value) { return ((hashci_cpp_t*)h->ptr)->insert(key, value); } int hci_del(hashci_t *h, const char *key) { return ((hashci_cpp_t*)h->ptr)->erase(key); } int hci_get(const hashci_t *h, const char *key, int *value) { return ((hashci_cpp_t*)h->ptr)->find(key, value); } u_int32_t hci_size(hashci_t *h) { return ((hashci_cpp_t*)h->ptr)->size(); } u_int32_t hci_capacity(hashci_t *h) { return ((hashci_cpp_t*)h->ptr)->capacity(); } int hci_resize(hashci_t *h, u_int32_t new_size) { return ((hashci_cpp_t*)h->ptr)->resize(new_size); } void hci_traverse(hashci_t *h, hashci_f func) { hashci_cpp_t *hash = (hashci_cpp_t*)h->ptr; hashci_cpp_t::iterator iter; for (iter = hash->begin(); iter != hash->end(); ++iter) { if (iter.isfilled()) { func(iter.key(), iter.value()); } } } // hashii typedef hash_map_misc hashii_cpp_t; hashii_t *hii_init() { hashii_t *h = (hashii_t*)malloc(sizeof(hashii_t)); h->ptr = new hashii_cpp_t; return h; } void hii_destroy(hashii_t *h) { delete (hashii_cpp_t*)h->ptr; free(h); } int hii_put(hashii_t *h, u_int32_t key, int value) { return ((hashii_cpp_t*)h->ptr)->insert(key, value); } int hii_del(hashii_t *h, u_int32_t key) { return ((hashii_cpp_t*)h->ptr)->erase(key); } int hii_get(const hashii_t *h, u_int32_t key, int *value) { return ((hashii_cpp_t*)h->ptr)->find(key, value); } u_int32_t hii_size(hashii_t *h) { return ((hashii_cpp_t*)h->ptr)->size(); } u_int32_t hii_capacity(hashii_t *h) { return ((hashii_cpp_t*)h->ptr)->capacity(); } int hii_resize(hashii_t *h, u_int32_t new_size) { return ((hashii_cpp_t*)h->ptr)->resize(new_size); } void hii_traverse(hashii_t *h, hashii_f func) { hashii_cpp_t *hash = (hashii_cpp_t*)h->ptr; hashii_cpp_t::iterator iter; for (iter = hash->begin(); iter != hash->end(); ++iter) { if (iter.isfilled()) { func(iter.key(), iter.value()); } } } maqview-0.2.5/uncompr.c0000644000265600020320000000404710761137604014154 0ustar tilleaadmin/* uncompr.c -- decompress a memory buffer * Copyright (C) 1995-2003 Jean-loup Gailly. * For conditions of distribution and use, see copyright notice in zlib.h */ /* @(#) $Id$ */ #define ZLIB_INTERNAL #include "zlib.h" /* =========================================================================== Decompresses the source buffer into the destination buffer. sourceLen is the byte length of the source buffer. Upon entry, destLen is the total size of the destination buffer, which must be large enough to hold the entire uncompressed data. (The size of the uncompressed data must have been saved previously by the compressor and transmitted to the decompressor by some mechanism outside the scope of this compression library.) Upon exit, destLen is the actual size of the compressed buffer. This function can be used to decompress a whole file at once if the input file is mmap'ed. uncompress returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_BUF_ERROR if there was not enough room in the output buffer, or Z_DATA_ERROR if the input data was corrupted. */ int ZEXPORT uncompress (dest, destLen, source, sourceLen) Bytef *dest; uLongf *destLen; const Bytef *source; uLong sourceLen; { z_stream stream; int err; stream.next_in = (Bytef*)source; stream.avail_in = (uInt)sourceLen; /* Check for source > 64K on 16-bit machine: */ if ((uLong)stream.avail_in != sourceLen) return Z_BUF_ERROR; stream.next_out = dest; stream.avail_out = (uInt)*destLen; if ((uLong)stream.avail_out != *destLen) return Z_BUF_ERROR; stream.zalloc = (alloc_func)0; stream.zfree = (free_func)0; err = inflateInit(&stream); if (err != Z_OK) return err; err = inflate(&stream, Z_FINISH); if (err != Z_STREAM_END) { inflateEnd(&stream); if (err == Z_NEED_DICT || (err == Z_BUF_ERROR && stream.avail_in == 0)) return Z_DATA_ERROR; return err; } *destLen = stream.total_out; err = inflateEnd(&stream); return err; } maqview-0.2.5/configure.ac0000644000265600020320000000225111117505274014604 0ustar tilleaadminAC_INIT(MAQVIEW, 0.2.5) AM_CONFIG_HEADER(config.h) AM_INIT_AUTOMAKE AC_CANONICAL_HOST AC_PROG_CC AC_PROG_CXX AC_PROG_INSTALL AC_STDC_HEADERS is_static=0 case ${prefix} in NONE);; *) is_static=1 AC_MSG_WARN([Library libglut will be statically linked.]) LDFLAGS="-L${prefix}/lib" CPPFLAGS="-I${prefix}/include";; esac # set CFLAGS and LDFLAGS true_CFLAGS="-g -O2 -Wall -W -DMAQ_LONGREADS" case "${host_os}" in darwin*) GLLIBS="-framework OpenGL -framework GLUT" AC_CHECK_HEADER(GLUT/glut.h, [isgl=1], [isgl=0]);; linux*) AC_CHECK_HEADER(GL/glut.h, [isgl=1], [isgl=0]) case "${host_cpu}" in i?86) CPPFLAGS="$CPPFLAGS -D_FILE_OFFSET_BITS=64";; esac AC_CHECK_LIB([glut], [glutMouseWheelFunc], [CPPFLAGS="$CPPFLAGS -DHAVE_FREEGLUT"]) AC_ARG_ENABLE(static, [ --enable-static statically link GLUT (Linux Only)], [is_static=1]) case $is_static in 1) GLLIBS="-Wl,-Bstatic -lglut -Wl,-Bdynamic -lGL -lGLU -lm";; 0) GLLIBS="-lGL -lglut -lm";; esac AC_SUBST([GLLIBS]);; # *) AC_MSG_ERROR([OS is not supported]);; esac AM_CONDITIONAL([HAVE_GL], [test "$isgl" = 1]) CFLAGS=$true_CFLAGS AC_CONFIG_FILES([Makefile]) AC_OUTPUT maqview-0.2.5/COPYING0000644000265600020320000004313110761137603013354 0ustar tilleaadmin GNU GENERAL PUBLIC LICENSE Version 2, June 1991 Copyright (C) 1989, 1991 Free Software Foundation, Inc. 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Library General Public License instead.) You can apply it to your programs, too. When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things. To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it. For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software. Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations. Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all. The precise terms and conditions for copying, distribution and modification follow. GNU GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you". Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does. 1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program. You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. 2. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions: a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change. b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License. c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.) These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it. Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program. In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License. 3. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following: a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, c) Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.) The source code for a work means the preferred form of the work for making modifications to it. For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to control compilation and installation of the executable. However, as a special exception, the source code distributed need not include anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable. If distribution of executable or object code is made by offering access to copy from a designated place, then offering equivalent access to copy the source code from the same place counts as distribution of the source code, even though third parties are not compelled to copy the source along with the object code. 4. You may not copy, modify, sublicense, or distribute the Program except as expressly provided under this License. Any attempt otherwise to copy, modify, sublicense or distribute the Program is void, and will automatically terminate your rights under this License. However, parties who have received copies, or rights, from you under this License will not have their licenses terminated so long as such parties remain in full compliance. 5. You are not required to accept this License, since you have not signed it. However, nothing else grants you permission to modify or distribute the Program or its derivative works. These actions are prohibited by law if you do not accept this License. Therefore, by modifying or distributing the Program (or any work based on the Program), you indicate your acceptance of this License to do so, and all its terms and conditions for copying, distributing or modifying the Program or works based on it. 6. Each time you redistribute the Program (or any work based on the Program), the recipient automatically receives a license from the original licensor to copy, distribute or modify the Program subject to these terms and conditions. You may not impose any further restrictions on the recipients' exercise of the rights granted herein. You are not responsible for enforcing compliance by third parties to this License. 7. If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to patent issues), conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot distribute so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not distribute the Program at all. For example, if a patent license would not permit royalty-free redistribution of the Program by all those who receive copies directly or indirectly through you, then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Program. If any portion of this section is held invalid or unenforceable under any particular circumstance, the balance of the section is intended to apply and the section as a whole is intended to apply in other circumstances. It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system, which is implemented by public license practices. Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice. This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License. 8. If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License. 9. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation. 10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. NO WARRANTY 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. Copyright (C) This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Also add information on how to contact you by electronic and paper mail. If the program is interactive, make it output a short notice like this when it starts in an interactive mode: Gnomovision version 69, Copyright (C) year name of author Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, the commands you use may be called something other than `show w' and `show c'; they could even be mouse-clicks or menu items--whatever suits your program. You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the program, if necessary. Here is a sample; alter the names: Yoyodyne, Inc., hereby disclaims all copyright interest in the program `Gnomovision' (which makes passes at compilers) written by James Hacker. , 1 April 1989 Ty Coon, President of Vice This General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Library General Public License instead of this License. maqview-0.2.5/maqview.pod0000644000265600020320000001067710761137602014506 0ustar tilleaadmin=head1 NAME Maqview - Maq alignment indexer and viewer =head1 SYNOPSIS B B<-i>|B<-v>|B<-b> [B<-c> F] F [I[:I[-I]] [...]] B [B<-c> F] I =head1 DESCRIPTION B is a set of programs that achieves fast random access to the alignment file generated by `B map', and displays the alignment with a nice GUI (Graphical User Interface). It is highly efficient in speed, memory and disk usage. B is based on OpenGL and is known to work on both Mac OS X and Linux. Porting to Windows is in principle easy. =head2 B B B<-i>|B<-v>|B<-b> [B<-c> F] F [I[:I[-I]] [...]] =over 9 =item B<-i> Index the alignment file =item B<-v> Print the alignment in the specified region in the `maq mapview' format =item B<-b> Dump the alignment in the specified region in the binary .map format =item B<-c> F Index the Maq consensus file for viewing in maqview at the same time =back Program B indexes a maq alignment file F or quickly retrieves all the reads in one or multiple regions. One of B<-i>, B<-v> and B<-b> must be used. For B<-v> or B<-b>, at least one region like `chrX', `chrX:1000' or `chrX:1,000-2,000' must be specified. Multiple regions are allowed. =head2 B B [B<-c> F] I =over 9 =item B<-c> F The Maq consensus file =back Program B displays the read alignment in a graphical window. When F is specified, the top sequence is the reference, followed by the Maq consensus sequence; otherwise, the majority-rule consensus will be calculated. Maqview has two views: sequence view and box view. In the sequence view, read sequences will be printed on the screen. Darker bases indicate lower base qualities and red ones show the differences in comparison to the reference if F is speficied or to the majority-rule consensus if not. In the box view, different types of nucleotides are represented as colour boxes with green for A, cyan for C, orange for G, red for T and dark gray for N. The saturation of colours indicates the base qualities and the thickness lines of reads shows the mapping qualities of read alignments. Zooming in/out is supported only in the box view. In both views, the status bar at the bottom of the window will show some information about the key touches, and read names and base qualities pointed by the mouse. Navigating the alignment is accomplished by vaious key bindings. =over 2 =item Key bindings: ? Display help Exit Sequence view Box view p Switch to the previous reference sequence n Switch to the next reference sequence r Refresh Move to the position pointed by h / Move left by one base l / Move right by one base k / Move up by one line j / Move down by one line > Move to the next read < Move to the previous read g / Move to the begining of the current reference G / Move to the end of the current reference u / Move left by one page / Move right by one page Move by 100 bases Move by 1000 bases + Add a new view - Remove the current view Toggle on/off right auto-scrolling ^b Toggle on/off left auto-scrolling + Zoom in - Zoom out 0 Zoom to the default scale q Toggle show/hide mapping qualities e Toggle display SE/PE mapping qualities o Open a new alignment file =item Enter an integer and then press to jump to the required position. =item Enter an integer and then press a key other than to speed up scrolling by the specified factor. =item Left click and drag the yellow cross in the square to move along the sequence. Right click the reference to highlight a column. =back =head1 LICENSE GNU General Public License (GPL) =head1 AVAILABILITY L =head1 AUTHORS Jue Ruan for writing and maintaining the whole software. Heng Li for testing the program and drafting the documentations. Mengyao Zhao for designing the color schemes. =cut maqview-0.2.5/zutil.h0000644000265600020320000001531310761137603013642 0ustar tilleaadmin/* zutil.h -- internal interface and configuration of the compression library * Copyright (C) 1995-2005 Jean-loup Gailly. * For conditions of distribution and use, see copyright notice in zlib.h */ /* WARNING: this file should *not* be used by applications. It is part of the implementation of the compression library and is subject to change. Applications should only use zlib.h. */ /* @(#) $Id$ */ #ifndef ZUTIL_H #define ZUTIL_H #define ZLIB_INTERNAL #include "zlib.h" #ifdef STDC # ifndef _WIN32_WCE # include # endif # include # include #endif #ifdef NO_ERRNO_H # ifdef _WIN32_WCE /* The Microsoft C Run-Time Library for Windows CE doesn't have * errno. We define it as a global variable to simplify porting. * Its value is always 0 and should not be used. We rename it to * avoid conflict with other libraries that use the same workaround. */ # define errno z_errno # endif extern int errno; #else # ifndef _WIN32_WCE # include # endif #endif #ifndef local # define local static #endif /* compile with -Dlocal if your debugger can't find static symbols */ typedef unsigned char uch; typedef uch FAR uchf; typedef unsigned short ush; typedef ush FAR ushf; typedef unsigned long ulg; extern const char * const z_errmsg[10]; /* indexed by 2-zlib_error */ /* (size given to avoid silly warnings with Visual C++) */ #define ERR_MSG(err) z_errmsg[Z_NEED_DICT-(err)] #define ERR_RETURN(strm,err) \ return (strm->msg = (char*)ERR_MSG(err), (err)) /* To be used only when the state is known to be valid */ /* common constants */ #ifndef DEF_WBITS # define DEF_WBITS MAX_WBITS #endif /* default windowBits for decompression. MAX_WBITS is for compression only */ #if MAX_MEM_LEVEL >= 8 # define DEF_MEM_LEVEL 8 #else # define DEF_MEM_LEVEL MAX_MEM_LEVEL #endif /* default memLevel */ #define STORED_BLOCK 0 #define STATIC_TREES 1 #define DYN_TREES 2 /* The three kinds of block type */ #define MIN_MATCH 3 #define MAX_MATCH 258 /* The minimum and maximum match lengths */ #define PRESET_DICT 0x20 /* preset dictionary flag in zlib header */ /* target dependencies */ #if defined(MSDOS) || (defined(WINDOWS) && !defined(WIN32)) # define OS_CODE 0x00 # if defined(__TURBOC__) || defined(__BORLANDC__) # if(__STDC__ == 1) && (defined(__LARGE__) || defined(__COMPACT__)) /* Allow compilation with ANSI keywords only enabled */ void _Cdecl farfree( void *block ); void *_Cdecl farmalloc( unsigned long nbytes ); # else # include # endif # else /* MSC or DJGPP */ # include # endif #endif #ifdef AMIGA # define OS_CODE 0x01 #endif #if defined(VAXC) || defined(VMS) # define OS_CODE 0x02 # define F_OPEN(name, mode) \ fopen((name), (mode), "mbc=60", "ctx=stm", "rfm=fix", "mrs=512") #endif #if defined(ATARI) || defined(atarist) # define OS_CODE 0x05 #endif #ifdef OS2 # define OS_CODE 0x06 # ifdef M_I86 #include # endif #endif #if defined(MACOS) || defined(TARGET_OS_MAC) # define OS_CODE 0x07 # if defined(__MWERKS__) && __dest_os != __be_os && __dest_os != __win32_os # include /* for fdopen */ # else # ifndef fdopen # define fdopen(fd,mode) NULL /* No fdopen() */ # endif # endif #endif #ifdef TOPS20 # define OS_CODE 0x0a #endif #ifdef WIN32 # ifndef __CYGWIN__ /* Cygwin is Unix, not Win32 */ # define OS_CODE 0x0b # endif #endif #ifdef __50SERIES /* Prime/PRIMOS */ # define OS_CODE 0x0f #endif #if defined(_BEOS_) || defined(RISCOS) # define fdopen(fd,mode) NULL /* No fdopen() */ #endif #if (defined(_MSC_VER) && (_MSC_VER > 600)) # if defined(_WIN32_WCE) # define fdopen(fd,mode) NULL /* No fdopen() */ # ifndef _PTRDIFF_T_DEFINED typedef int ptrdiff_t; # define _PTRDIFF_T_DEFINED # endif # else # define fdopen(fd,type) _fdopen(fd,type) # endif #endif /* common defaults */ #ifndef OS_CODE # define OS_CODE 0x03 /* assume Unix */ #endif #ifndef F_OPEN # define F_OPEN(name, mode) fopen((name), (mode)) #endif /* functions */ #if defined(STDC99) || (defined(__TURBOC__) && __TURBOC__ >= 0x550) # ifndef HAVE_VSNPRINTF # define HAVE_VSNPRINTF # endif #endif #if defined(__CYGWIN__) # ifndef HAVE_VSNPRINTF # define HAVE_VSNPRINTF # endif #endif #ifndef HAVE_VSNPRINTF # ifdef MSDOS /* vsnprintf may exist on some MS-DOS compilers (DJGPP?), but for now we just assume it doesn't. */ # define NO_vsnprintf # endif # ifdef __TURBOC__ # define NO_vsnprintf # endif # ifdef WIN32 /* In Win32, vsnprintf is available as the "non-ANSI" _vsnprintf. */ # if !defined(vsnprintf) && !defined(NO_vsnprintf) # define vsnprintf _vsnprintf # endif # endif # ifdef __SASC # define NO_vsnprintf # endif #endif #ifdef VMS # define NO_vsnprintf #endif #if defined(pyr) # define NO_MEMCPY #endif #if defined(SMALL_MEDIUM) && !defined(_MSC_VER) && !defined(__SC__) /* Use our own functions for small and medium model with MSC <= 5.0. * You may have to use the same strategy for Borland C (untested). * The __SC__ check is for Symantec. */ # define NO_MEMCPY #endif #if defined(STDC) && !defined(HAVE_MEMCPY) && !defined(NO_MEMCPY) # define HAVE_MEMCPY #endif #ifdef HAVE_MEMCPY # ifdef SMALL_MEDIUM /* MSDOS small or medium model */ # define zmemcpy _fmemcpy # define zmemcmp _fmemcmp # define zmemzero(dest, len) _fmemset(dest, 0, len) # else # define zmemcpy memcpy # define zmemcmp memcmp # define zmemzero(dest, len) memset(dest, 0, len) # endif #else extern void zmemcpy OF((Bytef* dest, const Bytef* source, uInt len)); extern int zmemcmp OF((const Bytef* s1, const Bytef* s2, uInt len)); extern void zmemzero OF((Bytef* dest, uInt len)); #endif /* Diagnostic functions */ #ifdef DEBUG # include extern int z_verbose; extern void z_error OF((char *m)); # define Assert(cond,msg) {if(!(cond)) z_error(msg);} # define Trace(x) {if (z_verbose>=0) fprintf x ;} # define Tracev(x) {if (z_verbose>0) fprintf x ;} # define Tracevv(x) {if (z_verbose>1) fprintf x ;} # define Tracec(c,x) {if (z_verbose>0 && (c)) fprintf x ;} # define Tracecv(c,x) {if (z_verbose>1 && (c)) fprintf x ;} #else # define Assert(cond,msg) # define Trace(x) # define Tracev(x) # define Tracevv(x) # define Tracec(c,x) # define Tracecv(c,x) #endif voidpf zcalloc OF((voidpf opaque, unsigned items, unsigned size)); void zcfree OF((voidpf opaque, voidpf ptr)); #define ZALLOC(strm, items, size) \ (*((strm)->zalloc))((strm)->opaque, (items), (size)) #define ZFREE(strm, addr) (*((strm)->zfree))((strm)->opaque, (voidpf)(addr)) #define TRY_FREE(s, p) {if (p) ZFREE(s, p);} #endif /* ZUTIL_H */ maqview-0.2.5/inflate.c0000644000265600020320000021551611075522732014117 0ustar tilleaadmin/* inflate.c -- zlib decompression * Copyright (C) 1995-2005 Mark Adler * For conditions of distribution and use, see copyright notice in zlib.h */ /* * Change history: * * 1.2.beta0 24 Nov 2002 * - First version -- complete rewrite of inflate to simplify code, avoid * creation of window when not needed, minimize use of window when it is * needed, make inffast.c even faster, implement gzip decoding, and to * improve code readability and style over the previous zlib inflate code * * 1.2.beta1 25 Nov 2002 * - Use pointers for available input and output checking in inffast.c * - Remove input and output counters in inffast.c * - Change inffast.c entry and loop from avail_in >= 7 to >= 6 * - Remove unnecessary second byte pull from length extra in inffast.c * - Unroll direct copy to three copies per loop in inffast.c * * 1.2.beta2 4 Dec 2002 * - Change external routine names to reduce potential conflicts * - Correct filename to inffixed.h for fixed tables in inflate.c * - Make hbuf[] unsigned char to match parameter type in inflate.c * - Change strm->next_out[-state->offset] to *(strm->next_out - state->offset) * to avoid negation problem on Alphas (64 bit) in inflate.c * * 1.2.beta3 22 Dec 2002 * - Add comments on state->bits assertion in inffast.c * - Add comments on op field in inftrees.h * - Fix bug in reuse of allocated window after inflateReset() * - Remove bit fields--back to byte structure for speed * - Remove distance extra == 0 check in inflate_fast()--only helps for lengths * - Change post-increments to pre-increments in inflate_fast(), PPC biased? * - Add compile time option, POSTINC, to use post-increments instead (Intel?) * - Make MATCH copy in inflate() much faster for when inflate_fast() not used * - Use local copies of stream next and avail values, as well as local bit * buffer and bit count in inflate()--for speed when inflate_fast() not used * * 1.2.beta4 1 Jan 2003 * - Split ptr - 257 statements in inflate_table() to avoid compiler warnings * - Move a comment on output buffer sizes from inffast.c to inflate.c * - Add comments in inffast.c to introduce the inflate_fast() routine * - Rearrange window copies in inflate_fast() for speed and simplification * - Unroll last copy for window match in inflate_fast() * - Use local copies of window variables in inflate_fast() for speed * - Pull out common write == 0 case for speed in inflate_fast() * - Make op and len in inflate_fast() unsigned for consistency * - Add FAR to lcode and dcode declarations in inflate_fast() * - Simplified bad distance check in inflate_fast() * - Added inflateBackInit(), inflateBack(), and inflateBackEnd() in new * source file infback.c to provide a call-back interface to inflate for * programs like gzip and unzip -- uses window as output buffer to avoid * window copying * * 1.2.beta5 1 Jan 2003 * - Improved inflateBack() interface to allow the caller to provide initial * input in strm. * - Fixed stored blocks bug in inflateBack() * * 1.2.beta6 4 Jan 2003 * - Added comments in inffast.c on effectiveness of POSTINC * - Typecasting all around to reduce compiler warnings * - Changed loops from while (1) or do {} while (1) to for (;;), again to * make compilers happy * - Changed type of window in inflateBackInit() to unsigned char * * * 1.2.beta7 27 Jan 2003 * - Changed many types to unsigned or unsigned short to avoid warnings * - Added inflateCopy() function * * 1.2.0 9 Mar 2003 * - Changed inflateBack() interface to provide separate opaque descriptors * for the in() and out() functions * - Changed inflateBack() argument and in_func typedef to swap the length * and buffer address return values for the input function * - Check next_in and next_out for Z_NULL on entry to inflate() * * The history for versions after 1.2.0 are in ChangeLog in zlib distribution. */ #include "zutil.h" #include "inftrees.h" #include "inflate.h" #include "inffast.h" #ifdef MAKEFIXED # ifndef BUILDFIXED # define BUILDFIXED # endif #endif /* function prototypes */ local void fixedtables OF((struct inflate_state FAR *state)); local int updatewindow OF((z_streamp strm, unsigned out)); #ifdef BUILDFIXED void makefixed OF((void)); #endif local unsigned syncsearch OF((unsigned FAR *have, unsigned char FAR *buf, unsigned len)); int ZEXPORT inflateReset(strm) z_streamp strm; { struct inflate_state FAR *state; if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR; state = (struct inflate_state FAR *)strm->state; strm->total_in = strm->total_out = state->total = 0; strm->msg = Z_NULL; strm->adler = 1; /* to support ill-conceived Java test suite */ state->mode = HEAD; state->last = 0; state->havedict = 0; state->dmax = 32768U; state->max_window_dist = 0; state->dist_window_tail = 0; state->dist_window = (unsigned short*)realloc(state->dist_window, state->dmax * sizeof(unsigned short)); memset(state->dist_window, 0, state->dmax * sizeof(unsigned short)); state->head = Z_NULL; state->wsize = 0; state->whave = 0; state->write = 0; state->hold = 0; state->bits = 0; state->lencode = state->distcode = state->next = state->codes; Tracev((stderr, "inflate: reset\n")); return Z_OK; } int ZEXPORT inflatePrime(strm, bits, value) z_streamp strm; int bits; int value; { struct inflate_state FAR *state; if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR; state = (struct inflate_state FAR *)strm->state; if (bits > 16 || state->bits + bits > 32) return Z_STREAM_ERROR; value &= (1L << bits) - 1; state->hold += value << state->bits; state->bits += bits; return Z_OK; } int ZEXPORT inflateInit2_(strm, windowBits, version, stream_size) z_streamp strm; int windowBits; const char *version; int stream_size; { struct inflate_state FAR *state; if (version == Z_NULL || version[0] != ZLIB_VERSION[0] || stream_size != (int)(sizeof(z_stream))) return Z_VERSION_ERROR; if (strm == Z_NULL) return Z_STREAM_ERROR; strm->msg = Z_NULL; /* in case we return an error */ if (strm->zalloc == (alloc_func)0) { strm->zalloc = zcalloc; strm->opaque = (voidpf)0; } if (strm->zfree == (free_func)0) strm->zfree = zcfree; state = (struct inflate_state FAR *) ZALLOC(strm, 1, sizeof(struct inflate_state)); if (state == Z_NULL) return Z_MEM_ERROR; Tracev((stderr, "inflate: allocated\n")); strm->state = (struct internal_state FAR *)state; if (windowBits < 0) { state->wrap = 0; windowBits = -windowBits; } else { state->wrap = (windowBits >> 4) + 1; #ifdef GUNZIP if (windowBits < 48) windowBits &= 15; #endif } if (windowBits < 8 || windowBits > 15) { ZFREE(strm, state); strm->state = Z_NULL; return Z_STREAM_ERROR; } state->wbits = (unsigned)windowBits; state->window = Z_NULL; state->dist_window = NULL; return inflateReset(strm); } int ZEXPORT inflateInit_(strm, version, stream_size) z_streamp strm; const char *version; int stream_size; { return inflateInit2_(strm, DEF_WBITS, version, stream_size); } /* Return state with length and distance decoding tables and index sizes set to fixed code decoding. Normally this returns fixed tables from inffixed.h. If BUILDFIXED is defined, then instead this routine builds the tables the first time it's called, and returns those tables the first time and thereafter. This reduces the size of the code by about 2K bytes, in exchange for a little execution time. However, BUILDFIXED should not be used for threaded applications, since the rewriting of the tables and virgin may not be thread-safe. */ local void fixedtables(state) struct inflate_state FAR *state; { #ifdef BUILDFIXED static int virgin = 1; static code *lenfix, *distfix; static code fixed[544]; /* build fixed huffman tables if first call (may not be thread safe) */ if (virgin) { unsigned sym, bits; static code *next; /* literal/length table */ sym = 0; while (sym < 144) state->lens[sym++] = 8; while (sym < 256) state->lens[sym++] = 9; while (sym < 280) state->lens[sym++] = 7; while (sym < 288) state->lens[sym++] = 8; next = fixed; lenfix = next; bits = 9; inflate_table(LENS, state->lens, 288, &(next), &(bits), state->work); /* distance table */ sym = 0; while (sym < 32) state->lens[sym++] = 5; distfix = next; bits = 5; inflate_table(DISTS, state->lens, 32, &(next), &(bits), state->work); /* do this just once */ virgin = 0; } #else /* !BUILDFIXED */ # include "inffixed.h" #endif /* BUILDFIXED */ state->lencode = lenfix; state->lenbits = 9; state->distcode = distfix; state->distbits = 5; } #ifdef MAKEFIXED #include /* Write out the inffixed.h that is #include'd above. Defining MAKEFIXED also defines BUILDFIXED, so the tables are built on the fly. makefixed() writes those tables to stdout, which would be piped to inffixed.h. A small program can simply call makefixed to do this: void makefixed(void); int main(void) { makefixed(); return 0; } Then that can be linked with zlib built with MAKEFIXED defined and run: a.out > inffixed.h */ void makefixed() { unsigned low, size; struct inflate_state state; fixedtables(&state); puts(" /* inffixed.h -- table for decoding fixed codes"); puts(" * Generated automatically by makefixed()."); puts(" */"); puts(""); puts(" /* WARNING: this file should *not* be used by applications."); puts(" It is part of the implementation of this library and is"); puts(" subject to change. Applications should only use zlib.h."); puts(" */"); puts(""); size = 1U << 9; printf(" static const code lenfix[%u] = {", size); low = 0; for (;;) { if ((low % 7) == 0) printf("\n "); printf("{%u,%u,%d}", state.lencode[low].op, state.lencode[low].bits, state.lencode[low].val); if (++low == size) break; putchar(','); } puts("\n };"); size = 1U << 5; printf("\n static const code distfix[%u] = {", size); low = 0; for (;;) { if ((low % 6) == 0) printf("\n "); printf("{%u,%u,%d}", state.distcode[low].op, state.distcode[low].bits, state.distcode[low].val); if (++low == size) break; putchar(','); } puts("\n };"); } #endif /* MAKEFIXED */ /* Update the window with the last wsize (normally 32K) bytes written before returning. If window does not exist yet, create it. This is only called when a window is already in use, or when output has been written during this inflate call, but the end of the deflate stream has not been reached yet. It is also called to create a window for dictionary data when a dictionary is loaded. Providing output buffers larger than 32K to inflate() should provide a speed advantage, since only the last 32K of output is copied to the sliding window upon return from inflate(), and since all distances after the first 32K of output will fall in the output data, making match copies simpler and faster. The advantage may be dependent on the size of the processor's data caches. */ local int updatewindow(strm, out) z_streamp strm; unsigned out; { struct inflate_state FAR *state; unsigned copy, dist; state = (struct inflate_state FAR *)strm->state; /* if it hasn't been done already, allocate space for the window */ if (state->window == Z_NULL) { state->window = (unsigned char FAR *) ZALLOC(strm, 1U << state->wbits, sizeof(unsigned char)); if (state->window == Z_NULL) return 1; } /* if window not in use yet, initialize */ if (state->wsize == 0) { state->wsize = 1U << state->wbits; state->write = 0; state->whave = 0; } /* copy state->wsize or less output bytes into the circular window */ copy = out - strm->avail_out; if (copy >= state->wsize) { zmemcpy(state->window, strm->next_out - state->wsize, state->wsize); state->write = 0; state->whave = state->wsize; } else { dist = state->wsize - state->write; if (dist > copy) dist = copy; zmemcpy(state->window + state->write, strm->next_out - copy, dist); copy -= dist; if (copy) { zmemcpy(state->window, strm->next_out - copy, copy); state->write = copy; state->whave = state->wsize; } else { state->write += dist; if (state->write == state->wsize) state->write = 0; if (state->whave < state->wsize) state->whave += dist; } } return 0; } /* Macros for inflate(): */ /* check function to use adler32() for zlib or crc32() for gzip */ #ifdef GUNZIP # define UPDATE(check, buf, len) \ (state->flags ? crc32(check, buf, len) : adler32(check, buf, len)) #else # define UPDATE(check, buf, len) adler32(check, buf, len) #endif /* check macros for header crc */ #ifdef GUNZIP # define CRC2(check, word) \ do { \ hbuf[0] = (unsigned char)(word); \ hbuf[1] = (unsigned char)((word) >> 8); \ check = crc32(check, hbuf, 2); \ } while (0) # define CRC4(check, word) \ do { \ hbuf[0] = (unsigned char)(word); \ hbuf[1] = (unsigned char)((word) >> 8); \ hbuf[2] = (unsigned char)((word) >> 16); \ hbuf[3] = (unsigned char)((word) >> 24); \ check = crc32(check, hbuf, 4); \ } while (0) #endif /* Load registers with state in inflate() for speed */ #define LOAD() \ do { \ put = strm->next_out; \ left = strm->avail_out; \ next = strm->next_in; \ have = strm->avail_in; \ hold = state->hold; \ bits = state->bits; \ } while (0) /* Restore state from registers in inflate() */ #define RESTORE() \ do { \ strm->next_out = put; \ strm->avail_out = left; \ strm->next_in = next; \ strm->avail_in = have; \ state->hold = hold; \ state->bits = bits; \ } while (0) /* Clear the input bit accumulator */ #define INITBITS() \ do { \ hold = 0; \ bits = 0; \ } while (0) /* Get a byte of input into the bit accumulator, or return from inflate() if there is no input available. */ #define PULLBYTE() \ do { \ if (have == 0) goto inf_leave; \ have--; \ hold += (unsigned long)(*next++) << bits; \ bits += 8; \ } while (0) /* Assure that there are at least n bits in the bit accumulator. If there is not enough available input to do that, then return from inflate(). */ #define NEEDBITS(n) \ do { \ while (bits < (unsigned)(n)) \ PULLBYTE(); \ } while (0) /* Return the low n bits of the bit accumulator (n < 16) */ #define BITS(n) \ ((unsigned)hold & ((1U << (n)) - 1)) /* Remove n bits from the bit accumulator */ #define DROPBITS(n) \ do { \ hold >>= (n); \ bits -= (unsigned)(n); \ } while (0) /* Remove zero to seven bits as needed to go to a byte boundary */ #define BYTEBITS() \ do { \ hold >>= bits & 7; \ bits -= bits & 7; \ } while (0) /* Reverse the bytes in a 32-bit value */ #define REVERSE(q) \ ((((q) >> 24) & 0xff) + (((q) >> 8) & 0xff00) + \ (((q) & 0xff00) << 8) + (((q) & 0xff) << 24)) /* inflate() uses a state machine to process as much input data and generate as much output data as possible before returning. The state machine is structured roughly as follows: for (;;) switch (state) { ... case STATEn: if (not enough input data or output space to make progress) return; ... make progress ... state = STATEm; break; ... } so when inflate() is called again, the same case is attempted again, and if the appropriate resources are provided, the machine proceeds to the next state. The NEEDBITS() macro is usually the way the state evaluates whether it can proceed or should return. NEEDBITS() does the return if the requested bits are not available. The typical use of the BITS macros is: NEEDBITS(n); ... do something with BITS(n) ... DROPBITS(n); where NEEDBITS(n) either returns from inflate() if there isn't enough input left to load n bits into the accumulator, or it continues. BITS(n) gives the low n bits in the accumulator. When done, DROPBITS(n) drops the low n bits off the accumulator. INITBITS() clears the accumulator and sets the number of available bits to zero. BYTEBITS() discards just enough bits to put the accumulator on a byte boundary. After BYTEBITS() and a NEEDBITS(8), then BITS(8) would return the next byte in the stream. NEEDBITS(n) uses PULLBYTE() to get an available byte of input, or to return if there is no input available. The decoding of variable length codes uses PULLBYTE() directly in order to pull just enough bytes to decode the next code, and no more. Some states loop until they get enough input, making sure that enough state information is maintained to continue the loop where it left off if NEEDBITS() returns in the loop. For example, want, need, and keep would all have to actually be part of the saved state in case NEEDBITS() returns: case STATEw: while (want < need) { NEEDBITS(n); keep[want++] = BITS(n); DROPBITS(n); } state = STATEx; case STATEx: As shown above, if the next state is also the next case, then the break is omitted. A state may also return if there is not enough output space available to complete that state. Those states are copying stored data, writing a literal byte, and copying a matching string. When returning, a "goto inf_leave" is used to update the total counters, update the check value, and determine whether any progress has been made during that inflate() call in order to return the proper return code. Progress is defined as a change in either strm->avail_in or strm->avail_out. When there is a window, goto inf_leave will update the window with the last output written. If a goto inf_leave occurs in the middle of decompression and there is no window currently, goto inf_leave will create one and copy output to the window for the next call of inflate(). In this implementation, the flush parameter of inflate() only affects the return code (per zlib.h). inflate() always writes as much as possible to strm->next_out, given the space available and the provided input--the effect documented in zlib.h of Z_SYNC_FLUSH. Furthermore, inflate() always defers the allocation of and copying into a sliding window until necessary, which provides the effect documented in zlib.h for Z_FINISH when the entire input stream available. So the only thing the flush parameter actually does is: when flush is set to Z_FINISH, inflate() cannot return Z_OK. Instead it will return Z_BUF_ERROR if it has not reached the end of the stream. */ int ZEXPORT inflate(strm, flush) z_streamp strm; int flush; { struct inflate_state FAR *state; unsigned char FAR *next; /* next input */ unsigned char FAR *put; /* next output */ unsigned have, left; /* available input and output */ unsigned long hold; /* bit buffer */ unsigned bits; /* bits in bit buffer */ unsigned in, out; /* save starting available input and output */ unsigned copy; /* number of stored or match bytes to copy */ unsigned char FAR *from; /* where to copy match bytes from */ code this; /* current decoding table entry */ code last; /* parent table entry */ unsigned len; /* length to copy for repeats, bits to drop */ int ret; /* return code */ #ifdef GUNZIP unsigned char hbuf[4]; /* buffer for gzip header crc calculation */ #endif static const unsigned short order[19] = /* permutation of code lengths */ {16, 17, 18, 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15}; if (strm == Z_NULL || strm->state == Z_NULL || strm->next_out == Z_NULL || (strm->next_in == Z_NULL && strm->avail_in != 0)) return Z_STREAM_ERROR; state = (struct inflate_state FAR *)strm->state; if (state->mode == TYPE) state->mode = TYPEDO; /* skip check */ LOAD(); in = have; out = left; ret = Z_OK; for (;;) switch (state->mode) { case HEAD: if (state->wrap == 0) { state->mode = TYPEDO; break; } NEEDBITS(16); #ifdef GUNZIP if ((state->wrap & 2) && hold == 0x8b1f) { /* gzip header */ state->check = crc32(0L, Z_NULL, 0); CRC2(state->check, hold); INITBITS(); state->mode = FLAGS; break; } state->flags = 0; /* expect zlib header */ if (state->head != Z_NULL) state->head->done = -1; if (!(state->wrap & 1) || /* check if zlib header allowed */ #else if ( #endif ((BITS(8) << 8) + (hold >> 8)) % 31) { strm->msg = (char *)"incorrect header check"; state->mode = BAD; break; } if (BITS(4) != Z_DEFLATED) { strm->msg = (char *)"unknown compression method"; state->mode = BAD; break; } DROPBITS(4); len = BITS(4) + 8; if (len > state->wbits) { strm->msg = (char *)"invalid window size"; state->mode = BAD; break; } state->dmax = 1U << len; state->max_window_dist = 0; state->dist_window_tail = 0; state->dist_window = (unsigned short*)realloc(state->dist_window, state->dmax * sizeof(unsigned short)); memset(state->dist_window, 0, state->dmax * sizeof(unsigned short)); Tracev((stderr, "inflate: zlib header ok\n")); strm->adler = state->check = adler32(0L, Z_NULL, 0); state->mode = hold & 0x200 ? DICTID : TYPE; INITBITS(); break; #ifdef GUNZIP case FLAGS: NEEDBITS(16); state->flags = (int)(hold); if ((state->flags & 0xff) != Z_DEFLATED) { strm->msg = (char *)"unknown compression method"; state->mode = BAD; break; } if (state->flags & 0xe000) { strm->msg = (char *)"unknown header flags set"; state->mode = BAD; break; } if (state->head != Z_NULL) state->head->text = (int)((hold >> 8) & 1); if (state->flags & 0x0200) CRC2(state->check, hold); INITBITS(); state->mode = TIME; case TIME: NEEDBITS(32); if (state->head != Z_NULL) state->head->time = hold; if (state->flags & 0x0200) CRC4(state->check, hold); INITBITS(); state->mode = OS; case OS: NEEDBITS(16); if (state->head != Z_NULL) { state->head->xflags = (int)(hold & 0xff); state->head->os = (int)(hold >> 8); } if (state->flags & 0x0200) CRC2(state->check, hold); INITBITS(); state->mode = EXLEN; case EXLEN: if (state->flags & 0x0400) { NEEDBITS(16); state->length = (unsigned)(hold); if (state->head != Z_NULL) state->head->extra_len = (unsigned)hold; if (state->flags & 0x0200) CRC2(state->check, hold); INITBITS(); } else if (state->head != Z_NULL) state->head->extra = Z_NULL; state->mode = EXTRA; case EXTRA: if (state->flags & 0x0400) { copy = state->length; if (copy > have) copy = have; if (copy) { if (state->head != Z_NULL && state->head->extra != Z_NULL) { len = state->head->extra_len - state->length; zmemcpy(state->head->extra + len, next, len + copy > state->head->extra_max ? state->head->extra_max - len : copy); } if (state->flags & 0x0200) state->check = crc32(state->check, next, copy); have -= copy; next += copy; state->length -= copy; } if (state->length) goto inf_leave; } state->length = 0; state->mode = NAME; case NAME: if (state->flags & 0x0800) { if (have == 0) goto inf_leave; copy = 0; do { len = (unsigned)(next[copy++]); if (state->head != Z_NULL && state->head->name != Z_NULL && state->length < state->head->name_max) state->head->name[state->length++] = len; } while (len && copy < have); if (state->flags & 0x0200) state->check = crc32(state->check, next, copy); have -= copy; next += copy; if (len) goto inf_leave; } else if (state->head != Z_NULL) state->head->name = Z_NULL; state->length = 0; state->mode = COMMENT; case COMMENT: if (state->flags & 0x1000) { if (have == 0) goto inf_leave; copy = 0; do { len = (unsigned)(next[copy++]); if (state->head != Z_NULL && state->head->comment != Z_NULL && state->length < state->head->comm_max) state->head->comment[state->length++] = len; } while (len && copy < have); if (state->flags & 0x0200) state->check = crc32(state->check, next, copy); have -= copy; next += copy; if (len) goto inf_leave; } else if (state->head != Z_NULL) state->head->comment = Z_NULL; state->mode = HCRC; case HCRC: if (state->flags & 0x0200) { NEEDBITS(16); if (hold != (state->check & 0xffff)) { strm->msg = (char *)"header crc mismatch"; state->mode = BAD; break; } INITBITS(); } if (state->head != Z_NULL) { state->head->hcrc = (int)((state->flags >> 9) & 1); state->head->done = 1; } strm->adler = state->check = crc32(0L, Z_NULL, 0); state->mode = TYPE; break; #endif case DICTID: NEEDBITS(32); strm->adler = state->check = REVERSE(hold); INITBITS(); state->mode = DICT; case DICT: if (state->havedict == 0) { RESTORE(); return Z_NEED_DICT; } strm->adler = state->check = adler32(0L, Z_NULL, 0); state->mode = TYPE; case TYPE: if (flush == Z_BLOCK) goto inf_leave; case TYPEDO: if (state->last) { BYTEBITS(); state->mode = CHECK; break; } NEEDBITS(3); state->last = BITS(1); DROPBITS(1); switch (BITS(2)) { case 0: /* stored block */ Tracev((stderr, "inflate: stored block%s\n", state->last ? " (last)" : "")); state->mode = STORED; break; case 1: /* fixed block */ fixedtables(state); Tracev((stderr, "inflate: fixed codes block%s\n", state->last ? " (last)" : "")); state->mode = LEN; /* decode codes */ break; case 2: /* dynamic block */ Tracev((stderr, "inflate: dynamic codes block%s\n", state->last ? " (last)" : "")); state->mode = TABLE; break; case 3: strm->msg = (char *)"invalid block type"; state->mode = BAD; } DROPBITS(2); break; case STORED: BYTEBITS(); /* go to byte boundary */ NEEDBITS(32); if ((hold & 0xffff) != ((hold >> 16) ^ 0xffff)) { strm->msg = (char *)"invalid stored block lengths"; state->mode = BAD; break; } state->length = (unsigned)hold & 0xffff; Tracev((stderr, "inflate: stored length %u\n", state->length)); INITBITS(); state->mode = COPY; case COPY: copy = state->length; if (copy) { if (copy > have) copy = have; if (copy > left) copy = left; if (copy == 0) goto inf_leave; zmemcpy(put, next, copy); have -= copy; next += copy; left -= copy; put += copy; state->length -= copy; break; } Tracev((stderr, "inflate: stored end\n")); state->mode = TYPE; break; case TABLE: NEEDBITS(14); state->nlen = BITS(5) + 257; DROPBITS(5); state->ndist = BITS(5) + 1; DROPBITS(5); state->ncode = BITS(4) + 4; DROPBITS(4); #ifndef PKZIP_BUG_WORKAROUND if (state->nlen > 286 || state->ndist > 30) { strm->msg = (char *)"too many length or distance symbols"; state->mode = BAD; break; } #endif Tracev((stderr, "inflate: table sizes ok\n")); state->have = 0; state->mode = LENLENS; case LENLENS: while (state->have < state->ncode) { NEEDBITS(3); state->lens[order[state->have++]] = (unsigned short)BITS(3); DROPBITS(3); } while (state->have < 19) state->lens[order[state->have++]] = 0; state->next = state->codes; state->lencode = (code const FAR *)(state->next); state->lenbits = 7; ret = inflate_table(CODES, state->lens, 19, &(state->next), &(state->lenbits), state->work); if (ret) { strm->msg = (char *)"invalid code lengths set"; state->mode = BAD; break; } Tracev((stderr, "inflate: code lengths ok\n")); state->have = 0; state->mode = CODELENS; case CODELENS: while (state->have < state->nlen + state->ndist) { for (;;) { this = state->lencode[BITS(state->lenbits)]; if ((unsigned)(this.bits) <= bits) break; PULLBYTE(); } if (this.val < 16) { NEEDBITS(this.bits); DROPBITS(this.bits); state->lens[state->have++] = this.val; } else { if (this.val == 16) { NEEDBITS(this.bits + 2); DROPBITS(this.bits); if (state->have == 0) { strm->msg = (char *)"invalid bit length repeat"; state->mode = BAD; break; } len = state->lens[state->have - 1]; copy = 3 + BITS(2); DROPBITS(2); } else if (this.val == 17) { NEEDBITS(this.bits + 3); DROPBITS(this.bits); len = 0; copy = 3 + BITS(3); DROPBITS(3); } else { NEEDBITS(this.bits + 7); DROPBITS(this.bits); len = 0; copy = 11 + BITS(7); DROPBITS(7); } if (state->have + copy > state->nlen + state->ndist) { strm->msg = (char *)"invalid bit length repeat"; state->mode = BAD; break; } while (copy--) state->lens[state->have++] = (unsigned short)len; } } /* handle error breaks in while */ if (state->mode == BAD) break; /* build code tables */ state->next = state->codes; state->lencode = (code const FAR *)(state->next); state->lenbits = 9; ret = inflate_table(LENS, state->lens, state->nlen, &(state->next), &(state->lenbits), state->work); if (ret) { strm->msg = (char *)"invalid literal/lengths set"; state->mode = BAD; break; } state->distcode = (code const FAR *)(state->next); state->distbits = 6; ret = inflate_table(DISTS, state->lens + state->nlen, state->ndist, &(state->next), &(state->distbits), state->work); if (ret) { strm->msg = (char *)"invalid distances set"; state->mode = BAD; break; } Tracev((stderr, "inflate: codes ok\n")); state->mode = LEN; case LEN: if (have >= 6 && left >= 258) { RESTORE(); inflate_fast(strm, out); LOAD(); break; } for (;;) { this = state->lencode[BITS(state->lenbits)]; if ((unsigned)(this.bits) <= bits) break; PULLBYTE(); } if (this.op && (this.op & 0xf0) == 0) { last = this; for (;;) { this = state->lencode[last.val + (BITS(last.bits + last.op) >> last.bits)]; if ((unsigned)(last.bits + this.bits) <= bits) break; PULLBYTE(); } DROPBITS(last.bits); } DROPBITS(this.bits); state->length = (unsigned)this.val; if ((int)(this.op) == 0) { Tracevv((stderr, this.val >= 0x20 && this.val < 0x7f ? "inflate: literal '%c'\n" : "inflate: literal 0x%02x\n", this.val)); state->mode = LIT; break; } if (this.op & 32) { Tracevv((stderr, "inflate: end of block\n")); state->mode = TYPE; break; } if (this.op & 64) { strm->msg = (char *)"invalid literal/length code"; state->mode = BAD; break; } state->extra = (unsigned)(this.op) & 15; state->mode = LENEXT; case LENEXT: if (state->extra) { NEEDBITS(state->extra); state->length += BITS(state->extra); DROPBITS(state->extra); } Tracevv((stderr, "inflate: length %u\n", state->length)); state->mode = DIST; case DIST: for (;;) { this = state->distcode[BITS(state->distbits)]; if ((unsigned)(this.bits) <= bits) break; PULLBYTE(); } if ((this.op & 0xf0) == 0) { last = this; for (;;) { this = state->distcode[last.val + (BITS(last.bits + last.op) >> last.bits)]; if ((unsigned)(last.bits + this.bits) <= bits) break; PULLBYTE(); } DROPBITS(last.bits); } DROPBITS(this.bits); if (this.op & 64) { strm->msg = (char *)"invalid distance code"; state->mode = BAD; break; } state->offset = (unsigned)this.val; state->extra = (unsigned)(this.op) & 15; state->mode = DISTEXT; case DISTEXT: if (state->extra) { NEEDBITS(state->extra); state->offset += BITS(state->extra); DROPBITS(state->extra); } #ifdef INFLATE_STRICT if (state->offset > state->dmax) { strm->msg = (char *)"invalid distance too far back"; state->mode = BAD; break; } #endif if (state->offset > state->whave + out - left) { strm->msg = (char *)"invalid distance too far back"; state->mode = BAD; break; } Tracevv((stderr, "inflate: distance %u\n", state->offset)); state->mode = MATCH; case MATCH: if (left == 0) goto inf_leave; copy = out - left; if (state->offset > copy) { /* copy from window */ copy = state->offset - copy; if (copy > state->write) { copy -= state->write; from = state->window + (state->wsize - copy); } else from = state->window + (state->write - copy); if (copy > state->length) copy = state->length; } else { /* copy from output */ from = put - state->offset; copy = state->length; } if (copy > left) copy = left; left -= copy; state->length -= copy; do { *put++ = *from++; } while (--copy); if (state->length == 0) state->mode = LEN; break; case LIT: if (left == 0) goto inf_leave; *put++ = (unsigned char)(state->length); left--; state->mode = LEN; break; case CHECK: if (state->wrap) { NEEDBITS(32); out -= left; strm->total_out += out; state->total += out; if (out) strm->adler = state->check = UPDATE(state->check, put - out, out); out = left; if (( #ifdef GUNZIP state->flags ? hold : #endif REVERSE(hold)) != state->check) { strm->msg = (char *)"incorrect data check"; state->mode = BAD; break; } INITBITS(); Tracev((stderr, "inflate: check matches trailer\n")); } #ifdef GUNZIP state->mode = LENGTH; case LENGTH: if (state->wrap && state->flags) { NEEDBITS(32); if (hold != (state->total & 0xffffffffUL)) { strm->msg = (char *)"incorrect length check"; state->mode = BAD; break; } INITBITS(); Tracev((stderr, "inflate: length matches trailer\n")); } #endif state->mode = DONE; case DONE: ret = Z_STREAM_END; goto inf_leave; case BAD: ret = Z_DATA_ERROR; goto inf_leave; case MEM: return Z_MEM_ERROR; case SYNC: default: return Z_STREAM_ERROR; } /* Return from inflate(), updating the total counts and the check value. If there was no progress during the inflate() call, return a buffer error. Call updatewindow() to create and/or update the window state. Note: a memory error from inflate() is non-recoverable. */ inf_leave: RESTORE(); if (state->wsize || (state->mode < CHECK && out != strm->avail_out)) if (updatewindow(strm, out)) { state->mode = MEM; return Z_MEM_ERROR; } in -= strm->avail_in; out -= strm->avail_out; strm->total_in += in; strm->total_out += out; state->total += out; if (state->wrap && out) strm->adler = state->check = UPDATE(state->check, strm->next_out - out, out); strm->data_type = state->bits + (state->last ? 64 : 0) + (state->mode == TYPE ? 128 : 0); if (((in == 0 && out == 0) || flush == Z_FINISH) && ret == Z_OK) ret = Z_BUF_ERROR; return ret; } int ZEXPORT inflate_zr(strm, flush) z_streamp strm; int flush; { struct inflate_state FAR *state; unsigned char FAR *next; /* next input */ unsigned char FAR *put; /* next output */ unsigned have, left; /* available input and output */ unsigned long hold; /* bit buffer */ unsigned bits; /* bits in bit buffer */ unsigned in, out; /* save starting available input and output */ unsigned copy; /* number of stored or match bytes to copy */ unsigned char FAR *from; /* where to copy match bytes from */ code this; /* current decoding table entry */ code last; /* parent table entry */ unsigned len; /* length to copy for repeats, bits to drop */ int ret; /* return code */ #ifdef GUNZIP unsigned char hbuf[4]; /* buffer for gzip header crc calculation */ #endif static const unsigned short order[19] = /* permutation of code lengths */ {16, 17, 18, 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15}; if (strm == Z_NULL || strm->state == Z_NULL || strm->next_out == Z_NULL || (strm->next_in == Z_NULL && strm->avail_in != 0)) return Z_STREAM_ERROR; state = (struct inflate_state FAR *)strm->state; if (state->mode == TYPE) state->mode = TYPEDO; /* skip check */ LOAD(); in = have; out = left; ret = Z_OK; for (;;) switch (state->mode) { case HEAD: if (state->wrap == 0) { state->mode = TYPEDO; break; } NEEDBITS(16); #ifdef GUNZIP if ((state->wrap & 2) && hold == 0x8b1f) { /* gzip header */ state->check = crc32(0L, Z_NULL, 0); CRC2(state->check, hold); INITBITS(); state->mode = FLAGS; break; } state->flags = 0; /* expect zlib header */ if (state->head != Z_NULL) state->head->done = -1; if (!(state->wrap & 1) || /* check if zlib header allowed */ #else if ( #endif ((BITS(8) << 8) + (hold >> 8)) % 31) { strm->msg = (char *)"incorrect header check"; state->mode = BAD; break; } if (BITS(4) != Z_DEFLATED) { strm->msg = (char *)"unknown compression method"; state->mode = BAD; break; } DROPBITS(4); len = BITS(4) + 8; if (len > state->wbits) { strm->msg = (char *)"invalid window size"; state->mode = BAD; break; } state->dmax = 1U << len; state->max_window_dist = 0; state->dist_window_tail = 0; state->dist_window = (unsigned short*)realloc(state->dist_window, state->dmax * sizeof(unsigned short)); memset(state->dist_window, 0, state->dmax * sizeof(unsigned short)); Tracev((stderr, "inflate: zlib header ok\n")); strm->adler = state->check = adler32(0L, Z_NULL, 0); state->mode = hold & 0x200 ? DICTID : TYPE; INITBITS(); break; #ifdef GUNZIP case FLAGS: NEEDBITS(16); state->flags = (int)(hold); if ((state->flags & 0xff) != Z_DEFLATED) { strm->msg = (char *)"unknown compression method"; state->mode = BAD; break; } if (state->flags & 0xe000) { strm->msg = (char *)"unknown header flags set"; state->mode = BAD; break; } if (state->head != Z_NULL) state->head->text = (int)((hold >> 8) & 1); if (state->flags & 0x0200) CRC2(state->check, hold); INITBITS(); state->mode = TIME; case TIME: NEEDBITS(32); if (state->head != Z_NULL) state->head->time = hold; if (state->flags & 0x0200) CRC4(state->check, hold); INITBITS(); state->mode = OS; case OS: NEEDBITS(16); if (state->head != Z_NULL) { state->head->xflags = (int)(hold & 0xff); state->head->os = (int)(hold >> 8); } if (state->flags & 0x0200) CRC2(state->check, hold); INITBITS(); state->mode = EXLEN; case EXLEN: if (state->flags & 0x0400) { NEEDBITS(16); state->length = (unsigned)(hold); if (state->head != Z_NULL) state->head->extra_len = (unsigned)hold; if (state->flags & 0x0200) CRC2(state->check, hold); INITBITS(); } else if (state->head != Z_NULL) state->head->extra = Z_NULL; state->mode = EXTRA; case EXTRA: if (state->flags & 0x0400) { copy = state->length; if (copy > have) copy = have; if (copy) { if (state->head != Z_NULL && state->head->extra != Z_NULL) { len = state->head->extra_len - state->length; zmemcpy(state->head->extra + len, next, len + copy > state->head->extra_max ? state->head->extra_max - len : copy); } if (state->flags & 0x0200) state->check = crc32(state->check, next, copy); have -= copy; next += copy; state->length -= copy; } if (state->length) goto inf_leave; } state->length = 0; state->mode = NAME; case NAME: if (state->flags & 0x0800) { if (have == 0) goto inf_leave; copy = 0; do { len = (unsigned)(next[copy++]); if (state->head != Z_NULL && state->head->name != Z_NULL && state->length < state->head->name_max) state->head->name[state->length++] = len; } while (len && copy < have); if (state->flags & 0x0200) state->check = crc32(state->check, next, copy); have -= copy; next += copy; if (len) goto inf_leave; } else if (state->head != Z_NULL) state->head->name = Z_NULL; state->length = 0; state->mode = COMMENT; case COMMENT: if (state->flags & 0x1000) { if (have == 0) goto inf_leave; copy = 0; do { len = (unsigned)(next[copy++]); if (state->head != Z_NULL && state->head->comment != Z_NULL && state->length < state->head->comm_max) state->head->comment[state->length++] = len; } while (len && copy < have); if (state->flags & 0x0200) state->check = crc32(state->check, next, copy); have -= copy; next += copy; if (len) goto inf_leave; } else if (state->head != Z_NULL) state->head->comment = Z_NULL; state->mode = HCRC; case HCRC: if (state->flags & 0x0200) { NEEDBITS(16); if (hold != (state->check & 0xffff)) { strm->msg = (char *)"header crc mismatch"; state->mode = BAD; break; } INITBITS(); } if (state->head != Z_NULL) { state->head->hcrc = (int)((state->flags >> 9) & 1); state->head->done = 1; } strm->adler = state->check = crc32(0L, Z_NULL, 0); state->mode = TYPE; break; #endif case DICTID: NEEDBITS(32); strm->adler = state->check = REVERSE(hold); INITBITS(); state->mode = DICT; case DICT: if (state->havedict == 0) { RESTORE(); return Z_NEED_DICT; } strm->adler = state->check = adler32(0L, Z_NULL, 0); state->mode = TYPE; case TYPE: if (flush == Z_BLOCK) goto inf_leave; case TYPEDO: if (state->last) { BYTEBITS(); state->mode = CHECK; break; } NEEDBITS(3); state->last = BITS(1); DROPBITS(1); switch (BITS(2)) { case 0: /* stored block */ Tracev((stderr, "inflate: stored block%s\n", state->last ? " (last)" : "")); state->mode = STORED; break; case 1: /* fixed block */ fixedtables(state); Tracev((stderr, "inflate: fixed codes block%s\n", state->last ? " (last)" : "")); state->mode = LEN; /* decode codes */ break; case 2: /* dynamic block */ Tracev((stderr, "inflate: dynamic codes block%s\n", state->last ? " (last)" : "")); state->mode = TABLE; break; case 3: strm->msg = (char *)"invalid block type"; state->mode = BAD; } DROPBITS(2); break; case STORED: BYTEBITS(); /* go to byte boundary */ NEEDBITS(32); if ((hold & 0xffff) != ((hold >> 16) ^ 0xffff)) { strm->msg = (char *)"invalid stored block lengths"; state->mode = BAD; break; } state->length = (unsigned)hold & 0xffff; Tracev((stderr, "inflate: stored length %u\n", state->length)); INITBITS(); state->mode = COPY; case COPY: copy = state->length; if (copy) { if (copy > have) copy = have; if (copy > left) copy = left; if (copy == 0) goto inf_leave; zmemcpy(put, next, copy); have -= copy; next += copy; left -= copy; put += copy; state->length -= copy; break; } Tracev((stderr, "inflate: stored end\n")); state->mode = TYPE; break; case TABLE: NEEDBITS(14); state->nlen = BITS(5) + 257; DROPBITS(5); state->ndist = BITS(5) + 1; DROPBITS(5); state->ncode = BITS(4) + 4; DROPBITS(4); #ifndef PKZIP_BUG_WORKAROUND if (state->nlen > 286 || state->ndist > 30) { strm->msg = (char *)"too many length or distance symbols"; state->mode = BAD; break; } #endif Tracev((stderr, "inflate: table sizes ok\n")); state->have = 0; state->mode = LENLENS; case LENLENS: while (state->have < state->ncode) { NEEDBITS(3); state->lens[order[state->have++]] = (unsigned short)BITS(3); DROPBITS(3); } while (state->have < 19) state->lens[order[state->have++]] = 0; state->next = state->codes; state->lencode = (code const FAR *)(state->next); state->lenbits = 7; ret = inflate_table(CODES, state->lens, 19, &(state->next), &(state->lenbits), state->work); if (ret) { strm->msg = (char *)"invalid code lengths set"; state->mode = BAD; break; } Tracev((stderr, "inflate: code lengths ok\n")); state->have = 0; state->mode = CODELENS; case CODELENS: while (state->have < state->nlen + state->ndist) { for (;;) { this = state->lencode[BITS(state->lenbits)]; if ((unsigned)(this.bits) <= bits) break; PULLBYTE(); } if (this.val < 16) { NEEDBITS(this.bits); DROPBITS(this.bits); state->lens[state->have++] = this.val; } else { if (this.val == 16) { NEEDBITS(this.bits + 2); DROPBITS(this.bits); if (state->have == 0) { strm->msg = (char *)"invalid bit length repeat"; state->mode = BAD; break; } len = state->lens[state->have - 1]; copy = 3 + BITS(2); DROPBITS(2); } else if (this.val == 17) { NEEDBITS(this.bits + 3); DROPBITS(this.bits); len = 0; copy = 3 + BITS(3); DROPBITS(3); } else { NEEDBITS(this.bits + 7); DROPBITS(this.bits); len = 0; copy = 11 + BITS(7); DROPBITS(7); } if (state->have + copy > state->nlen + state->ndist) { strm->msg = (char *)"invalid bit length repeat"; state->mode = BAD; break; } while (copy--) state->lens[state->have++] = (unsigned short)len; } } /* handle error breaks in while */ if (state->mode == BAD) break; /* build code tables */ state->next = state->codes; state->lencode = (code const FAR *)(state->next); state->lenbits = 9; ret = inflate_table(LENS, state->lens, state->nlen, &(state->next), &(state->lenbits), state->work); if (ret) { strm->msg = (char *)"invalid literal/lengths set"; state->mode = BAD; break; } state->distcode = (code const FAR *)(state->next); state->distbits = 6; ret = inflate_table(DISTS, state->lens + state->nlen, state->ndist, &(state->next), &(state->distbits), state->work); if (ret) { strm->msg = (char *)"invalid distances set"; state->mode = BAD; break; } Tracev((stderr, "inflate: codes ok\n")); state->mode = LEN; case LEN: if (have >= 6 && left >= 258) { RESTORE(); inflate_fast_zr(strm, out); LOAD(); break; } for (;;) { this = state->lencode[BITS(state->lenbits)]; if ((unsigned)(this.bits) <= bits) break; PULLBYTE(); } if (this.op && (this.op & 0xf0) == 0) { last = this; for (;;) { this = state->lencode[last.val + (BITS(last.bits + last.op) >> last.bits)]; if ((unsigned)(last.bits + this.bits) <= bits) break; PULLBYTE(); } DROPBITS(last.bits); } DROPBITS(this.bits); state->length = (unsigned)this.val; if ((int)(this.op) == 0) { Tracevv((stderr, this.val >= 0x20 && this.val < 0x7f ? "inflate: literal '%c'\n" : "inflate: literal 0x%02x\n", this.val)); state->mode = LIT; break; } if (this.op & 32) { Tracevv((stderr, "inflate: end of block\n")); state->mode = TYPE; break; } if (this.op & 64) { strm->msg = (char *)"invalid literal/length code"; state->mode = BAD; break; } state->extra = (unsigned)(this.op) & 15; state->mode = LENEXT; case LENEXT: if (state->extra) { NEEDBITS(state->extra); state->length += BITS(state->extra); DROPBITS(state->extra); } Tracevv((stderr, "inflate: length %u\n", state->length)); state->mode = DIST; case DIST: for (;;) { this = state->distcode[BITS(state->distbits)]; if ((unsigned)(this.bits) <= bits) break; PULLBYTE(); } if ((this.op & 0xf0) == 0) { last = this; for (;;) { this = state->distcode[last.val + (BITS(last.bits + last.op) >> last.bits)]; if ((unsigned)(last.bits + this.bits) <= bits) break; PULLBYTE(); } DROPBITS(last.bits); } DROPBITS(this.bits); if (this.op & 64) { strm->msg = (char *)"invalid distance code"; state->mode = BAD; break; } state->offset = (unsigned)this.val; state->extra = (unsigned)(this.op) & 15; state->mode = DISTEXT; case DISTEXT: if (state->extra) { NEEDBITS(state->extra); state->offset += BITS(state->extra); DROPBITS(state->extra); } #ifdef INFLATE_STRICT if (state->offset > state->dmax) { strm->msg = (char *)"invalid distance too far back"; state->mode = BAD; break; } #endif if (state->offset > state->whave + out - left) { strm->msg = (char *)"invalid distance too far back"; state->mode = BAD; break; } Tracevv((stderr, "inflate: distance %u\n", state->offset)); state->mode = MATCH; case MATCH: if (left == 0) goto inf_leave; copy = out - left; if (state->offset > copy) { /* copy from window */ copy = state->offset - copy; if (copy > state->write) { copy -= state->write; from = state->window + (state->wsize - copy); } else from = state->window + (state->write - copy); if (copy > state->length) copy = state->length; } else { /* copy from output */ from = put - state->offset; copy = state->length; } if (copy > left) copy = left; left -= copy; state->length -= copy; do { *put++ = *from++; } while (--copy); if (state->length == 0) state->mode = LEN; break; case LIT: if (left == 0) goto inf_leave; *put++ = (unsigned char)(state->length); left--; state->mode = LEN; break; case CHECK: if (state->wrap) { NEEDBITS(32); out -= left; strm->total_out += out; state->total += out; if (out) strm->adler = state->check = UPDATE(state->check, put - out, out); out = left; if (( #ifdef GUNZIP state->flags ? hold : #endif REVERSE(hold)) != state->check) { strm->msg = (char *)"incorrect data check"; state->mode = BAD; break; } INITBITS(); Tracev((stderr, "inflate: check matches trailer\n")); } #ifdef GUNZIP state->mode = LENGTH; case LENGTH: if (state->wrap && state->flags) { NEEDBITS(32); if (hold != (state->total & 0xffffffffUL)) { strm->msg = (char *)"incorrect length check"; state->mode = BAD; break; } INITBITS(); Tracev((stderr, "inflate: length matches trailer\n")); } #endif state->mode = DONE; case DONE: ret = Z_STREAM_END; goto inf_leave; case BAD: ret = Z_DATA_ERROR; goto inf_leave; case MEM: return Z_MEM_ERROR; case SYNC: default: return Z_STREAM_ERROR; } /* Return from inflate(), updating the total counts and the check value. If there was no progress during the inflate() call, return a buffer error. Call updatewindow() to create and/or update the window state. Note: a memory error from inflate() is non-recoverable. */ inf_leave: RESTORE(); if (state->wsize || (state->mode < CHECK && out != strm->avail_out)) if (updatewindow(strm, out)) { state->mode = MEM; return Z_MEM_ERROR; } in -= strm->avail_in; out -= strm->avail_out; strm->total_in += in; strm->total_out += out; state->total += out; if (state->wrap && out) strm->adler = state->check = UPDATE(state->check, strm->next_out - out, out); strm->data_type = state->bits + (state->last ? 64 : 0) + (state->mode == TYPE ? 128 : 0); if (((in == 0 && out == 0) || flush == Z_FINISH) && ret == Z_OK) ret = Z_BUF_ERROR; return ret; } int ZEXPORT inflateEnd(strm) z_streamp strm; { struct inflate_state FAR *state; if (strm == Z_NULL || strm->state == Z_NULL || strm->zfree == (free_func)0) return Z_STREAM_ERROR; state = (struct inflate_state FAR *)strm->state; if (state->window != Z_NULL) ZFREE(strm, state->window); if (state->dist_window != Z_NULL) ZFREE(strm, state->dist_window); ZFREE(strm, strm->state); strm->state = Z_NULL; Tracev((stderr, "inflate: end\n")); return Z_OK; } int ZEXPORT inflateSetDictionary(strm, dictionary, dictLength) z_streamp strm; const Bytef *dictionary; uInt dictLength; { struct inflate_state FAR *state; unsigned long id; /* check state */ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR; state = (struct inflate_state FAR *)strm->state; if (state->wrap != 0 && state->mode != DICT) return Z_STREAM_ERROR; /* check for correct dictionary id */ if (state->mode == DICT) { id = adler32(0L, Z_NULL, 0); id = adler32(id, dictionary, dictLength); if (id != state->check) return Z_DATA_ERROR; } /* copy dictionary to window */ if (updatewindow(strm, strm->avail_out)) { state->mode = MEM; return Z_MEM_ERROR; } if (dictLength > state->wsize) { zmemcpy(state->window, dictionary + dictLength - state->wsize, state->wsize); state->whave = state->wsize; } else { zmemcpy(state->window + state->wsize - dictLength, dictionary, dictLength); state->whave = dictLength; } state->havedict = 1; Tracev((stderr, "inflate: dictionary set\n")); return Z_OK; } int ZEXPORT inflateGetHeader(strm, head) z_streamp strm; gz_headerp head; { struct inflate_state FAR *state; /* check state */ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR; state = (struct inflate_state FAR *)strm->state; if ((state->wrap & 2) == 0) return Z_STREAM_ERROR; /* save header structure */ state->head = head; head->done = 0; return Z_OK; } /* Search buf[0..len-1] for the pattern: 0, 0, 0xff, 0xff. Return when found or when out of input. When called, *have is the number of pattern bytes found in order so far, in 0..3. On return *have is updated to the new state. If on return *have equals four, then the pattern was found and the return value is how many bytes were read including the last byte of the pattern. If *have is less than four, then the pattern has not been found yet and the return value is len. In the latter case, syncsearch() can be called again with more data and the *have state. *have is initialized to zero for the first call. */ local unsigned syncsearch(have, buf, len) unsigned FAR *have; unsigned char FAR *buf; unsigned len; { unsigned got; unsigned next; got = *have; next = 0; while (next < len && got < 4) { if ((int)(buf[next]) == (got < 2 ? 