From 3193f6774b111974d609ea5d5adc95ff50f92b68 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 10 Oct 2006 14:09:24 +0000
Subject: [PATCH] Remove growing hashtable

---
 src/jalview/datamodel/SequenceGroup.java |   21 ++++++---------------
 1 file changed, 6 insertions(+), 15 deletions(-)

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 04cfc2b..2eed50c 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -578,25 +578,16 @@ public class SequenceGroup
      */
     public SequenceI[] getSequencesInOrder(AlignmentI al)
     {
-        int sz = sequences.size();
-        java.util.Hashtable orderedSeqs = new java.util.Hashtable();
-        SequenceI[] seqs = new SequenceI[sz];
+        int sSize = sequences.size();
+        int alHeight = al.getHeight();
 
-        for (int i = 0; i < sz; i++)
-        {
-            SequenceI seq = (SequenceI) sequences.elementAt(i);
-            int index = al.findIndex(seq);
-            orderedSeqs.put(index + "", seq);
-        }
+        SequenceI[] seqs = new SequenceI[sSize];
 
         int index = 0;
-
-        for (int i = 0; i < al.getHeight(); i++)
+        for (int i = 0; i < alHeight && index<sSize; i++)
         {
-            if (orderedSeqs.containsKey(i + ""))
-            {
-                seqs[index++] = (SequenceI) orderedSeqs.get(i + "");
-            }
+          if(sequences.contains( al.getSequenceAt(i) ) )
+            seqs[index++] = al.getSequenceAt(i);
         }
 
         return seqs;
-- 
1.7.10.2