[med-svn] r1541 - in trunk/packages/clustalw/trunk: . debian

[charles-guest at alioth.debian.org]

Author: charles-guest
Date: 2008-03-09 13:40:46 +0000 (Sun, 09 Mar 2008)
New Revision: 1541

Modified:
   trunk/packages/clustalw/trunk/CHANGELOG
   trunk/packages/clustalw/trunk/debian/changelog
Log:
new upstream version

Modified: trunk/packages/clustalw/trunk/CHANGELOG
===================================================================
--- trunk/packages/clustalw/trunk/CHANGELOG	2008-03-09 13:27:55 UTC (rev 1540)
+++ trunk/packages/clustalw/trunk/CHANGELOG	2008-03-09 13:40:46 UTC (rev 1541)
@@ -1,9 +1,38 @@
+----------------------------------------------------------------------
+Version 2.0.4 
+----------------------------------------------------------------------
+
+* Updated URLs in help files
+
+* Fixed bug 96: error message when loading alignment with identical
+sequence names
+
+* Made console output look more like 1.83
+
+* Fixed bug 100: "Scores in clustalw2.0 don't match clustalw1.83"
+getMatrix was called with wrong scaling factor
+
+* Fixed bug 99: "stars in input not ignored"
+Asterisks were changed to gaps in alignment
+
+* New command line option: -fullhelp which dumps the built-in help
+file content.
+
+* Quickfix for bug 94 "quicktree seqfault"
+
+
+----------------------------------------------------------------------
+<= Version 2.0.3 
+----------------------------------------------------------------------
+
 * Added LICENSE file to distribution
-This file contains the information about commercial licensing of clustal as well as FAQ for licensing issues
+This file contains the information about commercial licensing of
+clustal as well as FAQ for licensing issues
 
 * Added README file to distribution
-This is the file that lists the files and directories on the Clustal FTP site.
-It also includes acknowledgements of people who have contributed binaries
+This is the file that lists the files and directories on the Clustal
+FTP site.  It also includes acknowledgements of people who have
+contributed binaries
 
 * Removed .pro Qt file from the distribution
 pro-file should be generated anew using qmake and modified according
@@ -25,14 +54,16 @@
 - http://www.openismus.com/documents/linux/automake/automake.shtml
 - http://www.bioinf.uni-freiburg.de/~mmann/HowTo/automake.html
 
-* clustalw files source files have been move to subdir
+* clustalw files source files have been moved to subdir
 
-* Fixed bug #53 change MAXNAMESTODISPLAY back to 10 from 30. This fixes problem of large amount of space between
-sequence name and actual alignment in clustal output files
+* Fixed bug #53 change MAXNAMESTODISPLAY back to 10 from 30.
+This fixes problem of large amount of space between sequence name and
+actual alignment in clustal output files
 
 * This solves bug #72 with long lines (5000+) in fasta files
-changed code to use strings rather than arrays.
-Needed to add delim parameter to getline in order to read files formatted for different OSs on different platforms.
+changed code to use strings rather than arrays.  Needed to add delim
+parameter to getline in order to read files formatted for different
+OSs on different platforms.
 
 * Fixed Bug 79:
 "The count of amino acids in the ClustalX Postscript output not correct"
@@ -51,9 +82,13 @@
 added in aminoacid code O for pyrrolysine
 
 * Fixed bug 89
-changed clustalw2.0 to conform to 1.83 behaviour for width of sequence ID and
-alignment
+changed clustalw2.0 to conform to 1.83 behaviour for width of sequence
+ID and alignment
 
 * Fixed bug 90
-changed clustalw2.0 to conform to 1.83 behaviour leading spaces are stripped
-from FASTA identifiers.
+changed clustalw2.0 to conform to 1.83 behaviour leading spaces are
+stripped from FASTA identifiers.
+
+* Fixed bug 91
+Clustalw2.0 now handles pseudo-FASTA/MoST format files. Strips out
+numbers and spaces.

Modified: trunk/packages/clustalw/trunk/debian/changelog
===================================================================
--- trunk/packages/clustalw/trunk/debian/changelog	2008-03-09 13:27:55 UTC (rev 1540)
+++ trunk/packages/clustalw/trunk/debian/changelog	2008-03-09 13:40:46 UTC (rev 1541)
@@ -1,4 +1,4 @@
-clustalw (2.0.3-1) UNRELEASED; urgency=low
+clustalw (2.0.4-1) UNRELEASED; urgency=low
 
   [ Steffen Moeller ]
   * New upstream release
@@ -6,6 +6,8 @@
     - Includes iterative alignment facility. (v. 2.0.0)
     - fixed bug where Pseudo -FASTA format files were not being processed
       as previously in v1.83 (v. 2.0.3)
+    - fixed other bugs to behave more like 1.83, and introduced a new
+      '-fullhelp' option. (v 2.0.4) 
   * updated debian/watch
   * moved clustalw.1 into debian folder (easier to work
     with svn-buildpackage)
@@ -26,7 +28,7 @@
   * debian/control:
     - fixed Debian capitalisation (see bug #456582)
 
- -- Steffen Moeller <moeller at debian.org>  Sun, 17 Feb 2008 15:18:34 +0100
+ -- Charles Plessy <charles-debian-nospam at plessy.org>  Sun, 09 Mar 2008 22:28:10 +0900
 
 clustalw (1.83-3) unstable; urgency=low