Sort Groups modified

[jalview.git] / src / jalview / datamodel / SequenceGroup.java

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 6f6850b..a262257 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -302,11 +302,11 @@ public class SequenceGroup
    * @param al Alignment\r
    * @return SequenceI[]\r
    */\r
-  public SequenceI[] getSequencesInOrder(Alignment al)\r
+  public SequenceI[] getSequencesInOrder(AlignmentI al)\r
   {\r
-    int sz;\r
+    int sz = sequences.size();\r
     java.util.Hashtable orderedSeqs = new java.util.Hashtable();\r
-    SequenceI[] seqs = new SequenceI[sz = sequences.size()];\r
+    SequenceI[] seqs = new SequenceI[sz];\r
 \r
     for (int i = 0; i < sz; i++)\r
     {\r
@@ -317,26 +317,12 @@ public class SequenceGroup
 \r
     int index = 0;\r
 \r
-    for (int i = 0; i < sz; i++)\r
+    for (int i = 0; i < al.getHeight(); i++)\r
     {\r
-      SequenceI seq = null;\r
-\r
-      while (seq == null)\r
-      {\r
-        if (orderedSeqs.containsKey(index + ""))\r
-        {\r
-          seq = (SequenceI) orderedSeqs.get(index + "");\r
-          index++;\r
-\r
-          break;\r
-        }\r
-        else\r
+        if (orderedSeqs.containsKey(i + ""))\r
         {\r
-          index++;\r
+          seqs[index++] =  (SequenceI) orderedSeqs.get(i + "");\r
         }\r
-      }\r
-\r
-      seqs[index] = seq;\r
     }\r
 \r
     return seqs;\r