[med-svn] r1866 - trunk/packages/emboss/trunk/debian/patches

[plessy at alioth.debian.org]

Author: plessy
Date: 2008-05-15 14:09:58 +0000 (Thu, 15 May 2008)
New Revision: 1866

Added:
   trunk/packages/emboss/trunk/debian/patches/clustalw2-fix.patch
Modified:
   trunk/packages/emboss/trunk/debian/patches/series
Log:
Patch for usage with clustalw2

Added: trunk/packages/emboss/trunk/debian/patches/clustalw2-fix.patch
===================================================================
--- trunk/packages/emboss/trunk/debian/patches/clustalw2-fix.patch	                        (rev 0)
+++ trunk/packages/emboss/trunk/debian/patches/clustalw2-fix.patch	2008-05-15 14:09:58 UTC (rev 1866)
@@ -0,0 +1,25 @@
+This patch allows to use versions of clustalw >= 2.0.
+(See http://lists.open-bio.org/pipermail/emboss/2008-April/003275.html )
+Index: EMBOSS-5.0.0/emboss/emma.c
+===================================================================
+--- EMBOSS-5.0.0.orig/emboss/emma.c
++++ EMBOSS-5.0.0/emboss/emma.c
+@@ -176,12 +176,12 @@
+     dna_matrix = ajAcdGetListSingle( "dnamatrix");
+     m2c = ajStrGetCharFirst(dna_matrix);
+ 
+-    if(m2c=='b')
+-	ajStrAssignC(&m2str,"iub");
+-    else if(m2c=='p')
+-	ajStrAssignC(&m2str,"clustalw");
+-    else if(m2c=='g')
+-	ajStrAssignC(&m2str,"own");
++    if(m2c=='i')
++        ajStrAssignC(&m2str,"iub");
++    else if(m2c=='c')
++        ajStrAssignC(&m2str,"clustalw");
++    else if(m2c=='o')
++        ajStrAssignC(&m2str,"own");
+ 
+ 
+     ma_matrix = ajAcdGetInfile("mamatrixfile");

Modified: trunk/packages/emboss/trunk/debian/patches/series
===================================================================
--- trunk/packages/emboss/trunk/debian/patches/series	2008-05-14 20:51:49 UTC (rev 1865)
+++ trunk/packages/emboss/trunk/debian/patches/series	2008-05-15 14:09:58 UTC (rev 1866)
@@ -1,2 +1,3 @@
+clustalw2-fix.patch
 using-pager-in-tfm.patch
 patch-1-9