From 00b702186f1676036db687a8df5d335a4d5da54d Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 3 May 2005 12:41:39 +0000
Subject: [PATCH] 1.1 compatible

---
 src/jalview/analysis/Conservation.java |   16 ++++++++--------
 src/jalview/analysis/NJTree.java       |   30 +++++++++++++++---------------
 src/jalview/datamodel/Alignment.java   |   19 ++++++++++---------
 src/jalview/datamodel/Sequence.java    |    8 ++------
 src/jalview/datamodel/SuperGroup.java  |   10 +++++-----
 5 files changed, 40 insertions(+), 43 deletions(-)

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 2b4ef63..74381fd 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -41,7 +41,7 @@ public class Conservation {
     if (i>-1 && i<sequences.size()) {
       sq = ((SequenceI)sequences.elementAt(i)).getSequence();
       if (seqNums.size()<=i) {
-        seqNums.add(new int[sq.length()+1]);
+        seqNums.addElement(new int[sq.length()+1]);
       }
       if (sq.hashCode()!=((int[])seqNums.elementAt(i))[0])
        {
@@ -58,7 +58,7 @@ public class Conservation {
            sqnum[j] = ( (Integer) jalview.schemes.ResidueProperties.aaHash.get(new
                String(sq.substring(j - 1, j)))).intValue(); // yuk
          }
-         seqNums.set(i, sqnum);
+         seqNums.setElementAt(sqnum, i);
        }
      } else {
        // JBPNote INFO level debug
@@ -156,7 +156,7 @@ public class Conservation {
           }
         }
       }
-      
+
       total.addElement(resultHash);
     }
   }
@@ -177,7 +177,7 @@ public class Conservation {
     }
     return count;
   }
-  /*** 
+  /***
    * countConsNGaps
    * returns gap count in int[0], and conserved residue count in int[1]
    */
@@ -191,7 +191,7 @@ public class Conservation {
     for (int i = 0; i < sequences.size();i++)
     {
       if( j >= ((Sequence)sequences.elementAt(i)).getSequence().length())
-      {  count++; 
+      {  count++;
       continue;}
 
       char c = ((Sequence)sequences.elementAt(i)).getSequence().charAt(j);
@@ -211,7 +211,7 @@ public class Conservation {
     r[0] = (nres==cons) ? 1 : 0;
     r[1] = count;
 
-    
+
     return r;
   }
 
@@ -336,7 +336,7 @@ public void findQuality(int start, int end) {
     int[] lengths = new int[size];
 
     for (int l = 0; l < size; l++)
-      lengths[l] = ((int[]) seqNums.get(l)).length-1;
+      lengths[l] = ((int[]) seqNums.elementAt(l)).length-1;
 
     for (int j=start; j <= end; j++) {
       double bigtot = 0;
@@ -363,7 +363,7 @@ public void findQuality(int start, int end) {
 	double[] xx = new double[24];
         int seqNum =
             (j<lengths[k])
-            ? ((int[]) seqNums.get(k))[j+1]
+            ? ((int[]) seqNums.elementAt(k))[j+1]
             : 23; // Sequence, or gap at the end
 
         // This is a loop over r
diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index fb0ec33..8f3483d 100755
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -538,8 +538,8 @@ public class NJTree {
 
       float dist = ((SequenceNode)node).dist;
       if (dist > maxDistValue) {
-	  maxdist      = (SequenceNode)node;
-	  maxDistValue = dist;
+          maxdist      = (SequenceNode)node;
+          maxDistValue = dist;
       }
     } else {
       findMaxDist((SequenceNode)node.left());
@@ -547,10 +547,10 @@ public class NJTree {
     }
   }
     public Vector getGroups() {
-	return groups;
+        return groups;
     }
     public float getMaxHeight() {
-	return maxheight;
+        return maxheight;
     }
   public void  groupNodes(SequenceNode node, float threshold) {
     if (node == null) {
@@ -639,8 +639,8 @@ public class NJTree {
   }
 
     public void reCount(SequenceNode node) {
-	ycount = 0;
-	_reCount(node);
+        ycount = 0;
+        _reCount(node);
     }
   public void _reCount(SequenceNode node) {
     if (node == null) {
@@ -664,13 +664,13 @@ public class NJTree {
 
   }
     public void swapNodes(SequenceNode node) {
-	if (node == null) {
-	    return;
-	}
-	SequenceNode tmp = (SequenceNode)node.left();
+        if (node == null) {
+            return;
+        }
+        SequenceNode tmp = (SequenceNode)node.left();
 
