1.1 compatible

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index e513e59..2355a20 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -11,7 +11,7 @@ public class Alignment implements AlignmentI
 \r
   protected Vector      sequences;\r
   protected Vector      groups = new Vector();\r
-  protected ArrayList   superGroup = new ArrayList();\r
+  protected Vector   superGroup = new Vector();\r
   protected char        gapCharacter = '-';\r
   public AlignmentAnnotation [] annotations;\r
   public Conservation conservation;\r
@@ -322,18 +322,19 @@ public class Alignment implements AlignmentI
   public SequenceGroup [] findAllGroups(SequenceI s)\r
   {\r
 \r
-    ArrayList temp = new ArrayList();\r
+    Vector temp = new Vector();\r
 \r
     for (int i = 0; i < this.groups.size();i++)\r
     {\r
       SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
 \r
       if (sg.sequences.contains(s))\r
-       temp.add(sg);\r
+       temp.addElement(sg);\r
     }\r
 \r
     SequenceGroup [] ret = new SequenceGroup[temp.size()];\r
-    temp.toArray( ret );\r
+    for(int i=0; i<temp.size(); i++)\r
+      ret[i] = (SequenceGroup)temp.elementAt(i);\r
 \r
     return ret;\r
 \r
@@ -358,19 +359,19 @@ public class Alignment implements AlignmentI
 \r
   public void addSuperGroup(SuperGroup sg)\r
   {\r
-    superGroup.add(sg);\r
+    superGroup.addElement(sg);\r
   }\r
 \r
   public void removeSuperGroup(SuperGroup sg)\r
   {\r
-    superGroup.remove(sg);\r
+    superGroup.removeElement(sg);\r
   }\r
 \r
   public SuperGroup     getSuperGroup(SequenceGroup sg)\r
   {\r
     for (int i = 0; i < this.superGroup.size(); i++)\r
     {\r
-      SuperGroup temp = (SuperGroup) superGroup.get(i);\r
+      SuperGroup temp = (SuperGroup) superGroup.elementAt(i);\r
       if (temp.sequenceGroups.contains(sg))\r
         return temp;\r
     }\r
@@ -385,8 +386,8 @@ public class Alignment implements AlignmentI
 \r
   public void deleteAllGroups()\r
   {\r
-    groups.clear();\r
-    superGroup.clear();\r
+    groups.removeAllElements();\r
+    superGroup.removeAllElements();\r
    int i=0;\r
     while (i < sequences.size()) {\r
      SequenceI s = getSequenceAt(i);\r