0 : 0xff)) got++; else if (buf[next]) got = 0; else got = 4 - got; next++; } *have = got; return next; } int ZEXPORT inflateSync(strm) z_streamp strm; { unsigned len; /* number of bytes to look at or looked at */ unsigned long in, out; /* temporary to save total_in and total_out */ unsigned char buf[4]; /* to restore bit buffer to byte string */ struct inflate_state FAR *state; /* check parameters */ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR; state = (struct inflate_state FAR *)strm->state; if (strm->avail_in == 0 && state->bits < 8) return Z_BUF_ERROR; /* if first time, start search in bit buffer */ if (state->mode != SYNC) { state->mode = SYNC; state->hold <<= state->bits & 7; state->bits -= state->bits & 7; len = 0; while (state->bits >= 8) { buf[len++] = (unsigned char)(state->hold); state->hold >>= 8; state->bits -= 8; } state->have = 0; syncsearch(&(state->have), buf, len); } /* search available input */ len = syncsearch(&(state->have), strm->next_in, strm->avail_in); strm->avail_in -= len; strm->next_in += len; strm->total_in += len; /* return no joy or set up to restart inflate() on a new block */ if (state->have != 4) return Z_DATA_ERROR; in = strm->total_in; out = strm->total_out; inflateReset(strm); strm->total_in = in; strm->total_out = out; state->mode = TYPE; return Z_OK; } /* Returns true if inflate is currently at the end of a block generated by Z_SYNC_FLUSH or Z_FULL_FLUSH. This function is used by one PPP implementation to provide an additional safety check. PPP uses Z_SYNC_FLUSH but removes the length bytes of the resulting empty stored block. When decompressing, PPP checks that at the end of input packet, inflate is waiting for these length bytes. */ int ZEXPORT inflateSyncPoint(strm) z_streamp strm; { struct inflate_state FAR *state; if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR; state = (struct inflate_state FAR *)strm->state; return state->mode == STORED && state->bits == 0; } int ZEXPORT inflateCopy(dest, source) z_streamp dest; z_streamp source; { struct inflate_state FAR *state; struct inflate_state FAR *copy; unsigned char FAR *window; unsigned wsize; /* check input */ if (dest == Z_NULL || source == Z_NULL || source->state == Z_NULL || source->zalloc == (alloc_func)0 || source->zfree == (free_func)0) return Z_STREAM_ERROR; state = (struct inflate_state FAR *)source->state; /* allocate space */ copy = (struct inflate_state FAR *) ZALLOC(source, 1, sizeof(struct inflate_state)); if (copy == Z_NULL) return Z_MEM_ERROR; window = Z_NULL; if (state->window != Z_NULL) { window = (unsigned char FAR *) ZALLOC(source, 1U << state->wbits, sizeof(unsigned char)); if (window == Z_NULL) { ZFREE(source, copy); return Z_MEM_ERROR; } } /* copy state */ zmemcpy(dest, source, sizeof(z_stream)); zmemcpy(copy, state, sizeof(struct inflate_state)); if (state->lencode >= state->codes && state->lencode <= state->codes + ENOUGH - 1) { copy->lencode = copy->codes + (state->lencode - state->codes); copy->distcode = copy->codes + (state->distcode - state->codes); } copy->next = copy->codes + (state->next - state->codes); if (window != Z_NULL) { wsize = 1U << state->wbits; zmemcpy(window, state->window, wsize); } copy->window = window; dest->state = (struct internal_state FAR *)copy; return Z_OK; } maqview-0.2.5/kstream.h0000644000265600020320000001035411100335457014134 0ustar tilleaadmin/* The MIT License Copyright (c) 2008, by Attractive Chaos Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef AC_KSTREAM_H #define AC_KSTREAM_H #include #include #include #define __KS_TYPE(type_t) \ typedef struct __kstream_t { \ char *buf; \ int begin, end, is_eof; \ type_t f; \ } kstream_t; #define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end) #define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0) #define __KS_BASIC(type_t, __bufsize) \ static inline kstream_t *ks_init(type_t f) \ { \ kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t)); \ ks->f = f; \ ks->buf = (char*)malloc(__bufsize); \ return ks; \ } \ static inline void ks_destroy(kstream_t *ks) \ { \ if (ks) { \ free(ks->buf); \ free(ks); \ } \ } #define __KS_GETC(__read, __bufsize) \ static inline int ks_getc(kstream_t *ks) \ { \ if (ks->is_eof && ks->begin >= ks->end) return -1; \ if (ks->begin >= ks->end) { \ ks->begin = 0; \ ks->end = __read(ks->f, ks->buf, __bufsize); \ if (ks->end < __bufsize) ks->is_eof = 1; \ if (ks->end == 0) return -1; \ } \ return (int)ks->buf[ks->begin++]; \ } typedef struct __kstring_t { size_t l, m; unsigned char *s; } kstring_t; #ifndef kroundup32 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) #endif #define __KS_GETUNTIL(__read, __bufsize) \ static int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \ { \ if (dret) *dret = 0; \ str->l = 0; \ if (ks->begin >= ks->end && ks->is_eof) return -1; \ for (;;) { \ int i; \ if (ks->begin >= ks->end) { \ if (!ks->is_eof) { \ ks->begin = 0; \ ks->end = __read(ks->f, ks->buf, __bufsize); \ if (ks->end < __bufsize) ks->is_eof = 1; \ if (ks->end == 0) break; \ } else break; \ } \ if (delimiter) { \ for (i = ks->begin; i < ks->end; ++i) \ if (ks->buf[i] == delimiter) break; \ } else { \ for (i = ks->begin; i < ks->end; ++i) \ if (isspace(ks->buf[i])) break; \ } \ if (str->m - str->l < i - ks->begin + 1) { \ str->m = str->l + (i - ks->begin) + 1; \ kroundup32(str->m); \ str->s = (unsigned char*)realloc(str->s, str->m); \ } \ memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \ str->l = str->l + (i - ks->begin); \ ks->begin = i + 1; \ if (i < ks->end) { \ if (dret) *dret = ks->buf[i]; \ break; \ } \ } \ str->s[str->l] = '\0'; \ return str->l; \ } #define KSTREAM_INIT(type_t, __read, __bufsize) \ __KS_TYPE(type_t) \ __KS_BASIC(type_t, __bufsize) \ __KS_GETC(__read, __bufsize) \ __KS_GETUNTIL(__read, __bufsize) #endif maqview-0.2.5/gl_gui.c0000644000265600020320000001271411051451754013735 0ustar tilleaadmin#include "gl_gui.h" static float default_colors[][3] = { {0.1, 0.1, 0.1}, //bgColor {.7, .7, .7}, //textColor {0, 0, 1}, //borderColor { 0, 1, 0 }, //highlightTextColor { 0.4, 0.4, 0.3 } //highlightBgColor }; void gui_default_window_colors(GContainer *win){ memcpy(win->bgColor, default_colors[0], 3 * sizeof(float)); memcpy(win->textColor, default_colors[1], 3 * sizeof(float)); memcpy(win->borderColor, default_colors[2], 3 * sizeof(float)); memcpy(win->highlightTextColor, default_colors[3], 3 * sizeof(float)); memcpy(win->highlightBgColor, default_colors[4], 3 * sizeof(float)); } void VP_addChild(ViewPanel *vp, void *child, CHILD_REPAINT func){ int i, j; if(child == NULL) return; j = -1; for(i=0;ichild_size;i++){ if(vp->childs[i*2] == NULL) j = i*2; if(child == vp->childs[i*2]) return; } if(j >= 0){ vp->childs[j] = child; vp->childs[j+1] = func; return; } if(vp->child_size * 2 >= vp->child_capacity){ vp->child_capacity = (vp->child_size + 1) * 2; vp->childs = (void**)realloc(vp->childs, sizeof(void*) * vp->child_capacity); } vp->childs[vp->child_size*2] = child; vp->childs[vp->child_size*2 + 1] = func; vp->child_size ++; } void* VP_removeChild(ViewPanel *vp, void *child){ int i; void *func; for(i=0;ichild_size;i++){ if(vp->childs[i*2] == child){ func = vp->childs[i*2+1]; vp->childs[i] = NULL; return func; } } return NULL; } GList *last_glist = NULL; GList* getCurrentGList(){ int win_id; win_id = glutGetWindow(); if(win_id > vps_size){ return last_glist; } else if(vp_types[win_id-1] == WINDOW_TYPE_GLIST){ last_glist = (GList*)vps[win_id-1]; return (GList*)vps[win_id-1]; } else { return last_glist; } } void GList_repaint(void *obj){ GList *list; int i; list = (GList*)obj; glutSetWindow(list->window.win_id); glClearColor(list->window.bgColor[0], list->window.bgColor[1], list->window.bgColor[2], 0); glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT); glColor3fv(list->window.borderColor); glBegin(GL_LINE_LOOP); glVertex3f(0, 0, 0); glVertex3f(list->window.win_width-1, 0, 0); glVertex3f(list->window.win_width-1, list->window.win_height-1, 0); glVertex3f(0, list->window.win_height-1, 0); glEnd(); for(i=0;idisp_size;i++){ if(i >0 && i < list->disp_size){ glColor3fv(list->window.borderColor); glBegin(GL_LINES); glVertex3f(0, list->cell_height * (list->disp_size - i), 0); glVertex3f(list->window.win_width, list->cell_height * (list->disp_size - i), 0); glEnd(); } if(i + list->disp_offset >= list->size) continue; if(i + list->disp_offset == list->selected){ /* glColor3fv(list->window.highlightBgColor); glRectf(0, list->cell_height * (list->disp_size - i), list->window.win_width, list->cell_height * (list->disp_size - i - 1)); */ glColor3fv(list->window.highlightTextColor); } else { glColor3fv(list->window.textColor); } drawString((list->cell_width - strlen(list->options[i + list->disp_offset]) * 8) / 2, (list->cell_height - 13) / 2 + list->cell_height * (list->disp_size - i - 1), list->options[i + list->disp_offset]); } glutSwapBuffers(); } void GList_display(){ GList *list; list = getCurrentGList(); GList_repaint(list); } void GList_resize(int w, int h){ glViewport(0, 0, w, h); glMatrixMode(GL_PROJECTION); glLoadIdentity(); glMatrixMode(GL_MODELVIEW); glLoadIdentity(); glOrtho(0, w, 0, h, -w, w); } void GList_mouse(int button, int state, int x, int y){ GList *list; list = getCurrentGList(); if(button == GLUT_LEFT_BUTTON && state == GLUT_DOWN){ list->selected = y / list->cell_height; if(list->valueChanged) list->valueChanged(list, list->selected); glutPostRedisplay(); } } GList* createGList(int id, ViewPanel *vp, float x, float y, float cell_w, float cell_h, int n_disp){ GList *list; list = (GList*)malloc(sizeof(GList)); list->window.parent = vp; list->window.visible = 1; list->window.win_x = x; list->window.win_y = y; list->window.border_size = 1; list->window.win_width = cell_w; list->window.win_height = cell_h * n_disp; gui_default_window_colors(&list->window); list->window.win_id = glutCreateSubWindow(vp->win_id, x, y, list->window.win_width, list->window.win_height); glEnable(GL_DEPTH_TEST); glutDisplayFunc(GList_display); glutReshapeFunc(GList_resize); glutMouseFunc(GList_mouse); register_window(list->window.win_id, list, WINDOW_TYPE_GLIST); list->cell_width = cell_w; list->cell_height = cell_h; list->id = id; list->selected = -1; list->disp_size = n_disp; list->disp_offset = 0; list->size = 0; list->capacity = 6; list->options = (char**)malloc(list->capacity * sizeof(char*)); list->valueChanged = NULL; VP_addChild(vp, list, GList_repaint); last_glist = list; return list; } int GList_addOption(GList *list, char *option){ char *str; str = (char*)malloc(sizeof(char) * (strlen(option) + 1)); strcpy(str, option); if(list->size > list->capacity){ list->capacity = list->size * 2; list->options = (char**)realloc(list->options, sizeof(char*) * list->capacity); } list->options[list->size++] = str; return list->size - 1; } char* GList_getOption(GList *list, int index){ if(index >= list->size || index < 0) return NULL; return list->options[index]; } void freeGList(GList *list){ int i; VP_removeChild(list->window.parent, list); for(i=0;isize;i++){ free(list->options[i]); } free(list->options); glutDestroyWindow(list->window.win_id); free(list); if(last_glist == list) last_glist = NULL; } maqview-0.2.5/MaqIndex.pm0000644000265600020320000000531311003261237014354 0ustar tilleaadminpackage MaqIndex; use strict; use warnings; use IO::Socket::INET; use FileHandle; sub new { my $invocant = shift; my $class = ref($invocant) || $invocant; my $self = { -host=>'127.0.0.1', -port=>'5321', @_ }; bless($self, $class); $self->init; return $self; } sub init { my $self = shift; my $server = qq/$self->{-host}:$self->{-port}/; $self->{_fh} = IO::Socket::INET->new(PeerAddr=>$server) || die("[MaqIndex::init] fail to connect server: '$server'"); my $fh = $self->{_fh}; binmode($fh); my $buf = ''; syswrite($fh, pack("C", 1)); read($fh, $buf, 4); # number of reference sequences ($self->{_n_ref}) = unpack("III", $buf); my $n_ref = $self->{_n_ref}; my $refs = \%{$self->{_refs}}; my @refa; for (0 .. $n_ref-1) { read($fh, $buf, 12); my ($len, $high, $nl) = unpack("III", $buf); # by default, Perl cannot really take 64-bit integers? read($fh, $buf, $nl); # ref name ($buf) = unpack("a$nl", $buf); @{$refs->{$buf}} = ($_, $len); push(@refa, $buf); } $self->{_lc} = 0; $self->{_refa} = \@refa; } sub DESTROY { my $self = shift; if (defined $self->{_fh}) { syswrite($self->{_fh}, pack("C", 0)); close($self->{_fh}); delete $self->{_fh}; } } sub get { my $self = shift; my $reg = shift; my @array; my $a = @_? shift : \@array; @$a = (); $reg =~ s/,//g; $reg =~ s/\s//g; unless ($reg =~ /^(\S+):(\d+)-(\d+)$/) { warn("[MaqIndex::get] Illegal region format: '$reg'. Skip!\n"); return; } my ($chr, $b, $e) = ($1, $2, $3); my $ref_id = $self->{_refs}{$chr}[0]; unless (defined $ref_id) { warn("[MaqIndex::get] Fail to find reference '$chr'. Skip!\n"); return; } my $fh = $self->{_fh}; my ($buf, $N, $dumb1, $dumb2); syswrite($fh, pack("CI6", 3, $self->{_lc}, $ref_id, $b-1, 0, $e-1, 0), 25); read($fh, $buf, 28); ($self->{_lc}, $ref_id, $b, $dumb1, $e, $dumb2, $N) = unpack("I7", $buf); for (1 .. $N) { read($fh, $buf, 120); push(@$a, $buf); read($fh, $buf, 8); # useless bits } return @array if (@array); } sub struct2array { my $self = shift; my $buf = shift; my $is_verbose = @_? $_ : 1; my $ref = $self->{_refa}; my @ACGT = ('A', 'C', 'G', 'T'); for my $i (0 .. @$buf-1) { my ($sq, @t); ($sq, @t[7,13,6,9..12,5,8,1,2,4,0]) = unpack("a63cC8I2iZ36", $buf->[$i]); @t[1..3] = ($ref->[$t[1]], ($t[2]>>1)+1, ($t[2]&1)?'-':'+', $t[9]&0xf); if ($is_verbose) { my @s = unpack("C$t[13]", $sq); my ($seq, $qual); foreach my $p (@s) { if ($p == 0) { $seq .= 'N'; } else { $seq .= $ACGT[$p>>6]; } $p = chr(33 + ($p&0x3f)); } push(@t, $seq, join('', @s)); } $buf->[$i] = \@t; } } sub mapview { my ($self, $bufs) = @_; $self->struct2array($bufs); for my $buf (@$bufs) { print join("\t", @$buf), "\n"; } } 1; maqview-0.2.5/ChangeLog0000644000265600020320000005707310771073704014107 0ustar tilleaadmin------------------------------------------------------------------------ r544 | ruanjue | 2008-03-15 16:04:01 +0000 (Sat, 15 Mar 2008) | 1 line Changed paths: M /branches/dev/maqview/btree.c M /branches/dev/maqview/maqmap_index.c fix a bug in btree indexing, small data will be displayed right ------------------------------------------------------------------------ r540 | lh3lh3 | 2008-03-15 12:26:48 +0000 (Sat, 15 Mar 2008) | 2 lines Changed paths: M /branches/dev/maqview/Makefile.generic M /branches/dev/maqview/NEWS M /branches/dev/maqview/configure.ac Release maqview-0.2.2 ------------------------------------------------------------------------ r539 | lh3lh3 | 2008-03-15 12:23:38 +0000 (Sat, 15 Mar 2008) | 2 lines Changed paths: M /branches/dev/maqview/btree.c M /branches/dev/maqview/view_goto.c bug fixes made by Jue ------------------------------------------------------------------------ r476 | lh3lh3 | 2008-01-26 09:57:17 +0000 (Sat, 26 Jan 2008) | 2 lines Changed paths: M /branches/dev/maqview/Makefile.am remove duplicated entries ------------------------------------------------------------------------ r475 | ruanjue | 2008-01-26 02:34:28 +0000 (Sat, 26 Jan 2008) | 1 line Changed paths: M /branches/dev/maqview/Makefile.am M /branches/dev/maqview/README M /branches/dev/maqview/view_panel.c ------------------------------------------------------------------------ r474 | lh3lh3 | 2008-01-25 22:49:08 +0000 (Fri, 25 Jan 2008) | 5 lines Changed paths: M /branches/dev/maqview/Makefile.am M /branches/dev/maqview/Makefile.generic A /branches/dev/maqview/caches.h M /branches/dev/maqview/cns_cache.c M /branches/dev/maqview/configure.ac M /branches/dev/maqview/maqmap_index_main.c M /branches/dev/maqview/maqview.h M /branches/dev/maqview/read_cache.c M /branches/dev/maqview/view_goto.c * maqview-0.2.1-1 * fix a bug on behalf of Jue * move GUI related codes to caches.h * fix a bug when .cns and .map contain different references ------------------------------------------------------------------------ r447 | lh3lh3 | 2007-12-06 16:16:03 +0000 (Thu, 06 Dec 2007) | 2 lines Changed paths: M /branches/dev/maqview/ChangeLog M /branches/dev/maqview/Makefile.generic M /branches/dev/maqview/NEWS M /branches/dev/maqview/configure.ac Release maqview-0.2.1 ------------------------------------------------------------------------ r445 | lh3lh3 | 2007-12-06 16:01:59 +0000 (Thu, 06 Dec 2007) | 3 lines Changed paths: M /branches/dev/maqview/MainFrame.c M /branches/dev/maqview/Makefile.am M /branches/dev/maqview/README M /branches/dev/maqview/btree.c M /branches/dev/maqview/cns_cache.c A /branches/dev/maqview/gl_gui.c (from /branches/dev/maqview-2/gl_gui.c:444) A /branches/dev/maqview/gl_gui.h (from /branches/dev/maqview-2/gl_gui.h:444) M /branches/dev/maqview/maqview.h M /branches/dev/maqview/view_goto.c M /branches/dev/maqview/view_panel.c M /branches/dev/maqview/zrio.c A /branches/dev/maqview/zrio_main.c (from /branches/dev/maqview-2/zrio_main.c:444) * merge from /branches/dev/maqview-2@444 * prepare to remove maqview-2. all development should happen here ------------------------------------------------------------------------ r389 | lh3lh3 | 2007-10-30 15:09:29 +0000 (Tue, 30 Oct 2007) | 2 lines Changed paths: M /branches/dev/maqview/ChangeLog M /branches/dev/maqview/NEWS Release maqview-0.2.0 ------------------------------------------------------------------------ r388 | lh3lh3 | 2007-10-30 14:51:51 +0000 (Tue, 30 Oct 2007) | 2 lines Changed paths: M /branches/dev/maqview/MainFrame.c M /branches/dev/maqview/Makefile.am M /branches/dev/maqview/Makefile.generic M /branches/dev/maqview/README M /branches/dev/maqview/btree.h A /branches/dev/maqview/cns_cache.c (from /branches/dev/maqview-2/cns_cache.c:387) M /branches/dev/maqview/configure.ac A /branches/dev/maqview/const.c (from /branches/dev/maqview-2/const.c:387) M /branches/dev/maqview/inffast.c M /branches/dev/maqview/inffast.h M /branches/dev/maqview/inflate.c M /branches/dev/maqview/inflate.h M /branches/dev/maqview/maqmap.h M /branches/dev/maqview/maqmap_index.c M /branches/dev/maqview/maqmap_index.h M /branches/dev/maqview/maqmap_index_main.c M /branches/dev/maqview/maqview.h M /branches/dev/maqview/maqview.pod M /branches/dev/maqview/read_cache.c A /branches/dev/maqview/stdhash.hh (from /branches/dev/maqview-2/stdhash.hh:387) A /branches/dev/maqview/stdhashc.cc (from /branches/dev/maqview-2/stdhashc.cc:387) A /branches/dev/maqview/stdhashc.h (from /branches/dev/maqview-2/stdhashc.h:387) M /branches/dev/maqview/view_goto.c A /branches/dev/maqview/view_panel.c (from /branches/dev/maqview-2/view_panel.c:387) M /branches/dev/maqview/zlib.h M /branches/dev/maqview/zrio.c M /branches/dev/maqview/zrio.h merge from maqview-2 ------------------------------------------------------------------------ r317 | lh3lh3 | 2007-09-27 14:49:38 +0100 (Thu, 27 Sep 2007) | 2 lines Changed paths: M /branches/dev/maqview/ChangeLog M /branches/dev/maqview/Makefile.am M /branches/dev/maqview/Makefile.generic M /branches/dev/maqview/NEWS M /branches/dev/maqview/configure.ac Release 0.1.1 ------------------------------------------------------------------------ r316 | ruanjue | 2007-09-26 15:13:48 +0100 (Wed, 26 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/Makefile.generic M /branches/dev/maqview/maqmap_index.c M /branches/dev/maqview/maqmap_index.h M /branches/dev/maqview/zrio.c M /branches/dev/maqview/zrio.h use lseek instead of fseek, fix an bug in zrseek ------------------------------------------------------------------------ r314 | lh3lh3 | 2007-09-26 11:03:20 +0100 (Wed, 26 Sep 2007) | 2 lines Changed paths: M /branches/dev/maqview/Makefile.am M /branches/dev/maqview/configure.ac M /branches/dev/maqview/maqview.pod for the new codes added by Jue ------------------------------------------------------------------------ r313 | ruanjue | 2007-09-26 04:35:47 +0100 (Wed, 26 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/Makefile.generic ------------------------------------------------------------------------ r312 | ruanjue | 2007-09-26 04:32:40 +0100 (Wed, 26 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/MainFrame.c M /branches/dev/maqview/btree.c M /branches/dev/maqview/btree.h M /branches/dev/maqview/maqmap_index.c M /branches/dev/maqview/maqmap_index.h M /branches/dev/maqview/maqmap_index_main.c M /branches/dev/maqview/maqview.h A /branches/dev/maqview/read_cache.c M /branches/dev/maqview/view_goto.c Add read_cache, speed up viewer ------------------------------------------------------------------------ r310 | ruanjue | 2007-09-25 10:52:28 +0100 (Tue, 25 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/MainFrame.c M /branches/dev/maqview/Makefile.generic M /branches/dev/maqview/maqview.h M /branches/dev/maqview/view_goto.c M /branches/dev/maqview/zrio.c fix an bug in zrio ------------------------------------------------------------------------ r306 | lh3lh3 | 2007-09-24 16:32:51 +0100 (Mon, 24 Sep 2007) | 2 lines Changed paths: M /branches/dev/maqview/AUTHORS M /branches/dev/maqview/ChangeLog A /branches/dev/maqview/FUTURES M /branches/dev/maqview/INSTALL M /branches/dev/maqview/MainFrame.c M /branches/dev/maqview/Makefile.generic M /branches/dev/maqview/NEWS M /branches/dev/maqview/configure.ac M /branches/dev/maqview/maqview.pod Release 0.1.0 ------------------------------------------------------------------------ r305 | lh3lh3 | 2007-09-24 12:43:36 +0100 (Mon, 24 Sep 2007) | 3 lines Changed paths: M /branches/dev/maqview/MainFrame.c M /branches/dev/maqview/configure.ac * 0.0.0-3 * a bug about information output ------------------------------------------------------------------------ r304 | ruanjue | 2007-09-24 10:02:24 +0100 (Mon, 24 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/MainFrame.c M /branches/dev/maqview/Makefile.generic ------------------------------------------------------------------------ r303 | lh3lh3 | 2007-09-24 09:56:49 +0100 (Mon, 24 Sep 2007) | 3 lines Changed paths: M /branches/dev/maqview/MainFrame.c M /branches/dev/maqview/configure.ac * 0.0.0-1 * change several key bindings ------------------------------------------------------------------------ r302 | ruanjue | 2007-09-24 09:08:42 +0100 (Mon, 24 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/MainFrame.c M /branches/dev/maqview/view_goto.c trifles ------------------------------------------------------------------------ r301 | ruanjue | 2007-09-24 05:57:14 +0100 (Mon, 24 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/MainFrame.c M /branches/dev/maqview/Makefile.generic M /branches/dev/maqview/maqview.h ------------------------------------------------------------------------ r300 | ruanjue | 2007-09-24 04:19:49 +0100 (Mon, 24 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/MainFrame.c Change "n"/"b" to ">"/"<"; enrich help in application ------------------------------------------------------------------------ r299 | ruanjue | 2007-09-24 03:48:34 +0100 (Mon, 24 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/MainFrame.c Add status bar ------------------------------------------------------------------------ r298 | ruanjue | 2007-09-24 02:47:53 +0100 (Mon, 24 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/MainFrame.c M /branches/dev/maqview/Makefile.generic M /branches/dev/maqview/README M /branches/dev/maqview/maqmap_index.c M /branches/dev/maqview/view_goto.c M /branches/dev/maqview/zrio.c Add "0" to restore zoom;, can speed up ------------------------------------------------------------------------ r297 | lh3lh3 | 2007-09-23 23:00:47 +0100 (Sun, 23 Sep 2007) | 3 lines Changed paths: A /branches/dev/maqview/AUTHORS A /branches/dev/maqview/COPYING A /branches/dev/maqview/ChangeLog A /branches/dev/maqview/INSTALL D /branches/dev/maqview/Makefile A /branches/dev/maqview/Makefile.am A /branches/dev/maqview/Makefile.generic (from /branches/dev/maqview/Makefile:296) A /branches/dev/maqview/NEWS A /branches/dev/maqview/autogen.sh A /branches/dev/maqview/cleanup.sh A /branches/dev/maqview/configure.ac M /branches/dev/maqview/maqmap_index_main.c M /branches/dev/maqview/view_goto.c * prepare files for GNU building systems * change the CLI for map_index ------------------------------------------------------------------------ r296 | lh3lh3 | 2007-09-21 14:36:37 +0100 (Fri, 21 Sep 2007) | 2 lines Changed paths: A /branches/dev/maqview/maqview.pod maqview manual page ------------------------------------------------------------------------ r295 | ruanjue | 2007-09-21 09:31:58 +0100 (Fri, 21 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/MainFrame.c ------------------------------------------------------------------------ r294 | ruanjue | 2007-09-21 09:07:05 +0100 (Fri, 21 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/MainFrame.c M /branches/dev/maqview/Makefile M /branches/dev/maqview/maqview.h M /branches/dev/maqview/view_goto.c Add new function: mouse wheel and +/- can zoom in/out ------------------------------------------------------------------------ r293 | lh3lh3 | 2007-09-20 23:07:37 +0100 (Thu, 20 Sep 2007) | 3 lines Changed paths: M /branches/dev/maqview/MainFrame.c M /branches/dev/maqview/Makefile M /branches/dev/maqview/maqview.h M /branches/dev/maqview/view_goto.c * change color scheme * visualize base qualities and mapping qualities in the square view ------------------------------------------------------------------------ r289 | ruanjue | 2007-09-20 13:54:54 +0100 (Thu, 20 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/MainFrame.c M /branches/dev/maqview/Makefile M /branches/dev/maqview/maqmap_index.c M /branches/dev/maqview/maqview.h M /branches/dev/maqview/view_goto.c M /branches/dev/maqview/zrio.c New function: Right mouse button click ------------------------------------------------------------------------ r287 | ruanjue | 2007-09-20 03:35:40 +0100 (Thu, 20 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/MainFrame.c M /branches/dev/maqview/view_goto.c correct caching in function append_left of view_goto.c ------------------------------------------------------------------------ r286 | lh3lh3 | 2007-09-19 16:50:43 +0100 (Wed, 19 Sep 2007) | 2 lines Changed paths: M /branches/dev/maqview/maqmap_index_main.c the output format is now identical maq-0.6.0 ------------------------------------------------------------------------ r285 | lh3lh3 | 2007-09-19 16:49:17 +0100 (Wed, 19 Sep 2007) | 2 lines Changed paths: M /branches/dev/maqview/Makefile an example to show how to statically link libglut, but dynamically link libGL. ------------------------------------------------------------------------ r283 | ruanjue | 2007-09-19 10:31:36 +0100 (Wed, 19 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/maqmap_index.c M /branches/dev/maqview/view_goto.c M /branches/dev/maqview/zrio.c M /branches/dev/maqview/zrio.h fix problem: zr->pos ------------------------------------------------------------------------ r282 | ruanjue | 2007-09-19 09:04:36 +0100 (Wed, 19 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/MainFrame.c M /branches/dev/maqview/btree.c M /branches/dev/maqview/btree.h M /branches/dev/maqview/maqmap_index.c M /branches/dev/maqview/maqview.h M /branches/dev/maqview/view_goto.c problematic ------------------------------------------------------------------------ r281 | ruanjue | 2007-09-19 07:36:17 +0100 (Wed, 19 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/MainFrame.c M /branches/dev/maqview/Makefile M /branches/dev/maqview/maqmap_index.c M /branches/dev/maqview/maqmap_index_main.c M /branches/dev/maqview/view_goto.c M /branches/dev/maqview/zrio.c ------------------------------------------------------------------------ r280 | ruanjue | 2007-09-19 03:23:44 +0100 (Wed, 19 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/MainFrame.c M /branches/dev/maqview/btree.c M /branches/dev/maqview/btree.h M /branches/dev/maqview/maqmap_index.c M /branches/dev/maqview/maqview.h M /branches/dev/maqview/view_goto.c M /branches/dev/maqview/zrio.c M /branches/dev/maqview/zrio.h Store compressed index files .idx and .vm ------------------------------------------------------------------------ r279 | ruanjue | 2007-09-18 15:12:01 +0100 (Tue, 18 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/zrio.c M /branches/dev/maqview/zrio.h change the return type of zrseek to int64_t ------------------------------------------------------------------------ r278 | ruanjue | 2007-09-18 15:06:03 +0100 (Tue, 18 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/MainFrame.c M /branches/dev/maqview/Makefile M /branches/dev/maqview/view_goto.c M /branches/dev/maqview/zrio.c M /branches/dev/maqview/zrio.h ------------------------------------------------------------------------ r277 | ruanjue | 2007-09-18 14:19:57 +0100 (Tue, 18 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/MainFrame.c fix an bug of switch mode ------------------------------------------------------------------------ r276 | ruanjue | 2007-09-18 14:11:07 +0100 (Tue, 18 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/btree.c M /branches/dev/maqview/btree.h M /branches/dev/maqview/maqmap_index.c M /branches/dev/maqview/maqmap_index.h M /branches/dev/maqview/maqmap_index_main.c M /branches/dev/maqview/zrio.h try support bit64 in zrio and map_index ------------------------------------------------------------------------ r275 | ruanjue | 2007-09-18 13:40:22 +0100 (Tue, 18 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/maqmap_index.c ------------------------------------------------------------------------ r274 | ruanjue | 2007-09-18 13:37:02 +0100 (Tue, 18 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/MainFrame.c M /branches/dev/maqview/Makefile M /branches/dev/maqview/maqview.h M /branches/dev/maqview/view_goto.c Add two mode: character and square ------------------------------------------------------------------------ r273 | lh3lh3 | 2007-09-18 12:58:47 +0100 (Tue, 18 Sep 2007) | 2 lines Changed paths: M /branches/dev/maqview/maqmap_index.c avoid using ->n_mapped_reads. Sometimes this information is wrong. ------------------------------------------------------------------------ r272 | ruanjue | 2007-09-18 10:01:23 +0100 (Tue, 18 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/zrio.c fixed load_access in zrio.c ------------------------------------------------------------------------ r271 | ruanjue | 2007-09-18 09:37:38 +0100 (Tue, 18 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/btree.c M /branches/dev/maqview/btree.h M /branches/dev/maqview/maqmap_index.c change file-format of .vm ------------------------------------------------------------------------ r270 | ruanjue | 2007-09-18 09:01:25 +0100 (Tue, 18 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/btree.h M /branches/dev/maqview/maqmap_index.c M /branches/dev/maqview/zrio.c ------------------------------------------------------------------------ r269 | ruanjue | 2007-09-18 06:02:05 +0100 (Tue, 18 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/maqmap_index.c M /branches/dev/maqview/zrio.c ------------------------------------------------------------------------ r268 | ruanjue | 2007-09-18 03:44:13 +0100 (Tue, 18 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/btree.c M /branches/dev/maqview/maqmap_index.c M /branches/dev/maqview/zrio.c ------------------------------------------------------------------------ r267 | lh3lh3 | 2007-09-17 13:28:35 +0100 (Mon, 17 Sep 2007) | 2 lines Changed paths: M /branches/dev/maqview/maqmap_index_main.c * change to 1-based coordinate ------------------------------------------------------------------------ r266 | ruanjue | 2007-09-17 11:03:32 +0100 (Mon, 17 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/MainFrame.c modify help context in application ------------------------------------------------------------------------ r265 | ruanjue | 2007-09-17 11:01:23 +0100 (Mon, 17 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/MainFrame.c M /branches/dev/maqview/Makefile D /branches/dev/maqview/maqmap.c M /branches/dev/maqview/maqmap.h M /branches/dev/maqview/maqmap_index.c M /branches/dev/maqview/maqmap_index_main.c M /branches/dev/maqview/maqview.h M /branches/dev/maqview/zrio.c M /branches/dev/maqview/zrio.h fix bugs in zrio ------------------------------------------------------------------------ r264 | ruanjue | 2007-09-17 04:30:51 +0100 (Mon, 17 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/MainFrame.c M /branches/dev/maqview/maqview.h M /branches/dev/maqview/view_goto.c Press or can toggle automaticly rolling ------------------------------------------------------------------------ r263 | ruanjue | 2007-09-15 05:44:56 +0100 (Sat, 15 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/MainFrame.c Add function: mouse`s right button can drag the reads layer ------------------------------------------------------------------------ r262 | ruanjue | 2007-09-15 05:06:15 +0100 (Sat, 15 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/MainFrame.c M /branches/dev/maqview/maqview.h M /branches/dev/maqview/view_goto.c ------------------------------------------------------------------------ r260 | ruanjue | 2007-09-14 09:20:46 +0100 (Fri, 14 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/MainFrame.c Fix selection, navigation will be first ------------------------------------------------------------------------ r259 | lh3lh3 | 2007-09-14 09:18:22 +0100 (Fri, 14 Sep 2007) | 2 lines Changed paths: M /branches/dev/maqview/zrio.c M /branches/dev/maqview/zrio.h add a header file for Mac OS X ------------------------------------------------------------------------ r258 | ruanjue | 2007-09-14 08:58:17 +0100 (Fri, 14 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/view_goto.c Fix a bug in guessing refer seqs ------------------------------------------------------------------------ r257 | ruanjue | 2007-09-14 08:26:41 +0100 (Fri, 14 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/MainFrame.c M /branches/dev/maqview/Makefile M /branches/dev/maqview/maqview.h M /branches/dev/maqview/view_goto.c Draw mismatch base in red color ------------------------------------------------------------------------ r256 | ruanjue | 2007-09-14 07:22:57 +0100 (Fri, 14 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/MainFrame.c remove line gap ------------------------------------------------------------------------ r255 | ruanjue | 2007-09-14 06:49:50 +0100 (Fri, 14 Sep 2007) | 1 line Changed paths: M /branches/dev/maqview/MainFrame.c M /branches/dev/maqview/Makefile M /branches/dev/maqview/btree.c M /branches/dev/maqview/gzio.c M /branches/dev/maqview/maqmap_index.c M /branches/dev/maqview/maqmap_index.h M /branches/dev/maqview/maqview.h M /branches/dev/maqview/view_goto.c M /branches/dev/maqview/zrio.c M /branches/dev/maqview/zrio.h an stable version 1.0 ------------------------------------------------------------------------ r254 | lh3lh3 | 2007-09-13 16:51:40 +0100 (Thu, 13 Sep 2007) | 2 lines Changed paths: D /branches/dev/maqview/example.c D /branches/dev/maqview/minigzip.c D /branches/dev/maqview/zconf.in.h D /branches/dev/maqview/zrio_main.c remove unused source codes ------------------------------------------------------------------------ r253 | lh3lh3 | 2007-09-13 16:44:30 +0100 (Thu, 13 Sep 2007) | 4 lines Changed paths: A /branches/dev/maqview A /branches/dev/maqview/MainFrame.c A /branches/dev/maqview/Makefile A /branches/dev/maqview/README A /branches/dev/maqview/adler32.c A /branches/dev/maqview/btree.c A /branches/dev/maqview/btree.h A /branches/dev/maqview/compress.c A /branches/dev/maqview/const.h A /branches/dev/maqview/crc32.c A /branches/dev/maqview/crc32.h A /branches/dev/maqview/deflate.c A /branches/dev/maqview/deflate.h A /branches/dev/maqview/example.c A /branches/dev/maqview/gzio.c A /branches/dev/maqview/infback.c A /branches/dev/maqview/inffast.c A /branches/dev/maqview/inffast.h A /branches/dev/maqview/inffixed.h A /branches/dev/maqview/inflate.c A /branches/dev/maqview/inflate.h A /branches/dev/maqview/inftrees.c A /branches/dev/maqview/inftrees.h A /branches/dev/maqview/maqmap.c A /branches/dev/maqview/maqmap.h A /branches/dev/maqview/maqmap_index.c A /branches/dev/maqview/maqmap_index.h A /branches/dev/maqview/maqmap_index_main.c A /branches/dev/maqview/maqview.h A /branches/dev/maqview/minigzip.c A /branches/dev/maqview/trees.c A /branches/dev/maqview/trees.h A /branches/dev/maqview/uncompr.c A /branches/dev/maqview/view_goto.c A /branches/dev/maqview/zconf.h A /branches/dev/maqview/zconf.in.h A /branches/dev/maqview/zlib.h A /branches/dev/maqview/zrio.c A /branches/dev/maqview/zrio.h A /branches/dev/maqview/zrio_main.c A /branches/dev/maqview/zutil.c A /branches/dev/maqview/zutil.h * 0.1.0 * the first version of maqview, a graphical alignment viewer * this is the great work done by Jue Ruan, not my me. I just check in on behalf him. ------------------------------------------------------------------------ maqview-0.2.5/socket_view.h0000644000265600020320000000302310777300177015015 0ustar tilleaadmin#ifndef __SOCKET_VIEW_RJ #define __SOCKET_VIEW_RJ #include "maqview.h" #include #include #include #include #include #include #include typedef struct ViewServer { RefSeq **srcs; int v_max; int socket; int stop; int debug; } ViewServer; ViewServer* createViewServer(const char *map_file, const char *cns_file, int listen_port, int max_conns); int runViewServer(ViewServer *server); void stopViewServer(ViewServer *server); void freeViewServer(ViewServer *server); typedef struct { int n_ref; char **ref_names; int64_t *ref_lengths; int last_code; int ref_id; int64_t start, end; Read *reads; int rd_size; int rd_cap; cns_t *seqs; int cns_size; int cns_cap; } ViewInfo; typedef struct ViewClient { ViewInfo *info; int socket; } ViewClient; ViewClient* connectViewClient(char *server, int port); void closeViewClient(ViewClient *client); int fetch_maq_data(ViewClient *client, int ref_id, int64_t start, int64_t end); #define VIEW_OP_CLOSE 0 #define VIEW_OP_INFO 1 #define VIEW_OP_GOTO 2 #define VIEW_OP_FETCH 3 #define VIEW_RES_ERROR -1 #define VIEW_RES_OK 0 int request_view_basement_info(int socket); int send_view_basement_info(int socket, RefSeq *src); ViewInfo* recv_view_basement_info(int socket); int request_maq_data(int socket, int last_code, int ref_id, int64_t start, int64_t end); int send_maq_data(int socket, RefSeq *src, int code, int64_t start, int64_t end); int recv_maq_data(int socket, ViewInfo *info); #endif maqview-0.2.5/compress.c0000644000265600020320000000467110761137603014326 0ustar tilleaadmin/* compress.c -- compress a memory buffer * Copyright (C) 1995-2003 Jean-loup Gailly. * For conditions of distribution and use, see copyright notice in zlib.h */ /* @(#) $Id$ */ #define ZLIB_INTERNAL #include "zlib.h" /* =========================================================================== Compresses the source buffer into the destination buffer. The level parameter has the same meaning as in deflateInit. sourceLen is the byte length of the source buffer. Upon entry, destLen is the total size of the destination buffer, which must be at least 0.1% larger than sourceLen plus 12 bytes. Upon exit, destLen is the actual size of the compressed buffer. compress2 returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_BUF_ERROR if there was not enough room in the output buffer, Z_STREAM_ERROR if the level parameter is invalid. */ int ZEXPORT compress2 (dest, destLen, source, sourceLen, level) Bytef *dest; uLongf *destLen; const Bytef *source; uLong sourceLen; int level; { z_stream stream; int err; stream.next_in = (Bytef*)source; stream.avail_in = (uInt)sourceLen; #ifdef MAXSEG_64K /* Check for source > 64K on 16-bit machine: */ if ((uLong)stream.avail_in != sourceLen) return Z_BUF_ERROR; #endif stream.next_out = dest; stream.avail_out = (uInt)*destLen; if ((uLong)stream.avail_out != *destLen) return Z_BUF_ERROR; stream.zalloc = (alloc_func)0; stream.zfree = (free_func)0; stream.opaque = (voidpf)0; err = deflateInit(&stream, level); if (err != Z_OK) return err; err = deflate(&stream, Z_FINISH); if (err != Z_STREAM_END) { deflateEnd(&stream); return err == Z_OK ? Z_BUF_ERROR : err; } *destLen = stream.total_out; err = deflateEnd(&stream); return err; } /* =========================================================================== */ int ZEXPORT compress (dest, destLen, source, sourceLen) Bytef *dest; uLongf *destLen; const Bytef *source; uLong sourceLen; { return compress2(dest, destLen, source, sourceLen, Z_DEFAULT_COMPRESSION); } /* =========================================================================== If the default memLevel or windowBits for deflateInit() is changed, then this function needs to be updated. */ uLong ZEXPORT compressBound (sourceLen) uLong sourceLen; { return sourceLen + (sourceLen >> 12) + (sourceLen >> 14) + 11; } maqview-0.2.5/zlib.h0000644000265600020320000020131411101572120013413 0ustar tilleaadmin/* zlib.h -- interface of the 'zlib' general purpose compression library version 1.2.3, July 18th, 2005 Copyright (C) 1995-2005 Jean-loup Gailly and Mark Adler This software is provided 'as-is', without any express or implied warranty. In no event will the authors be held liable for any damages arising from the use of this software. Permission is granted to anyone to use this software for any purpose, including commercial applications, and to alter it and redistribute it freely, subject to the following restrictions: 1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required. 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. 3. This notice may not be removed or altered from any source distribution. Jean-loup Gailly Mark Adler jloup@gzip.org madler@alumni.caltech.edu The data format used by the zlib library is described by RFCs (Request for Comments) 1950 to 1952 in the files http://www.ietf.org/rfc/rfc1950.txt (zlib format), rfc1951.txt (deflate format) and rfc1952.txt (gzip format). */ #ifndef ZLIB_H #define ZLIB_H #include "zconf.h" #ifdef __cplusplus extern "C" { #endif #define ZLIB_VERSION "1.2.3" #define ZLIB_VERNUM 0x1230 /* The 'zlib' compression library provides in-memory compression and decompression functions, including integrity checks of the uncompressed data. This version of the library supports only one compression method (deflation) but other algorithms will be added later and will have the same stream interface. Compression can be done in a single step if the buffers are large enough (for example if an input file is mmap'ed), or can be done by repeated calls of the compression function. In the latter case, the application must provide more input and/or consume the output (providing more output space) before each call. The compressed data format used by default by the in-memory functions is the zlib format, which is a zlib wrapper documented in RFC 1950, wrapped around a deflate stream, which is itself documented in RFC 1951. The library also supports reading and writing files in gzip (.gz) format with an interface similar to that of stdio using the functions that start with "gz". The gzip format is different from the zlib format. gzip is a gzip wrapper, documented in RFC 1952, wrapped around a deflate stream. This library can optionally read and write gzip streams in memory as well. The zlib format was designed to be compact and fast for use in memory and on communications channels. The gzip format was designed for single- file compression on file systems, has a larger header than zlib to maintain directory information, and uses a different, slower check method than zlib. The library does not install any signal handler. The decoder checks the consistency of the compressed data, so the library should never crash even in case of corrupted input. */ typedef voidpf (*alloc_func) OF((voidpf opaque, uInt items, uInt size)); typedef void (*free_func) OF((voidpf opaque, voidpf address)); struct internal_state; typedef struct z_stream_s { Bytef *next_in; /* next input byte */ uInt avail_in; /* number of bytes available at next_in */ uLong total_in; /* total nb of input bytes read so far */ Bytef *next_out; /* next output byte should be put there */ uInt avail_out; /* remaining free space at next_out */ uLong total_out; /* total nb of bytes output so far */ char *msg; /* last error message, NULL if no error */ struct internal_state FAR *state; /* not visible by applications */ alloc_func zalloc; /* used to allocate the internal state */ free_func zfree; /* used to free the internal state */ voidpf opaque; /* private data object passed to zalloc and zfree */ int data_type; /* best guess about the data type: binary or text */ uLong adler; /* adler32 value of the uncompressed data */ uLong reserved; /* reserved for future use */ } z_stream; typedef z_stream FAR *z_streamp; /* gzip header information passed to and from zlib routines. See RFC 1952 for more details on the meanings of these fields. */ typedef struct gz_header_s { int text; /* true if compressed data believed to be text */ uLong time; /* modification time */ int xflags; /* extra flags (not used when writing a gzip file) */ int os; /* operating system */ Bytef *extra; /* pointer to extra field or Z_NULL if none */ uInt extra_len; /* extra field length (valid if extra != Z_NULL) */ uInt extra_max; /* space at extra (only when reading header) */ Bytef *name; /* pointer to zero-terminated file name or Z_NULL */ uInt name_max; /* space at name (only when reading header) */ Bytef *comment; /* pointer to zero-terminated comment or Z_NULL */ uInt comm_max; /* space at comment (only when reading header) */ int hcrc; /* true if there was or will be a header crc */ int done; /* true when done reading gzip header (not used when writing a gzip file) */ } gz_header; typedef gz_header FAR *gz_headerp; /* The application must update next_in and avail_in when avail_in has dropped to zero. It must update next_out and avail_out when avail_out has dropped to zero. The application must initialize zalloc, zfree and opaque before calling the init function. All other fields are set by the compression library and must not be updated by the application. The opaque value provided by the application will be passed as the first parameter for calls of zalloc and zfree. This can be useful for custom memory management. The compression library attaches no meaning to the opaque value. zalloc must return Z_NULL if there is not enough memory for the object. If zlib is used in a multi-threaded application, zalloc and zfree must be thread safe. On 16-bit systems, the functions zalloc and zfree must be able to allocate exactly 65536 bytes, but will not be required to allocate more than this if the symbol MAXSEG_64K is defined (see zconf.h). WARNING: On MSDOS, pointers returned by zalloc for objects of exactly 65536 bytes *must* have their offset normalized to zero. The default allocation function provided by this library ensures this (see zutil.c). To reduce memory requirements and avoid any allocation of 64K objects, at the expense of compression ratio, compile the library with -DMAX_WBITS=14 (see zconf.h). The fields total_in and total_out can be used for statistics or progress reports. After compression, total_in holds the total size of the uncompressed data and may be saved for use in the decompressor (particularly if the decompressor wants to decompress everything in a single step). */ /* constants */ #define Z_NO_FLUSH 0 #define Z_PARTIAL_FLUSH 1 /* will be removed, use Z_SYNC_FLUSH instead */ #define Z_SYNC_FLUSH 2 #define Z_FULL_FLUSH 3 #define Z_FINISH 4 #define Z_BLOCK 5 /* Allowed flush values; see deflate() and inflate() below for details */ #define Z_OK 0 #define Z_STREAM_END 1 #define Z_NEED_DICT 2 #define Z_ERRNO (-1) #define Z_STREAM_ERROR (-2) #define Z_DATA_ERROR (-3) #define Z_MEM_ERROR (-4) #define Z_BUF_ERROR (-5) #define Z_VERSION_ERROR (-6) /* Return codes for the compression/decompression functions. Negative * values are errors, positive values are used for special but normal events. */ #define Z_NO_COMPRESSION 0 #define Z_BEST_SPEED 1 #define Z_BEST_COMPRESSION 9 #define Z_DEFAULT_COMPRESSION (-1) /* compression levels */ #define Z_FILTERED 1 #define Z_HUFFMAN_ONLY 2 #define Z_RLE 3 #define Z_FIXED 4 #define Z_DEFAULT_STRATEGY 0 /* compression strategy; see deflateInit2() below for details */ #define Z_BINARY 0 #define Z_TEXT 1 #define Z_ASCII Z_TEXT /* for compatibility with 1.2.2 and earlier */ #define Z_UNKNOWN 2 /* Possible values of the data_type field (though see inflate()) */ #define Z_DEFLATED 8 /* The deflate compression method (the only one supported in this version) */ #define Z_NULL 0 /* for initializing zalloc, zfree, opaque */ #define zlib_version zlibVersion() /* for compatibility with versions < 1.0.2 */ /* basic functions */ ZEXTERN const char * ZEXPORT zlibVersion OF((void)); /* The application can compare zlibVersion and ZLIB_VERSION for consistency. If the first character differs, the library code actually used is not compatible with the zlib.h header file used by the application. This check is automatically made by deflateInit and inflateInit. */ /* ZEXTERN int ZEXPORT deflateInit OF((z_streamp strm, int level)); Initializes the internal stream state for compression. The fields zalloc, zfree and opaque must be initialized before by the caller. If zalloc and zfree are set to Z_NULL, deflateInit updates them to use default allocation functions. The compression level must be Z_DEFAULT_COMPRESSION, or between 0 and 9: 1 gives best speed, 9 gives best compression, 0 gives no compression at all (the input data is simply copied a block at a time). Z_DEFAULT_COMPRESSION requests a default compromise between speed and compression (currently equivalent to level 6). deflateInit returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_STREAM_ERROR if level is not a valid compression level, Z_VERSION_ERROR if the zlib library version (zlib_version) is incompatible with the version assumed by the caller (ZLIB_VERSION). msg is set to null if there is no error message. deflateInit does not perform any compression: this will be done by deflate(). */ ZEXTERN int ZEXPORT deflate OF((z_streamp strm, int flush)); /* deflate compresses as much data as possible, and stops when the input buffer becomes empty or the output buffer becomes full. It may introduce some output latency (reading input without producing any output) except when forced to flush. The detailed semantics are as follows. deflate performs one or both of the following actions: - Compress more input starting at next_in and update next_in and avail_in accordingly. If not all input can be processed (because there is not enough room in the output buffer), next_in and avail_in are updated and processing will resume at this point for the next call of deflate(). - Provide more output starting at next_out and update next_out and avail_out accordingly. This action is forced if the parameter flush is non zero. Forcing flush frequently degrades the compression ratio, so this parameter should be set only when necessary (in interactive applications). Some output may be provided even if flush is not set. Before the call of deflate(), the application should ensure that at least one of the actions is possible, by providing more input and/or consuming more output, and updating avail_in or avail_out accordingly; avail_out should never be zero before the call. The application can consume the compressed output when it wants, for example when the output buffer is full (avail_out == 0), or after each call of deflate(). If deflate returns Z_OK and with zero avail_out, it must be called again after making room in the output buffer because there might be more output pending. Normally the parameter flush is set to Z_NO_FLUSH, which allows deflate to decide how much data to accumualte before producing output, in order to maximize compression. If the parameter flush is set to Z_SYNC_FLUSH, all pending output is flushed to the output buffer and the output is aligned on a byte boundary, so that the decompressor can get all input data available so far. (In particular avail_in is zero after the call if enough output space has been provided before the call.) Flushing may degrade compression for some compression algorithms and so it should be used only when necessary. If flush is set to Z_FULL_FLUSH, all output is flushed as with Z_SYNC_FLUSH, and the compression state is reset so that decompression can restart from this point if previous compressed data has been damaged or if random access is desired. Using Z_FULL_FLUSH too often can seriously degrade compression. If deflate returns with avail_out == 0, this function must be called again with the same value of the flush parameter and more output space (updated avail_out), until the flush is complete (deflate returns with non-zero avail_out). In the case of a Z_FULL_FLUSH or Z_SYNC_FLUSH, make sure that avail_out is greater than six to avoid repeated flush markers due to avail_out == 0 on return. If the parameter flush is set to Z_FINISH, pending input is processed, pending output is flushed and deflate returns with Z_STREAM_END if there was enough output space; if deflate returns with Z_OK, this function must be called again with Z_FINISH and more output space (updated avail_out) but no more input data, until it returns with Z_STREAM_END or an error. After deflate has returned Z_STREAM_END, the only possible operations on the stream are deflateReset or deflateEnd. Z_FINISH can be used immediately after deflateInit if all the compression is to be done in a single step. In this case, avail_out must be at least the value returned by deflateBound (see below). If deflate does not return Z_STREAM_END, then it must be called again as described above. deflate() sets strm->adler to the adler32 checksum of all input read so far (that is, total_in bytes). deflate() may update strm->data_type if it can make a good guess about the input data type (Z_BINARY or Z_TEXT). In doubt, the data is considered binary. This field is only for information purposes and does not affect the compression algorithm in any manner. deflate() returns Z_OK if some progress has been made (more input processed or more output produced), Z_STREAM_END if all input has been consumed and all output has been produced (only when flush is set to Z_FINISH), Z_STREAM_ERROR if the stream state was inconsistent (for example if next_in or next_out was NULL), Z_BUF_ERROR if no progress is possible (for example avail_in or avail_out was zero). Note that Z_BUF_ERROR is not fatal, and deflate() can be called again with more input and more output space to continue compressing. */ ZEXTERN int ZEXPORT deflateEnd OF((z_streamp strm)); /* All dynamically allocated data structures for this stream are freed. This function discards any unprocessed input and does not flush any pending output. deflateEnd returns Z_OK if success, Z_STREAM_ERROR if the stream state was inconsistent, Z_DATA_ERROR if the stream was freed prematurely (some input or output was discarded). In the error case, msg may be set but then points to a static string (which must not be deallocated). */ /* ZEXTERN int ZEXPORT inflateInit OF((z_streamp strm)); Initializes the internal stream state for decompression. The fields next_in, avail_in, zalloc, zfree and opaque must be initialized before by the caller. If next_in is not Z_NULL and avail_in is large enough (the exact value depends on the compression method), inflateInit determines the compression method from the zlib header and allocates all data structures accordingly; otherwise the allocation will be deferred to the first call of inflate. If zalloc and zfree are set to Z_NULL, inflateInit updates them to use default allocation functions. inflateInit returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_VERSION_ERROR if the zlib library version is incompatible with the version assumed by the caller. msg is set to null if there is no error message. inflateInit does not perform any decompression apart from reading the zlib header if present: this will be done by inflate(). (So next_in and avail_in may be modified, but next_out and avail_out are unchanged.) */ ZEXTERN int ZEXPORT inflate OF((z_streamp strm, int flush)); ZEXTERN int ZEXPORT inflate_zr OF((z_streamp strm, int flush)); /* inflate decompresses as much data as possible, and stops when the input buffer becomes empty or the output buffer becomes full. It may introduce some output latency (reading input without producing any output) except when forced to flush. The detailed semantics are as follows. inflate performs one or both of the following actions: - Decompress more input starting at next_in and update next_in and avail_in accordingly. If not all input can be processed (because there is not enough room in the output buffer), next_in is updated and processing will resume at this point for the next call of inflate(). - Provide more output starting at next_out and update next_out and avail_out accordingly. inflate() provides as much output as possible, until there is no more input data or no more space in the output buffer (see below about the flush parameter). Before the call of inflate(), the application should ensure that at least one of the actions is possible, by providing more input and/or consuming more output, and updating the next_* and avail_* values accordingly. The application can consume the uncompressed output when it wants, for example when the output buffer is full (avail_out == 0), or after each call of inflate(). If inflate returns Z_OK and with zero avail_out, it must be called again after making room in the output buffer because there might be more output pending. The flush parameter of inflate() can be Z_NO_FLUSH, Z_SYNC_FLUSH, Z_FINISH, or Z_BLOCK. Z_SYNC_FLUSH requests that inflate() flush as much output as possible to the output buffer. Z_BLOCK requests that inflate() stop if and when it gets to the next deflate block boundary. When decoding the zlib or gzip format, this will cause inflate() to return immediately after the header and before the first block. When doing a raw inflate, inflate() will go ahead and process the first block, and will return when it gets to the end of that block, or when it runs out of data. The Z_BLOCK option assists in appending to or combining deflate streams. Also to assist in this, on return inflate() will set strm->data_type to the number of unused bits in the last byte taken from strm->next_in, plus 64 if inflate() is currently decoding the last block in the deflate stream, plus 128 if inflate() returned immediately after decoding an end-of-block code or decoding the complete header up to just before the first byte of the deflate stream. The end-of-block will not be indicated until all of the uncompressed data from that block has been written to strm->next_out. The number of unused bits may in general be greater than seven, except when bit 7 of data_type is set, in which case the number of unused bits will be less than eight. inflate() should normally be called until it returns Z_STREAM_END or an error. However if all decompression is to be performed in a single step (a single call of inflate), the parameter flush should be set to Z_FINISH. In this case all pending input is processed and all pending output is flushed; avail_out must be large enough to hold all the uncompressed data. (The size of the uncompressed data may have been saved by the compressor for this purpose.) The next operation on this stream must be inflateEnd to deallocate the decompression state. The use of Z_FINISH is never required, but can be used to inform inflate that a faster approach may be used for the single inflate() call. In this implementation, inflate() always flushes as much output as possible to the output buffer, and always uses the faster approach on the first call. So the only effect of the flush parameter in this implementation is on the return value of inflate(), as noted below, or when it returns early because Z_BLOCK is used. If a preset dictionary is needed after this call (see inflateSetDictionary below), inflate sets strm->adler to the adler32 checksum of the dictionary chosen by the compressor and returns Z_NEED_DICT; otherwise it sets strm->adler to the adler32 checksum of all output produced so far (that is, total_out bytes) and returns Z_OK, Z_STREAM_END or an error code as described below. At the end of the stream, inflate() checks that its computed adler32 checksum is equal to that saved by the compressor and returns Z_STREAM_END only if the checksum is correct. inflate() will decompress and check either zlib-wrapped or gzip-wrapped deflate data. The header type is detected automatically. Any information contained in the gzip header is not retained, so applications that need that information should instead use raw inflate, see inflateInit2() below, or inflateBack() and perform their own processing of the gzip header and trailer. inflate() returns Z_OK if some progress has been made (more input processed or more output produced), Z_STREAM_END if the end of the compressed data has been reached and all uncompressed output has been produced, Z_NEED_DICT if a preset dictionary is needed at this point, Z_DATA_ERROR if the input data was corrupted (input stream not conforming to the zlib format or incorrect check value), Z_STREAM_ERROR if the stream structure was inconsistent (for example if next_in or next_out was NULL), Z_MEM_ERROR if there was not enough memory, Z_BUF_ERROR if no progress is possible or if there was not enough room in the output buffer when Z_FINISH is used. Note that Z_BUF_ERROR is not fatal, and inflate() can be called again with more input and more output space to continue decompressing. If Z_DATA_ERROR is returned, the application may then call inflateSync() to look for a good compression block if a partial recovery of the data is desired. */ ZEXTERN int ZEXPORT inflateEnd OF((z_streamp strm)); /* All dynamically allocated data structures for this stream are freed. This function discards any unprocessed input and does not flush any pending output. inflateEnd returns Z_OK if success, Z_STREAM_ERROR if the stream state was inconsistent. In the error case, msg may be set but then points to a static string (which must not be deallocated). */ /* Advanced functions */ /* The following functions are needed only in some special applications. */ /* ZEXTERN int ZEXPORT deflateInit2 OF((z_streamp strm, int level, int method, int windowBits, int memLevel, int strategy)); This is another version of deflateInit with more compression options. The fields next_in, zalloc, zfree and opaque must be initialized before by the caller. The method parameter is the compression method. It must be Z_DEFLATED in this version of the library. The windowBits parameter is the base two logarithm of the window size (the size of the history buffer). It should be in the range 8..15 for this version of the library. Larger values of this parameter result in better compression at the expense of memory usage. The default value is 15 if deflateInit is used instead. windowBits can also be -8..-15 for raw deflate. In this case, -windowBits determines the window size. deflate() will then generate raw deflate data with no zlib header or trailer, and will not compute an adler32 check value. windowBits can also be greater than 15 for optional gzip encoding. Add 16 to windowBits to write a simple gzip header and trailer around the compressed data instead of a zlib wrapper. The gzip header will have no file name, no extra data, no comment, no modification time (set to zero), no header crc, and the operating system will be set to 255 (unknown). If a gzip stream is being written, strm->adler is a crc32 instead of an adler32. The memLevel parameter specifies how much memory should be allocated for the internal compression state. memLevel=1 uses minimum memory but is slow and reduces compression ratio; memLevel=9 uses maximum memory for optimal speed. The default value is 8. See zconf.h for total memory usage as a function of windowBits and memLevel. The strategy parameter is used to tune the compression algorithm. Use the value Z_DEFAULT_STRATEGY for normal data, Z_FILTERED for data produced by a filter (or predictor), Z_HUFFMAN_ONLY to force Huffman encoding only (no string match), or Z_RLE to limit match distances to one (run-length encoding). Filtered data consists mostly of small values with a somewhat random distribution. In this case, the compression algorithm is tuned to compress them better. The effect of Z_FILTERED is to force more Huffman coding and less string matching; it is somewhat intermediate between Z_DEFAULT and Z_HUFFMAN_ONLY. Z_RLE is designed to be almost as fast as Z_HUFFMAN_ONLY, but give better compression for PNG image data. The strategy parameter only affects the compression ratio but not the correctness of the compressed output even if it is not set appropriately. Z_FIXED prevents the use of dynamic Huffman codes, allowing for a simpler decoder for special applications. deflateInit2 returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_STREAM_ERROR if a parameter is invalid (such as an invalid method). msg is set to null if there is no error message. deflateInit2 does not perform any compression: this will be done by deflate(). */ ZEXTERN int ZEXPORT deflateSetDictionary OF((z_streamp strm, const Bytef *dictionary, uInt dictLength)); /* Initializes the compression dictionary from the given byte sequence without producing any compressed output. This function must be called immediately after deflateInit, deflateInit2 or deflateReset, before any call of deflate. The compressor and decompressor must use exactly the same dictionary (see inflateSetDictionary). The dictionary should consist of strings (byte sequences) that are likely to be encountered later in the data to be compressed, with the most commonly used strings preferably put towards the end of the dictionary. Using a dictionary is most useful when the data to be compressed is short and can be predicted with good accuracy; the data can then be compressed better than with the default empty dictionary. Depending on the size of the compression data structures selected by deflateInit or deflateInit2, a part of the dictionary may in effect be discarded, for example if the dictionary is larger than the window size in deflate or deflate2. Thus the strings most likely to be useful should be put at the end of the dictionary, not at the front. In addition, the current implementation of deflate will use at most the window size minus 262 bytes of the provided dictionary. Upon return of this function, strm->adler is set to the adler32 value of the dictionary; the decompressor may later use this value to determine which dictionary has been used by the compressor. (The adler32 value applies to the whole dictionary even if only a subset of the dictionary is actually used by the compressor.) If a raw deflate was requested, then the adler32 value is not computed and strm->adler is not set. deflateSetDictionary returns Z_OK if success, or Z_STREAM_ERROR if a parameter is invalid (such as NULL dictionary) or the stream state is inconsistent (for example if deflate has already been called for this stream or if the compression method is bsort). deflateSetDictionary does not perform any compression: this will be done by deflate(). */ ZEXTERN int ZEXPORT deflateCopy OF((z_streamp dest, z_streamp source)); /* Sets the destination stream as a complete copy of the source stream. This function can be useful when several compression strategies will be tried, for example when there are several ways of pre-processing the input data with a filter. The streams that will be discarded should then be freed by calling deflateEnd. Note that deflateCopy duplicates the internal compression state which can be quite large, so this strategy is slow and can consume lots of memory. deflateCopy returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_STREAM_ERROR if the source stream state was inconsistent (such as zalloc being NULL). msg is left unchanged in both source and destination. */ ZEXTERN int ZEXPORT deflateReset OF((z_streamp strm)); /* This function is equivalent to deflateEnd followed by deflateInit, but does not free and reallocate all the internal compression state. The stream will keep the same compression level and any other attributes that may have been set by deflateInit2. deflateReset returns Z_OK if success, or Z_STREAM_ERROR if the source stream state was inconsistent (such as zalloc or state being NULL). */ ZEXTERN int ZEXPORT deflateParams OF((z_streamp strm, int level, int strategy)); /* Dynamically update the compression level and compression strategy. The interpretation of level and strategy is as in deflateInit2. This can be used to switch between compression and straight copy of the input data, or to switch to a different kind of input data requiring a different strategy. If the compression level is changed, the input available so far is compressed with the old level (and may be flushed); the new level will take effect only at the next call of deflate(). Before the call of deflateParams, the stream state must be set as for a call of deflate(), since the currently available input may have to be compressed and flushed. In particular, strm->avail_out must be non-zero. deflateParams returns Z_OK if success, Z_STREAM_ERROR if the source stream state was inconsistent or if a parameter was invalid, Z_BUF_ERROR if strm->avail_out was zero. */ ZEXTERN int ZEXPORT deflateTune OF((z_streamp strm, int good_length, int max_lazy, int nice_length, int max_chain)); /* Fine tune deflate's internal compression parameters. This should only be used by someone who understands the algorithm used by zlib's deflate for searching for the best matching string, and even then only by the most fanatic optimizer trying to squeeze out the last compressed bit for their specific input data. Read the deflate.c source code for the meaning of the max_lazy, good_length, nice_length, and max_chain parameters. deflateTune() can be called after deflateInit() or deflateInit2(), and returns Z_OK on success, or Z_STREAM_ERROR for an invalid deflate stream. */ ZEXTERN uLong ZEXPORT deflateBound OF((z_streamp strm, uLong sourceLen)); /* deflateBound() returns an upper bound on the compressed size after deflation of sourceLen bytes. It must be called after deflateInit() or deflateInit2(). This would be used to allocate an output buffer for deflation in a single pass, and so would be called before deflate(). */ ZEXTERN int ZEXPORT deflatePrime OF((z_streamp strm, int bits, int value)); /* deflatePrime() inserts bits in the deflate output stream. The intent is that this function is used to start off the deflate output with the bits leftover from a previous deflate stream when appending to it. As such, this function can only be used for raw deflate, and must be used before the first deflate() call after a deflateInit2() or deflateReset(). bits must be less than or equal to 16, and that many of the least significant bits of value will be inserted in the output. deflatePrime returns Z_OK if success, or Z_STREAM_ERROR if the source stream state was inconsistent. */ ZEXTERN int ZEXPORT deflateSetHeader OF((z_streamp strm, gz_headerp head)); /* deflateSetHeader() provides gzip header information for when a gzip stream is requested by deflateInit2(). deflateSetHeader() may be called after deflateInit2() or deflateReset() and before the first call of deflate(). The text, time, os, extra field, name, and comment information in the provided gz_header structure are written to the gzip header (xflag is ignored -- the extra flags are set according to the compression level). The caller must assure that, if not Z_NULL, name and comment are terminated with a zero byte, and that if extra is not Z_NULL, that extra_len bytes are available there. If hcrc is true, a gzip header crc is included. Note that the current versions of the command-line version of gzip (up through version 1.3.x) do not support header crc's, and will report that it is a "multi-part gzip file" and give up. If deflateSetHeader is not used, the default gzip header has text false, the time set to zero, and os set to 255, with no extra, name, or comment fields. The gzip header is returned to the default state by deflateReset(). deflateSetHeader returns Z_OK if success, or Z_STREAM_ERROR if the source stream state was inconsistent. */ /* ZEXTERN int ZEXPORT inflateInit2 OF((z_streamp strm, int windowBits)); This is another version of inflateInit with an extra parameter. The fields next_in, avail_in, zalloc, zfree and opaque must be initialized before by the caller. The windowBits parameter is the base two logarithm of the maximum window size (the size of the history buffer). It should be in the range 8..15 for this version of the library. The default value is 15 if inflateInit is used instead. windowBits must be greater than or equal to the windowBits value provided to deflateInit2() while compressing, or it must be equal to 15 if deflateInit2() was not used. If a compressed stream with a larger window size is given as input, inflate() will return with the error code Z_DATA_ERROR instead of trying to allocate a larger window. windowBits can also be -8..