debian/0000755000000000000000000000000012241150224007157 5ustar debian/control0000644000000000000000000000225512241143147010574 0ustar Source: amap-align Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9) Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/amap-align/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/amap-align/trunk/ X-Homepage: http://bio.math.berkeley.edu/amap/ - upstream seems to be dead Package: amap-align Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: Protein multiple alignment by sequence annealing AMAP is a command line tool to perform multiple alignment of peptidic sequences. It utilizes posterior decoding, and a sequence-annealing alignment, instead of the traditional progressive alignment method. It is the only alignment program that allows one to control the sensitivity / specificity tradeoff. It is based on the ProbCons source code, but uses alignment metric accuracy and eliminates the consistency transformation. . The java visualisation tool of AMAP 2.2 is not yet packaged in Debian. debian/install0000644000000000000000000000002312241143771010554 0ustar align/amap usr/bin debian/rules0000755000000000000000000000072312241147164010252 0ustar #!/usr/bin/make -f # -*- makefile -*- XP=xsltproc \ -''-nonet \ -''-param man.charmap.use.subset "0" \ -''-param make.year.ranges "1" \ -''-param make.single.year.ranges "1" \ -o debian/ pkg := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}') SRCDIR=align %: dh $@ --sourcedirectory=$(SRCDIR) --parallel override_dh_installexamples: dh_installexamples chmod 644 debian/$(pkg)/usr/share/doc/$(pkg)/examples/BB12020.tfa debian/manpages0000644000000000000000000000001312241143616010676 0ustar debian/*.1 debian/examples0000644000000000000000000000001312214301176010716 0ustar examples/* debian/watch0000644000000000000000000000040212214301176010210 0ustar ## Upstream homepage vanished - deactivate watch info #version=3 #http://baboon.math.berkeley.edu/amap/download/ amap\.(.*)\.tar\.gz # # Please note: The version hosted at # http://code.google.com/p/amap-align/ # is older than the Debian packaged version debian/upstream0000644000000000000000000000056312214301176010752 0ustar Reference: Author: Ariel S. Schwartz and Lior Pachter Title: Multiple alignment by sequence annealing Journal: Bioinformatics Year: 2007 Volume: 23 Number: 2 Pages: e24-e29 DOI: 10.1093/bioinformatics/btl311 URL: http://bioinformatics.oxfordjournals.org/content/23/2/e24 eprint: http://bioinformatics.oxfordjournals.org/content/23/2/e24.full.pdf+html debian/copyright0000644000000000000000000000473012241145240011120 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Author: Ariel Schwartz Source: http://bio.math.berkeley.edu/amap/download This download area as well as the homepage vanished Files: display/* Copyright: © 2007 Michael E. Smoot License: GPL-2+ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. . On Debian systems, the complete text of the GNU General Public License can be found in `/usr/share/common-licenses/GPL'. Files: * Copyright: 2005—2007 Ariel Schwartz License: PD License: PD The current version of AMAP uses the PROBCONS 1.09 code base for some of the input/output procedures, and for the calculation of posterior probabilities (see PROBCONS.README). . AMAP has been made freely available as PUBLIC DOMAIN software and hence is not subject to copyright in the United States. This system and/or any portion of the source code may be used, modified, or redistributed without restrictions. AMAP is distributed WITHOUT WARRANTY, express or implied. The authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for loss due to reliance on the program. . PROBCONS is copyright © 2004 Chuong Do . PROBCONS has been made freely available as PUBLIC DOMAIN software and hence is not subject