[med-svn] r1673 - trunk/packages/amap-align/trunk/debian

charles-guest at alioth.debian.org charles-guest at alioth.debian.org
Mon Mar 31 11:25:15 UTC 2008 

Author: charles-guest
Date: 2008-03-31 11:25:14 +0000 (Mon, 31 Mar 2008)
New Revision: 1673

Modified:
   trunk/packages/amap-align/trunk/debian/
   trunk/packages/amap-align/trunk/debian/amap.1
   trunk/packages/amap-align/trunk/debian/amap.1.xml
   trunk/packages/amap-align/trunk/debian/changelog
   trunk/packages/amap-align/trunk/debian/control
   trunk/packages/amap-align/trunk/debian/copyright
   trunk/packages/amap-align/trunk/debian/rules
Log:
Working on the 2.2 release ; the EXAMPLES section of the manpage has to be polished better.


Property changes on: trunk/packages/amap-align/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
   + 1

Modified: trunk/packages/amap-align/trunk/debian/amap.1
===================================================================
--- trunk/packages/amap-align/trunk/debian/amap.1	2008-03-31 09:14:42 UTC (rev 1672)
+++ trunk/packages/amap-align/trunk/debian/amap.1	2008-03-31 11:25:14 UTC (rev 1673)
@@ -1,11 +1,11 @@
 .\"     Title: AMAP
 .\"    Author: Ariel Schwartz <sariel at cs.berkeley.edu>
 .\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\"      Date: 03/04/2008
+.\"      Date: 03/31/2008
 .\"    Manual: User Manual
-.\"    Source: amap-align 2.2
+.\"    Source: amap 2.2
 .\"
-.TH "AMAP" "1" "03/04/2008" "amap-align 2.2" "User Manual"
+.TH "AMAP" "1" "03/31/2008" "amap 2.2" "User Manual"
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
@@ -21,7 +21,7 @@
 .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
+\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
@@ -138,6 +138,29 @@
 \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 <multi\-fasta\-file\-name>\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

Modified: trunk/packages/amap-align/trunk/debian/amap.1.xml
===================================================================
--- trunk/packages/amap-align/trunk/debian/amap.1.xml	2008-03-31 09:14:42 UTC (rev 1672)
+++ trunk/packages/amap-align/trunk/debian/amap.1.xml	2008-03-31 11:25:14 UTC (rev 1673)
@@ -10,7 +10,7 @@
   <!ENTITY dhemail     "charles-debian-nospam at plessy.org">
   <!ENTITY dhusername  "&dhfirstname; &dhsurname;">
   <!ENTITY dhucpackage "<refentrytitle>AMAP</refentrytitle>">
-  <!ENTITY dhpackage   "amap-align">
+  <!ENTITY dhpackage   "amap">
   <!ENTITY dhrelease   "2.2">
   <!ENTITY debian      "<productname>Debian</productname>">
   <!ENTITY gnu         "<acronym>GNU</acronym>">
@@ -265,6 +265,33 @@
   
   <refsect1>
     <title>
+      EXAMPLES
+    </title>
+    <para>
+      To run AMAP with the default options change to the <filename>align</filename> directory and type:
+    </para>
+    <para>
+        <command>% amap &lt;multi-fasta-file-name&gt;</command>
+    </para>
+    <para>
+      If no file name is provided the list of options are printed.
+    </para>
+    <para>
+      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:
+    </para>
+    <para>
+      <command>% align/amap -gui examples/BB12020.tfa &gt; examples/BB12020.tfa.out</command>
+    </para>
+    <para>
+      <command>% java -jar display/AmapDisplay.jar examples/BB12020.tfa.out</command>
+    </para>
+    <para>
+      (on Debian systems, the <filename>examples</filename> directory is in <filename>/usr/share/doc/amap-align/examples</filename>
+    </para>
+  </refsect1>
+  
+  <refsect1>
+    <title>
       NOTE
     </title>
     

Modified: trunk/packages/amap-align/trunk/debian/changelog
===================================================================
--- trunk/packages/amap-align/trunk/debian/changelog	2008-03-31 09:14:42 UTC (rev 1672)
+++ trunk/packages/amap-align/trunk/debian/changelog	2008-03-31 11:25:14 UTC (rev 1673)
@@ -1,14 +1,16 @@
-amap-align (2.2-1) unstable; urgency=low
+amap-align (2.2-1) UNRELEASED; 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: updated the manpage.
+  * 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/control: 
+    - Moved the 'Conflicts:' field from the source to the binary section.
 
- -- Charles Plessy <charles-debian-nospam at plessy.org>  Mon, 18 Feb 2008 22:34:20 +0900
+ -- Charles Plessy <charles-debian-nospam at plessy.org>  Fri, 21 Mar 2008 14:44:31 +0900
 
 amap-align (2.0-3) unstable; urgency=low
 

Modified: trunk/packages/amap-align/trunk/debian/control
===================================================================
--- trunk/packages/amap-align/trunk/debian/control	2008-03-31 09:14:42 UTC (rev 1672)
+++ trunk/packages/amap-align/trunk/debian/control	2008-03-31 11:25:14 UTC (rev 1673)
@@ -1,7 +1,6 @@
 Source: amap-align
 Section: science
 Priority: optional
-Conflicts: amap (<= 4.8-1)
 Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 DM-Upload-Allowed: yes
 Uploaders: Charles Plessy <charles-debian-nospam at plessy.org>,
@@ -16,6 +15,7 @@
 Package: amap-align
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}
+Conflicts: amap (<= 4.8-1)
 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

Modified: trunk/packages/amap-align/trunk/debian/copyright
===================================================================
--- trunk/packages/amap-align/trunk/debian/copyright	2008-03-31 09:14:42 UTC (rev 1672)
+++ trunk/packages/amap-align/trunk/debian/copyright	2008-03-31 11:25:14 UTC (rev 1673)
@@ -41,7 +41,7 @@
  authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for loss due to reliance on
  the program.
  .
- PROBCONS is copyright (C) 2004 Chuong Do <chuongdo at cs.stanford.edu>
+ PROBCONS is copyright © 2004 Chuong Do <chuongdo at cs.stanford.edu>
  .
  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

Modified: trunk/packages/amap-align/trunk/debian/rules
===================================================================
--- trunk/packages/amap-align/trunk/debian/rules	2008-03-31 09:14:42 UTC (rev 1672)
+++ trunk/packages/amap-align/trunk/debian/rules	2008-03-31 11:25:14 UTC (rev 1673)
@@ -5,10 +5,9 @@
 # As a special exception, when this file is copied by dh-make into a
 # dh-make output file, you may use that output file without restriction.
 # This special exception was added by Craig Small in version 0.37 of dh-make.
-# Modifications by Charles Plessy during the years 2006-7 can also
+# Modifications by Charles Plessy during the years 2006-8 can also
 # be used without restriction.
 
-DB2MAN   = "/usr/share/xml/docbook/stylesheet/nwalsh/manpages/docbook.xsl"
 
 XP=xsltproc  \
       -''-nonet \

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