-15 for raw inflate. In this case, -windowBits determines the window size. inflate() will then process raw deflate data, not looking for a zlib or gzip header, not generating a check value, and not looking for any check values for comparison at the end of the stream. This is for use with other formats that use the deflate compressed data format such as zip. Those formats provide their own check values. If a custom format is developed using the raw deflate format for compressed data, it is recommended that a check value such as an adler32 or a crc32 be applied to the uncompressed data as is done in the zlib, gzip, and zip formats. For most applications, the zlib format should be used as is. Note that comments above on the use in deflateInit2() applies to the magnitude of windowBits. windowBits can also be greater than 15 for optional gzip decoding. Add 32 to windowBits to enable zlib and gzip decoding with automatic header detection, or add 16 to decode only the gzip format (the zlib format will return a Z_DATA_ERROR). If a gzip stream is being decoded, strm->adler is a crc32 instead of an adler32. inflateInit2 returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_STREAM_ERROR if a parameter is invalid (such as a null strm). msg is set to null if there is no error message. inflateInit2 does not perform any decompression apart from reading the zlib header if present: this will be done by inflate(). (So next_in and avail_in may be modified, but next_out and avail_out are unchanged.) */ ZEXTERN int ZEXPORT inflateSetDictionary OF((z_streamp strm, const Bytef *dictionary, uInt dictLength)); /* Initializes the decompression dictionary from the given uncompressed byte sequence. This function must be called immediately after a call of inflate, if that call returned Z_NEED_DICT. The dictionary chosen by the compressor can be determined from the adler32 value returned by that call of inflate. The compressor and decompressor must use exactly the same dictionary (see deflateSetDictionary). For raw inflate, this function can be called immediately after inflateInit2() or inflateReset() and before any call of inflate() to set the dictionary. The application must insure that the dictionary that was used for compression is provided. inflateSetDictionary returns Z_OK if success, Z_STREAM_ERROR if a parameter is invalid (such as NULL dictionary) or the stream state is inconsistent, Z_DATA_ERROR if the given dictionary doesn't match the expected one (incorrect adler32 value). inflateSetDictionary does not perform any decompression: this will be done by subsequent calls of inflate(). */ ZEXTERN int ZEXPORT inflateSync OF((z_streamp strm)); /* Skips invalid compressed data until a full flush point (see above the description of deflate with Z_FULL_FLUSH) can be found, or until all available input is skipped. No output is provided. inflateSync returns Z_OK if a full flush point has been found, Z_BUF_ERROR if no more input was provided, Z_DATA_ERROR if no flush point has been found, or Z_STREAM_ERROR if the stream structure was inconsistent. In the success case, the application may save the current current value of total_in which indicates where valid compressed data was found. In the error case, the application may repeatedly call inflateSync, providing more input each time, until success or end of the input data. */ ZEXTERN int ZEXPORT inflateCopy OF((z_streamp dest, z_streamp source)); /* Sets the destination stream as a complete copy of the source stream. This function can be useful when randomly accessing a large stream. The first pass through the stream can periodically record the inflate state, allowing restarting inflate at those points when randomly accessing the stream. inflateCopy returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_STREAM_ERROR if the source stream state was inconsistent (such as zalloc being NULL). msg is left unchanged in both source and destination. */ ZEXTERN int ZEXPORT inflateReset OF((z_streamp strm)); /* This function is equivalent to inflateEnd followed by inflateInit, but does not free and reallocate all the internal decompression state. The stream will keep attributes that may have been set by inflateInit2. inflateReset returns Z_OK if success, or Z_STREAM_ERROR if the source stream state was inconsistent (such as zalloc or state being NULL). */ ZEXTERN int ZEXPORT inflatePrime OF((z_streamp strm, int bits, int value)); /* This function inserts bits in the inflate input stream. The intent is that this function is used to start inflating at a bit position in the middle of a byte. The provided bits will be used before any bytes are used from next_in. This function should only be used with raw inflate, and should be used before the first inflate() call after inflateInit2() or inflateReset(). bits must be less than or equal to 16, and that many of the least significant bits of value will be inserted in the input. inflatePrime returns Z_OK if success, or Z_STREAM_ERROR if the source stream state was inconsistent. */ ZEXTERN int ZEXPORT inflateGetHeader OF((z_streamp strm, gz_headerp head)); /* inflateGetHeader() requests that gzip header information be stored in the provided gz_header structure. inflateGetHeader() may be called after inflateInit2() or inflateReset(), and before the first call of inflate(). As inflate() processes the gzip stream, head->done is zero until the header is completed, at which time head->done is set to one. If a zlib stream is being decoded, then head->done is set to -1 to indicate that there will be no gzip header information forthcoming. Note that Z_BLOCK can be used to force inflate() to return immediately after header processing is complete and before any actual data is decompressed. The text, time, xflags, and os fields are filled in with the gzip header contents. hcrc is set to true if there is a header CRC. (The header CRC was valid if done is set to one.) If extra is not Z_NULL, then extra_max contains the maximum number of bytes to write to extra. Once done is true, extra_len contains the actual extra field length, and extra contains the extra field, or that field truncated if extra_max is less than extra_len. If name is not Z_NULL, then up to name_max characters are written there, terminated with a zero unless the length is greater than name_max. If comment is not Z_NULL, then up to comm_max characters are written there, terminated with a zero unless the length is greater than comm_max. When any of extra, name, or comment are not Z_NULL and the respective field is not present in the header, then that field is set to Z_NULL to signal its absence. This allows the use of deflateSetHeader() with the returned structure to duplicate the header. However if those fields are set to allocated memory, then the application will need to save those pointers elsewhere so that they can be eventually freed. If inflateGetHeader is not used, then the header information is simply discarded. The header is always checked for validity, including the header CRC if present. inflateReset() will reset the process to discard the header information. The application would need to call inflateGetHeader() again to retrieve the header from the next gzip stream. inflateGetHeader returns Z_OK if success, or Z_STREAM_ERROR if the source stream state was inconsistent. */ /* ZEXTERN int ZEXPORT inflateBackInit OF((z_streamp strm, int windowBits, unsigned char FAR *window)); Initialize the internal stream state for decompression using inflateBack() calls. The fields zalloc, zfree and opaque in strm must be initialized before the call. If zalloc and zfree are Z_NULL, then the default library- derived memory allocation routines are used. windowBits is the base two logarithm of the window size, in the range 8..15. window is a caller supplied buffer of that size. Except for special applications where it is assured that deflate was used with small window sizes, windowBits must be 15 and a 32K byte window must be supplied to be able to decompress general deflate streams. See inflateBack() for the usage of these routines. inflateBackInit will return Z_OK on success, Z_STREAM_ERROR if any of the paramaters are invalid, Z_MEM_ERROR if the internal state could not be allocated, or Z_VERSION_ERROR if the version of the library does not match the version of the header file. */ typedef unsigned (*in_func) OF((void FAR *, unsigned char FAR * FAR *)); typedef int (*out_func) OF((void FAR *, unsigned char FAR *, unsigned)); ZEXTERN int ZEXPORT inflateBack OF((z_streamp strm, in_func in, void FAR *in_desc, out_func out, void FAR *out_desc)); /* inflateBack() does a raw inflate with a single call using a call-back interface for input and output. This is more efficient than inflate() for file i/o applications in that it avoids copying between the output and the sliding window by simply making the window itself the output buffer. This function trusts the application to not change the output buffer passed by the output function, at least until inflateBack() returns. inflateBackInit() must be called first to allocate the internal state and to initialize the state with the user-provided window buffer. inflateBack() may then be used multiple times to inflate a complete, raw deflate stream with each call. inflateBackEnd() is then called to free the allocated state. A raw deflate stream is one with no zlib or gzip header or trailer. This routine would normally be used in a utility that reads zip or gzip files and writes out uncompressed files. The utility would decode the header and process the trailer on its own, hence this routine expects only the raw deflate stream to decompress. This is different from the normal behavior of inflate(), which expects either a zlib or gzip header and trailer around the deflate stream. inflateBack() uses two subroutines supplied by the caller that are then called by inflateBack() for input and output. inflateBack() calls those routines until it reads a complete deflate stream and writes out all of the uncompressed data, or until it encounters an error. The function's parameters and return types are defined above in the in_func and out_func typedefs. inflateBack() will call in(in_desc, &buf) which should return the number of bytes of provided input, and a pointer to that input in buf. If there is no input available, in() must return zero--buf is ignored in that case--and inflateBack() will return a buffer error. inflateBack() will call out(out_desc, buf, len) to write the uncompressed data buf[0..len-1]. out() should return zero on success, or non-zero on failure. If out() returns non-zero, inflateBack() will return with an error. Neither in() nor out() are permitted to change the contents of the window provided to inflateBackInit(), which is also the buffer that out() uses to write from. The length written by out() will be at most the window size. Any non-zero amount of input may be provided by in(). For convenience, inflateBack() can be provided input on the first call by setting strm->next_in and strm->avail_in. If that input is exhausted, then in() will be called. Therefore strm->next_in must be initialized before calling inflateBack(). If strm->next_in is Z_NULL, then in() will be called immediately for input. If strm->next_in is not Z_NULL, then strm->avail_in must also be initialized, and then if strm->avail_in is not zero, input will initially be taken from strm->next_in[0 .. strm->avail_in - 1]. The in_desc and out_desc parameters of inflateBack() is passed as the first parameter of in() and out() respectively when they are called. These descriptors can be optionally used to pass any information that the caller- supplied in() and out() functions need to do their job. On return, inflateBack() will set strm->next_in and strm->avail_in to pass back any unused input that was provided by the last in() call. The return values of inflateBack() can be Z_STREAM_END on success, Z_BUF_ERROR if in() or out() returned an error, Z_DATA_ERROR if there was a format error in the deflate stream (in which case strm->msg is set to indicate the nature of the error), or Z_STREAM_ERROR if the stream was not properly initialized. In the case of Z_BUF_ERROR, an input or output error can be distinguished using strm->next_in which will be Z_NULL only if in() returned an error. If strm->next is not Z_NULL, then the Z_BUF_ERROR was due to out() returning non-zero. (in() will always be called before out(), so strm->next_in is assured to be defined if out() returns non-zero.) Note that inflateBack() cannot return Z_OK. */ ZEXTERN int ZEXPORT inflateBackEnd OF((z_streamp strm)); /* All memory allocated by inflateBackInit() is freed. inflateBackEnd() returns Z_OK on success, or Z_STREAM_ERROR if the stream state was inconsistent. */ ZEXTERN uLong ZEXPORT zlibCompileFlags OF((void)); /* Return flags indicating compile-time options. Type sizes, two bits each, 00 = 16 bits, 01 = 32, 10 = 64, 11 = other: 1.0: size of uInt 3.2: size of uLong 5.4: size of voidpf (pointer) 7.6: size of z_off_t Compiler, assembler, and debug options: 8: DEBUG 9: ASMV or ASMINF -- use ASM code 10: ZLIB_WINAPI -- exported functions use the WINAPI calling convention 11: 0 (reserved) One-time table building (smaller code, but not thread-safe if true): 12: BUILDFIXED -- build static block decoding tables when needed 13: DYNAMIC_CRC_TABLE -- build CRC calculation tables when needed 14,15: 0 (reserved) Library content (indicates missing functionality): 16: NO_GZCOMPRESS -- gz* functions cannot compress (to avoid linking deflate code when not needed) 17: NO_GZIP -- deflate can't write gzip streams, and inflate can't detect and decode gzip streams (to avoid linking crc code) 18-19: 0 (reserved) Operation variations (changes in library functionality): 20: PKZIP_BUG_WORKAROUND -- slightly more permissive inflate 21: FASTEST -- deflate algorithm with only one, lowest compression level 22,23: 0 (reserved) The sprintf variant used by gzprintf (zero is best): 24: 0 = vs*, 1 = s* -- 1 means limited to 20 arguments after the format 25: 0 = *nprintf, 1 = *printf -- 1 means gzprintf() not secure! 26: 0 = returns value, 1 = void -- 1 means inferred string length returned Remainder: 27-31: 0 (reserved) */ /* utility functions */ /* The following utility functions are implemented on top of the basic stream-oriented functions. To simplify the interface, some default options are assumed (compression level and memory usage, standard memory allocation functions). The source code of these utility functions can easily be modified if you need special options. */ ZEXTERN int ZEXPORT compress OF((Bytef *dest, uLongf *destLen, const Bytef *source, uLong sourceLen)); /* Compresses the source buffer into the destination buffer. sourceLen is the byte length of the source buffer. Upon entry, destLen is the total size of the destination buffer, which must be at least the value returned by compressBound(sourceLen). Upon exit, destLen is the actual size of the compressed buffer. This function can be used to compress a whole file at once if the input file is mmap'ed. compress returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_BUF_ERROR if there was not enough room in the output buffer. */ ZEXTERN int ZEXPORT compress2 OF((Bytef *dest, uLongf *destLen, const Bytef *source, uLong sourceLen, int level)); /* Compresses the source buffer into the destination buffer. The level parameter has the same meaning as in deflateInit. sourceLen is the byte length of the source buffer. Upon entry, destLen is the total size of the destination buffer, which must be at least the value returned by compressBound(sourceLen). Upon exit, destLen is the actual size of the compressed buffer. compress2 returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_BUF_ERROR if there was not enough room in the output buffer, Z_STREAM_ERROR if the level parameter is invalid. */ ZEXTERN uLong ZEXPORT compressBound OF((uLong sourceLen)); /* compressBound() returns an upper bound on the compressed size after compress() or compress2() on sourceLen bytes. It would be used before a compress() or compress2() call to allocate the destination buffer. */ ZEXTERN int ZEXPORT uncompress OF((Bytef *dest, uLongf *destLen, const Bytef *source, uLong sourceLen)); /* Decompresses the source buffer into the destination buffer. sourceLen is the byte length of the source buffer. Upon entry, destLen is the total size of the destination buffer, which must be large enough to hold the entire uncompressed data. (The size of the uncompressed data must have been saved previously by the compressor and transmitted to the decompressor by some mechanism outside the scope of this compression library.) Upon exit, destLen is the actual size of the compressed buffer. This function can be used to decompress a whole file at once if the input file is mmap'ed. uncompress returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_BUF_ERROR if there was not enough room in the output buffer, or Z_DATA_ERROR if the input data was corrupted or incomplete. */ typedef voidp gzFile; ZEXTERN gzFile ZEXPORT gzopen OF((const char *path, const char *mode)); /* Opens a gzip (.gz) file for reading or writing. The mode parameter is as in fopen ("rb" or "wb") but can also include a compression level ("wb9") or a strategy: 'f' for filtered data as in "wb6f", 'h' for Huffman only compression as in "wb1h", or 'R' for run-length encoding as in "wb1R". (See the description of deflateInit2 for more information about the strategy parameter.) gzopen can be used to read a file which is not in gzip format; in this case gzread will directly read from the file without decompression. gzopen returns NULL if the file could not be opened or if there was insufficient memory to allocate the (de)compression state; errno can be checked to distinguish the two cases (if errno is zero, the zlib error is Z_MEM_ERROR). */ ZEXTERN gzFile ZEXPORT gzdopen OF((int fd, const char *mode)); /* gzdopen() associates a gzFile with the file descriptor fd. File descriptors are obtained from calls like open, dup, creat, pipe or fileno (in the file has been previously opened with fopen). The mode parameter is as in gzopen. The next call of gzclose on the returned gzFile will also close the file descriptor fd, just like fclose(fdopen(fd), mode) closes the file descriptor fd. If you want to keep fd open, use gzdopen(dup(fd), mode). gzdopen returns NULL if there was insufficient memory to allocate the (de)compression state. */ ZEXTERN int ZEXPORT gzsetparams OF((gzFile file, int level, int strategy)); /* Dynamically update the compression level or strategy. See the description of deflateInit2 for the meaning of these parameters. gzsetparams returns Z_OK if success, or Z_STREAM_ERROR if the file was not opened for writing. */ ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len)); /* Reads the given number of uncompressed bytes from the compressed file. If the input file was not in gzip format, gzread copies the given number of bytes into the buffer. gzread returns the number of uncompressed bytes actually read (0 for end of file, -1 for error). */ ZEXTERN int ZEXPORT gzwrite OF((gzFile file, voidpc buf, unsigned len)); /* Writes the given number of uncompressed bytes into the compressed file. gzwrite returns the number of uncompressed bytes actually written (0 in case of error). */ ZEXTERN int ZEXPORTVA gzprintf OF((gzFile file, const char *format, ...)); /* Converts, formats, and writes the args to the compressed file under control of the format string, as in fprintf. gzprintf returns the number of uncompressed bytes actually written (0 in case of error). The number of uncompressed bytes written is limited to 4095. The caller should assure that this limit is not exceeded. If it is exceeded, then gzprintf() will return return an error (0) with nothing written. In this case, there may also be a buffer overflow with unpredictable consequences, which is possible only if zlib was compiled with the insecure functions sprintf() or vsprintf() because the secure snprintf() or vsnprintf() functions were not available. */ ZEXTERN int ZEXPORT gzputs OF((gzFile file, const char *s)); /* Writes the given null-terminated string to the compressed file, excluding the terminating null character. gzputs returns the number of characters written, or -1 in case of error. */ ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len)); /* Reads bytes from the compressed file until len-1 characters are read, or a newline character is read and transferred to buf, or an end-of-file condition is encountered. The string is then terminated with a null character. gzgets returns buf, or Z_NULL in case of error. */ ZEXTERN int ZEXPORT gzputc OF((gzFile file, int c)); /* Writes c, converted to an unsigned char, into the compressed file. gzputc returns the value that was written, or -1 in case of error. */ ZEXTERN int ZEXPORT gzgetc OF((gzFile file)); /* Reads one byte from the compressed file. gzgetc returns this byte or -1 in case of end of file or error. */ ZEXTERN int ZEXPORT gzungetc OF((int c, gzFile file)); /* Push one character back onto the stream to be read again later. Only one character of push-back is allowed. gzungetc() returns the character pushed, or -1 on failure. gzungetc() will fail if a character has been pushed but not read yet, or if c is -1. The pushed character will be discarded if the stream is repositioned with gzseek() or gzrewind(). */ ZEXTERN int ZEXPORT gzflush OF((gzFile file, int flush)); /* Flushes all pending output into the compressed file. The parameter flush is as in the deflate() function. The return value is the zlib error number (see function gzerror below). gzflush returns Z_OK if the flush parameter is Z_FINISH and all output could be flushed. gzflush should be called only when strictly necessary because it can degrade compression. */ ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile file, z_off_t offset, int whence)); /* Sets the starting position for the next gzread or gzwrite on the given compressed file. The offset represents a number of bytes in the uncompressed data stream. The whence parameter is defined as in lseek(2); the value SEEK_END is not supported. If the file is opened for reading, this function is emulated but can be extremely slow. If the file is opened for writing, only forward seeks are supported; gzseek then compresses a sequence of zeroes up to the new starting position. gzseek returns the resulting offset location as measured in bytes from the beginning of the uncompressed stream, or -1 in case of error, in particular if the file is opened for writing and the new starting position would be before the current position. */ ZEXTERN int ZEXPORT gzrewind OF((gzFile file)); /* Rewinds the given file. This function is supported only for reading. gzrewind(file) is equivalent to (int)gzseek(file, 0L, SEEK_SET) */ ZEXTERN z_off_t ZEXPORT gztell OF((gzFile file)); /* Returns the starting position for the next gzread or gzwrite on the given compressed file. This position represents a number of bytes in the uncompressed data stream. gztell(file) is equivalent to gzseek(file, 0L, SEEK_CUR) */ ZEXTERN int ZEXPORT gzeof OF((gzFile file)); /* Returns 1 when EOF has previously been detected reading the given input stream, otherwise zero. */ ZEXTERN int ZEXPORT gzdirect OF((gzFile file)); /* Returns 1 if file is being read directly without decompression, otherwise zero. */ ZEXTERN int ZEXPORT gzclose OF((gzFile file)); /* Flushes all pending output if necessary, closes the compressed file and deallocates all the (de)compression state. The return value is the zlib error number (see function gzerror below). */ ZEXTERN const char * ZEXPORT gzerror OF((gzFile file, int *errnum)); /* Returns the error message for the last error which occurred on the given compressed file. errnum is set to zlib error number. If an error occurred in the file system and not in the compression library, errnum is set to Z_ERRNO and the application may consult errno to get the exact error code. */ ZEXTERN void ZEXPORT gzclearerr OF((gzFile file)); /* Clears the error and end-of-file flags for file. This is analogous to the clearerr() function in stdio. This is useful for continuing to read a gzip file that is being written concurrently. */ /* checksum functions */ /* These functions are not related to compression but are exported anyway because they might be useful in applications using the compression library. */ ZEXTERN uLong ZEXPORT adler32 OF((uLong adler, const Bytef *buf, uInt len)); /* Update a running Adler-32 checksum with the bytes buf[0..len-1] and return the updated checksum. If buf is NULL, this function returns the required initial value for the checksum. An Adler-32 checksum is almost as reliable as a CRC32 but can be computed much faster. Usage example: uLong adler = adler32(0L, Z_NULL, 0); while (read_buffer(buffer, length) != EOF) { adler = adler32(adler, buffer, length); } if (adler != original_adler) error(); */ ZEXTERN uLong ZEXPORT adler32_combine OF((uLong adler1, uLong adler2, z_off_t len2)); /* Combine two Adler-32 checksums into one. For two sequences of bytes, seq1 and seq2 with lengths len1 and len2, Adler-32 checksums were calculated for each, adler1 and adler2. adler32_combine() returns the Adler-32 checksum of seq1 and seq2 concatenated, requiring only adler1, adler2, and len2. */ ZEXTERN uLong ZEXPORT crc32 OF((uLong crc, const Bytef *buf, uInt len)); /* Update a running CRC-32 with the bytes buf[0..len-1] and return the updated CRC-32. If buf is NULL, this function returns the required initial value for the for the crc. Pre- and post-conditioning (one's complement) is performed within this function so it shouldn't be done by the application. Usage example: uLong crc = crc32(0L, Z_NULL, 0); while (read_buffer(buffer, length) != EOF) { crc = crc32(crc, buffer, length); } if (crc != original_crc) error(); */ ZEXTERN uLong ZEXPORT crc32_combine OF((uLong crc1, uLong crc2, z_off_t len2)); /* Combine two CRC-32 check values into one. For two sequences of bytes, seq1 and seq2 with lengths len1 and len2, CRC-32 check values were calculated for each, crc1 and crc2. crc32_combine() returns the CRC-32 check value of seq1 and seq2 concatenated, requiring only crc1, crc2, and len2. */ /* various hacks, don't look :) */ /* deflateInit and inflateInit are macros to allow checking the zlib version * and the compiler's view of z_stream: */ ZEXTERN int ZEXPORT deflateInit_ OF((z_streamp strm, int level, const char *version, int stream_size)); ZEXTERN int ZEXPORT inflateInit_ OF((z_streamp strm, const char *version, int stream_size)); ZEXTERN int ZEXPORT deflateInit2_ OF((z_streamp strm, int level, int method, int windowBits, int memLevel, int strategy, const char *version, int stream_size)); ZEXTERN int ZEXPORT inflateInit2_ OF((z_streamp strm, int windowBits, const char *version, int stream_size)); ZEXTERN int ZEXPORT inflateBackInit_ OF((z_streamp strm, int windowBits, unsigned char FAR *window, const char *version, int stream_size)); #define deflateInit(strm, level) \ deflateInit_((strm), (level), ZLIB_VERSION, sizeof(z_stream)) #define inflateInit(strm) \ inflateInit_((strm), ZLIB_VERSION, sizeof(z_stream)) #define deflateInit2(strm, level, method, windowBits, memLevel, strategy) \ deflateInit2_((strm),(level),(method),(windowBits),(memLevel),\ (strategy), ZLIB_VERSION, sizeof(z_stream)) #define inflateInit2(strm, windowBits) \ inflateInit2_((strm), (windowBits), ZLIB_VERSION, sizeof(z_stream)) #define inflateBackInit(strm, windowBits, window) \ inflateBackInit_((strm), (windowBits), (window), \ ZLIB_VERSION, sizeof(z_stream)) #if !defined(ZUTIL_H) && !defined(NO_DUMMY_DECL) struct internal_state {int dummy;}; /* hack for buggy compilers */ #endif ZEXTERN const char * ZEXPORT zError OF((int)); ZEXTERN int ZEXPORT inflateSyncPoint OF((z_streamp z)); ZEXTERN const uLongf * ZEXPORT get_crc_table OF((void)); #ifdef __cplusplus } #endif #endif /* ZLIB_H */ maqview-0.2.5/README0000644000265600020320000001170111054154215013171 0ustar tilleaadminM.A.Q. Viewer 1 ... install 2 ... zrio 3 ... maqindex 4 ... maqindex_socks 5 ... maqview 1, install maqview MAQViewer has been successly installed in linux and cygwin. $> tar -xzf maqview-XXX.tar.gz $> cd maqview $> ./autogen.sh $> ./configure $> make Or you can try: $> cd maqview $> make -f Makefile.generic 2, zrio Random Access GZ File Store points in every span of uncompressed source file, point contains 32k previous context, offsets in compressed and uncompressed file. Usage: ./zrio make | use make [] make index for gz-file,index filename will be .idx each level increasing the time for search whist decreasing the size of index level: default 1024, 1/1024 of source file level: 512, 1/512 of source file level: ... use [ ] use index .idx, exact from offset(source position) to stdout 3, mapindex Make Index for .map File for maq Uses BTREE index for reads in map-file, it writes an .vm file to store index Usage: maqindex <-i|-v|-b> [-l level] [-c cns] [chr[:begin[-end]] [...]] Options: -l INT level for indexing [1024] -c STR .cns file for this .map file -i index the map file -v display the alignment in the mapview format -b dump in the .map format e.g. 1, $> maqindex -i all.map 2, $> maqindex -i -c all.cns all.map 3, $> maqindex -i -c all.cns 4, $> maqindex -v all.map chrI:1-200 4, maqindex_socks Distribute MAQ-Data visa Networking When maq products huge result files, sharing those files among computers is required, maqindex_socks may help you. We had used it in our web-site to display alignment of HUMAN solexa reads. Usage: Setup Server: ./maqindex_socks -s [ [ []]] Run Client : ./maqindex_socks -c [ ] e.g. 1, $> maqindex_socks -s 1768 all.map >maqindex_server.log 2>&1 & 2, $> maqindex_socks -c locahost 1768 chrI 1 200 5, maqview Viewer For MAQ map File maqview is based on OpenGL, it requires gl, glx, glu and glut Usage: maqview [-c cns_file] [-w width:800] [-h height:600] map_file [ref_name:start_pos] Before uses maqview, you must run zrio and map_index on map-file, e.g. ./maqindex test.map ./maqview test.map If you have ref seq files named as in map-file, you can put them in working directory maqview will automatic treat them as ref seqs, those files must be plain text files contain only sequences without any additional format or characters, '\n' is also excluded It supports those keys in window: --------------------------------------------------------------------- ? : Display this help : Draw bases as characters : Draw bases as squares : Draw read as line p : Switch to the previous reference sequence n : Switch to the next reference sequence r : Show/Hide the menu of ref list a / h / [LEFT]: Move left by one base d / l / [RIGHT]: Move right by one base w / k / [UP]: Move view window down s / j / [DOWN]: Move view window up > : Move to next read < : Move to previous read g / [HOME]: Goto begin G / [END]: Goto end u [PAGE UP]: Move left one page [PAGE DOWN]: Move right one page + : Zoom in - : Zoom out + : Duplicate current view - : Close current view c : Input command 0 : Restore default scale q : Toggle display/undisplay mapping qualities e : Toggle display single-end/paired-end mapping qualities o : Open a new view file : exit hold [SHIFT] : Speed move 100 times hold [CTRL] : Speed move 1000 times : Toogle on/off automatic rolling on ^b : Toogle on/off automatic rolling back Enter an integer then press key to goto the position Enter an integer then press other key than can speed the integer times Mouse: left button to select; middle button temporarily drags the scene; right button sets marker Mouse: move over an entity to show description Press to exit help mode --------------------------------------------------------------------- Command: q|exit : close current view(euals -) c|clone : clone a copy of current view, and add it in the window (equals +) b|bind : binding current view to n'th view, n is 1 based B|unbind : unbinding r|ref : Move view to a new ref g|goto : goto a position, 1 based s|set : a list of commands i|interval : set the interval to n, interval is used in rooling s|step : set step to n, step is used in rolling maqview-0.2.5/deflate.c0000644000265600020320000017524311075263753014110 0ustar tilleaadmin/* deflate.c -- compress data using the deflation algorithm * Copyright (C) 1995-2005 Jean-loup Gailly. * For conditions of distribution and use, see copyright notice in zlib.h */ /* * ALGORITHM * * The "deflation" process depends on being able to identify portions * of the input text which are identical to earlier input (within a * sliding window trailing behind the input currently being processed). * * The most straightforward technique turns out to be the fastest for * most input files: try all possible matches and select the longest. * The key feature of this algorithm is that insertions into the string * dictionary are very simple and thus fast, and deletions are avoided * completely. Insertions are performed at each input character, whereas * string matches are performed only when the previous match ends. So it * is preferable to spend more time in matches to allow very fast string * insertions and avoid deletions. The matching algorithm for small * strings is inspired from that of Rabin & Karp. A brute force approach * is used to find longer strings when a small match has been found. * A similar algorithm is used in comic (by Jan-Mark Wams) and freeze * (by Leonid Broukhis). * A previous version of this file used a more sophisticated algorithm * (by Fiala and Greene) which is guaranteed to run in linear amortized * time, but has a larger average cost, uses more memory and is patented. * However the F&G algorithm may be faster for some highly redundant * files if the parameter max_chain_length (described below) is too large. * * ACKNOWLEDGEMENTS * * The idea of lazy evaluation of matches is due to Jan-Mark Wams, and * I found it in 'freeze' written by Leonid Broukhis. * Thanks to many people for bug reports and testing. * * REFERENCES * * Deutsch, L.P.,"DEFLATE Compressed Data Format Specification". * Available in http://www.ietf.org/rfc/rfc1951.txt * * A description of the Rabin and Karp algorithm is given in the book * "Algorithms" by R. Sedgewick, Addison-Wesley, p252. * * Fiala,E.R., and Greene,D.H. * Data Compression with Finite Windows, Comm.ACM, 32,4 (1989) 490-595 * */ /* @(#) $Id$ */ #include "deflate.h" const char deflate_copyright[] = " deflate 1.2.3 Copyright 1995-2005 Jean-loup Gailly "; /* If you use the zlib library in a product, an acknowledgment is welcome in the documentation of your product. If for some reason you cannot include such an acknowledgment, I would appreciate that you keep this copyright string in the executable of your product. */ /* =========================================================================== * Function prototypes. */ typedef enum { need_more, /* block not completed, need more input or more output */ block_done, /* block flush performed */ finish_started, /* finish started, need only more output at next deflate */ finish_done /* finish done, accept no more input or output */ } block_state; typedef block_state (*compress_func) OF((deflate_state *s, int flush)); /* Compression function. Returns the block state after the call. */ local void fill_window OF((deflate_state *s)); local block_state deflate_stored OF((deflate_state *s, int flush)); local block_state deflate_fast OF((deflate_state *s, int flush)); #ifndef FASTEST local block_state deflate_slow OF((deflate_state *s, int flush)); #endif local void lm_init OF((deflate_state *s)); local void putShortMSB OF((deflate_state *s, uInt b)); local void flush_pending OF((z_streamp strm)); local int read_buf OF((z_streamp strm, Bytef *buf, unsigned size)); #ifndef FASTEST #ifdef ASMV void match_init OF((void)); /* asm code initialization */ uInt longest_match OF((deflate_state *s, IPos cur_match)); #else local uInt longest_match OF((deflate_state *s, IPos cur_match)); #endif #endif local uInt longest_match_fast OF((deflate_state *s, IPos cur_match)); #ifdef DEBUG local void check_match OF((deflate_state *s, IPos start, IPos match, int length)); #endif /* =========================================================================== * Local data */ #define NIL 0 /* Tail of hash chains */ #ifndef TOO_FAR # define TOO_FAR 4096 #endif /* Matches of length 3 are discarded if their distance exceeds TOO_FAR */ #define MIN_LOOKAHEAD (MAX_MATCH+MIN_MATCH+1) /* Minimum amount of lookahead, except at the end of the input file. * See deflate.c for comments about the MIN_MATCH+1. */ /* Values for max_lazy_match, good_match and max_chain_length, depending on * the desired pack level (0..9). The values given below have been tuned to * exclude worst case performance for pathological files. Better values may be * found for specific files. */ typedef struct config_s { ush good_length; /* reduce lazy search above this match length */ ush max_lazy; /* do not perform lazy search above this match length */ ush nice_length; /* quit search above this match length */ ush max_chain; compress_func func; } config; #ifdef FASTEST local const config configuration_table[2] = { /* good lazy nice chain */ /* 0 */ {0, 0, 0, 0, deflate_stored}, /* store only */ /* 1 */ {4, 4, 8, 4, deflate_fast}}; /* max speed, no lazy matches */ #else local const config configuration_table[10] = { /* good lazy nice chain */ /* 0 */ {0, 0, 0, 0, deflate_stored}, /* store only */ /* 1 */ {4, 4, 8, 4, deflate_fast}, /* max speed, no lazy matches */ /* 2 */ {4, 5, 16, 8, deflate_fast}, /* 3 */ {4, 6, 32, 32, deflate_fast}, /* 4 */ {4, 4, 16, 16, deflate_slow}, /* lazy matches */ /* 5 */ {8, 16, 32, 32, deflate_slow}, /* 6 */ {8, 16, 128, 128, deflate_slow}, /* 7 */ {8, 32, 128, 256, deflate_slow}, /* 8 */ {32, 128, 258, 1024, deflate_slow}, /* 9 */ {32, 258, 258, 4096, deflate_slow}}; /* max compression */ #endif /* Note: the deflate() code requires max_lazy >= MIN_MATCH and max_chain >= 4 * For deflate_fast() (levels <= 3) good is ignored and lazy has a different * meaning. */ #define EQUAL 0 /* result of memcmp for equal strings */ #ifndef NO_DUMMY_DECL struct static_tree_desc_s {int dummy;}; /* for buggy compilers */ #endif /* =========================================================================== * Update a hash value with the given input byte * IN assertion: all calls to to UPDATE_HASH are made with consecutive * input characters, so that a running hash key can be computed from the * previous key instead of complete recalculation each time. */ #define UPDATE_HASH(s,h,c) (h = (((h)<hash_shift) ^ (c)) & s->hash_mask) /* =========================================================================== * Insert string str in the dictionary and set match_head to the previous head * of the hash chain (the most recent string with same hash key). Return * the previous length of the hash chain. * If this file is compiled with -DFASTEST, the compression level is forced * to 1, and no hash chains are maintained. * IN assertion: all calls to to INSERT_STRING are made with consecutive * input characters and the first MIN_MATCH bytes of str are valid * (except for the last MIN_MATCH-1 bytes of the input file). */ #ifdef FASTEST #define INSERT_STRING(s, str, match_head) \ (UPDATE_HASH(s, s->ins_h, s->window[(str) + (MIN_MATCH-1)]), \ match_head = s->head[s->ins_h], \ s->head[s->ins_h] = (Pos)(str)) #else #define INSERT_STRING(s, str, match_head) \ (UPDATE_HASH(s, s->ins_h, s->window[(str) + (MIN_MATCH-1)]), \ match_head = s->prev[(str) & s->w_mask] = s->head[s->ins_h], \ s->head[s->ins_h] = (Pos)(str)) #endif /* =========================================================================== * Initialize the hash table (avoiding 64K overflow for 16 bit systems). * prev[] will be initialized on the fly. */ #define CLEAR_HASH(s) \ s->head[s->hash_size-1] = NIL; \ zmemzero((Bytef *)s->head, (unsigned)(s->hash_size-1)*sizeof(*s->head)); /* ========================================================================= */ int ZEXPORT deflateInit_(strm, level, version, stream_size) z_streamp strm; int level; const char *version; int stream_size; { return deflateInit2_(strm, level, Z_DEFLATED, MAX_WBITS, DEF_MEM_LEVEL, Z_DEFAULT_STRATEGY, version, stream_size); /* To do: ignore strm->next_in if we use it as window */ } /* ========================================================================= */ int ZEXPORT deflateInit2_(strm, level, method, windowBits, memLevel, strategy, version, stream_size) z_streamp strm; int level; int method; int windowBits; int memLevel; int strategy; const char *version; int stream_size; { deflate_state *s; int wrap = 1; static const char my_version[] = ZLIB_VERSION; ushf *overlay; /* We overlay pending_buf and d_buf+l_buf. This works since the average * output size for (length,distance) codes is <= 24 bits. */ if (version == Z_NULL || version[0] != my_version[0] || stream_size != sizeof(z_stream)) { return Z_VERSION_ERROR; } if (strm == Z_NULL) return Z_STREAM_ERROR; strm->msg = Z_NULL; if (strm->zalloc == (alloc_func)0) { strm->zalloc = zcalloc; strm->opaque = (voidpf)0; } if (strm->zfree == (free_func)0) strm->zfree = zcfree; #ifdef FASTEST if (level != 0) level = 1; #else if (level == Z_DEFAULT_COMPRESSION) level = 6; #endif if (windowBits < 0) { /* suppress zlib wrapper */ wrap = 0; windowBits = -windowBits; } #ifdef GZIP else if (windowBits > 15) { wrap = 2; /* write gzip wrapper instead */ windowBits -= 16; } #endif if (memLevel < 1 || memLevel > MAX_MEM_LEVEL || method != Z_DEFLATED || windowBits < 8 || windowBits > 15 || level < 0 || level > 9 || strategy < 0 || strategy > Z_FIXED) { return Z_STREAM_ERROR; } if (windowBits == 8) windowBits = 9; /* until 256-byte window bug fixed */ s = (deflate_state *) ZALLOC(strm, 1, sizeof(deflate_state)); if (s == Z_NULL) return Z_MEM_ERROR; strm->state = (struct internal_state FAR *)s; s->strm = strm; s->wrap = wrap; s->gzhead = Z_NULL; s->w_bits = windowBits; s->w_size = 1 << s->w_bits; s->w_mask = s->w_size - 1; s->hash_bits = memLevel + 7; s->hash_size = 1 << s->hash_bits; s->hash_mask = s->hash_size - 1; s->hash_shift = ((s->hash_bits+MIN_MATCH-1)/MIN_MATCH); s->window = (Bytef *) ZALLOC(strm, s->w_size, 2*sizeof(Byte)); s->prev = (Posf *) ZALLOC(strm, s->w_size, sizeof(Pos)); s->head = (Posf *) ZALLOC(strm, s->hash_size, sizeof(Pos)); s->lit_bufsize = 1 << (memLevel + 6); /* 16K elements by default */ overlay = (ushf *) ZALLOC(strm, s->lit_bufsize, sizeof(ush)+2); s->pending_buf = (uchf *) overlay; s->pending_buf_size = (ulg)s->lit_bufsize * (sizeof(ush)+2L); if (s->window == Z_NULL || s->prev == Z_NULL || s->head == Z_NULL || s->pending_buf == Z_NULL) { s->status = FINISH_STATE; strm->msg = (char*)ERR_MSG(Z_MEM_ERROR); deflateEnd (strm); return Z_MEM_ERROR; } s->d_buf = overlay + s->lit_bufsize/sizeof(ush); s->l_buf = s->pending_buf + (1+sizeof(ush))*s->lit_bufsize; s->level = level; s->strategy = strategy; s->method = (Byte)method; return deflateReset(strm); } /* ========================================================================= */ int ZEXPORT deflateSetDictionary (strm, dictionary, dictLength) z_streamp strm; const Bytef *dictionary; uInt dictLength; { deflate_state *s; uInt length = dictLength; uInt n; IPos hash_head = 0; if (strm == Z_NULL || strm->state == Z_NULL || dictionary == Z_NULL || strm->state->wrap == 2 || (strm->state->wrap == 1 && strm->state->status != INIT_STATE)) return Z_STREAM_ERROR; s = strm->state; if (s->wrap) strm->adler = adler32(strm->adler, dictionary, dictLength); if (length < MIN_MATCH) return Z_OK; if (length > MAX_DIST(s)) { length = MAX_DIST(s); dictionary += dictLength - length; /* use the tail of the dictionary */ } zmemcpy(s->window, dictionary, length); s->strstart = length; s->block_start = (long)length; /* Insert all strings in the hash table (except for the last two bytes). * s->lookahead stays null, so s->ins_h will be recomputed at the next * call of fill_window. */ s->ins_h = s->window[0]; UPDATE_HASH(s, s->ins_h, s->window[1]); for (n = 0; n <= length - MIN_MATCH; n++) { INSERT_STRING(s, n, hash_head); } if (hash_head) hash_head = 0; /* to make compiler happy */ return Z_OK; } /* ========================================================================= */ int ZEXPORT deflateReset (strm) z_streamp strm; { deflate_state *s; if (strm == Z_NULL || strm->state == Z_NULL || strm->zalloc == (alloc_func)0 || strm->zfree == (free_func)0) { return Z_STREAM_ERROR; } strm->total_in = strm->total_out = 0; strm->msg = Z_NULL; /* use zfree if we ever allocate msg dynamically */ strm->data_type = Z_UNKNOWN; s = (deflate_state *)strm->state; s->pending = 0; s->pending_out = s->pending_buf; if (s->wrap < 0) { s->wrap = -s->wrap; /* was made negative by deflate(..., Z_FINISH); */ } s->status = s->wrap ? INIT_STATE : BUSY_STATE; strm->adler = #ifdef GZIP s->wrap == 2 ? crc32(0L, Z_NULL, 0) : #endif adler32(0L, Z_NULL, 0); s->last_flush = Z_NO_FLUSH; _tr_init(s); lm_init(s); return Z_OK; } /* ========================================================================= */ int ZEXPORT deflateSetHeader (strm, head) z_streamp strm; gz_headerp head; { if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR; if (strm->state->wrap != 2) return Z_STREAM_ERROR; strm->state->gzhead = head; return Z_OK; } /* ========================================================================= */ int ZEXPORT deflatePrime (strm, bits, value) z_streamp strm; int bits; int value; { if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR; strm->state->bi_valid = bits; strm->state->bi_buf = (ush)(value & ((1 << bits) - 1)); return Z_OK; } /* ========================================================================= */ int ZEXPORT deflateParams(strm, level, strategy) z_streamp strm; int level; int strategy; { deflate_state *s; compress_func func; int err = Z_OK; if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR; s = strm->state; #ifdef FASTEST if (level != 0) level = 1; #else if (level == Z_DEFAULT_COMPRESSION) level = 6; #endif if (level < 0 || level > 9 || strategy < 0 || strategy > Z_FIXED) { return Z_STREAM_ERROR; } func = configuration_table[s->level].func; if (func != configuration_table[level].func && strm->total_in != 0) { /* Flush the last buffer: */ err = deflate(strm, Z_PARTIAL_FLUSH); } if (s->level != level) { s->level = level; s->max_lazy_match = configuration_table[level].max_lazy; s->good_match = configuration_table[level].good_length; s->nice_match = configuration_table[level].nice_length; s->max_chain_length = configuration_table[level].max_chain; } s->strategy = strategy; return err; } /* ========================================================================= */ int ZEXPORT deflateTune(strm, good_length, max_lazy, nice_length, max_chain) z_streamp strm; int good_length; int max_lazy; int nice_length; int max_chain; { deflate_state *s; if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR; s = strm->state; s->good_match = good_length; s->max_lazy_match = max_lazy; s->nice_match = nice_length; s->max_chain_length = max_chain; return Z_OK; } /* ========================================================================= * For the default windowBits of 15 and memLevel of 8, this function returns * a close to exact, as well as small, upper bound on the compressed size. * They are coded as constants here for a reason--if the #define's are * changed, then this function needs to be changed as well. The return * value for 15 and 8 only works for those exact settings. * * For any setting other than those defaults for windowBits and memLevel, * the value returned is a conservative worst case for the maximum expansion * resulting from using fixed blocks instead of stored blocks, which deflate * can emit on compressed data for some combinations of the parameters. * * This function could be more sophisticated to provide closer upper bounds * for every combination of windowBits and memLevel, as well as wrap. * But even the conservative upper bound of about 14% expansion does not * seem onerous for output buffer allocation. */ uLong ZEXPORT deflateBound(strm, sourceLen) z_streamp strm; uLong sourceLen; { deflate_state *s; uLong destLen; /* conservative upper bound */ destLen = sourceLen + ((sourceLen + 7) >> 3) + ((sourceLen + 63) >> 6) + 11; /* if can't get parameters, return conservative bound */ if (strm == Z_NULL || strm->state == Z_NULL) return destLen; /* if not default parameters, return conservative bound */ s = strm->state; if (s->w_bits != 15 || s->hash_bits != 8 + 7) return destLen; /* default settings: return tight bound for that case */ return compressBound(sourceLen); } /* ========================================================================= * Put a short in the pending buffer. The 16-bit value is put in MSB order. * IN assertion: the stream state is correct and there is enough room in * pending_buf. */ local void putShortMSB (s, b) deflate_state *s; uInt b; { put_byte(s, (Byte)(b >> 8)); put_byte(s, (Byte)(b & 0xff)); } /* ========================================================================= * Flush as much pending output as possible. All deflate() output goes * through this function so some applications may wish to modify it * to avoid allocating a large strm->next_out buffer and copying into it. * (See also read_buf()). */ local void flush_pending(strm) z_streamp strm; { unsigned len = strm->state->pending; if (len > strm->avail_out) len = strm->avail_out; if (len == 0) return; zmemcpy(strm->next_out, strm->state->pending_out, len); strm->next_out += len; strm->state->pending_out += len; strm->total_out += len; strm->avail_out -= len; strm->state->pending -= len; if (strm->state->pending == 0) { strm->state->pending_out = strm->state->pending_buf; } } /* ========================================================================= */ int ZEXPORT deflate (strm, flush) z_streamp strm; int flush; { int old_flush; /* value of flush param for previous deflate call */ deflate_state *s; if (strm == Z_NULL || strm->state == Z_NULL || flush > Z_FINISH || flush < 0) { return Z_STREAM_ERROR; } s = strm->state; if (strm->next_out == Z_NULL || (strm->next_in == Z_NULL && strm->avail_in != 0) || (s->status == FINISH_STATE && flush != Z_FINISH)) { ERR_RETURN(strm, Z_STREAM_ERROR); } if (strm->avail_out == 0) ERR_RETURN(strm, Z_BUF_ERROR); s->strm = strm; /* just in case */ old_flush = s->last_flush; s->last_flush = flush; /* Write the header */ if (s->status == INIT_STATE) { #ifdef GZIP if (s->wrap == 2) { strm->adler = crc32(0L, Z_NULL, 0); put_byte(s, 31); put_byte(s, 139); put_byte(s, 8); if (s->gzhead == NULL) { put_byte(s, 0); put_byte(s, 0); put_byte(s, 0); put_byte(s, 0); put_byte(s, 0); put_byte(s, s->level == 9 ? 2 : (s->strategy >= Z_HUFFMAN_ONLY || s->level < 2 ? 4 : 0)); put_byte(s, OS_CODE); s->status = BUSY_STATE; } else { put_byte(s, (s->gzhead->text ? 1 : 0) + (s->gzhead->hcrc ? 2 : 0) + (s->gzhead->extra == Z_NULL ? 0 : 4) + (s->gzhead->name == Z_NULL ? 0 : 8) + (s->gzhead->comment == Z_NULL ? 0 : 16) ); put_byte(s, (Byte)(s->gzhead->time & 0xff)); put_byte(s, (Byte)((s->gzhead->time >> 8) & 0xff)); put_byte(s, (Byte)((s->gzhead->time >> 16) & 0xff)); put_byte(s, (Byte)((s->gzhead->time >> 24) & 0xff)); put_byte(s, s->level == 9 ? 2 : (s->strategy >= Z_HUFFMAN_ONLY || s->level < 2 ? 4 : 0)); put_byte(s, s->gzhead->os & 0xff); if (s->gzhead->extra != NULL) { put_byte(s, s->gzhead->extra_len & 0xff); put_byte(s, (s->gzhead->extra_len >> 8) & 0xff); } if (s->gzhead->hcrc) strm->adler = crc32(strm->adler, s->pending_buf, s->pending); s->gzindex = 0; s->status = EXTRA_STATE; } } else #endif { uInt header = (Z_DEFLATED + ((s->w_bits-8)<<4)) << 8; uInt level_flags; if (s->strategy >= Z_HUFFMAN_ONLY || s->level < 2) level_flags = 0; else if (s->level < 6) level_flags = 1; else if (s->level == 6) level_flags = 2; else level_flags = 3; header |= (level_flags << 6); if (s->strstart != 0) header |= PRESET_DICT; header += 31 - (header % 31); s->status = BUSY_STATE; putShortMSB(s, header); /* Save the adler32 of the preset dictionary: */ if (s->strstart != 0) { putShortMSB(s, (uInt)(strm->adler >> 16)); putShortMSB(s, (uInt)(strm->adler & 0xffff)); } strm->adler = adler32(0L, Z_NULL, 0); } } #ifdef GZIP if (s->status == EXTRA_STATE) { if (s->gzhead->extra != NULL) { uInt beg = s->pending; /* start of bytes to update crc */ while (s->gzindex < (s->gzhead->extra_len & 0xffff)) { if (s->pending == s->pending_buf_size) { if (s->gzhead->hcrc && s->pending > beg) strm->adler = crc32(strm->adler, s->pending_buf + beg, s->pending - beg); flush_pending(strm); beg = s->pending; if (s->pending == s->pending_buf_size) break; } put_byte(s, s->gzhead->extra[s->gzindex]); s->gzindex++; } if (s->gzhead->hcrc && s->pending > beg) strm->adler = crc32(strm->adler, s->pending_buf + beg, s->pending - beg); if (s->gzindex == s->gzhead->extra_len) { s->gzindex = 0; s->status = NAME_STATE; } } else s->status = NAME_STATE; } if (s->status == NAME_STATE) { if (s->gzhead->name != NULL) { uInt beg = s->pending; /* start of bytes to update crc */ int val; do { if (s->pending == s->pending_buf_size) { if (s->gzhead->hcrc && s->pending > beg) strm->adler = crc32(strm->adler, s->pending_buf + beg, s->pending - beg); flush_pending(strm); beg = s->pending; if (s->pending == s->pending_buf_size) { val = 1; break; } } val = s->gzhead->name[s->gzindex++]; put_byte(s, val); } while (val != 0); if (s->gzhead->hcrc && s->pending > beg) strm->adler = crc32(strm->adler, s->pending_buf + beg, s->pending - beg); if (val == 0) { s->gzindex = 0; s->status = COMMENT_STATE; } } else s->status = COMMENT_STATE; } if (s->status == COMMENT_STATE) { if (s->gzhead->comment != NULL) { uInt beg = s->pending; /* start of bytes to update crc */ int val; do { if (s->pending == s->pending_buf_size) { if (s->gzhead->hcrc && s->pending > beg) strm->adler = crc32(strm->adler, s->pending_buf + beg, s->pending - beg); flush_pending(strm); beg = s->pending; if (s->pending == s->pending_buf_size) { val = 1; break; } } val = s->gzhead->comment[s->gzindex++]; put_byte(s, val); } while (val != 0); if (s->gzhead->hcrc && s->pending > beg) strm->adler = crc32(strm->adler, s->pending_buf + beg, s->pending - beg); if (val == 0) s->status = HCRC_STATE; } else s->status = HCRC_STATE; } if (s->status == HCRC_STATE) { if (s->gzhead->hcrc) { if (s->pending + 2 > s->pending_buf_size) flush_pending(strm); if (s->pending + 2 <= s->pending_buf_size) { put_byte(s, (Byte)(strm->adler & 0xff)); put_byte(s, (Byte)((strm->adler >> 8) & 0xff)); strm->adler = crc32(0L, Z_NULL, 0); s->status = BUSY_STATE; } } else s->status = BUSY_STATE; } #endif /* Flush as much pending output as possible */ if (s->pending != 0) { flush_pending(strm); if (strm->avail_out == 0) { /* Since avail_out is 0, deflate will be called again with * more output space, but possibly with both pending and * avail_in equal to zero. There won't be anything to do, * but this is not an error situation so make sure we * return OK instead of BUF_ERROR at next call of deflate: */ s->last_flush = -1; return Z_OK; } /* Make sure there is something to do and avoid duplicate consecutive * flushes. For repeated and useless calls with Z_FINISH, we keep * returning Z_STREAM_END instead of Z_BUF_ERROR. */ } else if (strm->avail_in == 0 && flush <= old_flush && flush != Z_FINISH) { ERR_RETURN(strm, Z_BUF_ERROR); } /* User must not provide more input after the first FINISH: */ if (s->status == FINISH_STATE && strm->avail_in != 0) { ERR_RETURN(strm, Z_BUF_ERROR); } /* Start a new block or continue the current one. */ if (strm->avail_in != 0 || s->lookahead != 0 || (flush != Z_NO_FLUSH && s->status != FINISH_STATE)) { block_state bstate; bstate = (*(configuration_table[s->level].func))(s, flush); if (bstate == finish_started || bstate == finish_done) { s->status = FINISH_STATE; } if (bstate == need_more || bstate == finish_started) { if (strm->avail_out == 0) { s->last_flush = -1; /* avoid BUF_ERROR next call, see above */ } return Z_OK; /* If flush != Z_NO_FLUSH && avail_out == 0, the next call * of deflate should use the same flush parameter to make sure * that the flush is complete. So we don't have to output an * empty block here, this will be done at next call. This also * ensures that for a very small output buffer, we emit at most * one empty block. */ } if (bstate == block_done) { if (flush == Z_PARTIAL_FLUSH) { _tr_align(s); } else { /* FULL_FLUSH or SYNC_FLUSH */ _tr_stored_block(s, (char*)0, 0L, 0); /* For a full flush, this empty block will be recognized * as a special marker by inflate_sync(). */ if (flush == Z_FULL_FLUSH) { CLEAR_HASH(s); /* forget history */ } } flush_pending(strm); if (strm->avail_out == 0) { s->last_flush = -1; /* avoid BUF_ERROR at next call, see above */ return Z_OK; } } } Assert(strm->avail_out > 0, "bug2"); if (flush != Z_FINISH) return Z_OK; if (s->wrap <= 0) return Z_STREAM_END; /* Write the trailer */ #ifdef GZIP if (s->wrap == 2) { put_byte(s, (Byte)(strm->adler & 0xff)); put_byte(s, (Byte)((strm->adler >> 8) & 0xff)); put_byte(s, (Byte)((strm->adler >> 16) & 0xff)); put_byte(s, (Byte)((strm->adler >> 24) & 0xff)); put_byte(s, (Byte)(strm->total_in & 0xff)); put_byte(s, (Byte)((strm->total_in >> 8) & 0xff)); put_byte(s, (Byte)((strm->total_in >> 16) & 0xff)); put_byte(s, (Byte)((strm->total_in >> 24) & 0xff)); } else #endif { putShortMSB(s, (uInt)(strm->adler >> 16)); putShortMSB(s, (uInt)(strm->adler & 0xffff)); } flush_pending(strm); /* If avail_out is zero, the application will call deflate again * to flush the rest. */ if (s->wrap > 0) s->wrap = -s->wrap; /* write the trailer only once! */ return s->pending != 0 ? Z_OK : Z_STREAM_END; } /* ========================================================================= */ int ZEXPORT deflateEnd (strm) z_streamp strm; { int status; if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR; status = strm->state->status; if (status != INIT_STATE && status != EXTRA_STATE && status != NAME_STATE && status != COMMENT_STATE && status != HCRC_STATE && status != BUSY_STATE && status != FINISH_STATE) { return Z_STREAM_ERROR; } /* Deallocate in reverse order of allocations: */ TRY_FREE(strm, strm->state->pending_buf); TRY_FREE(strm, strm->state->head); TRY_FREE(strm, strm->state->prev); TRY_FREE(strm, strm->state->window); ZFREE(strm, strm->state); strm->state = Z_NULL; return status == BUSY_STATE ? Z_DATA_ERROR : Z_OK; } /* ========================================================================= * Copy the source state to the destination state. * To simplify the source, this is not supported for 16-bit MSDOS (which * doesn't have enough memory anyway to duplicate compression states). */ int ZEXPORT deflateCopy (dest, source) z_streamp dest; z_streamp source; { #ifdef MAXSEG_64K return Z_STREAM_ERROR; #else deflate_state *ds; deflate_state *ss; ushf *overlay; if (source == Z_NULL || dest == Z_NULL || source->state == Z_NULL) { return Z_STREAM_ERROR; } ss = source->state; zmemcpy(dest, source, sizeof(z_stream)); ds = (deflate_state *) ZALLOC(dest, 1, sizeof(deflate_state)); if (ds == Z_NULL) return Z_MEM_ERROR; dest->state = (struct internal_state FAR *) ds; zmemcpy(ds, ss, sizeof(deflate_state)); ds->strm = dest; ds->window = (Bytef *) ZALLOC(dest, ds->w_size, 2*sizeof(Byte)); ds->prev = (Posf *) ZALLOC(dest, ds->w_size, sizeof(Pos)); ds->head = (Posf *) ZALLOC(dest, ds->hash_size, sizeof(Pos)); overlay = (ushf *) ZALLOC(dest, ds->lit_bufsize, sizeof(ush)+2); ds->pending_buf = (uchf *) overlay; if (ds->window == Z_NULL || ds->prev == Z_NULL || ds->head == Z_NULL || ds->pending_buf == Z_NULL) { deflateEnd (dest); return Z_MEM_ERROR; } /* following zmemcpy do not work for 16-bit MSDOS */ zmemcpy(ds->window, ss->window, ds->w_size * 2 * sizeof(Byte)); zmemcpy(ds->prev, ss->prev, ds->w_size * sizeof(Pos)); zmemcpy(ds->head, ss->head, ds->hash_size * sizeof(Pos)); zmemcpy(ds->pending_buf, ss->pending_buf, (uInt)ds->pending_buf_size); ds->pending_out = ds->pending_buf + (ss->pending_out - ss->pending_buf); ds->d_buf = overlay + ds->lit_bufsize/sizeof(ush); ds->l_buf = ds->pending_buf + (1+sizeof(ush))*ds->lit_bufsize; ds->l_desc.dyn_tree = ds->dyn_ltree; ds->d_desc.dyn_tree = ds->dyn_dtree; ds->bl_desc.dyn_tree = ds->bl_tree; return Z_OK; #endif /* MAXSEG_64K */ } /* =========================================================================== * Read a new buffer from the current input stream, update the adler32 * and total number of bytes read. All deflate() input goes through * this function so some applications may wish to modify it to avoid * allocating a large strm->next_in buffer and copying from it. * (See also flush_pending()). */ local int read_buf(strm, buf, size) z_streamp strm; Bytef *buf; unsigned size; { unsigned len = strm->avail_in; if (len > size) len = size; if (len == 0) return 0; strm->avail_in -= len; if (strm->state->wrap == 1) { strm->adler = adler32(strm->adler, strm->next_in, len); } #ifdef GZIP else if (strm->state->wrap == 2) { strm->adler = crc32(strm->adler, strm->next_in, len); } #endif zmemcpy(buf, strm->next_in, len); strm->next_in += len; strm->total_in += len; return (int)len; } /* =========================================================================== * Initialize the "longest match" routines for a new zlib stream */ local void lm_init (s) deflate_state *s; { s->window_size = (ulg)2L*s->w_size; CLEAR_HASH(s); /* Set the default configuration parameters: */ s->max_lazy_match = configuration_table[s->level].max_lazy; s->good_match = configuration_table[s->level].good_length; s->nice_match = configuration_table[s->level].nice_length; s->max_chain_length = configuration_table[s->level].max_chain; s->strstart = 0; s->block_start = 0L; s->lookahead = 0; s->match_length = s->prev_length = MIN_MATCH-1; s->match_available = 0; s->ins_h = 0; #ifndef FASTEST #ifdef ASMV match_init(); /* initialize the asm code */ #endif #endif } #ifndef FASTEST /* =========================================================================== * Set match_start to the longest match starting at the given string and * return its length. Matches shorter or equal to prev_length are discarded, * in which case the result is equal to prev_length and match_start is * garbage. * IN assertions: cur_match is the head of the hash chain for the current * string (strstart) and its distance is <= MAX_DIST, and prev_length >= 1 * OUT assertion: the match length is not greater than s->lookahead. */ #ifndef ASMV /* For 80x86 and 680x0, an optimized version will be provided in match.asm or * match.S. The code will be functionally equivalent. */ local uInt longest_match(s, cur_match) deflate_state *s; IPos cur_match; /* current match */ { unsigned chain_length = s->max_chain_length;/* max hash chain length */ register Bytef *scan = s->window + s->strstart; /* current string */ register Bytef *match; /* matched string */ register int len; /* length of current match */ int best_len = s->prev_length; /* best match length so far */ int nice_match = s->nice_match; /* stop if match long enough */ IPos limit = s->strstart > (IPos)MAX_DIST(s) ? s->strstart - (IPos)MAX_DIST(s) : NIL; /* Stop when cur_match becomes <= limit. To simplify the code, * we prevent matches with the string of window index 0. */ Posf *prev = s->prev; uInt wmask = s->w_mask; #ifdef UNALIGNED_OK /* Compare two bytes at a time. Note: this is not always beneficial. * Try with and without -DUNALIGNED_OK to check. */ register Bytef *strend = s->window + s->strstart + MAX_MATCH - 1; register ush scan_start = *(ushf*)scan; register ush scan_end = *(ushf*)(scan+best_len-1); #else register Bytef *strend = s->window + s->strstart + MAX_MATCH; register Byte scan_end1 = scan[best_len-1]; register Byte scan_end = scan[best_len]; #endif /* The code is optimized for HASH_BITS >= 8 and MAX_MATCH-2 multiple of 16. * It is easy to get rid of this optimization if necessary. */ Assert(s->hash_bits >= 8 && MAX_MATCH == 258, "Code too clever"); /* Do not waste too much time if we already have a good match: */ if (s->prev_length >= s->good_match) { chain_length >>= 2; } /* Do not look for matches beyond the end of the input. This is necessary * to make deflate deterministic. */ if ((uInt)nice_match > s->lookahead) nice_match = s->lookahead; Assert((ulg)s->strstart <= s->window_size-MIN_LOOKAHEAD, "need lookahead"); do { Assert(cur_match < s->strstart, "no future"); match = s->window + cur_match; /* Skip to next match if the match length cannot increase * or if the match length is less than 2. Note that the checks below * for insufficient lookahead only occur occasionally for performance * reasons. Therefore uninitialized memory will be accessed, and * conditional jumps will be made that depend on those values. * However the length of the match is limited to the lookahead, so * the output of deflate is not affected by the uninitialized values. */ #if (defined(UNALIGNED_OK) && MAX_MATCH == 258) /* This code assumes sizeof(unsigned short) == 2. Do not use * UNALIGNED_OK if your compiler uses a different size. */ if (*(ushf*)(match+best_len-1) != scan_end || *(ushf*)match != scan_start) continue; /* It is not necessary to compare scan[2] and match[2] since they are * always equal when the other bytes match, given that the hash keys * are equal and that HASH_BITS >= 8. Compare 2 bytes at a time at * strstart+3, +5, ... up to strstart+257. We check for insufficient * lookahead only every 4th comparison; the 128th check will be made * at strstart+257. If MAX_MATCH-2 is not a multiple of 8, it is * necessary to put more guard bytes at the end of the window, or * to check more often for insufficient lookahead. */ Assert(scan[2] == match[2], "scan[2]?"); scan++, match++; do { } while (*(ushf*)(scan+=2) == *(ushf*)(match+=2) && *(ushf*)(scan+=2) == *(ushf*)(match+=2) && *(ushf*)(scan+=2) == *(ushf*)(match+=2) && *(ushf*)(scan+=2) == *(ushf*)(match+=2) && scan < strend); /* The funny "do {}" generates better code on most compilers */ /* Here, scan <= window+strstart+257 */ Assert(scan <= s->window+(unsigned)(s->window_size-1), "wild scan"); if (*scan == *match) scan++; len = (MAX_MATCH - 1) - (int)(strend-scan); scan = strend - (MAX_MATCH-1); #else /* UNALIGNED_OK */ if (match[best_len] != scan_end || match[best_len-1] != scan_end1 || *match != *scan || *++match != scan[1]) continue; /* The check at best_len-1 can be removed because it will be made * again later. (This heuristic is not always a win.) * It is not necessary to compare scan[2] and match[2] since they * are always equal when the other bytes match, given that * the hash keys are equal and that HASH_BITS >= 8. */ scan += 2, match++; Assert(*scan == *match, "match[2]?"); /* We check for insufficient lookahead only every 8th comparison; * the 256th check will be made at strstart+258. */ do { } while (*++scan == *++match && *++scan == *++match && *++scan == *++match && *++scan == *++match && *++scan == *++match && *++scan == *++match && *++scan == *++match && *++scan == *++match && scan < strend); Assert(scan <= s->window+(unsigned)(s->window_size-1), "wild scan"); len = MAX_MATCH - (int)(strend - scan); scan = strend - MAX_MATCH; #endif /* UNALIGNED_OK */ if (len > best_len) { s->match_start = cur_match; best_len = len; if (len >= nice_match) break; #ifdef UNALIGNED_OK scan_end = *(ushf*)(scan+best_len-1); #else scan_end1 = scan[best_len-1]; scan_end = scan[best_len]; #endif } } while ((cur_match = prev[cur_match & wmask]) > limit && --chain_length != 0); if ((uInt)best_len <= s->lookahead) return (uInt)best_len; return s->lookahead; } #endif /* ASMV */ #endif /* FASTEST */ /* --------------------------------------------------------------------------- * Optimized version for level == 1 or strategy == Z_RLE only */ local uInt longest_match_fast(s, cur_match) deflate_state *s; IPos cur_match; /* current match */ { register Bytef *scan = s->window + s->strstart; /* current string */ register Bytef *match; /* matched string */ register int len; /* length of current match */ register Bytef *strend = s->window + s->strstart + MAX_MATCH; /* The code is optimized for HASH_BITS >= 8 and MAX_MATCH-2 multiple of 16. * It is easy to get rid of this optimization if necessary. */ Assert(s->hash_bits >= 8 && MAX_MATCH == 258, "Code too clever"); Assert((ulg)s->strstart <= s->window_size-MIN_LOOKAHEAD, "need lookahead"); Assert(cur_match < s->strstart, "no future"); match = s->window + cur_match; /* Return failure if the match length is less than 2: */ if (match[0] != scan[0] || match[1] != scan[1]) return MIN_MATCH-1; /* The check at best_len-1 can be removed because it will be made * again later. (This heuristic is not always a win.) * It is not necessary to compare scan[2] and match[2] since they * are always equal when the other bytes match, given that * the hash keys are equal and that HASH_BITS >= 8. */ scan += 2, match += 2; Assert(*scan == *match, "match[2]?"); /* We check for insufficient lookahead only every 8th comparison; * the 256th check will be made at strstart+258. */ do { } while (*++scan == *++match && *++scan == *++match && *++scan == *++match && *++scan == *++match && *++scan == *++match && *++scan == *++match && *++scan == *++match && *++scan == *++match && scan < strend); Assert(scan <= s->window+(unsigned)(s->window_size-1), "wild scan"); len = MAX_MATCH - (int)(strend - scan); if (len < MIN_MATCH) return MIN_MATCH - 1; s->match_start = cur_match; return (uInt)len <= s->lookahead ? (uInt)len : s->lookahead; } #ifdef DEBUG /* =========================================================================== * Check that the match at match_start is indeed a match. */ local void check_match(s, start, match, length) deflate_state *s; IPos start, match; int length; { /* check that the match is indeed a match */ if (zmemcmp(s->window + match, s->window + start, length) != EQUAL) { fprintf(stderr, " start %u, match %u, length %d\n", start, match, length); do { fprintf(stderr, "%c%c", s->window[match++], s->window[start++]); } while (--length != 0); z_error("invalid match"); } if (z_verbose > 1) { fprintf(stderr,"\\[%d,%d]", start-match, length); do { putc(s->window[start++], stderr); } while (--length != 0); } } #else # define check_match(s, start, match, length) #endif /* DEBUG */ /* =========================================================================== * Fill the window when the lookahead becomes insufficient. * Updates strstart and lookahead. * * IN assertion: lookahead < MIN_LOOKAHEAD * OUT assertions: strstart <= window_size-MIN_LOOKAHEAD * At least one byte has been read, or avail_in == 0; reads are * performed for at least two bytes (required for the zip translate_eol * option -- not supported here). */ local void fill_window(s) deflate_state *s; { register unsigned n, m; register Posf *p; unsigned more; /* Amount of free space at the end of the window. */ uInt wsize = s->w_size; do { more = (unsigned)(s->window_size -(ulg)s->lookahead -(ulg)s->strstart); /* Deal with !