to copyright in the United States. This system and/or any portion of the source code may be used, modified, or redistributed without restrictions. PROBCONS is distributed WITHOUT WARRANTY, express or implied. The authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for loss due to reliance on the program. Files: debian/* Copyright: © 2007 David Paleino © 2006—2008 Charles Plessy © 2011-2013 Andreas Tille License: PD debian/source/0000755000000000000000000000000012214301176010463 5ustar debian/source/format0000644000000000000000000000001412214301176011671 0ustar 3.0 (quilt) debian/README.Debian0000644000000000000000000000073512214301176011231 0ustar amap for Debian =============== Please note that the previous upstream homepage http://bio.math.berkeley.edu/amap/ vanished and there is no information left about further updates of this program. The version hosted at http://code.google.com/p/amap-align/ is older than the Debian packaged version. If you have any knowledge about new location of the code, please drop a note to the address below. -- Andreas Tille Thu, 13 Jan 2011 13:50:30 +0100 debian/NEWS0000644000000000000000000000114112241147253007663 0ustar amap-align (2.0-2) unstable; urgency=low Previous versions of the package amap-align were shipping the program under a binary name (amap-align) which differed from the original one (amap) because there was already an amap program in Debian. Since this program has been removed from the Etch distribution, amap-align now provides its function through the program /usr/bin/align. To help the transition, a symbolic link, /usr/bin/amap-align, is provided, but may be supressed in the releases following Etch. -- Charles Plessy Sat, 10 Mar 2007 12:59:02 +0900 debian/amap.10000644000000000000000000001551412241144512010170 0ustar .\" Title: AMAP .\" Author: Ariel Schwartz .\" Generator: DocBook XSL Stylesheets v1.73.2 .\" Date: 03/31/2008 .\" Manual: User Manual .\" Source: amap 2.2 .\" .TH "AMAP" "1" "03/31/2008" "amap 2.2" "User Manual" .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .SH "NAME" amap - Protein multiple alignment by sequence annealing .SH "SYNOPSIS" .HP 5 \fBamap\fR [\fB\fIOPTION\fR\fR] [\fIMFAFILE\fR] [\fIMFAFILE\fR] .SH "DESCRIPTION" .PP AMAP is a tool to perform multiple alignment of peptidic sequences\. It utilizes posterior decoding, and a sequence\-annealing alignment, instead of the traditional progressive alignment method\. It is the only alignment program that allows one to control the sensitivity / specificity tradeoff\. It is based on the ProbCons source code, but uses alignment metric accuracy and eliminates the consistency transformation\. .PP In its default configuration, AMAP is tuned to maximize the expected Alignment Metric Accuracy (AMA) score \- a new alignment accuracy measure, based on a metric for the multiple\-alignment space, which integrates sensitivity and specificity into a single balanced measure\. AMA is defined as the fraction of correctly aligned residues (either to another residue or to a gap) out of the total number of residues in all the sequences\. .PP \fBamap\fR aligns sequences provided in MFA format\. This format consists of multiple sequences\. Each sequence in MFA format begins with a single\-line description, followed by lines of sequence data\. The description line is distinguished from the sequence data by a greater\-than (\(lq>\(rq) symbol in the first column\. .SH "OPTIONS" .PP \fB\-clustalw\fR .RS 4 use CLUSTALW output format instead of MFA .RE .PP \fB\-c\fR \fB\-\-consistency\fR \fIREPS\fR .RS 4 use 0 <= \fIREPS\fR <= 5 (default: 0) passes of consistency transformation .RE .PP \fB\-ir\fR \fB\-\-iterative\-refinement\fR \fIREPS\fR .RS 4 use 0 <= \fIREPS\fR <=1000 (default: 0) passes of iterative\-refinement .RE .PP \fB\-pre\fR \fB\-\-pre\-training\fR \fIREPS\fR .RS 4 use 0 <= \fIREPS\fR <= 20 (default: 0) rounds of pretraining .RE .PP \fB\-pairs\fR .RS 4 generate all\-pairs pairwise alignments .RE .PP \fB\-viterbi\fR .RS 4 use Viterbi algorithm to generate all pairs (automatically enables \fB\-pairs\fR) .RE .PP \fB\-v\fR \fB\-\-verbose\fR .RS 4 Report progress while aligning (default: off) .RE .PP \fB\-annot\fR \fIFILENAME\fR .RS 4 write annotation for multiple alignment to \fIFILENAME\fR .RE .PP \fB\-t\fR \fB\-\-train\fR \fIFILENAME\fR .RS 4 compute EM transition probabilities, store in \fIFILENAME\fR (default: no training) .RE .PP \fB\-e\fR \fB\-\-emissions\fR .RS 4 also reestimate emission probabilities (default: off) .RE .PP \fB\-p\fR \fB\-\-paramfile\fR \fIFILENAME\fR .RS 4 read parameters from \fIFILENAME\fR (default: ) .RE .PP \fB\-a\fR \fB\-\-alignment\-order\fR .RS 4 print sequences in alignment order rather than input order (default: off) .RE .PP \fB\-g\fR \fB\-\-gap\-factor\fR \fIGF\fR .RS 4 use \fIGF\fR as the gap\-factor parameter, set to 0 for best sensitivity, higher values for better specificity (default: 0\.5) .RE .PP \fB\-w\fR \fB\-\-edge\-weight\-threshold\fR \fIW\fR .RS 4 stop the sequence annealing process when best edge has lower weight than \fIW\fR, set to 0 for best sensitivity, higher values for better specificity (default: 0) .RE .PP \fB\-prog\fR \fB\-\-progressive\fR .RS 4 use progressive alignment instead of sequence annealing alignment (default: off) .RE .PP \fB\-noreorder\fR \fB\-\-no\-edge\-reordering\fR .RS 4 disable reordering of edges during sequence annealing alignment (default: off) .RE .PP \fB\-maxstep\fR \fB\-\-use\-max\-stepsize\fR .RS 4 use maximum improvement step size instead of tGf edge ranking (default: off) .RE .PP \fB\-print\fR \fB\-\-print\-posteriors\fR .RS 4 only print the posterior probability matrices (default: off) .RE .PP \fB\-gui\fR \fISTART\fR \fISTEP\fR .RS 4 print output for the AMAP Display Java based GUI (default: ) starting at weight \fISTART\fR (default: infinity) with step size \fISTEP\fR (default: ) .RE .SH "EXAMPLES" .PP To run AMAP with the default options change to the \fIalign\fR directory and type: .PP \fB% amap \fR .PP If no file name is provided the list of options are printed\. .PP In order to use the AMAP Display run AMAP with the \-gui option, and save the output to a file, then use the file as the input to AmapDisplay\. For example, type: .PP \fB% align/amap \-gui examples/BB12020\.tfa > examples/BB12020\.tfa\.out\fR .PP \fB% java \-jar display/AmapDisplay\.jar examples/BB12020\.tfa\.out\fR .PP (on Debian systems, the \fIexamples\fR directory is in \fI/usr/share/doc/amap\-align/examples\fR .SH "NOTE" .PP In older versions ( <\ 2\.0\-1) of the package for Debian(TM) systems, the \fBamap\fR command was renamed \fBamap\-align\fR because there was already another tool called \fBamap\fR (which performs some computer network diagnostics)\. A symbolic link \fBamap\-align\fR is still provided for upgrade purposes but will be removed in Debian releases posterior to Etch (Debian\ 4\.0)\. .SH "SEE ALSO" .PP The current version of AMAP uses the PROBCONS 1\.09 code base for some of the input/output procedures, and for the calculation of posterior probabilities (see PROBCONS\.README in \fI/usr/share/doc/amap\-align/\fR)\. Future releases might implement the algorithm using a new independent code base\. .PP On Debian(TM) systems, \fBprobcons\fR(1) is available in the probcons package\. .SH "REFERENCES" .PP For more details on AMAP and AMA, see Schwartz, Ariel S\., Myers, Eugene W\., and Pachter, Lior\. Alignment Metric Accuracy (Submitted for publication)\. For more details on sequence\-annealing, see Schwartz, Ariel S\. and Pachter, Lior\. Multiple Alignment by Sequence Annealing (Submitted for publication)\. .PP PROBCONS was published in Do, C\.B\., Mahabhashyam, M\.S\.P\., Brudno, M\., and Batzoglou, S\. 