queue : threadSpecificWaitQueues) {
OutputItem item = queue.peek();
while (item != null && item.rank == nextRank) {
if (allEmpty) {
allEmpty = false;
if (queue.size() > queueHighWaterMark)
queueHighWaterMark = queue.size();
}
try {
outputQueue.put(item);
} catch (InterruptedException e) {
Basic.caught(e);
}
nextRank++;
item = queue.poll(); // don't use take(), don't want to block here...
}
}
if (allEmpty) {
if (isClosing) {
outputQueue.put(SENTINEL);
return;
} else
try {
Thread.sleep(1);
} catch (InterruptedException e) {
Basic.caught(e);
}
}
}
} catch (InterruptedException ex) {
Basic.caught(ex);
}
});
thread1.start();
// this thread writes output to file
final Thread thread2 = new Thread(() -> {
try {
while (true) {
OutputItem item = outputQueue.take();
if (item == SENTINEL) {
hasFinishedOutput.countDown();
return;
}
byte[][] strings = item.strings;
if (strings != null) {
for (byte[] string : strings) {
byte b = 0;
for (byte aString : string) {
b = aString;
if (b == 0)
break; // zero-terminated byte string
writer.write((char) b);
}
if (b != '\t') // if this ends on a tab, don't add new line, it is the query-name for BlastTab or SAM
writer.write('\n');
}
}
}
} catch (Exception ex) {
Basic.caught(ex);
}
});
thread2.start();
}
/**
* close
*
* @throws java.io.IOException
*/
public void close() throws IOException {
isClosing = true;
try {
hasFinishedOutput.await();
} catch (InterruptedException e) {
Basic.caught(e);
}
if (fileFooter.length() > 0)
writer.write(fileFooter.toString());
writer.flush();
if (isFile)
writer.close();
/*
if (queueHighWaterMark > 1) {
System.err.println("(outputQueueHighWaterMark: " + queueHighWaterMark+")");
}
*/
}
/**
* Write byte strings to the out stream by rank.
* By rank means that output is generated only when all output of lower output
* has already been written
* Does not make a copy of the byte arrays, so shouldn't recycle because unclear when this will be written
* Then must not be overwritten
*
* @param rank each call must have a different rank and no rank can be skipped
* @param strings can be null
*/
public void writeByRank(int threadId, long rank, byte[][] strings) {
try {
threadSpecificWaitQueues[threadId].put(new OutputItem(rank, strings));
} catch (InterruptedException e) {
Basic.caught(e);
}
}
/**
* write a header and body by rank. By rank means that output is generated only when all output of lower output
* has already been written
* Does not make a copy of the byte arrays, so shouldn't recycle because unclear when this will be written
*
* @param rank
* @param header
* @param body
*/
public void writeByRank(int threadId, long rank, byte[] header, byte[] body) {
try {
threadSpecificWaitQueues[threadId].put(new OutputItem(rank, new byte[][]{header, body}));
} catch (InterruptedException e) {
Basic.caught(e);
}
}
/**
* skip a rank
*
* @param rank
*/
public void skipByRank(int threadId, int rank) {
try {
threadSpecificWaitQueues[threadId].put(new OutputItem(rank, null));
} catch (InterruptedException e) {
Basic.caught(e);
}
}
/**
* write this at the top of the file
*
* @param string
* @throws java.io.IOException
*/
public void writeFirst(String string) throws IOException {
writer.write(string);
}
/**
* write this at the end of the file
*
* @param string
* @throws java.io.IOException
*/
public void writeLast(String string) {
fileFooter.append(string);
}
}
/**
* output item consists of rank and bytes to write
*/
class OutputItem {
final long rank;
final byte[][] strings;
OutputItem(long rank, byte[][] strings) {
this.rank = rank;
this.strings = strings;
}
public String toString() {
StringBuilder buf = new StringBuilder();
buf.append("rank=").append(this.rank);
if (strings != null) {
for (byte[] string : strings) buf.append(Basic.toString(string));
}
return buf.toString();
}
}
malt-0.5.2/src/malt/io/RMA6Writer.java 0000664 0000000 0000000 00000027263 14004551276 0017371 0 ustar 00root root 0000000 0000000 /*
* RMA6Writer.java Copyright (C) 2020. Daniel H. Huson
*
* (Some files contain contributions from other authors, who are then mentioned separately.)
*
* 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 3 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, see .
*
*/
package malt.io;
import jloda.util.Basic;
import jloda.util.CanceledException;
import jloda.util.ProgressPercentage;
import malt.MaltOptions;
import malt.Version;
import malt.data.ReadMatch;
import malt.mapping.Mapping;
import malt.mapping.MappingManager;
import megan.classification.Classification;
import megan.core.ContaminantManager;
import megan.core.Document;
import megan.core.SyncArchiveAndDataTable;
import megan.data.IReadBlock;
import megan.data.IReadBlockIterator;
import megan.io.InputOutputReaderWriter;
import megan.rma6.MatchLineRMA6;
import megan.rma6.RMA6Connector;
import megan.rma6.RMA6FileCreator;
import java.io.IOException;
import java.util.Arrays;
/**
* Create an RMA6 file from SAM data in Malt
*
* Daniel Huson, 6.2015
*/
public class RMA6Writer {
private final RMA6FileCreator rma6FileCreator;
private final String rma6File;
private final boolean parseHeaders;
private final String[] cNames;
private final int maxMatchesPerQuery;
private final MaltOptions maltOptions;
private final MatchLineRMA6[] matches;
private final int[][] match2classification2id;
private byte[] queryText = new byte[10000];
private byte[] matchesText = new byte[10000];
/**
* constructor
*
* @param maltOptions
* @param rma6File
* @throws IOException
*/
public RMA6Writer(final MaltOptions maltOptions, String rma6File) throws IOException {
System.err.println("Starting file: " + rma6File);
this.maltOptions = maltOptions;
this.rma6File = rma6File;
this.parseHeaders = maltOptions.isParseHeaders();
maxMatchesPerQuery = maltOptions.getMaxAlignmentsPerQuery();
cNames = MappingManager.getCNames();
int taxonMapperIndex = Basic.getIndex(Classification.Taxonomy, Arrays.asList(cNames));
matches = new MatchLineRMA6[maxMatchesPerQuery];
for (int i = 0; i < matches.length; i++) {
matches[i] = new MatchLineRMA6(cNames.length, taxonMapperIndex);
}
match2classification2id = new int[maxMatchesPerQuery][cNames.length];
rma6FileCreator = new RMA6FileCreator(rma6File, true);
rma6FileCreator.writeHeader(Version.SHORT_DESCRIPTION, maltOptions.getMode(), cNames, false);
rma6FileCreator.startAddingQueries();
}
/**
* process the matches associated with a given query.
* This is used in malt1
*
* @param queryHeader
* @param matchesArray
* @param numberOfMatches
* @throws IOException
*/
public synchronized void processMatches(String queryHeader, String querySequence, ReadMatch[] matchesArray, int numberOfMatches) throws IOException {
// setup query text:
byte[] queryName = Basic.swallowLeadingGreaterSign(Basic.getFirstWord(queryHeader)).getBytes();
byte[] queryHeaderText = queryHeader.getBytes();
byte[] querySequenceText = querySequence.getBytes();
if (queryHeaderText.length + querySequenceText.length + 100 > queryText.length) {
queryText = new byte[100 + queryHeaderText.length + querySequenceText.length];
}
System.arraycopy(queryHeaderText, 0, queryText, 0, queryHeaderText.length);
int queryTextLength = queryHeaderText.length;
queryText[queryTextLength++] = '\n';
System.arraycopy(querySequenceText, 0, queryText, queryTextLength, querySequenceText.length);
queryTextLength += querySequenceText.length;
queryText[queryTextLength++] = '\n';
final String[] key = new String[cNames.length];
for (int i = 0; i < cNames.length; i++) {
key[i] = getKey(cNames[i]);
}
// setup matches text:
int matchesTextLength = 0;
numberOfMatches = Math.min(maxMatchesPerQuery, numberOfMatches);
for (int m = 0; m < numberOfMatches; m++) {
final ReadMatch match = matchesArray[m];
final byte[] matchText = match.getRMA6Text();
final int approximateLengthToAdd = matchesTextLength + matchText.length + queryName.length;
if (approximateLengthToAdd + 100 > matchesText.length) {
byte[] tmp = new byte[approximateLengthToAdd + 10000];
System.arraycopy(matchesText, 0, tmp, 0, matchesTextLength);
matchesText = tmp;
}
System.arraycopy(queryName, 0, matchesText, matchesTextLength, queryName.length);
matchesTextLength += queryName.length;
matchesText[matchesTextLength++] = '\t';
System.arraycopy(matchText, 0, matchesText, matchesTextLength, matchText.length);
matchesTextLength += matchText.length;
matchesText[matchesTextLength++] = '\n';
matches[m].setBitScore(match.getBitScore());
matches[m].setExpected(match.getExpected());
matches[m].setPercentIdentity(match.getPercentIdentity());
final String refHeader = (parseHeaders ? getWordAsString(match.getRMA6Text(), 2) : null);
for (int i = 0; i < cNames.length; i++) {
int id = 0;
if (parseHeaders)
id = parseIdInHeader(key[i], refHeader);
if (id == 0) {
Mapping mapping = MappingManager.getMapping(i);
if (mapping != null)
id = MappingManager.getMapping(i).get(match.getReferenceId());
}
match2classification2id[m][i] = id;
matches[m].setFId(i, id);
}
}
rma6FileCreator.addQuery(queryText, queryTextLength, numberOfMatches, matchesText, matchesTextLength, match2classification2id, 0);
}
private int parseIdInHeader(String key, String word) {
int pos = word.indexOf(key);
if (pos != -1) {
if (Basic.isInteger(word.substring(pos + key.length())))
return Basic.parseInt(word.substring(pos + key.length()));
}
return 0;
}
/**
* finish generation of RMA6 file
*
* @throws IOException
* @throws CanceledException
*/
public void close(String contaminantsFile) throws IOException {
try {
System.err.println("Finishing file: " + rma6File);
rma6FileCreator.endAddingQueries();
rma6FileCreator.writeClassifications(new String[0], null, null);
rma6FileCreator.close();
final boolean pairedReads = maltOptions.isPairedReads();
if (pairedReads) { // update paired reads info and then run dataprocessor
long count = 0;
try (InputOutputReaderWriter raf = new InputOutputReaderWriter(rma6File, "rw");
IReadBlockIterator it = (new RMA6Connector(rma6File)).getAllReadsIterator(0, 1000, false, false)) {
final ProgressPercentage progress = new ProgressPercentage("Linking paired reads");
progress.setProgress(0);
progress.setProgress(it.getMaximumProgress());
while (it.hasNext()) {
final IReadBlock readBlock = it.next();
if (readBlock.getMateUId() > 0) {
if (readBlock.getMateUId() > readBlock.getUId())
throw new IOException("Mate uid=" + readBlock.getMateUId() + ": too big");
raf.seek(readBlock.getMateUId());
raf.writeLong(readBlock.getUId());
count++;
}
progress.setProgress(it.getProgress());
}
progress.close();
System.err.printf("Number of pairs:%,14d%n", count);
}
}
// we need to run data processor
final Document doc = new Document();
doc.setTopPercent(maltOptions.getTopPercentLCA());
doc.setLcaAlgorithm(maltOptions.isUseWeightedLCA() ? Document.LCAAlgorithm.weighted : Document.LCAAlgorithm.naive);
doc.setLcaCoveragePercent(maltOptions.getLcaCoveragePercent());
doc.setMinSupportPercent(maltOptions.getMinSupportPercentLCA());
doc.setMinSupport(maltOptions.getMinSupportLCA());
doc.setMaxExpected((float) maltOptions.getMaxExpected());
doc.setMinScore((float) maltOptions.getMinBitScore());
doc.setPairedReads(pairedReads);
doc.setMaxExpected((float) maltOptions.getMaxExpected());
doc.setMinPercentIdentity(maltOptions.getMinPercentIdentityLCA());
doc.setUseIdentityFilter(maltOptions.isUsePercentIdentityFilterLCA());
doc.getActiveViewers().addAll(Arrays.asList(MappingManager.getCNames()));
doc.setReadAssignmentMode(Document.ReadAssignmentMode.readCount); // todo: make this an option
if (Basic.fileExistsAndIsNonEmpty(contaminantsFile)) {
ContaminantManager contaminantManager = new ContaminantManager();
contaminantManager.read(contaminantsFile);
doc.getDataTable().setContaminants(contaminantManager.getTaxonIdsString());
}
doc.getMeganFile().setFileFromExistingFile(rma6File, false);
doc.loadMeganFile();
doc.processReadHits();
// update and then save auxiliary data:
final String sampleName = Basic.replaceFileSuffix(Basic.getFileNameWithoutPath(rma6File), "");
SyncArchiveAndDataTable.syncRecomputedArchive2Summary(doc.getReadAssignmentMode(), sampleName, "LCA", doc.getBlastMode(), doc.getParameterString(), new RMA6Connector(rma6File), doc.getDataTable(), 0);
doc.saveAuxiliaryData();
} catch (CanceledException ex) {
throw new IOException(ex); // this can't happen because ProgressPercent never throws CanceledException
}
}
/**
* get key
*
* @param fName
* @return key
*/
private static String getKey(String fName) {
switch (fName.toLowerCase()) {
case "interpro2go":
return "ipr|";
case "eggnog":
return "cog|";
default:
return fName.toLowerCase() + "|";
}
}
/**
* get a word as string
*
* @param text
* @param whichWord
* @return string or null
*/
private static String getWordAsString(byte[] text, int whichWord) {
int start = -1;
whichWord--;
for (int i = 0; i < text.length; i++) {
if (Character.isWhitespace(text[i])) {
if (whichWord > 0) {
whichWord--;
if (whichWord == 0)
start = i;
} else if (whichWord == 0) {
return new String(text, start, i - start);
}
}
}
if (start >= 0)
return new String(text, start, text.length - start);
return null;
}
}
malt-0.5.2/src/malt/io/SAMHelper.java 0000664 0000000 0000000 00000041054 14004551276 0017241 0 ustar 00root root 0000000 0000000 /*
* SAMHelper.java Copyright (C) 2020. Daniel H. Huson
*
* (Some files contain contributions from other authors, who are then mentioned separately.)
*
* 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 3 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, see .