@#$% 64K limit: */ if (sizeof(int) <= 2) { if (more == 0 && s->strstart == 0 && s->lookahead == 0) { more = wsize; } else if (more == (unsigned)(-1)) { /* Very unlikely, but possible on 16 bit machine if * strstart == 0 && lookahead == 1 (input done a byte at time) */ more--; } } /* If the window is almost full and there is insufficient lookahead, * move the upper half to the lower one to make room in the upper half. */ if (s->strstart >= wsize+MAX_DIST(s)) { zmemcpy(s->window, s->window+wsize, (unsigned)wsize); s->match_start -= wsize; s->strstart -= wsize; /* we now have strstart >= MAX_DIST */ s->block_start -= (long) wsize; /* Slide the hash table (could be avoided with 32 bit values at the expense of memory usage). We slide even when level == 0 to keep the hash table consistent if we switch back to level > 0 later. (Using level 0 permanently is not an optimal usage of zlib, so we don't care about this pathological case.) */ /* %%% avoid this when Z_RLE */ n = s->hash_size; p = &s->head[n]; do { m = *--p; *p = (Pos)(m >= wsize ? m-wsize : NIL); } while (--n); n = wsize; #ifndef FASTEST p = &s->prev[n]; do { m = *--p; *p = (Pos)(m >= wsize ? m-wsize : NIL); /* If n is not on any hash chain, prev[n] is garbage but * its value will never be used. */ } while (--n); #endif more += wsize; } if (s->strm->avail_in == 0) return; /* If there was no sliding: * strstart <= WSIZE+MAX_DIST-1 && lookahead <= MIN_LOOKAHEAD - 1 && * more == window_size - lookahead - strstart * => more >= window_size - (MIN_LOOKAHEAD-1 + WSIZE + MAX_DIST-1) * => more >= window_size - 2*WSIZE + 2 * In the BIG_MEM or MMAP case (not yet supported), * window_size == input_size + MIN_LOOKAHEAD && * strstart + s->lookahead <= input_size => more >= MIN_LOOKAHEAD. * Otherwise, window_size == 2*WSIZE so more >= 2. * If there was sliding, more >= WSIZE. So in all cases, more >= 2. */ Assert(more >= 2, "more < 2"); n = read_buf(s->strm, s->window + s->strstart + s->lookahead, more); s->lookahead += n; /* Initialize the hash value now that we have some input: */ if (s->lookahead >= MIN_MATCH) { s->ins_h = s->window[s->strstart]; UPDATE_HASH(s, s->ins_h, s->window[s->strstart+1]); #if MIN_MATCH != 3 Call UPDATE_HASH() MIN_MATCH-3 more times #endif } /* If the whole input has less than MIN_MATCH bytes, ins_h is garbage, * but this is not important since only literal bytes will be emitted. */ } while (s->lookahead < MIN_LOOKAHEAD && s->strm->avail_in != 0); } /* =========================================================================== * Flush the current block, with given end-of-file flag. * IN assertion: strstart is set to the end of the current match. */ #define FLUSH_BLOCK_ONLY(s, eof) { \ _tr_flush_block(s, (s->block_start >= 0L ? \ (charf *)&s->window[(unsigned)s->block_start] : \ (charf *)Z_NULL), \ (ulg)((long)s->strstart - s->block_start), \ (eof)); \ s->block_start = s->strstart; \ flush_pending(s->strm); \ Tracev((stderr,"[FLUSH]")); \ } /* Same but force premature exit if necessary. */ #define FLUSH_BLOCK(s, eof) { \ FLUSH_BLOCK_ONLY(s, eof); \ if (s->strm->avail_out == 0) return (eof) ? finish_started : need_more; \ } /* =========================================================================== * Copy without compression as much as possible from the input stream, return * the current block state. * This function does not insert new strings in the dictionary since * uncompressible data is probably not useful. This function is used * only for the level=0 compression option. * NOTE: this function should be optimized to avoid extra copying from * window to pending_buf. */ local block_state deflate_stored(s, flush) deflate_state *s; int flush; { /* Stored blocks are limited to 0xffff bytes, pending_buf is limited * to pending_buf_size, and each stored block has a 5 byte header: */ ulg max_block_size = 0xffff; ulg max_start; if (max_block_size > s->pending_buf_size - 5) { max_block_size = s->pending_buf_size - 5; } /* Copy as much as possible from input to output: */ for (;;) { /* Fill the window as much as possible: */ if (s->lookahead <= 1) { Assert(s->strstart < s->w_size+MAX_DIST(s) || s->block_start >= (long)s->w_size, "slide too late"); fill_window(s); if (s->lookahead == 0 && flush == Z_NO_FLUSH) return need_more; if (s->lookahead == 0) break; /* flush the current block */ } Assert(s->block_start >= 0L, "block gone"); s->strstart += s->lookahead; s->lookahead = 0; /* Emit a stored block if pending_buf will be full: */ max_start = s->block_start + max_block_size; if (s->strstart == 0 || (ulg)s->strstart >= max_start) { /* strstart == 0 is possible when wraparound on 16-bit machine */ s->lookahead = (uInt)(s->strstart - max_start); s->strstart = (uInt)max_start; FLUSH_BLOCK(s, 0); } /* Flush if we may have to slide, otherwise block_start may become * negative and the data will be gone: */ if (s->strstart - (uInt)s->block_start >= MAX_DIST(s)) { FLUSH_BLOCK(s, 0); } } FLUSH_BLOCK(s, flush == Z_FINISH); return flush == Z_FINISH ? finish_done : block_done; } /* =========================================================================== * Compress as much as possible from the input stream, return the current * block state. * This function does not perform lazy evaluation of matches and inserts * new strings in the dictionary only for unmatched strings or for short * matches. It is used only for the fast compression options. */ local block_state deflate_fast(s, flush) deflate_state *s; int flush; { IPos hash_head = NIL; /* head of the hash chain */ int bflush; /* set if current block must be flushed */ for (;;) { /* Make sure that we always have enough lookahead, except * at the end of the input file. We need MAX_MATCH bytes * for the next match, plus MIN_MATCH bytes to insert the * string following the next match. */ if (s->lookahead < MIN_LOOKAHEAD) { fill_window(s); if (s->lookahead < MIN_LOOKAHEAD && flush == Z_NO_FLUSH) { return need_more; } if (s->lookahead == 0) break; /* flush the current block */ } /* Insert the string window[strstart .. strstart+2] in the * dictionary, and set hash_head to the head of the hash chain: */ if (s->lookahead >= MIN_MATCH) { INSERT_STRING(s, s->strstart, hash_head); } /* Find the longest match, discarding those <= prev_length. * At this point we have always match_length < MIN_MATCH */ if (hash_head != NIL && s->strstart - hash_head <= MAX_DIST(s)) { /* To simplify the code, we prevent matches with the string * of window index 0 (in particular we have to avoid a match * of the string with itself at the start of the input file). */ #ifdef FASTEST if ((s->strategy != Z_HUFFMAN_ONLY && s->strategy != Z_RLE) || (s->strategy == Z_RLE && s->strstart - hash_head == 1)) { s->match_length = longest_match_fast (s, hash_head); } #else if (s->strategy != Z_HUFFMAN_ONLY && s->strategy != Z_RLE) { s->match_length = longest_match (s, hash_head); } else if (s->strategy == Z_RLE && s->strstart - hash_head == 1) { s->match_length = longest_match_fast (s, hash_head); } #endif /* longest_match() or longest_match_fast() sets match_start */ } if (s->match_length >= MIN_MATCH) { check_match(s, s->strstart, s->match_start, s->match_length); _tr_tally_dist(s, s->strstart - s->match_start, s->match_length - MIN_MATCH, bflush); s->lookahead -= s->match_length; /* Insert new strings in the hash table only if the match length * is not too large. This saves time but degrades compression. */ #ifndef FASTEST if (s->match_length <= s->max_insert_length && s->lookahead >= MIN_MATCH) { s->match_length--; /* string at strstart already in table */ do { s->strstart++; INSERT_STRING(s, s->strstart, hash_head); /* strstart never exceeds WSIZE-MAX_MATCH, so there are * always MIN_MATCH bytes ahead. */ } while (--s->match_length != 0); s->strstart++; } else #endif { s->strstart += s->match_length; s->match_length = 0; s->ins_h = s->window[s->strstart]; UPDATE_HASH(s, s->ins_h, s->window[s->strstart+1]); #if MIN_MATCH != 3 Call UPDATE_HASH() MIN_MATCH-3 more times #endif /* If lookahead < MIN_MATCH, ins_h is garbage, but it does not * matter since it will be recomputed at next deflate call. */ } } else { /* No match, output a literal byte */ Tracevv((stderr,"%c", s->window[s->strstart])); _tr_tally_lit (s, s->window[s->strstart], bflush); s->lookahead--; s->strstart++; } if (bflush) FLUSH_BLOCK(s, 0); } FLUSH_BLOCK(s, flush == Z_FINISH); return flush == Z_FINISH ? finish_done : block_done; } #ifndef FASTEST /* =========================================================================== * Same as above, but achieves better compression. We use a lazy * evaluation for matches: a match is finally adopted only if there is * no better match at the next window position. */ local block_state deflate_slow(s, flush) deflate_state *s; int flush; { IPos hash_head = NIL; /* head of hash chain */ int bflush; /* set if current block must be flushed */ /* Process the input block. */ for (;;) { /* Make sure that we always have enough lookahead, except * at the end of the input file. We need MAX_MATCH bytes * for the next match, plus MIN_MATCH bytes to insert the * string following the next match. */ if (s->lookahead < MIN_LOOKAHEAD) { fill_window(s); if (s->lookahead < MIN_LOOKAHEAD && flush == Z_NO_FLUSH) { return need_more; } if (s->lookahead == 0) break; /* flush the current block */ } /* Insert the string window[strstart .. strstart+2] in the * dictionary, and set hash_head to the head of the hash chain: */ if (s->lookahead >= MIN_MATCH) { INSERT_STRING(s, s->strstart, hash_head); } /* Find the longest match, discarding those <= prev_length. */ s->prev_length = s->match_length, s->prev_match = s->match_start; s->match_length = MIN_MATCH-1; if (hash_head != NIL && s->prev_length < s->max_lazy_match && s->strstart - hash_head <= MAX_DIST(s)) { /* To simplify the code, we prevent matches with the string * of window index 0 (in particular we have to avoid a match * of the string with itself at the start of the input file). */ if (s->strategy != Z_HUFFMAN_ONLY && s->strategy != Z_RLE) { s->match_length = longest_match (s, hash_head); } else if (s->strategy == Z_RLE && s->strstart - hash_head == 1) { s->match_length = longest_match_fast (s, hash_head); } /* longest_match() or longest_match_fast() sets match_start */ if (s->match_length <= 5 && (s->strategy == Z_FILTERED #if TOO_FAR <= 32767 || (s->match_length == MIN_MATCH && s->strstart - s->match_start > TOO_FAR) #endif )) { /* If prev_match is also MIN_MATCH, match_start is garbage * but we will ignore the current match anyway. */ s->match_length = MIN_MATCH-1; } } /* If there was a match at the previous step and the current * match is not better, output the previous match: */ if (s->prev_length >= MIN_MATCH && s->match_length <= s->prev_length) { uInt max_insert = s->strstart + s->lookahead - MIN_MATCH; /* Do not insert strings in hash table beyond this. */ check_match(s, s->strstart-1, s->prev_match, s->prev_length); _tr_tally_dist(s, s->strstart -1 - s->prev_match, s->prev_length - MIN_MATCH, bflush); /* Insert in hash table all strings up to the end of the match. * strstart-1 and strstart are already inserted. If there is not * enough lookahead, the last two strings are not inserted in * the hash table. */ s->lookahead -= s->prev_length-1; s->prev_length -= 2; do { if (++s->strstart <= max_insert) { INSERT_STRING(s, s->strstart, hash_head); } } while (--s->prev_length != 0); s->match_available = 0; s->match_length = MIN_MATCH-1; s->strstart++; if (bflush) FLUSH_BLOCK(s, 0); } else if (s->match_available) { /* If there was no match at the previous position, output a * single literal. If there was a match but the current match * is longer, truncate the previous match to a single literal. */ Tracevv((stderr,"%c", s->window[s->strstart-1])); _tr_tally_lit(s, s->window[s->strstart-1], bflush); if (bflush) { FLUSH_BLOCK_ONLY(s, 0); } s->strstart++; s->lookahead--; if (s->strm->avail_out == 0) return need_more; } else { /* There is no previous match to compare with, wait for * the next step to decide. */ s->match_available = 1; s->strstart++; s->lookahead--; } } Assert (flush != Z_NO_FLUSH, "no flush?"); if (s->match_available) { Tracevv((stderr,"%c", s->window[s->strstart-1])); _tr_tally_lit(s, s->window[s->strstart-1], bflush); s->match_available = 0; } FLUSH_BLOCK(s, flush == Z_FINISH); return flush == Z_FINISH ? finish_done : block_done; } #endif /* FASTEST */ #if 0 /* =========================================================================== * For Z_RLE, simply look for runs of bytes, generate matches only of distance * one. Do not maintain a hash table. (It will be regenerated if this run of * deflate switches away from Z_RLE.) */ local block_state deflate_rle(s, flush) deflate_state *s; int flush; { int bflush; /* set if current block must be flushed */ uInt run; /* length of run */ uInt max; /* maximum length of run */ uInt prev; /* byte at distance one to match */ Bytef *scan; /* scan for end of run */ for (;;) { /* Make sure that we always have enough lookahead, except * at the end of the input file. We need MAX_MATCH bytes * for the longest encodable run. */ if (s->lookahead < MAX_MATCH) { fill_window(s); if (s->lookahead < MAX_MATCH && flush == Z_NO_FLUSH) { return need_more; } if (s->lookahead == 0) break; /* flush the current block */ } /* See how many times the previous byte repeats */ run = 0; if (s->strstart > 0) { /* if there is a previous byte, that is */ max = s->lookahead < MAX_MATCH ? s->lookahead : MAX_MATCH; scan = s->window + s->strstart - 1; prev = *scan++; do { if (*scan++ != prev) break; } while (++run < max); } /* Emit match if have run of MIN_MATCH or longer, else emit literal */ if (run >= MIN_MATCH) { check_match(s, s->strstart, s->strstart - 1, run); _tr_tally_dist(s, 1, run - MIN_MATCH, bflush); s->lookahead -= run; s->strstart += run; } else { /* No match, output a literal byte */ Tracevv((stderr,"%c", s->window[s->strstart])); _tr_tally_lit (s, s->window[s->strstart], bflush); s->lookahead--; s->strstart++; } if (bflush) FLUSH_BLOCK(s, 0); } FLUSH_BLOCK(s, flush == Z_FINISH); return flush == Z_FINISH ? finish_done : block_done; } #endif maqview-0.2.5/zrio_main.c0000644000265600020320000000373611051450600014447 0ustar tilleaadmin#include #include #include "zrio.h" void usage(FILE *out, char *prog){ fprintf(out, "Usage: %s make | use\n", prog); fprintf(out, "\tmake []\tmake index for gz-file,index filename will be .idx\n"); fprintf(out, "\t \teach level increasing the time for search whist decreasing the size of index\n"); fprintf(out, "\t \tlevel: default 1024, 1/1024 of source file\n"); fprintf(out, "\t \tlevel: 512, 1/512 of source file\n"); fprintf(out, "\t \tlevel: ...\n"); fprintf(out, "\tuse [ ]\tuse index .idx, exact from offset(source position) to stdout\n"); } int main(int argc, char **argv){ int64_t offset, offlen; int i, level, ret; zr_stream *zr; char buffer[WINSIZE + 1]; if(argc < 2) return usage(stderr, argv[0]), 1; if(strcmp(argv[1], "make") == 0){ if(argc < 3) return usage(stderr, argv[0]), 1; if(argc >= 4){ level = atoi(argv[3]); if(level < 2) level = 2; } else level = 1024; if(!zrmkindex(argv[2], level, NULL, NULL)){ fprintf(stderr, "Cannot make index for gzfile[%s]\n", argv[2]); return 1; } return 0; } else if(strcmp(argv[1], "use") == 0){ if(argc < 4) return usage(stderr, argv[0]), 1; zr = zropen(argv[2]); if(zr == NULL){ fprintf(stderr, "Cannot open %s\n", argv[2]); return 1; } offset = atol(argv[3]); if(argc == 4){ offlen = (int)((~((unsigned int)0)) >> 1); } else { offlen = atol(argv[4]); } if(zrseek(zr, offset) < 0){ fprintf(stderr, "Cannot seek to position %ld\n", offset); zrclose(zr); return 1; } while(offlen && !zreof(zr)){ ret = zrread(buffer, WINSIZE, zr); if(ret > offlen){ ret = offlen;} for(i=0;i= 199901L # ifndef STDC99 # define STDC99 # endif # endif #endif #if !defined(STDC) && (defined(__STDC__) || defined(__cplusplus)) # define STDC #endif #if !defined(STDC) && (defined(__GNUC__) || defined(__BORLANDC__)) # define STDC #endif #if !defined(STDC) && (defined(MSDOS) || defined(WINDOWS) || defined(WIN32)) # define STDC #endif #if !defined(STDC) && (defined(OS2) || defined(__HOS_AIX__)) # define STDC #endif #if defined(__OS400__) && !defined(STDC) /* iSeries (formerly AS/400). */ # define STDC #endif #ifndef STDC # ifndef const /* cannot use !defined(STDC) && !defined(const) on Mac */ # define const /* note: need a more gentle solution here */ # endif #endif /* Some Mac compilers merge all .h files incorrectly: */ #if defined(__MWERKS__)||defined(applec)||defined(THINK_C)||defined(__SC__) # define NO_DUMMY_DECL #endif /* Maximum value for memLevel in deflateInit2 */ #ifndef MAX_MEM_LEVEL # ifdef MAXSEG_64K # define MAX_MEM_LEVEL 8 # else # define MAX_MEM_LEVEL 9 # endif #endif /* Maximum value for windowBits in deflateInit2 and inflateInit2. * WARNING: reducing MAX_WBITS makes minigzip unable to extract .gz files * created by gzip. (Files created by minigzip can still be extracted by * gzip.) */ #ifndef MAX_WBITS # define MAX_WBITS 15 /* 32K LZ77 window */ #endif /* The memory requirements for deflate are (in bytes): (1 << (windowBits+2)) + (1 << (memLevel+9)) that is: 128K for windowBits=15 + 128K for memLevel = 8 (default values) plus a few kilobytes for small objects. For example, if you want to reduce the default memory requirements from 256K to 128K, compile with make CFLAGS="-O -DMAX_WBITS=14 -DMAX_MEM_LEVEL=7" Of course this will generally degrade compression (there's no free lunch). The memory requirements for inflate are (in bytes) 1 << windowBits that is, 32K for windowBits=15 (default value) plus a few kilobytes for small objects. */ /* Type declarations */ #ifndef OF /* function prototypes */ # ifdef STDC # define OF(args) args # else # define OF(args) () # endif #endif /* The following definitions for FAR are needed only for MSDOS mixed * model programming (small or medium model with some far allocations). * This was tested only with MSC; for other MSDOS compilers you may have * to define NO_MEMCPY in zutil.h. If you don't need the mixed model, * just define FAR to be empty. */ #ifdef SYS16BIT # if defined(M_I86SM) || defined(M_I86MM) /* MSC small or medium model */ # define SMALL_MEDIUM # ifdef _MSC_VER # define FAR _far # else # define FAR far # endif # endif # if (defined(__SMALL__) || defined(__MEDIUM__)) /* Turbo C small or medium model */ # define SMALL_MEDIUM # ifdef __BORLANDC__ # define FAR _far # else # define FAR far # endif # endif #endif #if defined(WINDOWS) || defined(WIN32) /* If building or using zlib as a DLL, define ZLIB_DLL. * This is not mandatory, but it offers a little performance increase. */ # ifdef ZLIB_DLL # if defined(WIN32) && (!defined(__BORLANDC__) || (__BORLANDC__ >= 0x500)) # ifdef ZLIB_INTERNAL # define ZEXTERN extern __declspec(dllexport) # else # define ZEXTERN extern __declspec(dllimport) # endif # endif # endif /* ZLIB_DLL */ /* If building or using zlib with the WINAPI/WINAPIV calling convention, * define ZLIB_WINAPI. * Caution: the standard ZLIB1.DLL is NOT compiled using ZLIB_WINAPI. */ # ifdef ZLIB_WINAPI # ifdef FAR # undef FAR # endif # include /* No need for _export, use ZLIB.DEF instead. */ /* For complete Windows compatibility, use WINAPI, not __stdcall. */ # define ZEXPORT WINAPI # ifdef WIN32 # define ZEXPORTVA WINAPIV # else # define ZEXPORTVA FAR CDECL # endif # endif #endif #if defined (__BEOS__) # ifdef ZLIB_DLL # ifdef ZLIB_INTERNAL # define ZEXPORT __declspec(dllexport) # define ZEXPORTVA __declspec(dllexport) # else # define ZEXPORT __declspec(dllimport) # define ZEXPORTVA __declspec(dllimport) # endif # endif #endif #ifndef ZEXTERN # define ZEXTERN extern #endif #ifndef ZEXPORT # define ZEXPORT #endif #ifndef ZEXPORTVA # define ZEXPORTVA #endif #ifndef FAR # define FAR #endif #if !defined(__MACTYPES__) typedef unsigned char Byte; /* 8 bits */ #endif typedef unsigned int uInt; /* 16 bits or more */ typedef unsigned long uLong; /* 32 bits or more */ #ifdef SMALL_MEDIUM /* Borland C/C++ and some old MSC versions ignore FAR inside typedef */ # define Bytef Byte FAR #else typedef Byte FAR Bytef; #endif typedef char FAR charf; typedef int FAR intf; typedef uInt FAR uIntf; typedef uLong FAR uLongf; #ifdef STDC typedef void const *voidpc; typedef void FAR *voidpf; typedef void *voidp; #else typedef Byte const *voidpc; typedef Byte FAR *voidpf; typedef Byte *voidp; #endif #if 0 /* HAVE_UNISTD_H -- this line is updated by ./configure */ # include /* for off_t */ # include /* for SEEK_* and off_t */ # ifdef VMS # include /* for off_t */ # endif # define z_off_t off_t #endif #ifndef SEEK_SET # define SEEK_SET 0 /* Seek from beginning of file. */ # define SEEK_CUR 1 /* Seek from current position. */ # define SEEK_END 2 /* Set file pointer to EOF plus "offset" */ #endif #ifndef z_off_t # define z_off_t long #endif #if defined(__OS400__) # define NO_vsnprintf #endif #if defined(__MVS__) # define NO_vsnprintf # ifdef FAR # undef FAR # endif #endif /* MVS linker does not support external names larger than 8 bytes */ #if defined(__MVS__) # pragma map(deflateInit_,"DEIN") # pragma map(deflateInit2_,"DEIN2") # pragma map(deflateEnd,"DEEND") # pragma map(deflateBound,"DEBND") # pragma map(inflateInit_,"ININ") # pragma map(inflateInit2_,"ININ2") # pragma map(inflateEnd,"INEND") # pragma map(inflateSync,"INSY") # pragma map(inflateSetDictionary,"INSEDI") # pragma map(compressBound,"CMBND") # pragma map(inflate_table,"INTABL") # pragma map(inflate_fast,"INFA") # pragma map(inflate_copyright,"INCOPY") #endif #endif /* ZCONF_H */ maqview-0.2.5/zrio.h0000644000265600020320000000256010761137604013457 0ustar tilleaadmin#ifndef __ZRIO_RJ #define __ZRIO_RJ #include #include #include "zutil.h" #include "inftrees.h" #include "inflate.h" #include "zlib.h" #define WINSIZE 32768 /* sliding window size */ #define CHUNK 16384 /* file input buffer size */ typedef struct point { int64_t out; int64_t in; int bits; unsigned char *window; } Point; typedef struct access { int have; /* number of list entries filled in */ int size; /* number of list entries allocated */ Point *list; /* allocated list */ } Access; typedef struct zr_stream { FILE *acc_file; Access *access; int64_t last_in, in, out; unsigned char window[WINSIZE]; int64_t pos; int fid; int z_eof; int z_err; void *inbuf; void *outbuf; z_stream *stream; } zr_stream; zr_stream* zropen(const char *filename); int zrmkindex(const char *filename, int level, void (*notify)(void *obj, unsigned char *buf, int buf_size, int64_t pos), void *obj); int64_t zrread(void *buf, int64_t len, zr_stream *stream); /** * More efficient than zrseek + zrread */ int64_t zrgets(void *buf, int64_t len, int64_t offset, zr_stream *stream); int zreof(zr_stream *stream); int zrerror(zr_stream *stream); int64_t zrtell(zr_stream *stream); int64_t zrseek(zr_stream *stream, int64_t offset); int zrskip(zr_stream *stream, int bytes); void zrclose(zr_stream *stream); #endif maqview-0.2.5/btree.h0000644000265600020320000000166411041565220013570 0ustar tilleaadmin#ifndef __BTREE_MAQVIEW_RJ #define __BTREE_MAQVIEW_RJ #include #include #include "zlib.h" typedef struct BTree { struct BTree *parent; struct BTree **childs; int64_t left, right; int64_t indexs[2]; int size; } BTree; #ifndef BTREE_MAX_ELEMENTS #define BTREE_MAX_ELEMENTS 1024 #endif #ifndef BTREE_MAX_NODES #define BTREE_MAX_NODES 32 #endif BTree* btree_init(); BTree* btree_bulid(int (*get_next)(void *obj, int64_t last_index, int64_t *value), void *obj); BTree* btree_append(BTree **tree_ref, BTree *last_node, int *layer, int64_t index, int64_t value); BTree* btree_find(BTree *tree, int64_t value, int64_t *left_index, int64_t *right_index); int btree_dump(FILE *out, BTree *tree); int btree_dump_gz(gzFile out, BTree *tree); BTree* btree_load(FILE *in); BTree* btree_load_gz(gzFile in); void btree_free(BTree *tree); int64_t _get_min_index(BTree *tree); int64_t _get_max_index(BTree *tree); #endif maqview-0.2.5/test_razf.c0000644000265600020320000000201511100513756014455 0ustar tilleaadmin#include "razf.h" #include "kstream.h" #include KSTREAM_INIT(RAZF*, razf_read, 4096) int main(int argc, char **argv){ RAZF *rz = razf_open_r(open(argv[1], O_RDONLY)); unsigned int n = 32 * 1024 * 1024; void *buffer = alloca(1<<12); clock_t t1 = clock(); int i; for(i=0;i>12;i++){ razf_read(rz, buffer, 1<<12); } t2 = clock(); fprintf(stderr, " -- time %.3lf , n = %u in %s -- %s:%d --\n", ((double)(t2-t1) / CLOCKS_PER_SEC), n, __FUNCTION__, __FILE__, __LINE__); razf_seek(rz, 0, SEEK_SET); kstream_t *ks = ks_init(rz); t1 = clock(); for(i=0;i for writing and maintaining the program. Heng Li for testing the program and drafting the documentations. Mengyao Zhao for designing the color schemes. maqview-0.2.5/view_goto.c0000644000265600020320000002442010777153206014473 0ustar tilleaadmin#include #include #include #include "maqview.h" #ifdef __APPLE__ #include #else #include #include #include "GL/glut.h" #ifdef HAVE_FREEGLUT #include "GL/freeglut_ext.h" #endif #endif static float mv_color_bg[3] = { 0, 0, 0 }, mv_color_A[3] = { 0.4, 0.8, 0.0 }, mv_color_C[3] = { 0.6, 1.0, 1.0 }, mv_color_G[3] = { 1.0, 0.6, 0.0 }, mv_color_T[3] = { 1.0, 0.0, 0.0 }, mv_color_N[3] = { 0.1, 0.1, 0.1 }, mv_color_ref[3] = { 1.0, 1.0, 1.0 }, mv_color_nav[3] = { 1.0, 1.0, 0.5 }, mv_color_tip[3] = { 1.0, 1.0, 0.5 }, mv_color_sel[3] = { 0.4, 0.4, 0.3 }, mv_color_lif[3] = { 0.7, 0.0, 0.3 }, mv_color_lib[3] = { 0.3, 0.0, 0.7 }, mv_color_def[3] = { 1.0, 1.0, 1.0 };; View* createView(const char *map_file, const char *cns_file, int width, int height, int style){ MapIndex *index; View *view; char *cns_name; int i; if(style != 0){ fprintf(stderr, "Cannot support style:%d\n", style); return NULL; } index = load_map_index(map_file, 0); if(index == NULL) return NULL; view = (View*)malloc(sizeof(View)); view->map_file = (char*)malloc(strlen(map_file) + 1); strcpy(view->map_file, map_file); view->style = style; view->font = GLUT_BITMAP_8_BY_13; view->big_font = GLUT_BITMAP_9_BY_15; view->width = width; view->height = height; view->font_width = 8; view->font_height = 13; view->font_line_height = 13; view->ch_width = width / view->font_width; view->mode = VIEW_MODE_CHARACTER; view->base_width = 5; view->base_margin = 0.5; view->base_height = 4; view->base_line_height = 5; view->line_width = 5; view->line_height = 6; view->scale_x = 1.0; view->scale_y = 1.0; view->nav.square_size = 10; view->nav.center_x = width / 2; view->nav.center_y = 4 * view->nav.square_size; view->nav.arrow_size = 20; view->nav.arrow_x = view->nav.center_x; view->nav.arrow_y = view->nav.center_y; view->nav.state = 0; memcpy(view->bgColor.rgb, mv_color_bg, sizeof(float) * 3); memcpy(view->ref_color.rgb, mv_color_ref, sizeof(float) * 3); memcpy(view->select_color.rgb, mv_color_sel, sizeof(float) * 3); memcpy(view->default_color.rgb, mv_color_def, sizeof(float) * 3); memcpy(view->line_forward_color.rgb, mv_color_lif, sizeof(float) * 3); memcpy(view->line_backward_color.rgb, mv_color_lib, sizeof(float) * 3); view->mismatch_color.rgb[0] = 1; view->mismatch_color.rgb[1] = 0; view->mismatch_color.rgb[2] = 0; memcpy(view->nav_color.rgb, mv_color_nav, sizeof(float) * 3); memcpy(view->tip_color.rgb, mv_color_tip, sizeof(float) * 3); i = 100; view->qual_color_table = (Color*)malloc(sizeof(Color) * (i + 1)); while (i >= 0) { float value = (float)((i >= MAX_BASE_Q)? MAX_BASE_Q : i) / MAX_BASE_Q; value = 0.8 * value + 0.2; view->qual_color_table[i].rgb[0] = value; view->qual_color_table[i].rgb[1] = value; view->qual_color_table[i].rgb[2] = value; i --; } view->base_color_table = (Color*)malloc(sizeof(Color) * 5); memcpy(view->base_color_table[0].rgb, mv_color_A, sizeof(float) * 3); memcpy(view->base_color_table[1].rgb, mv_color_C, sizeof(float) * 3); memcpy(view->base_color_table[2].rgb, mv_color_G, sizeof(float) * 3); memcpy(view->base_color_table[3].rgb, mv_color_T, sizeof(float) * 3); memcpy(view->base_color_table[4].rgb, mv_color_N, sizeof(float) * 3); view->default_ref_char = '-'; view->refs.cache = read_cache_init(index); view->refs.show_id = 0; view->refs.show_start = 0; view->refs.tooltips = (unsigned char*)malloc(TOOLTIP_SIZE); memset(view->refs.tooltips, 0, TOOLTIP_SIZE); cns_name = cns_file? (char*)cns_file : (char*)calloc(strlen(map_file)+6, 1); view->refs.cns = open_cns_cache(cns_name); if(view->refs.cns == NULL){ view->refs.cns = cns_cache_init(); } else { justify_cns_cache(view->refs.cns, view->refs.cache->index->mm->ref_name, view->refs.cache->index->mm->n_ref); for(i=0;irefs.cache->index->mm->n_ref;i++){ view->refs.cache->ref_lengths[i] = view->refs.cns->ref_lengths[i]; if(view->refs.cache->index->trees[i]->right < view->refs.cns->ref_lengths[i]){ view->refs.cache->index->trees[i]->right = view->refs.cns->ref_lengths[i]; } } } view->cns_file = (char*)malloc(strlen(cns_name) + 1); strcpy(view->cns_file, cns_name); if(!cns_file) free(cns_name); view->layer_offset = 1; // Deafult move down one line view->last_x = view->last_y = 0; view->old_x = view->old_y = 0; view->state = 0; view->rolling = 0; view->selecting = 0; view->step = 1; view->observer = (Observer*)malloc(sizeof(Observer)); view->observer->n_ob = 0; view->observer->objects = NULL; view->observer->notify = NULL; return view; } View* view_clone(View *view){ return createView(view->map_file, view->cns_file, view->width, view->height, view->style); } void observeView(View *view, void *observer, void (*notify)(void *obj, View *src, int event, int64_t last_x, int off_y)){ if(!notify) return; view->observer->n_ob ++; view->observer->objects = (void**)realloc(view->observer->objects, sizeof(void*) * view->observer->n_ob); view->observer->notify = (void*)realloc(view->observer->notify, sizeof(void*) * view->observer->n_ob); view->observer->objects[view->observer->n_ob-1] = observer; view->observer->notify[view->observer->n_ob-1] = notify; } void removeObserverView(View * view, void *object){ Observer *ob; int i; ob = view->observer; if(!ob) return; for(i=0;in_ob;i++){ if(ob->objects[i] == object){ ob->n_ob --; if(ob->n_ob && i < ob->n_ob){ memmove(ob->objects + i, ob->objects + i + 1, ob->n_ob - i); memmove(ob->notify + i, ob->notify + i + 1, ob->n_ob - i); } i --; } } } void notifyView(View *view, int evt, int64_t x, int y){ int i; for(i=0;iobserver->n_ob;i++){ view->observer->notify[i](view->observer->objects[i], view, evt, x, y); } } void view_resize(View *view, int w, int h){ switch(view->mode){ case VIEW_MODE_CHARACTER: view->ch_width = w / view->font_width; break; case VIEW_MODE_SQUARE: view->ch_width = w / (view->base_width * view->scale_x); break; case VIEW_MODE_LINE: view->ch_width = w / (view->line_width * view->scale_x); break; default: return; } memset(view->refs.tooltips, 0, TOOLTIP_SIZE); view->nav.center_x = w / 2; view->nav.center_y = 4 * view->nav.square_size; view->nav.arrow_x = view->nav.center_x; view->nav.arrow_y = view->nav.center_y; notifyView(view, VIEW_EVENT_RESIZE, view->refs.show_start, 0); view_goto(view, view->refs.show_id, view->refs.show_start); } void relayout(View *view){ int i, j, lay_size; int64_t *layers; Read *read; lay_size = 256; layers = (int64_t*)malloc(sizeof(int64_t) * lay_size); memset(layers, 0, sizeof(int64_t) * lay_size); for(i=0;irefs.cache->size;i++){ read = view->refs.cache->reads + view->refs.cache->offset + i; j = 0; REPEAT: for(;jread.pos) >= layers[j]){ read->y = j; layers[j] = read_pos(read->read.pos) + read->read.size + 1; break; } } if(j == lay_size){ lay_size += 256; layers = (int64_t*)realloc(layers, sizeof(int64_t) * lay_size); memset(layers + j, 0, sizeof(int64_t) * (lay_size - j)); goto REPEAT; } } free(layers); } int view_locate(View *view, char *ref_name, int64_t pos){ int ref_id; if(ref_name == NULL) return 0; for(ref_id=0;ref_idrefs.cache->index->mm->n_ref;ref_id++){ if(strcmp(ref_name, view->refs.cache->index->mm->ref_name[ref_id]) == 0){ return view_goto(view, ref_id, pos); } } return 0; } int view_goto(View *view, int ref_id, int64_t pos){ int i; int64_t start, end, last_start; int size, ret; RefSeq *refs; refs = &(view->refs); size = view->ch_width; start = pos - MAX_READ_SIZE; end = pos + size; last_start = view->refs.show_start; ret = read_cache_put(view->refs.cache, ref_id, start, end); if(ret < 0){ printf("[error]: %s:%d\n", __FILE__, __LINE__); return 0; } refs->show_start = pos; // refs->show_start = (pos<0)? 0:(pos); switch(ret){ case 1: notifyView(view, VIEW_EVENT_GOTO, last_start, 0); break; default: notifyView(view, VIEW_EVENT_MOVE, last_start, 0); } if(ret){ relayout(view); } if(refs->show_id != ref_id){ memset(refs->tooltips, 0, size); refs->show_id = ref_id; } else { if(refs->show_start < last_start + size && refs->show_start + size > last_start){ if(refs->show_start < last_start){ for(i=size-1;i>=last_start - refs->show_start;i--){ refs->tooltips[i] = refs->tooltips[i+refs->show_start-last_start]; } for(;i>=0;i--){ refs->tooltips[i] = 0; } } else { for(i=0;ishow_start + last_start;i++){ refs->tooltips[i] = refs->tooltips[i+refs->show_start-last_start]; } for(;itooltips[i] = 0; } } } else { memset(refs->tooltips, 0, size); } } if(refs->cns->stream && ref_id >= 0 && ref_id < refs->cns->n_mm_ref && refs->cns->mm_map[ref_id] >= 0){ cns_cache_put(refs->cns, refs->cns->mm_map[ref_id], start, end); } else { cns_cache_guess(refs->cns, refs->cache); } return 1; } void closeView(View *view){ RefSeq *refs; notifyView(view, VIEW_EVENT_CLOSE, 0, 0); free(view->observer->objects); free(view->observer->notify); free(view->observer); free(view->qual_color_table); free(view->base_color_table); refs = &(view->refs); close_cns_cache(refs->cns); free(refs->tooltips); read_cache_free(refs->cache); free(view->map_file); free(view->cns_file); free(view); } #ifdef MAIN_VIEW_GOTO void print_view(View *view){ int i; RefSeq *refs; Read *read; refs = &(view->refs); printf("------------------------ %lld %lld ---------------------------\n", refs->cache_start, refs->cache_end); for(i=0;iread_size;i++){ read = refs->reads + refs->read_offset + i; printf("%s\t%d\n", read->read.name, read_pos(read->read.pos) + 1); } printf("------------------------------------------------------------\n\n"); } int main(int argc, char **argv){ View *view; int i; if(argc < 2){ fprintf(stderr, "Usage: %s \n", argv[0]); return 1; } view = createView(argv[1], 1200, 800, 0); if(view == NULL){ printf("Cannot create view on file %s\n", argv[1]); return 1; } view_goto(view, 0, 1000); for(i=0;i<100;i++){ view_goto(view, 0, view->refs.show_start + 100); } for(;i>0;i--){ view_goto(view, 0, view->refs.show_start - 100); } closeView(view); return 0; } #endif maqview-0.2.5/gzio.c0000644000265600020320000007460410761137602013445 0ustar tilleaadmin/* gzio.c -- IO on .gz files * Copyright (C) 1995-2005 Jean-loup Gailly. * For conditions of distribution and use, see copyright notice in zlib.h * * Compile this file with -DNO_GZCOMPRESS to avoid the compression code. */ /* @(#) $Id$ */ #include #include "zutil.h" #ifdef NO_DEFLATE /* for compatibility with old definition */ # define NO_GZCOMPRESS #endif #ifndef NO_DUMMY_DECL struct internal_state {int dummy;}; /* for buggy compilers */ #endif #ifndef Z_BUFSIZE # ifdef MAXSEG_64K # define Z_BUFSIZE 4096 /* minimize memory usage for 16-bit DOS */ # else # define Z_BUFSIZE 16384 # endif #endif #ifndef Z_PRINTF_BUFSIZE # define Z_PRINTF_BUFSIZE 4096 #endif #ifdef __MVS__ # pragma map (fdopen , "\174\174FDOPEN") FILE *fdopen(int, const char *); #endif #ifndef STDC extern voidp malloc OF((uInt size)); extern void free OF((voidpf ptr)); #endif #define ALLOC(size) malloc(size) #define TRYFREE(p) {if (p) free(p);} static int const gz_magic[2] = {0x1f, 0x8b}; /* gzip magic header */ /* gzip flag byte */ #define ASCII_FLAG 0x01 /* bit 0 set: file probably ascii text */ #define HEAD_CRC 0x02 /* bit 1 set: header CRC present */ #define EXTRA_FIELD 0x04 /* bit 2 set: extra field present */ #define ORIG_NAME 0x08 /* bit 3 set: original file name present */ #define COMMENT 0x10 /* bit 4 set: file comment present */ #define RESERVED 0xE0 /* bits 5..7: reserved */ typedef struct gz_stream { z_stream stream; int z_err; /* error code for last stream operation */ int z_eof; /* set if end of input file */ FILE *file; /* .gz file */ Byte *inbuf; /* input buffer */ Byte *outbuf; /* output buffer */ uLong crc; /* crc32 of uncompressed data */ char *msg; /* error message */ char *path; /* path name for debugging only */ int transparent; /* 1 if input file is not a .gz file */ char mode; /* 'w' or 'r' */ z_off_t start; /* start of compressed data in file (header skipped) */ z_off_t in; /* bytes into deflate or inflate */ z_off_t out; /* bytes out of deflate or inflate */ int back; /* one character push-back */ int last; /* true if push-back is last character */ } gz_stream; local gzFile gz_open OF((const char *path, const char *mode, int fd)); local int do_flush OF((gzFile file, int flush)); local int get_byte OF((gz_stream *s)); local void check_header OF((gz_stream *s)); local int destroy OF((gz_stream *s)); local void putLong OF((FILE *file, uLong x)); local uLong getLong OF((gz_stream *s)); /* =========================================================================== Opens a gzip (.gz) file for reading or writing. The mode parameter is as in fopen ("rb" or "wb"). The file is given either by file descriptor or path name (if fd == -1). gz_open returns NULL if the file could not be opened or if there was insufficient memory to allocate the (de)compression state; errno can be checked to distinguish the two cases (if errno is zero, the zlib error is Z_MEM_ERROR). */ local gzFile gz_open (path, mode, fd) const char *path; const char *mode; int fd; { int err; int level = Z_DEFAULT_COMPRESSION; /* compression level */ int strategy = Z_DEFAULT_STRATEGY; /* compression strategy */ char *p = (char*)mode; gz_stream *s; char fmode[80]; /* copy of mode, without the compression level */ char *m = fmode; if (!path || !mode) return Z_NULL; s = (gz_stream *)ALLOC(sizeof(gz_stream)); if (!s) return Z_NULL; s->stream.zalloc = (alloc_func)0; s->stream.zfree = (free_func)0; s->stream.opaque = (voidpf)0; s->stream.next_in = s->inbuf = Z_NULL; s->stream.next_out = s->outbuf = Z_NULL; s->stream.avail_in = s->stream.avail_out = 0; s->file = NULL; s->z_err = Z_OK; s->z_eof = 0; s->in = 0; s->out = 0; s->back = EOF; s->crc = crc32(0L, Z_NULL, 0); s->msg = NULL; s->transparent = 0; s->path = (char*)ALLOC(strlen(path)+1); if (s->path == NULL) { return destroy(s), (gzFile)Z_NULL; } strcpy(s->path, path); /* do this early for debugging */ s->mode = '\0'; do { if (*p == 'r') s->mode = 'r'; if (*p == 'w' || *p == 'a') s->mode = 'w'; if (*p >= '0' && *p <= '9') { level = *p - '0'; } else if (*p == 'f') { strategy = Z_FILTERED; } else if (*p == 'h') { strategy = Z_HUFFMAN_ONLY; } else if (*p == 'R') { strategy = Z_RLE; } else { *m++ = *p; /* copy the mode */ } } while (*p++ && m != fmode + sizeof(fmode)); if (s->mode == '\0') return destroy(s), (gzFile)Z_NULL; if (s->mode == 'w') { #ifdef NO_GZCOMPRESS err = Z_STREAM_ERROR; #else err = deflateInit2(&(s->stream), level, Z_DEFLATED, -MAX_WBITS, DEF_MEM_LEVEL, strategy); /* windowBits is passed < 0 to suppress zlib header */ s->stream.next_out = s->outbuf = (Byte*)ALLOC(Z_BUFSIZE); #endif if (err != Z_OK || s->outbuf == Z_NULL) { return destroy(s), (gzFile)Z_NULL; } } else { s->stream.next_in = s->inbuf = (Byte*)ALLOC(Z_BUFSIZE); err = inflateInit2(&(s->stream), -MAX_WBITS); /* windowBits is passed < 0 to tell that there is no zlib header. * Note that in this case inflate *requires* an extra "dummy" byte * after the compressed stream in order to complete decompression and * return Z_STREAM_END. Here the gzip CRC32 ensures that 4 bytes are * present after the compressed stream. */ if (err != Z_OK || s->inbuf == Z_NULL) { return destroy(s), (gzFile)Z_NULL; } } s->stream.avail_out = Z_BUFSIZE; errno = 0; s->file = fd < 0 ? F_OPEN(path, fmode) : (FILE*)fdopen(fd, fmode); if (s->file == NULL) { return destroy(s), (gzFile)Z_NULL; } if (s->mode == 'w') { /* Write a very simple .gz header: */ fprintf(s->file, "%c%c%c%c%c%c%c%c%c%c", gz_magic[0], gz_magic[1], Z_DEFLATED, 0 /*flags*/, 0,0,0,0 /*time*/, 0 /*xflags*/, OS_CODE); s->start = 10L; /* We use 10L instead of ftell(s->file) to because ftell causes an * fflush on some systems. This version of the library doesn't use * start anyway in write mode, so this initialization is not * necessary. */ } else { check_header(s); /* skip the .gz header */ s->start = ftell(s->file) - s->stream.avail_in; } return (gzFile)s; } /* =========================================================================== Opens a gzip (.gz) file for reading or writing. */ gzFile ZEXPORT gzopen (path, mode) const char *path; const char *mode; { return gz_open (path, mode, -1); } /* =========================================================================== Associate a gzFile with the file descriptor fd. fd is not dup'ed here to mimic the behavio(u)r of fdopen. */ gzFile ZEXPORT gzdopen (fd, mode) int fd; const char *mode; { char name[46]; /* allow for up to 128-bit integers */ if (fd < 0) return (gzFile)Z_NULL; sprintf(name, "", fd); /* for debugging */ return gz_open (name, mode, fd); } /* =========================================================================== * Update the compression level and strategy */ int ZEXPORT gzsetparams (file, level, strategy) gzFile file; int level; int strategy; { gz_stream *s = (gz_stream*)file; if (s == NULL || s->mode != 'w') return Z_STREAM_ERROR; /* Make room to allow flushing */ if (s->stream.avail_out == 0) { s->stream.next_out = s->outbuf; if (fwrite(s->outbuf, 1, Z_BUFSIZE, s->file) != Z_BUFSIZE) { s->z_err = Z_ERRNO; } s->stream.avail_out = Z_BUFSIZE; } return deflateParams (&(s->stream), level, strategy); } /* =========================================================================== Read a byte from a gz_stream; update next_in and avail_in. Return EOF for end of file. IN assertion: the stream s has been sucessfully opened for reading. */ local int get_byte(s) gz_stream *s; { if (s->z_eof) return EOF; if (s->stream.avail_in == 0) { errno = 0; s->stream.avail_in = (uInt)fread(s->inbuf, 1, Z_BUFSIZE, s->file); if (s->stream.avail_in == 0) { s->z_eof = 1; if (ferror(s->file)) s->z_err = Z_ERRNO; return EOF; } s->stream.next_in = s->inbuf; } s->stream.avail_in--; return *(s->stream.next_in)++; } /* =========================================================================== Check the gzip header of a gz_stream opened for reading. Set the stream mode to transparent if the gzip magic header is not present; set s->err to Z_DATA_ERROR if the magic header is present but the rest of the header is incorrect. IN assertion: the stream s has already been created sucessfully; s->stream.avail_in is zero for the first time, but may be non-zero for concatenated .gz files. */ local void check_header(s) gz_stream *s; { int method; /* method byte */ int flags; /* flags byte */ uInt len; int c; /* Assure two bytes in the buffer so we can peek ahead -- handle case where first byte of header is at the end of the buffer after the last gzip segment */ len = s->stream.avail_in; if (len < 2) { if (len) s->inbuf[0] = s->stream.next_in[0]; errno = 0; len = (uInt)fread(s->inbuf + len, 1, Z_BUFSIZE >> len, s->file); if (len == 0 && ferror(s->file)) s->z_err = Z_ERRNO; s->stream.avail_in += len; s->stream.next_in = s->inbuf; if (s->stream.avail_in < 2) { s->transparent = s->stream.avail_in; return; } } /* Peek ahead to check the gzip magic header */ if (s->stream.next_in[0] != gz_magic[0] || s->stream.next_in[1] != gz_magic[1]) { s->transparent = 1; return; } s->stream.avail_in -= 2; s->stream.next_in += 2; /* Check the rest of the gzip header */ method = get_byte(s); flags = get_byte(s); if (method != Z_DEFLATED || (flags & RESERVED) != 0) { s->z_err = Z_DATA_ERROR; return; } /* Discard time, xflags and OS code: */ for (len = 0; len < 6; len++) (void)get_byte(s); if ((flags & EXTRA_FIELD) != 0) { /* skip the extra field */ len = (uInt)get_byte(s); len += ((uInt)get_byte(s))<<8; /* len is garbage if EOF but the loop below will quit anyway */ while (len-- != 0 && get_byte(s) != EOF) ; } if ((flags & ORIG_NAME) != 0) { /* skip the original file name */ while ((c = get_byte(s)) != 0 && c != EOF) ; } if ((flags & COMMENT) != 0) { /* skip the .gz file comment */ while ((c = get_byte(s)) != 0 && c != EOF) ; } if ((flags & HEAD_CRC) != 0) { /* skip the header crc */ for (len = 0; len < 2; len++) (void)get_byte(s); } s->z_err = s->z_eof ? Z_DATA_ERROR : Z_OK; } /* =========================================================================== * Cleanup then free the given gz_stream. Return a zlib error code. Try freeing in the reverse order of allocations. */ local int destroy (s) gz_stream *s; { int err = Z_OK; if (!s) return Z_STREAM_ERROR; TRYFREE(s->msg); if (s->stream.state != NULL) { if (s->mode == 'w') { #ifdef NO_GZCOMPRESS err = Z_STREAM_ERROR; #else err = deflateEnd(&(s->stream)); #endif } else if (s->mode == 'r') { err = inflateEnd(&(s->stream)); } } if (s->file != NULL && fclose(s->file)) { #ifdef ESPIPE if (errno != ESPIPE) /* fclose is broken for pipes in HP/UX */ #endif err = Z_ERRNO; } if (s->z_err < 0) err = s->z_err; TRYFREE(s->inbuf); TRYFREE(s->outbuf); TRYFREE(s->path); TRYFREE(s); return err; } /* =========================================================================== Reads the given number of uncompressed bytes from the compressed file. gzread returns the number of bytes actually read (0 for end of file). */ int ZEXPORT gzread (file, buf, len) gzFile file; voidp buf; unsigned len; { gz_stream *s = (gz_stream*)file; Bytef *start = (Bytef*)buf; /* starting point for crc computation */ Byte *next_out; /* == stream.next_out but not forced far (for MSDOS) */ if (s == NULL || s->mode != 'r') return Z_STREAM_ERROR; if (s->z_err == Z_DATA_ERROR || s->z_err == Z_ERRNO) return -1; if (s->z_err == Z_STREAM_END) return 0; /* EOF */ next_out = (Byte*)buf; s->stream.next_out = (Bytef*)buf; s->stream.avail_out = len; if (s->stream.avail_out && s->back != EOF) { *next_out++ = s->back; s->stream.next_out++; s->stream.avail_out--; s->back = EOF; s->out++; start++; if (s->last) { s->z_err = Z_STREAM_END; return 1; } } while (s->stream.avail_out != 0) { if (s->transparent) { /* Copy first the lookahead bytes: */ uInt n = s->stream.avail_in; if (n > s->stream.avail_out) n = s->stream.avail_out; if (n > 0) { zmemcpy(s->stream.next_out, s->stream.next_in, n); next_out += n; s->stream.next_out = next_out; s->stream.next_in += n; s->stream.avail_out -= n; s->stream.avail_in -= n; } if (s->stream.avail_out > 0) { s->stream.avail_out -= (uInt)fread(next_out, 1, s->stream.avail_out, s->file); } len -= s->stream.avail_out; s->in += len; s->out += len; if (len == 0) s->z_eof = 1; return (int)len; } if (s->stream.avail_in == 0 && !s->z_eof) { errno = 0; s->stream.avail_in = (uInt)fread(s->inbuf, 1, Z_BUFSIZE, s->file); if (s->stream.avail_in == 0) { s->z_eof = 1; if (ferror(s->file)) { s->z_err = Z_ERRNO; break; } } s->stream.next_in = s->inbuf; } s->in += s->stream.avail_in; s->out += s->stream.avail_out; s->z_err = inflate(&(s->stream), Z_NO_FLUSH); s->in -= s->stream.avail_in; s->out -= s->stream.avail_out; if (0 && s->z_err == Z_STREAM_END) { /* Check CRC and original size */ s->crc = crc32(s->crc, start, (uInt)(s->stream.next_out - start)); start = s->stream.next_out; if (getLong(s) != s->crc) { s->z_err = Z_DATA_ERROR; } else { (void)getLong(s); /* The uncompressed length returned by above getlong() may be * different from s->out in case of concatenated .gz files. * Check for such files: */ check_header(s); if (s->z_err == Z_OK) { inflateReset(&(s->stream)); s->crc = crc32(0L, Z_NULL, 0); } } } if (s->z_err != Z_OK || s->z_eof) break; } s->crc = crc32(s->crc, start, (uInt)(s->stream.next_out - start)); if (len == s->stream.avail_out && (s->z_err == Z_DATA_ERROR || s->z_err == Z_ERRNO)) return -1; return (int)(len - s->stream.avail_out); } /* =========================================================================== Reads one byte from the compressed file. gzgetc returns this byte or -1 in case of end of file or error. */ int ZEXPORT gzgetc(file) gzFile file; { unsigned char c; return gzread(file, &c, 1) == 1 ? c : -1; } /* =========================================================================== Push one byte back onto the stream. */ int ZEXPORT gzungetc(c, file) int c; gzFile file; { gz_stream *s = (gz_stream*)file; if (s == NULL || s->mode != 'r' || c == EOF || s->back != EOF) return EOF; s->back = c; s->out--; s->last = (s->z_err == Z_STREAM_END); if (s->last) s->z_err = Z_OK; s->z_eof = 0; return c; } /* =========================================================================== Reads bytes from the compressed file until len-1 characters are read, or a newline character is read and transferred to buf, or an end-of-file condition is encountered. The string is then terminated with a null character. gzgets returns buf, or Z_NULL in case of error. The current implementation is not optimized at all. */ char * ZEXPORT gzgets(file, buf, len) gzFile file; char *buf; int len; { char *b = buf; if (buf == Z_NULL || len <= 0) return Z_NULL; while (--len > 0 && gzread(file, buf, 1) == 1 && *buf++ != '\n') ; *buf = '\0'; return b == buf && len > 0 ? Z_NULL : b; } #ifndef NO_GZCOMPRESS /* =========================================================================== Writes the given number of uncompressed bytes into the compressed file. gzwrite returns the number of bytes actually written (0 in case of error). */ int ZEXPORT gzwrite (file, buf, len) gzFile file; voidpc buf; unsigned len; { gz_stream *s = (gz_stream*)file; if (s == NULL || s->mode != 'w') return Z_STREAM_ERROR; s->stream.next_in = (Bytef*)buf; s->stream.avail_in = len; while (s->stream.avail_in != 0) { if (s->stream.avail_out == 0) { s->stream.next_out = s->outbuf; if (fwrite(s->outbuf, 1, Z_BUFSIZE, s->file) != Z_BUFSIZE) { s->z_err = Z_ERRNO; break; } s->stream.avail_out = Z_BUFSIZE; } s->in += s->stream.avail_in; s->out += s->stream.avail_out; s->z_err = deflate(&(s->stream), Z_NO_FLUSH); s->in -= s->stream.avail_in; s->out -= s->stream.avail_out; if (s->z_err != Z_OK) break; } s->crc = crc32(s->crc, (const Bytef *)buf, len); return (int)(len - s->stream.avail_in); } /* =========================================================================== Converts, formats, and writes the args to the compressed file under control of the format string, as in fprintf. gzprintf returns the number of uncompressed bytes actually written (0 in case of error). */ #ifdef STDC #include int ZEXPORTVA gzprintf (gzFile file, const char *format, /* args */ ...) { char buf[Z_PRINTF_BUFSIZE]; va_list va; int len; buf[sizeof(buf) - 1] = 0; va_start(va, format); #ifdef NO_vsnprintf # ifdef HAS_vsprintf_void (void)vsprintf(buf, format, va); va_end(va); for (len = 0; len < sizeof(buf); len++) if (buf[len] == 0) break; # else len = vsprintf(buf, format, va); va_end(va); # endif #else # ifdef HAS_vsnprintf_void (void)vsnprintf(buf, sizeof(buf), format, va); va_end(va); len = strlen(buf); # else len = vsnprintf(buf, sizeof(buf), format, va); va_end(va); # endif #endif if (len <= 0 || len >= (int)sizeof(buf) || buf[sizeof(buf) - 1] != 0) return 0; return gzwrite(file, buf, (unsigned)len); } #else /* not ANSI C */ int ZEXPORTVA gzprintf (file, format, a1, a2, a3, a4, a5, a6, a7, a8, a9, a10, a11, a12, a13, a14, a15, a16, a17, a18, a19, a20) gzFile file; const char *format; int a1, a2, a3, a4, a5, a6, a7, a8, a9, a10, a11, a12, a13, a14, a15, a16, a17, a18, a19, a20; { char buf[Z_PRINTF_BUFSIZE]; int len; buf[sizeof(buf) - 1] = 0; #ifdef NO_snprintf # ifdef HAS_sprintf_void sprintf(buf, format, a1, a2, a3, a4, a5, a6, a7, a8, a9, a10, a11, a12, a13, a14, a15, a16, a17, a18, a19, a20); for (len = 0; len < sizeof(buf); len++) if (buf[len] == 0) break; # else len = sprintf(buf, format, a1, a2, a3, a4, a5, a6, a7, a8, a9, a10, a11, a12, a13, a14, a15, a16, a17, a18, a19, a20); # endif #else # ifdef HAS_snprintf_void snprintf(buf, sizeof(buf), format, a1, a2, a3, a4, a5, a6, a7, a8, a9, a10, a11, a12, a13, a14, a15, a16, a17, a18, a19, a20); len = strlen(buf); # else len = snprintf(buf, sizeof(buf), format, a1, a2, a3, a4, a5, a6, a7, a8, a9, a10, a11, a12, a13, a14, a15, a16, a17, a18, a19, a20); # endif #endif if (len <= 0 || len >= sizeof(buf) || buf[sizeof(buf) - 1] != 0) return 0; return gzwrite(file, buf, len); } #endif /* =========================================================================== Writes c, converted to an unsigned char, into the compressed file. gzputc returns the value that was written, or -1 in case of error. */ int ZEXPORT gzputc(file, c) gzFile file; int c; { unsigned char cc = (unsigned char) c; /* required for big endian systems */ return gzwrite(file, &cc, 1) == 1 ? (int)cc : -1; } /* =========================================================================== Writes the given null-terminated string to the compressed file, excluding the terminating null character. gzputs returns the number of characters written, or -1 in case of error. */ int ZEXPORT gzputs(file, s) gzFile file; const char *s; { return gzwrite(file, (char*)s, (unsigned)strlen(s)); } /* =========================================================================== Flushes all pending output into the compressed file. The parameter flush is as in the deflate() function. */ local int do_flush (file, flush) gzFile file; int flush; { uInt len; int done = 0; gz_stream *s = (gz_stream*)file; if (s == NULL || s->mode != 'w') return Z_STREAM_ERROR; s->stream.avail_in = 0; /* should be zero already anyway */ for (;;) { len = Z_BUFSIZE - s->stream.avail_out; if (len != 0) { if ((uInt)fwrite(s->outbuf, 1, len, s->file) != len) { s->z_err = Z_ERRNO; return Z_ERRNO; } s->stream.next_out = s->outbuf; s->stream.avail_out = Z_BUFSIZE; } if (done) break; s->out += s->stream.avail_out; s->z_err = deflate(&(s->stream), flush); s->out -= s->stream.avail_out; /* Ignore the second of two consecutive flushes: */ if (len == 0 && s->z_err == Z_BUF_ERROR) s->z_err = Z_OK; /* deflate has finished flushing only when it hasn't used up * all the available space in the output buffer: */ done = (s->stream.avail_out != 0 || s->z_err == Z_STREAM_END); if (s->z_err != Z_OK && s->z_err != Z_STREAM_END) break; } return s->z_err == Z_STREAM_END ? Z_OK : s->z_err; } int ZEXPORT gzflush (file, flush) gzFile file; int flush; { gz_stream *s = (gz_stream*)file; int err = do_flush (file, flush); if (err) return err; fflush(s->file); return s->z_err == Z_STREAM_END ? Z_OK : s->z_err; } #endif /* NO_GZCOMPRESS */ /* =========================================================================== Sets the starting position for the next gzread or gzwrite on the given compressed file. The offset represents a number of bytes in the gzseek returns the resulting offset location as measured in bytes from the beginning of the uncompressed stream, or -1 in case of error. SEEK_END is not implemented, returns error. In this version of the library, gzseek can be extremely slow. */ z_off_t ZEXPORT gzseek (file, offset, whence) gzFile file; z_off_t offset; int whence; { gz_stream *s = (gz_stream*)file; if (s == NULL || whence == SEEK_END || s->z_err == Z_ERRNO || s->z_err == Z_DATA_ERROR) { return -1L; } if (s->mode == 'w') { #ifdef NO_GZCOMPRESS return -1L; #else if (whence == SEEK_SET) { offset -= s->in; } if (offset < 0) return -1L; /* At this point, offset is the number of zero bytes to write. */ if (s->inbuf == Z_NULL) { s->inbuf = (Byte*)ALLOC(Z_BUFSIZE); /* for seeking */ if (s->inbuf == Z_NULL) return -1L; zmemzero(s->inbuf, Z_BUFSIZE); } while (offset > 0) { uInt size = Z_BUFSIZE; if (offset < Z_BUFSIZE) size = (uInt)offset; size = gzwrite(file, s->inbuf, size); if (size == 0) return -1L; offset -= size; } return s->in; #endif } /* Rest of function is for reading only */ /* compute absolute position */ if (whence == SEEK_CUR) { offset += s->out; } if (offset < 0) return -1L; if (s->transparent) { /* map to fseek */ s->back = EOF; s->stream.avail_in = 0; s->stream.next_in = s->inbuf; if (fseek(s->file, offset, SEEK_SET) < 0) return -1L; s->in = s->out = offset; return offset; } /* For a negative seek, rewind and use positive seek */ if (offset >= s->out) { offset -= s->out; } else if (gzrewind(file) < 0) { return -1L; } /* offset is now the number of bytes to skip. */ if (offset != 0 && s->outbuf == Z_NULL) { s->outbuf = (Byte*)ALLOC(Z_BUFSIZE); if (s->outbuf == Z_NULL) return -1L; } if (offset && s->back != EOF) { s->back = EOF; s->out++; offset--; if (s->last) s->z_err = Z_STREAM_END; } while (offset > 0) { int size = Z_BUFSIZE; if (offset < Z_BUFSIZE) size = (int)offset; size = gzread(file, s->outbuf, (uInt)size); if (size <= 0) return -1L; offset -= size; } return s->out; } /* =========================================================================== Rewinds input file. */ int ZEXPORT gzrewind (file) gzFile file; { gz_stream *s = (gz_stream*)file; if (s == NULL || s->mode != 'r') return -1; s->z_err = Z_OK; s->z_eof = 0; s->back = EOF; s->stream.avail_in = 0; s->stream.next_in = s->inbuf; s->crc = crc32(0L, Z_NULL, 0); if (!s->transparent) (void)inflateReset(&s->stream); s->in = 0; s->out = 0; return fseek(s->file, s->start, SEEK_SET); } /* =========================================================================== Returns the starting position for the next gzread or gzwrite on the given compressed file. This position represents a number of bytes in the uncompressed data stream. */ z_off_t ZEXPORT gztell (file) gzFile file; { return gzseek(file, 0L, SEEK_CUR); } /* =========================================================================== Returns 1 when EOF has previously been detected reading the given input stream, otherwise zero. */ int ZEXPORT gzeof (file) gzFile file; { gz_stream *s = (gz_stream*)file; /* With concatenated compressed files that can have embedded * crc trailers, z_eof is no longer the only/best indicator of EOF * on a gz_stream. Handle end-of-stream error explicitly here. */ if (s == NULL || s->mode != 'r') return 0; if (s->z_eof) return 1; return s->z_err == Z_STREAM_END; } /* =========================================================================== Returns 1 if reading and doing so transparently, otherwise zero. */ int ZEXPORT gzdirect (file) gzFile file; { gz_stream *s = (gz_stream*)file; if (s == NULL || s->mode != 'r') return 0; return s->transparent; } /* =========================================================================== Outputs a long in LSB order to the given file */ local void putLong (file, x) FILE *file; uLong x; { int n; for (n = 0; n < 4; n++) { fputc((int)(x & 0xff), file); x >>= 8; } } /* =========================================================================== Reads a long in LSB order from the given gz_stream. Sets z_err in case of error. */ local uLong getLong (s) gz_stream *s; { uLong x = (uLong)get_byte(s); int c; x += ((uLong)get_byte(s))<<8; x += ((uLong)get_byte(s))<<16; c = get_byte(s); if (c == EOF) s->z_err = Z_DATA_ERROR; x += ((uLong)c)<<24; return x; } /* =========================================================================== Flushes all pending output if necessary, closes the compressed file and deallocates all the (de)compression state. */ int ZEXPORT gzclose (file) gzFile file; { gz_stream *s = (gz_stream*)file; if (s == NULL) return Z_STREAM_ERROR; if (s->mode == 'w') { #ifdef NO_GZCOMPRESS return Z_STREAM_ERROR; #else if (do_flush (file, Z_FINISH) != Z_OK) return destroy((gz_stream*)file); putLong (s->file, s->crc); putLong (s->file, (uLong)(s->in & 0xffffffff)); #endif } return destroy((gz_stream*)file); } #ifdef STDC # define zstrerror(errnum) strerror(errnum) #else # define zstrerror(errnum) "" #endif /* =========================================================================== Returns the error message for the last error which occurred on the given compressed file. errnum is set to zlib error number. If an error occurred in the file system and not in the compression library, errnum is set to Z_ERRNO and the application may consult errno to get the exact error code. */ const char * ZEXPORT gzerror (file, errnum) gzFile file; int *errnum; { char *m; gz_stream *s = (gz_stream*)file; if (s == NULL) { *errnum = Z_STREAM_ERROR; return (const char*)ERR_MSG(Z_STREAM_ERROR); } *errnum = s->z_err; if (*errnum == Z_OK) return (const char*)""; m = (char*)(*errnum == Z_ERRNO ? zstrerror(errno) : s->stream.msg); if (m == NULL || *m == '\0') m = (char*)ERR_MSG(s->z_err); TRYFREE(s->msg); s->msg = (char*)ALLOC(strlen(s->path) + strlen(m) + 3); if (s->msg == Z_NULL) return (const char*)ERR_MSG(Z_MEM_ERROR); strcpy(s->msg, s->path); strcat(s->msg, ": "); strcat(s->msg, m); return (const char*)s->msg; } /* =========================================================================== Clear the error and end-of-file flags, and do the same for the real file. */ void ZEXPORT gzclearerr (file) gzFile file; { gz_stream *s = (gz_stream*)file; if (s == NULL) return; if (s->z_err != Z_STREAM_END) s->z_err = Z_OK; s->z_eof = 0; clearerr(s->file); } maqview-0.2.5/infback.c0000644000265600020320000005322410761137604014067 0ustar tilleaadmin/* infback.c -- inflate using a call-back interface * Copyright (C) 1995-2005 Mark Adler * For conditions of distribution and use, see copyright notice in zlib.h */ /* This code is largely copied from inflate.c. Normally either infback.o or inflate.o would be linked into an application--not both. The interface with inffast.c is retained so that optimized assembler-coded versions of inflate_fast() can be used with either inflate.c or infback.c. */ #include "zutil.h" #include "inftrees.h" #include "inflate.h" #include "inffast.h" /* function prototypes */ local void fixedtables OF((struct inflate_state FAR *state)); /* strm provides memory allocation functions in zalloc and zfree, or Z_NULL to use the library memory allocation functions. windowBits is in the range 8..15, and window is a user-supplied window and output buffer that is 2**windowBits bytes. */ int ZEXPORT inflateBackInit_(strm, windowBits, window, version, stream_size) z_streamp strm; int windowBits; unsigned char FAR *window; const char *version; int stream_size; { struct inflate_state FAR *state; if (version == Z_NULL || version[0] != ZLIB_VERSION[0] || stream_size != (int)(sizeof(z_stream))) return Z_VERSION_ERROR; if (strm == Z_NULL || window == Z_NULL || windowBits < 8 || windowBits > 15) return Z_STREAM_ERROR; strm->msg = Z_NULL; /* in case we return an error */ if (strm->zalloc == (alloc_func)0) { strm->zalloc = zcalloc; strm->opaque = (voidpf)0; } if (strm->zfree == (free_func)0) strm->zfree = zcfree; state = (struct inflate_state FAR *)ZALLOC(strm, 1, sizeof(struct inflate_state)); if (state == Z_NULL) return Z_MEM_ERROR; Tracev((stderr, "inflate: allocated\n")); strm->state = (struct internal_state FAR *)state; state->dmax = 32768U; state->wbits = windowBits; state->wsize = 1U << windowBits; state->window = window; state->write = 0; state->whave = 0; return Z_OK; } /* Return state with length and distance decoding tables and index sizes set to fixed code decoding. Normally this returns fixed tables from inffixed.h. If BUILDFIXED is defined, then instead this routine builds the tables the first time it's called, and returns those tables the first time and thereafter. This reduces the size of the code by about 2K bytes, in exchange for a little execution time. However, BUILDFIXED should not be used for threaded applications, since the rewriting of the tables and virgin may not be thread-safe. */ local void fixedtables(state) struct inflate_state FAR *state; { #ifdef BUILDFIXED static int virgin = 1; static code *lenfix, *distfix; static code fixed[544]; /* build fixed huffman tables if first call (may not be thread safe) */ if (virgin) { unsigned sym, bits; static code *next; /* literal/length table */ sym = 0; while (sym < 144) state->lens[sym++] = 8; while (sym < 256) state->lens[sym++] = 9; while (sym < 280) state->lens[sym++] = 7; while (sym < 288) state->lens[sym++] = 8; next = fixed; lenfix = next; bits = 9; inflate_table(LENS, state->lens, 288, &(next), &(bits), state->work); /* distance table */ sym = 0; while (sym < 32) state->lens[sym++] = 5; distfix = next; bits = 5; inflate_table(DISTS, state->lens, 32, &(next), &(bits), state->work); /* do this just once */ virgin = 0; } #else /* !BUILDFIXED */ # include "inffixed.h" #endif /* BUILDFIXED */ state->lencode = lenfix; state->lenbits = 9; state->distcode = distfix; state->distbits = 5; } /* Macros for inflateBack(): */ /* Load returned state from inflate_fast() */ #define LOAD() \ do { \ put = strm->next_out; \ left = strm->avail_out; \ next = strm->next_in; \ have = strm->avail_in; \ hold = state->hold; \ bits = state->bits; \ } while (0) /* Set state from registers for inflate_fast() */ #define RESTORE() \ do { \ strm->next_out = put; \ strm->avail_out = left; \ strm->next_in = next; \ strm->avail_in = have; \ state->hold = hold; \ state->bits = bits; \ } while (0) /* Clear the input bit accumulator */ #define INITBITS() \ do { \ hold = 0; \ bits = 0; \ } while (0) /* Assure that some input is available. If input is requested, but denied, then return a Z_BUF_ERROR from inflateBack(). */ #define PULL() \ do { \ if (have == 0) { \ have = in(in_desc, &next); \ if (have == 0) { \ next = Z_NULL; \ ret = Z_BUF_ERROR; \ goto inf_leave; \ } \ } \ } while (0) /* Get a byte of input into the bit accumulator, or return from inflateBack() with an error if there is no input available. */ #define PULLBYTE() \ do { \ PULL(); \ have--; \ hold += (unsigned long)(*next++) << bits; \ bits += 8; \ } while (0) /* Assure that there are at least n bits in the bit accumulator. If there is not enough available input to do that, then return from inflateBack() with an error. */ #define NEEDBITS(n) \ do { \ while (bits < (unsigned)(n)) \ PULLBYTE(); \ } while (0) /* Return the low n bits of the bit accumulator (n < 16) */ #define BITS(n) \ ((unsigned)hold & ((1U << (n)) - 1)) /* Remove n bits from the bit accumulator */ #define DROPBITS(n) \ do { \ hold >>= (n); \ bits -= (unsigned)(n); \ } while (0) /* Remove zero to seven bits as needed to go to a byte boundary */ #define BYTEBITS() \ do { \ hold >>= bits & 7; \ bits -= bits & 7; \ } while (0) /* Assure that some output space is available, by writing out the window if it's full. If the write fails, return from inflateBack() with a Z_BUF_ERROR. */ #define ROOM() \ do { \ if (left == 0) { \ put = state->window; \ left = state->wsize; \ state->whave = left; \ if (out(out_desc, put, left)) { \ ret = Z_BUF_ERROR; \ goto inf_leave; \ } \ } \ } while (0) /* strm provides the memory allocation functions and window buffer on input, and provides information on the unused input on return. For Z_DATA_ERROR returns, strm will also provide an error message. in() and out() are the call-back input and output functions. When inflateBack() needs more input, it calls in(). When inflateBack() has filled the window with output, or when it completes with data in the window, it calls out() to write out the data. The application must not change the provided input until in() is called again or inflateBack() returns. The application must not change the window/output buffer until inflateBack() returns. in() and out() are called with a descriptor parameter provided in the inflateBack() call. This parameter can be a structure that provides the information required to do the read or write, as well as accumulated information on the input and output such as totals and check values. in() should return zero on failure. out() should return non-zero on failure. If either in() or out() fails, than inflateBack() returns a Z_BUF_ERROR. strm->next_in can be checked for Z_NULL to see whether it was in() or out() that caused in the error. Otherwise, inflateBack() returns Z_STREAM_END on success, Z_DATA_ERROR for an deflate format error, or Z_MEM_ERROR if it could not allocate memory for the state. inflateBack() can also return Z_STREAM_ERROR if the input parameters are not correct, i.e. strm is Z_NULL or the state was not initialized. */ int ZEXPORT inflateBack(strm, in, in_desc, out, out_desc) z_streamp strm; in_func in; void FAR *in_desc; out_func out; void FAR *out_desc; { struct inflate_state FAR *state; unsigned char FAR *next; /* next input */ unsigned char FAR *put; /* next output */ unsigned have, left; /* available input and output */ unsigned long hold; /* bit buffer */ unsigned bits; /* bits in bit buffer */ unsigned copy; /* number of stored or match bytes to copy */ unsigned char FAR *from; /* where to copy match bytes from */ code this; /* current decoding table entry */ code last; /* parent table entry */ unsigned len; /* length to copy for repeats, bits to drop */ int ret; /* return code */ static const unsigned short order[19] = /* permutation of code lengths */ {16, 17, 18, 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15}; /* Check that the strm exists and that the state was initialized */ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR; state = (struct inflate_state FAR *)strm->state; /* Reset the state */ strm->msg = Z_NULL; state->mode = TYPE; state->last = 0; state->whave = 0; next = strm->next_in; have = next != Z_NULL ? strm->avail_in : 0; hold = 0; bits = 0; put = state->window; left = state->wsize; /* Inflate until end of block marked as last */ for (;;) switch (state->mode) { case TYPE: /* determine and dispatch block type */ if (state->last) { BYTEBITS(); state->mode = DONE; break; } NEEDBITS(3); state->last = BITS(1); DROPBITS(1); switch (BITS(2)) { case 0: /* stored block */ Tracev((stderr, "inflate: stored block%s\n", state->last ? " (last)" : "")); state->mode = STORED; break; case 1: /* fixed block */ fixedtables(state); Tracev((stderr, "inflate: fixed codes block%s\n", state->last ? " (last)" : "")); state->mode = LEN; /* decode codes */ break; case 2: /* dynamic block */ Tracev((stderr, "inflate: dynamic codes block%s\n", state->last ? " (last)" : "")); state->mode = TABLE; break; case 3: strm->msg = (char *)"invalid block type"; state->mode = BAD; } DROPBITS(2); break; case STORED: /* get and verify stored block length */ BYTEBITS(); /* go to byte boundary */ NEEDBITS(32); if ((hold & 0xffff) != ((hold >> 16) ^ 0xffff)) { strm->msg = (char *)"invalid stored block lengths"; state->mode = BAD; break; } state->length = (unsigned)hold & 0xffff; Tracev((stderr, "inflate: stored length %u\n", state->length)); INITBITS(); /* copy stored block from input to output */ while (state->length != 0) { copy = state->length; PULL(); ROOM(); if (copy > have) copy = have; if (copy > left) copy = left; zmemcpy(put, next, copy); have -= copy; next += copy; left -= copy; put += copy; state->length -= copy; } Tracev((stderr, "inflate: stored end\n")); state->mode = TYPE; break; case TABLE: /* get dynamic table entries descriptor */ NEEDBITS(14); state->nlen = BITS(5) + 257; DROPBITS(5); state->ndist = BITS(5) + 1; DROPBITS(5); state->ncode = BITS(4) + 4; DROPBITS(4); #ifndef PKZIP_BUG_WORKAROUND if (state->nlen > 286 || state->ndist > 30) { strm->msg = (char *)"too many length or distance symbols"; state->mode = BAD; break; } #endif Tracev((stderr, "inflate: table sizes ok\n")); /* get code length code lengths (not a typo) */ state->have = 0; while (state->have < state->ncode) { NEEDBITS(3); state->lens[order[state->have++]] = (unsigned short)BITS(3); DROPBITS(3); } while (state->have < 19) state->lens[order[state->have++]] = 0; state->next = state->codes; state->lencode = (code const FAR *)(state->next); state->lenbits = 7; ret = inflate_table(CODES, state->lens, 19, &(state->next), &(state->lenbits), state->work); if (ret) { strm->msg = (char *)"invalid code lengths set"; state->mode = BAD; break; } Tracev((stderr, "inflate: code lengths ok\n")); /* get length and distance code code lengths */ state->have = 0; while (state->have < state->nlen + state->ndist) { for (;;) { this = state->lencode[BITS(state->lenbits)]; if ((unsigned)(this.bits) <= bits) break; PULLBYTE(); } if (this.val < 16) { NEEDBITS(this.bits); DROPBITS(this.bits); state->lens[state->have++] = this.val; } else { if (this.val == 16) { NEEDBITS(this.bits + 2); DROPBITS(this.bits); if (state->have == 0) { strm->msg = (char *)"invalid bit length repeat"; state->mode = BAD; break; } len = (unsigned)(state->lens[state->have - 1]); copy = 3 + BITS(2); DROPBITS(2); } else if (this.val == 17) { NEEDBITS(this.bits + 3); DROPBITS(this.bits); len = 0; copy = 3 + BITS(3); DROPBITS(3); } else { NEEDBITS(this.bits + 7); DROPBITS(this.bits); len = 0; copy = 11 + BITS(7); DROPBITS(7); } if (state->have + copy > state->nlen + state->ndist) { strm->msg = (char *)"invalid bit length repeat"; state->mode = BAD; break; } while (copy--) state->lens[state->have++] = (unsigned short)len; } } /* handle error breaks in while */ if (state->mode == BAD) break; /* build code tables */ state->next = state->codes; state->lencode = (code const FAR *)(state->next); state->lenbits = 9; ret = inflate_table(LENS, state->lens, state->nlen, &(state->next), &(state->lenbits), state->work); if (ret) { strm->msg = (char *)"invalid literal/lengths set"; state->mode = BAD; break; } state->distcode = (code const FAR *)(state->next); state->distbits = 6; ret = inflate_table(DISTS, state->lens + state->nlen, state->ndist, &(state->next), &(state->distbits), state->work); if (ret) { strm->msg = (char *)"invalid distances set"; state->mode = BAD; break; } Tracev((stderr, "inflate: codes ok\n")); state->mode = LEN; case LEN: /* use inflate_fast() if we have enough input and output */ if (have >= 6 && left >= 258) { RESTORE(); if (state->whave < state->wsize) state->whave = state->wsize - left; inflate_fast(strm, state->wsize); LOAD(); break; } /* get a literal, length, or end-of-block code */ for (;;) { this = state->lencode[BITS(state->lenbits)]; if ((unsigned)(this.bits) <= bits) break; PULLBYTE(); } if (this.op && (this.op & 0xf0) == 0) { last = this; for (;;) { this = state->lencode[last.val + (BITS(last.bits + last.op) >> last.bits)]; if ((unsigned)(last.bits + this.bits) <= bits) break; PULLBYTE(); } DROPBITS(last.bits); } DROPBITS(this.bits); state->length = (unsigned)this.val; /* process literal */ if (this.op == 0) { Tracevv((stderr, this.val >= 0x20 && this.val < 0x7f ? "inflate: literal '%c'\n" : "inflate: literal 0x%02x\n", this.val)); ROOM(); *put++ = (unsigned char)(state->length); left--; state->mode = LEN; break; } /* process end of block */ if (this.op & 32) { Tracevv((stderr, "inflate: end of block\n")); state->mode = TYPE; break; } /* invalid code */ if (this.op & 64) { strm->msg = (char *)"invalid literal/length code"; state->mode = BAD; break; } /* length code -- get extra bits, if any */ state->extra = (unsigned)(this.op) & 15; if (state->extra != 0) { NEEDBITS(state->extra); state->length += BITS(state->extra); DROPBITS(state->extra); } Tracevv((stderr, "inflate: length %u\n", state->length)); /* get distance code */ for (;;) { this = state->distcode[BITS(state->distbits)]; if ((unsigned)(this.bits) <= bits) break; PULLBYTE(); } if ((this.op & 0xf0) == 0) { last = this; for (;;) { this = state->distcode[last.val + (BITS(last.bits + last.op) >> last.bits)]; if ((unsigned)(last.bits + this.bits) <= bits) break; PULLBYTE(); } DROPBITS(last.bits); } DROPBITS(this.bits); if (this.op & 64) { strm->msg = (char *)"invalid distance code"; state->mode = BAD; break; } state->offset = (unsigned)this.val; /* get distance extra bits, if any */ state->extra = (unsigned)(this.op) & 15; if (state->extra != 0) { NEEDBITS(state->extra); state->offset += BITS(state->extra); DROPBITS(state->extra); } if (state->offset > state->wsize - (state->whave < state->wsize ? left : 0)) { strm->msg = (char *)"invalid distance too far back"; state->mode = BAD; break; } Tracevv((stderr, "inflate: distance %u\n", state->offset)); /* copy match from window to output */ do { ROOM(); copy = state->wsize - state->offset; if (copy < left) { from = put + copy; copy = left - copy; } else { from = put - state->offset; copy = left; } if (copy > state->length) copy = state->length; state->length -= copy; left -= copy; do { *put++ = *from++; } while (--copy); } while (state->length != 0); break; case DONE: /* inflate stream terminated properly -- write leftover output */ ret = Z_STREAM_END; if (left < state->wsize) { if (out(out_desc, state->window, state->wsize - left)) ret = Z_BUF_ERROR; } goto inf_leave; case BAD: ret = Z_DATA_ERROR; goto inf_leave; default: /* can't happen, but makes compilers happy */ ret = Z_STREAM_ERROR; goto inf_leave; } /* Return unused input */ inf_leave: strm->next_in = next; strm->avail_in = have; return ret; } int ZEXPORT inflateBackEnd(strm) z_streamp strm; { if (strm == Z_NULL || strm->state == Z_NULL || strm->zfree == (free_func)0) return Z_STREAM_ERROR; ZFREE(strm, strm->state); strm->state = Z_NULL; Tracev((stderr, "inflate: end\n")); return Z_OK; } maqview-0.2.5/crc32.c0000644000265600020320000003161110761137602013400 0ustar tilleaadmin/* crc32.c -- compute the CRC-32 of a data stream * Copyright (C) 1995-2005 Mark Adler * For conditions of distribution and use, see copyright notice in zlib.h * * Thanks to Rodney Brown for his contribution of faster * CRC methods: exclusive-oring 32 bits of data at a time, and pre-computing * tables for updating the shift register in one step with three exclusive-ors * instead of four steps with four exclusive-ors. This results in about a * factor of two increase in speed on a Power PC G4 (PPC7455) using gcc -O3. */ /* @(#) $Id$ */ /* Note on the use of DYNAMIC_CRC_TABLE: there is no mutex or semaphore protection on the static variables used to control the first-use generation of the crc tables. Therefore, if you #define DYNAMIC_CRC_TABLE, you should first call get_crc_table() to initialize the tables before allowing more than one thread to use crc32(). */ #ifdef MAKECRCH # include # ifndef DYNAMIC_CRC_TABLE # define DYNAMIC_CRC_TABLE # endif /* !DYNAMIC_CRC_TABLE */ #endif /* MAKECRCH */ #include "zutil.h" /* for STDC and FAR definitions */ #define local static /* Find a four-byte integer type for crc32_little() and crc32_big(). */ #ifndef NOBYFOUR # ifdef STDC /* need ANSI C limits.h to determine sizes */ # include # define BYFOUR # if (UINT_MAX == 0xffffffffUL) typedef unsigned int u4; # else # if (ULONG_MAX == 0xffffffffUL) typedef unsigned long u4; # else # if (USHRT_MAX == 0xffffffffUL) typedef unsigned short u4; # else # undef BYFOUR /* can't find a four-byte integer type! */ # endif # endif # endif # endif /* STDC */ #endif /* !NOBYFOUR */ /* Definitions for doing the crc four data bytes at a time. */ #ifdef BYFOUR # define REV(w) (((w)>>24)+(((w)>>8)&0xff00)+ \ (((w)&0xff00)<<8)+(((w)&0xff)<<24)) local unsigned long crc32_little OF((unsigned long, const unsigned char FAR *, unsigned)); local unsigned long crc32_big OF((unsigned long, const unsigned char FAR *, unsigned)); # define TBLS 8 #else # define TBLS 1 #endif /* BYFOUR */ /* Local functions for crc concatenation */ local unsigned long gf2_matrix_times OF((unsigned long *mat, unsigned long vec)); local void gf2_matrix_square OF((unsigned long *square, unsigned long *mat)); #ifdef DYNAMIC_CRC_TABLE local volatile int crc_table_empty = 1; local unsigned long FAR crc_table[TBLS][256]; local void make_crc_table OF((void)); #ifdef MAKECRCH local void write_table OF((FILE *, const unsigned long FAR *)); #endif /* MAKECRCH */ /* Generate tables for a byte-wise 32-bit CRC calculation on the polynomial: x^32+x^26+x^23+x^22+x^16+x^12+x^11+x^10+x^8+x^7+x^5+x^4+x^2+x+1. Polynomials over GF(2) are represented in binary, one bit per coefficient, with the lowest powers in the most significant bit. Then adding polynomials is just exclusive-or, and multiplying a polynomial by x is a right shift by one. If we call the above polynomial p, and represent a byte as the polynomial q, also with the lowest power in the most significant bit (so the byte 0xb1 is the polynomial x^7+x^3+x+1), then the CRC is (q*x^32) mod p, where a mod b means the remainder after dividing a by b. This calculation is done using the shift-register method of multiplying and taking the remainder. The register is initialized to zero, and for each incoming bit, x^32 is added mod p to the register if the bit is a one (where x^32 mod p is p+x^32 = x^26+...