From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 23 Nov 2006 18:27:11 +0000 (+0000)
Subject: Dont make groups of hidden sequences
X-Git-Tag: Release_2_2~38
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6d58edc047af16d3d632842be665ff990de74607;p=jalview.git

Dont make groups of hidden sequences
---

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 71e76af..6051aa6 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -259,7 +259,26 @@ public class Alignment implements AlignmentI
     {
         if (!groups.contains(sg))
         {
-            groups.addElement(sg);
+          if(hiddenSequences.getSize()>0)
+          {
+            //We're not going to make groups of
+            //Hidden sequences
+            int i, iSize = sg.getSize(false);
+            for (i = 0; i < iSize; i++)
+            {
+              if (!sequences.contains(sg.getSequenceAt(i)))
+              {
+                sg.deleteSequence(sg.getSequenceAt(i), false);
+                iSize--;
+                i--;
+              }
+            }
+
+            if (sg.getSize(true) < 1)
+              return;
+          }
+
+          groups.addElement(sg);
         }
     }