*
*/
package malt.io;
import jloda.util.BlastMode;
import malt.data.DNA5;
/**
* helps to create a SAM line from an alignment
* Daniel Huson, 8.2014
*/
public class SAMHelper {
private static final String FILE_HEADER_BLASTN_TEMPLATE = "@HD\tVN:1.5\tSO:unsorted\tGO:query\n@PG\tID:1\tPN:MALT\tCL:%s\tDS:BlastN\n@RG\tID:1\tPL:unknown\tSM:unknown\n@CO\tBlastN-like alignments\n" +
"@CO\tReporting AS: bitScore, ZR: rawScore, ZE: expected, ZI: percent identity, ZL: reference length\n";
private static final String FILE_HEADER_BLASTP_TEMPLATE = "@HD\tVN:1.5\tSO:unsorted\tGO:query\n@PG\tID:1\tPN:MALT\tCL:%s\tDS:BlastP\n@RG\tID:1\tPL:unknown\tSM:unknown\n@CO\tBlastP-like alignments\n" +
"@CO\tReporting AS: bitScore, ZR: rawScore, ZE: expected, ZI: percent identity, ZL: reference length\n";
private static final String FILE_HEADER_BLASTX_TEMPLATE = "@HD\tVN:1.5\tSO:unsorted\tGO:query\n@PG\tID:1\tPN:MALT\tCL:%s\tDS:BlastX\n@RG\tID:1\tPL:unknown\tSM:unknown\n@CO\tBlastX-like alignments\n" +
"@CO\tReporting AS: bitScore, ZR: rawScore, ZE: expected, ZI: percent identity, ZL: reference length, ZF: frame, ZS: query start DNA coordinate\n";
/*
0 QNAME String
1 FLAG Int
2 RNAME String
3 POS Int
4 MAPQ Int
5 CIGAR String
6 RNEXT String
7 PNEXT Int
8 TLEN Int
9 SEQ String
10 QUAL String Regexp/Range [!-?A-~]{1,255} [0,216 -1] \*|[!-()+-<>-~][!-~]* [0,229 -1][0,28 -1] \*|([0-9]+[MIDNSHPX=])+ \*|=|[!-()+-<>-~][!-~]* [0,229 -1] [-229 +1,229 -1] \*|[A-Za-z=.]+ [!-~]+
11 additional stuff including score and MD
*/
/**
* creates a SAM line. If queryHeader==null, does not output the initial query token
*
* @param mode
* @param queryHeader
* @param queryStart
* @param queryStartBlastX
* @param queryEnd
* @param queryLength
* @param alignedQuery
* @param referenceHeader
* @param referenceStart
* @param referenceEnd
* @param alignedReference
* @param referenceLength
* @param bitScore
* @param rawScore
* @param expected
* @param percentIdentity
* @param frame
* @param softClipped
* @return
*/
public static String createSAMLine(final BlastMode mode, final byte[] queryHeader, final byte[] querySequence, final int queryStart, final int queryStartBlastX, final int queryEnd, final int queryLength, final byte[] alignedQuery,
final byte[] referenceHeader, final int referenceStart, final int referenceEnd, final byte[] alignedReference, final int referenceLength,
final double bitScore, final int rawScore, final double expected, final float percentIdentity, int frame, final byte[] qualityValues, boolean softClipped) {
if (querySequence == null && softClipped)
softClipped = false;
final StringBuilder buffer = new StringBuilder();
// QNAME:
boolean first = true;
if (queryHeader != null) {
for (byte a : queryHeader) {
if (first && a == '>') {
first = false;
continue;
}
if (a == 0 || Character.isSpaceChar(a))
break;
buffer.append((char) a);
}
buffer.append('\t');
}
// FLAG
final boolean reverseComplemented = ((queryStart < queryEnd) != (referenceStart < referenceEnd));
final int queryOffset;
switch (mode) {
case BlastN:
if (reverseComplemented) {
queryOffset = queryLength - queryEnd;
buffer.append(0x10); // SEQ is reverse complemented
} else {
queryOffset = queryStart;
buffer.append(0);
}
break;
case BlastX:
if (reverseComplemented)
buffer.append(0x10); // SEQ is reverse complemented
else
buffer.append(0);
queryOffset = 0; // will explicitly save query start and query end
break;
default:
case BlastP:
queryOffset = queryStart;
buffer.append(0);
}
buffer.append('\t');
// RNAME:
first = true;
for (byte a : referenceHeader) {
if (first && a == '>') {
first = false;
continue;
}
if (a == 0 || Character.isSpaceChar(a))
break;
buffer.append((char) a);
}
buffer.append('\t');
// POS:
int pos = Math.min(referenceStart, referenceEnd);
buffer.append(pos);
buffer.append('\t');
// MAPQ
buffer.append("255"); // unknown
buffer.append('\t');
// CIGAR
appendCigar(alignedQuery, queryOffset, queryLength, alignedReference, reverseComplemented, softClipped, buffer);
buffer.append('\t');
// RNEXT
buffer.append("*"); // unknown
buffer.append('\t');
// PNEXT
buffer.append("0"); // unknown
buffer.append('\t');
// TLEN
buffer.append("0");
buffer.append('\t');
// SEQ
if (softClipped && querySequence != null) {
if (reverseComplemented) {
for (int i = queryLength - 1; i >= 0; i--) {
buffer.append((char) DNA5.getInstance().getBaseComplement(querySequence[i]));
}
} else {
for (int i = 0; i < queryLength; i++)
buffer.append((char) querySequence[i]);
}
} else {
if (reverseComplemented) {
for (int i = alignedQuery.length - 1; i >= 0; i--) {
byte a = alignedQuery[i];
if (a != '-')
buffer.append((char) DNA5.getInstance().getBaseComplement(a));
}
} else {
for (byte a : alignedQuery) {
if (a != '-')
buffer.append((char) a);
}
}
}
buffer.append('\t');
// QUAL
if (qualityValues == null)
buffer.append("*");
else {
if (softClipped) {
if (reverseComplemented) {
for (int i = queryLength - 1; i >= 0; i--)
buffer.append((char) qualityValues[i]);
} else {
for (int i = 0; i < queryLength; i++)
buffer.append((char) qualityValues[i]);
}
} else {
if (reverseComplemented) {
for (int i = queryStart; i < queryEnd; i++)
buffer.append((char) qualityValues[queryLength - (i + 1)]);
} else {
for (int i = queryStart; i < queryEnd; i++)
buffer.append((char) qualityValues[i]);
}
}
}
buffer.append('\t');
// optional stuff:
buffer.append(String.format("AS:i:%d\t", (int) Math.round(bitScore)));
buffer.append(String.format("NM:i:%d\t", computeEditDistance(alignedQuery, alignedReference)));
buffer.append(String.format("ZL:i:%d\t", referenceLength));
buffer.append(String.format("ZR:i:%d\t", rawScore));
buffer.append(String.format("ZE:f:%g\t", (float) expected));
buffer.append(String.format("ZI:i:%d\t", (int) Math.round(percentIdentity)));
if (mode == BlastMode.BlastX) {
buffer.append(String.format("ZF:i:%d\t", frame));
buffer.append(String.format("ZS:i:%d\t", queryStartBlastX));
}
appendMDString(alignedQuery, alignedReference, reverseComplemented, buffer);
return buffer.toString();
}
/**
* append the cigar string
*
* @param alignedQuery
* @param queryOffset
* @param queryLength
* @param alignedReference
* @param reverseComplemented
* @param softClipped
* @param buffer
*/
private static void appendCigar(byte[] alignedQuery, int queryOffset, int queryLength, byte[] alignedReference, boolean reverseComplemented, boolean softClipped, StringBuilder buffer) {
int clip = (!reverseComplemented ? queryOffset : (queryLength - queryOffset - alignedQuery.length));
if (clip > 0) {
buffer.append(clip).append(softClipped ? "S" : "H");
}
if (reverseComplemented) {
char state = 'M'; // M in match, I insert, D deletion
int count = 0;
for (int i = alignedQuery.length - 1; i >= 0; i--) {
if (alignedQuery[i] == '-') {
if (state == 'D') {
count++;
} else if (count > 0) {
buffer.append(count).append(state);
state = 'D';
count = 1;
}
} else if (alignedReference[i] == '-') {
if (state == 'I') {
count++;
} else if (count > 0) {
buffer.append(count).append(state);
state = 'I';
count = 1;
}
} else { // match or mismatch
if (state == 'M') {
count++;
} else if (count > 0) {
buffer.append(count).append(state);
state = 'M';
count = 1;
}
}
}
if (count > 0) {
buffer.append(count).append(state);
}
} else {
char cigarState = 'M'; // M in match, D deletion, I insertion
int count = 0;
for (int i = 0; i < alignedQuery.length; i++) {
if (alignedQuery[i] == '-') {
if (cigarState == 'D') {
count++;
} else if (count > 0) {
buffer.append(count).append(cigarState);
cigarState = 'D';
count = 1;
}
} else if (alignedReference[i] == '-') {
if (cigarState == 'I') {
count++;
} else if (count > 0) {
buffer.append(count).append(cigarState);
cigarState = 'I';
count = 1;
}
} else { // match or mismatch
if (cigarState == 'M') {
count++;
} else if (count > 0) {
buffer.append(count).append(cigarState);
cigarState = 'M';
count = 1;
}
}
}
if (count > 0) {
buffer.append(count).append(cigarState);
}
}
clip = (reverseComplemented ? queryOffset : (queryLength - queryOffset - alignedQuery.length));
if (clip > 0) {
buffer.append(clip).append(softClipped ? "S" : "H");
}
}
/**
* append the MD string
*
* @param alignedQuery
* @param alignedReference
* @param reverseComplemented
* @param buffer
*/
private static void appendMDString(final byte[] alignedQuery, final byte[] alignedReference, final boolean reverseComplemented, final StringBuilder buffer) {
buffer.append("MD:Z:");
if (reverseComplemented) {
int countMatches = 0;
boolean inDeletion = false;
for (int i = alignedQuery.length - 1; i >= 0; i--) {
if (alignedQuery[i] == '-') { // gap in query
if (countMatches > 0) {
buffer.append(countMatches);
countMatches = 0;
}
if (!inDeletion) {
buffer.append("^");
inDeletion = true;
}
buffer.append((char) (DNA5.getInstance().getBaseComplement(alignedReference[i])));
} else if (alignedReference[i] != '-') { // match or mismatch
if (alignedQuery[i] == alignedReference[i]) {
countMatches++;
} else {
if (inDeletion)
buffer.append(0);
if (countMatches > 0) {
buffer.append(countMatches);
countMatches = 0;
}
buffer.append((char) (DNA5.getInstance().getBaseComplement(alignedReference[i])));
}
if (inDeletion)
inDeletion = false;
}
// else alignedReference[i] == '-': this has no effect
}
if (countMatches > 0)
buffer.append(countMatches);
else if (inDeletion)
buffer.append(0);
} else {
int countMatches = 0;
boolean inDeletion = false;
for (int i = 0; i < alignedQuery.length; i++) {
if (alignedQuery[i] == '-') { // gap in query
if (countMatches > 0) {
buffer.append(countMatches);
countMatches = 0;
}
if (!inDeletion) {
buffer.append("^");
inDeletion = true;
}
buffer.append((char) alignedReference[i]);
} else if (alignedReference[i] != '-') { // match or mismatch
if (alignedQuery[i] == alignedReference[i]) {
countMatches++;
} else {
if (inDeletion)
buffer.append("0");
if (countMatches > 0) {
buffer.append(countMatches);
countMatches = 0;
}
buffer.append((char) alignedReference[i]);
}
if (inDeletion)
inDeletion = false;
}
// else alignedReference[i] == '-': this has no effect
}
if (countMatches > 0)
buffer.append(countMatches);
else if (inDeletion)
buffer.append(0);
}
}
/**
* compute edit distance from alignment
*
* @param alignedQuery
* @param alignedReference
* @return edit distance
*/
private static int computeEditDistance(byte[] alignedQuery, byte[] alignedReference) {
int distance = 0;
for (int i = 0; i < alignedQuery.length; i++) {
if (alignedQuery[i] == '-' || alignedReference[i] == '-' || alignedQuery[i] != alignedReference[i])
distance++;
}
return distance;
}
/**
* gets the SAM header line
*
* @param mode
* @return SAM header line or null
*/
public static String getSAMHeader(BlastMode mode, String commandLine) {
switch (mode) {
case BlastN:
return String.format(FILE_HEADER_BLASTN_TEMPLATE, (commandLine != null ? commandLine : ""));
case BlastP:
return String.format(FILE_HEADER_BLASTP_TEMPLATE, (commandLine != null ? commandLine : ""));
case BlastX:
return String.format(FILE_HEADER_BLASTX_TEMPLATE, (commandLine != null ? commandLine : ""));
default:
return "???";
}
}
}
malt-0.5.2/src/malt/mapping/ 0000775 0000000 0000000 00000000000 14004551276 0015636 5 ustar 00root root 0000000 0000000 malt-0.5.2/src/malt/mapping/Mapping.java 0000664 0000000 0000000 00000016274 14004551276 0020106 0 ustar 00root root 0000000 0000000 /*
* Mapping.java Copyright (C) 2020. Daniel H. Huson
*
* (Some files contain contributions from other authors, who are then mentioned separately.)
*
* 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 3 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, see .
*
*/
package malt.mapping;
import jloda.util.Basic;
import jloda.util.CanceledException;
import jloda.util.ProgressListener;
import jloda.util.ProgressPercentage;
import malt.data.ISequenceAccessor;
import malt.data.RefIndex2ClassId;
import megan.accessiondb.AccessAccessionMappingDatabase;
import megan.classification.Classification;
import megan.classification.IdParser;
import java.io.File;
import java.io.IOException;
import java.sql.SQLException;
import java.util.Collection;
import java.util.HashMap;
import java.util.Map;
/**
* Maintains mapping from Reference indices to classification
* Daniel Huson, 2.2016
*/
public class Mapping extends RefIndex2ClassId {
private final static String version = "V1.1";
private final String fName;
/**
* construct a table
*
* @param maxIndex
*/
public Mapping(String fName, int maxIndex) {
super(maxIndex);
this.fName = fName;
}
/**
* compute the mapping for the given reference database
*
* @param referencesDB
* @param progress
*/
public static Mapping create(String fName, ISequenceAccessor referencesDB, IdParser classificationMapper, ProgressListener progress) throws IOException {
final Mapping mapping = new Mapping(fName, referencesDB.getNumberOfSequences());
final String tag = Classification.createShortTag(fName);
progress.setMaximum(referencesDB.getNumberOfSequences());
progress.setProgress(0);
for (int i = 0; i < referencesDB.getNumberOfSequences(); i++) {
String header = Basic.toString(referencesDB.getHeader(i));
int classId = classificationMapper.getIdFromHeaderLine(header);
if (classId != 0) {
mapping.put(i, classId);
referencesDB.extendHeader(i, tag, classId);
}
progress.incrementProgress();
}
if (progress instanceof ProgressPercentage)
progress.close();
return mapping;
}
/**
* compute the mapping for the given reference database
*
* @param referencesDB
* @param progress
*/
public static Map create(Collection namesToUse, ISequenceAccessor referencesDB, AccessAccessionMappingDatabase mappingDatabase, ProgressListener progress) throws IOException, SQLException {
final Collection cNames = mappingDatabase.getClassificationNames();
final int maxIndex = cNames.stream().mapToInt(name -> {
try {
return mappingDatabase.getClassificationIndex(name);
} catch (SQLException throwables) {
throwables.printStackTrace();
return 0;
}
}).max().orElse(-1);
final Map mappings = new HashMap<>();
final String[] cIndex2Name = new String[maxIndex + 1];
final String[] tags = new String[maxIndex + 1];
{
int c = 0;
for (String cName : cNames) {
final int index = mappingDatabase.getClassificationIndex(cName) - 2;
if (namesToUse.contains(cName)) {
mappings.put(cName, new Mapping(cName, referencesDB.getNumberOfSequences()));
cIndex2Name[index] = cName;
tags[c] = Classification.createShortTag(cName);
}
c++;
}
}
progress.setMaximum(referencesDB.getNumberOfSequences());
progress.setProgress(0);
final int chunkSize = 10000;
final String[] accessions = new String[chunkSize];
for (int offset = 0; offset < referencesDB.getNumberOfSequences(); offset += chunkSize) {
final int numberInChunk = Math.min(chunkSize, referencesDB.getNumberOfSequences() - offset * chunkSize);
for (int r = 0; r < numberInChunk; r++) {
accessions[r] = getFirstWordAccession(referencesDB.getHeader(offset + r));
}
final Map accession2ids = mappingDatabase.getValues(accessions, numberInChunk);
for (int r = 0; r < numberInChunk; r++) {
if (accessions[r].length() > 0) {
final int[] ids = accession2ids.get(accessions[r]);
if (ids != null) {
//System.err.println((offset+r)+" -> "+Basic.toString(referencesDB.getHeader(offset + r))+" -> "+accessions[r]);
for (int c = 0; c < cIndex2Name.length; c++) {
if (cIndex2Name[c] != null) {
final int index = ids[c];
if (index != 0) {
//System.err.println(cIndex2Name[c]+" -> "+index);
mappings.get(cIndex2Name[c]).put(offset + r, index);
referencesDB.extendHeader(c, tags[c], index);
}
}
}
}
}
}
progress.setProgress(offset + numberInChunk);
}
return mappings;
}
public static String getFirstWordAccession(byte[] bytes) {
final String aLine = Basic.toString(bytes);
int a = 0;
while (a < aLine.length()) {
if (aLine.charAt(a) == '>' || aLine.charAt(a) == '@' || Character.isWhitespace(aLine.charAt(a)))
a++;
else
break;
}
int b = a + 1;
while (b < aLine.length()) {
if (Character.isLetterOrDigit(aLine.charAt(b)) || aLine.charAt(b) == '_')
b++;
else
break;
}
if (b - a > 4) {
return aLine.substring(a, b);
} else
return "";
}
/**
* save to a stream and then close the stream
*
* @param file
* @throws IOException
*/
public void save(File file) throws IOException {
super.save(file, makeMagicNumber(fName));
}
/**
* construct from an existing file
*
* @param file
* @throws IOException
* @throws CanceledException
*/
public Mapping(String fName, File file) throws IOException, CanceledException {
super(file, makeMagicNumber(fName));
this.fName = fName;
}
private static byte[] makeMagicNumber(String fName) {
return ("MA" + fName + version).getBytes();
}
}
malt-0.5.2/src/malt/mapping/MappingManager.java 0000664 0000000 0000000 00000007264 14004551276 0021400 0 ustar 00root root 0000000 0000000 /*
* MappingManager.java Copyright (C) 2020. Daniel H. Huson
*
* (Some files contain contributions from other authors, who are then mentioned separately.)