+1), and the register is multiplied mod p by x (which is shifting right by one and adding x^32 mod p if the bit shifted out is a one). We start with the highest power (least significant bit) of q and repeat for all eight bits of q. The first table is simply the CRC of all possible eight bit values. This is all the information needed to generate CRCs on data a byte at a time for all combinations of CRC register values and incoming bytes. The remaining tables allow for word-at-a-time CRC calculation for both big-endian and little- endian machines, where a word is four bytes. */ local void make_crc_table() { unsigned long c; int n, k; unsigned long poly; /* polynomial exclusive-or pattern */ /* terms of polynomial defining this crc (except x^32): */ static volatile int first = 1; /* flag to limit concurrent making */ static const unsigned char p[] = {0,1,2,4,5,7,8,10,11,12,16,22,23,26}; /* See if another task is already doing this (not thread-safe, but better than nothing -- significantly reduces duration of vulnerability in case the advice about DYNAMIC_CRC_TABLE is ignored) */ if (first) { first = 0; /* make exclusive-or pattern from polynomial (0xedb88320UL) */ poly = 0UL; for (n = 0; n < sizeof(p)/sizeof(unsigned char); n++) poly |= 1UL << (31 - p[n]); /* generate a crc for every 8-bit value */ for (n = 0; n < 256; n++) { c = (unsigned long)n; for (k = 0; k < 8; k++) c = c & 1 ? poly ^ (c >> 1) : c >> 1; crc_table[0][n] = c; } #ifdef BYFOUR /* generate crc for each value followed by one, two, and three zeros, and then the byte reversal of those as well as the first table */ for (n = 0; n < 256; n++) { c = crc_table[0][n]; crc_table[4][n] = REV(c); for (k = 1; k < 4; k++) { c = crc_table[0][c & 0xff] ^ (c >> 8); crc_table[k][n] = c; crc_table[k + 4][n] = REV(c); } } #endif /* BYFOUR */ crc_table_empty = 0; } else { /* not first */ /* wait for the other guy to finish (not efficient, but rare) */ while (crc_table_empty) ; } #ifdef MAKECRCH /* write out CRC tables to crc32.h */ { FILE *out; out = fopen("crc32.h", "w"); if (out == NULL) return; fprintf(out, "/* crc32.h -- tables for rapid CRC calculation\n"); fprintf(out, " * Generated automatically by crc32.c\n */\n\n"); fprintf(out, "local const unsigned long FAR "); fprintf(out, "crc_table[TBLS][256] =\n{\n {\n"); write_table(out, crc_table[0]); # ifdef BYFOUR fprintf(out, "#ifdef BYFOUR\n"); for (k = 1; k < 8; k++) { fprintf(out, " },\n {\n"); write_table(out, crc_table[k]); } fprintf(out, "#endif\n"); # endif /* BYFOUR */ fprintf(out, " }\n};\n"); fclose(out); } #endif /* MAKECRCH */ } #ifdef MAKECRCH local void write_table(out, table) FILE *out; const unsigned long FAR *table; { int n; for (n = 0; n < 256; n++) fprintf(out, "%s0x%08lxUL%s", n % 5 ? "" : " ", table[n], n == 255 ? "\n" : (n % 5 == 4 ? ",\n" : ", ")); } #endif /* MAKECRCH */ #else /* !DYNAMIC_CRC_TABLE */ /* ======================================================================== * Tables of CRC-32s of all single-byte values, made by make_crc_table(). */ #include "crc32.h" #endif /* DYNAMIC_CRC_TABLE */ /* ========================================================================= * This function can be used by asm versions of crc32() */ const unsigned long FAR * ZEXPORT get_crc_table() { #ifdef DYNAMIC_CRC_TABLE if (crc_table_empty) make_crc_table(); #endif /* DYNAMIC_CRC_TABLE */ return (const unsigned long FAR *)crc_table; } /* ========================================================================= */ #define DO1 crc = crc_table[0][((int)crc ^ (*buf++)) & 0xff] ^ (crc >> 8) #define DO8 DO1; DO1; DO1; DO1; DO1; DO1; DO1; DO1 /* ========================================================================= */ unsigned long ZEXPORT crc32(crc, buf, len) unsigned long crc; const unsigned char FAR *buf; unsigned len; { if (buf == Z_NULL) return 0UL; #ifdef DYNAMIC_CRC_TABLE if (crc_table_empty) make_crc_table(); #endif /* DYNAMIC_CRC_TABLE */ #ifdef BYFOUR if (sizeof(void *) == sizeof(ptrdiff_t)) { u4 endian; endian = 1; if (*((unsigned char *)(&endian))) return crc32_little(crc, buf, len); else return crc32_big(crc, buf, len); } #endif /* BYFOUR */ crc = crc ^ 0xffffffffUL; while (len >= 8) { DO8; len -= 8; } if (len) do { DO1; } while (--len); return crc ^ 0xffffffffUL; } #ifdef BYFOUR /* ========================================================================= */ #define DOLIT4 c ^= *buf4++; \ c = crc_table[3][c & 0xff] ^ crc_table[2][(c >> 8) & 0xff] ^ \ crc_table[1][(c >> 16) & 0xff] ^ crc_table[0][c >> 24] #define DOLIT32 DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4 /* ========================================================================= */ local unsigned long crc32_little(crc, buf, len) unsigned long crc; const unsigned char FAR *buf; unsigned len; { register u4 c; register const u4 FAR *buf4; c = (u4)crc; c = ~c; while (len && ((ptrdiff_t)buf & 3)) { c = crc_table[0][(c ^ *buf++) & 0xff] ^ (c >> 8); len--; } buf4 = (const u4 FAR *)(const void FAR *)buf; while (len >= 32) { DOLIT32; len -= 32; } while (len >= 4) { DOLIT4; len -= 4; } buf = (const unsigned char FAR *)buf4; if (len) do { c = crc_table[0][(c ^ *buf++) & 0xff] ^ (c >> 8); } while (--len); c = ~c; return (unsigned long)c; } /* ========================================================================= */ #define DOBIG4 c ^= *++buf4; \ c = crc_table[4][c & 0xff] ^ crc_table[5][(c >> 8) & 0xff] ^ \ crc_table[6][(c >> 16) & 0xff] ^ crc_table[7][c >> 24] #define DOBIG32 DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4 /* ========================================================================= */ local unsigned long crc32_big(crc, buf, len) unsigned long crc; const unsigned char FAR *buf; unsigned len; { register u4 c; register const u4 FAR *buf4; c = REV((u4)crc); c = ~c; while (len && ((ptrdiff_t)buf & 3)) { c = crc_table[4][(c >> 24) ^ *buf++] ^ (c << 8); len--; } buf4 = (const u4 FAR *)(const void FAR *)buf; buf4--; while (len >= 32) { DOBIG32; len -= 32; } while (len >= 4) { DOBIG4; len -= 4; } buf4++; buf = (const unsigned char FAR *)buf4; if (len) do { c = crc_table[4][(c >> 24) ^ *buf++] ^ (c << 8); } while (--len); c = ~c; return (unsigned long)(REV(c)); } #endif /* BYFOUR */ #define GF2_DIM 32 /* dimension of GF(2) vectors (length of CRC) */ /* ========================================================================= */ local unsigned long gf2_matrix_times(mat, vec) unsigned long *mat; unsigned long vec; { unsigned long sum; sum = 0; while (vec) { if (vec & 1) sum ^= *mat; vec >>= 1; mat++; } return sum; } /* ========================================================================= */ local void gf2_matrix_square(square, mat) unsigned long *square; unsigned long *mat; { int n; for (n = 0; n < GF2_DIM; n++) square[n] = gf2_matrix_times(mat, mat[n]); } /* ========================================================================= */ uLong ZEXPORT crc32_combine(crc1, crc2, len2) uLong crc1; uLong crc2; z_off_t len2; { int n; unsigned long row; unsigned long even[GF2_DIM]; /* even-power-of-two zeros operator */ unsigned long odd[GF2_DIM]; /* odd-power-of-two zeros operator */ /* degenerate case */ if (len2 == 0) return crc1; /* put operator for one zero bit in odd */ odd[0] = 0xedb88320L; /* CRC-32 polynomial */ row = 1; for (n = 1; n < GF2_DIM; n++) { odd[n] = row; row <<= 1; } /* put operator for two zero bits in even */ gf2_matrix_square(even, odd); /* put operator for four zero bits in odd */ gf2_matrix_square(odd, even); /* apply len2 zeros to crc1 (first square will put the operator for one zero byte, eight zero bits, in even) */ do { /* apply zeros operator for this bit of len2 */ gf2_matrix_square(even, odd); if (len2 & 1) crc1 = gf2_matrix_times(even, crc1); len2 >>= 1; /* if no more bits set, then done */ if (len2 == 0) break; /* another iteration of the loop with odd and even swapped */ gf2_matrix_square(odd, even); if (len2 & 1) crc1 = gf2_matrix_times(odd, crc1); len2 >>= 1; /* if no more bits set, then done */ } while (len2 != 0); /* return combined crc */ crc1 ^= crc2; return crc1; } maqview-0.2.5/cns_cache.c0000644000265600020320000003111011062204465014361 0ustar tilleaadmin#include #include #include #include "caches.h" #include "stdhashc.h" struct CNSObj { CNSCache *cache; unsigned char buf[1024]; int buf_size; int64_t skips; int heading; int n; int count; }; #define old_read_buf(target, size) if(obj->buf_size >= size){ \ memcpy(target, obj->buf, size);\ obj->buf_size -= size;\ } else if(obj->buf_size){\ if(obj->buf_size + buf_size >= size){\ memcpy(target, obj->buf, obj->buf_size);\ memcpy(target + obj->buf_size, buf, size - obj->buf_size);\ buf += size - obj->buf_size;\ buf_size -= size - obj->buf_size;\ obj->buf_size = 0;\ } else {\ memcpy(obj->buf + obj->buf_size, buf, buf_size);\ obj->buf_size += buf_size;\ return;\ }\ } else if(buf_size < size){\ if(buf_size) memcpy(obj->buf, buf, buf_size);\ obj->buf_size = buf_size;\ return;\ } else {\ memcpy(target, buf, size);\ buf += size;\ buf_size -= size;\ } static int read_buf(struct CNSObj *obj, void *target, unsigned char **buf_ptr, int *buf_size_ptr, int size){ if(obj->buf_size >= size){ memcpy(target, obj->buf, size); obj->buf_size -= size; } else if(obj->buf_size){ if(obj->buf_size + *buf_size_ptr >= size){ memcpy(target, obj->buf, obj->buf_size); memcpy(target + obj->buf_size, *buf_ptr, size - obj->buf_size); *buf_ptr += size - obj->buf_size; *buf_size_ptr -= size - obj->buf_size; obj->buf_size = 0; } else { memcpy(obj->buf + obj->buf_size, *buf_ptr, *buf_size_ptr); obj->buf_size += *buf_size_ptr; return 0; } } else if(*buf_size_ptr < size){ if(*buf_size_ptr) memcpy(obj->buf, *buf_ptr, *buf_size_ptr); obj->buf_size = *buf_size_ptr; return 0; } else { memcpy(target, *buf_ptr, size); *buf_ptr += size; *buf_size_ptr -= size; } return 1; } void cns_notify(void *object, unsigned char *buf, int buf_size, int64_t pos){ struct CNSObj *obj; obj = (struct CNSObj*)object; AGAIN: if(!obj->heading){ if(buf_size > obj->skips){ buf_size -= obj->skips; buf += obj->skips; obj->skips = 0; obj->heading = 1; obj->cache->ref_id = obj->cache->n_ref; obj->cache->n_ref ++; obj->cache->ref_name = (char**)realloc(obj->cache->ref_name, sizeof(char*) * obj->cache->n_ref); obj->cache->ref_offsets = (int64_t*)realloc(obj->cache->ref_offsets, sizeof(int64_t) * obj->cache->n_ref); obj->cache->ref_lengths = (int64_t*)realloc(obj->cache->ref_lengths, sizeof(int64_t) * obj->cache->n_ref); obj->cache->ref_states = (int*)realloc(obj->cache->ref_states, sizeof(int) * obj->cache->n_ref); obj->cache->last_ref_pos = pos - buf_size; } else { obj->skips -= buf_size; return; } } switch(obj->heading){ case 1: if(!read_buf(obj, &obj->n, &buf, &buf_size, sizeof(int))) return; obj->cache->ref_offsets[obj->cache->ref_id] = obj->cache->last_ref_pos + sizeof(int) + obj->n + sizeof(int); obj->cache->ref_name[obj->cache->ref_id] = (char*)malloc(obj->n + 1); obj->heading = 2; case 2: if(!read_buf(obj, obj->cache->ref_name[obj->cache->ref_id], &buf, &buf_size, obj->n)) return; obj->cache->ref_name[obj->cache->ref_id][obj->n] = 0; obj->heading = 3; case 3: if(!read_buf(obj, &obj->skips, &buf, &buf_size, sizeof(int))) return; obj->cache->ref_lengths[obj->cache->ref_id] = obj->skips; obj->cache->ref_states[obj->cache->ref_id] = 1; obj->skips *= sizeof(cns_t); obj->heading = 0; if(obj->skips <= obj->buf_size){ obj->buf_size -= obj->skips; obj->skips = 0; goto AGAIN; } obj->skips -= obj->buf_size; obj->buf_size = 0; if(obj->skips < buf_size){ buf_size -= obj->skips; buf += obj->skips; obj->skips = 0; goto AGAIN; } obj->skips -= buf_size; return; } } CNSCache* make_cns_index(const char *filename, int level){ CNSCache *cache; struct CNSObj obj; char *index_name; FILE *file; int i; cache = cns_cache_init(); if((cache->stream = zropen(filename)) == NULL){ close_cns_cache(cache); return NULL; } obj.cache = cache; obj.heading = 0; obj.skips = 0; obj.buf_size = 0; zrmkindex(filename, level, cns_notify, &obj); //cache->n_ref --; index_name = (char*)malloc(strlen(filename) + 9); strcpy(index_name, filename); strcat(index_name, ".summary"); if((file = fopen(index_name, "w")) == NULL){ free(index_name); close_cns_cache(cache); return NULL; } fprintf(file, "N_REF: %d\n", cache->n_ref); for(i=0;in_ref;i++){ fprintf(file, "REF_NAME:%s\n", cache->ref_name[i]); fprintf(file, "REF_LENGTH:%ld\n", cache->ref_lengths[i]); fprintf(file, "REF_OFFSET:%ld\n", cache->ref_offsets[i]); } fclose(file); return cache; } void close_cns_cache(CNSCache * cache){ int i; if(cache == NULL) return; for(i=0;in_ref;i++){ free(cache->ref_name[i]); } if(cache->ref_name) free(cache->ref_name); if(cache->ref_lengths) free(cache->ref_lengths); if(cache->ref_offsets) free(cache->ref_offsets); if(cache->ref_states) free(cache->ref_states); if (cache->mm_map) free(cache->mm_map); if (cache->cns_map) free(cache->cns_map); free(cache->seqs); if(cache->stream) zrclose(cache->stream); free(cache); } CNSCache *cns_cache_init(){ CNSCache *cns; cns = (CNSCache*)calloc(1, sizeof(CNSCache)); cns->ref_id = -1; cns->capacity = 512; cns->seqs = (cns_t*)malloc(sizeof(cns_t) * cns->capacity); return cns; } CNSCache* open_cns_cache(const char *filename){ CNSCache *cns; char *index_name; FILE *file; int i; index_name = (char*)malloc(strlen(filename) + 9); strcpy(index_name, filename); strcat(index_name, ".summary"); if((file = fopen(index_name, "r")) == NULL){ free(index_name); return NULL; } cns = (CNSCache*)calloc(1, sizeof(CNSCache)); fscanf(file, "N_REF: %d\n", &cns->n_ref); cns->ref_name = (char**)malloc(sizeof(char*) * cns->n_ref); cns->ref_lengths = (int64_t*)malloc(sizeof(int64_t) * cns->n_ref); cns->ref_offsets = (int64_t*)malloc(sizeof(int64_t) * cns->n_ref); cns->ref_states = (int*)calloc(cns->n_ref, sizeof(int)); cns->capacity = 512; cns->seqs = (cns_t*)malloc(sizeof(cns_t) * cns->capacity); cns->ref_id = -1; for(i=0;in_ref;i++){ cns->ref_name[i] = (char*)malloc(120); fscanf(file, "REF_NAME:%s\n", cns->ref_name[i]); fscanf(file, "REF_LENGTH:%ld\n", cns->ref_lengths + i); fscanf(file, "REF_OFFSET:%ld\n", cns->ref_offsets + i); } fclose(file); if((cns->stream = zropen(filename)) == NULL){ close_cns_cache(cns); return NULL;} return cns; } static void synchronize_ref(CNSCache *cns, int n_ref, char **ref_name) { hashci_t *h; int i, val; cns->n_mm_ref = n_ref; cns->mm_map = (int*)calloc(cns->n_mm_ref, sizeof(int)); cns->cns_map = (int*)calloc(cns->n_ref, sizeof(int)); h = hci_init(); for (i = 0; i != cns->n_ref; ++i) hci_put(h, cns->ref_name[i], i); for (i = 0; i != cns->n_mm_ref; ++i) cns->mm_map[i] = hci_get(h, ref_name[i], &val)? val : -1; hci_destroy(h); h = hci_init(); for (i = 0; i != cns->n_mm_ref; ++i) hci_put(h, ref_name[i], i); for (i = 0; i != cns->n_ref; ++i) cns->cns_map[i] = hci_get(h, cns->ref_name[i], &val)? val : -1; hci_destroy(h); } void justify_cns_cache(CNSCache *cns, char **ref_name, int n_ref){ cns->offset = 0; cns->size = 0; cns->start = 0; cns->end = 0; cns->ref_id = 0; cns->last_ref_pos = 0; synchronize_ref(cns, n_ref, ref_name); } int cns_cache_put(CNSCache *cns, int ref_id, int64_t start, int64_t end){ int64_t offset; int64_t size; if(cns->stream == NULL) return -2; if(ref_id < 0 || ref_id >= cns->n_ref) return -2; cns->src_type = CNS_SRC_FILE; if(start < 0) start = 0; if(start >= cns->ref_lengths[ref_id]) start = cns->ref_lengths[ref_id] - 1; if(end < 0) end = 0; if(end >= cns->ref_lengths[ref_id]) end = cns->ref_lengths[ref_id] - 1; if (cns->ref_id < 0 || ref_id != cns->mm_map[cns->ref_id]){ cns->ref_id = cns->cns_map[ref_id]; goto RESET; } if(start < cns->start){ if(end < cns->start || end > cns->end){ goto RESET; } else { goto APPEND_LEFT; } } else if(start >= cns->end){ goto RESET; } else { if(end > cns->end){ goto APPEND_RIGHT; } else { return 0; } } RESET: offset = cns->ref_offsets[ref_id] + start * sizeof(cns_t); if(zrseek(cns->stream, offset) < 0){ fprintf(stderr, "Read Error: at %s:%d\n", __FILE__, __LINE__); return -1; } cns->offset = 0; cns->size = end - start + 1; if(cns->capacity < cns->size){ cns->capacity = cns->size; cns->seqs = (cns_t*)realloc(cns->seqs, sizeof(cns_t) * cns->capacity); } offset = zrread(cns->seqs, sizeof(cns_t) * cns->size, cns->stream); if(offset != cns->size * sizeof(cns_t)){ fprintf(stderr, "Read Error: at %s:%d\n", __FILE__, __LINE__); return -1; } cns->last_ref_pos = zrtell(cns->stream); cns->start = start; cns->end = end; return cns->size; APPEND_LEFT: start -= 1024 * 5; if(start < 0) start = 0; offset = cns->ref_offsets[ref_id] + start * sizeof(cns_t); if(zrseek(cns->stream, offset) < 0){ fprintf(stderr, "Read Error: at %s:%d\n", __FILE__, __LINE__); return -1; } size = cns->start - start; if(cns->offset < size){ if(cns->size + size > cns->capacity){ if(end - start + 1 > cns->capacity){ size = end - start + 1; cns->capacity = size; cns->offset = cns->capacity; cns->size = 0; cns->seqs = (cns_t*)realloc(cns->seqs, sizeof(cns_t) * cns->capacity); } else { cns->size = cns->capacity - size; memmove(cns->seqs + size, cns->seqs + cns->offset, sizeof(cns_t) * cns->size); cns->offset = size; } } else { memmove(cns->seqs + cns->capacity - cns->size, cns->seqs + cns->offset, sizeof(cns_t) * (cns->size)); cns->offset = cns->capacity - cns->size; } } offset = zrread(cns->seqs + cns->offset - size, sizeof(cns_t) * size, cns->stream); if(offset != size * sizeof(cns_t)){ fprintf(stderr, "Read Error: at %s:%d\n", __FILE__, __LINE__); return -1; } cns->last_ref_pos = zrtell(cns->stream); cns->size += size; cns->offset -= size; cns->start = start; cns->end = start + cns->size - 1; return end - start + 1; APPEND_RIGHT: end += 1024; if(end >= cns->ref_lengths[ref_id]) end = cns->ref_lengths[ref_id] - 1; size = end - cns->end; if(cns->offset + cns->size + size > cns->capacity){ if(cns->size + size <= cns->capacity){ memmove(cns->seqs, cns->seqs + cns->offset, cns->size * sizeof(cns_t)); cns->offset = 0; } else { if(end - start + 1 > cns->capacity){ size = end - start + 1; cns->capacity = size; cns->offset = 0; cns->size = 0; cns->seqs = (cns_t*)realloc(cns->seqs, sizeof(cns_t) * cns->capacity); } else { memmove(cns->seqs, cns->seqs + cns->offset + cns->size - (cns->capacity - size), sizeof(cns_t) * (cns->capacity - size)); cns->offset = 0; cns->size = cns->capacity - size; } } } offset = cns->ref_offsets[ref_id] + (end - size + 1) * sizeof(cns_t); if(zrseek(cns->stream, offset) < 0){ fprintf(stderr, "Read Error: at %s:%d\n", __FILE__, __LINE__); return -1; } offset = zrread(cns->seqs + cns->offset + cns->size, sizeof(cns_t) * size, cns->stream); if(offset != size * sizeof(cns_t)){ fprintf(stderr, "Read Error: at %s:%d\n", __FILE__, __LINE__); return -1; } cns->last_ref_pos = zrtell(cns->stream); cns->size += size; cns->start = end - cns->size + 1; cns->end = end; return end - start + 1; } int cns_cache_guess(CNSCache *cns, ReadCache *cache){ int i, n, l; int *guess_seqs; int64_t r; int trans_table[] = {1, 2, 4, 8, 15}; cns->src_type = CNS_SRC_GUESS; if(cns->ref_id == cache->ref_id && cache->start >= cns->start && cache->end <= cns->end){ return 0; } if(cns->capacity < cache->end - cache->start + 1){ cns->capacity = cache->end - cache->start + 1; cns->seqs = (cns_t*)realloc(cns->seqs, sizeof(cns_t) * cns->capacity); } cns->offset = 0; cns->size = cache->end - cache->start + 1; cns->start = cache->start; cns->end = cache->end; cns->ref_id = cache->ref_id; guess_seqs = (int*)malloc(sizeof(int) * cns->size * 4); if(guess_seqs == NULL){ fprintf(stderr, "Maqview ** Out of memory %ld M **\n", sizeof(int) * cns->size * 4 / (1024 * 1024)); fprintf(stderr, "Maqview ** cache %ld - %ld **\n", cache->start, cache->end); return -1; } memset(guess_seqs, 0, sizeof(int) * cns->size * 4); for(i=0;isize;i++){ r = read_pos(cache->reads[cache->offset + i].read.pos); for(l=0;lreads[cache->offset + i].read.size;l++){ if(r + l > cns->end) break; guess_seqs[(r + l - cns->start) * 4 + (cache->reads[cache->offset + i].read.seq[l]>>6&3)] ++; } } memset(cns->seqs, 0, sizeof(cns_t) * cns->size); for(i=0;isize;i++){ r = 4; n = 0; for(l=0;l<4;l++){ if(guess_seqs[i * 4 + l] > n){ r = l; n = guess_seqs[i * 4 + l]; } } cns_set_ref(cns->seqs[i], 0); cns_set_cns(cns->seqs[i], trans_table[r]); } free(guess_seqs); return cns->size; } maqview-0.2.5/maqmap_index_main.c0000644000265600020320000001325411051451011016120 0ustar tilleaadmin#include #include #include #include #include #include #include "zrio.h" #include "maqmap_index.h" #include "caches.h" #include "stdhashc.h" static gzFile global_fp; static int usage() { fprintf(stderr, "\n"); fprintf(stderr, "Usage: maqindex <-i|-v|-b> [-l level] [-c cns] [chr[:begin[-end]] [...]]\n\n"); fprintf(stderr, "Options: -l INT level for indexing [1024]\n"); fprintf(stderr, " -c STR .cns file for this .map file\n"); fprintf(stderr, " -i index the map file\n"); fprintf(stderr, " -v display the alignment in the mapview format\n"); fprintf(stderr, " -b dump in the .map format\n\n"); return 1; } hashci_t *mv_mk_hashci(int n, char **keys) { hashci_t *h; int i; h = hci_init(); for (i = 0; i != n; ++i) hci_put(h, keys[i], i); return h; } void mv_get_region(const hashci_t *h, const char *str, int *ref_id, int *begin, int *end) { char *s, *p; int i, l, k; l = strlen(str); p = s = (char*)malloc(l+1); /* squeeze out "," */ for (i = k = 0; i != l; ++i) if (str[i] != ',' && !isspace(str[i])) s[k++] = str[i]; s[k] = 0; for (i = 0; i != k; ++i) if (s[i] == ':') break; s[i] = 0; assert(hci_get(h, p, ref_id)); /* get the ref_id */ if (i == k) { /* dump the whole sequence */ *begin = 0; *end = 0x7fffffff; return; } for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break; *begin = atoi(p); if (i < k) { p = s + i + 1; *end = atoi(p); } else { *end = 0x7fffffff; } if (*begin > 0) --*begin; if (*end > 0) --*end; /* change to 0 based coordinate */ assert(*begin <= *end); free(s); } static int dump_map(void *obj, maplet *m1) { return gzwrite(global_fp, m1, sizeof(maplet)); } int print_map(void *obj, maplet *m1){ int j; maqmap_t *m; FILE *fpout; m = (maqmap_t*)obj; fpout = stdout; fprintf(fpout, "%s\t%s\t%d\t%c\t%d\t%u\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t", m1->name, m->ref_name[m1->seqid], (m1->pos>>1) + 1, (m1->pos&1)? '-' : '+', m1->dist, m1->flag, m1->map_qual, (signed char)m1->seq[MAX_READLEN-1], m1->alt_qual, m1->info1&0xf, m1->info2, m1->c[0], m1->c[1], m1->size); for (j = 0; j != m1->size; ++j) { if (m1->seq[j] == 0) fputc('n', fpout); else if ((m1->seq[j]&0x3f) < 27) fputc("acgt"[m1->seq[j]>>6&3], fpout); else fputc("ACGT"[m1->seq[j]>>6&3], fpout); } fputc('\t', fpout); for (j = 0; j != m1->size; ++j) fputc((m1->seq[j]&0x3f) + 33, fpout); fputc('\n', fpout); return 1; } int main(int argc, char *argv[]) { int c, i, level, task = 0; int64_t j; char *cns_name = 0; CNSCache *cns; MapIndex *mi; level = 1024; cns_name = NULL; while ((c = getopt(argc, argv, "l:c:ivb")) >= 0) { switch (c) { case 'l': level = atoi(optarg); break; case 'c': cns_name = strdup(optarg); break; case 'i': task = 'i'; break; case 'v': task = 'v'; break; case 'b': task = 'b'; break; } } if(cns_name){ if(task != 'i' && task != 'v'){ fprintf(stderr, "** One of '-i' and '-v' must be specified for cns.\n"); return 1; } } else { if (optind == argc) return usage(); if (task != 'i' && task != 'v' && task != 'b') { fprintf(stderr, "** One of '-i', '-v' and '-b' must be specified.\n"); return 1; } else if (task == 'v' || task == 'b') { if (optind+1 == argc) { fprintf(stderr, "** A region like 'chr' or 'chr:begin-end' must be specified with '-v' or '-b'.\n"); return 1; } } } if (level < 2) level = 2; if (task == 'i') { /* index */ if(optind < argc){ fprintf(stderr, "-- Indexing the alignment file '%s' ... ", argv[optind]); assert(mi = make_map_index(argv[optind], level)); close_map_index(mi); fprintf(stderr, "DONE!\n"); } if (cns_name) { fprintf(stderr, "-- Indexing the consensus file '%s' ... ", cns_name); assert(cns = make_cns_index(cns_name, level)); fprintf(stderr, "DONE!\n"); close_cns_cache(cns); free(cns_name); } } else { /* use */ int ref_id, begin, end, (*func)(void*, maplet*); hashci_t *h; if(cns_name){ if(task != 'v') return usage(); CNSCache *cns; cns_t *seq; cns = open_cns_cache(cns_name); if(cns == NULL){ fprintf(stderr, " -- Cannot open %s in %s -- %s:%d --\n", cns_name, __FUNCTION__, __FILE__, __LINE__); } justify_cns_cache(cns, cns->ref_name, cns->n_ref); h = mv_mk_hashci(cns->n_ref, cns->ref_name); for (i = optind; i != argc; ++i) { mv_get_region(h, argv[i], &ref_id, &begin, &end); if(cns_cache_put(cns, ref_id, (int64_t)begin, (int64_t)end) < 0){ fprintf(stderr, " -- Error in %s -- %s:%d --\n", __FUNCTION__, __FILE__, __LINE__); break; } for(j=0;jsize;j++){ if(j + cns->start < begin || j + cns->start > end) continue; seq = cns->seqs + j + cns->offset; printf("%s\t%ld\t%c\t%c\t%d\t%d\t%.2f\t%d\t%d\n", cns->ref_name[ref_id], j+cns->start+1, nst_nt16_rev_table[seq->ref_base], nst_nt16_rev_table[seq->base], seq->qual, seq->depth, seq->avg01/16.0, seq->qMax, seq->qNei<<1); } } hci_destroy(h); close_cns_cache(cns); return 0; } if(optind >= argc) return usage(); func = (task == 'v')? print_map : dump_map; mi = load_map_index(argv[optind], 1); if (mi == 0) { fprintf(stderr, "** The index for '%s' is broken. Please rebuild the index.\n", argv[optind]); return 1; } if (task == 'b') { global_fp = gzdopen(fileno(stdout), "w"); maqmap_write_header(global_fp, mi->mm); } h = mv_mk_hashci(mi->mm->n_ref, mi->mm->ref_name); for (i = optind+1; i != argc; ++i) { mv_get_region(h, argv[i], &ref_id, &begin, &end); iter_map_index(mi, ref_id, begin, end, func, mi->mm); } hci_destroy(h); if (task == 'b') gzclose(global_fp); /* BAD: close_map_index(mi); */ } return 0; } maqview-0.2.5/caches.h0000644000265600020320000000415711005617221013714 0ustar tilleaadmin#ifndef __CACHES_RJ #define __CACHES_RJ #include "maqmap.h" #include "maqmap_index.h" #define READ_SELECT 0x00000001 #define READ_SHOWTIP 0x00000002 #ifndef MAX_READ_SIZE #define MAX_READ_SIZE 128 #endif typedef struct Read { maqmap1_t read; unsigned int flag; int y; } Read; #define free_read(r) free(r) typedef struct ReadCache { MapIndex *index; Read *reads; int offset; int size; int capacity; int64_t start; int64_t end; int64_t length; int n_ref; int64_t *ref_lengths; int ref_id; int64_t stream_pos; } ReadCache; ReadCache* read_cache_init(MapIndex *index); void read_cache_free(ReadCache *cache); int read_cache_put(ReadCache *cache, int ref_id, int64_t start, int64_t end); typedef struct { // bit32_t avg01:12, qDiff:5, het:1, qMax:6, depth:8; bit32_t depth:8, qMax:6, het:1, qNei:5, avg01:12; // bit32_t ref_base:4, base:4; qual:8, base2:4, base3:4, qual2:8; bit32_t qual2:8, base3:4, base2:4, qual:8, base:4, ref_base:4; } cns_t; #define cns_get_cns(seq) nst_nt16_rev_table[(seq).base] #define cns_set_cns(seq, val) (seq).base = (val)&0xF #define cns_get_ref(seq) nst_nt16_rev_table[(seq).ref_base] #define cns_set_ref(seq, val) (seq).ref_base = (val)&0xF #define CNS_SRC_FILE 0 #define CNS_SRC_GUESS 1 typedef struct { zr_stream *stream; char **ref_name; int n_ref; int64_t *ref_offsets; int64_t *ref_lengths; int *ref_states; int ref_id; int64_t last_ref_pos; cns_t *seqs; int offset; int size; int capacity; int src_type; int n_mm_ref, *mm_map, *cns_map; int64_t start, end; } CNSCache; CNSCache* cns_cache_init(); CNSCache* make_cns_index(const char * filename, int level); CNSCache* open_cns_cache(const char *filename); void justify_cns_cache(CNSCache *cache, char **ref_name, int n_ref); void close_cns_cache(CNSCache *cache); int cns_cache_put(CNSCache *cache, int ref_id, int64_t start, int64_t end); int cns_cache_guess(CNSCache *cns, ReadCache *cache); typedef struct RefSeq { ReadCache *cache; int show_id; int64_t show_start; unsigned char *tooltips; /* char *seqs; int **guess_seqs; int64_t seq_start; int seq_size; int seq_capacity; */ CNSCache *cns; } RefSeq; #endif maqview-0.2.5/crc32.h0000644000265600020320000007355010761137603013416 0ustar tilleaadmin/* crc32.h -- tables for rapid CRC calculation * Generated automatically by crc32.c */ local const unsigned long FAR crc_table[TBLS][256] = { { 0x00000000UL, 0x77073096UL, 0xee0e612cUL, 0x990951baUL, 0x076dc419UL, 0x706af48fUL, 0xe963a535UL, 0x9e6495a3UL, 0x0edb8832UL, 0x79dcb8a4UL, 0xe0d5e91eUL, 0x97d2d988UL, 0x09b64c2bUL, 0x7eb17cbdUL, 0xe7b82d07UL, 0x90bf1d91UL, 0x1db71064UL, 0x6ab020f2UL, 0xf3b97148UL, 0x84be41deUL, 0x1adad47dUL, 0x6ddde4ebUL, 0xf4d4b551UL, 0x83d385c7UL, 0x136c9856UL, 0x646ba8c0UL, 0xfd62f97aUL, 0x8a65c9ecUL, 0x14015c4fUL, 0x63066cd9UL, 0xfa0f3d63UL, 0x8d080df5UL, 0x3b6e20c8UL, 0x4c69105eUL, 0xd56041e4UL, 0xa2677172UL, 0x3c03e4d1UL, 0x4b04d447UL, 0xd20d85fdUL, 0xa50ab56bUL, 0x35b5a8faUL, 0x42b2986cUL, 0xdbbbc9d6UL, 0xacbcf940UL, 0x32d86ce3UL, 0x45df5c75UL, 0xdcd60dcfUL, 0xabd13d59UL, 0x26d930acUL, 0x51de003aUL, 0xc8d75180UL, 0xbfd06116UL, 0x21b4f4b5UL, 0x56b3c423UL, 0xcfba9599UL, 0xb8bda50fUL, 0x2802b89eUL, 0x5f058808UL, 0xc60cd9b2UL, 0xb10be924UL, 0x2f6f7c87UL, 0x58684c11UL, 0xc1611dabUL, 0xb6662d3dUL, 0x76dc4190UL, 0x01db7106UL, 0x98d220bcUL, 0xefd5102aUL, 0x71b18589UL, 0x06b6b51fUL, 0x9fbfe4a5UL, 0xe8b8d433UL, 0x7807c9a2UL, 0x0f00f934UL, 0x9609a88eUL, 0xe10e9818UL, 0x7f6a0dbbUL, 0x086d3d2dUL, 0x91646c97UL, 0xe6635c01UL, 0x6b6b51f4UL, 0x1c6c6162UL, 0x856530d8UL, 0xf262004eUL, 0x6c0695edUL, 0x1b01a57bUL, 0x8208f4c1UL, 0xf50fc457UL, 0x65b0d9c6UL, 0x12b7e950UL, 0x8bbeb8eaUL, 0xfcb9887cUL, 0x62dd1ddfUL, 0x15da2d49UL, 0x8cd37cf3UL, 0xfbd44c65UL, 0x4db26158UL, 0x3ab551ceUL, 0xa3bc0074UL, 0xd4bb30e2UL, 0x4adfa541UL, 0x3dd895d7UL, 0xa4d1c46dUL, 0xd3d6f4fbUL, 0x4369e96aUL, 0x346ed9fcUL, 0xad678846UL, 0xda60b8d0UL, 0x44042d73UL, 0x33031de5UL, 0xaa0a4c5fUL, 0xdd0d7cc9UL, 0x5005713cUL, 0x270241aaUL, 0xbe0b1010UL, 0xc90c2086UL, 0x5768b525UL, 0x206f85b3UL, 0xb966d409UL, 0xce61e49fUL, 0x5edef90eUL, 0x29d9c998UL, 0xb0d09822UL, 0xc7d7a8b4UL, 0x59b33d17UL, 0x2eb40d81UL, 0xb7bd5c3bUL, 0xc0ba6cadUL, 0xedb88320UL, 0x9abfb3b6UL, 0x03b6e20cUL, 0x74b1d29aUL, 0xead54739UL, 0x9dd277afUL, 0x04db2615UL, 0x73dc1683UL, 0xe3630b12UL, 0x94643b84UL, 0x0d6d6a3eUL, 0x7a6a5aa8UL, 0xe40ecf0bUL, 0x9309ff9dUL, 0x0a00ae27UL, 0x7d079eb1UL, 0xf00f9344UL, 0x8708a3d2UL, 0x1e01f268UL, 0x6906c2feUL, 0xf762575dUL, 0x806567cbUL, 0x196c3671UL, 0x6e6b06e7UL, 0xfed41b76UL, 0x89d32be0UL, 0x10da7a5aUL, 0x67dd4accUL, 0xf9b9df6fUL, 0x8ebeeff9UL, 0x17b7be43UL, 0x60b08ed5UL, 0xd6d6a3e8UL, 0xa1d1937eUL, 0x38d8c2c4UL, 0x4fdff252UL, 0xd1bb67f1UL, 0xa6bc5767UL, 0x3fb506ddUL, 0x48b2364bUL, 0xd80d2bdaUL, 0xaf0a1b4cUL, 0x36034af6UL, 0x41047a60UL, 0xdf60efc3UL, 0xa867df55UL, 0x316e8eefUL, 0x4669be79UL, 0xcb61b38cUL, 0xbc66831aUL, 0x256fd2a0UL, 0x5268e236UL, 0xcc0c7795UL, 0xbb0b4703UL, 0x220216b9UL, 0x5505262fUL, 0xc5ba3bbeUL, 0xb2bd0b28UL, 0x2bb45a92UL, 0x5cb36a04UL, 0xc2d7ffa7UL, 0xb5d0cf31UL, 0x2cd99e8bUL, 0x5bdeae1dUL, 0x9b64c2b0UL, 0xec63f226UL, 0x756aa39cUL, 0x026d930aUL, 0x9c0906a9UL, 0xeb0e363fUL, 0x72076785UL, 0x05005713UL, 0x95bf4a82UL, 0xe2b87a14UL, 0x7bb12baeUL, 0x0cb61b38UL, 0x92d28e9bUL, 0xe5d5be0dUL, 0x7cdcefb7UL, 0x0bdbdf21UL, 0x86d3d2d4UL, 0xf1d4e242UL, 0x68ddb3f8UL, 0x1fda836eUL, 0x81be16cdUL, 0xf6b9265bUL, 0x6fb077e1UL, 0x18b74777UL, 0x88085ae6UL, 0xff0f6a70UL, 0x66063bcaUL, 0x11010b5cUL, 0x8f659effUL, 0xf862ae69UL, 0x616bffd3UL, 0x166ccf45UL, 0xa00ae278UL, 0xd70dd2eeUL, 0x4e048354UL, 0x3903b3c2UL, 0xa7672661UL, 0xd06016f7UL, 0x4969474dUL, 0x3e6e77dbUL, 0xaed16a4aUL, 0xd9d65adcUL, 0x40df0b66UL, 0x37d83bf0UL, 0xa9bcae53UL, 0xdebb9ec5UL, 0x47b2cf7fUL, 0x30b5ffe9UL, 0xbdbdf21cUL, 0xcabac28aUL, 0x53b39330UL, 0x24b4a3a6UL, 0xbad03605UL, 0xcdd70693UL, 0x54de5729UL, 0x23d967bfUL, 0xb3667a2eUL, 0xc4614ab8UL, 0x5d681b02UL, 0x2a6f2b94UL, 0xb40bbe37UL, 0xc30c8ea1UL, 0x5a05df1bUL, 0x2d02ef8dUL #ifdef BYFOUR }, { 0x00000000UL, 0x191b3141UL, 0x32366282UL, 0x2b2d53c3UL, 0x646cc504UL, 0x7d77f445UL, 0x565aa786UL, 0x4f4196c7UL, 0xc8d98a08UL, 0xd1c2bb49UL, 0xfaefe88aUL, 0xe3f4d9cbUL, 0xacb54f0cUL, 0xb5ae7e4dUL, 0x9e832d8eUL, 0x87981ccfUL, 0x4ac21251UL, 0x53d92310UL, 0x78f470d3UL, 0x61ef4192UL, 0x2eaed755UL, 0x37b5e614UL, 0x1c98b5d7UL, 0x05838496UL, 0x821b9859UL, 0x9b00a918UL, 0xb02dfadbUL, 0xa936cb9aUL, 0xe6775d5dUL, 0xff6c6c1cUL, 0xd4413fdfUL, 0xcd5a0e9eUL, 0x958424a2UL, 0x8c9f15e3UL, 0xa7b24620UL, 0xbea97761UL, 0xf1e8e1a6UL, 0xe8f3d0e7UL, 0xc3de8324UL, 0xdac5b265UL, 0x5d5daeaaUL, 0x44469febUL, 0x6f6bcc28UL, 0x7670fd69UL, 0x39316baeUL, 0x202a5aefUL, 0x0b07092cUL, 0x121c386dUL, 0xdf4636f3UL, 0xc65d07b2UL, 0xed705471UL, 0xf46b6530UL, 0xbb2af3f7UL, 0xa231c2b6UL, 0x891c9175UL, 0x9007a034UL, 0x179fbcfbUL, 0x0e848dbaUL, 0x25a9de79UL, 0x3cb2ef38UL, 0x73f379ffUL, 0x6ae848beUL, 0x41c51b7dUL, 0x58de2a3cUL, 0xf0794f05UL, 0xe9627e44UL, 0xc24f2d87UL, 0xdb541cc6UL, 0x94158a01UL, 0x8d0ebb40UL, 0xa623e883UL, 0xbf38d9c2UL, 0x38a0c50dUL, 0x21bbf44cUL, 0x0a96a78fUL, 0x138d96ceUL, 0x5ccc0009UL, 0x45d73148UL, 0x6efa628bUL, 0x77e153caUL, 0xbabb5d54UL, 0xa3a06c15UL, 0x888d3fd6UL, 0x91960e97UL, 0xded79850UL, 0xc7cca911UL, 0xece1fad2UL, 0xf5facb93UL, 0x7262d75cUL, 0x6b79e61dUL, 0x4054b5deUL, 0x594f849fUL, 0x160e1258UL, 0x0f152319UL, 0x243870daUL, 0x3d23419bUL, 0x65fd6ba7UL, 0x7ce65ae6UL, 0x57cb0925UL, 0x4ed03864UL, 0x0191aea3UL, 0x188a9fe2UL, 0x33a7cc21UL, 0x2abcfd60UL, 0xad24e1afUL, 0xb43fd0eeUL, 0x9f12832dUL, 0x8609b26cUL, 0xc94824abUL, 0xd05315eaUL, 0xfb7e4629UL, 0xe2657768UL, 0x2f3f79f6UL, 0x362448b7UL, 0x1d091b74UL, 0x04122a35UL, 0x4b53bcf2UL, 0x52488db3UL, 0x7965de70UL, 0x607eef31UL, 0xe7e6f3feUL, 0xfefdc2bfUL, 0xd5d0917cUL, 0xcccba03dUL, 0x838a36faUL, 0x9a9107bbUL, 0xb1bc5478UL, 0xa8a76539UL, 0x3b83984bUL, 0x2298a90aUL, 0x09b5fac9UL, 0x10aecb88UL, 0x5fef5d4fUL, 0x46f46c0eUL, 0x6dd93fcdUL, 0x74c20e8cUL, 0xf35a1243UL, 0xea412302UL, 0xc16c70c1UL, 0xd8774180UL, 0x9736d747UL, 0x8e2de606UL, 0xa500b5c5UL, 0xbc1b8484UL, 0x71418a1aUL, 0x685abb5bUL, 0x4377e898UL, 0x5a6cd9d9UL, 0x152d4f1eUL, 0x0c367e5fUL, 0x271b2d9cUL, 0x3e001cddUL, 0xb9980012UL, 0xa0833153UL, 0x8bae6290UL, 0x92b553d1UL, 0xddf4c516UL, 0xc4eff457UL, 0xefc2a794UL, 0xf6d996d5UL, 0xae07bce9UL, 0xb71c8da8UL, 0x9c31de6bUL, 0x852aef2aUL, 0xca6b79edUL, 0xd37048acUL, 0xf85d1b6fUL, 0xe1462a2eUL, 0x66de36e1UL, 0x7fc507a0UL, 0x54e85463UL, 0x4df36522UL, 0x02b2f3e5UL, 0x1ba9c2a4UL, 0x30849167UL, 0x299fa026UL, 0xe4c5aeb8UL, 0xfdde9ff9UL, 0xd6f3cc3aUL, 0xcfe8fd7bUL, 0x80a96bbcUL, 0x99b25afdUL, 0xb29f093eUL, 0xab84387fUL, 0x2c1c24b0UL, 0x350715f1UL, 0x1e2a4632UL, 0x07317773UL, 0x4870e1b4UL, 0x516bd0f5UL, 0x7a468336UL, 0x635db277UL, 0xcbfad74eUL, 0xd2e1e60fUL, 0xf9ccb5ccUL, 0xe0d7848dUL, 0xaf96124aUL, 0xb68d230bUL, 0x9da070c8UL, 0x84bb4189UL, 0x03235d46UL, 0x1a386c07UL, 0x31153fc4UL, 0x280e0e85UL, 0x674f9842UL, 0x7e54a903UL, 0x5579fac0UL, 0x4c62cb81UL, 0x8138c51fUL, 0x9823f45eUL, 0xb30ea79dUL, 0xaa1596dcUL, 0xe554001bUL, 0xfc4f315aUL, 0xd7626299UL, 0xce7953d8UL, 0x49e14f17UL, 0x50fa7e56UL, 0x7bd72d95UL, 0x62cc1cd4UL, 0x2d8d8a13UL, 0x3496bb52UL, 0x1fbbe891UL, 0x06a0d9d0UL, 0x5e7ef3ecUL, 0x4765c2adUL, 0x6c48916eUL, 0x7553a02fUL, 0x3a1236e8UL, 0x230907a9UL, 0x0824546aUL, 0x113f652bUL, 0x96a779e4UL, 0x8fbc48a5UL, 0xa4911b66UL, 0xbd8a2a27UL, 0xf2cbbce0UL, 0xebd08da1UL, 0xc0fdde62UL, 0xd9e6ef23UL, 0x14bce1bdUL, 0x0da7d0fcUL, 0x268a833fUL, 0x3f91b27eUL, 0x70d024b9UL, 0x69cb15f8UL, 0x42e6463bUL, 0x5bfd777aUL, 0xdc656bb5UL, 0xc57e5af4UL, 0xee530937UL, 0xf7483876UL, 0xb809aeb1UL, 0xa1129ff0UL, 0x8a3fcc33UL, 0x9324fd72UL }, { 0x00000000UL, 0x01c26a37UL, 0x0384d46eUL, 0x0246be59UL, 0x0709a8dcUL, 0x06cbc2ebUL, 0x048d7cb2UL, 0x054f1685UL, 0x0e1351b8UL, 0x0fd13b8fUL, 0x0d9785d6UL, 0x0c55efe1UL, 0x091af964UL, 0x08d89353UL, 0x0a9e2d0aUL, 0x0b5c473dUL, 0x1c26a370UL, 0x1de4c947UL, 0x1fa2771eUL, 0x1e601d29UL, 0x1b2f0bacUL, 0x1aed619bUL, 0x18abdfc2UL, 0x1969b5f5UL, 0x1235f2c8UL, 0x13f798ffUL, 0x11b126a6UL, 0x10734c91UL, 0x153c5a14UL, 0x14fe3023UL, 0x16b88e7aUL, 0x177ae44dUL, 0x384d46e0UL, 0x398f2cd7UL, 0x3bc9928eUL, 0x3a0bf8b9UL, 0x3f44ee3cUL, 0x3e86840bUL, 0x3cc03a52UL, 0x3d025065UL, 0x365e1758UL, 0x379c7d6fUL, 0x35dac336UL, 0x3418a901UL, 0x3157bf84UL, 0x3095d5b3UL, 0x32d36beaUL, 0x331101ddUL, 0x246be590UL, 0x25a98fa7UL, 0x27ef31feUL, 0x262d5bc9UL, 0x23624d4cUL, 0x22a0277bUL, 0x20e69922UL, 0x2124f315UL, 0x2a78b428UL, 0x2bbade1fUL, 0x29fc6046UL, 0x283e0a71UL, 0x2d711cf4UL, 0x2cb376c3UL, 0x2ef5c89aUL, 0x2f37a2adUL, 0x709a8dc0UL, 0x7158e7f7UL, 0x731e59aeUL, 0x72dc3399UL, 0x7793251cUL, 0x76514f2bUL, 0x7417f172UL, 0x75d59b45UL, 0x7e89dc78UL, 0x7f4bb64fUL, 0x7d0d0816UL, 0x7ccf6221UL, 0x798074a4UL, 0x78421e93UL, 0x7a04a0caUL, 0x7bc6cafdUL, 0x6cbc2eb0UL, 0x6d7e4487UL, 0x6f38fadeUL, 0x6efa90e9UL, 0x6bb5866cUL, 0x6a77ec5bUL, 0x68315202UL, 0x69f33835UL, 0x62af7f08UL, 0x636d153fUL, 0x612bab66UL, 0x60e9c151UL, 0x65a6d7d4UL, 0x6464bde3UL, 0x662203baUL, 0x67e0698dUL, 0x48d7cb20UL, 0x4915a117UL, 0x4b531f4eUL, 0x4a917579UL, 0x4fde63fcUL, 0x4e1c09cbUL, 0x4c5ab792UL, 0x4d98dda5UL, 0x46c49a98UL, 0x4706f0afUL, 0x45404ef6UL, 0x448224c1UL, 0x41cd3244UL, 0x400f5873UL, 0x4249e62aUL, 0x438b8c1dUL, 0x54f16850UL, 0x55330267UL, 0x5775bc3eUL, 0x56b7d609UL, 0x53f8c08cUL, 0x523aaabbUL, 0x507c14e2UL, 0x51be7ed5UL, 0x5ae239e8UL, 0x5b2053dfUL, 0x5966ed86UL, 0x58a487b1UL, 0x5deb9134UL, 0x5c29fb03UL, 0x5e6f455aUL, 0x5fad2f6dUL, 0xe1351b80UL, 0xe0f771b7UL, 0xe2b1cfeeUL, 0xe373a5d9UL, 0xe63cb35cUL, 0xe7fed96bUL, 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0x07694ca1UL, 0xbe519b3cUL, 0xdb362784UL, 0x35999296UL, 0x50fe2e2eUL, 0x99b95426UL, 0xfcdee89eUL, 0x12715d8cUL, 0x7716e134UL, 0xce2e36a9UL, 0xab498a11UL, 0x45e63f03UL, 0x208183bbUL, 0x7691e0e3UL, 0x13f65c5bUL, 0xfd59e949UL, 0x983e55f1UL, 0x2106826cUL, 0x44613ed4UL, 0xaace8bc6UL, 0xcfa9377eUL, 0x38417fd6UL, 0x5d26c36eUL, 0xb389767cUL, 0xd6eecac4UL, 0x6fd61d59UL, 0x0ab1a1e1UL, 0xe41e14f3UL, 0x8179a84bUL, 0xd769cb13UL, 0xb20e77abUL, 0x5ca1c2b9UL, 0x39c67e01UL, 0x80fea99cUL, 0xe5991524UL, 0x0b36a036UL, 0x6e511c8eUL, 0xa7166686UL, 0xc271da3eUL, 0x2cde6f2cUL, 0x49b9d394UL, 0xf0810409UL, 0x95e6b8b1UL, 0x7b490da3UL, 0x1e2eb11bUL, 0x483ed243UL, 0x2d596efbUL, 0xc3f6dbe9UL, 0xa6916751UL, 0x1fa9b0ccUL, 0x7ace0c74UL, 0x9461b966UL, 0xf10605deUL #endif } }; maqview-0.2.5/const.h0000644000265600020320000000063410761137604013622 0ustar tilleaadmin#ifndef NST_CONST_H #define NST_CONST_H #define MAX_ULL 0xffffffffffffffffull typedef unsigned long long bit64_t; typedef unsigned bit32_t; typedef unsigned short bit16_t; typedef unsigned char bit8_t; extern bit8_t nst_nt4_table[]; extern bit8_t nst_nt16_table[]; extern char *nst_nt4_rev_table; extern char *nst_nt16_rev_table; extern bit8_t nst_nt16_nt4_table[]; extern int nst_nt16_count_table[]; #endif maqview-0.2.5/Makefile.generic0000644000265600020320000000335511042300371015363 0ustar tilleaadminCC= gcc CXX= g++ CFLAGS= -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -DHAVE_FREEGLUT# -pg -fprofile-arcs -ftest-coverage CXXFLAGS= $(CFLAGS) DFLAGS= ZOBJS= adler32.o compress.o crc32.o deflate.o gzio.o inffast.o inflate.o \ infback.o inftrees.o trees.o uncompr.o zutil.o OBJS= zrio.o btree.o maqmap_index.o read_cache.o cns_cache.o const.o stdhashc.o PROGS= maqindex maqview zrio VERSION= 0.2.4 LIBS= -lm #For Mac #GLLIBS= -framework openGL -framework glut #For Linux #GLLIBS= -lGL -lglut GLLIBS= -Wl,-Bstatic -lglut -Wl,-Bdynamic -lGL -lGLU .SUFFIXES:.c .o .cc .c.o: $(CC) -c $(CFLAGS) $(DFLAGS) $< -o $@ .cc.o: $(CXX) -c $(CXXFLAGS) $(DFLAGS) $< -o $@ all:$(PROGS) zrio:$(ZOBJS) zrio_main.o $(CC) $(CFLAGS) -o $@ -DMAIN_ZRIO zrio_main.o zrio.o $(ZOBJS) maqindex:$(ZOBJS) $(OBJS) maqmap_index_main.o $(CXX) $(CFLAGS) -o $@ $(ZOBJS) $(OBJS) maqmap_index_main.o maqview:$(ZOBJS) $(OBJS) view_goto.o MainFrame.o view_panel.o gl_gui.o $(CXX) $(CFLAGS) -o $@ $(ZOBJS) $(OBJS) view_goto.o view_panel.o gl_gui.o MainFrame.o $(GLLIBS) maqview.1:maqview.pod pod2man --center "Bioinformatics Tools" --release "maqview-$(VERSION)" maqview.pod > $@ adler32.o: zlib.h zconf.h compress.o: zlib.h zconf.h crc32.o: crc32.h zlib.h zconf.h deflate.o: deflate.h zutil.h zlib.h zconf.h gzio.o: zutil.h zlib.h zconf.h inffast.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h inflate.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h infback.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h inftrees.o: zutil.h zlib.h zconf.h inftrees.h trees.o: deflate.h zutil.h zlib.h zconf.h trees.h uncompr.o: zlib.h zconf.h zutil.o: zutil.h zlib.h zconf.h clear: rm -f *.o a.out *~ *.a clean: rm -f *.o a.out *~ *.a $(PROGS) maqview.1 *.gc* gmont.out maqview-0.2.5/inftrees.h0000644000265600020320000000450510761137604014314 0ustar tilleaadmin/* inftrees.h -- header to use inftrees.c * Copyright (C) 1995-2005 Mark Adler * For conditions of distribution and use, see copyright notice in zlib.h */ /* WARNING: this file should *not* be used by applications. It is part of the implementation of the compression library and is subject to change. Applications should only use zlib.h. */ /* Structure for decoding tables. Each entry provides either the information needed to do the operation requested by the code that indexed that table entry, or it provides a pointer to another table that indexes more bits of the code. op indicates whether the entry is a pointer to another table, a literal, a length or distance, an end-of-block, or an invalid code. For a table pointer, the low four bits of op is the number of index bits of that table. For a length or distance, the low four bits of op is the number of extra bits to get after the code. bits is the number of bits in this code or part of the code to drop off of the bit buffer. val is the actual byte to output in the case of a literal, the base length or distance, or the offset from the current table to the next table. Each entry is four bytes. */ typedef struct { unsigned char op; /* operation, extra bits, table bits */ unsigned char bits; /* bits in this part of the code */ unsigned short val; /* offset in table or code value */ } code; /* op values as set by inflate_table(): 00000000 - literal 0000tttt - table link, tttt != 0 is the number of table index bits 0001eeee - length or distance, eeee is the number of extra bits 01100000 - end of block 01000000 - invalid code */ /* Maximum size of dynamic tree. The maximum found in a long but non- exhaustive search was 1444 code structures (852 for length/literals and 592 for distances, the latter actually the result of an exhaustive search). The true maximum is not known, but the value below is more than safe. */ #define ENOUGH 2048 #define MAXD 592 /* Type of code to build for inftable() */ typedef enum { CODES, LENS, DISTS } codetype; extern int inflate_table OF((codetype type, unsigned short FAR *lens, unsigned codes, code FAR * FAR *table, unsigned FAR *bits, unsigned short FAR *work)); maqview-0.2.5/NEWS0000644000265600020320000000456210771073704013027 0ustar tilleaadminBeta Release 0.2.3 (17 March 2008) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Another bug in maqindex gets fixed. (0.2.3: 15 March 2008, r547) Beta Release 0.2.2 (15 March 2008) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ This is mainly a bugfix release. (0.2.2: 15 March 2008, r541) Beta Release 0.2.1 (06 December, 2007) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Notable changes in this release include: * Fixed a bug which may cause segfault in rare cases. * Added codes to show a list of reference names to faciliate switching reference sequences. (0.2.1: 06 December 2007, r448) Beta Release 0.2.0 (30 October, 2007) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The most important change in this release is that the reference sequence and Maq consensus can be displayed in Maqview. Other improvements include: * For maqindex, a region can be specified with a string like: `chrX', `chrX:1000' or `chrX:1,000-2,000'. * In maqview, the window can be split into more to view the different part of the alignments at the same time. * All the coordinates are now 1-based. That is, the coordinate of the first base is 1. (0.2.0: 30 October 2007, r390) Beta Release 0.1.1 (27 September, 2007) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ This is a release with minor changes. Since this release, maqview has been accelerated. The building system is also improved, which makes it a little easier to compile maqview in Linux. LFS (Large File Support) has been implemented. Maqview compiled on the i386 architecture can be used to view a alignment file larger than 2Gb. (0.1.1: 27 September 2007, r318) Beta Release 0.1.0 (24 September, 2007) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ This is the first release of maqview, the graphical viewer for the maq alignment files. A command-line tool, maqindex, also comes with this package to achieve quick retrieval of reads in any specified regions. Maqview is highly efficient in speed, memory and disk usage. It is known to work with a 8Gb maq alignment file. The graphical user interface (GUI) of maqview is based on OpenGL, and therefore installing OpenGL is required. GLUT is optional, though. It has been statically linked in the binary distribution. Maqview simply works, but in this first release, probably you will not find all the features you are expecting. We are still working on it, and hope you enjoy this software. (0.1.0: 24 September 2007, r307)maqview-0.2.5/inflate.h0000644000265600020320000001356410761137604014124 0ustar tilleaadmin/* inflate.h -- internal inflate state definition * Copyright (C) 1995-2004 Mark Adler * For conditions of distribution and use, see copyright notice in zlib.h */ /* WARNING: this file should *not* be used by applications. It is part of the implementation of the compression library and is subject to change. Applications should only use zlib.h. */ /* define NO_GZIP when compiling if you want to disable gzip header and trailer decoding by inflate(). NO_GZIP would be used to avoid linking in the crc code when it is not needed. For shared libraries, gzip decoding should be left enabled. */ #ifndef NO_GZIP # define GUNZIP #endif /* Possible inflate modes between inflate() calls */ typedef enum { HEAD, /* i: waiting for magic header */ FLAGS, /* i: waiting for method and flags (gzip) */ TIME, /* i: waiting for modification time (gzip) */ OS, /* i: waiting for extra flags and operating system (gzip) */ EXLEN, /* i: waiting for extra length (gzip) */ EXTRA, /* i: waiting for extra bytes (gzip) */ NAME, /* i: waiting for end of file name (gzip) */ COMMENT, /* i: waiting for end of comment (gzip) */ HCRC, /* i: waiting for header crc (gzip) */ DICTID, /* i: waiting for dictionary check value */ DICT, /* waiting for inflateSetDictionary() call */ TYPE, /* i: waiting for type bits, including last-flag bit */ TYPEDO, /* i: same, but skip check to exit inflate on new block */ STORED, /* i: waiting for stored size (length and complement) */ COPY, /* i/o: waiting for input or output to copy stored block */ TABLE, /* i: waiting for dynamic block table lengths */ LENLENS, /* i: waiting for code length code lengths */ CODELENS, /* i: waiting for length/lit and distance code lengths */ LEN, /* i: waiting for length/lit code */ LENEXT, /* i: waiting for length extra bits */ DIST, /* i: waiting for distance code */ DISTEXT, /* i: waiting for distance extra bits */ MATCH, /* o: waiting for output space to copy string */ LIT, /* o: waiting for output space to write literal */ CHECK, /* i: waiting for 32-bit check value */ LENGTH, /* i: waiting for 32-bit length (gzip) */ DONE, /* finished check, done -- remain here until reset */ BAD, /* got a data error -- remain here until reset */ MEM, /* got an inflate() memory error -- remain here until reset */ SYNC /* looking for synchronization bytes to restart inflate() */ } inflate_mode; /* State transitions between above modes - (most modes can go to the BAD or MEM mode -- not shown for clarity) Process header: HEAD -> (gzip) or (zlib) (gzip) -> FLAGS -> TIME -> OS -> EXLEN -> EXTRA -> NAME NAME -> COMMENT -> HCRC -> TYPE (zlib) -> DICTID or TYPE DICTID -> DICT -> TYPE Read deflate blocks: TYPE -> STORED or TABLE or LEN or CHECK STORED -> COPY -> TYPE TABLE -> LENLENS -> CODELENS -> LEN Read deflate codes: LEN -> LENEXT or LIT or TYPE LENEXT -> DIST -> DISTEXT -> MATCH -> LEN LIT -> LEN Process trailer: CHECK -> LENGTH -> DONE */ /* state maintained between inflate() calls. Approximately 7K bytes. */ struct inflate_state { inflate_mode mode; /* current inflate mode */ int last; /* true if processing last block */ int wrap; /* bit 0 true for zlib, bit 1 true for gzip */ int havedict; /* true if dictionary provided */ int flags; /* gzip header method and flags (0 if zlib) */ unsigned dmax; /* zlib header max distance (INFLATE_STRICT) */ unsigned short max_window_dist; int dist_window_tail; unsigned short *dist_window; unsigned long check; /* protected copy of check value */ unsigned long total; /* protected copy of output count */ gz_headerp head; /* where to save gzip header information */ /* sliding window */ unsigned wbits; /* log base 2 of requested window size */ unsigned wsize; /* window size or zero if not using window */ unsigned whave; /* valid bytes in the window */ unsigned write; /* window write index */ unsigned char FAR *window; /* allocated sliding window, if needed */ /* bit accumulator */ unsigned long hold; /* input bit accumulator */ unsigned bits; /* number of bits in "in" */ /* for string and stored block copying */ unsigned length; /* literal or length of data to copy */ unsigned offset; /* distance back to copy string from */ /* for table and code decoding */ unsigned extra; /* extra bits needed */ /* fixed and dynamic code tables */ code const FAR *lencode; /* starting table for length/literal codes */ code const FAR *distcode; /* starting table for distance codes */ unsigned lenbits; /* index bits for lencode */ unsigned distbits; /* index bits for distcode */ /* dynamic table building */ unsigned ncode; /* number of code length code lengths */ unsigned nlen; /* number of length code lengths */ unsigned ndist; /* number of distance code lengths */ unsigned have; /* number of code lengths in lens[] */ code FAR *next; /* next available space in codes[] */ unsigned short lens[320]; /* temporary storage for code lengths */ unsigned short work[288]; /* work area for code table building */ code codes[ENOUGH]; /* space for code tables */ }; maqview-0.2.5/deflate.h0000644000265600020320000002752210761137602014103 0ustar tilleaadmin/* deflate.h -- internal compression state * Copyright (C) 1995-2004 Jean-loup Gailly * For conditions of distribution and use, see copyright notice in zlib.h */ /* WARNING: this file should *not* be used by applications. It is part of the implementation of the compression library and is subject to change. Applications should only use zlib.h. */ /* @(#) $Id$ */ #ifndef DEFLATE_H #define DEFLATE_H #include "zutil.h" /* define NO_GZIP when compiling if you want to disable gzip header and trailer creation by deflate(). NO_GZIP would be used to avoid linking in the crc code when it is not needed. For shared libraries, gzip encoding should be left enabled. */ #ifndef NO_GZIP # define GZIP #endif /* =========================================================================== * Internal compression state. */ #define LENGTH_CODES 29 /* number of length codes, not counting the special END_BLOCK code */ #define LITERALS 256 /* number of literal bytes 0..255 */ #define L_CODES (LITERALS+1+LENGTH_CODES) /* number of Literal or Length codes, including the END_BLOCK code */ #define D_CODES 30 /* number of distance codes */ #define BL_CODES 19 /* number of codes used to transfer the bit lengths */ #define HEAP_SIZE (2*L_CODES+1) /* maximum heap size */ #define MAX_BITS 15 /* All codes must not exceed MAX_BITS bits */ #define INIT_STATE 42 #define EXTRA_STATE 69 #define NAME_STATE 73 #define COMMENT_STATE 91 #define HCRC_STATE 103 #define BUSY_STATE 113 #define FINISH_STATE 666 /* Stream status */ /* Data structure describing a single value and its code string. */ typedef struct ct_data_s { union { ush freq; /* frequency count */ ush code; /* bit string */ } fc; union { ush dad; /* father node in Huffman tree */ ush len; /* length of bit string */ } dl; } FAR ct_data; #define Freq fc.freq #define Code fc.code #define Dad dl.dad #define Len dl.len typedef struct static_tree_desc_s static_tree_desc; typedef struct tree_desc_s { ct_data *dyn_tree; /* the dynamic tree */ int max_code; /* largest code with non zero frequency */ static_tree_desc *stat_desc; /* the corresponding static tree */ } FAR tree_desc; typedef ush Pos; typedef Pos FAR Posf; typedef unsigned IPos; /* A Pos is an index in the character window. We use short instead of int to * save space in the various tables. IPos is used only for parameter passing. */ typedef struct internal_state { z_streamp strm; /* pointer back to this zlib stream */ int status; /* as the name implies */ Bytef *pending_buf; /* output still pending */ ulg pending_buf_size; /* size of pending_buf */ Bytef *pending_out; /* next pending byte to output to the stream */ uInt pending; /* nb of bytes in the pending buffer */ int wrap; /* bit 0 true for zlib, bit 1 true for gzip */ gz_headerp gzhead; /* gzip header information to write */ uInt gzindex; /* where in extra, name, or comment */ Byte method; /* STORED (for zip only) or DEFLATED */ int last_flush; /* value of flush param for previous deflate call */ /* used by deflate.c: */ uInt w_size; /* LZ77 window size (32K by default) */ uInt w_bits; /* log2(w_size) (8..16) */ uInt w_mask; /* w_size - 1 */ Bytef *window; /* Sliding window. Input bytes are read into the second half of the window, * and move to the first half later to keep a dictionary of at least wSize * bytes. With this organization, matches are limited to a distance of * wSize-MAX_MATCH bytes, but this ensures that IO is always * performed with a length multiple of the block size. Also, it limits * the window size to 64K, which is quite useful on MSDOS. * To do: use the user input buffer as sliding window. */ ulg window_size; /* Actual size of window: 2*wSize, except when the user input buffer * is directly used as sliding window. */ Posf *prev; /* Link to older string with same hash index. To limit the size of this * array to 64K, this link is maintained only for the last 32K strings. * An index in this array is thus a window index modulo 32K. */ Posf *head; /* Heads of the hash chains or NIL. */ uInt ins_h; /* hash index of string to be inserted */ uInt hash_size; /* number of elements in hash table */ uInt hash_bits; /* log2(hash_size) */ uInt hash_mask; /* hash_size-1 */ uInt hash_shift; /* Number of bits by which ins_h must be shifted at each input * step. It must be such that after MIN_MATCH steps, the oldest * byte no longer takes part in the hash key, that is: * hash_shift * MIN_MATCH >= hash_bits */ long block_start; /* Window position at the beginning of the current output block. Gets * negative when the window is moved backwards. */ uInt match_length; /* length of best match */ IPos prev_match; /* previous match */ int match_available; /* set if previous match exists */ uInt strstart; /* start of string to insert */ uInt match_start; /* start of matching string */ uInt lookahead; /* number of valid bytes ahead in window */ uInt prev_length; /* Length of the best match at previous step. Matches not greater than this * are discarded. This is used in the lazy match evaluation. */ uInt max_chain_length; /* To speed up deflation, hash chains are never searched beyond this * length. A higher limit improves compression ratio but degrades the * speed. */ uInt max_lazy_match; /* Attempt to find a better match only when the current match is strictly * smaller than this value. This mechanism is used only for compression * levels >= 4. */ # define max_insert_length max_lazy_match /* Insert new strings in the hash table only if the match length is not * greater than this length. This saves time but degrades compression. * max_insert_length is used only for compression levels <= 3. */ int level; /* compression level (1..9) */ int strategy; /* favor or force Huffman coding*/ uInt good_match; /* Use a faster search when the previous match is longer than this */ int nice_match; /* Stop searching when current match exceeds this */ /* used by trees.c: */ /* Didn't use ct_data typedef below to supress compiler warning */ struct ct_data_s dyn_ltree[HEAP_SIZE]; /* literal and length tree */ struct ct_data_s dyn_dtree[2*D_CODES+1]; /* distance tree */ struct ct_data_s bl_tree[2*BL_CODES+1]; /* Huffman tree for bit lengths */ struct tree_desc_s l_desc; /* desc. for literal tree */ struct tree_desc_s d_desc; /* desc. for distance tree */ struct tree_desc_s bl_desc; /* desc. for bit length tree */ ush bl_count[MAX_BITS+1]; /* number of codes at each bit length for an optimal tree */ int heap[2*L_CODES+1]; /* heap used to build the Huffman trees */ int heap_len; /* number of elements in the heap */ int heap_max; /* element of largest frequency */ /* The sons of heap[n] are heap[2*n] and heap[2*n+1]. heap[0] is not used. * The same heap array is used to build all trees. */ uch depth[2*L_CODES+1]; /* Depth of each subtree used as tie breaker for trees of equal frequency */ uchf *l_buf; /* buffer for literals or lengths */ uInt lit_bufsize; /* Size of match buffer for literals/lengths. There are 4 reasons for * limiting lit_bufsize to 64K: * - frequencies can be kept in 16 bit counters * - if compression is not successful for the first block, all input * data is still in the window so we can still emit a stored block even * when input comes from standard input. (This can also be done for * all blocks if lit_bufsize is not greater than 32K.) * - if compression is not successful for a file smaller than 64K, we can * even emit a stored file instead of a stored block (saving 5 bytes). * This is applicable only for zip (not gzip or zlib). * - creating new Huffman trees less frequently may not provide fast * adaptation to changes in the input data statistics. (Take for * example a binary file with poorly compressible code followed by * a highly compressible string table.) Smaller buffer sizes give * fast adaptation but have of course the overhead of transmitting * trees more frequently. * - I can't count above 4 */ uInt last_lit; /* running index in l_buf */ ushf *d_buf; /* Buffer for distances. To simplify the code, d_buf and l_buf have * the same number of elements. To use different lengths, an extra flag * array would be necessary. */ ulg opt_len; /* bit length of current block with optimal trees */ ulg static_len; /* bit length of current block with static trees */ uInt matches; /* number of string matches in current block */ int last_eob_len; /* bit length of EOB code for last block */ #ifdef DEBUG ulg compressed_len; /* total bit length of compressed file mod 2^32 */ ulg bits_sent; /* bit length of compressed data sent mod 2^32 */ #endif ush bi_buf; /* Output buffer. bits are inserted starting at the bottom (least * significant bits). */ int bi_valid; /* Number of valid bits in bi_buf. All bits above the last valid bit * are always zero. */ } FAR deflate_state; /* Output a byte on the stream. * IN assertion: there is enough room in pending_buf. */ #define put_byte(s, c) {s->pending_buf[s->pending++] = (c);} #define MIN_LOOKAHEAD (MAX_MATCH+MIN_MATCH+1) /* Minimum amount of lookahead, except at the end of the input file. * See deflate.c for comments about the MIN_MATCH+1. */ #define MAX_DIST(s) ((s)->w_size-MIN_LOOKAHEAD) /* In order to simplify the code, particularly on 16 bit machines, match * distances are limited to MAX_DIST instead of WSIZE. */ /* in trees.c */ void _tr_init OF((deflate_state *s)); int _tr_tally OF((deflate_state *s, unsigned dist, unsigned lc)); void _tr_flush_block OF((deflate_state *s, charf *buf, ulg stored_len, int eof)); void _tr_align OF((deflate_state *s)); void _tr_stored_block OF((deflate_state *s, charf *buf, ulg stored_len, int eof)); #define d_code(dist) \ ((dist) < 256 ? _dist_code[dist] : _dist_code[256+((dist)>>7)]) /* Mapping from a distance to a distance code. dist is the distance - 1 and * must not have side effects. _dist_code[256] and _dist_code[257] are never * used. */ #ifndef DEBUG /* Inline versions of _tr_tally for speed: */ #if defined(GEN_TREES_H) || !defined(STDC) extern uch _length_code[]; extern uch _dist_code[]; #else extern const uch _length_code[]; extern const uch _dist_code[]; #endif # define _tr_tally_lit(s, c, flush) \ { uch cc = (c); \ s->d_buf[s->last_lit] = 0; \ s->l_buf[s->last_lit++] = cc; \ s->dyn_ltree[cc].Freq++; \ flush = (s->last_lit == s->lit_bufsize-1); \ } # define _tr_tally_dist(s, distance, length, flush) \ { uch len = (length); \ ush dist = (distance); \ s->d_buf[s->last_lit] = dist; \ s->l_buf[s->last_lit++] = len; \ dist--; \ s->dyn_ltree[_length_code[len]+LITERALS+1].Freq++; \ s->dyn_dtree[d_code(dist)].Freq++; \ flush = (s->last_lit == s->lit_bufsize-1); \ } #else # define _tr_tally_lit(s, c, flush) flush = _tr_tally(s, 0, c) # define _tr_tally_dist(s, distance, length, flush) \ flush = _tr_tally(s, distance, length) #endif #endif /* DEFLATE_H */ maqview-0.2.5/autogen.sh0000755000265600020320000000027710761137603014326 0ustar tilleaadmin#!