From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Sat, 25 May 2013 04:44:21 +0000 (+0000)
Subject: inprogress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3491e0d3c56167d6f6e8f291572e40367efd7fca;p=jalview.git

inprogress
---

diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
index cc0cd46..abcd31f 100644
--- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java
+++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
@@ -175,7 +175,7 @@ public final class SurfacingUtil {
         final Set<String> da = new HashSet<String>();
         domain_architecutures.put( genome, da );
         for( final Protein protein : protein_list ) {
-            final String da_str = ( ( BasicProtein ) protein ).toDomainArchitectureString( "~" );
+            final String da_str = ( ( BasicProtein ) protein ).toDomainArchitectureString( "~", 3, "=" );
             if ( !da.contains( da_str ) ) {
                 if ( !distinct_domain_architecuture_counts.containsKey( da_str ) ) {
                     distinct_domain_architecuture_counts.put( da_str, 1 );