*
* 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 3 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, see .
*
*/
package malt.mapping;
import jloda.util.Basic;
import jloda.util.CanceledException;
import megan.classification.Classification;
import megan.classification.ClassificationManager;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
/**
* manages MALT mapping files
* Daniel Huson, 2.2016
*/
public class MappingManager {
private static String[] cNames;
private static int taxonomyIndex;
private static Mapping[] mappings;
/**
* load all mappings
*
* @param cNames
* @param indexDirectory
* @throws IOException
* @throws CanceledException
*/
public static void loadMappings(String[] cNames, String indexDirectory) throws IOException, CanceledException {
MappingManager.cNames = cNames;
mappings = new Mapping[cNames.length];
taxonomyIndex = -1;
for (int i = 0; i < cNames.length; i++) {
String cName = cNames[i];
if (cName.equals(Classification.Taxonomy))
taxonomyIndex = i;
String fileName = cName.toLowerCase() + ".idx";
ClassificationManager.ensureTreeIsLoaded(cName);
final File file = new File(indexDirectory, fileName);
if (file.exists())
mappings[i] = new Mapping(cName, file);
else
mappings[i] = null;
}
}
/**
* get all names of loaded mappings
*
* @return names
*/
public static String[] getCNames() {
return cNames;
}
/**
* gets the appopriate mapping for the given fID
*
* @param fID
* @return mapping
*/
public static Mapping getMapping(int fID) {
return mappings[fID];
}
/**
* gets the taxonomy mapping
*
* @return taxonomy mapping
*/
public static Mapping getTaxonomyMapping() {
if (taxonomyIndex >= 0)
return getMapping(taxonomyIndex);
else
return null;
}
/**
* determine all available classifications
*
* @param indexDirectory
* @return list of available classifications
*/
public static String[] determineAvailableMappings(String indexDirectory) {
File[] files = (new File(indexDirectory)).listFiles();
if (files != null) {
ArrayList cNames = new ArrayList<>(files.length);
for (File file : files) {
String name = file.getName();
if (name.endsWith(".tre")) {
name = Basic.replaceFileSuffix(name, "");
for (String cName : ClassificationManager.getAllSupportedClassifications()) {
if (cName.equalsIgnoreCase(name))
cNames.add(cName);
}
}
}
return cNames.toArray(new String[0]);
} else
return new String[0];
}
}
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malt-0.5.2/src/malt/resources/icons/malt-run48.png 0000664 0000000 0000000 00000010505 14004551276 0021752 0 ustar 00root root 0000000 0000000 PNG
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* Alphabet.java Copyright (C) 2020. Daniel H. Huson
*
* (Some files contain contributions from other authors, who are then mentioned separately.)
*
* 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 3 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, see .
*
*/
package malt.sequence;
import malt.data.INormalizer;
/**
* Alphabet base class
*
* Created by huson on 9/30/14.
*/
public class Alphabet implements INormalizer {
protected final byte alphabetSize;
protected final long[] letter2code;
protected final byte[] letter2normalized;
protected final byte[] code2letter;
protected final int bitsPerLetter;
protected final int unusedBits;
protected final int lettersPerWord;
protected final long letterMask;
protected final byte undefinedLetterCode;
protected final String definitionString;
/**
* constructor
*
* @param definitionString
* @param undefinedLetter
*/
public Alphabet(String definitionString, byte undefinedLetter) {
boolean isUndefinedContained = (definitionString.indexOf(undefinedLetter) != -1);
this.definitionString = definitionString.replaceAll("\\[", "").replaceAll("]", "").replaceAll("\\s+", " ");
String[] letterGroups = this.definitionString.split(" ");
alphabetSize = (byte) (letterGroups.length + (isUndefinedContained ? 0 : 1));
{
int bits = 1;
while (!(Math.pow(2, bits) > alphabetSize)) {
bits++;
}
bitsPerLetter = bits;
}
letterMask = (1L << bitsPerLetter) - 1;
lettersPerWord = 64 / bitsPerLetter;
unusedBits = 64 - lettersPerWord * bitsPerLetter;
System.err.println("Alphabet: " + definitionString + " bits: " + bitsPerLetter);
code2letter = new byte[alphabetSize + 1];
undefinedLetterCode = alphabetSize;
letter2code = new long[127];
letter2normalized = new byte[127];
for (int i = 0; i < 127; i++) {
letter2code[i] = undefinedLetterCode;
letter2normalized[i] = undefinedLetter;
}
code2letter[undefinedLetterCode] = undefinedLetter;
int bits = 1;
for (String letterGroup : letterGroups) {
for (int j = 0; j < letterGroup.length(); j++) {
int letter = Character.toLowerCase(letterGroup.charAt(j));
letter2code[letter] = bits;
letter = Character.toUpperCase(letterGroup.charAt(j));
letter2code[letter] = bits;
letter2normalized[letter] = (byte) letterGroup.charAt(0);
if (j == 0)
code2letter[bits] = (byte) letter;
}
// System.err.println(letterGroups[i]+" -> "+Integer.toBinaryString(bits)+" -> "+(char)code2letter[bits]);
bits++;
}
}
/**
* gets the alphabet size
*
* @return alphabet size
*/
public byte getAlphabetSize() {
return alphabetSize;
}
/**
* gets the number of bits used to encode a letter
*
* @return number of bits
*/
public int getBitsPerLetter() {
return bitsPerLetter;
}
/**
* gets the letter to code mapping
*
* @return letter to code
*/
public long[] getLetter2Code() {
return letter2code;
}
/**
* gets the code to letter mapping
*
* @return code to letter
*/
public byte[] getCode2Letter() {
return code2letter;
}
/**
* gets the mask used for a single letter
*
* @return letter mask
*/
public long getLetterMask() {
return letterMask;
}
/**
* gets the number of letters per 64-bit word
*
* @return letters per word
*/
public int getLettersPerWord() {
return lettersPerWord;
}
/**
* gets the number of unused bits
*
* @return number of unused (per 64-bit word)
*/
public int getUnusedBits() {
return unusedBits;
}
/**
* gets the code assigned to undefined letter
*
* @return code
*/
public byte getUndefinedLetterCode() {
return undefinedLetterCode;
}
/**
* gets the definition string
*
* @return defintion
*/
public String getDefinitionString() {
return definitionString;
}
/**
* returns normalized letter
*
* @param letter
* @return normalized letter
*/
@Override
public byte getNormalized(byte letter) {
return letter2normalized[letter];
}
}
malt-0.5.2/src/malt/sequence/DNA5Alphabet.java 0000664 0000000 0000000 00000004673 14004551276 0021020 0 ustar 00root root 0000000 0000000 /*
* DNA5Alphabet.java Copyright (C) 2020. Daniel H. Huson
*
* (Some files contain contributions from other authors, who are then mentioned separately.)
*
* 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 3 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, see .
*
*/
package malt.sequence;
/**
* DNA5 alphabet
* Created by huson on 9/30/14.
*/
public class DNA5Alphabet extends Alphabet {
private static DNA5Alphabet instance;
final static private byte[] normalizedComplement = {
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', '-', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'T',
'N', 'G', 'N', 'N', 'N', 'C', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'A', 'A', 'N', 'N',
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'T', 'N', 'G', 'N', 'N', 'N', 'C', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', 'N', 'N', 'A', 'A', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N'
};
/**
* gets the single instance of the protein alphabet
*
* @return instance
*/
public static DNA5Alphabet getInstance() {
if (instance == null)
instance = new DNA5Alphabet();
return instance;
}
/**
* constructor
*/
private DNA5Alphabet() {
super("A C G TU", (byte) 'N');
}
/**
* gets the reverse complement
*
* @param sequence
* @param reverseComplement
*/
public static void reverseComplement(byte[] sequence, byte[] reverseComplement) {
for (int i = 0; i < sequence.length; i++) {
reverseComplement[sequence.length - (i + 1)] = normalizedComplement[sequence[i]];
}
}
}
malt-0.5.2/src/malt/sequence/FastAFileIteratorCode.java 0000664 0000000 0000000 00000020421 14004551276 0022760 0 ustar 00root root 0000000 0000000 /*
* FastAFileIteratorCode.java Copyright (C) 2020. Daniel H. Huson
*
* (Some files contain contributions from other authors, who are then mentioned separately.)
*
* 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 3 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, see .
*
*/
package malt.sequence;
import jloda.util.Basic;
import java.io.BufferedInputStream;
import java.io.IOException;
/**
* Reads in a multifast file and places all headers in byte arrays and all sequences in encoded arrays
* Daniel Huson, 8.2014
*/
public class FastAFileIteratorCode {
private final SequenceEncoder sequenceEncoder;
private byte[] buffer = new byte[10000000];
private int length = 0;
private long position = 0;
private final long maxProgress;
private boolean expectingHeader = true;
private final BufferedInputStream inputStream;
private boolean isFastQ = false;
private boolean ok = true; // haven't seen next() fail yet
private boolean nextIsLoaded = false; // have already loaded the next item
/**
* constructor
*
* @param fileName
* @throws java.io.FileNotFoundException
*/
public FastAFileIteratorCode(final String fileName, final SequenceEncoder sequenceEncoder) throws IOException {
this.sequenceEncoder = sequenceEncoder;
inputStream = new BufferedInputStream(Basic.getInputStreamPossiblyZIPorGZIP(fileName), 8192);
maxProgress = Basic.guessUncompressedSizeOfFile(fileName);
try {
int value = inputStream.read();
isFastQ = (value == '@');
} catch (IOException e) {
}
}
/**
* has next header or sequence
*
* @return true if has a header or sequence
*/
public boolean hasNext() {
if (!ok)
return false;
else if (nextIsLoaded)
return true;
try {
if (isFastQ) { // expect four lines per read
try {
length = 0;
if (expectingHeader) {
buffer[length++] = (byte) '>';
int value = inputStream.read();
if (value == -1)
return ok = false;
if (value != '@')
buffer[length++] = (byte) value;
length = readLineIntoBuffer(inputStream, length);
position += length;
return ok = (length > 1);
} else {
length = readLineIntoBuffer(inputStream, length);
if (length == 0)
return ok = false;
position += length;
position += skipLine(inputStream); // skip comment line
position += skipLine(inputStream); // skip quality line
return ok = true;
}
} catch (IOException e) {
return ok = false;
}
} else {
int value;
length = 0;
boolean first = true;
try {
while (true) {
value = inputStream.read();
if (expectingHeader) {
if (value == -1)
return ok = false;
if (first) {
first = false;
if (value != '>')
buffer[length++] = '>';
}
if (value == '\n' || value == '\r') {
position += length;
return ok = (length > 0);
}
} else {
if (Character.isWhitespace(value))
continue; // skip white space
if (value == '>' || value == -1) {
position += length;
return ok = (length > 0);
}
}
if (length >= buffer.length)
growBuffer();
buffer[length++] = (byte) value;
}
} catch (IOException e) {
return ok = false;
}
}
} finally {
nextIsLoaded = true;
}
}
/**
* get next header
*
* @return header
*/
public byte[] nextHeader() {
try {
if (!nextIsLoaded && !hasNext())
return null;
if (expectingHeader)
expectingHeader = false;
else
nextSequenceCode(); // skip sequence
if (length > 0 || hasNext()) {
byte[] result = new byte[length];
System.arraycopy(buffer, 0, result, 0, length);
length = 0;
return result;
}
return null;
} finally {
nextIsLoaded = false;
}
}
/**
* get next sequence
*
* @return sequence
*/
public long[] nextSequenceCode() {
try {
if (!nextIsLoaded && !hasNext())
return null;
if (expectingHeader)
nextHeader(); // skip header
else
expectingHeader = true;
if (length > 0 || hasNext()) {
long[] result = sequenceEncoder.encode(buffer, length);
length = 0;
return result;
}
return null;
} finally {
nextIsLoaded = false;
}
}
/**
* read the next line into the buffer
*
* @param inputStream
* @param offset
* @return position of next available position in buffer
*/
private int readLineIntoBuffer(BufferedInputStream inputStream, int offset) throws IOException {
int value = inputStream.read();
while (value != '\r' && value != '\n' && value != -1) {
if (offset >= buffer.length) { // need to grow buffer
growBuffer();
}
buffer[offset++] = (byte) value;
value = inputStream.read();
}
return offset;
}
/**
* grows the line buffer
*/
private void growBuffer() {
byte[] nextBuffer = new byte[(int) Math.min(Integer.MAX_VALUE - 10L, 2 * buffer.length)];
System.arraycopy(buffer, 0, nextBuffer, 0, buffer.length);
buffer = nextBuffer;
}
/**
* skip the current line
*
* @param inputStream
* @throws java.io.IOException
*/
private int skipLine(BufferedInputStream inputStream) throws IOException {
int skipped = 0;
int value = inputStream.read();
while (value != '\r' && value != '\n' && value != -1) {
value = inputStream.read();
skipped++;
}
return skipped;
}
public void remove() {
}
/**
* close the stream
*
* @throws java.io.IOException
*/
public void close() throws IOException {
inputStream.close();
}
/**
* gets the maximum progress value
*
* @return maximum progress value
*/
public long getMaximumProgress() {
return maxProgress;
}
/**
* gets the current progress value
*
* @return current progress value
*/
public long getProgress() {
return position;
}
/**
* is the file we are reading actually a fastQ file?