/bin/sh run () { echo "running: $*" eval $* if test $? != 0 ; then echo "error: while running '$*'" exit 1 fi } run aclocal run autoheader run automake -a run autoconf maqview-0.2.5/INSTALL0000644000265600020320000000062711052304776013356 0ustar tilleaadmin Maqview GUI is based on OpenGL. It is known to work in Linux and Mac OS X and in principle can be ported to any POSIX/BSD platforms with OpenGL supported. Maqview is built with GNU building systems. To compile it, just run "./autogen.sh; ./configure; make". OpenGL and GLUT are required for building graphical user interface. If you just like to use maqindex, type "make -f Makefile.generic" to compile. maqview-0.2.5/MainFrame.c0000644000265600020320000001543711062071756014335 0ustar tilleaadmin#ifdef __APPLE__ #include #else #include #include #include "GL/glut.h" #ifdef HAVE_FREEGLUT #include "GL/freeglut_ext.h" #endif #endif #include #include #include #include #include "maqview.h" static int main_window = 0; static ViewPanel **main_vps = NULL; static int n_vp = 0; static int win_width = 800; static int win_height = 600; static char msg_string[] = "\ ? : Display this help\n\ : exit\n\ : Draw bases as characters\n\ : Draw bases as squares\n\ p : Switch to the previous reference sequence\n\ n : Switch to the next reference sequence\n\ r : Show/Hide the menu of ref list\n\ : Move to the position pointed by \n\ h / : Move left by one base\n\ l / : Move right by one base\n\ k / : Move view window down\n\ j / : Move view window up\n\ > : Move to next read\n\ < : Move to previous read\n\ g / : Goto begin\n\ G / : Goto end\n\ u / : Move left one page\n\ / : Move right one page\n\ : Move by 100 bases\n\ : Move by 1000 bases\n\ + : Add a new view\n\ - : Remove the current view\n\ : Toogle on/off automatic rolling on\n\ ^b : Toogle on/off automatic rolling back\n\ + : Zoom in\n\ - : Zoom out\n\ 0 : Zoom to the default scale\n\ q : Toggle display/undisplay mapping qualities\n\ e : Toggle display single-end/paired-end mapping qualities\n\ o : Open a new view file\n\ c : Input command, see README\n\n\ Enter an integer then press key to goto the position\n\ Enter an integer then press a key other than can speed the integer times\n\ Mouse:\n\ left button to select;\n\ middle button temporarily drags the scene;\n\ right button sets marker\n\ Mouse: move over an entity to show description\n\ \n\ \n\ Please see README for more function, Press / to return"; void main_display(){ glClearColor(0, 0, 0, 0); glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT); glColor3f(1, 1, 1); drawString(20, win_height - 20, msg_string); glutSwapBuffers(); } void main_reshape(int w, int h){ int i; win_width = w; win_height = h; glViewport(0, 0, win_width, win_height); glMatrixMode(GL_PROJECTION); glLoadIdentity(); glMatrixMode(GL_MODELVIEW); glLoadIdentity(); glOrtho(0, win_width, 0, win_height, -1, 1); if(!n_vp) return; for(i=0;iwin_id); main_vps[i]->off_x = 0; main_vps[i]->off_y = i * h / n_vp; glutPositionWindow(0, i * h / n_vp); glutReshapeWindow(w, h / n_vp); //main_vps[i]->resize(main_vps[i], w, h / n_vp); } glutSetWindow(main_vps[0]->win_id); glutPostRedisplay(); } void main_keyboard(unsigned char key, int x, int y){ ViewPanel *vp; vp = getCurrentViewPanel(); if(vp && vp->keyTyped){ vp->keyTyped(vp, key, x, y); } else { } } void main_mouse(int button, int state, int x, int y){ ViewPanel *vp = getCurrentViewPanel(); if(vp == NULL) return; if(state == GLUT_DOWN){ if(vp->mousePressed) vp->mousePressed(vp, button, x, y); } else { if(vp->mouseReleased) vp->mouseReleased(vp, button, x, y); } } void main_special_key(int key, int x, int y){ ViewPanel *vp = getCurrentViewPanel(); if(vp == NULL) return; if(vp->specialKey) vp->specialKey(vp, key, x, y); } ViewPanel* addViewPanel(ViewPanel * parent, const char *map_name, const char *cns_name, int view_style){ View *view; view = createView(map_name, cns_name, win_width, win_height, view_style); if(view == NULL){ fprintf(stderr, "Cannot open view on %s\n", map_name); return 0; } main_vps = (ViewPanel**)realloc(main_vps, sizeof(ViewPanel*) * (++n_vp)); main_vps[n_vp-1] = createViewPanel(main_window, view, 0, 0, win_width, win_height); if(parent){ main_vps[n_vp-1]->owner = parent; observeView(parent->view, main_vps[n_vp-1], main_vps[n_vp-1]->synchronize); } main_reshape(win_width, win_height); return main_vps[n_vp-1]; } void removeViewPanel(ViewPanel *vp){ int i; if(n_vp < 2) return; for(i=0;iobserver; for(i=0;in_ob;i++){ if(ob->objects[i] == vp) return 1; else { if(check_circle_binding(vp, ((ViewPanel*)ob->objects[i])->view)) return 1; } } return 0; } void bindViewPanel(ViewPanel *observer, int n){ if(n < 0 || n > n_vp) return; if(check_circle_binding(main_vps[n], observer->view)){ fprintf(stderr,"Might bring circled binding, break now\n\n"); return; } observeView(main_vps[n]->view, observer, observer->synchronize); observer->owner = main_vps[n]; } int maqview_usage(){ fprintf(stderr, "MaqView 0.2.4(%s) was written by Ruan Jue ,Li Heng and Zhao MengYao\n", "2008.09"); fprintf(stderr, "Usage: maqview [-c cns_file] [-w width:800] [-h height:600] map_file [ref_name:start_pos]\n"); return 1; } int main(int argc, char **argv){ int w, h, c; int i, n; ViewPanel *vp; char *map_file, *cns_file; char *location; glutInit(&argc, argv); cns_file = NULL; w = win_width; h = win_height; while((c = getopt(argc, argv, "c:w:h:")) >= 0){ switch(c){ case 'c': cns_file = optarg; break; case 'w': win_width = atoi(optarg); break; case 'h': win_height = atoi(optarg); break; } } if(optind == argc) return maqview_usage(); map_file = argv[optind]; glutInitDisplayMode(GLUT_DOUBLE | GLUT_RGB | GLUT_DEPTH); glutInitWindowSize(win_width, win_height); glutInitWindowPosition(200, 200); main_window = glutCreateWindow("M.A.Q Viewer"); vp = addViewPanel(NULL, map_file, cns_file, 0); if(optind + 1 < argc){ n = strlen(argv[optind+1]); location = (char*)malloc(n + 1); memcpy(location, argv[optind+1], n + 1); for(i=0;iview, location, str2num(location + i + 1)); break; } } free(location); } atexit(closeViewPanels); glutSetWindow(main_window); glutReshapeFunc(main_reshape); glutDisplayFunc(main_display); glutKeyboardFunc(main_keyboard); glutSpecialFunc(main_special_key); // glutMouseFunc(main_mouse); // glutMotionFunc(main_motion); // glutPassiveMotionFunc(main_mouseMoved); #ifdef __APPLE__ #else #ifdef HAVE_FREEGLUT // glutMouseWheelFunc(main_mouseWheel); #endif #endif // glutTimerFunc(100, timer, 0); glutMainLoop(); return 0; } maqview-0.2.5/adler32.c0000644000265600020320000001071710761137604013726 0ustar tilleaadmin/* adler32.c -- compute the Adler-32 checksum of a data stream * Copyright (C) 1995-2004 Mark Adler * For conditions of distribution and use, see copyright notice in zlib.h */ /* @(#) $Id$ */ #define ZLIB_INTERNAL #include "zlib.h" #define BASE 65521UL /* largest prime smaller than 65536 */ #define NMAX 5552 /* NMAX is the largest n such that 255n(n+1)/2 + (n+1)(BASE-1) <= 2^32-1 */ #define DO1(buf,i) {adler += (buf)[i]; sum2 += adler;} #define DO2(buf,i) DO1(buf,i); DO1(buf,i+1); #define DO4(buf,i) DO2(buf,i); DO2(buf,i+2); #define DO8(buf,i) DO4(buf,i); DO4(buf,i+4); #define DO16(buf) DO8(buf,0); DO8(buf,8); /* use NO_DIVIDE if your processor does not do division in hardware */ #ifdef NO_DIVIDE # define MOD(a) \ do { \ if (a >= (BASE << 16)) a -= (BASE << 16); \ if (a >= (BASE << 15)) a -= (BASE << 15); \ if (a >= (BASE << 14)) a -= (BASE << 14); \ if (a >= (BASE << 13)) a -= (BASE << 13); \ if (a >= (BASE << 12)) a -= (BASE << 12); \ if (a >= (BASE << 11)) a -= (BASE << 11); \ if (a >= (BASE << 10)) a -= (BASE << 10); \ if (a >= (BASE << 9)) a -= (BASE << 9); \ if (a >= (BASE << 8)) a -= (BASE << 8); \ if (a >= (BASE << 7)) a -= (BASE << 7); \ if (a >= (BASE << 6)) a -= (BASE << 6); \ if (a >= (BASE << 5)) a -= (BASE << 5); \ if (a >= (BASE << 4)) a -= (BASE << 4); \ if (a >= (BASE << 3)) a -= (BASE << 3); \ if (a >= (BASE << 2)) a -= (BASE << 2); \ if (a >= (BASE << 1)) a -= (BASE << 1); \ if (a >= BASE) a -= BASE; \ } while (0) # define MOD4(a) \ do { \ if (a >= (BASE << 4)) a -= (BASE << 4); \ if (a >= (BASE << 3)) a -= (BASE << 3); \ if (a >= (BASE << 2)) a -= (BASE << 2); \ if (a >= (BASE << 1)) a -= (BASE << 1); \ if (a >= BASE) a -= BASE; \ } while (0) #else # define MOD(a) a %= BASE # define MOD4(a) a %= BASE #endif /* ========================================================================= */ uLong ZEXPORT adler32(adler, buf, len) uLong adler; const Bytef *buf; uInt len; { unsigned long sum2; unsigned n; /* split Adler-32 into component sums */ sum2 = (adler >> 16) & 0xffff; adler &= 0xffff; /* in case user likes doing a byte at a time, keep it fast */ if (len == 1) { adler += buf[0]; if (adler >= BASE) adler -= BASE; sum2 += adler; if (sum2 >= BASE) sum2 -= BASE; return adler | (sum2 << 16); } /* initial Adler-32 value (deferred check for len == 1 speed) */ if (buf == Z_NULL) return 1L; /* in case short lengths are provided, keep it somewhat fast */ if (len < 16) { while (len--) { adler += *buf++; sum2 += adler; } if (adler >= BASE) adler -= BASE; MOD4(sum2); /* only added so many BASE's */ return adler | (sum2 << 16); } /* do length NMAX blocks -- requires just one modulo operation */ while (len >= NMAX) { len -= NMAX; n = NMAX / 16; /* NMAX is divisible by 16 */ do { DO16(buf); /* 16 sums unrolled */ buf += 16; } while (--n); MOD(adler); MOD(sum2); } /* do remaining bytes (less than NMAX, still just one modulo) */ if (len) { /* avoid modulos if none remaining */ while (len >= 16) { len -= 16; DO16(buf); buf += 16; } while (len--) { adler += *buf++; sum2 += adler; } MOD(adler); MOD(sum2); } /* return recombined sums */ return adler | (sum2 << 16); } /* ========================================================================= */ uLong ZEXPORT adler32_combine(adler1, adler2, len2) uLong adler1; uLong adler2; z_off_t len2; { unsigned long sum1; unsigned long sum2; unsigned rem; /* the derivation of this formula is left as an exercise for the reader */ rem = (unsigned)(len2 % BASE); sum1 = adler1 & 0xffff; sum2 = rem * sum1; MOD(sum2); sum1 += (adler2 & 0xffff) + BASE - 1; sum2 += ((adler1 >> 16) & 0xffff) + ((adler2 >> 16) & 0xffff) + BASE - rem; if (sum1 > BASE) sum1 -= BASE; if (sum1 > BASE) sum1 -= BASE; if (sum2 > (BASE << 1)) sum2 -= (BASE << 1); if (sum2 > BASE) sum2 -= BASE; return sum1 | (sum2 << 16); } maqview-0.2.5/zutil.c0000644000265600020320000001574010761137602013640 0ustar tilleaadmin/* zutil.c -- target dependent utility functions for the compression library * Copyright (C) 1995-2005 Jean-loup Gailly. * For conditions of distribution and use, see copyright notice in zlib.h */ /* @(#) $Id$ */ #include "zutil.h" #ifndef NO_DUMMY_DECL struct internal_state {int dummy;}; /* for buggy compilers */ #endif const char * const z_errmsg[10] = { "need dictionary", /* Z_NEED_DICT 2 */ "stream end", /* Z_STREAM_END 1 */ "", /* Z_OK 0 */ "file error", /* Z_ERRNO (-1) */ "stream error", /* Z_STREAM_ERROR (-2) */ "data error", /* Z_DATA_ERROR (-3) */ "insufficient memory", /* Z_MEM_ERROR (-4) */ "buffer error", /* Z_BUF_ERROR (-5) */ "incompatible version",/* Z_VERSION_ERROR (-6) */ ""}; const char * ZEXPORT zlibVersion() { return ZLIB_VERSION; } uLong ZEXPORT zlibCompileFlags() { uLong flags; flags = 0; switch (sizeof(uInt)) { case 2: break; case 4: flags += 1; break; case 8: flags += 2; break; default: flags += 3; } switch (sizeof(uLong)) { case 2: break; case 4: flags += 1 << 2; break; case 8: flags += 2 << 2; break; default: flags += 3 << 2; } switch (sizeof(voidpf)) { case 2: break; case 4: flags += 1 << 4; break; case 8: flags += 2 << 4; break; default: flags += 3 << 4; } switch (sizeof(z_off_t)) { case 2: break; case 4: flags += 1 << 6; break; case 8: flags += 2 << 6; break; default: flags += 3 << 6; } #ifdef DEBUG flags += 1 << 8; #endif #if defined(ASMV) || defined(ASMINF) flags += 1 << 9; #endif #ifdef ZLIB_WINAPI flags += 1 << 10; #endif #ifdef BUILDFIXED flags += 1 << 12; #endif #ifdef DYNAMIC_CRC_TABLE flags += 1 << 13; #endif #ifdef NO_GZCOMPRESS flags += 1L << 16; #endif #ifdef NO_GZIP flags += 1L << 17; #endif #ifdef PKZIP_BUG_WORKAROUND flags += 1L << 20; #endif #ifdef FASTEST flags += 1L << 21; #endif #ifdef STDC # ifdef NO_vsnprintf flags += 1L << 25; # ifdef HAS_vsprintf_void flags += 1L << 26; # endif # else # ifdef HAS_vsnprintf_void flags += 1L << 26; # endif # endif #else flags += 1L << 24; # ifdef NO_snprintf flags += 1L << 25; # ifdef HAS_sprintf_void flags += 1L << 26; # endif # else # ifdef HAS_snprintf_void flags += 1L << 26; # endif # endif #endif return flags; } #ifdef DEBUG # ifndef verbose # define verbose 0 # endif int z_verbose = verbose; void z_error (m) char *m; { fprintf(stderr, "%s\n", m); exit(1); } #endif /* exported to allow conversion of error code to string for compress() and * uncompress() */ const char * ZEXPORT zError(err) int err; { return ERR_MSG(err); } #if defined(_WIN32_WCE) /* The Microsoft C Run-Time Library for Windows CE doesn't have * errno. We define it as a global variable to simplify porting. * Its value is always 0 and should not be used. */ int errno = 0; #endif #ifndef HAVE_MEMCPY void zmemcpy(dest, source, len) Bytef* dest; const Bytef* source; uInt len; { if (len == 0) return; do { *dest++ = *source++; /* ??? to be unrolled */ } while (--len != 0); } int zmemcmp(s1, s2, len) const Bytef* s1; const Bytef* s2; uInt len; { uInt j; for (j = 0; j < len; j++) { if (s1[j] != s2[j]) return 2*(s1[j] > s2[j])-1; } return 0; } void zmemzero(dest, len) Bytef* dest; uInt len; { if (len == 0) return; do { *dest++ = 0; /* ??? to be unrolled */ } while (--len != 0); } #endif #ifdef SYS16BIT #ifdef __TURBOC__ /* Turbo C in 16-bit mode */ # define MY_ZCALLOC /* Turbo C malloc() does not allow dynamic allocation of 64K bytes * and farmalloc(64K) returns a pointer with an offset of 8, so we * must fix the pointer. Warning: the pointer must be put back to its * original form in order to free it, use zcfree(). */ #define MAX_PTR 10 /* 10*64K = 640K */ local int next_ptr = 0; typedef struct ptr_table_s { voidpf org_ptr; voidpf new_ptr; } ptr_table; local ptr_table table[MAX_PTR]; /* This table is used to remember the original form of pointers * to large buffers (64K). Such pointers are normalized with a zero offset. * Since MSDOS is not a preemptive multitasking OS, this table is not * protected from concurrent access. This hack doesn't work anyway on * a protected system like OS/2. Use Microsoft C instead. */ voidpf zcalloc (voidpf opaque, unsigned items, unsigned size) { voidpf buf = opaque; /* just to make some compilers happy */ ulg bsize = (ulg)items*size; /* If we allocate less than 65520 bytes, we assume that farmalloc * will return a usable pointer which doesn't have to be normalized. */ if (bsize < 65520L) { buf = farmalloc(bsize); if (*(ush*)&buf != 0) return buf; } else { buf = farmalloc(bsize + 16L); } if (buf == NULL || next_ptr >= MAX_PTR) return NULL; table[next_ptr].org_ptr = buf; /* Normalize the pointer to seg:0 */ *((ush*)&buf+1) += ((ush)((uch*)buf-0) + 15) >> 4; *(ush*)&buf = 0; table[next_ptr++].new_ptr = buf; return buf; } void zcfree (voidpf opaque, voidpf ptr) { int n; if (*(ush*)&ptr != 0) { /* object < 64K */ farfree(ptr); return; } /* Find the original pointer */ for (n = 0; n < next_ptr; n++) { if (ptr != table[n].new_ptr) continue; farfree(table[n].org_ptr); while (++n < next_ptr) { table[n-1] = table[n]; } next_ptr--; return; } ptr = opaque; /* just to make some compilers happy */ Assert(0, "zcfree: ptr not found"); } #endif /* __TURBOC__ */ #ifdef M_I86 /* Microsoft C in 16-bit mode */ # define MY_ZCALLOC #if (!defined(_MSC_VER) || (_MSC_VER <= 600)) # define _halloc halloc # define _hfree hfree #endif voidpf zcalloc (voidpf opaque, unsigned items, unsigned size) { if (opaque) opaque = 0; /* to make compiler happy */ return _halloc((long)items, size); } void zcfree (voidpf opaque, voidpf ptr) { if (opaque) opaque = 0; /* to make compiler happy */ _hfree(ptr); } #endif /* M_I86 */ #endif /* SYS16BIT */ #ifndef MY_ZCALLOC /* Any system without a special alloc function */ #ifndef STDC extern voidp malloc OF((uInt size)); extern voidp calloc OF((uInt items, uInt size)); extern void free OF((voidpf ptr)); #endif voidpf zcalloc (opaque, items, size) voidpf opaque; unsigned items; unsigned size; { if (opaque) items += size - size; /* make compiler happy */ return sizeof(uInt) > 2 ? (voidpf)malloc(items * size) : (voidpf)calloc(items, size); } void zcfree (opaque, ptr) voidpf opaque; voidpf ptr; { free(ptr); if (opaque) return; /* make compiler happy */ } #endif /* MY_ZCALLOC */ maqview-0.2.5/const.c0000644000265600020320000000400310761137604013607 0ustar tilleaadmin#include "const.h" bit8_t nst_nt4_table[256] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5 /*'-'*/, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 }; char *nst_nt4_rev_table = "ACGTN-"; unsigned char nst_nt16_table[256] = { 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15 /*'-'*/,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15, 15,15, 5, 6, 8,15, 7, 9, 0,10,15,15, 15,15,15,15, 15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15, 15,15, 5, 6, 8,15, 7, 9, 0,10,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15 }; char *nst_nt16_rev_table = "XACMGRSVTWYHKDBN"; bit8_t nst_nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 }; int nst_nt16_count_table[] = { 4, 1, 1, 2, 1, 2, 2, 3, 1, 2, 2, 3, 2, 3, 3, 4 }; maqview-0.2.5/gl_gui.h0000644000265600020320000000165210761137604013743 0ustar tilleaadmin#ifndef __GL_LIST_RJ #define __GL_LIST_RJ #include "maqview.h" typedef struct GContainer { int win_id; ViewPanel *parent; int visible; float win_x, win_y; float win_width, win_height; float border_size; float bgColor[3]; float textColor[3]; float borderColor[3]; float highlightTextColor[3]; float highlightBgColor[3]; } GContainer; typedef void (*VALUE_CHANGED)(void *obj, int new_value); typedef struct GList { GContainer window; float cell_width, cell_height; int id; int selected; int disp_offset; int disp_size; int size; int capacity; char **options; VALUE_CHANGED valueChanged; } GList; GList* createGList(int id, ViewPanel *vp, float x, float y, float cell_width, float cell_height, int n_disp); void GList_valueChangedFunc(GList *list, VALUE_CHANGED *valueChanged); int GList_addOption(GList *list, char *option); char* GList_getOption(GList *list, int index); void freeGList(GList *list); #endif maqview-0.2.5/read_cache.c0000644000265600020320000001250510777153022014524 0ustar tilleaadmin#include #include #include #include "caches.h" ReadCache* read_cache_init(MapIndex *index){ int i; ReadCache *cache; cache = (ReadCache*)malloc(sizeof(ReadCache)); cache->index = index; cache->ref_id = -1; cache->capacity = 2 * 1024; cache->reads = (Read*)malloc(sizeof(Read) * cache->capacity); cache->size = 0; cache->offset = 0; cache->start = 0; cache->end = 0; cache->n_ref = index->mm->n_ref; cache->ref_lengths = (int64_t*)malloc(sizeof(int64_t) * cache->n_ref); for(i=0;in_ref;i++){ cache->ref_lengths[i] = index->trees[i]->right + MAX_READ_SIZE; } return cache; } void read_cache_free(ReadCache *cache){ close_map_index(cache->index); free(cache->reads); free(cache); } #define let2read(let, reads) memcpy(&((reads)->read), let, sizeof(maplet)); (reads)->flag = 0; (reads)->y = 0 int read_cache_put(ReadCache *cache, int ref_id, int64_t start, int64_t end){ maplet *let; BTree *tree; int i, m, n; int64_t t; if(ref_id < 0 || ref_id >= cache->index->mm->n_ref) return -2; tree = cache->index->trees[ref_id]; if(start < tree->left) start = tree->left; if(end > tree->right + MAX_READ_SIZE) end = tree->right + MAX_READ_SIZE; if(ref_id != cache->ref_id){ cache->ref_id = ref_id; cache->length = cache->ref_lengths[ref_id]; goto RELOAD; } if(start < cache->start){ if(end < cache->start){ goto RELOAD; } else if(end <= cache->end){ goto APPEND_LEFT; } else { goto RELOAD; } } else if(start <= cache->end){ if(end <= cache->end){ return 0; } else { goto APPEND_RIGHT; } } else { goto RELOAD; } RELOAD: let = read_map_index(cache->index, ref_id, start, end, &n); cache->stream_pos = zrtell(cache->index->stream); if(let == NULL) return -1; if(n > cache->capacity){ cache->capacity = n; cache->reads = (Read*)realloc(cache->reads, sizeof(Read) * cache->capacity);} cache->offset = 0; memset(cache->reads, 0, sizeof(Read) * cache->capacity); for(i=0;ireads + i); } cache->size = n; free(let); if(n){ cache->start = read_pos(cache->reads[cache->offset].read.pos); if(cache->start > start) cache->start = start; cache->end = read_pos(cache->reads[cache->offset+cache->size-1].read.pos); if(cache->end < end) cache->end = end; } else { cache->start = start; cache->end = end; } return 1; APPEND_LEFT: t = end; end = cache->start; if(start >= end) return 0; let = read_map_index(cache->index, ref_id, start, end, &n); cache->stream_pos = zrtell(cache->index->stream); if(let == NULL) return -1; m = n; for(;n>0;n--){ if(read_pos(let[n-1].pos) <= cache->start) break; } if(n <= 0){ cache->start = start; return 0; } if(n + cache->size > cache->capacity){ if(read_pos(let[m-1].pos) >= t){ if(m > cache->capacity){ cache->capacity = m; cache->reads = (Read*)realloc(cache->reads, sizeof(Read) * cache->capacity); } n = m; cache->offset = cache->capacity; cache->size = 0; cache->end = read_pos(let[n-1].pos); } else { cache->capacity = cache->size + n; cache->reads = (Read*)realloc(cache->reads, sizeof(Read) * cache->capacity); } } if(cache->offset < n){ if(cache->size) memmove(cache->reads + cache->capacity - cache->size, cache->reads + cache->offset, sizeof(Read) * cache->size); cache->offset = cache->capacity - cache->size; } for(;n>0;n--){ cache->offset --; cache->size ++; let2read(let + n - 1, cache->reads + cache->offset); } free(let); cache->start = read_pos(cache->reads[cache->offset].read.pos); if(cache->start > start) cache->start = start; return 2; APPEND_RIGHT: t = start; start = cache->end; if(start >= end) return 0; if(cache->stream_pos == zrtell(cache->index->stream)){ let = read_map_next_to(cache->index, ref_id, end + MAX_READ_SIZE, &n); } else { let = read_map_index(cache->index, ref_id, start, end, &n); } cache->stream_pos = zrtell(cache->index->stream); if(let == NULL) return -1; m = n; for(n=0;n cache->end) break; } if(n == m){ cache->end = end; return 0; } if(m - n + cache->size > cache->capacity){ if(read_pos(let[0].pos) <= t - MAX_READ_SIZE){ if(m > cache->capacity){ cache->capacity = m; cache->reads = (Read*)realloc(cache->reads, sizeof(Read) * cache->capacity); } n = 0; cache->offset = 0; cache->size = 0; cache->start = read_pos(let[0].pos); } else { for(i=cache->size-1;i>=0;i--){ if(read_pos(cache->reads[cache->offset + i].read.pos) < t - MAX_READ_SIZE) break; } i ++; if(i > 0){ cache->size -= i; if(cache->size){ memmove(cache->reads, cache->reads + cache->offset + i, sizeof(Read) * cache->size); cache->start = read_pos(cache->reads[0].read.pos); } else { cache->start = read_pos(let[0].pos); } cache->offset = 0; } if(m - n + cache->size > cache->capacity){ cache->capacity = m - n + cache->size; cache->reads = (Read*)realloc(cache->reads, sizeof(Read) * cache->capacity); } } } if(cache->offset){ memmove(cache->reads, cache->reads + cache->offset, sizeof(Read) * cache->size); cache->offset = 0; } for(;nreads + cache->offset + cache->size); cache->size ++; } cache->end = read_pos(cache->reads[cache->offset+cache->size-1].read.pos); if(cache->end < end) cache->end = end; return 3; } maqview-0.2.5/maqmap_index.h0000644000265600020320000000154210761137604015136 0ustar tilleaadmin#ifndef __MAQMAP_INDEX_RJ #define __MAQMAP_INDEX_RJ #include "maqmap.h" #include "zrio.h" #include "btree.h" #define maplet maqmap1_t #define read_pos(p) ((int64_t)((p)>>1)) #define read_strand(p) (p&1) typedef struct { maqmap_t *mm; BTree **trees; zr_stream *stream; int head_size; } MapIndex; MapIndex* load_map_index(const char *filename, int auto_make_index_if_no); MapIndex* make_map_index(const char *filename, int level); int iter_map_index(MapIndex *mi, int ref_id, int64_t start, int64_t end, int (*handle_maqmap1_t)(void *obj, maplet *let), void *obj); maplet* read_map_index(MapIndex *mi, int ref_id, int64_t start, int64_t end, int *n_let); maplet* read_map_next_to(MapIndex *mi, int ref_id, int64_t pos, int *n_let); void close_map_index(MapIndex *mi); void num2str(int64_t number, char *string); int64_t str2num(char *string); #endif maqview-0.2.5/maqindex_socket.pl0000755000265600020320000000054111003261421016017 0ustar tilleaadmin#!/usr/bin/perl -w use strict; use warnings; use MaqIndex; my $mi = MaqIndex->new(-port=>1768); #print $mi->{_n_ref}, "\n"; #for my $ref (keys %{$mi->{_refs}}) { # print join("\t", $ref, @{$mi->{_refs}{$ref}}), "\n"; #} my @bufs; $mi->get("1:100-110", \@bufs); $mi->mapview(\@bufs); $mi->get("2:100-110", \@bufs); $mi->mapview(\@bufs); $mi->destroy; maqview-0.2.5/zrio.c0000644000265600020320000004026711064440355013455 0ustar tilleaadmin#include #include #include #include #include #include #include "zrio.h" #define Z_BUFSIZE 16384 Access * load_access(FILE *in); zr_stream * zropen(const char *filename){ zr_stream *zr; int fid; char * accname; int ret; fid = open(filename, O_RDONLY); if(fid == -1){ return NULL; } zr = (zr_stream*)malloc(sizeof(zr_stream)); zr->stream = (z_stream*)malloc(sizeof(z_stream)); zr->fid = fid; zr->acc_file= NULL; zr->access = NULL; zr->in = 0; zr->last_in = 0; zr->pos = 0; zr->z_eof = 0; zr->z_err = 0; zr->inbuf = (void*)malloc(WINSIZE); zr->stream->next_in = Z_NULL; zr->stream->avail_in = 0; zr->outbuf = (void*)malloc(WINSIZE); zr->stream->next_out = Z_NULL; zr->stream->avail_out = 0; zr->stream->zalloc = Z_NULL; zr->stream->zfree = Z_NULL; zr->stream->opaque = Z_NULL; ret = inflateInit2(zr->stream, 47); /* automatic zlib or gzip decoding */ if(ret != Z_OK){ zrclose(zr); return NULL; } accname = (char*)malloc(strlen(filename) + 4); strcpy(accname, filename); strcat(accname, ".zr"); zr->acc_file = fopen(accname, "r"); free(accname); return zr; } int64_t zrread(void *buf, int64_t len, zr_stream *zr){ int ret; if(zr->z_err || zr->z_eof) return 0; zr->stream->next_out = buf; zr->stream->avail_out = len; zr->out += len; while(zr->stream->avail_out){ if(!zr->stream->avail_in){ zr->stream->avail_in = read(zr->fid, zr->inbuf, WINSIZE); zr->in += zr->stream->avail_in; zr->stream->next_in = zr->inbuf; } if(zr->stream->avail_in == 0){ inflateEnd(zr->stream); zr->z_eof = 1; goto END; } ret = inflate(zr->stream, Z_NO_FLUSH); if (ret == Z_NEED_DICT){ break; } if (ret == Z_MEM_ERROR || ret == Z_DATA_ERROR){ fprintf(stderr, "** Error in inflating data at %s:%d **\n", __FILE__, __LINE__); zr->z_err = 1; goto END; } if (ret == Z_STREAM_END) { zr->z_eof = 1; break; } } END: zr->out -= zr->stream->avail_out; zr->pos += len - zr->stream->avail_out; return len - zr->stream->avail_out; } int zreof(zr_stream *zr){ return zr->z_eof; } int zrerror(zr_stream *zr){ return zr->z_err; } int64_t zrtell(zr_stream *zr){ return zr->pos; } int zrskip(zr_stream *zr, int bytes){ int m, n; unsigned char input[CHUNK]; if(bytes < 0) return 0; n = 0; while(bytes > n){ if(bytes - n >= CHUNK){ m = CHUNK; } else { m = bytes - n; } m = zrread(input, m, zr); n += m; if(zr->z_eof || zr->z_err) return n; } return n; } int64_t set_z_pos(zr_stream *zr, Point *here, int64_t offset){ int ret; int64_t off; z_stream *strm; ret = lseek(zr->fid, here->in - (here->bits ? 1 : 0), SEEK_SET); if(ret == -1) return -1; strm = zr->stream; if(!zr->z_eof) inflateEnd(zr->stream); strm->zalloc = Z_NULL; strm->zfree = Z_NULL; strm->opaque = Z_NULL; strm->avail_in = 0; strm->next_in = Z_NULL; ret = inflateInit2(strm, -15); if (ret != Z_OK) return ret; if(here->bits){ ret = 0; if(read(zr->fid, &ret, 1) == 0){ return -1; } (void)inflatePrime(strm, here->bits, ret >> (8 - here->bits)); } (void)inflateSetDictionary(strm, here->window, WINSIZE); off = offset - here->out; strm->avail_in = 0; #ifdef ZRSKIP zr->pos = here->out; zr->z_eof = 0; zr->z_err = 0; zrskip(zr, (int)off); #else do { if (off > WINSIZE) { /* skip WINSIZE bytes */ strm->avail_out = WINSIZE; strm->next_out = zr->outbuf; off -= WINSIZE; } else if (off != 0) { /* last skip */ strm->avail_out = (unsigned)off; strm->next_out = zr->outbuf; off = 0; } /* uncompress until avail_out filled, or end of stream */ do { if (strm->avail_in == 0) { strm->avail_in = read(zr->fid, zr->inbuf, WINSIZE); if (strm->avail_in == 0) { return -1; } strm->next_in = zr->inbuf; } ret = inflate(strm, Z_NO_FLUSH); /* normal inflate */ if (ret == Z_NEED_DICT) ret = Z_DATA_ERROR; if (ret == Z_MEM_ERROR || ret == Z_DATA_ERROR){ printf("Inflate Error: %s:%d\n", __FILE__, __LINE__); return -1; } if (ret == Z_STREAM_END){ break; } } while (strm->avail_out != 0); /* if reach end of stream, then don't keep trying to get more */ if (ret == Z_STREAM_END){ return (off == 0)? offset:-1; } } while(off); zr->pos = offset; zr->z_eof = 0; zr->z_err = 0; #endif return offset; } int64_t zrseek(zr_stream *zr, int64_t offset){ int i; Point *here; if(offset < 0) return -1; if(offset >= zr->pos && offset <= zr->pos + WINSIZE){ zrskip(zr, (int)(offset - zr->pos)); return offset; } if(zr->access == NULL){ if(zr->acc_file != NULL){ if((zr->access = load_access(zr->acc_file)) == NULL) return -1; } else return -1; } for(i=0;iaccess->have;i+=128){ if(zr->access->list[i].out > offset){ break; } } if(i >= zr->access->have) i = zr->access->have - 1; for(;i>0;i--){ if(zr->access->list[i].out <= offset) break; } here = zr->access->list + i; if(offset > zr->pos && here->out < zr->pos + WINSIZE / 64){ zrskip(zr, (int)(offset - zr->pos)); return offset; } if(here->window == NULL){ if(fseek(zr->acc_file, sizeof(int) + (sizeof(int) + 2 * sizeof(int64_t)) * zr->access->have + WINSIZE * i, SEEK_SET)) return -1; here->window = (unsigned char*)malloc(WINSIZE); if((i = fread(here->window, 1, WINSIZE, zr->acc_file)) != WINSIZE){ return -1; } } return set_z_pos(zr, here, offset); } int64_t zrgets(void *buf, int64_t len, int64_t offset, zr_stream *zr){ int i; int64_t l; Point *here; if(offset < 0) return -1; if(offset == zr->pos){ return zrread(buf, len, zr); } if(offset > zr->pos && offset <= zr->pos + WINSIZE){ zrskip(zr, (int)(offset - zr->pos)); return zrread(buf, len, zr); } if(zr->access == NULL){ if(zr->acc_file != NULL){ if((zr->access = load_access(zr->acc_file)) == NULL) return -1; } else return -1; } for(i=0;iaccess->have;i+=128){ if(zr->access->list[i].out > offset){ break; } } if(i >= zr->access->have) i = zr->access->have - 1; for(;i>0;i--){ if(zr->access->list[i].out <= offset) break; if(zr->access->list[i].out - WINSIZE <= offset) goto SPEC_WAY; } here = zr->access->list + i; if(offset > zr->pos && here->out < zr->pos + WINSIZE/64){ zrskip(zr, (int)(offset - zr->pos)); return zrread(buf, len, zr); } if(here->window == NULL){ if(fseek(zr->acc_file, sizeof(int) + (sizeof(int) + 2 * sizeof(int64_t)) * zr->access->have + WINSIZE * i, SEEK_SET)) return -1; here->window = (unsigned char*)malloc(WINSIZE); if(fread(here->window, 1, WINSIZE, zr->acc_file) != WINSIZE) return -1; } if(set_z_pos(zr, here, offset) < 0) return -1; return zrread(buf, len, zr); SPEC_WAY: here = zr->access->list + i; if(here->window == NULL){ if(fseek(zr->acc_file, sizeof(int) + (sizeof(int) + 2 * sizeof(int64_t)) * zr->access->have + WINSIZE * i, SEEK_SET)) return -1; here->window = (unsigned char*)malloc(WINSIZE); if(fread(here->window, 1, WINSIZE, zr->acc_file) != WINSIZE) return -1; } l = offset - zr->access->list[i].out; if(l > len) l = len; memcpy(buf, here->window + WINSIZE - l, l); if(l == len) return len; len -= l; if(set_z_pos(zr, here, here->out) < 0) return -1; return zrread(buf + l, len, zr) + l; } void zrclose(zr_stream *zr){ if(zr->fid != -1) close(zr->fid); if(zr->acc_file) fclose(zr->acc_file); if(zr->access){ free(zr->access->list); free(zr->access); } if(zr->inbuf) free(zr->inbuf); if(zr->outbuf) free(zr->outbuf); (void)inflateEnd(zr->stream); free(zr->stream); free(zr); } /* Save the access in a file */ #define my_write(file, buf, len) fwrite(buf, 1, len, file) int save_access(FILE *out, Access *index){ int i; Point *p; my_write(out, &(index->have), sizeof(int)); for(i=0;ihave;i++){ p = index->list + i; my_write(out, &(p->out), sizeof(int64_t)); my_write(out, &(p->in), sizeof(int64_t)); my_write(out, &(p->bits), sizeof(int)); } for(i=0;ihave;i++){ p = index->list + i; my_write(out, p->window, WINSIZE); } return i; } /* Load an access from file */ #define my_read(file, buf, len) fread(buf, 1, len, file) Access * load_access(FILE *in){ int i, size; Access *index; Point *p; my_read(in, &size, sizeof(int)); if(size < 0){ return NULL; } index = (Access*)malloc(sizeof(Access)); index->have = index->size = size; index->list = (Point*)malloc(sizeof(Point) * size); for(i=0;ilist + i; p->window = NULL; my_read(in, &(p->out), sizeof(int64_t)); my_read(in, &(p->in), sizeof(int64_t)); my_read(in, &(p->bits), sizeof(int)); } /* for(i=0;ilist + i; p->window = (unsigned char *)malloc(WINSIZE); my_read(in, p->window, WINSIZE); } */ return index; } /* Deallocate an index built by build_index() */ void free_index(struct access *index) { if (index != NULL) { free(index->list); free(index); } } /* Add an entry to the access point list. If out of memory, deallocate the existing list and return NULL. */ struct access *addpoint(struct access *index, int bits, int64_t in, int64_t out, unsigned left, unsigned char *window) { struct point *next; /* if list is empty, create it (start with eight points) */ if (index == NULL) { index = malloc(sizeof(struct access)); if (index == NULL) return NULL; index->list = malloc(sizeof(struct point) << 3); if (index->list == NULL) { free(index); return NULL; } index->size = 8; index->have = 0; } /* if list is full, make it bigger */ else if (index->have == index->size) { index->size <<= 1; next = realloc(index->list, sizeof(struct point) * index->size); if (next == NULL) { free_index(index); return NULL; } index->list = next; } /* fill in entry and increment how many we have */ next = index->list + index->have; next->bits = bits; next->in = in; next->out = out; next->window = (unsigned char*)malloc(WINSIZE); if (left) memcpy(next->window, window + WINSIZE - left, left); if (left < WINSIZE) memcpy(next->window + left, window, WINSIZE - left); index->have++; /* return list, possibly reallocated */ return index; } unsigned short get_max_dist(struct inflate_state *state){ int i, dmax; dmax = 0; for(i=state->dist_window_tail;idmax;i++){ if(dmax + (i - state->dist_window_tail) < state->dist_window[i]) dmax = state->dist_window[i] - (i - state->dist_window_tail); } for(i=0;idist_window_tail;i++){ if(dmax + (i + state->dmax - state->dist_window_tail) < state->dist_window[i]) dmax = state->dist_window[i] - (i + state->dmax - state->dist_window_tail); } return (unsigned short)dmax; } /* Make one entire pass through the compressed stream and build an index, with access points about every span bytes of uncompressed output -- span is chosen to balance the speed of random access against the memory requirements of the list, about 32K bytes per access point. Note that data after the end of the first zlib or gzip stream in the file is ignored. build_index() returns the number of access points on success (>= 1), Z_MEM_ERROR for out of memory, Z_DATA_ERROR for an error in the input file, or Z_ERRNO for a file read error. On success, *built points to the resulting index. */ int build_index(int in, int64_t span, struct access **built, void (*notify)(void *obj, unsigned char *buf, int buf_size, int64_t pos), void *obj) { int ret; int64_t totin, totout, tmp; /* our own total counters to avoid 4GB limit */ int64_t last; /* totout value of last access point */ struct access *index; /* access points being generated */ z_stream strm; unsigned char input[CHUNK]; unsigned char discard[WINSIZE]; unsigned char *window = discard; struct inflate_state *state; memset(window, 0, WINSIZE); /* initialize inflate */ strm.zalloc = Z_NULL; strm.zfree = Z_NULL; strm.opaque = Z_NULL; strm.avail_in = 0; strm.next_in = Z_NULL; ret = inflateInit2(&strm, 47); /* automatic zlib or gzip decoding */ if (ret != Z_OK) return ret; /* inflate the input, maintain a sliding window, and build an index -- this also validates the integrity of the compressed data using the check information at the end of the gzip or zlib stream */ totin = totout = last = 0; index = NULL; /* will be allocated by first addpoint() */ strm.avail_out = 0; state = (struct inflate_state *)strm.state; do { /* get some compressed data from input file */ strm.avail_in = read(in, input, CHUNK); if (strm.avail_in == 0) { ret = Z_DATA_ERROR; goto build_index_error; } strm.next_in = input; /* process all of that, or until end of stream */ do { /* reset sliding window if necessary */ if (strm.avail_out == 0) { strm.avail_out = WINSIZE; strm.next_out = window; // printf("MARK: dist = %d / %d %s:%d\n", get_max_dist(state), state->dmax, __FILE__, __LINE__); } /* inflate until out of input, output, or at end of block -- update the total input and output counters */ totin += strm.avail_in; totout += strm.avail_out; tmp = strm.avail_out; ret = inflate_zr(&strm, Z_BLOCK); /* return at end of block */ totin -= strm.avail_in; totout -= strm.avail_out; if(notify) notify(obj, window + WINSIZE - tmp, tmp - strm.avail_out, totout); if (ret == Z_NEED_DICT) ret = Z_DATA_ERROR; if (ret == Z_MEM_ERROR || ret == Z_DATA_ERROR) goto build_index_error; if (ret == Z_STREAM_END) break; /* if at end of block, consider adding an index entry (note that if data_type indicates an end-of-block, then all of the uncompressed data from that block has been delivered, and none of the compressed data after that block has been consumed, except for up to seven bits) -- the totout == 0 provides an entry point after the zlib or gzip header, and assures that the index always has at least one access point; we avoid creating an access point after the last block by checking bit 6 of data_type */ if ((strm.data_type & 128) && !(strm.data_type & 64) && (totout == 0 || totout - last > span)) { index = addpoint(index, strm.data_type & 7, totin, totout, strm.avail_out, window); if (index == NULL) { ret = Z_MEM_ERROR; goto build_index_error; } last = totout; } } while (strm.avail_in != 0); } while (ret != Z_STREAM_END); /* clean up and return index (release unused entries in list) */ (void)inflateEnd(&strm); index = realloc(index, sizeof(struct point) * index->have); index->size = index->have; *built = index; return index->size; /* return error */ build_index_error: (void)inflateEnd(&strm); if (index != NULL) free_index(index); return 0; } int zrmkindex(const char *filename, int level, void (*notify)(void *obj, unsigned char *buf, int buf_size, int64_t pos), void *obj){ int fid; FILE *file; Access *index; int64_t span; char *accname; if(level <= 1) return 0; span = level * WINSIZE; if((fid = open(filename, O_RDONLY)) == -1) return 0; if(!build_index(fid, span, &index, notify, obj)){ close(fid); return 0; } close(fid); accname = (char*)malloc(strlen(filename) + 4); strcpy(accname, filename); strcat(accname, ".zr"); file = fopen(accname, "w"); free(accname); if(file == NULL){ free_index(index); return 0; } save_access(file, index); free_index(index); fclose(file); return 1; } maqview-0.2.5/MaqDataClient.java0000644000265600020320000001244411010215165015622 0ustar tilleaadmin/* * Author: Ruan Jue */ import java.io.*; import java.net.*; import java.util.*; public class MaqDataClient { public static int VIEW_OP_CLOSE = 0; public static int VIEW_OP_INFO = 1; public static int VIEW_OP_GOTO = 2; public static int VIEW_OP_FETCH = 3; public static char[] nst_nt16_rev_table = {'X', 'A', 'C', 'M', 'G', 'R', 'S', 'V', 'T', 'W', 'Y', 'H', 'K', 'D', 'B', 'N'}; Socket socket = null; int n_ref = 0; ArrayList ref_names = new ArrayList(); ArrayList ref_lengths = new ArrayList(); ArrayList reads = new ArrayList(1024); StringBuffer ref_seqs = new StringBuffer(256); StringBuffer cns_seqs = new StringBuffer(256); int last_code = 0; int ref_id = 0; long start = 0; long end = -1; class Read { byte seq[] = new byte[64]; byte size; byte map_qual; byte info1; byte info2; byte c[] = new byte[2]; byte flag; byte alt_qual; int seqid; int pos; int dist; byte name[] = new byte[36]; public int getRefId(){ return seqid; } public long getPos(){ return (long)(pos>>1); } public boolean isComplement(){ return (pos&0x1) == 1; } public String getSeq(){ char ACGT[] = {'A', 'C', 'G', 'T'}; char acgt[] = {'a', 'c', 'g', 't'}; int i; char[] str = new char[size]; for(i=0;i>6)&0x03]; } else { str[i] = ACGT[seq[i]>>6]; } } return new String(str); } public byte[] getSeqQuals(){ byte[] qual = new byte[size]; for(int i=0;i>24)&0xFF; v2 = (v>>16)&0xFF; v3 = (v>>8)&0xFF; v4 = (v)&0xFF; return v1 | (v2<<8) | (v3<<16) | (v4<<24); } public static long converseLong(long v){ long vs[] = new long[8]; for(int i=0;i<8;i++){ vs[i] = (v>>((7-i)*8))&0xFF; } v = 0; for(int i=0;i<8;i++){ v |= vs[i] << (i * 8); } return v; } public static MaqDataClient connect(String host, int port) throws Exception { MaqDataClient client; DataInputStream input; client = new MaqDataClient(); client.socket = new Socket(host, port); client.socket.getOutputStream().write(VIEW_OP_INFO); client.socket.getOutputStream().flush(); input = new DataInputStream(client.socket.getInputStream()); client.n_ref = converseInt(input.readInt()); for(int i=0;i>4]); } } public void close() throws Exception{ socket.getOutputStream().write(VIEW_OP_CLOSE); socket.close(); } public static void main(String[] argv) throws Exception { if(argv.length < 5){ System.out.println("Params: "); return; } MaqDataClient client = MaqDataClient.connect(argv[0], Integer.parseInt(argv[1])); client.getMaqData(Integer.parseInt(argv[2]), Long.parseLong(argv[3]), Long.parseLong(argv[4])); System.out.println(client.ref_seqs); System.out.println(client.cns_seqs); for(int i=0;i #include #include #include "maqview.h" #include "gl_gui.h" void** vps = NULL; int *vp_types = NULL; int vps_size = 0; static ViewPanel *last_vp = NULL; static char acgt[4] = {'a', 'c', 'g', 't'}; static char ACGT[4] = {'A', 'C', 'G', 'T'}; void register_window(int win_id, void *obj, int win_type){ if(vps_size < win_id){ vps = (void**)realloc(vps, sizeof(void*) * win_id); vp_types = (int*)realloc(vp_types, sizeof(int) * win_id); memset(vp_types + vps_size, 0, sizeof(int) * (win_id - vps_size)); memset(vps + vps_size, 0, sizeof(void*) * (win_id - vps_size)); vps_size = win_id; } vps[win_id-1] = obj; vp_types[win_id-1] = win_type; if(win_type == WINDOW_TYPE_VIEWPANEL) last_vp = (ViewPanel*)obj; } ViewPanel* getViewPanel(int win_id){ if(win_id > vps_size) return NULL; if(vp_types[win_id-1] != WINDOW_TYPE_VIEWPANEL) return NULL; return (ViewPanel*)vps[win_id-1]; } int getMaxWindow_id(){ return vps_size; } ViewPanel* getCurrentViewPanel(){ ViewPanel *vp; int id = glutGetWindow(); vp = getViewPanel(id); if(vp == NULL){ vp = last_vp; } else { last_vp = vp; } return vp; } void hideSubWindows(){ int i, pid; pid = 0; for(i=0;iwin_id); glutHideWindow(); pid = ((ViewPanel*)vps[i])->parent_win_id; } } if(pid) glutSetWindow(pid); } void showSubWindows(){ int i; for(i=0;iwin_id); glutShowWindow(); } } } int execute_cmd(ViewPanel *vp, char *cmd){ int cmd_len; int off, next_pos; char argv[6][80]; int argc; if(cmd == NULL) return 0; if(vp == NULL) return 0; cmd_len = strlen(cmd); /* Parse command */ off = 0; argc = 0; while(offview->map_file){ addViewPanel(NULL, vp->view->map_file, vp->view->cns_file, vp->view->style); glutSetWindow(vp->win_id); return 1; } } } else if(argc == 2){ if(strcmp(argv[0], "b") == 0 || strcmp(argv[0], "bind") == 0){ bindViewPanel(vp, atoi(argv[1]) - 1); return 1; } else if(strcmp(argv[0], "B") == 0 || strcmp(argv[0], "unbind") == 0){ removeObserverView(vp->owner->view, vp); vp->owner = NULL; return 1; } else if(strcmp(argv[0], "g") == 0 || strcmp(argv[0], "goto") == 0){ view_goto(vp->view, vp->view->refs.show_id, str2num(argv[1]) - 1); glutPostRedisplay(); return 1; } else if(strcmp(argv[0], "r") == 0 || strcmp(argv[0], "ref") == 0){ if(view_locate(vp->view, argv[1], 0)){ glutPostRedisplay(); return 1; } else return 0; } } else if(argc == 3){ if(strcmp(argv[0], "s") == 0 || strcmp(argv[0], "set") == 0){ if(strcmp(argv[1], "i") == 0 || strcmp(argv[1], "interval") == 0){ off = atoi(argv[2]); if(off <= 0) return 0; vp->interval = off; } else if(strcmp(argv[1], "s") == 0 || strcmp(argv[1], "step") == 0){ vp->view->step = atoi(argv[2]); } } } return 0; } void synchronize(void *observer, View *view, int event, int64_t last_x, int off_y){ ViewPanel *vp; Read *read; int win_id, i; vp = (ViewPanel*)observer; win_id = glutGetWindow(); switch(event){ case VIEW_EVENT_GOTO: if(view->refs.show_id != vp->view->refs.show_id){ view_goto(vp->view, view->refs.show_id, view->refs.show_start); glutSetWindow(vp->win_id); glutPostRedisplay(); break; } case VIEW_EVENT_MOVE: if(last_x != view->refs.show_start){ view_goto(vp->view, view->refs.show_id, vp->view->refs.show_start + view->refs.show_start - last_x); glutSetWindow(vp->win_id); glutPostRedisplay(); } break; case VIEW_EVENT_MARK_COL: last_x -= vp->view->refs.show_start; if(last_x >= 0 && last_x <= vp->view->ch_width){ if(off_y){ vp->view->refs.tooltips[(int)last_x] |= 0x02; } else { vp->view->refs.tooltips[(int)last_x] &= ~0x02; } glutSetWindow(vp->win_id); glutPostRedisplay(); } break; case VIEW_EVENT_MARK_REF: last_x -= vp->view->refs.show_start; if(last_x >= 0 && last_x <= vp->view->ch_width){ if(off_y){ vp->view->refs.tooltips[(int)last_x] |= 0x01; } else { vp->view->refs.tooltips[(int)last_x] &= ~0x01; } glutSetWindow(vp->win_id); glutPostRedisplay(); } break; case VIEW_EVENT_SELECT_READ: view_goto(vp->view, view->refs.show_id, last_x + off_y - (int)(vp->view->ch_width) / 2); for(i=0;iview->refs.cache->size;i++){ read = vp->view->refs.cache->reads + vp->view->refs.cache->offset + i; if(read_pos(read->read.pos) + read->read.size < last_x + off_y) continue; if(read_pos(read->read.pos) + read->read.size > last_x + off_y) break; if(read->read.dist + off_y == 0){ read->flag |= READ_SHOWTIP; vp->view->layer_offset = - read->y; printf("offset = %d %s:%d\n", read->y, __FILE__, __LINE__); break; } } glutSetWindow(vp->win_id); glutPostRedisplay(); break; case VIEW_EVENT_CLOSE: if(vp->owner && vp->owner->view == view){ vp->owner = NULL; } break; } if(win_id) glutSetWindow(win_id); } void reshape(int w, int h){ ViewPanel *vp = getCurrentViewPanel(); vp->resize(vp, w, h); } void display(){ ViewPanel *vp = getCurrentViewPanel(); vp->paint(vp); } void display_bar(){ ViewPanel *vp = getCurrentViewPanel(); vp->paintStatusBar(vp); } void timer(int win_id){ ViewPanel *vp = getViewPanel(win_id); if(vp->timer) vp->timer(vp, win_id); } void mouse(int button, int state, int x, int y){ ViewPanel *vp = getCurrentViewPanel(); if(state == GLUT_DOWN){ if(vp->mousePressed) vp->mousePressed(vp, button, x, y); } else { if(vp->mouseReleased) vp->mouseReleased(vp, button, x, y); } } void motion(int x, int y){ ViewPanel *vp = getCurrentViewPanel(); if(vp->mouseDragged) vp->mouseDragged(vp, x, y); } void mouse_move(int x, int y){ ViewPanel *vp = getCurrentViewPanel(); if(vp->mouseMoved) vp->mouseMoved(vp, x, y); } void mouse_wheel(int wheel, int direction, int x, int y){ ViewPanel *vp = getCurrentViewPanel(); if(vp->mouseWheel) vp->mouseWheel(vp, wheel, direction, x, y); } void keyboard(unsigned char key, int x, int y){ ViewPanel *vp = getCurrentViewPanel(); if(vp->keyTyped) vp->keyTyped(vp, key, x, y); } void special_key(int code, int x, int y){ ViewPanel *vp = getCurrentViewPanel(); if(vp->specialKey) vp->specialKey(vp, code, x, y); } void resetMatrixs(ViewPanel *vp){ glMatrixMode(GL_PROJECTION); glLoadIdentity(); glMatrixMode(GL_MODELVIEW); glLoadIdentity(); glOrtho(0, vp->width, 0, vp->height, -vp->width, vp->width); } void resetPickMatrixs(ViewPanel *vp, GLdouble x, GLdouble y, float size, GLint *viewport){ glMatrixMode(GL_PROJECTION); glLoadIdentity(); gluPickMatrix((GLdouble)x, (GLdouble) y, size, size, viewport); glMatrixMode(GL_MODELVIEW); glLoadIdentity(); glOrtho(0, vp->width, 0, vp->height, -vp->width, vp->width); } void bar_resize(int w, int h){ glViewport(0, 0, w, h); glMatrixMode(GL_PROJECTION); glLoadIdentity(); glMatrixMode(GL_MODELVIEW); glLoadIdentity(); glOrtho(0, w, 0, h, -w, w); } void default_resize(ViewPanel *vp, int w, int h){ vp->width = w; vp->height = h - vp->status_height; vp->status_width = w; view_resize(vp->view, vp->width, vp->height); glutSetWindow(vp->win_id); //glutReshapeWindow(w, h); glViewport(0, 0, w, h); resetMatrixs(vp); glutPostRedisplay(); glutSetWindow(vp->status_id); glutPositionWindow(0, vp->height); glutReshapeWindow(vp->status_width, vp->status_height); bar_resize(vp->status_width, vp->status_height); glutSetWindow(vp->win_id); } void default_timer(ViewPanel *vp, int win_id){ int next_pos; if(vp->view->nav.state){ glutTimerFunc(vp->interval, timer, win_id); next_pos = vp->view->refs.show_start + vp->view->nav.arrow_x - vp->view->nav.center_x; if(next_pos < 0 || next_pos >= vp->view->refs.cache->length){ } else { view_goto(vp->view, vp->view->refs.show_id, next_pos); vp->paint(vp); } } else if(vp->view->rolling){ next_pos = vp->view->refs.show_start + vp->view->rolling; if(next_pos < 0 || next_pos > vp->view->refs.cache->length){ vp->view->rolling = 0; } else { glutTimerFunc(vp->interval, timer, win_id); view_goto(vp->view, vp->view->refs.show_id, next_pos); vp->paint(vp); } } } void drawString(float x, float y, char *str){ char *c; glRasterPos3f(x, y, 0); c = str; for(;*c != '\0'; c++){ if(*c == '\n' || *c == '\r'){ y -= 15; glRasterPos3f(x, y, 0); } else { glutBitmapCharacter(GLUT_BITMAP_8_BY_13, *c); } } } /* void drawString(float x, float y, char *str){ char *c; float font_width = 8, font_height = 13, off_x; glPushMatrix(); glTranslatef(x, y, 0); glScalef(font_width / 104.76, font_height / 152.38, 1); c = str; off_x = 0; for(;*c != '\0'; c++){ if(*c == '\n' || *c == '\r'){ glTranslatef(off_x, -152.38, 0); off_x = 0; } else { off_x -= 104.76; glutStrokeCharacter(GLUT_STROKE_MONO_ROMAN, *c); } } glPopMatrix(); } */ void drawToolTip(ViewPanel *vp, float x, float y, char *str){ int i, size; View *view; float z; view = vp->view; z = 2; size = strlen(str); glColor3fv(view->select_color.rgb); glBegin(GL_POLYGON); glVertex3f(x, y, z); glVertex3f(x + size * view->font_width / 2 + 1, y + view->font_line_height - view->font_height - 2, z); glVertex3f(x + size * view->font_width / 2 + 1, y + view->font_line_height, z); glVertex3f(x - size * view->font_width / 2 - 1, y + view->font_line_height, z); glVertex3f(x - size * view->font_width / 2 - 1, y + view->font_line_height - view->font_height - 2, z); glEnd(); glColor3fv(view->tip_color.rgb); z += 0.1; glBegin(GL_LINE_LOOP); glVertex3f(x, y - 5, z); glVertex3f(x + 3, y, z); glVertex3f(x + size * view->font_width / 2 + 1, y, z); glVertex3f(x + size * view->font_width / 2 + 1, y + view->font_line_height, z); glVertex3f(x - size * view->font_width / 2 - 1, y + view->font_line_height, z); glVertex3f(x - size * view->font_width / 2 - 1, y, z); glVertex3f(x - 3, y, z); glEnd(); if(x - size * view->font_width / 2 < 0){ i = ((- x + size * view->font_width / 2) / view->font_width); if(i * view->font_width != (- x + size * view->font_width / 2)) i++; } else { i = 0; } glRasterPos3f(x - size * view->font_width / 2 + i * view->font_width, y + view->font_line_height - view->font_height, z + 1); for(;ifont, str[i]); } void drawRect(float x1, float y1, float x2, float y2, float z){ glBegin(GL_POLYGON); glVertex3f(x1, y1, z); glVertex3f(x2, y1, z); glVertex3f(x2, y2, z); glVertex3f(x1, y2, z); glEnd(); } void setBaseColor(View *view, char ch, int q){ float rgb[3], tmp; switch(ch){ case 'A': case 'a': memcpy(rgb, view->base_color_table[0].rgb, 3 * sizeof(float)); break; case 'T': case 't': memcpy(rgb, view->base_color_table[1].rgb, 3 * sizeof(float)); break; case 'G': case 'g': memcpy(rgb, view->base_color_table[2].rgb, 3 * sizeof(float)); break; case 'C': case 'c': memcpy(rgb, view->base_color_table[3].rgb, 3 * sizeof(float)); break; default: memcpy(rgb, view->base_color_table[4].rgb, 3 * sizeof(float)); } tmp = 1.0 * q / MAX_BASE_Q; if (tmp > 1.0) tmp = 1.0; rgb[0] = rgb[0] * (0.8 * tmp + 0.2); rgb[1] = rgb[1] * (0.8 * tmp + 0.2); rgb[2] = rgb[2] * (0.8 * tmp + 0.2); glColor3fv(rgb); } void drawRefSeq_ch(ViewPanel *vp, float x, float y, int size){ int i; char ch, ch2; char str[81]; View *view; RefSeq *refs; view = vp->view; refs = &view->refs; for(i=0;ishow_start + i > refs->cns->end || refs->show_start + i < 0 || refs->show_start + i < refs->cns->start){ ch = view->default_ref_char; ch2= view->default_ref_char; } else { ch = cns_get_ref(refs->cns->seqs[refs->cns->offset + refs->show_start + i - refs->cns->start]); ch2 = cns_get_cns(refs->cns->seqs[refs->cns->offset + refs->show_start + i - refs->cns->start]); } if(refs->tooltips[i] & 1){ glColor3fv(view->select_color.rgb); drawRect(x + i * view->font_width, y, x + (i+1) * view->font_width, y + view->font_height, -1); num2str(i + refs->show_start + 1, str); drawToolTip(vp, x + (i + 0.5f) * view->font_width, y + view->font_height, str); } if(refs->tooltips[i] & 2){ glColor3fv(view->select_color.rgb); drawRect(x + i * view->font_width, y, x + (i+1) * view->font_width, 0, -1); } glColor3fv(view->ref_color.rgb); glRasterPos3f(x + i * view->font_width, y, 0); glutBitmapCharacter(view->font, ch); glRasterPos3f(x + i * view->font_width, y - view->font_height, 0); glutBitmapCharacter(view->font, ch2); } } void drawRefSeq_sq(ViewPanel *vp, float x, float y, int size){ int i; char ch, ch2; char str[81]; View *view; RefSeq *refs; view = vp->view; refs = &view->refs; for(i=0;ishow_start + i > refs->cns->end || refs->show_start + i < 0 || refs->show_start + i < refs->cns->start){ ch = view->default_ref_char; ch2= view->default_ref_char; } else { ch = cns_get_ref(refs->cns->seqs[refs->cns->offset + refs->show_start + i - refs->cns->start]); ch2= cns_get_cns(refs->cns->seqs[refs->cns->offset + refs->show_start + i - refs->cns->start]); } if(refs->tooltips[i] & 1){ glColor3fv(view->select_color.rgb); drawRect(x + i * view->base_width * view->scale_x, y, x + (i+1) * view->base_width * view->scale_x, y + view->base_height * view->scale_y, -1); sprintf(str, "%ld[%c]", i + refs->show_start + 1, ch); drawToolTip(vp, x + (i + 0.5f) * view->base_width * view->scale_x, y + view->base_height * view->scale_y, str); } if(refs->tooltips[i] & 2){ glColor3fv(view->select_color.rgb); drawRect(x + i * view->line_width * view->scale_x, y, x + (i+1) * view->line_width * view->scale_x, 0, -1); } setBaseColor(view, ch, MAX_BASE_Q); glRectf(x + i * view->line_width * view->scale_x + view->base_margin * view->scale_x, y, x + (i + 1) * view->line_width * view->scale_x - view->base_margin * view->scale_x, y + view->base_height * view->scale_y); if(ch2 != ch) setBaseColor(view, ch2, MAX_BASE_Q); glRectf(x + i * view->line_width * view->scale_x + view->base_margin * view->scale_x, y - view->line_height * view->scale_y, x + (i + 1) * view->line_width * view->scale_x - view->base_margin * view->scale_x, y - view->line_height * view->scale_y + view->base_height * view->scale_y); } } void drawRefSeq_li(ViewPanel *vp, float x, float y, int size){ int i; char ch, ch2; char str[81]; View *view; RefSeq *refs; view = vp->view; refs = &view->refs; for(i=0;ishow_start + i > refs->cns->end || refs->show_start + i < 0 || refs->show_start + i < refs->cns->start){ ch = view->default_ref_char; ch2= view->default_ref_char; } else { ch = cns_get_ref(refs->cns->seqs[refs->cns->offset + refs->show_start + i - refs->cns->start]); ch2= cns_get_cns(refs->cns->seqs[refs->cns->offset + refs->show_start + i - refs->cns->start]); } if(refs->tooltips[i] & 1){ glColor3fv(view->select_color.rgb); drawRect(x + i * view->line_width * view->scale_x, y, x + (i+1) * view->line_width * view->scale_x, y + view->line_height * view->scale_y, -1); sprintf(str, "%ld[%c]", i + refs->show_start + 1, ch); drawToolTip(vp, x + (i + 0.5f) * view->line_width * view->scale_x, y + view->line_height * view->scale_y, str); } if(refs->tooltips[i] & 2){ glColor3fv(view->select_color.rgb); drawRect(x + i * view->line_width * view->scale_x, y, x + (i+1) * view->line_width * view->scale_x, 0, -1); } setBaseColor(view, ch, MAX_BASE_Q); glRectf(x + i * view->line_width * view->scale_x, y, x + (i + 1) * view->line_width * view->scale_x, y + view->line_height * view->scale_y); if(ch != ch2) setBaseColor(view, ch2, MAX_BASE_Q); glRectf(x + i * view->line_width * view->scale_x, y - view->line_height * view->scale_y, x + (i + 1) * view->line_width * view->scale_x, y - view->line_height * view->scale_y + view->line_height * view->scale_y); } } void drawRefSeq(ViewPanel *vp, float x, float y, int size){ switch(vp->view->mode){ case VIEW_MODE_CHARACTER: return drawRefSeq_ch(vp, x, y, size); case VIEW_MODE_SQUARE: return drawRefSeq_sq(vp, x, y, size); case VIEW_MODE_LINE: return drawRefSeq_li(vp, x, y, size); } } int selectRefSeq_ch(ViewPanel *vp, float x, float y, int size, int id){ int i; i = 0; for(;iview->font_width, y + vp->view->font_height, x + (i+1) * vp->view->font_width, y); glRectf(x + i * vp->view->font_width, y - vp->view->font_line_height + vp->view->font_height, x + (i+1) * vp->view->font_width, y - vp->view->font_line_height); } return i; } int selectRefSeq_sq(ViewPanel *vp, float x, float y, int size, int id){ int i; float y2; View *view; view = vp->view; i = 0; y2 = y - view->line_height * view->scale_y; for(;ibase_width * view->scale_x, y + view->base_height * view->scale_y, x + (i+1) * view->base_width * view->scale_x, y); glRectf(x + i * view->base_width * view->scale_x, y2 + view->base_height * view->scale_y, x + (i+1) * view->base_width * view->scale_x, y2); } return i; } int selectRefSeq_li(ViewPanel *vp, float x, float y, int size, int id){ int i; float y2; View *view; view = vp->view; i = 0; y2 = y - view->line_height * view->scale_y; for(;iline_width * view->scale_x, y + view->line_height * view->scale_y, x + (i+1) * view->line_width * view->scale_x, y); glRectf(x + i * view->base_width * view->scale_x, y2 + view->base_height * view->scale_y, x + (i+1) * view->base_width * view->scale_x, y2); } return i; } int selectRefSeq(ViewPanel *vp, float x, float y, int size, int id){ switch(vp->view->mode){ case VIEW_MODE_CHARACTER: return selectRefSeq_ch(vp, x, y, size, id); case VIEW_MODE_SQUARE: return selectRefSeq_sq(vp, x, y, size, id); case VIEW_MODE_LINE: return selectRefSeq_li(vp, x, y, size, id); } return 0; } void drawRead_ch(ViewPanel *vp, Read *read, float x, float y){ int i, q; char ch, ref; float r, g, b; View *view; view = vp->view; if((read->flag & READ_SELECT && view->selecting) || read->flag & READ_SHOWTIP){ r = 0.7; g = 0.0; b = 0.3; for(i=0;iread.size;i++){ r /= 1.03; b *= 1.03; glColor3f(r, g, b); if(read_strand(read->read.pos)) drawRect(x + (read->read.size - i)* view->font_width, y, x + (read->read.size - i - 1) * view->font_width, y + view->font_height, -2); else drawRect(x + i * view->font_width, y, x + (i + 1) * view->font_width, y + view->font_height, -2); } } else { read->flag &= ~READ_SELECT; } for(i=0;iread.size;i++){ q = read->read.seq[i] & 0x3f; if (read->read.seq[i] == 0) ch = 'n'; else if (q < 27) ch = acgt[read->read.seq[i]>>6&3]; else ch = ACGT[read->read.seq[i]>>6&3]; if(x + i * view->font_width < 0) continue; if(x + i * view->font_width >= vp->width) continue; if(view->refs.cns->src_type == CNS_SRC_FILE){ ref = cns_get_ref(view->refs.cns->seqs[view->refs.cns->offset + read_pos(read->read.pos) + i - view->refs.cns->start]); } else { ref = cns_get_cns(view->refs.cns->seqs[view->refs.cns->offset + read_pos(read->read.pos) + i - view->refs.cns->start]); } if((ch>='a'? ch-'a'+'A':ch) != ref){ glColor3fv(view->mismatch_color.rgb); } else { glColor3fv(view->qual_color_table[q].rgb); } glRasterPos3f(x + i * view->font_width, y, 0); glutBitmapCharacter(view->font, ch); } } void drawRead_sq(ViewPanel *vp, Read *read, float x, float y){ int i, q, h, map_qual; char ch; float r, g, b; View *view; view = vp->view; map_qual = (vp->global_flag & GF_IS_SINGLEQ)? read->read.seq[MAX_READLEN-1] : read->read.map_qual; if((view->selecting && read->flag & READ_SELECT) || (read->flag & READ_SHOWTIP)){ r = 0.7; g = 0.3; b = 0.3; for(i=0;iread.size;i++){ r /= 1.03; g /= 1.03; b *= 1.03; glColor3f(r, g, b); if(read_strand(read->read.pos)) drawRect(x + (read->read.size - i)* view->base_width * view->scale_x, y, x + (read->read.size - i - 1) * view->base_width * view->scale_x , y + view->base_height * view->scale_y, -2); else drawRect(x + i * view->base_width * view->scale_x, y, x + (i + 1) * view->base_width * view->scale_x, y + view->base_height * view->scale_y, -2); } } else { read->flag &= ~READ_SELECT; } for(i=0;iread.size;i++){ q = read->read.seq[i] & 0x3f; if (read->read.seq[i] == 0) ch = 'n'; else if (q < 27) ch = acgt[read->read.seq[i]>>6&3]; else ch = ACGT[read->read.seq[i]>>6&3]; if(x + i * view->base_width * view->scale_x < 0) continue; if(x + i * view->base_width * view->scale_x >= vp->width) continue; setBaseColor(view, ch, q); h = view->base_height * view->scale_y; /* h is the height of the box */ if (!