tidied up system.out messages and moved many to stderr.

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index e513e59..d953598 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -11,10 +11,9 @@ 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
 \r
   public boolean featuresAdded = false;\r
 \r
@@ -292,10 +291,10 @@ public class Alignment implements AlignmentI
       len = getHeight()/2;\r
     } else {\r
       len = (getHeight()+1)/2;\r
-      System.out.println("Sort len is odd = " + len);\r
+      System.out.println("DEBUG:Sort len is odd = " + len); // log.\r
     }\r
     for (int i = 0; i < len; i++) {\r
-      System.out.println("Swapping " + seqs[i].getName() + " and " + seqs[getHeight()-i-1].getName());\r
+      System.out.println("DEBUG:Swapping " + seqs[i].getName() + " and " + seqs[getHeight()-i-1].getName()); // log.\r
       SequenceI tmp = seqs[i];\r
       sequences.setElementAt(seqs[getHeight()-i-1],i);\r
       sequences.setElementAt(tmp,getHeight()-i-1);\r
@@ -322,18 +321,19 @@ 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 +358,19 @@ 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 +385,8 @@ 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