Remove growing hashtable

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