2005\. PROBCONS: Probabilistic Consistency\-based Multiple Sequence Alignment\. Genome Research 15: 330\-340\. .SH "AUTHORS" .PP \fBAriel Schwartz\fR <\&sariel@cs\.berkeley\.edu\&> .sp -1n .IP "" 4 Upstream author of AMAP .PP \fBChuong Do\fR .sp -1n .IP "" 4 Wrote Probcons, on which AMAP is based\. .PP \fBCharles Plessy>\fR <\&charles\-debian\-nospam@plessy\.org\&> .sp -1n .IP "" 4 Wrote this manpage in DocBook XML for the Debian distribution\. .SH "COPYRIGHT" .PP AMAP, PROBCONS, and this manual page have been made freely available as PUBLIC DOMAIN software and hence are not subject to copyright in the United States\. This system and/or any portion of the source code may be used, modified, or redistributed without restrictions\. AMAP, PROBCONS and this manual page are distributed WITHOUT WARRANTY, express or implied\. The authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for loss due to reliance on the program\. .sp debian/changelog0000644000000000000000000000707412241150224011041 0ustar amap-align (2.2-4) unstable; urgency=low * debian/README.Debian: Mentioning that latest source is not available online any more * debian/source/format: 3.0 (quilt) * debian/upstream: Add citation information * debian/control: - cme fix dpkg-control - canonical Vcs fields - debhelper 9 * remove unneeded amap-align wrapper as announced previously (NEWS) * debian/patches/hardening.patch: Propagate hardening options -- Andreas Tille Thu, 14 Nov 2013 13:46:11 +0100 amap-align (2.2-3) unstable; urgency=low * Standards-Version: 3.9.2 (no changes needed) * Debhelper 8 (compat+control) * debian/patches/fix-gcc-4.6.diff: Fix gcc-4.6 build error Closes: #624990 -- Andreas Tille Mon, 02 May 2011 16:30:17 +0200 amap-align (2.2-2) unstable; urgency=low [ Charles Plessy ] * Updated my email address. [ David Paleino ] * debian/control: removed myself from Uploaders [ Andreas Tille ] * debian/control: - Standards-Version: 3.9.1 (no changes needed) - Debhelper 7 - Fixed Debian Med spelling in maintainer address - Commented Homepage which simply vanished and added a hint about dead upstream * debian/watch: deactivated useless code because the donwload area vanished * debian/copyright: Mention missing homepage / download * debian/rules: - s/dh_clean -k/dh_prep/ - fix permissions of example which should not be executable * debian/README.{Debian,source}: added some information -- Andreas Tille Thu, 13 Jan 2011 13:50:30 +0100 amap-align (2.2-1) unstable; urgency=low [ Charles Plessy ] * New upstream release: - Corrected DNA alignment parameters file. Improved debug output. (2.01) - Includes new output for the AMAP Display Java based GUI. (2.1) * debian/amap.1, debian/amap.1.xml: updated the manpage. * debian/watch: changed URI to monitor. * debian/patches, debian/rules, debian/control: switched to quilt. * debian/patches/fix-gcc-4.3.diff: updated for version 2.2 (Closes: #468060). * debian/control: - Moved the 'Conflicts:' field from the source to the binary section. -- Charles Plessy Thu, 10 Apr 2008 09:17:01 +0900 amap-align (2.0-3) unstable; urgency=low [ Charles Plessy ] * Moved the Homepage: field out from the package's description. [ David Paleino ] * debian/amap.1 - the manpage is now generated offline: this saves buildd time and B-D space. * debian/control: - XS-Vcs-* fields moved to Vcs-* and fixed - added myself to Uploaders - B-D fixed (see above) - Using DM-Upload-Allowed instead of the XS- version * debian/rules - minor changes [ Andreas Tille ] * Added myself as uploader * Reformatted debian/NEWS according to Developers Reference, section 6.3.4 -- Andreas Tille Wed, 20 Feb 2008 10:59:46 +0100 amap-align (2.0-2) unstable; urgency=low * Added Subversion