*
* @return true, if fastQ
*/
public boolean isFastQ() {
return isFastQ;
}
}
malt-0.5.2/src/malt/sequence/ISeedExtractor.java 0000664 0000000 0000000 00000003521 14004551276 0021544 0 ustar 00root root 0000000 0000000 /*
* ISeedExtractor.java Copyright (C) 2020. Daniel H. Huson
*
* (Some files contain contributions from other authors, who are then mentioned separately.)
*
* 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 3 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, see .
*
*/
package malt.sequence;
/**
* seed extract
* Daniel Huson, 2014
*/
public interface ISeedExtractor {
byte[] decodeSeed(long seedCode, int seedWeight);
/**
* extract a seed from a sequence code
*
* @param seedShape
* @param seedWeight
* @param sequenceCode
* @param pos @return seed
*/
long getSeedCode(boolean[] seedShape, int seedWeight, long[] sequenceCode, int pos);
/**
* extract a seed from a sequence code
*
* @param seedShape
* @param seedWeight
* @param sequenceCode
* @param pos
* @param failValue value returned if sequence too short @return seed
*/
long getSeedCode(boolean[] seedShape, int seedWeight, long[] sequenceCode, int pos, int failValue);
/**
* is this a good seed?
*
* @param seedCode
* @return true, if good
*/
boolean isGoodSeed(long seedCode, int seedWeight);
/**
* get the number of bits per letter
*
* @return bits
*/
int getBitsPerLetter();
}
malt-0.5.2/src/malt/sequence/ProteinAlphabet.java 0000664 0000000 0000000 00000002570 14004551276 0021743 0 ustar 00root root 0000000 0000000 /*
* ProteinAlphabet.java Copyright (C) 2020. Daniel H. Huson
*
* (Some files contain contributions from other authors, who are then mentioned separately.)
*
* 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 3 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, see .
*
*/
package malt.sequence;
/**
* protein alphabet
* Daniel Huson, 2014
*/
public class ProteinAlphabet extends Alphabet {
private static ProteinAlphabet instance;
/**
* gets the single instance of the protein alphabet
*
* @return instance
*/
public static ProteinAlphabet getInstance() {
if (instance == null)
instance = new ProteinAlphabet();
return instance;
}
/**
* constructor
*/
private ProteinAlphabet() {
super("A C D E F G H I K L M N P Q R S T V W Y", (byte) 'X');
}
}
malt-0.5.2/src/malt/sequence/ProteinSequenceEncoder.java 0000664 0000000 0000000 00000014436 14004551276 0023277 0 ustar 00root root 0000000 0000000 /*
* ProteinSequenceEncoder.java Copyright (C) 2020. Daniel H. Huson
*
* (Some files contain contributions from other authors, who are then mentioned separately.)
*
* 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 3 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, see .
*
*/
package malt.sequence;
import jloda.util.Basic;
import jloda.util.ProgressPercentage;
import malt.data.SeedShape;
import java.io.IOException;
import java.util.Iterator;
/**
* test protein sequence encoder
* Created by huson on 9/30/14.
*/
public class ProteinSequenceEncoder {
/**
* test program
*
* @param args
* @throws java.io.IOException
*/
public static void main(String[] args) throws IOException {
SequenceEncoder encoder = new SequenceEncoder(ProteinAlphabet.getInstance());
ReducedAlphabet reducedAlphabet = new ReducedAlphabet(ProteinAlphabet.getInstance(), "DIAMOND_11");
byte[] sequence1 = "MKTKSSNNIKKIYYISSILVGIYLCWQIIIQIIFLMDNSIAILEAIGMVVFISVYSLAVAINGWILVGRMKKSSKKAQYE".getBytes();
System.err.println("set: " + Basic.toString(sequence1));
long[] encoded = encoder.encode(sequence1, sequence1.length, null);
byte[] sequence2 = encoder.decode(encoded);
System.err.println("get: " + Basic.toString(sequence2));
System.err.println("SAME: " + Basic.equal(sequence1, sequence2));
for (int i = 0; i < sequence2.length; i++) {
if (sequence2[i] != encoder.decode(encoder.getLetterCode(encoded, i)))
System.err.println((char) sequence2[i] + " != " + (char) encoder.getLetterCode(encoded, i));
}
System.err.print("It.: ");
for (Iterator it = encoder.getLetterIterator(encoded); it.hasNext(); ) {
System.err.print((char) (byte) it.next());
}
System.err.println();
int skip = 30;
System.err.print("It.: ");
for (int i = 0; i < skip; i++)
System.err.print(" ");
for (Iterator it = encoder.getLetterIterator(encoded, skip); it.hasNext(); ) {
System.err.print((char) (byte) it.next());
}
System.err.println();
int rev = 30;
System.err.print("It.: ");
for (Iterator it = encoder.getLetterReverseIterator(encoded, rev); it.hasNext(); ) {
System.err.print((char) (byte) it.next());
}
System.err.println(" reverse " + rev);
SeedShape2 seedShape = new SeedShape2(SeedShape.SINGLE_PROTEIN_SEED);
System.err.println("SeedShape: " + seedShape);
for (int i = 0; i < 5; i++) {
System.err.print("Span at " + i + ": ");
long[] span = encoder.getSeedSpanCode(seedShape.getLength(), encoded, i, null);
System.err.print(Basic.toString(encoder.decode(span)));
System.err.println();
long seedCode = encoder.getSeedCode(seedShape.getMask(), seedShape.getWeight(), encoded, i);
System.err.println("Full seed at " + i + ": " + Basic.toString(encoder.decodeSeed(seedCode, seedShape.getWeight()))
+ " " + Basic.toBinaryString(seedCode));
long reducedSeedCode = reducedAlphabet.getSeedCode(seedShape.getMask(), seedShape.getWeight(), encoded, i);
System.err.println("Reduced seed at " + i + ": " +
Basic.toString(reducedAlphabet.decodeSeed(reducedSeedCode, seedShape.getWeight()))
+ " " + Basic.toBinaryString(reducedSeedCode));
}
int limit = sequence1.length - seedShape.getLength();
long[] seeds = new long[2 * limit];
for (int i = 0; i < limit; i++) {
seeds[2 * i] = reducedAlphabet.getSeedCode(seedShape.getMask(), seedShape.getWeight(), encoded, i);
seeds[2 * i + 1] = i;
}
seeds = ProteinSequenceEncoder.radixSort2(seeds, seeds.length, 64 - reducedAlphabet.unusedBits, reducedAlphabet.bitsPerLetter, new ProgressPercentage("Sorting..."));
for (int i = 0; i < seeds.length; i += 2) {
System.err.printf("i=%3d pos=%3d seed=%s%n", i, seeds[i + 1], Basic.toString(reducedAlphabet.decodeSeed(seeds[i], seedShape.getWeight())));
}
}
/**
* radix sort list of longs, using entries with even index as keys and entries with odd indices as associated values
*
* @param array
* @param length
* @param w number of bits to use (64 to sort full numbers)
* @param d number of bits to consider at a time - in the case of 4-bit encoded letters: 4
* @return sorted array
*/
public static long[] radixSort2(long[] array, int length, int w, int d, final ProgressPercentage progress) {
if (length % 2 != 0)
throw new RuntimeException("radixSort2(length=" + length + "): length must be even");
final int steps = w / d;
long[] a = array;
long[] b = new long[length];
if (progress != null) {
progress.setMaximum(steps);
progress.setProgress(0);
}
for (int p = 0; p < steps; p++) {
final int[] c = new int[1 << d];
// the next three for loops implement counting-sort
for (int i = 0; i < length; i += 2) {
c[(int) ((a[i] >> d * p) & ((1 << d) - 1))]++;
}
for (int i = 1; i < 1 << d; i++)
c[i] += c[i - 1];
for (int i = length - 2; i >= 0; i -= 2) {
final int index = (--c[(int) ((a[i] >> d * p) & ((1 << d) - 1))]) << 1;
b[index] = a[i];
b[index + 1] = a[i + 1];
}
// swap arrays
final long[] tmp = b;
b = a;
a = tmp;
if (progress != null)
progress.setProgress(p);
}
return a;
}
}
malt-0.5.2/src/malt/sequence/ReducedAlphabet.java 0000664 0000000 0000000 00000020133 14004551276 0021671 0 ustar 00root root 0000000 0000000 /*
* ReducedAlphabet.java Copyright (C) 2020. Daniel H. Huson
*
* (Some files contain contributions from other authors, who are then mentioned separately.)
*
* 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 3 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, see .
*
*/
package malt.sequence;
import java.io.IOException;
import java.util.Map;
import java.util.TreeMap;
/**
* Reduced protein alphabet
* Daniel Huson, 9.2014
*/
public class ReducedAlphabet extends Alphabet implements ISeedExtractor {
private final Alphabet proteinAlphabet;
private final long[] proteinCode2ReducedCode;
private static Map reductions;
/**
* constructor
*
* @param proteinAlphabet
* @param reductionDefinition
*/
public ReducedAlphabet(final Alphabet proteinAlphabet, String reductionDefinition) throws IOException {
super(getReductionDefinition(reductionDefinition), (byte) 'X');
this.proteinAlphabet = proteinAlphabet;
proteinCode2ReducedCode = new long[proteinAlphabet.getCode2Letter().length];
for (int i = 1; i < proteinCode2ReducedCode.length; i++) {
proteinCode2ReducedCode[i] = getLetter2Code()[proteinAlphabet.getCode2Letter()[i]];
/*
System.err.println(Integer.toBinaryString(i)+" -> "+(char)proteinAlphabet.getCode2Letter()[i]+" -> "
+Integer.toBinaryString((int)proteinCode2ReducedCode[i]));
*/
}
}
/**
* decode a sequenceCode
*
* @param sequenceCode
* @param bytes sequence
* @return sequence length
*/
public int decode(long[] sequenceCode, byte[] bytes) {
int shift = 64 - bitsPerLetter;
int word = 0;
int length = 0;
while (true) {
byte bits = (byte) ((sequenceCode[word] & (letterMask << shift)) >>> shift);
if (bits == 0)
break;
bytes[length++] = code2letter[bits];
shift -= bitsPerLetter;
if (shift < 0) {
if (++word == sequenceCode.length)
break;
shift = 64 - bitsPerLetter;
}
}
return length;
}
/**
* decode a sequence
*
* @param seedCode
* @param seedWeight
* @return seed sequence
*/
@Override
public byte[] decodeSeed(long seedCode, int seedWeight) {
byte[] sequence = new byte[seedWeight];
decode(new long[]{seedCode << (64 - seedWeight * bitsPerLetter)}, sequence);
return sequence;
}
/**
* gets a seed code using the reduced alphabet
*
* @param seedShape
* @param seedWeight
* @param sequenceCode
* @param pos
* @return reduced code
*/
public long getSeedCode(final boolean[] seedShape, int seedWeight, long[] sequenceCode, int pos) {
return getSeedCode(seedShape, seedWeight, sequenceCode, pos, 0);
}
/**
* gets a seed code using the reduced alphabet
*
* @param seedShape
* @param seedWeight
* @param sequenceCode
* @param pos
* @param failValue value to return if seed extraction fails due to sequence being too short @return reduced code
*/
public long getSeedCode(final boolean[] seedShape, int seedWeight, long[] sequenceCode, int pos, int failValue) {
// this code is a bit tricky:
// we need to use protein alphabet encoding parameters to step through the sequence code
// we need to use reduced protein alphabet encoding parameters to compute seed code
long seed = 0;
int seedShift = (seedWeight - 1) * bitsPerLetter;
int word = pos / proteinAlphabet.lettersPerWord;
int letterInWord = pos - proteinAlphabet.lettersPerWord * word;
int shift = 64 - (letterInWord + 1) * proteinAlphabet.bitsPerLetter;
for (boolean aSeedShape : seedShape) {
if (aSeedShape) {
long bits = (sequenceCode[word] & (proteinAlphabet.letterMask << shift)) >>> shift;
if (bits == 0)
return failValue;
bits = proteinCode2ReducedCode[(int) bits];
seed |= (bits << seedShift);
seedShift -= bitsPerLetter;
}
shift -= proteinAlphabet.bitsPerLetter;
if (shift < 0) {
shift = 64 - proteinAlphabet.bitsPerLetter;
word++;
if (word == sequenceCode.length)
return failValue;
}
}
return seed;
}
/**
* get a reduction by name
*
* @param name
* @return reduction definition string or null
*/
public static String getReductionDefinition(String name) throws IOException {
if (reductions == null)
reductions = initReductions();
String value = reductions.get(name);
if (value == null) {
if (name.split(" ").length > 1)
return name;
else
throw new IOException("Unknown reduction: " + name);
}
return value;
}
/**
* is this a good seed? Yes, if it contains at least three different letters and none is undefined
*
* @param seedCode
* @return true, if good
*/
public boolean isGoodSeed(long seedCode, int seedWeight) {
int shift = 0;
byte a = 0;
byte b = 0;
byte c = 0;
while (shift < 64) {
byte bits = (byte) ((seedCode & (letterMask << shift)) >>> shift);
if (bits == 0)
break;
else if (bits == undefinedLetterCode)
return false;
if (a == 0)
a = bits;
else if (bits != a && b == 0)
b = bits;
else if (bits != a && bits != b && c == 0)
c = bits;
shift += bitsPerLetter;
}
return c != 0;
}
/**
* setup the set of all known reductions
*
* @return reductions
*/
private static Map initReductions() {
Map reductions = new TreeMap<>();
// From: Bioinformatics. 2009 June 1; 25(11): 1356–1362. Published online 2009 April 7. doi: 10.1093/bioinformatics/btp164:
reductions.put("GBMR4", "[ADKERNTSQ] [YFLIVMCWH*X] G P");
reductions.put("SDM12", "A D [KER] N [STQ] [YF] [LIVM*X] C W H G P");
reductions.put("HSDM17", "A D [KE] R N T S Q Y F [LIV*X] M C W H G P");
// Murphy, Lynne Reed and Wallqvist, Anders and Levy, Ronald M., 2000 :
reductions.put("BLOSUM50_4", "[LVIMC*] [AGSTP] [FYW] [EDNQKRH]");
reductions.put("BLOSUM50_8", "[LVIMC*] [AG] [ST] P [FYW] [EDNQ] [KR] H");
reductions.put("BLOSUM50_10", "[LVIM*] C A G [ST] P [FYW] [EDNQ] [KR] H");
reductions.put("BLOSUM50_11", "[LVIM*] C A G S T P [FYW] [EDNQ] [KR] H"); // this was produced from BLOSUM50_10 by separating S and T
reductions.put("BLOSUM50_15", "[LVIM*] C A G S T P [FY] W E D N Q [KR] H");
reductions.put("DIAMOND_11", "[KREDQN*] C G H [ILV] M F Y W P [STA]"); // DIAMOND default
// produced especially for MALT:
reductions.put("MALT_10", "[LVIM*X] C [AST] G P [WYF] [DEQ] N [RK] H");
// use these together to get good sensitivity:
reductions.put("MALT_12A", " [LVMI*WYF] C [AST] G P D E Q N R K H");
reductions.put("MALT_12B", " [LVM*I] W Y F C A S T G P [DEQNRK] H");
reductions.put("MALT_12C", "[LVIM*] C [AST] G P [FY] [DE] W N Q [KR] H");
reductions.put("UNREDUCED", "A D K E R N T S Q Y F L I V M C W H G P *");
return reductions;
}
}
malt-0.5.2/src/malt/sequence/SeedShape2.java 0000664 0000000 0000000 00000007062 14004551276 0020606 0 ustar 00root root 0000000 0000000 /*
* SeedShape2.java Copyright (C) 2020. Daniel H. Huson
*
* (Some files contain contributions from other authors, who are then mentioned separately.)
