X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=dd02bc12626f3b396b3109ee24a6a0aa92747c9d;hb=44d9bd9b511490baec5302be3b7756be0adebde3;hp=3fa137978c21b059ab486913635a49afe9424547;hpb=a013236e12d46fbb87df79447cc3031c542606e1;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 3fa1379..dd02bc1 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -112,7 +112,7 @@ public class Alignment implements AlignmentI
         if (current.getLength() > i)
         {
 	    /* MC Should move this to a method somewhere */
-          if (current.getCharAt(i)!='-' && current.getCharAt(i)!='.' && current.getCharAt(i)!=' ')
+          if ( !jalview.util.Comparison.isGap(current.getCharAt(i)))
             delete = false;
 
         }
@@ -318,6 +318,24 @@ public class Alignment implements AlignmentI
 
     }
     return null;
+  }
+
+  public SequenceGroup [] findAllGroups(SequenceI s)
+  {
+
+    ArrayList temp = new ArrayList();
+
+    for (int i = 0; i < this.groups.size();i++)
+    {
+      SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
+      if (sg.sequences.contains(s))
+       temp.add(sg);
+    }
+
+    SequenceGroup [] ret = new SequenceGroup[temp.size()];
+    temp.toArray( ret );
+
+    return ret;
 
   }
   /**    */
@@ -385,12 +403,14 @@ public class Alignment implements AlignmentI
   }
 
   /**    */
-  public int findIndex(SequenceI s) {
+  public int findIndex(SequenceI s)
+  {
     int i=0;
-    while (i < sequences.size()) {
-      if (s == getSequenceAt(i)) {
+    while (i < sequences.size())
+    {
+      if (s == getSequenceAt(i))
         return i;
-      }
+
       i++;
     }
     return -1;