repository URL to debian/control. * Patched for building with gcc-4.3. Many thanks to Martin Michlmayr (Closes:413477) * Renamed /usr/bin/amap-align to /usr/bin/amap, providing a wrapper for compatibility. * Included /usr/share/dpatch/dpatch.make in debian/rules. * Improved manpage using the template of docbook-xsl 1.71.0.dfsg.1-1.1. * Fixed double-building in debian/rules. -- Charles Plessy Sat, 17 Mar 2007 22:16:34 +0900 amap-align (2.0-1) unstable; urgency=low * Initial release Closes: #366321 -- Charles Plessy Sun, 9 Jul 2006 12:53:25 +0900 debian/patches/0000755000000000000000000000000012241144731010614 5ustar debian/patches/fix-gcc-4.6.diff0000644000000000000000000000057312241142545013301 0ustar Author: Andreas Tille LastChanged: Mon, 02 May 2011 16:30:17 +0200 Description: Add header file needed for gcc-4.6 --- amap-align-2.2.orig/align/SafeVector.h +++ amap-align-2.2/align/SafeVector.h @@ -10,6 +10,7 @@ #include #include +#include ///////////////////////////////////////////////////////////////// // SafeVector debian/patches/rename-amap.diff0000644000000000000000000000161312214301176013630 0ustar Since version 2.0-2, this patch is not applied anymore, because the old amap package related to networking has been removed from Debian. --- a/align/Amap.cc +++ b/align/Amap.cc @@ -660,7 +660,12 @@ << "files README and README.PROBCONS for details." << endl << endl << "Usage:" << endl - << " amap [OPTION]... [MFAFILE]..." << endl + << " amap-align [OPTION]... [MFAFILE]..." << endl + << endl + << "Note:" << endl + << "On Debian systems, amap is renamed amap-align because there is already" << endl + << "an amap program in our archives. On other systems, it is possible that " << endl + << "you will find this program under its original amap name." << endl << endl << "Description:" << endl << " Align sequences in MFAFILE(s) and print result to standard output" << endl debian/patches/hardening.patch0000644000000000000000000000174312241144731013601 0ustar Authoe: Andreas Tille LastChanged: Thu, 14 Nov 2013 13:46:11 +0100 Description: Propagate hardening options --- a/align/Makefile +++ b/align/Makefile @@ -26,7 +26,7 @@ OTHERFLAGS = -DNumInsertStates=1 -DVERSI # release mode #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer -CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops +CXXFLAGS += -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops ################################################################################ # 3) Dependencies @@ -38,7 +38,7 @@ TARGETS = amap all : $(TARGETS) amap : MultiSequenceDag.h MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Amap.cc - $(CXX) $(CXXFLAGS) -lm -o amap Amap.cc + $(CXX) $(CXXFLAGS) -lm -o amap Amap.cc $(LDFLAGS) .PHONY : clean clean: debian/patches/fix-gcc-4.3.diff0000644000000000000000000000152212214301176013266 0ustar Description: Allows building with gcc-4.3. Author: Martin Michlmayr (http://bugs.debian.org/413477) Anibal Avelar (http://bugs.debian.org/468060) Forwarded: Ariel Schwartz --- a/align/Amap.cc +++ b/align/Amap.cc @@ -12,6 +12,8 @@ #include "ProbabilisticModel.h" #include "EvolutionaryTree.h" #include "SparseMatrix.h" +#include +#include #include #include #include @@ -23,6 +25,7 @@ #include #include #include +#include string parametersInputFilename = ""; string parametersOutputFilename = "no training"; --- a/align/MultiSequenceDag.h +++ b/align/MultiSequenceDag.h @@ -13,6 +13,7 @@ #include #include #include +#include #include "MultiSequence.h" #include "SparseMatrix.h" debian/patches/series0000644000000000000000000000006212241144600012022 0ustar fix-gcc-4.3.diff fix-gcc-4.6.diff hardening.patch debian/compat0000644000000000000000000000000212241142742010363 0ustar 9 debian/docs0000644000000000000000000000003512214301176010034 0ustar align/PROBCONS.README README