*
* 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 3 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, see .
*
*/
package malt.sequence;
import java.io.IOException;
/**
* seed shape
* Daniel Huson, 8.2014
*/
public class SeedShape2 {
private final boolean[] mask;
private final String shape;
private final int weight;
private int jumpToFirstZero = -1;
// Source for all seed patterns: Ilie et al. BMC Genomics 2011, 12:280 http://www.biomedcentral.com/1471-2164/12/280
public static final String SINGLE_DNA_SEED = "111110111011110110111111";
public static final String SINGLE_PROTEIN_SEED = "111101101110111";
public static final String[] PROTEIN_SEEDS = new String[]{"111101101110111", "1111000101011001111", "11101001001000100101111", "11101001000010100010100111"};
private int id; // id is 0,..,number of seed shapes-1
/**
* constructor
*
* @param shape
* @throws java.io.IOException
*/
public SeedShape2(String shape) throws IOException {
this.shape = shape;
mask = new boolean[shape.length()];
int ones = 0;
for (int i = 0; i < shape.length(); i++) {
if (shape.charAt(i) != '0') {
mask[i] = true;
ones++;
} else {
if (jumpToFirstZero == -1)
jumpToFirstZero = i;
}
}
weight = ones;
}
/**
* string representation of shaped seed
*
* @return string
*/
public String toString() {
return shape;
}
/**
* get bytes
*
* @return string as bytes
*/
public byte[] getBytes() {
return shape.getBytes();
}
/**
* length of spaced seed
*
* @return length
*/
public int getLength() {
return mask.length;
}
/**
* weight of spaced seed
*
* @return weight
*/
public int getWeight() {
return weight;
}
/**
* create correct size byte array for holding seed results
*
* @return bytes
*/
public byte[] createBuffer() {
return new byte[getWeight()];
}
/**
* compute the number of positions to jump over to get to first 0
*
* @return number of ones before first zero
*/
public int getJumpToFirstZero() {
return jumpToFirstZero;
}
/**
* gets the expected number of seeds
*
* @param numberOfSequences
* @param numberOfLetters
* @return expected number of seeds
*/
public long getMaxSeedCount(int numberOfSequences, long numberOfLetters, int numberOfJobs) {
return Math.max(1, numberOfLetters - numberOfSequences * (weight - 1)) / numberOfJobs;
}
public void setId(int id) {
this.id = id;
}
public int getId() {
return id;
}
public boolean[] getMask() {
return mask;
}
}
malt-0.5.2/src/malt/sequence/SequenceEncoder.java 0000664 0000000 0000000 00000027762 14004551276 0021744 0 ustar 00root root 0000000 0000000 /*
* SequenceEncoder.java Copyright (C) 2020. Daniel H. Huson
*
* (Some files contain contributions from other authors, who are then mentioned separately.)
*
* 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 3 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, see .
*
*/
package malt.sequence;
import java.util.Iterator;
/**
* sequence encoder
* Daniel Huson, 2014
*/
public class SequenceEncoder implements ISeedExtractor {
protected final int bitsPerLetter;
protected final int lettersPerWord;
protected final long letterMask;
protected final int unusedBits;
protected final long[] letter2code;
protected final byte[] code2letter;
protected final byte undefinedLetterCode;
/**
* constructor
*
* @param alphabet
*/
public SequenceEncoder(final Alphabet alphabet) {
bitsPerLetter = alphabet.getBitsPerLetter();
lettersPerWord = 64 / bitsPerLetter;
letterMask = alphabet.getLetterMask();
unusedBits = alphabet.getUnusedBits();
letter2code = alphabet.getLetter2Code();
code2letter = alphabet.getCode2Letter();
undefinedLetterCode = alphabet.getUndefinedLetterCode();
}
/**
* encode a sequence
*
* @param sequence
* @param length
* @param sequenceCode array to use or null
* @return encoded sequence
*/
public long[] encode(byte[] sequence, int length, long[] sequenceCode) {
int numberOfWords = length / lettersPerWord + 1;
if (sequenceCode == null || sequenceCode.length < numberOfWords)
sequenceCode = new long[numberOfWords];
int shift = 64 - bitsPerLetter;
int word = 0;
for (int i = 0; i < length; i++) {
sequenceCode[word] |= letter2code[sequence[i]] << shift;
shift -= bitsPerLetter;
if (shift < 0) {
shift = 64 - bitsPerLetter;
word++;
}
}
/*
for (int i = 0; i < numberOfWords; i++) {
System.err.println(Long.toBinaryString(sequenceCode[i]));
}
*/
return sequenceCode;
}
/**
* encode a sequence
*
* @param sequence
* @param length
* @return encoded sequence
*/
public long[] encode(byte[] sequence, int length) {
return encode(sequence, length, new long[length / lettersPerWord + 1]);
}
/**
* encode a sequence
*
* @param sequence
* @return encoded sequence
*/
public long[] encode(byte[] sequence) {
return encode(sequence, sequence.length, new long[sequence.length / lettersPerWord + 1]);
}
/**
* encode a single letter
*
* @param letter
* @return code
*/
public byte encode(byte letter) {
return (byte) letter2code[letter];
}
/**
* decode a sequenceCode
*
* @param sequenceCode
* @param bytes sequence
* @return sequence length
*/
public int decode(long[] sequenceCode, byte[] bytes) {
int shift = 64 - bitsPerLetter;
int word = 0;
int length = 0;
while (true) {
byte bits = (byte) ((sequenceCode[word] & (letterMask << shift)) >>> shift);
if (bits == 0)
break;
bytes[length++] = code2letter[bits];
shift -= bitsPerLetter;
if (shift < 0) {
if (++word == sequenceCode.length)
break;
shift = 64 - bitsPerLetter;
}
}
return length;
}
/**
* decode a sequence
*
* @param sequenceCode
* @return sequence
*/
public byte[] decode(long[] sequenceCode) {
byte[] sequence = new byte[computeLength(sequenceCode)];
decode(sequenceCode, sequence);
return sequence;
}
/**
* compute the length of the sequence. It is not stored explicitly.
*
* @param sequenceCode
* @return sequence length
*/
public int computeLength(long[] sequenceCode) {
int length = lettersPerWord * (sequenceCode.length - 1); // assume all but last word are full
int shift = 64 - bitsPerLetter;
final int word = sequenceCode.length - 1;
while (shift >= 0) {
byte bits = (byte) ((sequenceCode[word] & (letterMask << shift)) >>> shift);
if (bits == 0)
break;
length++;
shift -= bitsPerLetter;
}
return length;
}
/**
* get a letter
*
* @param sequenceCode
* @param pos
* @return letter
*/
public byte getLetterCode(long[] sequenceCode, int pos) {
int word = pos / lettersPerWord;
int letterInWord = pos - lettersPerWord * word;
int shift = 64 - (letterInWord + 1) * bitsPerLetter;
return (byte) ((sequenceCode[word] & (letterMask << shift)) >>> shift);
}
/**
* gets an getLetterCodeIterator over all letters
*
* @param sequenceCode
* @return getLetterCodeIterator
*/
public Iterator getLetterIterator(final long[] sequenceCode) {
return getLetterIterator(sequenceCode, 0);
}
/**
* gets an iterator over all letters.
* No check is performed to see whether pos is in range
*
* @param sequenceCode
* @return iterator
*/
public Iterator getLetterIterator(final long[] sequenceCode, final int pos) {
return new Iterator<>() {
private int word = pos / lettersPerWord;
private int shift = 64 - ((pos - lettersPerWord * word) + 1) * bitsPerLetter;
byte bits = (byte) ((sequenceCode[word] & (letterMask << shift)) >>> shift);
public boolean hasNext() {
return bits > 0;
}
public Byte next() {
byte result = decode(bits);
// get next bits:
shift -= bitsPerLetter;
if (shift < 0) {
word++;
shift = 64 - bitsPerLetter;
}
if (word < sequenceCode.length)
bits = (byte) ((sequenceCode[word] & (letterMask << shift)) >>> shift);
else
bits = 0;
// else done
return result;
}
public void remove() {
}
};
}
/**
* gets a reverse iterator over all letters.
* No check is performed to see whether pos is in range
*
* @param sequenceCode
* @return iterator
*/
public Iterator getLetterReverseIterator(final long[] sequenceCode, final int pos) {
return new Iterator<>() {
private int word = pos / lettersPerWord;
private int shift = 64 - ((pos - lettersPerWord * word) + 1) * bitsPerLetter;
byte bits = (byte) ((sequenceCode[word] & (letterMask << shift)) >>> shift);
public boolean hasNext() {
return bits > 0;
}
public Byte next() {
byte result = decode(bits);
shift += bitsPerLetter;
if (shift >= 64) {
shift = unusedBits;
word--;
}
if (word >= 0)
bits = (byte) ((sequenceCode[word] & (letterMask << shift)) >>> shift);
else
bits = 0;
return result;
}
public void remove() {
}
};
}
/**
* gets a seed code using the reduced alphabet
*
* @param seedShape
* @param seedWeight
* @param sequenceCode
* @param pos @return reduced code
*/
public long getSeedCode(final boolean[] seedShape, int seedWeight, long[] sequenceCode, int pos) {
return getSeedCode(seedShape, seedWeight, sequenceCode, pos, 0);
}
/**
* get the code for a given seed
*
* @param seedShape
* @param seedWeight
* @param sequenceCode
* @param pos
* @param failValue @return code
*/
public long getSeedCode(boolean[] seedShape, int seedWeight, long[] sequenceCode, int pos, int failValue) {
long seed = 0;
int seedShift = (seedWeight - 1) * bitsPerLetter;
int word = pos / lettersPerWord;
int letterInWord = pos - lettersPerWord * word;
int shift = 64 - (letterInWord + 1) * bitsPerLetter;
for (boolean aSeedShape : seedShape) {
if (aSeedShape) {
long bits = (sequenceCode[word] & (letterMask << shift)) >>> shift;
if (bits == 0)
return failValue;
// System.err.println(Long.toBinaryString(bits));
seed |= (bits << seedShift);
seedShift -= bitsPerLetter;
}
shift -= bitsPerLetter;
if (shift < 0) {
shift = 64 - bitsPerLetter;
word++;
if (word == sequenceCode.length)
return failValue;
}
}
return seed;
}
/**
* decodes a seed code. For debugging only
*
* @param seedCode
* @return bytes for seed
*/
public byte[] decodeSeed(long seedCode, int seedWeight) {
return decode(new long[]{seedCode << (64 - seedWeight * bitsPerLetter)});
}
/**
* decodes a letter code
*
* @param letterCode
* @return letter
*/
public byte decode(byte letterCode) {
return code2letter[letterCode];
}
/**
* get the code for sequence spanned by a seed
*
* @param seedLength
* @param sequenceCode
* @param pos
* @param seedWords
* @return
*/
public long[] getSeedSpanCode(int seedLength, long[] sequenceCode, int pos, long[] seedWords) {
if (seedWords == null)
seedWords = new long[1 + seedLength / lettersPerWord];
int seedWord = 0;
long seed = 0;
int seedShift = 64 - bitsPerLetter;
int word = pos / lettersPerWord;
int letterInWord = pos - lettersPerWord * word;
int shift = 64 - (letterInWord + 1) * bitsPerLetter;
for (int i = 0; i < seedLength; i++) {
long bits = (sequenceCode[word] & (letterMask << shift)) >>> shift;
seed |= (bits << seedShift);
seedShift -= bitsPerLetter;
shift -= bitsPerLetter;
if (shift < 0) {
shift = 64 - bitsPerLetter;
word++;
}
if (seedShift < 0) {
seedShift = 64 - bitsPerLetter;
seedWords[seedWord++] = seed;
seed = 0;
}
}
seedWords[seedWord] = seed;
return seedWords;
}
/**
* is this a good seed? Yes, if it contains at least two different letters and none is undefined
*
* @param seedCode
* @return true, if good
*/
public boolean isGoodSeed(long seedCode, int seedWeight) {
int shift = 0;
byte a = 0;
byte b = 0;
while (shift < 64) {
byte bits = (byte) ((seedCode & (letterMask << shift)) >>> shift);
if (bits == 0)
break;
else if (bits == undefinedLetterCode)
return false;
if (a == 0)
a = bits;
else if (bits != a && b == 0)
b = bits;
shift += bitsPerLetter;
}
return b != 0;
}
public int getBitsPerLetter() {
return bitsPerLetter;
}
}
malt-0.5.2/src/malt/sequence/SequenceStore.java 0000664 0000000 0000000 00000016563 14004551276 0021456 0 ustar 00root root 0000000 0000000 /*
* SequenceStore.java Copyright (C) 2020. Daniel H. Huson
*
* (Some files contain contributions from other authors, who are then mentioned separately.)
*
* 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 3 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, see .
*
*/
package malt.sequence;
import jloda.util.Basic;
import jloda.util.CanceledException;
import jloda.util.ProgressListener;
import jloda.util.ProgressPercentage;
import megan.io.OutputWriter;
import java.io.DataInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
/**
* Sequence store using encoded sequenceCodes
* Created by huson on 10/1/14.