(vp->global_flag & GF_HIDE_MAPQ)) { if (map_qual >= 60) h = view->base_height * view->scale_y; else if (map_qual >= 30) h = 3; else if (map_qual >= 13) h = 2; else h = 1; } glRectf(x + i * view->base_width * view->scale_x + view->base_margin * view->scale_x, y, x + (i + 1) * view->base_width * view->scale_x - view->base_margin * view->scale_x, y + h); } } void drawRead_li(ViewPanel *vp, Read *read, float x, float y){ View *view; view = vp->view; if((view->selecting && read->flag & READ_SELECT) || (read->flag & READ_SHOWTIP)){ glColor3fv(view->select_color.rgb); } else { read->flag &= ~READ_SELECT; if(read_strand(read->read.pos)) glColor3fv(view->line_backward_color.rgb); else glColor3fv(view->line_forward_color.rgb); } drawRect(x, y + view->line_height * view->scale_y / 3, x + read->read.size * view->line_width * view->scale_x, y + view->line_height * view->scale_y * 2 / 3, 0); if(read->read.dist > 0){ glBegin(GL_POLYGON); glVertex3f(x + (read->read.size - 1) * view->line_width * view->scale_x, y + view->line_height * view->scale_y, 0); glVertex3f(x + (read->read.size - 1) * view->line_width * view->scale_x, y, 0); glVertex3f(x + (read->read.size) * view->line_width * view->scale_x, y + view->line_height * view->scale_y / 3, 0); glVertex3f(x + (read->read.size) * view->line_width * view->scale_x, y + view->line_height * view->scale_y * 2 / 3, 0); glEnd(); } else if(read->read.dist < 0){ glBegin(GL_POLYGON); glVertex3f(x + (1) * view->line_width * view->scale_x, y + view->line_height * view->scale_y, 0); glVertex3f(x + (1) * view->line_width * view->scale_x, y, 0); glVertex3f(x, y + view->line_height * view->scale_y / 3, 0); glVertex3f(x, y + view->line_height * view->scale_y * 2 / 3, 0); glEnd(); } } void drawRead(ViewPanel *vp, Read *read, float x, float y){ switch(vp->view->mode){ case VIEW_MODE_CHARACTER: return drawRead_ch(vp, read, x, y); case VIEW_MODE_SQUARE: return drawRead_sq(vp, read, x, y); case VIEW_MODE_LINE: return drawRead_li(vp, read, x, y); } } int selectRead_ch(ViewPanel *vp, Read *read, float x, float y, int id){ int i; for(i=0;iread.size;i++){ glLoadName(id+i); glRectf(x + i * vp->view->font_width, y + vp->view->font_height, x + (i+1) * vp->view->font_width, y); } return i; } int selectRead_sq(ViewPanel *vp, Read *read, float x, float y, int id){ int i; for(i=0;iread.size;i++){ glLoadName(id+i); glRectf(x + i * vp->view->base_width * vp->view->scale_x, y + vp->view->base_height * vp->view->scale_y, x + (i+1) * vp->view->base_width * vp->view->scale_x, y); } return i; } int selectRead_li(ViewPanel *vp, Read *read, float x, float y, int id){ glLoadName(id); glRectf(x , y, x + (read->read.size) * vp->view->line_width * vp->view->scale_x, y + vp->view->line_height * vp->view->scale_y); return 1; } int selectRead(ViewPanel *vp, Read *read, float x, float y, int id){ switch(vp->view->mode){ case VIEW_MODE_CHARACTER: return selectRead_ch(vp, read, x, y, id); case VIEW_MODE_SQUARE: return selectRead_sq(vp, read, x, y, id); case VIEW_MODE_LINE: return selectRead_li(vp, read, x, y, id); default: return 0; } } void default_paint(ViewPanel *vp){ int i, f; float x, y; int view_layer; float layer_offset; float font_width, ch_width, line_height; View *view; Read *read; RefSeq *refs; glutSetWindow(vp->win_id); resetMatrixs(vp); view = vp->view; glClearColor(0, 0, 0, 0); glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT); switch(view->mode){ case VIEW_MODE_CHARACTER: font_width = view->font_width; ch_width = view->ch_width; line_height = view->font_line_height; break; case VIEW_MODE_SQUARE: font_width = view->base_width * view->scale_x; ch_width = view->ch_width; line_height = view->base_line_height * view->scale_y; break; case VIEW_MODE_LINE: font_width = view->line_width * view->scale_x; ch_width = view->ch_width; line_height = view->line_height * view->scale_y; break; default: return; } layer_offset = view->font_line_height + line_height * 2; view_layer = (vp->height - layer_offset) / (line_height); refs = &(view->refs); drawRefSeq(vp, (float)0, (vp->height - line_height - view->font_line_height), ch_width); f = 0; if(vp->show_help){ drawToolTip(vp, vp->width/2 - 100, (vp->height - line_height), "Reference Sequences(maybe null)"); drawToolTip(vp, vp->width/2 + 100, (vp->height - line_height - line_height), "Consensus Sequences"); drawToolTip(vp, 160, vp->status_height + 5, "It is Status Bar"); f = 0; } for(i=0;icache->size;i++){ read = refs->cache->reads + refs->cache->offset + i; if(read_pos(read->read.pos) > refs->show_start + ch_width) break; if(read->y + view->layer_offset < 0) continue; if(read->y + view->layer_offset > view_layer) continue; x = (read_pos(read->read.pos) - refs->show_start) * font_width; y = vp->height - layer_offset - ((read->y + 1 + view->layer_offset)) * line_height; if(read_pos(read->read.pos) + read->read.size < refs->show_start) continue; drawRead(vp, read, x, y); if(!f && x > 0){ f = 1; if(vp->show_help){ drawToolTip(vp, x + 60, y + line_height, "This is a Read"); } } } glutSwapBuffers(); for(i=0;ichild_size;i++){ if(vp->childs[i*2] && vp->childs[i*2+1]){ ((CHILD_REPAINT)vp->childs[i*2+1])(vp->childs[i*2]); } } vp->paintStatusBar(vp); } void default_paintStatusBar(ViewPanel *vp){ char str[120]; glutSetWindow(vp->status_id); glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT); glColor3f(1.0, 1.0, 1.0); if(vp->view_number){ num2str(vp->view_number, str); sprintf(vp->msg_string, "Input:[%s_]", str); drawString(10, 5, vp->msg_string); } else if(vp->string_f && vp->string_n){ sprintf(vp->msg_string, "%s:[%s_]", vp->err_string, vp->view_string); drawString(10, 5, vp->msg_string); } else if(vp->err){ drawString(10, 5, vp->err_string); } else { sprintf(vp->msg_string, "Ref[%s] Position[%ld-%ld] Caching[%ld-%ld] Cacheing seqs[%ld-%ld]", vp->view->refs.cache->index->mm->ref_name[vp->view->refs.show_id], vp->view->refs.show_start + 1, vp->view->refs.show_start + (int64_t)vp->view->ch_width + 1, vp->view->refs.cache->start + 1, vp->view->refs.cache->end + 1, vp->view->refs.cns->start + 1, vp->view->refs.cns->end + 1 ); drawString(10, 5, vp->msg_string); } if(vp->show_help && !vp->err) vp->show_help = 0; glutSwapBuffers(); glutSetWindow(vp->win_id); } #define BUFSIZE 24 int default_pick(ViewPanel *vp, float x, float y, float size, void (*handle)(ViewPanel *vp, SelectObject *obj, int id)){ GLuint selectBuf[BUFSIZE]; GLint hits, viewport[4]; int i, j, id, count; int view_layer; float font_width, ch_width, line_height; float rect[4]; View *view; Read *read; RefSeq *refs; SelectObject *obj, *root; glutSetWindow(vp->win_id); view = vp->view; switch(view->mode){ case VIEW_MODE_CHARACTER: font_width = view->font_width; ch_width = view->ch_width; line_height = view->font_line_height; break; case VIEW_MODE_SQUARE: font_width = view->base_width * view->scale_x; ch_width = view->ch_width; line_height = view->base_line_height * view->scale_y; break; case VIEW_MODE_LINE: font_width = view->line_width * view->scale_x; ch_width = view->ch_width; line_height = view->line_height * view->scale_y; break; default: return 0; } root = NULL; glGetIntegerv(GL_VIEWPORT, viewport); glSelectBuffer(BUFSIZE, selectBuf); glRenderMode(GL_SELECT); glInitNames(); glPushName(0); resetPickMatrixs(vp, (GLdouble)x, (GLdouble)(viewport[3] - y), size, viewport); rect[0] = x - size/2; rect[1] = (float)(vp->height - y) - size/2; rect[2] = x + size/2; rect[3] = (float)(vp->height + vp->status_height - y) + size/2; id = 1; view_layer = vp->height / (line_height) - 2; if(view_layer < 1) goto END; refs = &(view->refs); obj = (SelectObject*)malloc(sizeof(SelectObject)); obj->id_start = id; obj->ptr = refs; obj->type = SELECT_TYPE_REFSEQ; obj->next = NULL; root = obj; count = selectRefSeq(vp, (float)0, (float)(vp->height - line_height - view->font_line_height), ch_width, id); id += count; obj->id_end = id; for(i=0;icache->size;i++){ read = refs->cache->reads + refs->cache->offset + i; if(read_pos(read->read.pos) > refs->show_start + ch_width) break; if(read->y + view->layer_offset < 0) continue; if(read->y + view->layer_offset > view_layer) continue; x = (read_pos(read->read.pos) - refs->show_start) * font_width; y = vp->height - (2 + (read->y + 1 + view->layer_offset)) * line_height - view->font_line_height; if(read_pos(read->read.pos) + read->read.size < refs->show_start) continue; if(x + read->read.size * font_width < rect[0] || x > rect[2]) continue; if(y + line_height < rect[1] || y > rect[3]) continue; count = selectRead(vp, read, x, y, id); if(count > 0){ obj->next = (SelectObject*)malloc(sizeof(SelectObject)); obj = obj->next; obj->id_start = id; id += count; obj->id_end = id; obj->ptr = read; obj->type = SELECT_TYPE_READ; obj->next = NULL; } } END: glFlush(); hits = glRenderMode(GL_RENDER); resetMatrixs(vp); if(hits > 0){ count = 0; for(i=0;iid_start <= id && obj->id_end > id){ if(handle) handle(vp, obj, id); break; } else { obj = obj->next; } } } if(root){ obj = root->next; free(root); while(obj != NULL){ root = obj; obj = root->next; free(root); } } return hits; } int print_map(void *obj, maplet *m1){ int j; maqmap_t *m; FILE *fpout; m = (maqmap_t*)obj; fpout = stdout; fprintf(fpout, "%s\t%s\t%d\t%c\t%d\t%u\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t", m1->name, m->ref_name[m1->seqid], (m1->pos>>1) + 1, (m1->pos&1)? '-' : '+', m1->dist, m1->flag, m1->map_qual, (signed char)m1->seq[MAX_READLEN-1], m1->alt_qual, m1->info1&0xf, m1->info2, m1->c[0], m1->c[1], m1->size); for (j = 0; j != m1->size; ++j) { if (m1->seq[j] == 0) fputc('n', fpout); else if ((m1->seq[j]&0x3f) < 27) fputc("acgt"[m1->seq[j]>>6&3], fpout); else fputc("ACGT"[m1->seq[j]>>6&3], fpout); } fputc('\t', fpout); for (j = 0; j != m1->size; ++j) fputc((m1->seq[j]&0x3f) + 33, fpout); fputc('\n', fpout); fflush(fpout); return 1; } void handle_left_pick(ViewPanel *vp, SelectObject *obj, int id){ RefSeq * refs; Read *read; switch(obj->type){ case SELECT_TYPE_NAVIGATION: ((Navigation*)(obj->ptr))->state = 1; return; case SELECT_TYPE_REFSEQ: refs = (RefSeq*)obj->ptr; id = id - obj->id_start; if(refs->tooltips[id] & 1){ refs->tooltips[id] &= ~0x01; notifyView(vp->view, VIEW_EVENT_MARK_REF, refs->show_start + id, 0); } else { refs->tooltips[id] |= 0x01; notifyView(vp->view, VIEW_EVENT_MARK_REF, refs->show_start + id, 1); } return; case SELECT_TYPE_READ: read = (Read*)obj->ptr; print_map(vp->view->refs.cache->index->mm, &(read->read)); id = id - obj->id_start; (read->flag & READ_SELECT)? (read->flag &= ~READ_SELECT) : (read->flag |= READ_SELECT); if(read->read.dist) notifyView(vp->view, VIEW_EVENT_SELECT_READ, read->read.dist>0? read_pos(read->read.pos):read_pos(read->read.pos)+read->read.size, read->read.dist); return; } } void handle_right_pick(ViewPanel *vp, SelectObject *obj, int id){ RefSeq * refs; Read *read; switch(obj->type){ case SELECT_TYPE_REFSEQ: refs = (RefSeq*)obj->ptr; id = id - obj->id_start; if(refs->tooltips[id] & 0x02){ refs->tooltips[id] &= ~(0x02); notifyView(vp->view, VIEW_EVENT_MARK_COL, refs->show_start + id, 0); } else { refs->tooltips[id] |= 0x02; notifyView(vp->view, VIEW_EVENT_MARK_COL, refs->show_start + id, 1); } return; case SELECT_TYPE_READ: read = (Read*)obj->ptr; id = id - obj->id_start; (read->flag & READ_SHOWTIP)? (read->flag &= ~READ_SHOWTIP) : (read->flag |= READ_SHOWTIP); return; } } void handle_mouse_over(ViewPanel *vp, SelectObject *obj, int id){ RefSeq * refs; Read *read; Navigation *nav; int q; char ch; switch(obj->type){ case SELECT_TYPE_NAVIGATION: nav = (Navigation*)(obj->ptr); sprintf(vp->err_string, "Drag navigation to move left/right"); return; case SELECT_TYPE_REFSEQ: refs = (RefSeq*)obj->ptr; id = id - obj->id_start; sprintf(vp->err_string, "Refs[%s] %ld", refs->cache->index->mm->ref_name[refs->show_id], refs->show_start + id + 1); return; case SELECT_TYPE_READ: read = (Read*)obj->ptr; id = id - obj->id_start; q = read->read.seq[id] & 0x3f; switch(vp->view->mode){ case VIEW_MODE_CHARACTER: case VIEW_MODE_SQUARE: if (read->read.seq[id] == 0) ch = 'n'; else if (q < 27) ch = acgt[read->read.seq[id]>>6&3]; else ch = ACGT[read->read.seq[id]>>6&3]; sprintf(vp->err_string, "Read: %ld|%c|%s[%d]|%c %d", read_pos(read->read.pos) + 1, read_strand(read->read.pos)? '-':'+', read->read.name, id + 1, ch, q); return; case VIEW_MODE_LINE: sprintf(vp->err_string, "Read: %ld|%c|%s", read_pos(read->read.pos) + 1, read_strand(read->read.pos)? '-':'+', read->read.name); return; } } } void default_mousePressed(ViewPanel *vp, int button, int x, int y){ glutSetWindow(vp->win_id); if(button == GLUT_RIGHT_BUTTON){ if(vp->pick && vp->handle_right_pick && vp->pick(vp, x, y, 1, vp->handle_right_pick)){ } else { vp->err = 1; sprintf(vp->err_string, "enter '?' to get help"); vp->show_help = 1; } glutSetCursor(GLUT_CURSOR_CROSSHAIR); glutPostRedisplay(); return; } if(button == GLUT_MIDDLE_BUTTON){ vp->view->state = 1; vp->view->last_x = x; vp->view->last_y = y; vp->view->old_x = vp->view->refs.show_start; vp->view->old_y = vp->view->layer_offset; return; } vp->view->selecting = 1; if(vp->pick && vp->handle_left_pick && vp->pick(vp, x, y, 1, vp->handle_left_pick)){ } else { vp->err = 1; sprintf(vp->err_string, "enter '?' to get help"); vp->show_help = 1; } glutSetCursor(GLUT_CURSOR_CROSSHAIR); glutPostRedisplay(); } void default_mouseReleased(ViewPanel *vp, int button, int x, int y){ if(vp->msg) return; glutSetWindow(vp->win_id); if(button == GLUT_RIGHT_BUTTON){ glutSetCursor(GLUT_CURSOR_LEFT_ARROW); return; } if(button == GLUT_MIDDLE_BUTTON){ vp->view->state = 0; vp->view->refs.show_start = vp->view->old_x; vp->view->layer_offset = vp->view->old_y; glutPostRedisplay(); return; } glutSetCursor(GLUT_CURSOR_LEFT_ARROW); vp->view->selecting = 0; if(vp->view->nav.state){ vp->view->nav.arrow_x = vp->view->nav.center_x; vp->view->nav.arrow_y = vp->view->nav.center_y; vp->view->nav.state = 0; } glutPostRedisplay(); } void default_mouseDragged(ViewPanel *vp, int x, int y){ if(vp->view == NULL) return; if(vp->msg) return; glutSetWindow(vp->win_id); if(vp->view->state){ vp->view->layer_offset = vp->view->old_y + (y - vp->view->last_y) / vp->view->font_line_height; vp->view->refs.show_start = vp->view->old_x - (x - vp->view->last_x) / vp->view->font_width; glutPostRedisplay(); } } void default_mouseMoved(ViewPanel *vp, int x, int y){ if(vp->msg) return; glutSetWindow(vp->win_id); vp->_x = x; vp->_y = y; if(vp->pick){ if(vp->handle_mouse_over && vp->pick(vp, x, y, 1, vp->handle_mouse_over)){ vp->err = 1; } else { vp->err = 0; } vp->paintStatusBar(vp); } glutPostRedisplay(); } static void select_ref(void *obj, int val){ ViewPanel *vp; vp = ((GList*)obj)->window.parent; if(val != vp->view->refs.show_id){ view_goto(vp->view, val, 1); vp->paint(vp); } } void default_mouseWheel(ViewPanel *vp, int wheel, int direction, int x, int y){ if(vp->view->mode == VIEW_MODE_CHARACTER) return; if(vp->msg) return; if(direction > 0){ vp->view->scale_x *= 1.2; vp->view->scale_y *= 1.2; } else if(vp->view->scale_x > 0.33){ vp->view->scale_x /= 1.2; vp->view->scale_y /= 1.2; } vp->view->ch_width = vp->width/(vp->view->base_width * vp->view->scale_x); glutPostRedisplay(); } void default_keyTyped(ViewPanel *vp, unsigned char key, int x, int y){ View *view; int cell_w, cell_h, n_disp; int i; int64_t t; int modifiers, multiple; glutSetWindow(vp->win_id); modifiers = glutGetModifiers(); if(modifiers & GLUT_ACTIVE_SHIFT){ multiple = 100; } else if(modifiers & GLUT_ACTIVE_CTRL){ multiple = 1000; } else { multiple = 1; } if(vp->msg){ if(key != 13 && key != 27) return; showSubWindows(); vp->msg = 0; glutPostRedisplay(); return; } if(!vp->string_f && key == '?'){ vp->msg = 1; hideSubWindows(); glutPostRedisplay(); return; } if(vp->view == NULL) return; if(vp->string_f){ if(key == 27){ vp->string_f = 0; vp->string_n = 0; vp->view_string[0] = '\0'; vp->err = 0; } else if(key == 13){ switch(vp->command){ case VP_CMD_OPEN: view = createView(vp->view_string, NULL, vp->width, vp->height, 0); if(view == NULL){ vp->err = 1; sprintf(vp->err_string, "Cannot open view %s", vp->view_string); } else { closeView(vp->view); vp->view = view; vp->err = 1; sprintf(vp->err_string, "set view to %s", vp->view_string); vp->view_string[0] = '\0'; vp->string_f = 0; vp->string_n = 0; goto REFRESH; } break; case VP_CMD_CMD: vp->err = 0; execute_cmd(vp, vp->view_string); break; } vp->view_string[0] = '\0'; vp->string_f = 0; vp->string_n = 0; } else if(key == '\b'){ if(!vp->string_n) return; vp->string_n --; vp->view_string[vp->string_n] = '\0'; } else { vp->view_string[vp->string_n++] = key; vp->view_string[vp->string_n] = '\0'; } glutPostRedisplay(); return; } else if(key >= '0' && key <= '9'){ if(key == '0' && vp->view_number == 0){ vp->view->scale_x = 1; vp->view->scale_y = 1; if(vp->view->mode != VIEW_MODE_CHARACTER) vp->view->ch_width = vp->width / vp->view->base_width; } else { vp->view_number = vp->view_number * 10 + key - '0'; } glutPostRedisplay(); return; } else if(key == 13){ if(vp->view_number){ vp->view->rolling = 0; view_goto(vp->view, vp->view->refs.show_id, vp->view_number - 1); vp->err = 1; sprintf(vp->err_string, "goto: %ld", vp->view_number); vp->view_number = 0; } else { vp->err = 0; if(vp->view->rolling) vp->view->rolling = 0; else { vp->view->rolling = vp->view->step; if(vp->timer) vp->timer(vp, glutGetWindow()); } } glutPostRedisplay(); return; } else if(key == 2){ if(vp->view_number){ vp->view_number /= 10; glutPostRedisplay(); return; } if(vp->view->rolling) vp->view->rolling = 0; else { vp->view->rolling = -vp->view->step; if(vp->timer) vp->timer(vp, glutGetWindow()); } return; } // for(i=0;iview->refs.tooltips[i] &= ~(0x02); if(vp->view_number > 0){ if(key == 27){ vp->view_number = 0; glutPostRedisplay(); return; } else { vp->view->step = vp->view_number; } } vp->view_number = 0; switch(key){ case 'f': glutSetWindow(vp->parent_win_id); glutFullScreen(); glutSetWindow(vp->win_id); break; case 'q': if (vp->global_flag & GF_HIDE_MAPQ) { vp->global_flag &= ~GF_HIDE_MAPQ; vp->err = 1; sprintf(vp->err_string, "hide mapping qualities"); } else { vp->global_flag |= GF_HIDE_MAPQ; vp->err = 1; sprintf(vp->err_string, "show mapping qualities"); } glutPostRedisplay(); break; case 'e': vp->global_flag &= ~GF_HIDE_MAPQ; if (vp->global_flag & GF_IS_SINGLEQ) { vp->global_flag &= ~GF_IS_SINGLEQ; vp->err = 1; sprintf(vp->err_string, "visualize paired-end mapping qualities"); } else { vp->global_flag |= GF_IS_SINGLEQ; vp->err = 1; sprintf(vp->err_string, "visualize single-end mapping qualities"); } glutPostRedisplay(); break; case 27: exit(0); case 'o': vp->command = VP_CMD_OPEN; vp->string_f = 1; vp->string_n = 0; vp->view_string[0] = '\0'; vp->err = 1; sprintf(vp->err_string, "try open new view, please input filename"); glutPostRedisplay(); break; case 'c': vp->command = VP_CMD_CMD; vp->string_f = 1; vp->string_n = 0; vp->view_string[0] = '\0'; vp->err = 1; sprintf(vp->err_string, "input command"); glutPostRedisplay(); break; case '=': case '+': if(modifiers & GLUT_ACTIVE_CTRL){ if(vp->view->map_file){ addViewPanel(NULL, vp->view->map_file, vp->view->cns_file, vp->view->style); glutSetWindow(vp->win_id); } break; } if(vp->view->mode == VIEW_MODE_CHARACTER){ vp->err = 1; sprintf(vp->err_string, "Cannot zoom in in character mode"); } else { vp->view->scale_x *= 1.2; vp->view->scale_y *= 1.2; switch(vp->view->mode){ case VIEW_MODE_SQUARE: vp->view->ch_width = vp->width/(vp->view->base_width * vp->view->scale_x); break; case VIEW_MODE_LINE: vp->view->ch_width = vp->width/(vp->view->line_width * vp->view->scale_x); break; } } view_goto(vp->view, vp->view->refs.show_id, vp->view->refs.show_start); glutPostRedisplay(); break; case 31: removeViewPanel(vp); break; /* for Mac OS X */ case '-': if(modifiers & GLUT_ACTIVE_CTRL){ removeViewPanel(vp); break; } if(vp->view->mode == VIEW_MODE_CHARACTER){ vp->err = 1; sprintf(vp->err_string, "Cannot zoom out in character mode"); } else if(vp->view->scale_x > 0.33){ vp->view->scale_x /= 1.2; vp->view->scale_y /= 1.2; switch(vp->view->mode){ case VIEW_MODE_SQUARE: vp->view->ch_width = vp->width/(vp->view->base_width * vp->view->scale_x); break; case VIEW_MODE_LINE: vp->view->ch_width = vp->width/(vp->view->line_width * vp->view->scale_x); break; } } view_goto(vp->view, vp->view->refs.show_id, vp->view->refs.show_start); glutPostRedisplay(); break; case 'r': if(vp->ref_menu){ freeGList(vp->ref_menu); vp->ref_menu = NULL; } else { cell_w = 100; cell_h = 20; n_disp = vp->view->refs.cache->index->mm->n_ref; if(n_disp * cell_h > vp->height - vp->status_height){ n_disp = (vp->height - vp->status_height) / cell_h; } vp->ref_menu = createGList(0, vp, 5, vp->height - (n_disp * cell_h), cell_w, cell_h, n_disp); for(i=0;iview->refs.cache->index->mm->n_ref;i++){ GList_addOption(vp->ref_menu, vp->view->refs.cache->index->mm->ref_name[i]); } vp->ref_menu->valueChanged = select_ref; } glutPostRedisplay(); break; vp->err = 1; sprintf(vp->err_string, "Refresh"); REFRESH: vp->view->refs.cache->offset = 0; vp->view->refs.cache->size = 0; vp->view->refs.cache->start = 0; vp->view->refs.cache->end = 0; vp->view->refs.cns->ref_id = -1; t = vp->view->refs.show_start; vp->view->refs.show_start = t + 1; view_goto(vp->view, vp->view->refs.show_id, t); glutPostRedisplay(); case 8: case 'H': case 'h': vp->err = 0; if (key == 8) multiple = 1000; else if (key == 'H') multiple = 100; if(vp->view->refs.show_start > 0){ view_goto(vp->view, vp->view->refs.show_id, vp->view->refs.show_start - vp->view->step * multiple); glutPostRedisplay(); } break; case 12: case 'L': case 'l': vp->err = 0; if (key == 12) multiple = 1000; else if (key == 'L') multiple = 100; if(vp->view->refs.show_start < vp->view->refs.cache->length){ view_goto(vp->view, vp->view->refs.show_id, vp->view->refs.show_start + vp->view->step * multiple); glutPostRedisplay(); } break; case 'k': vp->err = 1; vp->view->layer_offset += multiple; if(vp->view->layer_offset > 2) vp->view->layer_offset = 2; sprintf(vp->err_string, "move view offset to %d line", vp->view->layer_offset); glutPostRedisplay(); break; case 'j': vp->err = 1; vp->view->layer_offset -= multiple; sprintf(vp->err_string, "move view offset to %d line", vp->view->layer_offset); glutPostRedisplay(); break; case ' ': vp->err = 0; if(vp->view->refs.show_start < vp->view->refs.cache->length){ view_goto(vp->view, vp->view->refs.show_id, vp->view->refs.show_start + vp->view->ch_width); glutPostRedisplay(); } break; case 'u': vp->err = 0; if(vp->view->refs.show_start > 0){ view_goto(vp->view, vp->view->refs.show_id, vp->view->refs.show_start - vp->view->ch_width); glutPostRedisplay(); } break; case 'g': view_goto(vp->view, vp->view->refs.show_id, 0); vp->err = 1; sprintf(vp->err_string, "goto begin"); glutPostRedisplay(); break; case 'G': view_goto(vp->view, vp->view->refs.show_id, vp->view->refs.cache->length); vp->err = 1; sprintf(vp->err_string, "goto end"); glutPostRedisplay(); break; case '>': vp->err = 0; t = vp->view->refs.show_start; while(1){ for(i=0;iview->refs.cache->size;i++){ if(read_pos(vp->view->refs.cache->reads[vp->view->refs.cache->offset + i].read.pos) > t){ view_goto(vp->view, vp->view->refs.show_id, read_pos(vp->view->refs.cache->reads[vp->view->refs.cache->offset + i].read.pos)); glutPostRedisplay(); return; } } if(vp->view->refs.show_start + vp->view->ch_width < vp->view->refs.cache->length && view_goto(vp->view, vp->view->refs.show_id, vp->view->refs.cache->end + 1) && vp->view->refs.cache->size){ } else { vp->err = 1; sprintf(vp->err_string, "No more read available"); glutPostRedisplay(); return; } } break; case '<': vp->err = 0; t = vp->view->refs.show_start; while(1){ for(i=vp->view->refs.cache->size-1;i>=0;i--){ if(read_pos(vp->view->refs.cache->reads[vp->view->refs.cache->offset + i].read.pos) < t){ view_goto(vp->view, vp->view->refs.show_id, read_pos(vp->view->refs.cache->reads[vp->view->refs.cache->offset + i].read.pos)); glutPostRedisplay(); return; } } if(vp->view->refs.show_start > 0 && view_goto(vp->view, vp->view->refs.show_id, vp->view->refs.cache->start - vp->view->ch_width)){ } else { vp->err = 1; sprintf(vp->err_string, "No more read available"); glutPostRedisplay(); return; } } break; case 'n': vp->err = 1; if(vp->view->refs.cache->index->mm->n_ref > 1){ i = (vp->view->refs.show_id + 1) % vp->view->refs.cache->index->mm->n_ref; view_goto(vp->view, i, 0); sprintf(vp->err_string, "Switch to ref seq [%s]", vp->view->refs.cache->index->mm->ref_name[i]); } else { sprintf(vp->err_string, "Cannot switch: only one ref seq [%s]", vp->view->refs.cache->index->mm->ref_name[vp->view->refs.show_id]); } glutPostRedisplay(); break; case 'p': vp->err = 1; if(vp->view->refs.cache->index->mm->n_ref > 1){ i = (vp->view->refs.show_id - 1 + vp->view->refs.cache->index->mm->n_ref) % vp->view->refs.cache->index->mm->n_ref; view_goto(vp->view, i, 0); sprintf(vp->err_string, "Switch to ref seq [%s]", vp->view->refs.cache->index->mm->ref_name[i]); // if(view_goto(vp->view, i, 0)){ // } else { // sprintf(err_string, "Cannot switch to ref seq [%s]", vp->view->refs.index->mm->ref_name[i]); // } } else { sprintf(vp->err_string, "Cannot switch: only one ref seq [%s]", vp->view->refs.cache->index->mm->ref_name[vp->view->refs.show_id]); } glutPostRedisplay(); break; default: vp->err = 1; sprintf(vp->err_string, "unknown key binding: %d[%c]", key, key); glutPostRedisplay(); } } void default_specialKey(ViewPanel *vp, int key, int x, int y){ if(!vp->view) return; glutSetWindow(vp->win_id); switch(key){ case GLUT_KEY_F1: vp->view->mode = VIEW_MODE_CHARACTER; vp->view->ch_width = vp->width/vp->view->font_width; view_goto(vp->view, vp->view->refs.show_id, vp->view->refs.show_start); glutPostRedisplay(); return; case GLUT_KEY_F2: vp->view->mode = VIEW_MODE_SQUARE; vp->view->ch_width = vp->width/(vp->view->base_width * vp->view->scale_x); view_goto(vp->view, vp->view->refs.show_id, vp->view->refs.show_start); glutPostRedisplay(); return; case GLUT_KEY_F3: vp->view->mode = VIEW_MODE_LINE; vp->view->ch_width = vp->width/(vp->view->line_width * vp->view->scale_x); view_goto(vp->view, vp->view->refs.show_id, vp->view->refs.show_start); glutPostRedisplay(); return; case GLUT_KEY_LEFT: return default_keyTyped(vp, 'h', x, y); case GLUT_KEY_RIGHT: return default_keyTyped(vp, 'l', x, y); case GLUT_KEY_UP: return default_keyTyped(vp, 'k', x, y); case GLUT_KEY_DOWN: return default_keyTyped(vp, 'j', x, y); case GLUT_KEY_PAGE_UP: return default_keyTyped(vp, 'u', x, y); case GLUT_KEY_PAGE_DOWN: return default_keyTyped(vp, ' ', x, y); case GLUT_KEY_HOME: return default_keyTyped(vp, 'g', x, y); case GLUT_KEY_END: return default_keyTyped(vp, 'G', x, y); } } ViewPanel* createViewPanel(int pw_id, View *view, float off_x, float off_y, float width, float height){ int win_id; int status_height; ViewPanel *vp; status_height = 20; win_id = glutCreateSubWindow(pw_id, off_x, off_y, width, height); glClearColor(0, 0, 0, 0); glEnable(GL_DEPTH_TEST); vp = (ViewPanel*)malloc(sizeof(ViewPanel)); vp->parent_win_id = pw_id; vp->win_id = win_id; vp->status_id = glutCreateSubWindow(win_id, 0, height - status_height, width, status_height); glClearColor(0.2, 0.2, 0.2, 0); glEnable(GL_DEPTH_TEST); glutDisplayFunc(display_bar); glutReshapeFunc(bar_resize); vp->off_x = off_x; vp->off_y = off_y; vp->width = width; vp->height = height - status_height; vp->status_width = width; vp->status_height = status_height; vp->view = view; vp->view_number = 0; vp->string_f = 0; vp->string_n = 0; vp->err = 0; vp->msg = 0; vp->show_help = 0; vp->interval = 180; vp->command = 0; vp->_x = 0; vp->_x1 = 0; vp->_x2 = 0; vp->_y = 0; vp->_y1 = 0; vp->_y2 = 0; vp->global_flag = 0; vp->resize = (void*)default_resize; vp->paint = (void*)default_paint; vp->pick = (void*)default_pick; vp->paintStatusBar = (void*)default_paintStatusBar; vp->handle_left_pick = (void*)handle_left_pick; vp->handle_right_pick = (void*)handle_right_pick; vp->handle_mouse_over = (void*)handle_mouse_over; vp->mousePressed = (void*)default_mousePressed; vp->mouseReleased = (void*)default_mouseReleased; vp->mouseDragged = (void*)default_mouseDragged; vp->mouseMoved = (void*)default_mouseMoved; vp->mouseWheel = (void*)default_mouseWheel; vp->keyTyped = (void*)default_keyTyped; vp->specialKey = (void*)default_specialKey; vp->timer = (void*)default_timer; vp->synchronize = (void*)synchronize; vp->owner = NULL; vp->childs = NULL; vp->child_size = 0; vp->child_capacity = 0; vp->ref_menu = NULL; register_window(vp->win_id, vp, WINDOW_TYPE_VIEWPANEL); glutSetWindow(vp->win_id); glutReshapeFunc(reshape); glutDisplayFunc(display); glutMouseFunc(mouse); glutMotionFunc(motion); glutPassiveMotionFunc(mouse_move); glutKeyboardFunc(keyboard); glutSpecialFunc(special_key); #ifdef HAVE_FREEGLUT glutMouseWheelFunc(mouse_wheel); #endif vp->resize(vp, width, height); view_resize(view, vp->width, vp->height); return vp; } void closeViewPanel(ViewPanel *vp){ int i; closeView(vp->view); glutDestroyWindow(vp->status_id); glutDestroyWindow(vp->win_id); if(vps_size >= vp->win_id && vps[vp->win_id-1] == vp){ vps[vp->win_id-1] = NULL; } for(i=0;iview, vp); } free(vp); } void closeViewPanels(){ int i; for(i=0;i #endif /* =========================================================================== * Constants */ #define MAX_BL_BITS 7 /* Bit length codes must not exceed MAX_BL_BITS bits */ #define END_BLOCK 256 /* end of block literal code */ #define REP_3_6 16 /* repeat previous bit length 3-6 times (2 bits of repeat count) */ #define REPZ_3_10 17 /* repeat a zero length 3-10 times (3 bits of repeat count) */ #define REPZ_11_138 18 /* repeat a zero length 11-138 times (7 bits of repeat count) */ local const int extra_lbits[LENGTH_CODES] /* extra bits for each length code */ = {0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0}; local const int extra_dbits[D_CODES] /* extra bits for each distance code */ = {0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13}; local const int extra_blbits[BL_CODES]/* extra bits for each bit length code */ = {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,3,7}; local const uch bl_order[BL_CODES] = {16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15}; /* The lengths of the bit length codes are sent in order of decreasing * probability, to avoid transmitting the lengths for unused bit length codes. */ #define Buf_size (8 * 2*sizeof(char)) /* Number of bits used within bi_buf. (bi_buf might be implemented on * more than 16 bits on some systems.) */ /* =========================================================================== * Local data. These are initialized only once. */ #define DIST_CODE_LEN 512 /* see definition of array dist_code below */ #if defined(GEN_TREES_H) || !defined(STDC) /* non ANSI compilers may not accept trees.h */ local ct_data static_ltree[L_CODES+2]; /* The static literal tree. Since the bit lengths are imposed, there is no * need for the L_CODES extra codes used during heap construction. However * The codes 286 and 287 are needed to build a canonical tree (see _tr_init * below). */ local ct_data static_dtree[D_CODES]; /* The static distance tree. (Actually a trivial tree since all codes use * 5 bits.) */ uch _dist_code[DIST_CODE_LEN]; /* Distance codes. The first 256 values correspond to the distances * 3 .. 258, the last 256 values correspond to the top 8 bits of * the 15 bit distances. */ uch _length_code[MAX_MATCH-MIN_MATCH+1]; /* length code for each normalized match length (0 == MIN_MATCH) */ local int base_length[LENGTH_CODES]; /* First normalized length for each code (0 = MIN_MATCH) */ local int base_dist[D_CODES]; /* First normalized distance for each code (0 = distance of 1) */ #else # include "trees.h" #endif /* GEN_TREES_H */ struct static_tree_desc_s { const ct_data *static_tree; /* static tree or NULL */ const intf *extra_bits; /* extra bits for each code or NULL */ int extra_base; /* base index for extra_bits */ int elems; /* max number of elements in the tree */ int max_length; /* max bit length for the codes */ }; local static_tree_desc static_l_desc = {static_ltree, extra_lbits, LITERALS+1, L_CODES, MAX_BITS}; local static_tree_desc static_d_desc = {static_dtree, extra_dbits, 0, D_CODES, MAX_BITS}; local static_tree_desc static_bl_desc = {(const ct_data *)0, extra_blbits, 0, BL_CODES, MAX_BL_BITS}; /* =========================================================================== * Local (static) routines in this file. */ local void tr_static_init OF((void)); local void init_block OF((deflate_state *s)); local void pqdownheap OF((deflate_state *s, ct_data *tree, int k)); local void gen_bitlen OF((deflate_state *s, tree_desc *desc)); local void gen_codes OF((ct_data *tree, int max_code, ushf *bl_count)); local void build_tree OF((deflate_state *s, tree_desc *desc)); local void scan_tree OF((deflate_state *s, ct_data *tree, int max_code)); local void send_tree OF((deflate_state *s, ct_data *tree, int max_code)); local int build_bl_tree OF((deflate_state *s)); local void send_all_trees OF((deflate_state *s, int lcodes, int dcodes, int blcodes)); local void compress_block OF((deflate_state *s, ct_data *ltree, ct_data *dtree)); local void set_data_type OF((deflate_state *s)); local unsigned bi_reverse OF((unsigned value, int length)); local void bi_windup OF((deflate_state *s)); local void bi_flush OF((deflate_state *s)); local void copy_block OF((deflate_state *s, charf *buf, unsigned len, int header)); #ifdef GEN_TREES_H local void gen_trees_header OF((void)); #endif #ifndef DEBUG # define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len) /* Send a code of the given tree. c and tree must not have side effects */ #else /* DEBUG */ # define send_code(s, c, tree) \ { if (z_verbose>2) fprintf(stderr,"\ncd %3d ",(c)); \ send_bits(s, tree[c].Code, tree[c].Len); } #endif /* =========================================================================== * Output a short LSB first on the stream. * IN assertion: there is enough room in pendingBuf. */ #define put_short(s, w) { \ put_byte(s, (uch)((w) & 0xff)); \ put_byte(s, (uch)((ush)(w) >> 8)); \ } /* =========================================================================== * Send a value on a given number of bits. * IN assertion: length <= 16 and value fits in length bits. */ #ifdef DEBUG local void send_bits OF((deflate_state *s, int value, int length)); local void send_bits(s, value, length) deflate_state *s; int value; /* value to send */ int length; /* number of bits */ { Tracevv((stderr," l %2d v %4x ", length, value)); Assert(length > 0 && length <= 15, "invalid length"); s->bits_sent += (ulg)length; /* If not enough room in bi_buf, use (valid) bits from bi_buf and * (16 - bi_valid) bits from value, leaving (width - (16-bi_valid)) * unused bits in value. */ if (s->bi_valid > (int)Buf_size - length) { s->bi_buf |= (value << s->bi_valid); put_short(s, s->bi_buf); s->bi_buf = (ush)value >> (Buf_size - s->bi_valid); s->bi_valid += length - Buf_size; } else { s->bi_buf |= value << s->bi_valid; s->bi_valid += length; } } #else /* !DEBUG */ #define send_bits(s, value, length) \ { int len = length;\ if (s->bi_valid > (int)Buf_size - len) {\ int val = value;\ s->bi_buf |= (val << s->bi_valid);\ put_short(s, s->bi_buf);\ s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\ s->bi_valid += len - Buf_size;\ } else {\ s->bi_buf |= (value) << s->bi_valid;\ s->bi_valid += len;\ }\ } #endif /* DEBUG */ /* the arguments must not have side effects */ /* =========================================================================== * Initialize the various 'constant' tables. */ local void tr_static_init() { #if defined(GEN_TREES_H) || !defined(STDC) static int static_init_done = 0; int n; /* iterates over tree elements */ int bits; /* bit counter */ int length; /* length value */ int code; /* code value */ int dist; /* distance index */ ush bl_count[MAX_BITS+1]; /* number of codes at each bit length for an optimal tree */ if (static_init_done) return; /* For some embedded targets, global variables are not initialized: */ static_l_desc.static_tree = static_ltree; static_l_desc.extra_bits = extra_lbits; static_d_desc.static_tree = static_dtree; static_d_desc.extra_bits = extra_dbits; static_bl_desc.extra_bits = extra_blbits; /* Initialize the mapping length (0..255) -> length code (0..28) */ length = 0; for (code = 0; code < LENGTH_CODES-1; code++) { base_length[code] = length; for (n = 0; n < (1< dist code (0..29) */ dist = 0; for (code = 0 ; code < 16; code++) { base_dist[code] = dist; for (n = 0; n < (1<>= 7; /* from now on, all distances are divided by 128 */ for ( ; code < D_CODES; code++) { base_dist[code] = dist << 7; for (n = 0; n < (1<<(extra_dbits[code]-7)); n++) { _dist_code[256 + dist++] = (uch)code; } } Assert (dist == 256, "tr_static_init: 256+dist != 512"); /* Construct the codes of the static literal tree */ for (bits = 0; bits <= MAX_BITS; bits++) bl_count[bits] = 0; n = 0; while (n <= 143) static_ltree[n++].Len = 8, bl_count[8]++; while (n <= 255) static_ltree[n++].Len = 9, bl_count[9]++; while (n <= 279) static_ltree[n++].Len = 7, bl_count[7]++; while (n <= 287) static_ltree[n++].Len = 8, bl_count[8]++; /* Codes 286 and 287 do not exist, but we must include them in the * tree construction to get a canonical Huffman tree (longest code * all ones) */ gen_codes((ct_data *)static_ltree, L_CODES+1, bl_count); /* The static distance tree is trivial: */ for (n = 0; n < D_CODES; n++) { static_dtree[n].Len = 5; static_dtree[n].Code = bi_reverse((unsigned)n, 5); } static_init_done = 1; # ifdef GEN_TREES_H gen_trees_header(); # endif #endif /* defined(GEN_TREES_H) || !defined(STDC) */ } /* =========================================================================== * Genererate the file trees.h describing the static trees. */ #ifdef GEN_TREES_H # ifndef DEBUG # include # endif # define SEPARATOR(i, last, width) \ ((i) == (last)? "\n};\n\n" : \ ((i) % (width) == (width)-1 ? ",\n" : ", ")) void gen_trees_header() { FILE *header = fopen("trees.h", "w"); int i; Assert (header != NULL, "Can't open trees.h"); fprintf(header, "/* header created automatically with -DGEN_TREES_H */\n\n"); fprintf(header, "local const ct_data static_ltree[L_CODES+2] = {\n"); for (i = 0; i < L_CODES+2; i++) { fprintf(header, "{{%3u},{%3u}}%s", static_ltree[i].Code, static_ltree[i].Len, SEPARATOR(i, L_CODES+1, 5)); } fprintf(header, "local const ct_data static_dtree[D_CODES] = {\n"); for (i = 0; i < D_CODES; i++) { fprintf(header, "{{%2u},{%2u}}%s", static_dtree[i].Code, static_dtree[i].Len, SEPARATOR(i, D_CODES-1, 5)); } fprintf(header, "const uch _dist_code[DIST_CODE_LEN] = {\n"); for (i = 0; i < DIST_CODE_LEN; i++) { fprintf(header, "%2u%s", _dist_code[i], SEPARATOR(i, DIST_CODE_LEN-1, 20)); } fprintf(header, "const uch _length_code[MAX_MATCH-MIN_MATCH+1]= {\n"); for (i = 0; i < MAX_MATCH-MIN_MATCH+1; i++) { fprintf(header, "%2u%s", _length_code[i], SEPARATOR(i, MAX_MATCH-MIN_MATCH, 20)); } fprintf(header, "local const int base_length[LENGTH_CODES] = {\n"); for (i = 0; i < LENGTH_CODES; i++) { fprintf(header, "%1u%s", base_length[i], SEPARATOR(i, LENGTH_CODES-1, 20)); } fprintf(header, "local const int base_dist[D_CODES] = {\n"); for (i = 0; i < D_CODES; i++) { fprintf(header, "%5u%s", base_dist[i], SEPARATOR(i, D_CODES-1, 10)); } fclose(header); } #endif /* GEN_TREES_H */ /* =========================================================================== * Initialize the tree data structures for a new zlib stream. */ void _tr_init(s) deflate_state *s; { tr_static_init(); s->l_desc.dyn_tree = s->dyn_ltree; s->l_desc.stat_desc = &static_l_desc; s->d_desc.dyn_tree = s->dyn_dtree; s->d_desc.stat_desc = &static_d_desc; s->bl_desc.dyn_tree = s->bl_tree; s->bl_desc.stat_desc = &static_bl_desc; s->bi_buf = 0; s->bi_valid = 0; s->last_eob_len = 8; /* enough lookahead for inflate */ #ifdef DEBUG s->compressed_len = 0L; s->bits_sent = 0L; #endif /* Initialize the first block of the first file: */ init_block(s); } /* =========================================================================== * Initialize a new block. */ local void init_block(s) deflate_state *s; { int n; /* iterates over tree elements */ /* Initialize the trees. */ for (n = 0; n < L_CODES; n++) s->dyn_ltree[n].Freq = 0; for (n = 0; n < D_CODES; n++) s->dyn_dtree[n].Freq = 0; for (n = 0; n < BL_CODES; n++) s->bl_tree[n].Freq = 0; s->dyn_ltree[END_BLOCK].Freq = 1; s->opt_len = s->static_len = 0L; s->last_lit = s->matches = 0; } #define SMALLEST 1 /* Index within the heap array of least frequent node in the Huffman tree */ /* =========================================================================== * Remove the smallest element from the heap and recreate the heap with * one less element. Updates heap and heap_len. */ #define pqremove(s, tree, top) \ {\ top = s->heap[SMALLEST]; \ s->heap[SMALLEST] = s->heap[s->heap_len--]; \ pqdownheap(s, tree, SMALLEST); \ } /* =========================================================================== * Compares to subtrees, using the tree depth as tie breaker when * the subtrees have equal frequency. This minimizes the worst case length. */ #define smaller(tree, n, m, depth) \ (tree[n].Freq < tree[m].Freq || \ (tree[n].Freq == tree[m].Freq && depth[n] <= depth[m])) /* =========================================================================== * Restore the heap property by moving down the tree starting at node k, * exchanging a node with the smallest of its two sons if necessary, stopping * when the heap property is re-established (each father smaller than its * two sons). */ local void pqdownheap(s, tree, k) deflate_state *s; ct_data *tree; /* the tree to restore */ int k; /* node to move down */ { int v = s->heap[k]; int j = k << 1; /* left son of k */ while (j <= s->heap_len) { /* Set j to the smallest of the two sons: */ if (j < s->heap_len && smaller(tree, s->heap[j+1], s->heap[j], s->depth)) { j++; } /* Exit if v is smaller than both sons */ if (smaller(tree, v, s->heap[j], s->depth)) break; /* Exchange v with the smallest son */ s->heap[k] = s->heap[j]; k = j; /* And continue down the tree, setting j to the left son of k */ j <<= 1; } s->heap[k] = v; } /* =========================================================================== * Compute the optimal bit lengths for a tree and update the total bit length * for the current block. * IN assertion: the fields freq and dad are set, heap[heap_max] and * above are the tree nodes sorted by increasing frequency. * OUT assertions: the field len is set to the optimal bit length, the * array bl_count contains the frequencies for each bit length. * The length opt_len is updated; static_len is also updated if stree is * not null. */ local void gen_bitlen(s, desc) deflate_state *s; tree_desc *desc; /* the tree descriptor */ { ct_data *tree = desc->dyn_tree; int max_code = desc->max_code; const ct_data *stree = desc->stat_desc->static_tree; const intf *extra = desc->stat_desc->extra_bits; int base = desc->stat_desc->extra_base; int max_length = desc->stat_desc->max_length; int h; /* heap index */ int n, m; /* iterate over the tree elements */ int bits; /* bit length */ int xbits; /* extra bits */ ush f; /* frequency */ int overflow = 0; /* number of elements with bit length too large */ for (bits = 0; bits <= MAX_BITS; bits++) s->bl_count[bits] = 0; /* In a first pass, compute the optimal bit lengths (which may * overflow in the case of the bit length tree). */ tree[s->heap[s->heap_max]].Len = 0; /* root of the heap */ for (h = s->heap_max+1; h < HEAP_SIZE; h++) { n = s->heap[h]; bits = tree[tree[n].Dad].Len + 1; if (bits > max_length) bits = max_length, overflow++; tree[n].Len = (ush)bits; /* We overwrite tree[n].Dad which is no longer needed */ if (n > max_code) continue; /* not a leaf node */ s->bl_count[bits]++; xbits = 0; if (n >= base) xbits = extra[n-base]; f = tree[n].Freq; s->opt_len += (ulg)f * (bits + xbits); if (stree) s->static_len += (ulg)f * (stree[n].Len + xbits); } if (overflow == 0) return; Trace((stderr,"\nbit length overflow\n")); /* This happens for example on obj2 and pic of the Calgary corpus */ /* Find the first bit length which could increase: */ do { bits = max_length-1; while (s->bl_count[bits] == 0) bits--; s->bl_count[bits]--; /* move one leaf down the tree */ s->bl_count[bits+1] += 2; /* move one overflow item as its brother */ s->bl_count[max_length]--; /* The brother of the overflow item also moves one step up, * but this does not affect bl_count[max_length] */ overflow -= 2; } while (overflow > 0); /* Now recompute all bit lengths, scanning in increasing frequency. * h is still equal to HEAP_SIZE. (It is simpler to reconstruct all * lengths instead of fixing only the wrong ones. This idea is taken * from 'ar' written by Haruhiko Okumura.) */ for (bits = max_length; bits != 0; bits--) { n = s->bl_count[bits]; while (n != 0) { m = s->heap[--h]; if (m > max_code) continue; if ((unsigned) tree[m].Len != (unsigned) bits) { Trace((stderr,"code %d bits %d->%d\n", m, tree[m].Len, bits)); s->opt_len += ((long)bits - (long)tree[m].Len) *(long)tree[m].Freq; tree[m].Len = (ush)bits; } n--; } } } /* =========================================================================== * Generate the codes for a given tree and bit counts (which need not be * optimal). * IN assertion: the array bl_count contains the bit length statistics for * the given tree and the field len is set for all tree elements. * OUT assertion: the field code is set for all tree elements of non * zero code length. */ local void gen_codes (tree, max_code, bl_count) ct_data *tree; /* the tree to decorate */ int max_code; /* largest code with non zero frequency */ ushf *bl_count; /* number of codes at each bit length */ { ush next_code[MAX_BITS+1]; /* next code value for each bit length */ ush code = 0; /* running code value */ int bits; /* bit index */ int n; /* code index */ /* The distribution counts are first used to generate the code values * without bit reversal. */ for (bits = 1; bits <= MAX_BITS; bits++) { next_code[bits] = code = (code + bl_count[bits-1]) << 1; } /* Check that the bit counts in bl_count are consistent. The last code * must be all ones. */ Assert (code + bl_count[MAX_BITS]-1 == (1<dyn_tree; const ct_data *stree = desc->stat_desc->static_tree; int elems = desc->stat_desc->elems; int n, m; /* iterate over heap elements */ int max_code = -1; /* largest code with non zero frequency */ int node; /* new node being created */ /* Construct the initial heap, with least frequent element in * heap[SMALLEST]. The sons of heap[n] are heap[2*n] and heap[2*n+1]. * heap[0] is not used. */ s->heap_len = 0, s->heap_max = HEAP_SIZE; for (n = 0; n < elems; n++) { if (tree[n].Freq != 0) { s->heap[++(s->heap_len)] = max_code = n; s->depth[n] = 0; } else { tree[n].Len = 0; } } /* The pkzip format requires that at least one distance code exists, * and that at least one bit should be sent even if there is only one * possible code. So to avoid special checks later on we force at least * two codes of non zero frequency. */ while (s->heap_len < 2) { node = s->heap[++(s->heap_len)] = (max_code < 2 ? ++max_code : 0); tree[node].Freq = 1; s->depth[node] = 0; s->opt_len--; if (stree) s->static_len -= stree[node].Len; /* node is 0 or 1 so it does not have extra bits */ } desc->max_code = max_code; /* The elements heap[heap_len/2+1 .. heap_len] are leaves of the tree, * establish sub-heaps of increasing lengths: */ for (n = s->heap_len/2; n >= 1; n--) pqdownheap(s, tree, n); /* Construct the Huffman tree by repeatedly combining the least two * frequent nodes. */ node = elems; /* next internal node of the tree */ do { pqremove(s, tree, n); /* n = node of least frequency */ m = s->heap[SMALLEST]; /* m = node of next least frequency */ s->heap[--(s->heap_max)] = n; /* keep the nodes sorted by frequency */ s->heap[--(s->heap_max)] = m; /* Create a new node father of n and m */ tree[node].Freq = tree[n].Freq + tree[m].Freq; s->depth[node] = (uch)((s->depth[n] >= s->depth[m] ? s->depth[n] : s->depth[m]) + 1); tree[n].Dad = tree[m].Dad = (ush)node; #ifdef DUMP_BL_TREE if (tree == s->bl_tree) { fprintf(stderr,"\nnode %d(%d), sons %d(%d) %d(%d)", node, tree[node].Freq, n, tree[n].Freq, m, tree[m].Freq); } #endif /* and insert the new node in the heap */ s->heap[SMALLEST] = node++; pqdownheap(s, tree, SMALLEST); } while (s->heap_len >= 2); s->heap[--(s->heap_max)] = s->heap[SMALLEST]; /* At this point, the fields freq and dad are set. We can now * generate the bit lengths. */ gen_bitlen(s, (tree_desc *)desc); /* The field len is now set, we can generate the bit codes */ gen_codes ((ct_data *)tree, max_code, s->bl_count); } /* =========================================================================== * Scan a literal or distance tree to determine the frequencies of the codes * in the bit length tree. */ local void scan_tree (s, tree, max_code) deflate_state *s; ct_data *tree; /* the tree to be scanned */ int max_code; /* and its largest code of non zero frequency */ { int n; /* iterates over all tree elements */ int prevlen = -1; /* last emitted length */ int curlen; /* length of current code */ int nextlen = tree[0].Len; /* length of next code */ int count = 0; /* repeat count of the current code */ int max_count = 7; /* max repeat count */ int min_count = 4; /* min repeat count */ if (nextlen == 0) max_count = 138, min_count = 3; tree[max_code+1].Len = (ush)0xffff; /* guard */ for (n = 0; n <= max_code; n++) { curlen = nextlen; nextlen = tree[n+1].Len; if (++count < max_count && curlen == nextlen) { continue; } else if (count < min_count) { s->bl_tree[curlen].Freq += count; } else if (curlen != 0) { if (curlen != prevlen) s->bl_tree[curlen].Freq++; s->bl_tree[REP_3_6].Freq++; } else if (count <= 10) { s->bl_tree[REPZ_3_10].Freq++; } else { s->bl_tree[REPZ_11_138].Freq++; } count = 0; prevlen = curlen; if (nextlen == 0) { max_count = 138, min_count = 3; } else if (curlen == nextlen) { max_count = 6, min_count = 3; } else { max_count = 7, min_count = 4; } } } /* =========================================================================== * Send a literal or distance tree in compressed form, using the codes in * bl_tree. */ local void send_tree (s, tree, max_code) deflate_state *s; ct_data *tree; /* the tree to be scanned */ int max_code; /* and its largest code of non zero frequency */ { int n; /* iterates over all tree elements */ int prevlen = -1; /* last emitted length */ int curlen; /* length of current code */ int nextlen = tree[0].Len; /* length of next code */ int count = 0; /* repeat count of the current code */ int max_count = 7; /* max repeat count */ int min_count = 4; /* min repeat count */ /* tree[max_code+1].Len = -1; */ /* guard already set */ if (nextlen == 0) max_count = 138, min_count = 3; for (n = 0; n <= max_code; n++) { curlen = nextlen; nextlen = tree[n+1].Len; if (++count < max_count && curlen == nextlen) { continue; } else if (count < min_count) { do { send_code(s, curlen, s->bl_tree); } while (--count != 0); } else if (curlen != 0) { if (curlen != prevlen) { send_code(s, curlen, s->bl_tree); count--; } Assert(count >= 3 && count <= 6, " 3_6?"); send_code(s, REP_3_6, s->bl_tree); send_bits(s, count-3, 2); } else if (count <= 10) { send_code(s, REPZ_3_10, s->bl_tree); send_bits(s, count-3, 3); } else { send_code(s, REPZ_11_138, s->bl_tree); send_bits(s, count-11, 7); } count = 0; prevlen = curlen; if (nextlen == 0) { max_count = 138, min_count = 3; } else if (curlen == nextlen) { max_count = 6, min_count = 3; } else { max_count = 7, min_count = 4; } } } /* =========================================================================== * Construct the Huffman tree for the bit lengths and return the index in * bl_order of the last bit length code to send. */ local int build_bl_tree(s) deflate_state *s; { int max_blindex; /* index of last bit length code of non zero freq */ /* Determine the bit length frequencies for literal and distance trees */ scan_tree(s, (ct_data *)s->dyn_ltree, s->l_desc.max_code); scan_tree(s, (ct_data *)s->dyn_dtree, s->d_desc.max_code); /* Build the bit length tree: */ build_tree(s, (tree_desc *)(&(s->bl_desc))); /* opt_len now includes the length of the tree representations, except * the lengths of the bit lengths codes and the 5+5+4 bits for the counts. */ /* Determine the number of bit length codes to send. The pkzip format * requires that at least 4 bit length codes be sent. (appnote.txt says * 3 but the actual value used is 4.) */ for (max_blindex = BL_CODES-1; max_blindex >= 3; max_blindex--) { if (s->bl_tree[bl_order[max_blindex]].Len != 0) break; } /* Update opt_len to include the bit length tree and counts */ s->opt_len += 3*(max_blindex+1) + 5+5+4; Tracev((stderr, "\ndyn trees: dyn %ld, stat %ld", s->opt_len, s->static_len)); return max_blindex; } /* =========================================================================== * Send the header for a block using dynamic Huffman trees: the counts, the * lengths of the bit length codes, the literal tree and the distance tree. * IN assertion: lcodes >= 257, dcodes >= 1, blcodes >= 4. */ local void send_all_trees(s, lcodes, dcodes, blcodes) deflate_state *s; int lcodes, dcodes, blcodes; /* number of codes for each tree */ { int rank; /* index in bl_order */ Assert (lcodes >= 257 && dcodes >= 1 && blcodes >= 4, "not enough codes"); Assert (lcodes <= L_CODES && dcodes <= D_CODES && blcodes <= BL_CODES, "too many codes"); Tracev((stderr, "\nbl counts: ")); send_bits(s, lcodes-257, 5); /* not +255 as stated in appnote.txt */ send_bits(s, dcodes-1, 5); send_bits(s, blcodes-4, 4); /* not -3 as stated in appnote.txt */ for (rank = 0; rank < blcodes; rank++) { Tracev((stderr, "\nbl code %2d ", bl_order[rank])); send_bits(s, s->bl_tree[bl_order[rank]].Len, 3); } Tracev((stderr, "\nbl tree: sent %ld", s->bits_sent)); send_tree(s, (ct_data *)s->dyn_ltree, lcodes-1); /* literal tree */ Tracev((stderr, "\nlit tree: sent %ld", s->bits_sent)); send_tree(s, (ct_data *)s->dyn_dtree, dcodes-1); /* distance tree */ Tracev((stderr, "\ndist tree: sent %ld", s->bits_sent)); } /* =========================================================================== * Send a stored block */ void _tr_stored_block(s, buf, stored_len, eof) deflate_state *s; charf *buf; /* input block */ ulg stored_len; /* length of input block */ int eof; /* true if this is the last block for a file */ { send_bits(s, (STORED_BLOCK<<1)+eof, 3); /* send block type */ #ifdef DEBUG s->compressed_len = (s->compressed_len + 3 + 7) & (ulg)~7L; s->compressed_len += (stored_len + 4) << 3; #endif copy_block(s, buf, (unsigned)stored_len, 1); /* with header */ } /* =========================================================================== * Send one empty static block to give enough lookahead for inflate. * This takes 10 bits, of which 7 may remain in the bit buffer. * The current inflate code requires 9 bits of lookahead. If the * last two codes for the previous block (real code plus EOB) were coded * on 5 bits or less, inflate may have only 5+3 bits of lookahead to decode * the last real code. In this case we send two empty static blocks instead * of one. (There are no problems if the previous block is stored or fixed.) * To simplify the code, we assume the worst case of last real code encoded * on one bit only. */ void _tr_align(s) deflate_state *s; { send_bits(s, STATIC_TREES<<1, 3); send_code(s, END_BLOCK, static_ltree); #ifdef DEBUG s->compressed_len += 10L; /* 3 for block type, 7 for EOB */ #endif bi_flush(s); /* Of the 10 bits for the empty block, we have already sent * (10 - bi_valid) bits. The lookahead for the last real code (before * the EOB of the previous block) was thus at least one plus the length * of the EOB plus what we have just sent of the empty static block. */ if (1 + s->last_eob_len + 10 - s->bi_valid < 9) { send_bits(s, STATIC_TREES<<1, 3); send_code(s, END_BLOCK, static_ltree); #ifdef DEBUG s->compressed_len += 10L; #endif bi_flush(s); } s->last_eob_len = 7; } /* =========================================================================== * Determine the best encoding for the current block: dynamic trees, static * trees or store, and output the encoded block to the zip file. */ void _tr_flush_block(s, buf, stored_len, eof) deflate_state *s; charf *buf; /* input block, or NULL if too old */ ulg stored_len; /* length of input block */ int eof; /* true if this is the last block for a file */ { ulg opt_lenb, static_lenb; /* opt_len and static_len in bytes */ int max_blindex = 0; /* index of last bit length code of non zero freq */ /* Build the Huffman trees unless a stored block is forced */ if (s->level > 0) { /* Check if the file is binary or text */ if (stored_len > 0 && s->strm->data_type == Z_UNKNOWN) set_data_type(s); /* Construct the literal and distance trees */ build_tree(s, (tree_desc *)(&(s->l_desc))); Tracev((stderr, "\nlit data: dyn %ld, stat %ld", s->opt_len, s->static_len)); build_tree(s, (tree_desc *)(&(s->d_desc))); Tracev((stderr, "\ndist data: dyn %ld, stat %ld", s->opt_len, s->static_len)); /* At this point, opt_len and static_len are the total bit lengths of * the compressed block data, excluding the tree representations. */ /* Build the bit length tree for the above two trees, and get the index * in bl_order of the last bit length code to send. */ max_blindex = build_bl_tree(s); /* Determine the best encoding. Compute the block lengths in bytes. */ opt_lenb = (s->opt_len+3+7)>>3; static_lenb = (s->static_len+3+7)>>3; Tracev((stderr, "\nopt %lu(%lu) stat %lu(%lu) stored %lu lit %u ", opt_lenb, s->opt_len, static_lenb, s->static_len, stored_len, s->last_lit)); if (static_lenb <= opt_lenb) opt_lenb = static_lenb; } else { Assert(buf != (char*)0, "lost buf"); opt_lenb = static_lenb = stored_len + 5; /* force a stored block */ } #ifdef FORCE_STORED if (buf != (char*)0) { /* force stored block */ #else if (stored_len+4 <= opt_lenb && buf != (char*)0) { /* 4: two words for the lengths */ #endif /* The test buf != NULL is only necessary if LIT_BUFSIZE > WSIZE. * Otherwise we can't have processed more than WSIZE input bytes since * the last block flush, because compression would have been * successful. If LIT_BUFSIZE <= WSIZE, it is never too late to * transform a block into a stored block. */ _tr_stored_block(s, buf, stored_len, eof); #ifdef FORCE_STATIC } else if (static_lenb >= 0) { /* force static trees */ #else } else if (s->strategy == Z_FIXED || static_lenb == opt_lenb) { #endif send_bits(s, (STATIC_TREES<<1)+eof, 3); compress_block(s, (ct_data *)static_ltree, (ct_data *)static_dtree); #ifdef DEBUG s->compressed_len += 3 + s->static_len; #endif } else { send_bits(s, (DYN_TREES<<1)+eof, 3); send_all_trees(s, s->l_desc.max_code+1, s->d_desc.max_code+1, max_blindex+1); compress_block(s, (ct_data *)s->dyn_ltree, (ct_data *)s->dyn_dtree); #ifdef DEBUG s->compressed_len += 3 + s->opt_len; #endif } Assert (s->compressed_len == s->bits_sent, "bad compressed size"); /* The above check is made mod 2^32, for files larger than 512 MB * and uLong implemented on 32 bits. */ init_block(s); if (eof) { bi_windup(s); #ifdef DEBUG s->compressed_len += 7; /* align on byte boundary */ #endif } Tracev((stderr,"\ncomprlen %lu(%lu) ", s->compressed_len>>3, s->compressed_len-7*eof)); } /* =========================================================================== * Save the match info and tally the frequency counts. Return true if * the current block must be flushed. */ int _tr_tally (s, dist, lc) deflate_state *s; unsigned dist; /* distance of matched string */ unsigned lc; /* match length-MIN_MATCH or unmatched char (if dist==0) */ { s->d_buf[s->last_lit] = (ush)dist; s->l_buf[s->last_lit++] = (uch)lc; if (dist == 0) { /* lc is the unmatched char */ s->dyn_ltree[lc].Freq++; } else { s->matches++; /* Here, lc is the match length - MIN_MATCH */ dist--; /* dist = match distance - 1 */ Assert((ush)dist < (ush)MAX_DIST(s) && (ush)lc <= (ush)(MAX_MATCH-MIN_MATCH) && (ush)d_code(dist) < (ush)D_CODES, "_tr_tally: bad match"); s->dyn_ltree[_length_code[lc]+LITERALS+1].Freq++; s->dyn_dtree[d_code(dist)].Freq++; } #ifdef TRUNCATE_BLOCK /* Try to guess if it is profitable to stop the current block here */ if ((s->last_lit & 0x1fff) == 0 && s->level > 2) { /* Compute an upper bound for the compressed length */ ulg out_length = (ulg)s->last_lit*8L; ulg in_length = (ulg)((long)s->strstart - s->block_start); int dcode; for (dcode = 0; dcode < D_CODES; dcode++) { out_length += (ulg)s->dyn_dtree[dcode].Freq * (5L+extra_dbits[dcode]); } out_length >>= 3; Tracev((stderr,"\nlast_lit %u, in %ld, out ~%ld(%ld%%) ", s->last_lit, in_length, out_length, 100L - out_length*100L/in_length)); if (s->matches < s->last_lit/2 && out_length < in_length/2) return 1; } #endif return (s->last_lit == s->lit_bufsize-1); /* We avoid equality with lit_bufsize because of wraparound at 64K * on 16 bit machines and because stored blocks are restricted to * 64K-1 bytes. */ } /* =========================================================================== * Send the block data compressed using the given Huffman trees */ local void compress_block(s, ltree, dtree) deflate_state *s; ct_data *ltree; /* literal tree */ ct_data *dtree; /* distance tree */ { unsigned dist; /* distance of matched string */ int lc; /* match length or unmatched char (if dist == 0) */ unsigned lx = 0; /* running index in l_buf */ unsigned code; /* the code to send */ int extra; /* number of extra bits to send */ if (s->last_lit != 0) do { dist = s->d_buf[lx]; lc = s->l_buf[lx++]; if (dist == 0) { send_code(s, lc, ltree); /* send a literal byte */ Tracecv(isgraph(lc), (stderr," '%c' ", lc)); } else { /* Here, lc is the match length - MIN_MATCH */ code = _length_code[lc]; send_code(s, code+LITERALS+1, ltree); /* send the length code */ extra = extra_lbits[code]; if (extra != 0) { lc -= base_length[code]; send_bits(s, lc, extra); /* send the extra length bits */ } dist--; /* dist is now the match distance - 1 */ code = d_code(dist); Assert (code < D_CODES, "bad d_code"); send_code(s, code, dtree); /* send the distance code */ extra = extra_dbits[code]; if (extra != 0) { dist -= base_dist[code]; send_bits(s, dist, extra); /* send the extra distance bits */ } } /* literal or match pair ? */ /* Check that the overlay between pending_buf and d_buf+l_buf is ok: */ Assert((uInt)(s->pending) < s->lit_bufsize + 2*lx, "pendingBuf overflow"); } while (lx < s->last_lit); send_code(s, END_BLOCK, ltree); s->last_eob_len = ltree[END_BLOCK].Len; } /* =========================================================================== * Set the data type to BINARY or TEXT, using a crude approximation: * set it to Z_TEXT if all symbols are either printable characters (33 to 255) * or white spaces (9 to 13, or 32); or set it to Z_BINARY otherwise. * IN assertion: the fields Freq of dyn_ltree are set. */ local void set_data_type(s) deflate_state *s; { int n; for (n = 0; n < 9; n++) if (s->dyn_ltree[n].Freq != 0) break; if (n == 9) for (n = 14; n < 32; n++) if (s->dyn_ltree[n].Freq != 0) break; s->strm->data_type = (n == 32) ? Z_TEXT : Z_BINARY; } /* =========================================================================== * Reverse the first len bits of a code, using straightforward code (a faster * method would use a table) * IN assertion: 1 <= len <= 15 */ local unsigned bi_reverse(code, len) unsigned code; /* the value to invert */ int len; /* its bit length */ { register unsigned res = 0; do { res |= code & 1; code >>= 1, res <<= 1; } while (--len > 0); return res >> 1; } /* =========================================================================== * Flush the bit buffer, keeping at most 7 bits in it. */ local void bi_flush(s) deflate_state *s; { if (s->bi_valid == 16) { put_short(s, s->bi_buf); s->bi_buf = 0; s->bi_valid = 0; } else if (s->bi_valid >= 8) { put_byte(s, (Byte)s->bi_buf); s->bi_buf >>= 8; s->bi_valid -= 8; } } /* =========================================================================== * Flush the bit buffer and align the output on a byte boundary */ local void bi_windup(s) deflate_state *s; { if (s->bi_valid > 8) { put_short(s, s->bi_buf); } else if (s->bi_valid > 0) { put_byte(s, (Byte)s->bi_buf); } s->bi_buf = 0; s->bi_valid = 0; #ifdef DEBUG s->bits_sent = (s->bits_sent+7) & ~7; #endif } /* =========================================================================== * Copy a stored block, storing first the length and its * one's complement if requested. */ local void copy_block(s, buf, len, header) deflate_state *s; charf *buf; /* the input data */ unsigned len; /* its length */ int header; /* true if block header must be written */ { bi_windup(s); /* align on byte boundary */ s->last_eob_len = 8; /* enough lookahead for inflate */ if (header) { put_short(s, (ush)len); put_short(s, (ush)~len); #ifdef DEBUG s->bits_sent += 2*16; #endif } #ifdef DEBUG s->bits_sent += (ulg)len<<3; #endif while (len--) { put_byte(s, *buf++); } } maqview-0.2.5/maqmap.h0000644000265600020320000000321511117475430013744 0ustar tilleaadmin#ifndef MAQMAP_H_ #define MAQMAP_H_ #ifdef MAQ_LONGREADS #define MAX_READLEN 128 #else #define MAX_READLEN 64 #endif #ifndef MAX_NAMELEN #define MAX_NAMELEN 36 #endif #define MAQMAP_FORMAT_OLD 0 #define MAQMAP_FORMAT_NEW -1 #define PAIRFLAG_FF 0x01 #define PAIRFLAG_FR 0x02 #define PAIRFLAG_RF 0x04 #define PAIRFLAG_RR 0x08 #define PAIRFLAG_PAIRED 0x10 #define PAIRFLAG_DIFFCHR 0x20 #define PAIRFLAG_NOMATCH 0x40 #define PAIRFLAG_SW 0x80 #include #include "zrio.h" #include "const.h" /* name: read name size: the length of the read seq: read sequence (see also below) seq[MAX_READLEN-1]: single end mapping quality (equals to map_qual if not paired) map_qual: the final mapping quality alt_qual: the lower quality of the two ends (equals to map_qual if not paired) flag: status of the pair dist: offset of the mate (zero if not paired) info1: mismatch and rough sum of errors of the best hit info2: mismatch and rough sum of errors of the second best hit c[2]: count of all 0- and 1-mismatch hits on the reference */ typedef struct { bit8_t seq[MAX_READLEN]; /* the last base is the single-end mapping quality. */ bit8_t size, map_qual, info1, info2, c[2], flag, alt_qual; bit32_t seqid, pos; int dist; char name[MAX_NAMELEN]; } maqmap1_t; typedef struct { int format, n_ref; char **ref_name; bit64_t n_mapped_reads; maqmap1_t *mapped_reads; } maqmap_t; #define maqmap_read1(fp, m1) gzread((fp), (m1), sizeof(maqmap1_t)) #ifdef __cplusplus extern "C" { #endif maqmap_t *maqmap_read_header(zr_stream *fp); void maqmap_write_header(gzFile fp, const maqmap_t *mm); #ifdef __cplusplus } #endif #endif maqview-0.2.5/trees.h0000644000265600020320000002037410761137603013620 0ustar tilleaadmin/* header created automatically with -DGEN_TREES_H */ local const ct_data static_ltree[L_CODES+2] = { {{ 12},{ 8}}, {{140},{ 8}}, {{ 76},{ 8}}, {{204},{ 8}}, {{ 44},{ 8}}, {{172},{ 8}}, {{108},{ 8}}, {{236},{ 8}}, {{ 28},{ 8}}, {{156},{ 8}}, {{ 92},{ 8}}, {{220},{ 8}}, {{ 60},{ 8}}, {{188},{ 8}}, {{124},{ 8}}, {{252},{ 8}}, {{ 2},{ 8}}, {{130},{ 8}}, {{ 66},{ 8}}, {{194},{ 8}}, {{ 34},{ 8}}, {{162},{ 8}}, {{ 98},{ 8}}, {{226},{ 8}}, {{ 18},{ 8}}, {{146},{ 8}}, {{ 82},{ 8}}, {{210},{ 8}}, {{ 50},{ 8}}, {{178},{ 8}}, {{114},{ 8}}, {{242},{ 8}}, {{ 10},{ 8}}, {{138},{ 8}}, {{ 74},{ 8}}, {{202},{ 8}}, {{ 42},{ 8}}, {{170},{ 8}}, {{106},{ 8}}, {{234},{ 8}}, {{ 26},{ 8}}, {{154},{ 8}}, {{ 90},{ 8}}, {{218},{ 8}}, {{ 58},{ 8}}, {{186},{ 8}}, {{122},{ 8}}, {{250},{ 8}}, {{ 6},{ 8}}, {{134},{ 8}}, {{ 70},{ 8}}, {{198},{ 8}}, {{ 38},{ 8}}, {{166},{ 8}}, {{102},{ 8}}, {{230},{ 8}}, {{ 22},{ 8}}, {{150},{ 8}}, {{ 86},{ 8}}, {{214},{ 8}}, {{ 54},{ 8}}, {{182},{ 8}}, {{118},{ 8}}, {{246},{ 8}}, {{ 14},{ 8}}, {{142},{ 8}}, {{ 78},{ 8}}, {{206},{ 8}}, {{ 46},{ 8}}, {{174},{ 8}}, {{110},{ 8}}, {{238},{ 8}}, {{ 30},{ 8}}, {{158},{ 8}}, {{ 94},{ 8}}, {{222},{ 8}}, {{ 62},{ 8}}, {{190},{ 8}}, {{126},{ 8}}, {{254},{ 8}}, {{ 1},{ 8}}, {{129},{ 8}}, {{ 65},{ 8}}, {{193},{ 8}}, {{ 33},{ 8}}, {{161},{ 8}}, {{ 97},{ 8}}, {{225},{ 8}}, {{ 17},{ 8}}, {{145},{ 8}}, {{ 81},{ 8}}, {{209},{ 8}}, {{ 49},{ 8}}, {{177},{ 8}}, {{113},{ 8}}, {{241},{ 8}}, {{ 9},{ 8}}, {{137},{ 8}}, {{ 73},{ 8}}, {{201},{ 8}}, {{ 41},{ 8}}, {{169},{ 8}}, {{105},{ 8}}, {{233},{ 8}}, {{ 25},{ 8}}, {{153},{ 8}}, {{ 89},{ 8}}, {{217},{ 8}}, {{ 57},{ 8}}, {{185},{ 8}}, {{121},{ 8}}, {{249},{ 8}}, {{ 5},{ 8}}, {{133},{ 8}}, {{ 69},{ 8}}, {{197},{ 8}}, {{ 37},{ 8}}, {{165},{ 8}}, {{101},{ 8}}, {{229},{ 8}}, {{ 21},{ 8}}, {{149},{ 8}}, {{ 85},{ 8}}, {{213},{ 8}}, {{ 53},{ 8}}, {{181},{ 8}}, {{117},{ 8}}, {{245},{ 8}}, {{ 13},{ 8}}, {{141},{ 8}}, {{ 77},{ 8}}, {{205},{ 8}}, {{ 45},{ 8}}, {{173},{ 8}}, {{109},{ 8}}, {{237},{ 8}}, {{ 29},{ 8}}, {{157},{ 8}}, {{ 93},{ 8}}, {{221},{ 8}}, {{ 61},{ 8}}, {{189},{ 8}}, {{125},{ 8}}, {{253},{ 8}}, {{ 19},{ 9}}, {{275},{ 9}}, {{147},{ 9}}, {{403},{ 9}}, {{ 83},{ 9}}, {{339},{ 9}}, {{211},{ 9}}, {{467},{ 9}}, {{ 51},{ 9}}, {{307},{ 9}}, {{179},{ 9}}, {{435},{ 9}}, {{115},{ 9}}, {{371},{ 9}}, {{243},{ 9}}, {{499},{ 9}}, {{ 11},{ 9}}, {{267},{ 9}}, {{139},{ 9}}, {{395},{ 9}}, {{ 75},{ 9}}, {{331},{ 9}}, {{203},{ 9}}, {{459},{ 9}}, {{ 43},{ 9}}, {{299},{ 9}}, {{171},{ 9}}, {{427},{ 9}}, {{107},{ 9}}, {{363},{ 9}}, {{235},{ 9}}, {{491},{ 9}}, {{ 27},{ 9}}, {{283},{ 9}}, {{155},{ 9}}, {{411},{ 9}}, {{ 91},{ 9}}, {{347},{ 9}}, {{219},{ 9}}, {{475},{ 9}}, {{ 59},{ 9}}, {{315},{ 9}}, {{187},{ 9}}, {{443},{ 9}}, {{123},{ 9}}, {{379},{ 9}}, {{251},{ 9}}, {{507},{ 9}}, {{ 7},{ 9}}, {{263},{ 9}}, {{135},{ 9}}, {{391},{ 9}}, {{ 71},{ 9}}, {{327},{ 9}}, {{199},{ 9}}, {{455},{ 9}}, {{ 39},{ 9}}, {{295},{ 9}}, {{167},{ 9}}, {{423},{ 9}}, {{103},{ 9}}, {{359},{ 9}}, {{231},{ 9}}, {{487},{ 9}}, {{ 23},{ 9}}, {{279},{ 9}}, {{151},{ 9}}, {{407},{ 9}}, {{ 87},{ 9}}, {{343},{ 9}}, {{215},{ 9}}, {{471},{ 9}}, {{ 55},{ 9}}, {{311},{ 9}}, {{183},{ 9}}, {{439},{ 9}}, {{119},{ 9}}, {{375},{ 9}}, {{247},{ 9}}, {{503},{ 9}}, {{ 15},{ 9}}, {{271},{ 9}}, {{143},{ 9}}, {{399},{ 9}}, {{ 79},{ 9}}, {{335},{ 9}}, {{207},{ 9}}, {{463},{ 9}}, {{ 47},{ 9}}, {{303},{ 9}}, {{175},{ 9}}, {{431},{ 9}}, {{111},{ 9}}, {{367},{ 9}}, {{239},{ 9}}, {{495},{ 9}}, {{ 31},{ 9}}, {{287},{ 9}}, {{159},{ 9}}, {{415},{ 9}}, {{ 95},{ 9}}, {{351},{ 9}}, {{223},{ 9}}, {{479},{ 9}}, {{ 63},{ 9}}, {{319},{ 9}}, {{191},{ 9}}, {{447},{ 9}}, {{127},{ 9}}, {{383},{ 9}}, {{255},{ 9}}, {{511},{ 9}}, {{ 0},{ 7}}, {{ 64},{ 7}}, {{ 32},{ 7}}, {{ 96},{ 7}}, {{ 16},{ 7}}, {{ 80},{ 7}}, {{ 48},{ 7}}, {{112},{ 7}}, {{ 8},{ 7}}, {{ 72},{ 7}}, {{ 40},{ 7}}, {{104},{ 7}}, {{ 24},{ 7}}, {{ 88},{ 7}}, {{ 56},{ 7}}, {{120},{ 7}}, {{ 4},{ 7}}, {{ 68},{ 7}}, {{ 36},{ 7}}, {{100},{ 7}}, {{ 20},{ 7}}, {{ 84},{ 7}}, {{ 52},{ 7}}, {{116},{ 7}}, {{ 3},{ 8}}, {{131},{ 8}}, {{ 67},{ 8}}, {{195},{ 8}}, {{ 35},{ 8}}, {{163},{ 8}}, {{ 99},{ 8}}, {{227},{ 8}} }; local const ct_data static_dtree[D_CODES] = { {{ 0},{ 5}}, {{16},{ 5}}, {{ 8},{ 5}}, {{24},{ 5}}, {{ 4},{ 5}}, {{20},{ 5}}, {{12},{ 5}}, {{28},{ 5}}, {{ 2},{ 5}}, {{18},{ 5}}, {{10},{ 5}}, {{26},{ 5}}, {{ 6},{ 5}}, {{22},{ 5}}, {{14},{ 5}}, {{30},{ 5}}, {{ 1},{ 5}}, {{17},{ 5}}, {{ 9},{ 5}}, {{25},{ 5}}, {{ 5},{ 5}}, {{21},{ 5}}, {{13},{ 5}}, {{29},{ 5}}, {{ 3},{ 5}}, {{19},{ 5}}, {{11},{ 5}}, {{27},{ 5}}, {{ 7},{ 5}}, {{23},{ 5}} }; const uch _dist_code[DIST_CODE_LEN] = { 0, 1, 2, 3, 4, 4, 5, 5, 6, 6, 6, 6, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 0, 0, 16, 17, 18, 18, 19, 19, 20, 20, 20, 20, 21, 21, 21, 21, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29 }; const uch _length_code[MAX_MATCH-MIN_MATCH+1]= { 0, 1, 2, 3, 4, 5, 6, 7, 8, 8, 9, 9, 10, 10, 11, 11, 12, 12, 12, 12, 13, 13, 13, 13, 14, 14, 14, 14, 15, 15, 15, 15, 16, 16, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 17, 17, 17, 18, 18, 18, 18, 18, 18, 18, 18, 19, 19, 19, 19, 19, 19, 19, 19, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 28 }; local const int base_length[LENGTH_CODES] = { 0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 12, 14, 16, 20, 24, 28, 32, 40, 48, 56, 64, 80, 96, 112, 128, 160, 192, 224, 0 }; local const int base_dist[D_CODES] = { 0, 1, 2, 3, 4, 6, 8, 12, 16, 24, 32, 48, 64, 96, 128, 192, 256, 384, 512, 768, 1024, 1536, 2048, 3072, 4096, 6144, 8192, 12288, 16384, 24576 }; maqview-0.2.5/maqmap_index.c0000644000265600020320000002742111117504741015131 0ustar tilleaadmin#include "maqmap_index.h" #include #include #include struct CallbackObj { MapIndex *mi; maqmap_t *mm; BTree *tree, *last_node; int last_ref_id, layer; int64_t index; unsigned char buf[1024]; // I never expect ref_name[x] exceed this length int buf_size; int heading; int count; int n; }; #define read_buf(target, size) if(obj->buf_size >= size){ \ memcpy(target, obj->buf, size);\ obj->buf_size -= size;\ } else if(obj->buf_size){\ if(obj->buf_size + buf_size >= size){\ memcpy(target, obj->buf, obj->buf_size);\ memcpy(target + obj->buf_size, buf, size - obj->buf_size);\ buf += size - obj->buf_size;\ buf_size -= size - obj->buf_size;\ obj->buf_size = 0;\ } else {\ memcpy(obj->buf + obj->buf_size, buf, buf_size);\ obj->buf_size += buf_size;\ return;\ }\ } else if(buf_size < size){\ memcpy(obj->buf, buf, buf_size);\ obj->buf_size = buf_size;\ return;\ } else {\ memcpy(target, buf, size);\ buf += size;\ buf_size -= size;\ } void notify(void *object, unsigned char *buf, int buf_size, int64_t pos){ struct CallbackObj *obj; maplet *let; int i; obj = (struct CallbackObj*)object; while(obj->heading){ switch(obj->heading){ case 1: obj->mi->head_size = 0; read_buf(&obj->mm->format, (int)sizeof(int)); if (obj->mm->format != MAQMAP_FORMAT_NEW) { if (obj->mm->format > 0) { fprintf(stderr, "** Obsolete map format is detected (%d). Please use 'mapass2maq' command to convert the format.\n", obj->mm->format); exit(3); } } obj->mi->head_size += sizeof(int); obj->heading = 2; case 2: read_buf(&obj->mm->n_ref, (int)sizeof(int)); obj->mm->ref_name = (char**)calloc(obj->mm->n_ref, sizeof(char*)); obj->mi->trees = (BTree**)malloc(sizeof(BTree*) * obj->mm->n_ref); for(i=0;imm->n_ref;i++) obj->mi->trees[i] = NULL; obj->count = 0; obj->mi->head_size += sizeof(int); obj->heading = 3; case 3: if(obj->count == obj->mm->n_ref){ obj->heading = 5; break; } read_buf(&obj->n, (int)sizeof(int)); obj->mi->head_size += sizeof(int); obj->mm->ref_name[obj->count] = (char*)malloc(obj->n + 1); memset(obj->mm->ref_name[obj->count], 0, obj->n+1); obj->heading = 4; case 4: read_buf(obj->mm->ref_name[obj->count], obj->n); obj->mm->ref_name[obj->count][obj->n] = 0; obj->count ++; obj->mi->head_size += obj->n; obj->heading = 3; break; case 5: read_buf(&obj->mm->n_mapped_reads, (int)sizeof(bit64_t)); obj->mi->head_size += sizeof(bit64_t); obj->heading = 0; } } while(buf_size + obj->buf_size >= (int)sizeof(maplet)){ if(obj->buf_size){ memcpy(obj->buf + obj->buf_size, buf, sizeof(maplet) - obj->buf_size); buf += sizeof(maplet) - obj->buf_size; buf_size -= sizeof(maplet) - obj->buf_size; obj->buf_size = 0; let = (maplet*)obj->buf; } else { let = (maplet*)buf; buf += sizeof(maplet); buf_size -= sizeof(maplet); } if((int)let->seqid != obj->last_ref_id){ if(obj->tree != NULL){ obj->mi->trees[obj->last_ref_id] = obj->tree; } obj->tree = btree_init(); obj->last_node = obj->tree; obj->last_node->left = obj->last_node->right = (int64_t)read_pos(let->pos); obj->last_node->indexs[0] = obj->last_node->indexs[1] = obj->index; obj->layer = 1; obj->last_ref_id = let->seqid; } else { obj->last_node = btree_append(&obj->tree, obj->last_node, &obj->layer, obj->index, (int64_t)read_pos(let->pos)); } obj->index ++; } if(buf_size){ memcpy(obj->buf + obj->buf_size, buf, buf_size); obj->buf_size += buf_size; } } maqmap_t *maq_new_maqmap() { maqmap_t *mm = (maqmap_t*)calloc(1, sizeof(maqmap_t)); mm->format = MAQMAP_FORMAT_NEW; return mm; } MapIndex * make_map_index(const char *filename, int level){ MapIndex *mi; maqmap_t *mm; struct CallbackObj obj; zr_stream *zr; char *index_name; gzFile file; int i; // if((zr = zropen(filename)) == NULL) return NULL; mm = maq_new_maqmap(); mi = (MapIndex*)malloc(sizeof(MapIndex)); mi->mm = mm; // mi->trees = (BTree**)malloc(sizeof(BTree*) * mm->n_ref); // for(i=0;in_ref;i++) mi->trees[i] = NULL; // zrclose(zr); obj.mi = mi; obj.mm = mm; obj.tree = NULL; obj.last_node = NULL; obj.n = 0; obj.count = 0; obj.buf_size = 0; obj.heading = 1; obj.index = 0; obj.layer = 1; obj.last_ref_id = -1; zrmkindex(filename, level, notify, &obj); if(obj.tree != NULL) obj.mi->trees[obj.last_ref_id] = obj.tree; if((zr = zropen(filename)) == NULL) return NULL; mi->stream = zr; index_name = (char*)malloc(strlen(filename) + 4); strcpy(index_name, filename); strcat(index_name, ".vm"); if((file = gzopen(index_name, "w")) == NULL){ free(index_name); close_map_index(mi); return NULL; } free(index_name); gzwrite(file, &mi->head_size, sizeof(int)); gzwrite(file, &(mm->n_ref), sizeof(int)); for(i=0;in_ref;i++){ btree_dump_gz(file, mi->trees[i]); } gzclose(file); return mi; } MapIndex * make_map_index_old(const char *filename){ MapIndex *mi; maqmap_t *mm; maplet let; BTree *tree, *last_node; zr_stream *zr; char *index_name; gzFile file; int i, last_ref_id, layer, head_size; int64_t index; if((zr = zropen(filename)) == NULL) return NULL; index_name = (char*)malloc(strlen(filename) + 4); strcpy(index_name, filename); strcat(index_name, ".vm"); mm = maqmap_read_header(zr); mi = (MapIndex*)malloc(sizeof(MapIndex)); mi->mm = mm; head_size = sizeof(int) * 2 + sizeof(bit64_t); for(i=0;in_ref;i++){ head_size += sizeof(int) + strlen(mm->ref_name[i]) + 1; } mi->head_size = head_size; mi->trees = (BTree**)malloc(sizeof(BTree*) * mm->n_ref); for(i=0;in_ref;i++) mi->trees[i] = NULL; mi->stream = zr; index = 0; layer = 1; last_node = NULL; last_ref_id = -1; tree = NULL; while(zrread(&let, sizeof(maplet), zr) == sizeof(maplet)){ if((int)let.seqid != last_ref_id){ if(tree != NULL){ mi->trees[last_ref_id] = tree; } tree = btree_init(); last_node = tree; last_node->left = last_node->right = (int64_t)read_pos(let.pos); last_node->indexs[0] = last_node->indexs[1] = index; layer = 1; last_ref_id = let.seqid; } else { last_node = btree_append(&tree, last_node, &layer, index, (int64_t)read_pos(let.pos)); } index ++; } if(tree != NULL) mi->trees[last_ref_id] = tree; if((file = gzopen(index_name, "w")) == NULL){ free(index_name); close_map_index(mi); return NULL; } free(index_name); gzwrite(file, &head_size, sizeof(int)); gzwrite(file, &(mm->n_ref), sizeof(int)); for(i=0;in_ref;i++) btree_dump_gz(file, mi->trees[i]); gzclose(file); return mi; } void maqmap_write_header(gzFile fp, const maqmap_t *mm) { int i, len; gzwrite(fp, &mm->format, sizeof(int)); gzwrite(fp, &mm->n_ref, sizeof(int)); for (i = 0; i != mm->n_ref; ++i) { len = strlen(mm->ref_name[i]) + 1; gzwrite(fp, &len, sizeof(int)); gzwrite(fp, mm->ref_name[i], len); } gzwrite(fp, &mm->n_mapped_reads, sizeof(bit64_t)); } maqmap_t *maqmap_read_header(zr_stream *fp) { maqmap_t *mm; int k, len; mm = maq_new_maqmap(); zrread(&mm->format, sizeof(int), fp); if (mm->format != MAQMAP_FORMAT_NEW) { if (mm->format > 0) { fprintf(stderr, "** Obsolete map format is detected. Please use 'mapass2maq' command to convert the format.