[med-svn] r825 - trunk/packages/amap-align/trunk/debian

hanska-guest at alioth.debian.org hanska-guest at alioth.debian.org
Sun Nov 18 09:48:15 UTC 2007 

Author: hanska-guest
Date: 2007-11-18 09:48:14 +0000 (Sun, 18 Nov 2007)
New Revision: 825

Added:
   trunk/packages/amap-align/trunk/debian/amap.1
Modified:
   trunk/packages/amap-align/trunk/debian/changelog
   trunk/packages/amap-align/trunk/debian/control
   trunk/packages/amap-align/trunk/debian/rules
Log:
* 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-*
  - added myself to Uploaders
  - B-D fixed (see above)
* debian/rules - minor changes

Added: trunk/packages/amap-align/trunk/debian/amap.1
===================================================================
--- trunk/packages/amap-align/trunk/debian/amap.1	                        (rev 0)
+++ trunk/packages/amap-align/trunk/debian/amap.1	2007-11-18 09:48:14 UTC (rev 825)
@@ -0,0 +1,179 @@
+.\"     Title: AMAP
+.\"    Author: Ariel Schwartz <sariel at cs.berkeley.edu>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\"      Date: March 10, 2007
+.\"    Manual: User Manual
+.\"    Source: amap-align 2.0
+.\"
+.TH "AMAP" "1" "March 10, 2007" "amap-align 2.0" "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 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\-align\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
+.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 at 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 at 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

Modified: trunk/packages/amap-align/trunk/debian/changelog
===================================================================
--- trunk/packages/amap-align/trunk/debian/changelog	2007-11-18 00:07:16 UTC (rev 824)
+++ trunk/packages/amap-align/trunk/debian/changelog	2007-11-18 09:48:14 UTC (rev 825)
@@ -1,9 +1,19 @@
-amap-align (2.0-3) unreleased; urgency=low
+amap-align (2.0-3) UNRELEASED; urgency=low
 
+  [ Charles Plessy ]
   * Moved the Homepage: field out from the package's description.
 
- -- Charles Plessy <charles-debian-nospam at plessy.org>  Fri, 21 Sep 2007 22:49:14 +0900
+  [ 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-*
+    - added myself to Uploaders
+    - B-D fixed (see above)
+  * debian/rules - minor changes
 
+ -- David Paleino <d.paleino at gmail.com>  Sun, 18 Nov 2007 10:34:44 +0100
+
 amap-align (2.0-2) unstable; urgency=low
 
   * Added Subversion repository URL to debian/control.

Modified: trunk/packages/amap-align/trunk/debian/control
===================================================================
--- trunk/packages/amap-align/trunk/debian/control	2007-11-18 00:07:16 UTC (rev 824)
+++ trunk/packages/amap-align/trunk/debian/control	2007-11-18 09:48:14 UTC (rev 825)
@@ -1,13 +1,14 @@
 Source: amap-align
 Section: science
 Priority: optional
-Conflicts: amap ( <= 4.8-1 )
+Conflicts: amap (<= 4.8-1)
 Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Charles Plessy <charles-debian-nospam at plessy.org>
-Build-Depends: debhelper (>= 5), xsltproc, docbook-xml, docbook-xsl, dpatch
+Uploaders: Charles Plessy <charles-debian-nospam at plessy.org>,
+ David Paleino <d.paleino at gmail.com>
+Build-Depends: debhelper (>= 5), dpatch
 Standards-Version: 3.7.2
-XS-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/amap-align/trunk/
-XS-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/amap-align
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/amap-align/trunk/
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/amap-align
 Homepage: http://bio.math.berkeley.edu/amap/
 
 Package: amap-align

Modified: trunk/packages/amap-align/trunk/debian/rules
===================================================================
--- trunk/packages/amap-align/trunk/debian/rules	2007-11-18 00:07:16 UTC (rev 824)
+++ trunk/packages/amap-align/trunk/debian/rules	2007-11-18 09:48:14 UTC (rev 825)
@@ -27,22 +27,20 @@
 include /usr/share/dpatch/dpatch.make
 
 build: build-stamp
-
-build-stamp: patch amap.1
+build-stamp: patch
 	dh_testdir
 	$(MAKE)
-	touch build-stamp
+	touch $@
 
-amap.1: debian/amap.1.xml
+debian/amap.1: debian/amap.1.xml
 	$(XP) $<
 
-
 clean: unpatch
 	dh_testdir
 	dh_testroot
 	rm -f build-stamp
 	[ ! -f Makefile ] || $(MAKE) clean
-	dh_clean amap.1
+	dh_clean
 
 install: build
 	dh_testdir
@@ -51,7 +49,6 @@
 	dh_installdirs
 
 binary-indep: build install
-
 binary-arch: build install
 	dh_testdir
 	dh_testroot
@@ -59,7 +56,7 @@
 	dh_installdocs
 	dh_installexamples
 	dh_install	amap debian/wrapper/amap-align usr/bin/
-	dh_installman	amap.1
+	dh_installman	debian/amap.1
 	dh_link		usr/share/man/man1/amap.1 usr/share/man/man1/amap-align.1
 	dh_strip
 	dh_compress
@@ -71,4 +68,4 @@
 	dh_builddeb
 
 binary: binary-indep binary-arch
-.PHONY: build clean binary-indep binary-arch binary install configure
+.PHONY: build clean binary-indep binary-arch binary install

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