*/
public class SequenceStore {
public final static int MAX_ARRAY_SIZE = Integer.MAX_VALUE - 8;
private final SequenceEncoder sequenceEncoder;
private int numberOfSequences;
private byte[][] headers;
private long[][] sequenceCodes;
/**
* constructor
*
* @param sequenceEncoder
* @param size
*/
public SequenceStore(final SequenceEncoder sequenceEncoder, final int size) {
this.sequenceEncoder = sequenceEncoder;
headers = new byte[size][];
sequenceCodes = new long[size][];
}
/**
* read sequences from a fastA or fastQ file
*
* @param it
* @param numberToRead
* @return number of sequences read
*/
public int readFromFastA(FastAFileIteratorCode it, int numberToRead, ProgressListener progress) throws CanceledException {
progress.setMaximum(numberToRead);
progress.setProgress(0);
numberOfSequences = 0;
while (it.hasNext()) {
if (numberOfSequences >= headers.length) {
grow();
}
headers[numberOfSequences] = it.nextHeader();
sequenceCodes[numberOfSequences] = it.nextSequenceCode();
numberOfSequences++;
if (numberOfSequences >= numberToRead)
break;
progress.incrementProgress();
}
return numberOfSequences;
}
/**
* write to a file in binary format
*
* @param fileName
*/
public void write(final String fileName) throws IOException {
try (OutputWriter outs = new OutputWriter(new File(fileName)); ProgressPercentage progress = new ProgressPercentage("Writing file: " + fileName, numberOfSequences)) {
outs.writeInt(numberOfSequences);
for (int i = 0; i < numberOfSequences; i++) {
{
int length = headers[i].length;
outs.writeInt(length);
outs.write(headers[i], 0, length);
}
{
int length = sequenceCodes[i].length;
outs.writeInt(length);
for (int j = 0; j < length; j++)
outs.writeLong(sequenceCodes[i][j]);
}
progress.incrementProgress();
}
}
}
/**
* read a file in binary format
*
* @param fileName
* @return number of sequences read
* @throws IOException
*/
public int read(final String fileName) throws IOException {
DataInputStream ins = new DataInputStream(new FileInputStream(fileName));
numberOfSequences = ins.readInt();
if (headers.length < numberOfSequences) { // resize
headers = new byte[numberOfSequences][];
sequenceCodes = new long[numberOfSequences][];
}
ProgressPercentage progress = new ProgressPercentage("Reading file: " + fileName, numberOfSequences);
for (int i = 0; i < numberOfSequences; i++) {
{
int length = ins.readInt();
for (int j = 0; j < length; j++)
headers[i][j] = (byte) ins.read();
}
{
int length = ins.readInt();
for (int j = 0; j < length; j++)
sequenceCodes[i][j] = ins.readLong();
}
progress.incrementProgress();
}
ins.close();
progress.close();
return numberOfSequences;
}
/**
* get the number of sequences
*
* @return
*/
public int getNumberOfSequences() {
return numberOfSequences;
}
/**
* gets the i-th header
*
* @param i
* @return header
*/
public byte[] getHeader(int i) {
return headers[i];
}
/**
* gets the i-th sequence
*
* @param i
* @return sequence
*/
public byte[] getSequence(int i) {
return sequenceEncoder.decode(sequenceCodes[i]);
}
/**
* gets the i-th sequence code
*
* @param i
* @return sequence code
*/
public long[] getSequenceCode(int i) {
return sequenceCodes[i];
}
/**
* gets the sequence encoder
*
* @return
*/
public SequenceEncoder getSequenceEncoder() {
return sequenceEncoder;
}
/**
* grow the data arrays
*/
private void grow() {
final int newLength = (int) Math.min(MAX_ARRAY_SIZE, 2L * Math.max(16, headers.length));
System.err.print("[Grow: " + headers.length + " -> " + newLength + "]");
{
byte[][] tmp = new byte[newLength][];
System.arraycopy(headers, 0, tmp, 0, headers.length);
headers = tmp;
}
{
long[][] tmp = new long[newLength][];
System.arraycopy(sequenceCodes, 0, tmp, 0, sequenceCodes.length);
sequenceCodes = tmp;
}
}
public static void main(String[] args) throws IOException {
String fileName = "/Users/huson/data/megan/ecoli/x.fna";
SequenceStore sequenceStore = new SequenceStore(new SequenceEncoder(DNA5Alphabet.getInstance()), 2000);
FastAFileIteratorCode fastAFileIteratorCode = new FastAFileIteratorCode(fileName, sequenceStore.getSequenceEncoder());
ProgressPercentage progress = new ProgressPercentage("Reading file: " + fileName);
sequenceStore.readFromFastA(fastAFileIteratorCode, 2000, progress);
progress.close();
System.err.println("Got:");
for (int i = 0; i < Math.min(5, sequenceStore.getNumberOfSequences()); i++) {
System.err.println(Basic.toString(sequenceStore.getHeader(i)));
System.err.println(Basic.toString(sequenceStore.getSequence(i)));
}
String binFile = "/Users/huson/tmp/x.idx";
sequenceStore.write(binFile);
sequenceStore.read(binFile);
System.err.println("Read: " + sequenceStore.numberOfSequences);
System.err.println("Got:");
for (int i = 0; i < Math.min(5, sequenceStore.getNumberOfSequences()); i++) {
System.err.println(Basic.toString(sequenceStore.getHeader(i)));
System.err.println(Basic.toString(sequenceStore.getSequence(i)));
}
}
}
malt-0.5.2/src/malt/tools/ 0000775 0000000 0000000 00000000000 14004551276 0015343 5 ustar 00root root 0000000 0000000 malt-0.5.2/src/malt/tools/DumpReferencesFromMaltIndex.java 0000664 0000000 0000000 00000007051 14004551276 0023552 0 ustar 00root root 0000000 0000000 /*
* DumpReferencesFromMaltIndex.java Copyright (C) 2020. Daniel H. Huson
*
* (Some files contain contributions from other authors, who are then mentioned separately.)
*
* 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 3 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, see .
*
*/
package malt.tools;
import jloda.swing.util.ArgsOptions;
import jloda.util.*;
import malt.MaltOptions;
import malt.data.ReferencesDBAccess;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
public class DumpReferencesFromMaltIndex {
/**
* dump references from malt index
*/
public static void main(String[] args) {
try {
ProgramProperties.setProgramName("DumpReferencesFromMaltIndex");
ProgramProperties.setProgramVersion(megan.main.Version.SHORT_DESCRIPTION);
PeakMemoryUsageMonitor.start();
(new DumpReferencesFromMaltIndex()).run(args);
System.err.println("Total time: " + PeakMemoryUsageMonitor.getSecondsSinceStartString());
System.err.println("Peak memory: " + PeakMemoryUsageMonitor.getPeakUsageString());
System.exit(0);
} catch (Exception ex) {
Basic.caught(ex);
System.exit(1);
}
}
/**
* run the program
*/
public void run(String[] args) throws IOException, UsageException {
final ArgsOptions options = new ArgsOptions(args, this, "Dump references from MALT index");
options.setVersion(ProgramProperties.getProgramVersion());
options.setLicense("Copyright (C) 2020 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.");
options.setAuthors("Daniel H. Huson");
options.comment("Input Output");
final String indexDirectory = options.getOptionMandatory("-d", "index", "Index directory", "");
final String outputFile = options.getOptionMandatory("-o", "output", "Output file (.gz ok)", "");
options.comment(ArgsOptions.OTHER);
final boolean headersOnly = options.getOption("-ho", "headersOnly", "Only save headers", false);
options.done();
System.err.println("Loading references from: " + indexDirectory);
final ReferencesDBAccess referencesDB = new ReferencesDBAccess(MaltOptions.MemoryMode.load, new File(indexDirectory, "ref.idx"), new File(indexDirectory, "ref.db"), new File(indexDirectory, "ref.inf"));
int count = 0;
try (BufferedWriter w = new BufferedWriter(new FileWriter(outputFile)); ProgressPercentage progress = new ProgressPercentage("Writing file: " + outputFile, referencesDB.getNumberOfSequences())) {
for (int i = 0; i < referencesDB.getNumberOfSequences(); i++) {
w.write(Basic.toString(referencesDB.getHeader(i)) + "\n");
if (!headersOnly) w.write(Basic.toString(referencesDB.getSequence(i)) + "\n");
progress.incrementProgress();
count++;
}
}
System.err.printf("Lines: %,d%n", count);
}
}
malt-0.5.2/src/malt/tools/RandomReadExtractor.java 0000664 0000000 0000000 00000013033 14004551276 0022116 0 ustar 00root root 0000000 0000000 /*
* RandomReadExtractor.java Copyright (C) 2020. Daniel H. Huson
*
* (Some files contain contributions from other authors, who are then mentioned separately.)
*
* 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 3 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, see .
*
*/
package malt.tools;
import jloda.swing.util.ArgsOptions;
import jloda.util.*;
import java.io.*;
import java.util.ArrayList;
import java.util.Random;
public class RandomReadExtractor {
/**
* convert feature tables to gene table
*/
public static void main(String[] args) throws Exception {
try {
ProgramProperties.setProgramName("RandomReadExtractor");
ProgramProperties.setProgramVersion(megan.main.Version.SHORT_DESCRIPTION);
PeakMemoryUsageMonitor.start();
(new RandomReadExtractor()).run(args);
System.err.println("Total time: " + PeakMemoryUsageMonitor.getSecondsSinceStartString());
System.err.println("Peak memory: " + PeakMemoryUsageMonitor.getPeakUsageString());
System.exit(0);
} catch (Exception ex) {
Basic.caught(ex);
System.exit(1);
}
}
/**
* run the program
*/
public void run(String[] args) throws IOException, UsageException {
final ArgsOptions options = new ArgsOptions(args, this, "Randomly cuts out reads from a single DNA sequence");
options.setVersion(ProgramProperties.getProgramVersion());
options.setLicense("Copyright (C) 2020 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.");
options.setAuthors("Daniel H. Huson");
options.comment("Input Output");
final String inputFile = options.getOptionMandatory("-i", "input", "FastA file containing a single sequence", "");
final String outputFile = options.getOptionMandatory("-o", "output", "Output file (.gz ok)", "");
options.comment("Options");
final String startsFile = options.getOption("-sf", "startsFile", "Select the reads from the list of start positions given in this file (overrides -n)", "");
final int numberOfReads = options.getOption("-n", "num", "Number of reads to extract", 10000);
final int readLength = options.getOption("-l", "length", "Length of reads to extract", 100);
final boolean forwardStrand = options.getOption("-fs", "forwardStrand", "From forward strand", true);
final boolean backwardStrand = options.getOption("-bs", "backwardtrand", "From backward strand", true);
final int randomSeed = options.getOption("-rs", "randomSeed", "Random number seed", 666);
options.done();
final Random random = new Random(randomSeed);
int count = 0;
final FastA fastA = new FastA();
try (Reader r = new InputStreamReader(Basic.getInputStreamPossiblyZIPorGZIP(inputFile))) {
fastA.read(r);
System.err.printf("Sequence '%s' length: %,d%n", Basic.getFirstWord(fastA.getHeader(0)), fastA.getSequence(0).length());
}
final String genome = fastA.getSequence(0);
final ArrayList starts = new ArrayList<>();
if (startsFile.length() > 0) {
try (FileLineIterator it = new FileLineIterator(startsFile, true)) {
while (it.hasNext()) {
String aLine = it.next();
if (Basic.isInteger(aLine))
starts.add(Basic.parseInt(aLine)); // either start or -start to indicate reverse complement
}
}
} else {
for (int i = 0; i < numberOfReads; i++) {
final boolean forward = forwardStrand && !backwardStrand || (!backwardStrand || forwardStrand) && random.nextBoolean();
final int start = random.nextInt(genome.length() - readLength);
if (forward)
starts.add(start);
else
starts.add(-start);
}
}
try (BufferedWriter w = new BufferedWriter(new FileWriter(outputFile)); ProgressPercentage progress = new ProgressPercentage("Writing file: " + outputFile, starts.size())) {
for (int r = 0; r < starts.size(); r++) {
final boolean forward = (starts.get(r) > 0);
final int start = Math.abs(starts.get(r));
final int end = start + readLength;
final String header = String.format(">r%06d %d-%d from %s", (r + 1), (start + 1), (end + 1), fastA.getHeader(0));
final String sequence;
if (forward) {
sequence = genome.substring(start, end);
} else {
sequence = SequenceUtils.getReverseComplement(genome.substring(start, end));
}
w.write(header);
w.write("\n");
w.write(sequence);
w.write("\n");
progress.incrementProgress();
count++;
}
}
System.err.printf("Lines: %,d%n", count);
}
}
malt-0.5.2/src/malt/util/ 0000775 0000000 0000000 00000000000 14004551276 0015160 5 ustar 00root root 0000000 0000000 malt-0.5.2/src/malt/util/FixedSizePriorityQueue.java 0000664 0000000 0000000 00000006623 14004551276 0022473 0 ustar 00root root 0000000 0000000 /*
* FixedSizePriorityQueue.java Copyright (C) 2020. Daniel H. Huson
*
* (Some files contain contributions from other authors, who are then mentioned separately.)
*
* 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 3 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, see .
*
*/
package malt.util;
import java.util.Comparator;
import java.util.PriorityQueue;
/**
* A priority queue implementation with a fixed size
*/
public class FixedSizePriorityQueue {
private final PriorityQueue priorityQueue; /* backing data structure */
private final Comparator comparator;
private final int maxSize;
/**
* Constructs a {@link FixedSizePriorityQueue} with the specified {@code maxSize}
* and {@code comparator}.
*
* @param maxSize - The maximum size the queue can reach, must be a positive integer.
* @param comparator - The comparator to be used to compare the elements in the queue, must be non-null.
*/
public FixedSizePriorityQueue(final int maxSize, final Comparator comparator) {
super();
if (maxSize <= 0) {
throw new IllegalArgumentException("maxSize = " + maxSize + "; expected a positive integer.");
}
if (comparator == null) {
throw new NullPointerException("Comparator is null.");
}
this.maxSize = maxSize;
this.comparator = comparator;
this.priorityQueue = new PriorityQueue<>(maxSize, comparator);
}
/**
* Adds an element to the queue. If the queue contains {@code maxSize} elements, {@code e} will
* be compared to the lowest element in the queue using {@code comparator}.
* If {@code e} is greater than or equalOverShorterOfBoth to the lowest element, that element will be removed and
* {@code e} will be added instead. Otherwise, the queue will not be modified
* and {@code e} will not be added.
*
* @param e - Element to be added, must be non-null.
* @return returns true if added
*/
public boolean add(final E e) {
if (e == null) {
throw new NullPointerException("e is null.");
}
if (priorityQueue.size() >= maxSize) {
if (comparator.compare(e, priorityQueue.peek()) <= 0)
return false;
priorityQueue.poll(); // remove smallest element
}
return priorityQueue.add(e);
}
public int getMaxSize() {
return maxSize;
}
public E poll() {
return priorityQueue.poll();
}
public int size() {
return priorityQueue.size();
}
public void clear() {
priorityQueue.clear();
}
public boolean remove(E entry) {
return priorityQueue.remove(entry);
}
/**
* get as collection
*
* @return collection
*/
public java.util.Collection getCollection() {
return priorityQueue;
}
}
malt-0.5.2/src/malt/util/TaxonomyUtilities.java 0000664 0000000 0000000 00000012215 14004551276 0021536 0 ustar 00root root 0000000 0000000 /*
* TaxonomyUtilities.java Copyright (C) 2020. Daniel H. Huson
*
* (Some files contain contributions from other authors, who are then mentioned separately.)
*
* 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 3 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, see .
