From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 11 Oct 2013 16:20:08 +0000 (+0100)
Subject: JAL-1164 regression on JAL-1292 use bitset to mark graphGroup as rendered
X-Git-Tag: Release_2_8_0b1~1^2~44^2
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=a16fd1b3b74c14b058b297a91d48de0dd85f2a0d

JAL-1164 regression on JAL-1292 use bitset to mark graphGroup as rendered
---

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index dc352f4..dca968e 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -41,6 +41,7 @@ import jalview.workers.ConsensusThread;
 import jalview.workers.StrucConsensusThread;
 
 import java.util.ArrayList;
+import java.util.BitSet;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
@@ -1413,7 +1414,7 @@ public abstract class AlignmentViewport implements AlignViewportI
     int charHeight = getCharHeight();
     if (aa != null)
     {
-      boolean graphgrp[] = null;
+      BitSet graphgrp = new BitSet();
       for (int i = 0; i < aa.length; i++)
       {
         if (aa[i] == null)
@@ -1427,17 +1428,13 @@ public abstract class AlignmentViewport implements AlignViewportI
         }
         if (aa[i].graphGroup > -1)
         {
-          if (graphgrp == null)
-          {
-            graphgrp = new boolean[aa.length];
-          }
-          if (graphgrp[aa[i].graphGroup])
+          if (graphgrp.get(aa[i].graphGroup))
           {
             continue;
           }
           else
           {
-            graphgrp[aa[i].graphGroup] = true;
+            graphgrp.set(aa[i].graphGroup);
           }
         }
         aa[i].height = 0;