\n"); exit(3); } } zrread(&mm->n_ref, sizeof(int), fp); mm->ref_name = (char**)calloc(mm->n_ref, sizeof(char*)); for (k = 0; k != mm->n_ref; ++k) { zrread(&len, sizeof(int), fp); mm->ref_name[k] = (char*)malloc(len * sizeof(char) + 1); zrread(mm->ref_name[k], (size_t)len, fp); mm->ref_name[k][len] = 0; } /* read number of mapped reads */ zrread(&mm->n_mapped_reads, sizeof(bit64_t), fp); return mm; } MapIndex* load_map_index(const char *filename, int auto_mk){ zr_stream *zr; MapIndex *mi; maqmap_t *mm; char *index_name; gzFile file; int i, n; if((zr = zropen(filename)) == NULL) return NULL; index_name = (char*)malloc(strlen(filename) + 4); strcpy(index_name, filename); strcat(index_name, ".vm"); if((file = gzopen(index_name, "r")) == NULL){ zrclose(zr); free(index_name); if(auto_mk){ return make_map_index(filename, 1024); } else { return NULL; } } free(index_name); mm = maqmap_read_header(zr); mi = (MapIndex*)malloc(sizeof(MapIndex)); mi->mm = mm; mi->trees = (BTree**)malloc(sizeof(BTree*) * mm->n_ref); for(i=0;in_ref;i++) mi->trees[i] = NULL; mi->stream = zr; gzread(file, &(mi->head_size), sizeof(int)); gzread(file,&n, sizeof(int)); if(n != mm->n_ref){ close_map_index(mi); gzclose(file); } for(i=0;in_ref;i++){ mi->trees[i] = btree_load_gz(file); } gzclose(file); return mi; } void close_map_index(MapIndex *mi){ int i; if(mi->stream) zrclose(mi->stream); if(mi->mm){ if(mi->trees){ for(i=0;imm->n_ref;i++){ btree_free(mi->trees[i]); } free(mi->trees); } if(mi->mm->ref_name){ for(i=0;imm->n_ref;i++) free(mi->mm->ref_name[i]); free(mi->mm->ref_name); } if(mi->mm->mapped_reads) free(mi->mm->mapped_reads); free(mi->mm); } free(mi); } int iter_map_index(MapIndex *mi, int ref_id, int64_t start, int64_t end, int (*handle)(void *obj, maplet *let), void *obj){ BTree *tree; int64_t offset; int64_t left, right, i, l, r; maplet let; tree = mi->trees[ref_id]; btree_find(tree, start, &l, &r); left = l; btree_find(tree, end, &l, &r); right = r; if(left > right) return 0; offset = mi->head_size + sizeof(maplet) * left; if(zrseek(mi->stream, offset) < 0){ return -1; } l = 0; for(i=left;i<=right;i++){ offset = sizeof(maplet); while(offset){ r = zrread((void*)(&let) + sizeof(maplet) - offset, offset, mi->stream); if(r <= 0){ fprintf(stderr, "Read_map_index Error: %s:%d\n", __FILE__, __LINE__); exit(1); } else { offset -= r; } } if(read_pos(let.pos) < start || read_pos(let.pos) > end) continue; if(handle && !handle(obj, &let)) break; l ++; } return l; } maplet* read_map_index(MapIndex *mi, int ref_id, int64_t start, int64_t end, int *n_let){ BTree *tree; int64_t left, right, offset; int64_t l, r; maplet *let; tree = mi->trees[ref_id]; btree_find(tree, start, &l, &r); left = l; btree_find(tree, end, &l, &r); right = r; if(left > right){ return NULL; *n_let = -1; } offset = mi->head_size + sizeof(maplet) * left; /* if(zrseek(mi->stream, offset) < 0){ *n_let=-1; return NULL; } l = right - left + 1; let = (maplet*)malloc(sizeof(maplet) * l); offset = zrread((void*)let, sizeof(maplet) * l, mi->stream); */ l = right - left + 1; let = (maplet*)malloc(sizeof(maplet) * l); offset = zrgets((void*)let, sizeof(maplet) * l, offset, mi->stream); if(offset != l * sizeof(maplet)){ fprintf(stderr, "Read_map_index Error: %s:%d\n", __FILE__, __LINE__); *n_let = 0; return NULL; } *n_let = l; return let; } maplet* read_map_next_to(MapIndex *mi, int ref_id, int64_t pos, int *n_let){ maplet *let; int size, capacity; capacity = 64; size = 0; let = (maplet*)malloc(sizeof(maplet) * capacity); while(zrread(let + size, sizeof(maplet), mi->stream) == sizeof(maplet)){ if(let[size].seqid != ref_id) break; if(read_pos(let[size].pos) > pos) break; size ++; if(size == capacity){ capacity += 64; let = (maplet*)realloc(let, sizeof(maplet) * capacity); } } *n_let = size; return let; } void num2str(int64_t number, char *string){ int n, m; char *str; sprintf(string, "%ld", number); n = strlen(string); m = ((n - 1) / 3); string[n + m] = '\0'; str = string + n - 3; 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This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA */ /** Standalone hash library is a free C++ template library for hash tables. It implements open-address hashing with the "double hashing" technique, which makes this library different from most of other implementations, such as STL and TR1 hash based classes, which are all based on chained hashing. However, fewer implementations do not mean open-address hashing is less efficient. As a matter of fact, this hash library is at least as efficient, in terms of both time and space, as STL and TR1 libraries, and in some cases outperforms others. */ /* 2007-07-18, 1.9.2: fixed a bug in hash_*_char when an element is erased. */ #ifndef LH3_STDHASH_H_ #define LH3_STDHASH_H_ #include #include #define LH3_STDHASH_VERSION "1.9.2" typedef unsigned int bit32_t; typedef unsigned long long bit64_t; typedef unsigned short bit16_t; // even on 64-bit systems, hashint_t should be bit32_t typedef bit32_t hashint_t; /* * Hash functions */ // Do a web search "g_str_hash X31_HASH" for more information. /** hash function for strings (char*) */ inline bit32_t __lh3_X31_hash_string(const char *s) { bit32_t h = 0; for ( ; *s; s++) h = (h << 5) - h + *s; return h; } /** Jenkins' hash function for 32-bit integers. Not used in this library. */ inline bit32_t __lh3_Jenkins_hash_int(bit32_t key) { key += (key << 12); key ^= (key >> 22); key += (key << 4); key ^= (key >> 9); key += (key << 10); key ^= (key >> 2); key += (key << 7); key ^= (key >> 12); return key; } /** Jenkins' hash function for 64-bit integers. Used when LH3_HASH_INT macro is set. */ inline bit64_t __lh3_Jenkins_hash_64(bit64_t key) { key += ~(key << 32); key ^= (key >> 22); key += ~(key << 13); key ^= (key >> 8); key += (key << 3); key ^= (key >> 15); key += ~(key << 27); key ^= (key >> 31); return key; } /** Wang's hash function for 32-bit inegers. Used when LH3_HASH_INT macro is set. */ inline bit32_t __lh3_Wang_hash_int(bit32_t key) { key += ~(key << 15); key ^= (key >> 10); key += (key << 3); key ^= (key >> 6); key += ~(key << 11); key ^= (key >> 16); return key; } /** hash function for 16-bit integers */ inline bit32_t __lh3_hash_fun(bit16_t key) { #ifndef LH3_HASH_INT return __lh3_Wang_hash_int(bit32_t(key)); #else return bit32_t(key); #endif } /** hash function for 32-bit integers */ inline bit32_t __lh3_hash_fun(bit32_t key) { #ifndef LH3_HASH_INT return __lh3_Wang_hash_int(key); #else return key; #endif } /** hash function for 64-bit integers */ inline bit32_t __lh3_hash_fun(bit64_t key) { #ifdef LH3_HASH_INT return bit32_t(__lh3_Jenkins_hash_64(key)); #else return bit32_t(key>>16) ^ bit32_t(key); #endif } /** hash function for strings (char*) */ inline bit32_t __lh3_hash_fun(const char *key) { return __lh3_X31_hash_string(key); } /* * Equality operator "==" */ /** "==" for 16-bit integers */ inline bool __lh3_key_equal(bit16_t a, bit16_t b) { return a == b; } /** "==" for 32-bit integers */ inline bool __lh3_key_equal(bit32_t a, bit32_t b) { return a == b; } /** "==" for 64-bit integers */ inline bool __lh3_key_equal(bit64_t a, bit64_t b) { return a == b; } /** "==" for strings (char*) */ inline bool __lh3_key_equal(const char *a, const char *b) { return (a && b && strcmp(a, b) == 0); } /* * Table for primes */ const int __lh3_HASH_PRIME_SIZE = 32; static const bit32_t __lh3_prime_list[__lh3_HASH_PRIME_SIZE] = { 0ul, 3ul, 11ul, 23ul, 53ul, 97ul, 193ul, 389ul, 769ul, 1543ul, 3079ul, 6151ul, 12289ul, 24593ul, 49157ul, 98317ul, 196613ul, 393241ul, 786433ul, 1572869ul, 3145739ul, 6291469ul, 12582917ul, 25165843ul, 50331653ul, 100663319ul, 201326611ul, 402653189ul, 805306457ul, 1610612741ul, 3221225473ul, 4294967291ul }; /** Threshold for rehashing */ const double __lh3_HASH_UPPER = 0.77; /* * Constants and macros for retrieve/set flags "isempty" and "isdel". */ typedef bit32_t __lh3_flag_t; const int __lh3_FLAG_SHIFT = 4; const int __lh3_FLAG_MASK = 0xful; const __lh3_flag_t __lh3_FLAG_DEFAULT = 0xaaaaaaaaul; #define __lh3_isempty(flag, i) ((flag[i>>__lh3_FLAG_SHIFT]>>((i&__lh3_FLAG_MASK)<<1))&2) #define __lh3_isdel(flag, i) ((flag[i>>__lh3_FLAG_SHIFT]>>((i&__lh3_FLAG_MASK)<<1))&1) #define __lh3_isboth(flag, i) ((flag[i>>__lh3_FLAG_SHIFT]>>((i&__lh3_FLAG_MASK)<<1))&3) #define __lh3_set_isdel_false(flag, i) (flag[i>>__lh3_FLAG_SHIFT]&=~(1ul<<((i&__lh3_FLAG_MASK)<<1))) #define __lh3_set_isempty_false(flag, i) (flag[i>>__lh3_FLAG_SHIFT]&=~(2ul<<((i&__lh3_FLAG_MASK)<<1))) #define __lh3_set_isboth_false(flag, i) (flag[i>>__lh3_FLAG_SHIFT]&=~(3ul<<((i&__lh3_FLAG_MASK)<<1))) #define __lh3_set_isdel_true(flag, i) (flag[i>>__lh3_FLAG_SHIFT]|=1ul<<((i&__lh3_FLAG_MASK)<<1)) /* * Auxiliary functions for search/insert/erase. */ template inline hashint_t __lh3_hash_search_aux(const keytype_t &key, hashint_t m, const keytype_t *keys, const __lh3_flag_t *flag) { if (!m) return 0; hashint_t inc, k, i; k = __lh3_hash_fun(key); i = k % m; inc = 1 + k % (m - 1); hashint_t last = i; while (!__lh3_isempty(flag, i) && !__lh3_key_equal(keys[i], key)) { if (i + inc >= m) i = i + inc - m; // inc < m, and so never write this line as: "i += inc - m;" else i += inc; if (i == last) return m; // fail to find } return i; } template inline hashint_t __lh3_hash_insert_aux(const keytype_t &key, hashint_t m, const keytype_t *keys, const __lh3_flag_t *flag) { hashint_t inc, k, i, site; site = m; k = __lh3_hash_fun(key); i = k % m; inc = 1 + k % (m - 1); hashint_t last = i; while (!__lh3_isempty(flag, i) && !__lh3_key_equal(keys[i], key)) { if (__lh3_isdel(flag, i)) site = i; if (i + inc >= m) i = i + inc - m; else i += inc; if (i == last) return site; } if (__lh3_isempty(flag, i) && site != m) return site; else return i; } template inline hashint_t __lh3_hash_erase_aux(const keytype_t &key, hashint_t m, const keytype_t *keys, __lh3_flag_t *flag) { if (!m) return 0; hashint_t i; i = __lh3_hash_search_aux(key, m, keys, flag); if (i != m && !__lh3_isempty(flag, i)) { if (__lh3_isdel(flag, i)) return m; // has been deleted __lh3_set_isdel_true(flag, i); // set "isdel" flag as "true" return i; } else return m; } /** "iterator" class for "hash_set_char" and "hash_set_misc" */ template class __lh3_hash_base_iterator { protected: hashint_t i; keytype_t *keys; __lh3_flag_t *flags; public: __lh3_hash_base_iterator() {} // No initialization. This is unsafe, but reasonable use will not cause any problems. __lh3_hash_base_iterator(hashint_t _i, keytype_t *_keys, __lh3_flag_t *_flags) { i = _i; keys = _keys; flags = _flags; } inline const keytype_t &operator & () { return keys[i]; } // Keys should never be changed by an iterator. inline const keytype_t &key() { return keys[i]; } // an alias of the operator "&" inline bool operator != (const __lh3_hash_base_iterator &iter) { return i != iter.i; } inline bool operator == (const __lh3_hash_base_iterator &iter) { return i == iter.i; } inline bool operator < (const __lh3_hash_base_iterator &iter) { return i < iter.i; } inline bool operator > (const __lh3_hash_base_iterator &iter) { return i > iter.i; } inline void operator ++ () { ++i; } inline void operator ++ (int) { ++i; } inline void operator -- () { --i; } inline void operator -- (int) { --i; } inline bool isfilled() { return !__lh3_isboth(flags, i); } inline bool operator + () { return isfilled(); } // an alias of "isfilled()" }; /** "iterator" class for "hash_map_char" and "hash_map_misc" */ template class __lh3_hash_val_iterator : public __lh3_hash_base_iterator { protected: valtype_t *vals; public: __lh3_hash_val_iterator() {} __lh3_hash_val_iterator(hashint_t _i, keytype_t *_keys, __lh3_flag_t *_flags, valtype_t *_vals) { this->i = _i; this->keys = _keys; this->flags = _flags; vals = _vals; } inline valtype_t &operator * () { return vals[this->i]; } // Values can be changed here. inline const valtype_t &value() { return vals[this->i]; } // the following two functions are alternatives to the operator "*". inline void value(const valtype_t &v) { vals[this->i] = v; } }; /** Base class of all hash classes */ template class __lh3_hash_base_class { protected: hashint_t n_capacity; /**< maximum size of the hash table */ hashint_t n_size; /**< number of elements in hash table */ hashint_t n_occupied; /**< number of cells that have not been flaged as "isempty" (n_capacity >= n_occupied >= n_size) */ hashint_t upper_bound; /**< The upper bound. When n_occupied exceeds this, rehashing will be performed. */ __lh3_flag_t *flags; /**< flag array which stores the status "isempty" or "isdel" of each hash cell. */ keytype_t *keys; /**< array that stores hash keys */ // return 0 for unchanged, 1 for empty, 2 for deleted inline int direct_insert_aux(const keytype_t &key, hashint_t m, keytype_t *K, __lh3_flag_t *F, hashint_t *i) { *i = __lh3_hash_insert_aux(key, m, K, F); if (__lh3_isempty(F, *i)) { K[*i] = key; __lh3_set_isboth_false(F, *i); return 1; } else if (__lh3_isdel(F, *i)) { K[*i] = key; __lh3_set_isboth_false(F, *i); return 2; } else return 0; } inline bool resize_aux1(hashint_t *new_capacity, __lh3_flag_t **new_flags) { hashint_t t; t = __lh3_HASH_PRIME_SIZE - 1; while (__lh3_prime_list[t] > *new_capacity) --t; *new_capacity = __lh3_prime_list[t+1]; if (n_size >= hashint_t(*new_capacity * __lh3_HASH_UPPER + 0.5)) return false; // do not rehash keys = (keytype_t*)realloc(keys, *new_capacity * sizeof(keytype_t)); if (keys == 0) return false; // insufficient memory? *new_flags = (__lh3_flag_t*)malloc(*new_capacity * sizeof(__lh3_flag_t)); if (*new_flags == 0) { // insufficient memory? ::free(*new_flags); return false; } for (t = 0; t < ((*new_capacity>>__lh3_FLAG_SHIFT) + 1); ++t) (*new_flags)[t] = __lh3_FLAG_DEFAULT; return true; } inline void resize_aux2(hashint_t new_capacity, __lh3_flag_t *new_flags) { ::free(flags); flags = new_flags; n_capacity = new_capacity; n_occupied = n_size; upper_bound = hashint_t(n_capacity * __lh3_HASH_UPPER + 0.5); } /** Test whether rehashing is needed and perform rehashing if this is the fact. */ inline void rehash() { if (n_occupied >= upper_bound) { if (n_capacity > (n_size<<1)) resize(n_capacity - 1); // do not enlarge else resize(n_capacity + 1); // enlarge the capacity } } public: typedef __lh3_hash_base_iterator iterator; __lh3_hash_base_class(void) { keys = 0; flags = 0; n_capacity = n_size = n_occupied = upper_bound = 0;; } ~__lh3_hash_base_class(void) { ::free(keys); ::free(flags); } /** resize the hash table and perform rehashing */ inline bool resize(hashint_t new_capacity) { __lh3_flag_t *new_flags; if (!resize_aux1(&new_capacity, &new_flags)) return false; for (hashint_t j = 0; j != n_capacity; ++j) { if (__lh3_isboth(flags, j) == 0) { keytype_t key = keys[j]; // take out the key __lh3_set_isdel_true(flags, j); // mark "deleted" while (1) { hashint_t inc, k, i; k = __lh3_hash_fun(key); i = k % new_capacity; // calculate the new position inc = 1 + k % (new_capacity - 1); while (!__lh3_isempty(new_flags, i)) { if (i + inc >= new_capacity) i = i + inc - new_capacity; else i += inc; } __lh3_set_isempty_false(new_flags, i); if (i < this->n_capacity && __lh3_isboth(flags, i) == 0) { // something is here { keytype_t tmp = keys[i]; keys[i] = key; key = tmp; } // take it out __lh3_set_isdel_true(flags, i); } else { // put key and quit the loop keys[i] = key; break; } } } } resize_aux2(new_capacity, new_flags); return true; } /** get n_size */ inline hashint_t size(void) const { return n_size; }; /** get n_capacity */ inline hashint_t capacity(void) const { return n_capacity; }; /** the first iterator */ inline iterator begin() { return iterator(0, keys, flags); } /** the last iterator */ inline iterator end() { return iterator(n_capacity, keys, flags); } /** clear the hash table, but do not free the memory */ inline void clear(void) { if (flags) { for (hashint_t t = 0; t < ((n_capacity>>__lh3_FLAG_SHIFT) + 1); ++t) flags[t] = __lh3_FLAG_DEFAULT; } n_size = 0; } /** clear the hash table and free the memory */ inline void free() { ::free(keys); ::free(flags); keys = 0; flags = 0; n_capacity = n_size = n_occupied = upper_bound = 0;; } }; /** hash_set_misc class */ template class hash_set_misc : public __lh3_hash_base_class { public: hash_set_misc(void) {}; ~hash_set_misc(void) {}; /** search a key */ inline bool find(const keytype_t &key) const { hashint_t i = __lh3_hash_search_aux(key, this->n_capacity, this->keys, this->flags); return (i != this->n_capacity && __lh3_isboth(this->flags, i) == 0)? true : false; } /** insert a key */ inline bool insert(const keytype_t &key) { __lh3_hash_base_class::rehash(); hashint_t i; int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); if (ret == 0) return true; if (ret == 1) { ++(this->n_size); ++(this->n_occupied); } else ++(this->n_size); // then ret == 2 return false; } /** delete a key */ inline bool erase(const keytype_t &key) { hashint_t i = __lh3_hash_erase_aux(key, this->n_capacity, this->keys, this->flags); if (i != this->n_capacity) { --(this->n_size); return true; } else return false; } }; /** hash_map_misc class */ template class hash_map_misc : public hash_set_misc { valtype_t *vals; /** a copy of __lh3_hash_base_class::rehash() */ inline void rehash() { if (this->n_occupied >= this->upper_bound) { if (this->n_capacity > (this->n_size<<1)) resize(this->n_capacity - 1); else resize(this->n_capacity + 1); } } public: hash_map_misc(void) { vals = 0; }; ~hash_map_misc(void) { ::free(vals); }; typedef __lh3_hash_val_iterator iterator; /** analogy of __lh3_hash_base_class::resize(hashint_t) */ inline bool resize(hashint_t new_capacity) { __lh3_flag_t *new_flags; if (!__lh3_hash_base_class::resize_aux1(&new_capacity, &new_flags)) return false; vals = (valtype_t*)realloc(vals, sizeof(valtype_t) * new_capacity); if (vals == 0) { // insufficient enough memory? ::free(new_flags); return false; } for (hashint_t j = 0; j != this->n_capacity; ++j) { if (__lh3_isboth(this->flags, j) == 0) { keytype_t key = this->keys[j]; // take out the key valtype_t val = vals[j]; __lh3_set_isdel_true(this->flags, j); // mark "deleted" while (1) { hashint_t inc, k, i; k = __lh3_hash_fun(key); i = k % new_capacity; // calculate the new position inc = 1 + k % (new_capacity - 1); while (!__lh3_isempty(new_flags, i)) { if (i + inc >= new_capacity) i = i + inc - new_capacity; else i += inc; } __lh3_set_isempty_false(new_flags, i); if (i < this->n_capacity && __lh3_isboth(this->flags, i) == 0) { // something is here { keytype_t tmp = this->keys[i]; this->keys[i] = key; key = tmp; } // take it out { valtype_t tmp = vals[i]; vals[i] = val; val = tmp; } // take it out __lh3_set_isdel_true(this->flags, i); } else { // clear this->keys[i] = key; vals[i] = val; break; } } } } __lh3_hash_base_class::resize_aux2(new_capacity, new_flags); return true; } inline bool find(const keytype_t &key, valtype_t *q) const { hashint_t i = __lh3_hash_search_aux(key, this->n_capacity, this->keys, this->flags); if (i != this->n_capacity && __lh3_isboth(this->flags, i) == 0) { *q = vals[i]; return true; } else return false; } inline bool insert(const keytype_t &key, const valtype_t &val) { rehash(); hashint_t i; int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); vals[i] = val; if (ret == 0) return true; if (ret == 1) { ++(this->n_size); ++(this->n_occupied); } else ++(this->n_size); // then ret == 2 return false; } inline bool insert(const keytype_t &key, valtype_t **q) { rehash(); hashint_t i; int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); *q = vals + i; if (ret == 0) return true; if (ret == 1) { ++(this->n_size); ++(this->n_occupied); } else ++(this->n_size); // then ret == 2 return false; } inline bool erase(const keytype_t &key) { return hash_set_misc::erase(key); } inline bool erase(const keytype_t &key, valtype_t **q) { hashint_t i = __lh3_hash_erase_aux(key, this->n_capacity, this->keys, this->flags); if (i != this->n_capacity) { --(this->n_size); *q = vals + i; return true; } else return false; } inline iterator begin() { return iterator(0, this->keys, this->flags, vals); } inline iterator end() { return iterator(this->n_capacity, this->keys, this->flags, vals); } inline void free() { hash_set_misc::free(); ::free(vals); vals = 0; } }; typedef char *__lh3_char_t; /** hash_set_char class */ class hash_set_char : public __lh3_hash_base_class { protected: inline int insert_aux(const char *key, hashint_t m, char **K, __lh3_flag_t *F, hashint_t *i) { *i = __lh3_hash_insert_aux((const __lh3_char_t)key, m, K, F); if (__lh3_isempty(F, *i)) { K[*i] = strdup(key); __lh3_set_isboth_false(F, *i); return 1; } else if (__lh3_isdel(F, *i)) { K[*i] = strdup(key); __lh3_set_isboth_false(F, *i); return 2; } else return 0; } public: hash_set_char(void) {}; ~hash_set_char(void) { clear(); }; inline bool find(const char *key) const { hashint_t i = __lh3_hash_search_aux((const __lh3_char_t)key, this->n_capacity, this->keys, this->flags); return (i != this->n_capacity && __lh3_isboth(this->flags, i) == 0)? true : false; } inline bool insert(const char *key) { rehash(); hashint_t i; int ret = insert_aux(key, this->n_capacity, this->keys, this->flags, &i); if (ret == 0) return true; if (ret == 1) { ++(this->n_size); ++(this->n_occupied); } else ++(this->n_size); // then ret == 2 return false; } inline bool erase(const char *key) { hashint_t i = __lh3_hash_erase_aux((const __lh3_char_t)key, this->n_capacity, this->keys, this->flags); if (i != this->n_capacity) { ::free(this->keys[i]); this->keys[i] = 0; --(this->n_size); return true; } else return false; } inline void clear(void) { for (hashint_t i = 0; i != this->n_capacity; ++i) if (!__lh3_isboth(this->flags, i)) { ::free(this->keys[i]); this->keys[i] = 0; } __lh3_hash_base_class::clear(); } inline void free() { clear(); __lh3_hash_base_class::free(); } }; /** hash_map_char class */ template class hash_map_char : public hash_set_char { valtype_t *vals; inline void rehash() { if (this->n_occupied >= this->upper_bound) { if (this->n_capacity > (this->n_size<<1)) resize(this->n_capacity - 1); else resize(this->n_capacity + 1); } } public: typedef __lh3_hash_val_iterator iterator; hash_map_char(void) { vals = 0; }; ~hash_map_char(void) { clear(); ::free(vals); }; inline valtype_t &val(hashint_t i) { return vals[i]; } inline void val(hashint_t i, const valtype_t &v) { return vals[i] = v; } inline bool resize(hashint_t new_capacity) { __lh3_flag_t *new_flags; if (!resize_aux1(&new_capacity, &new_flags)) return false; vals = (valtype_t*)realloc(vals, sizeof(valtype_t) * new_capacity); if (vals == 0) { // insufficient enough memory? ::free(new_flags); return false; } for (hashint_t j = 0; j != this->n_capacity; ++j) { if (__lh3_isboth(this->flags, j) == 0) { char *key = this->keys[j]; // take out the key valtype_t val = vals[j]; __lh3_set_isdel_true(this->flags, j); // mark "deleted" while (1) { hashint_t inc, k, i; k = __lh3_hash_fun(key); i = k % new_capacity; // calculate the new position inc = 1 + k % (new_capacity - 1); while (!__lh3_isempty(new_flags, i)) { if (i + inc >= new_capacity) i = i + inc - new_capacity; else i += inc; } __lh3_set_isempty_false(new_flags, i); if (i < this->n_capacity && __lh3_isboth(this->flags, i) == 0) { // something is here { char* tmp = this->keys[i]; this->keys[i] = key; key = tmp; } // take it out { valtype_t tmp = vals[i]; vals[i] = val; val = tmp; } // take it out __lh3_set_isdel_true(this->flags, i); } else { // clear this->keys[i] = key; vals[i] = val; break; } } } } resize_aux2(new_capacity, new_flags); return true; } inline bool find(const char *key, valtype_t *q) const { hashint_t i = __lh3_hash_search_aux((const __lh3_char_t)key, this->n_capacity, this->keys, this->flags); if (i != this->n_capacity && __lh3_isboth(this->flags, i) == 0) { *q = vals[i]; return true; } else return false; } inline bool insert(const char *key, const valtype_t &val) { rehash(); hashint_t i; int ret = insert_aux(key, this->n_capacity, this->keys, this->flags, &i); vals[i] = val; if (ret == 0) return true; if (ret == 1) { ++(this->n_size); ++(this->n_occupied); } else ++(this->n_size); // then ret == 2 return false; } inline bool insert(const char *key, valtype_t **q) { rehash(); hashint_t i; int ret = insert_aux(key, this->n_capacity, this->keys, this->flags, &i); *q = vals + i; if (ret == 0) return true; if (ret == 1) { ++(this->n_size); ++(this->n_occupied); } else ++(this->n_size); // then ret == 2 return false; } inline bool erase(const char *key) { return hash_set_char::erase(key); } inline bool erase(const char *key, valtype_t **q) { hashint_t i = __lh3_hash_erase_aux((const __lh3_char_t)key, this->n_capacity, this->keys, this->flags); if (i != this->n_capacity) { ::free(this->keys[i]); this->keys[i] = 0; --(this->n_size); *q = vals + i; return true; } else return false; } inline iterator begin() { return iterator(0, this->keys, this->flags, vals); } inline iterator end() { return iterator(this->n_capacity, this->keys, this->flags, vals); } inline void free() { hash_set_char::free(); ::free(vals); vals = 0; } }; #endif // LH3_STDHASH_H_ maqview-0.2.5/MaqDataClient$Read.class0000644000265600020320000000375611010215174016654 0ustar tilleaadminÊþº¾2p E F G H I J K LM N O PQR S T U VW X YZ [\] ^`seq[BsizeBmap_qualinfo1info2cflagalt_qualseqidIposdistnamethis$0LMaqDataClient;(LMaqDataClient;)VCodeLineNumberTablegetRefId()IgetPos()J isComplement()Z StackMapTablegetSeq()Ljava/lang/String;`c getSeqQuals()[B getMapQualgetNametoStringMdM SourceFileMaqDataClient.java )* +e  ! ( $% &% java/lang/String +f  +g$name[%s] seq[%s] qual[%d] pos[%d] %sjava/lang/Object >7 67 =0h ij 12k il 34 ComplementForward mnoMaqDataClient$ReadRead InnerClasses[C[Ljava/lang/Object;()V([C)V([BII)Vjava/lang/IntegervalueOf(I)Ljava/lang/Integer;java/lang/Long(J)Ljava/lang/Long;format9(Ljava/lang/String;[Ljava/lang/Object;)Ljava/lang/String; MaqDataClient   !"#$%&%'%()* +,-E!*+µ*·*@¼µ*¼µ*$¼µ±. "(/0-*´¬.+12- *´z…­./34-3*´~ §¬.35@67-õ•¼YAUYCUYGUYTUL¼YaUYcUYgUYtUM*´¼:>*´¢L*´3š NU§4*´3?~¢,*´3z~4U§+*´3z4U„§ÿ²» Y· °.. 780:8;B<K=T>b?vA…;‹D5ÿ:8999!:;-`&*´¼L=*´¢+*´3?~‘T„§ÿè+°.HIJI$L5 ý <ú=0-*´ ¬.P>7-R%<$¢*´3™ „§ÿî» Y*´· °.TUV5ü?7-ˆ= ½Y*¶SY*¶SY*¶¸SY*¶¸SY*¶™§S¸°.Z5-ÿ68@AAÿ8@AABCDb _amaqview-0.2.5/stdhashc.h0000644000265600020320000000226010761137603014271 0ustar tilleaadmin#ifndef STDHASHC_H #define STDHASHC_H #include /* hashci */ typedef struct { void *ptr; } hashci_t; typedef int (*hashci_f)(const char *key, int value); #ifdef __cplusplus extern "C" { #endif hashci_t *hci_init(); void hci_destroy(hashci_t *h); int hci_put(hashci_t *h, const char *key, int value); int hci_del(hashci_t *h, const char *key); int hci_get(const hashci_t *h, const char *key, int *value); u_int32_t hci_size(hashci_t *h); u_int32_t hci_capacity(hashci_t *h); int hci_resize(hashci_t *h, u_int32_t new_size); void hci_traverse(hashci_t *h, hashci_f func); #ifdef __cplusplus } #endif /* hashii */ typedef struct { void *ptr; } hashii_t; typedef int (*hashii_f)(u_int32_t key, int value); #ifdef __cplusplus extern "C" { #endif hashii_t *hii_init(); void hii_destroy(hashii_t *h); int hii_put(hashii_t *h, u_int32_t key, int value); int hii_del(hashii_t *h, u_int32_t key); int hii_get(const hashii_t *h, u_int32_t key, int *value); u_int32_t hii_size(hashii_t *h); u_int32_t hii_capacity(hashii_t *h); int hii_resize(hashii_t *h, u_int32_t new_size); void hii_traverse(hashii_t *h, hashii_f func); #ifdef __cplusplus } #endif #endif maqview-0.2.5/btree.c0000644000265600020320000002043411051450644013563 0ustar tilleaadmin#include #include "btree.h" BTree* btree_init(){ BTree *tree; tree = (BTree*)malloc(sizeof(BTree)); tree->parent = NULL; tree->size = 0; tree->childs = NULL; tree->left = 0; tree->right = 0; tree->indexs[0] = tree->indexs[1] = 0; return tree; } void _trim_tree(BTree *tree){ int i; if(tree->childs){ if(tree->size < BTREE_MAX_NODES){ tree->childs = (BTree**)realloc(tree->childs, sizeof(BTree*) * tree->size); } for(i=0;isize;i++) _trim_tree(tree->childs[i]); } } /** * Return last node */ BTree* btree_append(BTree **root, BTree *last_node, int *layer_ref, int64_t index, int64_t value){ BTree *tree, *node, *n; int i, layer; layer = *layer_ref; node = last_node; if(value == node->right){ node->size ++; node->indexs[1] = index; return node; } else if(value < node->right){ fprintf(stderr, "** Value appended to BTree was not sorted(ASC), ignored %ld (%ld) at %s:%d\n", value, node->right, __FILE__, __LINE__); return node; } if(node->size < BTREE_MAX_ELEMENTS){ node->size ++; node->indexs[1] = index; n = node; for(i=1;i<=layer;i++){ n->right = value; n = n->parent; } return node; } for(i=1;iparent; if(node->size < BTREE_MAX_NODES){ break; } } if(i == layer){ layer ++; tree = btree_init(); tree->childs = (BTree**)malloc(sizeof(BTree*) * BTREE_MAX_NODES); tree->childs[0] = node; tree->size = 1; tree->left = node->left; node->parent = tree; node = tree; *root = tree; *layer_ref = layer; } for(;i>1;i--){ n = btree_init(); n->left = value; n->childs = (BTree**)malloc(sizeof(BTree*) * BTREE_MAX_NODES); n->parent = node; node->childs[node->size++] = n; node = n; } n = btree_init(); n->left = value; n->right = value; n->indexs[0] = index; n->indexs[1] = index; n->size = 1; n->parent = node; node->childs[node->size++] = n; node = n; for(i=1;i<=layer;i++){ n->right = value; n = n->parent; } return node; } BTree* btree_build(int (*get_next)(void *obj, int64_t last_index, int64_t *value), void *obj){ int i, layer; int64_t index; int64_t value; BTree *tree, *node, *n; tree = btree_init(); node = tree; index = 0; layer = 1; if(get_next(obj, index, &value)){ node->left = node->right = value; node->indexs[0] = node->indexs[1] = index; node->size ++; } else { return NULL; } while(get_next(obj, index, &value)){ index ++; if(value != node->right && node->size >= BTREE_MAX_ELEMENTS){ for(i=1;iparent; if(node->size < BTREE_MAX_NODES){ break; } } if(i == layer){ layer ++; tree = btree_init(); tree->childs = (BTree**)malloc(sizeof(BTree*) * BTREE_MAX_NODES); tree->childs[0] = node; tree->size = 1; tree->left = node->left; node->parent = tree; node = tree; } for(;i>1;i--){ n = btree_init(); n->left = value; n->childs = (BTree**)malloc(sizeof(BTree*) * BTREE_MAX_NODES); n->parent = node; node->childs[node->size++] = n; node = n; } n = btree_init(); n->left = value; n->right = value - 1; n->indexs[0] = index; n->parent = node; node->childs[node->size++] = n; node = n; } node->indexs[1] = index; if(node->right != value){ node->size ++; node->right = value; n = node; for(i=1;i<=layer;i++){ n->right = value; n = n->parent; } } } // _trim_tree(tree); return tree; } int64_t _get_min_index(BTree *tree){ while(tree->childs){ tree = tree->childs[0]; } return tree->indexs[0]; } int64_t _get_max_index(BTree *tree){ while(tree->childs){ tree = tree->childs[tree->size-1]; } return tree->indexs[1]; } /** * left : the index of element that no more than value * right: the index + 1 of element that no less than value * RETURN true, if find, visa verse */ BTree* btree_find(BTree *tree, int64_t value, int64_t *left, int64_t *right){ int i; if(value < tree->left){ *left = _get_min_index(tree); *right = *left; return NULL; } if(value > tree->right){ *left = _get_max_index(tree); *right = *left; return NULL; } while(tree->childs){ for(i=0;isize;i++){ if(value <= tree->childs[i]->right) break; } if(i == tree->size) return NULL; if(value < tree->childs[i]->left){ *right = _get_min_index(tree->childs[i]); while(1){ if(i){ *left = _get_max_index(tree->childs[i-1]); break; } else { for(i=0;iparent->size;i++){ if(tree == tree->parent->childs[i]) break; } tree = tree->parent; } } return NULL; } tree = tree->childs[i]; } *left = tree->indexs[0]; *right = tree->indexs[1]; return tree; } int btree_dump_core(FILE *out, BTree *tree){ int i, n; unsigned char ch; ch = (tree->childs != NULL); fwrite(&ch, 1, 1, out); fwrite(&tree->left, sizeof(int64_t), 1, out); fwrite(&tree->right, sizeof(int64_t), 1, out); fwrite(tree->indexs, sizeof(int64_t), 2, out); fwrite(&tree->size, sizeof(int), 1, out); n = 1; if(tree->childs){ for(i=0;isize;i++){ n += btree_dump_core(out, tree->childs[i]); } } return n; } int btree_dump(FILE *out, BTree *tree){ int n; if(tree == NULL){ n = 2; // Write signal 2 in output fwrite(&n, 1, 1, out); fflush(out); return 1; } n = btree_dump_core(out, tree); fflush(out); return n; } int btree_dump_gz_core(gzFile out, BTree *tree){ int i, n; unsigned char ch; ch = (tree->childs != NULL); gzwrite(out, &ch, 1); gzwrite(out, &tree->left, sizeof(int64_t)); gzwrite(out, &tree->right, sizeof(int64_t)); gzwrite(out, tree->indexs, 2 * sizeof(int64_t)); gzwrite(out, &tree->size, sizeof(int)); n = 1; if(ch){ for(i=0;isize;i++){ n += btree_dump_gz_core(out, tree->childs[i]); } } return n; } int btree_dump_gz(gzFile out, BTree *tree){ int n; if(tree == NULL){ n = 2; // Write signal 2 in output gzwrite(out, &n, 1); return 1; } n = btree_dump_gz_core(out, tree); return n; } BTree* btree_load(FILE *in){ BTree *tree, *node; int i; unsigned char ch; tree = (BTree*)malloc(sizeof(BTree)); tree->parent = NULL; fread(&ch, 1, 1, in); // Empty tree read, signal 2 if(ch == 2){ tree->left = 0; tree->right = 0; tree->size = 0; tree->indexs[0] = -1; tree->indexs[1] = -1; tree->childs = NULL; return tree; } fread(&tree->left, sizeof(int64_t), 1, in); fread(&tree->right, sizeof(int64_t), 1, in); fread(tree->indexs, sizeof(int64_t), 2, in); fread(&tree->size, sizeof(int), 1, in); if(ch){ tree->childs = (BTree**)malloc(sizeof(BTree*) * tree->size); for(i=0;isize;i++){ node = btree_load(in); node->parent = tree; tree->childs[i] = node; } } else { tree->childs = NULL; } return tree; } BTree* btree_load_gz(gzFile in){ BTree *tree, *node; int i; unsigned char ch; tree = (BTree*)malloc(sizeof(BTree)); tree->parent = NULL; gzread(in, &ch, 1); // Empty tree read, signal 2 if(ch == 2){ tree->left = 0; tree->right = 0; tree->size = 0; tree->indexs[0] = -1; tree->indexs[1] = -1; tree->childs = NULL; return tree; } gzread(in, &tree->left, sizeof(int64_t)); gzread(in, &tree->right, sizeof(int64_t)); gzread(in, tree->indexs, 2 * sizeof(int64_t)); gzread(in, &tree->size, sizeof(int)); if(ch){ tree->childs = (BTree**)malloc(sizeof(BTree*) * tree->size); for(i=0;isize;i++){ node = btree_load_gz(in); node->parent = tree; tree->childs[i] = node; } } else { tree->childs = NULL; } return tree; } void btree_free(BTree *tree){ int i; if(tree == NULL) return; if(tree->childs){ for(i=0;isize;i++) btree_free(tree->childs[i]); free(tree->childs); } free(tree); } #ifdef MAIN_BTREE int main(){ int i, l, r, layer; FILE *file; BTree *tree, *node; tree = btree_init(); node = tree; layer = 1; node->left = node->right = 0; node->indexs[0] = node->indexs[1] = 0; node->size ++; for(i=1;i<10240;i++){ node = btree_append(&tree, node, &layer, i, i); } if(btree_find(tree, 1234, &l, &r)){ printf("%d is between %d and %d\n", 1234, l, r); } else { printf("Error\n"); } file = fopen("test.idx", "w+"); if(file == NULL) perror("FILE OPEN FAILED"); btree_dump(file, tree); btree_free(tree); fseek(file, 0, SEEK_SET); tree = btree_load(file); fclose(file); if(btree_find(tree, 1234, &l, &r)){ printf("%d is between %d and %d\n", 1234, l, r); } else { printf("Error\n"); } btree_free(tree); return 0; } #endif maqview-0.2.5/socket_view.c0000644000265600020320000003463611051452465015020 0ustar tilleaadmin#include "socket_view.h" void custom_socket(int sock){ int yes, no; yes = 1; no = 0; setsockopt(sock, SOL_SOCKET, SO_DEBUG, &yes, sizeof(int)); setsockopt(sock, SOL_SOCKET, SO_KEEPALIVE, &yes, sizeof(int)); } int read_full(int fds, void *buffer, size_t size){ int num, count; count = 0; while(1){ num = read(fds, buffer + count, size - count); if(num < 0){ break; } else { count += num; if(count == size) break; } } return count; } #define my_write(fds, val) if(write(fds, &(val), sizeof(val)) != sizeof(val)) return -1 #define my_write_full(fds, buffer, size) if(write(fds, buffer, size) != size) return -1 int request_view_basement_info(int sock){ const unsigned char op = VIEW_OP_INFO; my_write(sock, op); return 1; } int send_view_basement_info(int sock, RefSeq *src){ int i, size; my_write(sock, src->cache->n_ref); for(i=0;icache->n_ref;i++){ my_write(sock, src->cache->ref_lengths[i]); size = strlen(src->cache->index->mm->ref_name[i]); my_write(sock, size); my_write_full(sock, src->cache->index->mm->ref_name[i], size); } return 1; } #define my_read(fds, val) if(read_full(fds, &(val), sizeof(val)) != sizeof(val)) return NULL #define my_read_full(fds, buffer, size) if(read_full(fds, buffer, size) != size) return NULL #define my_read2(fds, val) if(read_full(fds, &(val), sizeof(val)) != sizeof(val)) return -1 #define my_read_full2(fds, buffer, size) if(read_full(fds, buffer, size) != size) return -1 ViewInfo* recv_view_basement_info(int sock){ ViewInfo *info; int i, len; info = (ViewInfo*)malloc(sizeof(ViewInfo)); my_read(sock, info->n_ref); info->ref_names = (char**)malloc(sizeof(char*) * info->n_ref); info->ref_lengths = (int64_t*)malloc(sizeof(int64_t) * info->n_ref); for(i=0;in_ref;i++){ my_read(sock, info->ref_lengths[i]); my_read(sock, len); info->ref_names[i] = (char*)malloc(len + 1); my_read_full(sock, info->ref_names[i], len); info->ref_names[i][len] = 0; } info->last_code = 0; info->ref_id = 0; info->start = 0; info->end = -1; info->rd_size = 0; info->rd_cap = 1024; info->reads = (Read*)malloc(sizeof(Read) * info->rd_cap); info->cns_size = 0; info->cns_cap = 1024; info->seqs = (cns_t*)malloc(sizeof(cns_t) * info->cns_cap); return info; } int request_maq_data(int sock, int last_code, int ref_id, int64_t start, int64_t end){ const unsigned char op = VIEW_OP_FETCH; my_write(sock, op); my_write(sock, last_code); my_write(sock, ref_id); my_write(sock, start); my_write(sock, end); return 1; } int send_maq_data(int sock, RefSeq *refs, int code, int64_t start, int64_t end){ int s, e, size, i; int64_t pos, m; my_write(sock, code); my_write(sock, refs->cache->ref_id); i = 0; while(icache->size-1 && read_pos(refs->cache->reads[i].read.pos) < start){ i++; } s = i; while(icache->size-2 && read_pos(refs->cache->reads[i+1].read.pos) <= end) i++; e = i; size = e - s + 1; if(size > 0){ pos = read_pos(refs->cache->reads[s].read.pos); my_write(sock, pos); pos = read_pos(refs->cache->reads[e].read.pos); my_write(sock, pos); my_write(sock, size); my_write_full(sock, refs->cache->reads + refs->cache->offset + s, sizeof(Read) * size); m = start - refs->cns->start; size = refs->cns->size - m; my_write(sock, size); my_write_full(sock, refs->cns->seqs + refs->cns->offset + m, sizeof(cns_t) * (size)); } else { size = 0; my_write(sock, start); my_write(sock, start); my_write(sock, size); my_write(sock, size); } return 1; } int recv_maq_data(int sock, ViewInfo *info){ my_read2(sock, info->last_code); my_read2(sock, info->ref_id); my_read2(sock, info->start); my_read2(sock, info->end); my_read2(sock, info->rd_size); if(info->rd_size >= info->rd_cap){ info->rd_cap = info->rd_size; info->reads = (Read*)realloc(info->reads, sizeof(Read) * info->rd_cap); } if(info->rd_size) my_read_full2(sock, info->reads, sizeof(Read) * info->rd_size); my_read2(sock, info->cns_size); if(info->cns_size >= info->cns_cap){ info->cns_cap = info->cns_size; info->seqs = (cns_t*)realloc(info->seqs, sizeof(cns_t) * info->cns_cap); } if(info->cns_size) my_read_full2(sock, info->seqs, sizeof(cns_t) * info->cns_size); return 1; } ViewServer* createViewServer(const char *map_file, const char *cns_file, int listen_port, int max_conns){ ViewServer *server; MapIndex *index; RefSeq *refs; int i, j; struct sockaddr_in name; if(max_conns < 1) return NULL; server = (ViewServer*)malloc(sizeof(ViewServer)); server->v_max = max_conns; server->srcs = (RefSeq**)malloc(sizeof(RefSeq*) * server->v_max); for(i=0;iv_max;i++){ index = load_map_index(map_file, 0); if(index == NULL){ return NULL; } refs = (RefSeq*)malloc(sizeof(RefSeq)); refs->cache = read_cache_init(index); refs->show_id = 0; refs->show_start = 0; refs->tooltips = NULL; refs->cns = NULL; if(cns_file) refs->cns = open_cns_cache(cns_file); if(refs->cns == NULL) refs->cns = cns_cache_init(); else { justify_cns_cache(refs->cns, refs->cache->index->mm->ref_name, refs->cache->index->mm->n_ref); for(j=0;jcache->index->mm->n_ref;j++){ refs->cache->ref_lengths[j] = refs->cns->ref_lengths[j]; if(refs->cache->index->trees[j]->right < refs->cns->ref_lengths[j]){ refs->cache->index->trees[j]->right = refs->cns->ref_lengths[j]; } } } server->srcs[i] = refs; } server->socket = -1; server->socket = socket(PF_INET, SOCK_STREAM, 0); if(server->socket < 0){ perror("socket"); freeViewServer(server); return NULL; } name.sin_family = AF_INET; name.sin_port = htons(listen_port); name.sin_addr.s_addr = htonl(INADDR_ANY); if(bind(server->socket, (struct sockaddr *)&name, sizeof(name)) < 0){ perror("bind"); freeViewServer(server); return NULL; } server->stop = 1; server->debug = 0; return server; } int service_core(ViewServer *server, int sock){ unsigned char op; int i, ref_id, idx, last_idx, ret; int64_t start, end; RefSeq *refs; switch(read(sock, &op, 1)){ case 1: break; case 0: default: return -1; } switch(op){ case VIEW_OP_CLOSE: if(server->debug){ fprintf(stderr, " -- Server recv VIEW_OP_CLOSE in %s -- %s:%d --\n", __FUNCTION__, __FILE__, __LINE__); } return -1; case VIEW_OP_INFO: if(server->debug){ fprintf(stderr, " -- Server recv VIEW_OP_INFO in %s -- %s:%d --\n", __FUNCTION__, __FILE__, __LINE__); } return send_view_basement_info(sock, server->srcs[0]); case VIEW_OP_FETCH: if(server->debug){ fprintf(stderr, " -- Server recv VIEW_OP_FETCH in %s -- %s:%d --\n", __FUNCTION__, __FILE__, __LINE__); } my_read2(sock, last_idx); my_read2(sock, ref_id); my_read2(sock, start); my_read2(sock, end); if(last_idx < 0 || last_idx >= server->v_max) return -1; refs = server->srcs[last_idx]; idx = last_idx; for(i=0;iv_max;i++){ if(i == last_idx) continue; if(server->srcs[i]->show_id == ref_id){ if(refs->show_id != ref_id){ refs = server->srcs[i]; idx = i; } else { if(server->srcs[i]->show_start >= start && server->srcs[i]->show_start <= start + 32 * 1024){ if(refs->show_start >= start && refs->show_start <= start + 32 * 1024){ if(server->srcs[i]->show_start < refs->show_start){ refs = server->srcs[i]; idx = i; } } else { refs = server->srcs[i]; idx = i; } } } } } ret = read_cache_put(refs->cache, ref_id, start, end); if(ret < 0) return -1; refs->show_id = ref_id; refs->show_start = start; if(refs->cns->stream && ref_id >= 0 && ref_id < refs->cns->n_mm_ref && refs->cns->mm_map[ref_id] >= 0){ cns_cache_put(refs->cns, refs->cns->mm_map[ref_id], start, end); } else { cns_cache_guess(refs->cns, refs->cache); } if(server->debug){ fprintf(stderr, " -- Server fetch %d %ld %ld in %s -- %s:%d --\n", ref_id, start, end, __FUNCTION__, __FILE__, __LINE__); } return send_maq_data(sock, refs, idx, start, end); default: return 0; } } int runViewServer(ViewServer *server){ int i, sock, state; size_t size; fd_set active_fd_set, read_fd_set; struct timeval timeout; struct sockaddr_in clientname; if(listen(server->socket, server->v_max) < 0){ perror("listen"); return -1; } FD_ZERO(&active_fd_set); FD_SET(server->socket, &active_fd_set); server->stop = 0; while(!server->stop){ read_fd_set = active_fd_set; timeout.tv_sec = 5; timeout.tv_usec = 0; state = select(FD_SETSIZE, &read_fd_set, NULL, NULL, &timeout); if(state != 1) continue; for(i=0;isocket){ size = sizeof(clientname); sock = accept(server->socket, (struct sockaddr *)&clientname, &size); if(sock < 0){ perror("accept"); continue; } if(server->debug){ fprintf(stdout, "Server: connect from host %s, port %hd client_id(%d).\n", inet_ntoa(clientname.sin_addr), ntohs(clientname.sin_port), sock); } custom_socket(sock); FD_SET(sock, &active_fd_set); } else { switch(service_core(server, i)){ case VIEW_RES_ERROR: close(i); if(server->debug){ fprintf(stderr, " -- Close client(%d) in %s -- %s:%d --\n", i, __FUNCTION__, __FILE__, __LINE__); } FD_CLR(i, &active_fd_set); break; } } } } } for(i=0;isocket) continue; if(!FD_ISSET(i, &active_fd_set)) continue; close(i); } return 0; } void stopViewServer(ViewServer *server){ server->stop = 1; } void freeViewServer(ViewServer *server){ int i; if(server->socket >= 0) close(server->socket); for(i=0;iv_max;i++){ read_cache_free(server->srcs[i]->cache); close_cns_cache(server->srcs[i]->cns); free(server->srcs[i]); } free(server->srcs); free(server); } void freeViewInfo(ViewInfo *info){ int i; free(info->ref_lengths); free(info->reads); free(info->seqs); for(i=0;in_ref;i++){ free(info->ref_names[i]); } free(info->ref_names); free(info); } void freeViewClient(ViewClient *client){ if(client->info) freeViewInfo(client->info); free(client); } ViewClient* connectViewClient(char *host, int port){ ViewClient *client; int sock; struct sockaddr_in name; struct hostent *hostinfo; sock = socket(PF_INET, SOCK_STREAM, 0); if(sock < 0){ perror("socket"); return NULL; } custom_socket(sock); name.sin_family = AF_INET; name.sin_port = htons (port); hostinfo = gethostbyname (host); if (hostinfo == NULL){ fprintf (stderr, "Unknown host %s:%d.\n", host, port); return NULL; } name.sin_addr = *(struct in_addr *) hostinfo->h_addr; if(connect(sock, (struct sockaddr *) &name, sizeof(name)) < 0){ perror("connect"); return NULL; } client = (ViewClient*)malloc(sizeof(ViewClient)); client->socket = sock; if(request_view_basement_info(client->socket) == -1){ free(client); perror("write"); return NULL; } client->info = recv_view_basement_info(client->socket); if(client->info == NULL){ free(client); return NULL; } return client; } int fetch_maq_data(ViewClient *client, int ref_id, int64_t start, int64_t end){ if(request_maq_data(client->socket, client->info->last_code, ref_id, start, end) == VIEW_RES_ERROR) return VIEW_RES_ERROR; if(recv_maq_data(client->socket, client->info) == VIEW_RES_ERROR) return VIEW_RES_ERROR; return 1; } void closeViewClient(ViewClient *client){ const unsigned char op = VIEW_OP_CLOSE; if(client->socket >= 0){ write(client->socket, &op, sizeof(op)); close(client->socket); } freeViewClient(client); } void socketview_usage(char *prog){ printf( "Setup Server: %s -s [ [ []]]\n" "Run Client : %s -c [ ]\n", prog, prog); exit(0); } int print_map(char* ref_name, maplet *m1){ int j; FILE *fpout; fpout = stdout; fprintf(fpout, "%s\t%s\t%d\t%c\t%d\t%u\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t", m1->name, ref_name, (m1->pos>>1) + 1, (m1->pos&1)? '-' : '+', m1->dist, m1->flag, m1->map_qual, (signed char)m1->seq[MAX_READLEN-1], m1->alt_qual, m1->info1&0xf, m1->info2, m1->c[0], m1->c[1], m1->size); for (j = 0; j != m1->size; ++j) { if (m1->seq[j] == 0) fputc('n', fpout); else if ((m1->seq[j]&0x3f) < 27) fputc("acgt"[m1->seq[j]>>6&3], fpout); else fputc("ACGT"[m1->seq[j]>>6&3], fpout); } fputc('\t', fpout); for (j = 0; j != m1->size; ++j) fputc((m1->seq[j]&0x3f) + 33, fpout); fputc('\n', fpout); return 1; } int main(int argc, char **argv){ ViewServer *server; ViewClient *client; int i, c; int ref_id; int64_t start, end; char *host, *map_file, *cns_file; int port; c = 0; c = getopt(argc, argv, "sc"); if(c == -1) socketview_usage(argv[0]); host = map_file = cns_file = NULL; if(c == 's'){ if(argc > optind) port = atoi(argv[optind++]); else socketview_usage(argv[0]); if(argc > optind) map_file = argv[optind++]; else socketview_usage(argv[0]); if(argc > optind) cns_file = argv[optind++]; else cns_file = NULL; server = createViewServer(map_file, cns_file, port, 6); server->debug = 1; if(server == NULL){ printf("Cannot create View\n"); return 1; } runViewServer(server); exit(0); } else if(c == 'c'){ if(argc > optind) host = argv[optind++]; else socketview_usage(argv[0]); if(argc > optind) port = atoi(argv[optind++]); else socketview_usage(argv[0]); if(argc > optind) ref_id = atoi(argv[optind++]); else ref_id = -1; if(argc > optind) start = atol(argv[optind++]) - 1; else start = 0; if(argc > optind) end = atol(argv[optind++]) - 1; else end = 0; client = connectViewClient(host, port); if(client == NULL){ fprintf(stderr, "Cannot connect to %s:%d\n", host, port); return 1; } if(ref_id == -1){ printf("Number of references: %d\n", client->info->n_ref); for(i=0;iinfo->n_ref;i++){ printf("%d\t%s\t%ld\n", i, client->info->ref_names[i], client->info->ref_lengths[i]); } } else { if(fetch_maq_data(client, ref_id, start, end) == -1){ fprintf(stderr, "Error in fetching maq data\n"); } else { for(i=0;iinfo->cns_size;i++){ printf("%c", cns_get_ref(client->info->seqs[i])); } printf("\n"); for(i=0;iinfo->cns_size;i++){ printf("%c", cns_get_cns(client->info->seqs[i])); } printf("\n"); for(i=0;iinfo->rd_size;i++){ print_map(client->info->ref_names[client->info->ref_id], &(client->info->reads[i].read)); } } } closeViewClient(client); } else { printf("Unknown option %c\n", c); socketview_usage(argv[0]); } return 0; } maqview-0.2.5/inffast.h0000644000265600020320000000072210761137603014123 0ustar tilleaadmin/* inffast.h -- header to use inffast.c * Copyright (C) 1995-2003 Mark Adler * For conditions of distribution and use, see copyright notice in zlib.h */ /* WARNING: this file should *not* be used by applications. It is part of the implementation of the compression library and is subject to change. Applications should only use zlib.h. */ void inflate_fast OF((z_streamp strm, unsigned start)); void inflate_fast_zr OF((z_streamp strm, unsigned start)); maqview-0.2.5/maqview.h0000644000265600020320000001735011051452004014133 0ustar tilleaadmin#ifndef __MAQVIEW_RJ #define __MAQVIEW_RJ #ifdef __APPLE__ #include "GLUT/glut.h" #else #include #include #include "GL/glut.h" #ifdef HAVE_FREEGLUT #include "GL/freeglut_ext.h" #endif #endif #include #include #include #include "maqmap.h" #include "zrio.h" #include "maqmap_index.h" #include "caches.h" #define MAX_BASE_Q 30 /** * Stack */ typedef struct Stack { void **elements; int offset; int ptr; int capacity; } Stack; #define check_alloc(ptr) if(ptr == NULL){fprintf(stderr, "Cannot alloc memeory at %s line %d", __FILE__, __LINE__);exit(1);} #define stack_init(stack, n) stack=(Stack*)malloc(sizeof(Stack));\ check_alloc(stack);\ (stack)->offset=0;\ (stack)->ptr=0;\ (stack)->capacity=n;\ (stack)->elements=(void**)malloc(sizeof(void*)*(stack)->capacity);\ check_alloc(stack->elements) #define stack_free(stack) free((stack)->elements);free(stack) #define stack_push(stack,e) if(((stack)->ptr + (stack)->offset) >= (stack)->capacity){\ if((stack)->offset){\ memmove((stack)->elements, (stack)->elements + (stack)->offset, (stack)->offset * sizeof(void*));\ (stack)->offset = 0;\ } else {\ (stack)->capacity = (int)(((stack)->capacity)*1.5) + 1;\ (stack)->elements=(void**)realloc((stack)->elements, sizeof(void*) * ((stack)->capacity));\ check_alloc((stack)->elements);\ }\ }\ (stack)->elements[(stack)->ptr++] = (void*)(e) #define stack_pop(stack) ((stack)->elements[--(stack)->ptr + (stack)->offset]) #define stack_shift(stack, value) value = (stack)->element[(stack)->offset ++]; (stack)->ptr-- #define stack_unshift(stack, value) if((stack)->offset == 0){\ if((stack)->ptr + 4 > (stack)->capacity){\ (stack)->capacity = (stack)->ptr + 4;\ (stack)->elements=(void**)realloc((stack)->elements, sizeof(void*) * ((stack)->capacity));\ check_alloc((stack)->elements);\ memmove((stack)->elements + 4, (stack)->elements, 4 * sizeof(void*));\ (stack)->offset = 4;\ }\ }\ (stack)->elements[--(stack)->offset] = value;\ (stack)->ptr ++ #define stack_peer(stack,i) (stack)->elements[(stack)->offset + (stack)->ptr - (i)] #define stack_get(stack, i) (stack)->elements[(stack)->offset + (i)] #define stack_clear(stack) (stack)->ptr = 0 #define stack_size(stack) (stack->ptr) #define stack_clone(stack, clone) stack_init(clone, stack_size(stack));\ memcopy((clone)->elements, (stack)->elements, sizeof(void*) * stack_size(stack));\ (clone)->ptr = (stack)->ptr typedef struct RGBColor { float rgb[3]; } Color; typedef struct Bounds { int x; int y; int w; int h; } Bounds; #define SELECT_TYPE_NAVIGATION 1 #define SELECT_TYPE_REFSEQ 2 #define SELECT_TYPE_READ 3 typedef struct SelectObject { int id_start; int id_end; void *ptr; int type; struct SelectObject *next; } SelectObject; typedef struct { int center_x; int center_y; int square_size; int arrow_x; int arrow_y; int arrow_size; int state; /* 0: not selected; 1: selected */ } Navigation; struct View; #define NOTIFY (*notify)(void *observer, struct View *src, int event, int64_t last_x, int off_y) typedef struct { void **objects; void (**notify)(void *observer, struct View *src, int event, int64_t last_x, int off_y); int n_ob; } Observer; #define VIEW_MODE_CHARACTER 0 #define VIEW_MODE_SQUARE 1 #define VIEW_MODE_LINE 2 #define TOOLTIP_SIZE 4096 #define VIEW_EVENT_CLOSE 0 #define VIEW_EVENT_RESIZE 1 #define VIEW_EVENT_MOVE 2 #define VIEW_EVENT_GOTO 3 #define VIEW_EVENT_MARK_COL 4 #define VIEW_EVENT_MARK_REF 5 #define VIEW_EVENT_SELECT_READ 6 typedef struct View { char *map_file; char *cns_file; int width; int height; int style; float ch_width; /* max characters in refer sequence are showed */ Color *qual_color_table; Color *base_color_table; Color bgColor; Color default_color; Color ref_color; Color select_color; Color tip_color; Color nav_color; Color mismatch_color; Color line_forward_color; Color line_backward_color; void *font; void *big_font; float font_width; float font_height; float font_line_height; float base_width; float base_margin; float base_height; float base_line_height; float line_width; float line_height; float scale_x; float scale_y; int mode; char default_ref_char; RefSeq refs; Navigation nav; int layer_offset; int last_x, last_y; int old_x, old_y; int state; int rolling; int step; int selecting; Observer *observer; } View; /** * Default style : 0 */ View* createView(const char *map_file, const char *cns_file, int width, int height, int style); void observeView(View *view, void *observer, void (*notify)(void *obj, View *src, int event, int64_t last_x, int off_y)); void removeObserverView(View *view, void *object); void notifyView(View *view, int evt, int64_t x, int y); int view_goto(View *view, int ref_id, int64_t pos); int view_locate(View *view, char *ref_name, int64_t pos); void view_resize(View *view, int width, int height); View* view_clone(View *view); void closeView(View *view); #define MAX_LAYER 600 /* bit-wise flag for global_flag */ #define GF_HIDE_MAPQ 0x00000001u #define GF_HIDE_BASEQ 0x00000002u #define GF_IS_SINGLEQ 0x00000004u #define VP_CMD_OPEN 1 #define VP_CMD_CMD 2 struct GList; typedef struct ViewPanel { int parent_win_id; int win_id; int status_id; float off_x; float off_y; float width; float height; float status_width; float status_height; int64_t view_number; char view_string[120]; int string_n; int string_f; char err_string[120]; int err; char msg_string[120]; int msg; int _x, _y, _x1, _x2, _y1, _y2; // Register int command; int show_help; int interval; //time for rolling View *view; u_int32_t global_flag; void (*resize)(struct ViewPanel *vp, int w, int h); void (*paint)(struct ViewPanel *vp); int (*pick)(struct ViewPanel *vp, float x, float y, float size, void (*handle)(struct ViewPanel *vp, SelectObject *obj, int id)); void (*handle_left_pick)(struct ViewPanel *vp, SelectObject *obj, int id); void (*handle_right_pick)(struct ViewPanel *vp, SelectObject *obj, int id); void (*handle_mouse_over)(struct ViewPanel *vp, SelectObject *obj, int id); void (*paintStatusBar)(struct ViewPanel *vp); void (*timer)(struct ViewPanel *vp, int t); void (*mousePressed)(struct ViewPanel *vp, int button, int x, int y); void (*mouseReleased)(struct ViewPanel *vp, int button, int x, int y); void (*mouseDragged)(struct ViewPanel *vp, int x, int y); void (*mouseMoved)(struct ViewPanel *vp, int x, int y); void (*mouseWheel)(struct ViewPanel *vp, int wheel, int direction, int x, int y); void (*keyTyped)(struct ViewPanel *vp, unsigned char key, int x, int y); void (*specialKey)(struct ViewPanel *vp, int code, int x, int y); void (*synchronize)(void *observer, View *view, int event, int64_t last_x, int y); struct ViewPanel *owner; void **childs; int child_size; int child_capacity; struct GList* ref_menu; } ViewPanel; void drawString(float x, float y, char *str); ViewPanel* createViewPanel(int pw_id, View *view, float off_x, float off_y, float width, float height); int execute_cmd(ViewPanel *vp, char *cmd); ViewPanel* addViewPanel(ViewPanel *owner, const char *map_file, const char *cns_file, int view_style); void bindViewPanel(ViewPanel *self, int n); void unbindViewPanel(ViewPanel *self, int n); void removeViewPanel(ViewPanel *vp); typedef void (*CHILD_REPAINT)(void *child); void VP_addChild(ViewPanel *vp, void *child, CHILD_REPAINT repaint); void* VP_removeChild(ViewPanel *vp, void *child); #define WINDOW_TYPE_VIEWPANEL 1 #define WINDOW_TYPE_GLIST 2 extern void **vps; extern int *vp_types; extern int vps_size; ViewPanel* getCurrentViewPanel(); ViewPanel* getViewPanel(int win_id); void register_window(int win_id, void *obj, int win_type); int getMaxWin_id(); void closeViewPanel(ViewPanel *vp); void closeViewPanels(); #endif maqview-0.2.5/inffast.c0000644000265600020320000005505410761137603014126 0ustar tilleaadmin/* inffast.c -- fast decoding * Copyright (C) 1995-2004 Mark Adler * For conditions of distribution and use, see copyright notice in zlib.h */ #include "zutil.h" #include "inftrees.h" #include "inflate.h" #include "inffast.h" #ifndef ASMINF /* Allow machine dependent optimization for post-increment or pre-increment. Based on testing to date, Pre-increment preferred for: - PowerPC G3 (Adler) - MIPS R5000 (Randers-Pehrson) Post-increment preferred for: - none No measurable difference: - Pentium III (Anderson) - M68060 (Nikl) */ #ifdef POSTINC # define OFF 0 # define PUP(a) *(a)++ #else # define OFF 1 # define PUP(a) *++(a) #endif /* Decode literal, length, and distance codes and write out the resulting literal and match bytes until either not enough input or output is available, an end-of-block is encountered, or a data error is encountered. When large enough input and output buffers are supplied to inflate(), for example, a 16K input buffer and a 64K output buffer, more than 95% of the inflate execution time is spent in this routine. Entry assumptions: state->mode == LEN strm->avail_in >= 6 strm->avail_out >= 258 start >= strm->avail_out state->bits < 8 On return, state->mode is one of: LEN -- ran out of enough output space or enough available input TYPE -- reached end of block code, inflate() to interpret next block BAD -- error in block data Notes: - The maximum input bits used by a length/distance pair is 15 bits for the length code, 5 bits for the length extra, 15 bits for the distance code, and 13 bits for the distance extra. This totals 48 bits, or six bytes. Therefore if strm->avail_in >= 6, then there is enough input to avoid checking for available input while decoding. - The maximum bytes that a single length/distance pair can output is 258 bytes, which is the maximum length that can be coded. inflate_fast() requires strm->avail_out >= 258 for each loop to avoid checking for output space. */ void inflate_fast(strm, start) z_streamp strm; unsigned start; /* inflate()'s starting value for strm->avail_out */ { struct inflate_state FAR *state; unsigned char FAR *in; /* local strm->next_in */ unsigned char FAR *last; /* while in < last, enough input available */ unsigned char FAR *out; /* local strm->next_out */ unsigned char FAR *beg; /* inflate()'s initial strm->next_out */ unsigned char FAR *end; /* while out < end, enough space available */ #ifdef INFLATE_STRICT unsigned dmax; /* maximum distance from zlib header */ #endif unsigned wsize; /* window size or zero if not using window */ unsigned whave; /* valid bytes in the window */ unsigned write; /* window write index */ unsigned char FAR *window; /* allocated sliding window, if wsize != 0 */ unsigned long hold; /* local strm->hold */ unsigned bits; /* local strm->bits */ code const FAR *lcode; /* local strm->lencode */ code const FAR *dcode; /* local strm->distcode */ unsigned lmask; /* mask for first level of length codes */ unsigned dmask; /* mask for first level of distance codes */ code this; /* retrieved table entry */ unsigned op; /* code bits, operation, extra bits, or */ /* window position, window bytes to copy */ unsigned len; /* match length, unused bytes */ unsigned dist; /* match distance */ unsigned char FAR *from; /* where to copy match from */ /* copy state to local variables */ state = (struct inflate_state FAR *)strm->state; in = strm->next_in - OFF; last = in + (strm->avail_in - 5); out = strm->next_out - OFF; beg = out - (start - strm->avail_out); end = out + (strm->avail_out - 257); #ifdef INFLATE_STRICT dmax = state->dmax; #endif wsize = state->wsize; whave = state->whave; write = state->write; window = state->window; hold = state->hold; bits = state->bits; lcode = state->lencode; dcode = state->distcode; lmask = (1U << state->lenbits) - 1; dmask = (1U << state->distbits) - 1; /* decode literals and length/distances until end-of-block or not enough input data or output space */ do { if (bits < 15) { hold += (unsigned long)(PUP(in)) << bits; bits += 8; hold += (unsigned long)(PUP(in)) << bits; bits += 8; } this = lcode[hold & lmask]; dolen: op = (unsigned)(this.bits); hold >>= op; bits -= op; op = (unsigned)(this.op); if (op == 0) { /* literal */ Tracevv((stderr, this.val >= 0x20 && this.val < 0x7f ? "inflate: literal '%c'\n" : "inflate: literal 0x%02x\n", this.val)); PUP(out) = (unsigned char)(this.val); } else if (op & 16) { /* length base */ len = (unsigned)(this.val); op &= 15; /* number of extra bits */ if (op) { if (bits < op) { hold += (unsigned long)(PUP(in)) << bits; bits += 8; } len += (unsigned)hold & ((1U << op) - 1); hold >>= op; bits -= op; } Tracevv((stderr, "inflate: length %u\n", len)); if (bits < 15) { hold += (unsigned long)(PUP(in)) << bits; bits += 8; hold += (unsigned long)(PUP(in)) << bits; bits += 8; } this = dcode[hold & dmask]; dodist: op = (unsigned)(this.bits); hold >>= op; bits -= op; op = (unsigned)(this.op); if (op & 16) { /* distance base */ dist = (unsigned)(this.val); op &= 15; /* number of extra bits */ if (bits < op) { hold += (unsigned long)(PUP(in)) << bits; bits += 8; if (bits < op) { hold += (unsigned long)(PUP(in)) << bits; bits += 8; } } dist += (unsigned)hold & ((1U << op) - 1); #ifdef INFLATE_STRICT if (dist > dmax) { strm->msg = (char *)"invalid distance too far back"; state->mode = BAD; break; } #endif hold >>= op; bits -= op; Tracevv((stderr, "inflate: distance %u\n", dist)); op = (unsigned)(out - beg); /* max distance in output */ if (dist > op) { /* see if copy from window */ op = dist - op; /* distance back in window */ if (op > whave) { strm->msg = (char *)"invalid distance too far back"; state->mode = BAD; break; } from = window - OFF; if (write == 0) { /* very common case */ from += wsize - op; if (op < len) { /* some from window */ len -= op; do { PUP(out) = PUP(from); } while (--op); from = out - dist; /* rest from output */ } } else if (write < op) { /* wrap around window */ from += wsize + write - op; op -= write; if (op < len) { /* some from end of window */ len -= op; do { PUP(out) = PUP(from); } while (--op); from = window - OFF; if (write < len) { /* some from start of window */ op = write; len -= op; do { PUP(out) = PUP(from); } while (--op); from = out - dist; /* rest from output */ } } } else { /* contiguous in window */ from += write - op; if (op < len) { /* some from window */ len -= op; do { PUP(out) = PUP(from); } while (--op); from = out - dist; /* rest from output */ } } while (len > 2) { PUP(out) = PUP(from); PUP(out) = PUP(from); PUP(out) = PUP(from); len -= 3; } if (len) { PUP(out) = PUP(from); if (len > 1){ PUP(out) = PUP(from); } } } else { from = out - dist; /* copy direct from output */ do { /* minimum length is three */ PUP(out) = PUP(from); PUP(out) = PUP(from); PUP(out) = PUP(from); len -= 3; } while (len > 2); if (len) { PUP(out) = PUP(from); if (len > 1){ PUP(out) = PUP(from); } } } } else if ((op & 64) == 0) { /* 2nd level distance code */ this = dcode[this.val + (hold & ((1U << op) - 1))]; goto dodist; } else { strm->msg = (char *)"invalid distance code"; state->mode = BAD; break; } } else if ((op & 64) == 0) { /* 2nd level length code */ this = lcode[this.val + (hold & ((1U << op) - 1))]; goto dolen; } else if (op & 32) { /* end-of-block */ Tracevv((stderr, "inflate: end of block\n")); state->mode = TYPE; break; } else { strm->msg = (char *)"invalid literal/length code"; state->mode = BAD; break; } } while (in < last && out < end); /* return unused bytes (on entry, bits < 8, so in won't go too far back) */ len = bits >> 3; in -= len; bits -= len << 3; hold &= (1U << bits) - 1; /* update state and return */ strm->next_in = in + OFF; strm->next_out = out + OFF; strm->avail_in = (unsigned)(in < last ? 5 + (last - in) : 5 - (in - last)); strm->avail_out = (unsigned)(out < end ? 257 + (end - out) : 257 - (out - end)); state->hold = hold; state->bits = bits; return; } /* inflate_fast() speedups that turned out slower (on a PowerPC G3 750CXe): - Using bit fields for code structure - Different op definition to avoid & for extra bits (do & for table bits) - Three separate decoding do-loops for direct, window, and write == 0 - Special case for distance > 1 copies to do overlapped load and store copy - Explicit branch predictions (based on measured branch probabilities) - Deferring match copy and interspersed it with decoding subsequent codes - Swapping literal/length else - Swapping window/direct else - Larger unrolled copy loops (three is about right) - Moving len -= 3 statement into middle of loop */ #define append_dist_window(state, val) if(state->dist_window_tail >= state->dmax) state->dist_window_tail = 0;\ state->dist_window[state->dist_window_tail++] = (unsigned short)val void inflate_fast_zr(strm, start) z_streamp strm; unsigned start; /* inflate()'s starting value for strm->avail_out */ { struct inflate_state FAR *state; unsigned char FAR *in; /* local strm->next_in */ unsigned char FAR *last; /* while in < last, enough input available */ unsigned char FAR *out; /* local strm->next_out */ unsigned char FAR *beg; /* inflate()'s initial strm->next_out */ unsigned char FAR *end; /* while out < end, enough space available */ #ifdef INFLATE_STRICT unsigned dmax; /* maximum distance from zlib header */ #endif unsigned wsize; /* window size or zero if not using window */ unsigned whave; /* valid bytes in the window */ unsigned write; /* window write index */ unsigned char FAR *window; /* allocated sliding window, if wsize != 0 */ unsigned long hold; /* local strm->hold */ unsigned bits; /* local strm->bits */ code const FAR *lcode; /* local strm->lencode */ code const FAR *dcode; /* local strm->distcode */ unsigned lmask; /* mask for first level of length codes */ unsigned dmask; /* mask for first level of distance codes */ code this; /* retrieved table entry */ unsigned op; /* code bits, operation, extra bits, or */ /* window position, window bytes to copy */ unsigned len; /* match length, unused bytes */ unsigned dist; /* match distance */ unsigned char FAR *from; /* where to copy match from */ /* copy state to local variables */ state = (struct inflate_state FAR *)strm->state; in = strm->next_in - OFF; last = in + (strm->avail_in - 5); out = strm->next_out - OFF; beg = out - (start - strm->avail_out); end = out + (strm->avail_out - 257); #ifdef INFLATE_STRICT dmax = state->dmax; #endif wsize = state->wsize; whave = state->whave; write = state->write; window = state->window; hold = state->hold; bits = state->bits; lcode = state->lencode; dcode = state->distcode; lmask = (1U << state->lenbits) - 1; dmask = (1U << state->distbits) - 1; /* decode literals and length/distances until end-of-block or not enough input data or output space */ do { if (bits < 15) { hold += (unsigned long)(PUP(in)) << bits; bits += 8; hold += (unsigned long)(PUP(in)) << bits; bits += 8; } this = lcode[hold & lmask]; dolen: op = (unsigned)(this.bits); hold >>= op; bits -= op; op = (unsigned)(this.op); if (op == 0) { /* literal */ Tracevv((stderr, this.val >= 0x20 && this.val < 0x7f ? "inflate: literal '%c'\n" : "inflate: literal 0x%02x\n", this.val)); PUP(out) = (unsigned char)(this.val); append_dist_window(state, 0); } else if (op & 16) { /* length base */ len = (unsigned)(this.val); op &= 15; /* number of extra bits */ if (op) { if (bits < op) { hold += (unsigned long)(PUP(in)) << bits; bits += 8; } len += (unsigned)hold & ((1U << op) - 1); hold >>= op; bits -= op; } Tracevv((stderr, "inflate: length %u\n", len)); if (bits < 15) { hold += (unsigned long)(PUP(in)) << bits; bits += 8; hold += (unsigned long)(PUP(in)) << bits; bits += 8; } this = dcode[hold & dmask]; dodist: op = (unsigned)(this.bits); hold >>= op; bits -= op; op = (unsigned)(this.op); if (op & 16) { /* distance base */ dist = (unsigned)(this.val); op &= 15; /* number of extra bits */ if (bits < op) { hold += (unsigned long)(PUP(in)) << bits; bits += 8; if (bits < op) { hold += (unsigned long)(PUP(in)) << bits; bits += 8; } } dist += (unsigned)hold & ((1U << op) - 1); #ifdef INFLATE_STRICT if (dist > dmax) { strm->msg = (char *)"invalid distance too far back"; state->mode = BAD; break; } #endif hold >>= op; bits -= op; Tracevv((stderr, "inflate: distance %u\n", dist)); op = (unsigned)(out - beg); /* max distance in output */ if (dist > op) { /* see if copy from window */ op = dist - op; /* distance back in window */ if (op > whave) { strm->msg = (char *)"invalid distance too far back"; state->mode = BAD; break; } from = window - OFF; if (write == 0) { /* very common case */ from += wsize - op; if (op < len) { /* some from window */ len -= op; do { PUP(out) = PUP(from); } while (--op); from = out - dist; /* rest from output */ } } else if (write < op) { /* wrap around window */ from += wsize + write - op; op -= write; if (op < len) { /* some from end of window */ len -= op; do { PUP(out) = PUP(from); append_dist_window(state, dist); } while (--op); from = window - OFF; if (write < len) { /* some from start of window */ op = write; len -= op; do { PUP(out) = PUP(from); append_dist_window(state, dist); } while (--op); from = out - dist; /* rest from output */ } } } else { /* contiguous in window */ from += write - op; if (op < len) { /* some from window */ len -= op; do { PUP(out) = PUP(from); append_dist_window(state, dist); } while (--op); from = out - dist; /* rest from output */ } } while (len > 2) { PUP(out) = PUP(from); append_dist_window(state, dist); PUP(out) = PUP(from); append_dist_window(state, dist); PUP(out) = PUP(from); append_dist_window(state, dist); len -= 3; } if (len) { PUP(out) = PUP(from); append_dist_window(state, dist); if (len > 1){ PUP(out) = PUP(from); append_dist_window(state, dist); } } } else { from = out - dist; /* copy direct from output */ do { /* minimum length is three */ PUP(out) = PUP(from); append_dist_window(state, dist); PUP(out) = PUP(from); append_dist_window(state, dist); PUP(out) = PUP(from); append_dist_window(state, dist); len -= 3; } while (len > 2); if (len) { PUP(out) = PUP(from); append_dist_window(state, dist); if (len > 1){ PUP(out) = PUP(from); append_dist_window(state, dist); } } } } else if ((op & 64) == 0) { /* 2nd level distance code */ this = dcode[this.val + (hold & ((1U << op) - 1))]; goto dodist; } else { strm->msg = (char *)"invalid distance code"; state->mode = BAD; break; } } else if ((op & 64) == 0) { /* 2nd level length code */ this = lcode[this.val + (hold & ((1U << op) - 1))]; goto dolen; } else if (op & 32) { /* end-of-block */ Tracevv((stderr, "inflate: end of block\n")); state->mode = TYPE; break; } else { strm->msg = (char *)"invalid literal/length code"; state->mode = BAD; break; } } while (in < last && out < end); /* return unused bytes (on entry, bits < 8, so in won't go too far back) */ len = bits >> 3; in -= len; bits -= len << 3; hold &= (1U << bits) - 1; /* update state and return */ strm->next_in = in + OFF; strm->next_out = out + OFF; strm->avail_in = (unsigned)(in < last ? 5 + (last - in) : 5 - (in - last)); strm->avail_out = (unsigned)(out < end ? 257 + (end - out) : 257 - (out - end)); state->hold = hold; state->bits = bits; return; } #endif /* !ASMINF */