*
*/
package malt.util;
import jloda.graph.Node;
import megan.classification.Classification;
import megan.classification.ClassificationManager;
import megan.viewer.TaxonomicLevels;
import java.util.ArrayList;
import java.util.List;
/**
* simple utilities
* Daniel Huson, 8.2014
*/
public class TaxonomyUtilities {
/**
* get the species for the taxon
*
* @param taxonId
* @return species
*/
public static String getContainingSpecies(Integer taxonId) {
final Classification classification = ClassificationManager.get(Classification.Taxonomy, false);
Node v = classification.getFullTree().getTaxon2Node(taxonId);
while (v != null) {
taxonId = (Integer) v.getInfo();
int level = classification.getName2IdMap().getRank(taxonId);
if (level == TaxonomicLevels.getSpeciesId())
return classification.getName2IdMap().get(taxonId);
if (v.getInDegree() > 0)
v = v.getFirstInEdge().getSource();
else
v = null;
}
return null;
}
/**
* get the genus
*
* @param taxonId
* @return genus
*/
public static String getContainingGenus(Integer taxonId) {
final Classification classification = ClassificationManager.get(Classification.Taxonomy, false);
Node v = classification.getFullTree().getTaxon2Node(taxonId);
while (v != null) {
taxonId = (Integer) v.getInfo();
int level = classification.getName2IdMap().getRank(taxonId);
if (level == TaxonomicLevels.getGenusId())
return classification.getName2IdMap().get(taxonId);
if (v.getInDegree() > 0)
v = v.getFirstInEdge().getSource();
else
v = null;
}
return null;
}
/**
* gets the strain
*
* @param taxonId
* @return
*/
public static String getStrain(int taxonId) {
final Classification classification = ClassificationManager.get(Classification.Taxonomy, false);
final int speciesId = TaxonomicLevels.getSpeciesId();
final int subspeciesId = TaxonomicLevels.getSubspeciesId();
Node v = classification.getFullTree().getTaxon2Node(taxonId);
while (v != null && v.getInDegree() > 0 && v.getInfo() != null) {
v = v.getFirstInEdge().getSource();
taxonId = (Integer) v.getInfo();
String name = classification.getName2IdMap().get(taxonId);
if (name != null && (name.equals("root") || name.equals("cellular organisms")))
break;
int level = classification.getName2IdMap().getRank(taxonId);
if (level > speciesId)
break;
if (level > subspeciesId)
break;
if (level != subspeciesId)
break;
}
return null;
}
/**
* gets the taxonomic path to the named taxon
*
* @param taxonId
* @return
*/
public static String getPath(int taxonId) {
final Classification classification = ClassificationManager.get(Classification.Taxonomy, false);
final int genus = TaxonomicLevels.getGenusId();
if (taxonId == 1)// root taxon
return classification.getName2IdMap().get(taxonId);
List path = new ArrayList<>();
Node v = classification.getFullTree().getTaxon2Node(taxonId);
while (v != null) {
taxonId = (Integer) v.getInfo();
if (classification.getName2IdMap().getRank(taxonId) != 0) // ignore unranked nodes
path.add(taxonId);
if (v.getInDegree() > 0)
v = v.getFirstInEdge().getSource();
else
v = null;
}
StringBuilder buf = new StringBuilder();
if (path.size() > 0) {
boolean isFirst = true;
for (int i = path.size() - 1; i >= 0; i--) {
if (isFirst)
isFirst = false;
else
buf.append("; ");
buf.append(classification.getName2IdMap().get(path.get(i)));
}
int level = classification.getName2IdMap().getRank(path.get(path.size() - 1));
if (level == genus)
buf.append(".");
}
return buf.toString();
}
}
malt-0.5.2/src/malt/util/Tester.java 0000664 0000000 0000000 00000007764 14004551276 0017307 0 ustar 00root root 0000000 0000000 /*
* Tester.java Copyright (C) 2020. Daniel H. Huson
*
* (Some files contain contributions from other authors, who are then mentioned separately.)
*
* 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 3 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, see .
*
*/
package malt.util;
/**
* tester
* Daniel Huson, 2014
*/
public class Tester {
/**
* shows that modulo takes three times as long as bitwise-and or shift
*
* @param args
*/
public static void main(String[] args) {
System.err.println("MAX: " + Integer.MAX_VALUE + " bin: " + Integer.toBinaryString(Integer.MAX_VALUE));
System.err.println("MIN+1: " + (Integer.MIN_VALUE + 1));
System.err.println("-MIN+1: " + (-(Integer.MIN_VALUE + 1)) + " equals MAX? " + (Integer.MAX_VALUE == (-(Integer.MIN_VALUE + 1))));
int hash = Integer.MAX_VALUE;
System.err.print("hash: " + hash);
if ((long) hash == Integer.MAX_VALUE || (long) hash <= Integer.MIN_VALUE + 1)
hash = 0;
System.err.println(" -> " + hash);
hash = Integer.MIN_VALUE;
System.err.print("hash: " + hash);
if ((long) hash == Integer.MAX_VALUE || (long) hash <= Integer.MIN_VALUE + 1)
hash = 0;
System.err.println(" -> " + hash);
hash = Integer.MIN_VALUE + 1;
System.err.print("hash: " + hash);
if ((long) hash == Integer.MAX_VALUE || (long) hash <= Integer.MIN_VALUE + 1)
hash = 0;
System.err.println(" -> " + hash);
/*
for(int i=0;i<32;i++) {
System.err.println("i="+i+" (1<= Integer.MAX_VALUE) {
tableSize = Integer.MAX_VALUE;
} else {
tableSize = 1;
while (numberOfSeeds > tableSize) {
tableSize *= 2;
}
}
final int mask = tableSize - 1;
System.err.println("tableSize: " + tableSize);
System.err.println("mask: " + mask + " bits: " + Integer.toBinaryString(mask));
for (int i = tableSize - 5; i < tableSize + 5; i++) {
System.err.println("i=" + i + " i&mask=" + (i & mask));
}
for (int i = tableSize - 5; i < tableSize + 5; i++) {
System.err.println("i=" + (-i) + " (-i)&mask=" + ((i) & mask));
}
if (true) {
int top = Integer.MAX_VALUE >>> 8;
System.err.println("top: " + top);
System.err.println("aMask: " + Integer.toBinaryString(top));
{
long start = System.currentTimeMillis();
long sum = 0;
for (int i = 0; i < Integer.MAX_VALUE; i++) {
sum += (i % top);
}
System.err.println("Time: " + ((System.currentTimeMillis() - start) / 1000.0));
System.err.println("Sum: " + sum);
}
{
long start = System.currentTimeMillis();
long sum = 0;
for (int i = 0; i < Integer.MAX_VALUE; i++) {
sum += (i & top);
}
System.err.println("Time: " + ((System.currentTimeMillis() - start) / 1000.0));
System.err.println("Sum: " + sum);
}
}
System.exit(0);
}
}
malt-0.5.2/src/malt/util/Utilities.java 0000664 0000000 0000000 00000031504 14004551276 0020001 0 ustar 00root root 0000000 0000000 /*
* Utilities.java Copyright (C) 2020. Daniel H. Huson
*
* (Some files contain contributions from other authors, who are then mentioned separately.)
*
* 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 3 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, see .
*
*/
package malt.util;
import jloda.util.Basic;
import jloda.util.BlastMode;
import jloda.util.UsageException;
import malt.data.ReadMatch;
import malt.data.Row;
import malt.data.SequenceType;
import megan.classification.IdMapper;
import megan.classification.commandtemplates.LoadMappingFileCommand;
import megan.io.IIntPutter;
import java.io.File;
import java.io.IOException;
import java.util.Random;
/**
* some utilities
* Daniel Huson, 8.2014
*/
public class Utilities {
/**
* randomize array of longs using (Durstenfeld 1964)
*
* @param array
* @param offset start of numbers to be randomized
* @param length number of numbers to be randomized
* @param random
*/
public static void randomize(long[] array, int offset, int length, Random random) {
for (int i = offset + length - 1; i >= offset + 1; i--) {
int j = random.nextInt(i - offset) + offset;
long tmp = array[i];
array[i] = array[j];
array[j] = tmp;
}
}
/**
* randomize array of integers using (Durstenfeld 1964) in consecutive pairs
*
* @param array
* @param offset start of numbers to be randomized
* @param length number of numbers to be randomized. Must be even for this to make sense
* @param random
*/
public static void randomizePairs(int[] array, int offset, int length, Random random) {
int end = offset + length / 2;
for (int i = end - 1; i >= offset + 1; i--) {
int j = random.nextInt(i - offset) + offset;
int i2 = 2 * i - offset;
int j2 = 2 * j - offset;
int tmp = array[i2];
array[i2] = array[j2];
array[j2] = tmp;
i2++;
j2++;
tmp = array[i2];
array[i2] = array[j2];
array[j2] = tmp;
}
}
/**
* randomize array of integers using (Durstenfeld 1964) in consecutive pairs
*
* @param array
* @param offset start of numbers to be randomized
* @param length number of numbers to be randomized. Must be even for this to make sense
* @param random
*/
public static void randomizePairs(IIntPutter array, long offset, int length, Random random) {
long end = offset + length / 2;
for (long i = end - 1; i >= offset + 1; i--) {
long j = random.nextInt((int) (i - offset)) + offset;
long i2 = 2 * i - offset;
long j2 = 2 * j - offset;
int tmp = array.get(i2);
array.put(i2, array.get(j2));
array.put(j2, tmp);
i2++;
j2++;
tmp = array.get(i2);
array.put(i2, array.get(j2));
array.put(j2, tmp);
}
}
/**
* resize array
*
* @param array
* @return new array
*/
public static int[] resize(int[] array, int newSize) {
int[] result = new int[newSize];
System.arraycopy(array, 0, result, 0, Math.min(newSize, array.length));
return result;
}
/**
* resize array
*
* @param array
* @return new array
*/
public static Row[] resizeAndConstructEntries(Row[] array, int newSize) {
Row[] result = new Row[newSize];
for (int i = array.length; i < newSize; i++)
result[i] = new Row();
System.arraycopy(array, 0, result, 0, Math.min(newSize, array.length));
return result;
}
/**
* resize array
*
* @param array
* @return new array
*/
public static ReadMatch[] resize(ReadMatch[] array, int newSize) {
ReadMatch[] result = new ReadMatch[newSize];
System.arraycopy(array, 0, result, 0, Math.min(newSize, array.length));
return result;
}
/**
* get first word of header
*
* @param header
* @return first word
*/
public static byte[] getFirstWordSkipLeadingGreaterSign(byte[] header) {
int start = 0;
while (start < header.length) {
byte ch = header[start];
if (ch != '>' && !Character.isWhitespace(ch))
break;
start++;
}
int finish = start;
while (finish < header.length) {
byte ch = header[finish];
if (ch == 0 || Character.isWhitespace(ch))
break;
finish++;
}
byte[] result = new byte[finish - start];
System.arraycopy(header, start, result, 0, finish - start);
return result;
}
/**
* get first word of header and make sure it starts with a greater sign
*
* @param header
* @return first word
*/
public static byte[] getFirstWordEnsureLeadingGreaterSign(byte[] header) {
int length = 0;
boolean hasLeadingGreaterSign = (header.length > 0 && header[0] == '>');
while (length < header.length) {
if (header[length] == 0 || Character.isWhitespace(header[length])) {
if (hasLeadingGreaterSign) {
byte[] result = new byte[length];
System.arraycopy(header, 0, result, 0, length);
return result;
} else {
byte[] result = new byte[length + 1];
result[0] = '>';
System.arraycopy(header, 0, result, 1, length);
return result;
}
}
length++;
}
return header;
}
/**
* copy a 0-terminated byte array
*
* @param bytes
* @return copy (up to first 0)
*/
public static byte[] copy0Terminated(byte[] bytes) {
int length = 0;
while (length < bytes.length) {
if (bytes[length] == 0)
break;
length++;
}
byte[] result = new byte[length];
System.arraycopy(bytes, 0, result, 0, length);
return result;
}
/**
* get first word of header and write it to result
*
* @param header
* @return first word
*/
public static int getFirstWordSkipLeadingGreaterSign(byte[] header, byte[] result) {
int start = (header.length > 0 && header[0] == '>' ? 1 : 0);
while (start < header.length && Character.isWhitespace(header[start])) {
start++;
}
if (start == header.length)
return 0;
int end = start;
while (end < header.length && !Character.isWhitespace(header[end]) && header[end] != 0) {
end++;
}
int length = Math.min(result.length, end - start);
if (length > 0)
System.arraycopy(header, start, result, 0, length);
return length;
}
public static void checkFileExists(File file) throws IOException {
checkFileExists(file.getPath(), false);
}
public static void checkFileExists(String fileName, boolean allowToAddGZSuffix) throws IOException {
if ((new File(fileName)).exists())
return; // ok
if (!allowToAddGZSuffix) {
throw new IOException("File not found: " + fileName);
} else if (!(new File(fileName + ".gz")).exists()) {
throw new IOException("File not found: " + fileName + " nor " + fileName + ".gz");
}
}
/**
* remove all existing index files
*
* @param indexDirectory
*/
public static void cleanIndexDirectory(File indexDirectory) throws IOException {
if (!indexDirectory.isDirectory())
throw new IOException("Not a directory: " + indexDirectory);
File[] files = indexDirectory.listFiles((file, s) -> s.endsWith(".idx") || s.contains(".idx."));
if (files != null) {
System.err.println("Deleting index files: " + files.length);
for (File file : files)
if (!file.delete())
throw new IOException("Failed to delete file: " + file);
}
}
/**
* gets the query sequence type from the alignment program mode
*
* @param mode
* @return query type
* @throws UsageException
*/
public static SequenceType getQuerySequenceTypeFromMode(BlastMode mode) throws IOException {
switch (mode) {
case BlastN:
case BlastX:
return SequenceType.DNA;
case BlastP:
return SequenceType.Protein;
default:
throw new IOException("Unsupported mode: " + mode);
}
}
/**
