[med-svn] r174 - in trunk/packages/clustalw/trunk: . debian

[Steffen Möller]

Author: smoe-guest
Date: 2007-01-08 10:37:25 +0100 (Mon, 08 Jan 2007)
New Revision: 174

Modified:
   trunk/packages/clustalw/trunk/clustalx.c
   trunk/packages/clustalw/trunk/debian/changelog
   trunk/packages/clustalw/trunk/debian/control
   trunk/packages/clustalw/trunk/xmenu.c
Log:
* Help now works in ClustalX (Closes:#215414)
* debian/control:
  - improved wording/formatting
  - suggesting alignment pretty-printers
 


Modified: trunk/packages/clustalw/trunk/clustalx.c
===================================================================
--- trunk/packages/clustalw/trunk/clustalx.c	2006-12-29 14:40:50 UTC (rev 173)
+++ trunk/packages/clustalw/trunk/clustalx.c	2007-01-08 09:37:25 UTC (rev 174)
@@ -26,7 +26,7 @@
 #ifdef MSDOS
         char *help_file_name = "clustalx.hlp";
 #else
-        char *help_file_name = "/usr/share/clustalw/clustalw_help";
+        char *help_file_name = "/usr/share/clustalw/clustalx_help";
 #endif
 
 sint max_names; /* maximum length of names in current alignment file */

Modified: trunk/packages/clustalw/trunk/debian/changelog
===================================================================
--- trunk/packages/clustalw/trunk/debian/changelog	2006-12-29 14:40:50 UTC (rev 173)
+++ trunk/packages/clustalw/trunk/debian/changelog	2007-01-08 09:37:25 UTC (rev 174)
@@ -1,3 +1,9 @@
+clustalw (1.83-3) unstable; urgency=low
+
+  * Help now works in ClustalX (Closes:#215414).
+
+ -- Steffen Moeller <steffen_moeller at gmx.de>  Sun,  7 Jan 2007 19:25:12 +0100
+
 clustalw (1.83-2) unstable; urgency=low
 
   * FreeDesktop menu added (Closes: #380715)

Modified: trunk/packages/clustalw/trunk/debian/control
===================================================================
--- trunk/packages/clustalw/trunk/debian/control	2006-12-29 14:40:50 UTC (rev 173)
+++ trunk/packages/clustalw/trunk/debian/control	2007-01-08 09:37:25 UTC (rev 174)
@@ -24,7 +24,7 @@
  http://www.techfak.uni-bielefeld.de/bcd/Curric/MulAli/welcome.html.
  .
  The output of ClustalW can be edited manually but preferably with an alignment
- editor like seaview or within its companion clustalx.
+ editor like seaview or within its companion ClustalX.
  When building a model from your alignment, this can be applied for improved
  database searches. The debian package hmmer creates such in form of an HMM. 
  .
@@ -34,20 +34,23 @@
 Package: clustalx
 Architecture: any
 Depends: ${shlibs:Depends}, clustalw
+Suggests: texshade|texlive-latex-extra, boxshade
 Description: [Biology] GUI for clustalw
- GUI interface for the ClustalW multiple sequence alignment program. It
- provides an integrated environment for performing multiple sequence
- and profile alignments and analysing the results. The sequence alignment is
- displayed in a window on the screen. A versatile coloring scheme has been
- incorporated allowing you to highlight conserved features  in the alignment.
+ This package offers a GUI interface for the ClustalW multiple sequence
+ alignment program. It provides an integrated environment for performing
+ multiple sequence- and profile-alignments to analyse the results.
+ The sequence alignment is displayed in a window on the screen.
+ A versatile coloring scheme has been incorporated to highlight conserved
+ features in the alignment. For professional presentations, one should
+ use the texshade LaTeX package or boxshade.
+ .
  The pull-down menus at the top of the window allow you to select all the
  options required for traditional multiple sequence and profile alignment.
- .
  You can cut-and-paste sequences to change the order of the alignment; you can
  select a subset of sequences to be aligned; you can select a sub-range of the
  alignment to be realigned and inserted back into the original alignment.
  .
- Alignment quality analysis can be performed and low-scoring segments or
+ An alignment quality analysis can be performed and low-scoring segments or
  exceptional residues can be highlighted.
  .
   URL: ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/

Modified: trunk/packages/clustalw/trunk/xmenu.c
===================================================================
--- trunk/packages/clustalw/trunk/xmenu.c	2006-12-29 14:40:50 UTC (rev 173)
+++ trunk/packages/clustalw/trunk/xmenu.c	2007-01-08 09:37:25 UTC (rev 174)
@@ -4411,7 +4411,7 @@
 	while(TRUE) {
 		if(fgets(temp,MAXLINE+1,fd) == NULL) {
 			if(!found_help)
-				error("No help found in help file");
+				error("No help found in help file [%s]",help_file);
 			fclose(fd);
 			return;
 		}