* gets the reference sequence type from the alignment program mode
*
* @param mode
* @return query type
* @throws UsageException
*/
public static SequenceType getReferenceSequenceTypeFromMode(BlastMode mode) throws IOException {
switch (mode) {
case BlastN:
return SequenceType.DNA;
case BlastX:
case BlastP:
return SequenceType.Protein;
default:
throw new IOException("Unsupported mode: " + mode);
}
}
/**
* determines how many different frames are possible for a given query
*
* @param mode
* @param dnaDoForward
* @param dnaDoReverse
* @return number of frames
* @throws IOException
*/
public static int getMaxFramesPerQuery(BlastMode mode, boolean dnaDoForward, boolean dnaDoReverse) throws IOException {
switch (mode) {
case BlastN:
return (dnaDoForward ? 1 : 0) + (dnaDoReverse ? 1 : 0);
case BlastX:
return 3 * ((dnaDoForward ? 1 : 0) + (dnaDoReverse ? 1 : 0));
case BlastP:
return 1;
default:
throw new IOException("Unsupported mode: " + mode);
}
}
/**
* count the number of gaps ('-') in a sequence
*
* @param sequence
* @return number of gaps
*/
public static int countGaps(byte[] sequence, int offset, int length) {
int count = 0;
for (int i = 0; i < length; i++) {
int a = sequence[offset + i];
if (a == '-')
count++;
}
return count;
}
/**
* does this contain only at most two different letters
*
* @param seq
* @return True at most two different letters occur
*/
public static boolean hasAtMostTwoLetters(byte[] seq) {
byte a = seq[0];
byte b = 0;
int pos = 1;
while (pos < seq.length) {
if (seq[pos] != a) {
b = seq[pos];
break;
}
pos++;
}
while (pos < seq.length) {
if (seq[pos] != a && seq[pos] != b)
return false;
pos++;
}
return true;
}
public static int getNextPowerOf2(int value) {
long i = 1;
for (; i < Integer.MAX_VALUE; i <<= 1) {
if (i > value)
return (int) i;
}
return Integer.MAX_VALUE;
}
/**
* gets a file for a given directory with a given name, if it exists. If gzippedOk, also tries adding .gz or replacing the suffix by .gz
*
* @param directory
* @param name
* @param gzippedOk
* @return file or null
*/
public static File getFile(String directory, String name, boolean gzippedOk) {
File file = new File(directory, name);
if (file.exists())
return file;
if (gzippedOk) {
file = new File(directory, name + ".gz");
if (file.exists())
return file;
file = new File(directory, Basic.replaceFileSuffix(name, ".gz"));
if (file.exists())
return file;
}
return null;
}
/**
* load a mapping file
*
* @param fileName
* @param mapType
* @param cName
* @throws Exception
*/
public static void loadMapping(String fileName, IdMapper.MapType mapType, String cName) throws Exception {
if (fileName.length() > 0)
(new LoadMappingFileCommand()).apply("load mapFile='" + fileName + "' mapType=" + mapType.toString() + " cName=" + cName + ";");
}
}
malt-0.5.2/src/module-info.java 0000664 0000000 0000000 00000000231 14004551276 0016323 0 ustar 00root root 0000000 0000000 module malt {
requires transitive jloda;
requires transitive megan;
exports malt.tools;
exports malt;
opens malt.resources.icons;
} malt-0.5.2/tex/ 0000775 0000000 0000000 00000000000 14004551276 0013257 5 ustar 00root root 0000000 0000000 malt-0.5.2/tex/manual/ 0000775 0000000 0000000 00000000000 14004551276 0014534 5 ustar 00root root 0000000 0000000 malt-0.5.2/tex/manual/Makefile 0000664 0000000 0000000 00000000305 14004551276 0016172 0 ustar 00root root 0000000 0000000 manual.pdf: manual.tex clean
pdflatex manual
bibtex manual
pdflatex manual
pdflatex manual
makeindex manual
pdflatex manual
clean:
rm -f manual.dvi manu.idx manual.aux manual.ps manual.pdf
malt-0.5.2/tex/manual/definitions.tex 0000664 0000000 0000000 00000011216 14004551276 0017572 0 ustar 00root root 0000000 0000000 % Show optional stuff:
\newcommand{\optional}[1]{{#1}}
% Hide optional stuff:
\renewcommand{\optional}[1]{}
% link stuff using hyperlinks:
\newcommand{\link}[2]{\hyperlink{#2}{#1}}
% a todo command:
\newcommand{\todo}[1]{
\optional{\marginpar{\raggedright \tiny \textbf{todo:} {#1}}}}
% use \mylabel instead of \label to see labels in print out
\newcommand{\mylabel}[1]{
\optional{\marginpar{\raggedright\tiny{#1}}}
\label{#1}
\hypertarget{#1}{}
}
% use \target instead of \hypertarget to see targets in print out
\newcommand{\target}[2]{
\hypertarget{#2}{#1}
\optional{\marginpar{\raggedright\tiny{#2}}}
}
% use \mysection instead of \section to produce labels and hyperlink targets
\newcommand{\mysection}[1]{\section{#1}\mylabel{sec:#1}}
% use \mysubsection instead of \section to produce labels and hyperlink targets
\newcommand{\mysubsection}[1]{\subsection{#1}\mylabel{subsec:#1}}
\newcommand{\menu}[1]{
\link{{\tt #1}}{menu:#1}}
\newcommand{\pmenu}[1]{
\target{{\tt #1}}{menu:#1}
\index{#1}\hspace{-0.3cm}
}
\newcommand{\program}[1]{
\link{{\tt #1}}{program:#1}}
\newcommand{\pprogram}[1]{
\target{{\tt #1}}{program:#1}
\index{#1}\hspace{-0.3cm}
}
\newcommand{\windowmenu}[2]{
\link{{\tt $#2}}{windowmenu:#1-#2}\index{#2}\index{#2}}
\newcommand{\pwindowmenu}[2]
{\target{{\tt#2}}{windowmenu:#1-#2}
\index{#2}\index{#2}}
\newcommand{\submenu}[1]{
\link{{\tt #1}}{submenu:#1}}
\newcommand{\psubmenu}[1]{
\target{{\tt #1}}{submenu:#1}
\index{#1}}
\newcommand{\menuitem}[2]{
\link{{\tt #1$\to$#2}}{menuitem:#1-#2}
\index{#1$\to$#2}\index{#2}}
\newcommand{\pmenuitem}[2]{\index{#1$\to$#2}\index{#2}
\target{{\tt #1$\to$#2}}{menuitem:#1-#2}\hspace{-0.3cm}
}
\newcommand{\menuitemh}[3]{
\link{{\tt #1$\to$#2$\to$#3}}{menuitem:#1-#2-#3}\index{#1$\to$#2$\to$#3}\index{#3}}
\newcommand{\pmenuitemh}[3]
{\target{{\tt#1$\to$#2$\to$#3}}{menuitem:#1-#2-#3}
\index{#1$\to$#2$\to$#3}\index{#3}}
\newcommand{\windowmenuitem}[3]{
\link{{\tt #2$\to$#3}}{windowmenuitem:#1-#2-#3}\index{#2$\to$#3}\index{#3}}
\newcommand{\pwindowmenuitem}[3]
{\target{{\tt#2$\to$#3}}{windowmenuitem:#1-#2-#3}
\index{#2$\to$#3}\index{#3}}
\newcommand{\ppopupmenu}[1]{
\target{{\tt #1}}{popupmenu:#1}
\index{#1}}
\newcommand{\popupmenu}[1]{
\link{{\tt #1}}{popupmenu:#1}
\index{#1}}
\newcommand{\ppopupmenuitem}[2]{
\target{{\tt #2}}{popupmenuitem:#1-#2}
\index{#1$\to$#2}\index{#2}}
\newcommand{\popupmenuitem}[2]{
\link{{\tt #2}}{popupmenuitem:#1-#2}
\index{#1$\to$#2}\index{#2}}
\newcommand{\block}[1]{
\link{{\tt #1}}{block:#1}}
\newcommand{\pblock}[1]{
\target{{\tt #1}}{block:#1}
\index{#1}}
\newcommand{\button}[1]{
\link{{\tt #1}}{button:#1}}
\newcommand{\pbutton}[1]{\hspace{-0.3cm}
\target{{\tt #1}}{button:#1}
\index{#1}\hspace{-0.3cm}}
\newcommand{\method}[1]{
\link{{\tt #1}}{method:#1}}
\newcommand{\pmethod}[1]{
\target{{\tt #1}}{method:#1}
\index{#1}}
\newcommand{\window}[1]{
\link{{\tt #1}}{window:#1}}
\newcommand{\pwindow}[1]{\hspace{-0.3cm}
\target{{\tt #1}}{window:#1}
\index{#1}\hspace{-0.3cm}}
\newcommand{\tab}[2]{
\link{{\tt #1:#2}}{tab:#1-#2}}
\newcommand{\ptab}[2]{
\target{{\tt #1:#2}}{tab:#1-#2}
\index{#1:#2}}
\newcommand{\tabtab}[3]{
\link{{\tt #1:#2:#3}}{tabtab:#1-#2-#3}}
\newcommand{\ptabtab}[3]{
\target{{\tt #1:#2:#3}}{tabtab:#1-#2-#3}
\index{#1:#2:#3}}
\newcommand{\concept}[1]{
\link{{#1}}{concept:#1}}
\newcommand{\pconcept}[1]{\hspace{-0.3cm}
\target{{\em #1}}{concept:#1}\index{#1}\hspace{-0.2cm}}
%%% The following commands are to help make hyperlinks:
% use this to emphasize a word and to put it into the index:
\newcommand{\iem}[1]{{\em #1}\index{#1}}
\newcommand{\irm}[1]{{#1}\index{#1}}
\newcommand{\itt}[1]{{\tt #1}\index{#1}}
\newcommand{\ibf}[1]{{\bf #1}\index{#1}}
\newcommand{\iit}[1]{{\it #1}\index{#1}}
\newcommand{\isc}[1]{{\sc #1}\index{#1}}
% use this to emphasize a word and to put it into the index and link it
% to it's primary occurrence:
\newcommand{\ieml}[1]{\link{{\em #1}}{#1}\index{#1}}
\newcommand{\irml}[1]{\link{#1}{#1}\index{#1}}
\newcommand{\ittl}[1]{\link{{\tt #1}}{#1}\index{#1}}
\newcommand{\iitl}[1]{\link{{\it #1}}{#1}\index{#1}}
\newcommand{\iscl}[1]{\link{{\sc #1}}{#1}\index{#1}}
\newcommand{\il}[1]{\link{#1}{#1}\index{#1}}
% use this to emphasize the primary occurrence of
% word and to put it into the index, also make this occurrence of the word
% a hyperlink target:
\newcommand{\pem}[1]{{\em \hypertarget{#1}{#1}}\index{#1}
\optional{{\marginpar{\raggedright\tiny{#1}}}}}
% use this to ignore stuff:
\newcommand{\ignore}[1]{}
% some definitions:
\def\kb{{\rm kb }}
\def\bp{{\rm bp }}
\def\Gb{{\rm Gb }}
\def\Mb{{\rm Mb }}
\def\this{.}
% Headings
%\pagestyle{myheadings}
%\markboth{}{$ $Date: 2006-04-26 19:12:01 $ $\hfil User Manual \Megan v4b25}
malt-0.5.2/tex/manual/manual.bbl 0000664 0000000 0000000 00000011137 14004551276 0016475 0 ustar 00root root 0000000 0000000 \begin{thebibliography}{10}
\bibitem{GeneOntology2000}
M.~Ashburner, C.~A. Ball, J.~A. Blake, D.~Botstein, H.~Butler, J.~M. Cherry,
A.~P. Davis, K.~Dolinski, S.~S. Dwight, J.~T. Eppig, M.~A. Harris, D.~P.
Hill, L.~Issel-Tarver, A.~Kasarskis, S.~Lewis, J.~C. Matese, J.~E.
Richardson, M.~Ringwald, G.~M. Rubin, and G.~Sherlock.
\newblock Gene ontology: tool for the unification of biology. the gene ontology
consortium.
\newblock {\em Nat Genet}, 25(1):25--29, May 2000.
\bibitem{Burkhardt01}
Stefan Burkhardt and Juha K{\"a}rkk{\"a}inen.
\newblock Better filtering with gapped q-grams.
\newblock {\em Fundamenta Informaticae}, XXIII:1001--1018, 2001.
\bibitem{ChaoPM92}
Kun-Mao Chao, William~R. Pearson, and Webb Miller.
\newblock Aligning two sequences within a specified diagonal band.
\newblock {\em Computer Applications in the Biosciences}, 8(5):481--487, 1992.
\bibitem{MEGAN2007}
D.~H. Huson, A.~F. Auch, J.~Qi, and S.~C. Schuster.
\newblock {MEGAN} analysis of metagenomic data.
\newblock {\em Genome Res}, 17(3):377--386, March 2007.
\bibitem{MEGAN2011}
D.~H. Huson, S.~Mitra, N.~Weber, H.-J. Ruscheweyh, and S.~C. Schuster.
\newblock Integrative analysis of environmental sequences using {MEGAN\,4}.
\newblock {\em Genome Research}, 21:1552--1560, 2011.
\bibitem{Ilie:2011fk}
Lucian Ilie, Silvana Ilie, Shima Khoshraftar, and Anahita~Mansouri Bigvand.
\newblock Seeds for effective oligonucleotide design.
\newblock {\em BMC Genomics}, 12:280, 2011.
\bibitem{Kanehisa2000}
M.~Kanehisa and S.~Goto.
\newblock {KEGG}: {Kyoto} encyclopedia of genes and genomes.
\newblock {\em Nucleic Acids Res}, 28(1):27--30, Jan 2000.
\bibitem{Ma02}
Bin Ma, John Tromp, and Ming Li.
\newblock {PatternHunter}: faster and more sensitive homology search.
\newblock {\em Bioinformatics}, 18(3):440--445, 2002.
\bibitem{Mitchell2015}
Alex Mitchell, Hsin-Yu Chang, Louise Daugherty, Matthew Fraser, Sarah Hunter,
Rodrigo Lopez, Craig McAnulla, Conor McMenamin, Gift Nuka, Sebastien Pesseat,
Amaia Sangrador-Vegas, Maxim Scheremetjew, Claudia Rato, Siew-Yit Yong, Alex
Bateman, Marco Punta, Teresa~K. Attwood, Christian~J.A. Sigrist, Nicole
Redaschi, Catherine Rivoire, Ioannis Xenarios, Daniel Kahn, Dominique Guyot,
Peer Bork, Ivica Letunic, Julian Gough, Matt Oates, Daniel Haft, Hongzhan
Huang, Darren~A. Natale, Cathy~H. Wu, Christine Orengo, Ian Sillitoe, Huaiyu
Mi, Paul~D. Thomas, and Robert~D. Finn.
\newblock The interpro protein families database: the classification resource
after 15 years.
\newblock {\em Nucleic Acids Research}, 43(D1):D213--D221, 2015.
\bibitem{Murphy2000}
Lynne~Reed Murphy, Anders Wallqvist, and Ronald~M. Levy.
\newblock Simplified amino acid alphabets for protein fold recognition and
implications for folding.
\newblock {\em Protein Engineering}, 13:149--152(4), 2000.
\bibitem{SSAHA}
Z.~Ning, A.~J. Cox, and J.~C. Mullikin.
\newblock {SSAHA}: a fast search method for large {DNA} databases.
\newblock {\em Genome Res}, 11(10):1725--1729, 2001.
\bibitem{SEED2005}
Ross Overbeek, Tadhg Begley, Ralph~M Butler, Jomuna~V Choudhuri, Han-Yu Chuang,
Matthew Cohoon, Val\'erie de~Cr\'ecy-Lagard, Naryttza Diaz, Terry Disz,
Robert Edwards, Michael Fonstein, Ed~D Frank, Svetlana Gerdes, Elizabeth~M
Glass, Alexander Goesmann, Andrew Hanson, Dirk Iwata-Reuyl, Roy Jensen, Neema
Jamshidi, Lutz Krause, Michael Kubal, Niels Larsen, Burkhard Linke, Alice~C
McHardy, Folker Meyer, Heiko Neuweger, Gary Olsen, Robert Olson, Andrei
Osterman, Vasiliy Portnoy, Gordon~D Pusch, Dmitry~A Rodionov, Christian
R\"uckert, Jason Steiner, Rick Stevens, Ines Thiele, Olga Vassieva, Yuzhen
Ye, Olga Zagnitko, and Veronika Vonstein.
\newblock The subsystems approach to genome annotation and its use in the
project to annotate 1000 genomes.
\newblock {\em Nucleic Acids Res}, 33(17):5691--5702, 2005.
\bibitem{eggNOG}
Sean Powell, Damian Szklarczyk, Kalliopi Trachana, Alexander Roth, Michael
Kuhn, Jean Muller, Roland Arnold, Thomas Rattei, Ivica Letunic, Tobias
Doerks, Lars~Juhl Jensen, Christian von Mering, and Peer Bork.
\newblock {eggNOG} v3.0: orthologous groups covering 1133 organisms at 41
different taxonomic ranges.
\newblock {\em Nucleic Acids Research}, 40(Database-Issue):284--289, 2012.
\bibitem{Tatusov1997}
R.~L. Tatusov, E.~V. Koonin, and D.~J. Lipman.
\newblock A genomic perspective on protein families.
\newblock {\em Science}, 278(5338):631--637, Oct 1997.
\bibitem{RapSearch2}
Yongan Zhao, Haixu Tang, and Yuzhen Ye.
\newblock {RAPSearch2}: a fast and memory-efficient protein similarity search
tool for next-generation sequencing data.
\newblock {\em Bioinformatics}, 28(1):125--126, 2012.
\end{thebibliography}
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