-	node.setLeft(node.right());
-	node.setRight(tmp);
+        node.setLeft(node.right());
+        node.setRight(tmp);
     }
   public void changeDirection(SequenceNode node, SequenceNode dir) {
     if (node == null) {
@@ -710,13 +710,13 @@ public class NJTree {
     }
   }
     public void setMaxDist(SequenceNode node) {
-	this.maxdist = maxdist;
+        this.maxdist = maxdist;
     }
     public SequenceNode getMaxDist() {
-	return maxdist;
+        return maxdist;
     }
     public SequenceNode getTopNode() {
-	return top;
+        return top;
     }
 
 }
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index e513e59..2355a20 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -11,7 +11,7 @@ public class Alignment implements AlignmentI
 
   protected Vector      sequences;
   protected Vector      groups = new Vector();
-  protected ArrayList   superGroup = new ArrayList();
+  protected Vector   superGroup = new Vector();
   protected char        gapCharacter = '-';
   public AlignmentAnnotation [] annotations;
   public Conservation conservation;
@@ -322,18 +322,19 @@ public class Alignment implements AlignmentI
   public SequenceGroup [] findAllGroups(SequenceI s)
   {
 
-    ArrayList temp = new ArrayList();
+    Vector temp = new Vector();
 
     for (int i = 0; i < this.groups.size();i++)
     {
       SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
 
       if (sg.sequences.contains(s))
-       temp.add(sg);
+       temp.addElement(sg);
     }
 
     SequenceGroup [] ret = new SequenceGroup[temp.size()];
-    temp.toArray( ret );
+    for(int i=0; i<temp.size(); i++)
+      ret[i] = (SequenceGroup)temp.elementAt(i);
 
     return ret;
 
@@ -358,19 +359,19 @@ public class Alignment implements AlignmentI
 
   public void addSuperGroup(SuperGroup sg)
   {
-    superGroup.add(sg);
+    superGroup.addElement(sg);
   }
 
   public void removeSuperGroup(SuperGroup sg)
   {
-    superGroup.remove(sg);
+    superGroup.removeElement(sg);
   }
 
   public SuperGroup     getSuperGroup(SequenceGroup sg)
   {
     for (int i = 0; i < this.superGroup.size(); i++)
     {
-      SuperGroup temp = (SuperGroup) superGroup.get(i);
+      SuperGroup temp = (SuperGroup) superGroup.elementAt(i);
       if (temp.sequenceGroups.contains(sg))
         return temp;
     }
@@ -385,8 +386,8 @@ public class Alignment implements AlignmentI
 
   public void deleteAllGroups()
   {
-    groups.clear();
-    superGroup.clear();
+    groups.removeAllElements();
+    superGroup.removeAllElements();
    int i=0;
     while (i < sequences.size()) {
      SequenceI s = getSequenceAt(i);
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 5db051a..7a48c2b 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -212,16 +212,12 @@ public class Sequence implements SequenceI
 
   public void deleteCharAt(int i)
   {
-    StringBuffer sbuffer = new StringBuffer(sequence);
-    sbuffer.deleteCharAt(i);
-    sequence = sbuffer.toString();
+    sequence = sequence.substring(0,i) + sequence.substring(i+1);
   }
 
   public void deleteChars(int i, int j)
   {
-    StringBuffer sbuffer = new StringBuffer(sequence);
-    sbuffer.delete(i,j);
-    sequence = sbuffer.toString();
+    sequence = sequence.substring(0,i) + sequence.substring(j);
   }
 
   public void insertCharAt(int i, char c)
diff --git a/src/jalview/datamodel/SuperGroup.java b/src/jalview/datamodel/SuperGroup.java
index 6c4da29..4e2ac1c 100755
--- a/src/jalview/datamodel/SuperGroup.java
+++ b/src/jalview/datamodel/SuperGroup.java
@@ -12,7 +12,7 @@ public class SuperGroup
   boolean displayText;
   boolean colourText;
   public ColourSchemeI cs;
-  ArrayList sequenceGroups = new ArrayList();
+  Vector sequenceGroups = new Vector();
 
   public SuperGroup()
   {
@@ -49,7 +49,7 @@ public class SuperGroup
   public void addGroup(SequenceGroup sg)
   {
     if(!sequenceGroups.contains(sg))
-      sequenceGroups.add(sg);
+      sequenceGroups.addElement(sg);
   }
 
   public void addOrRemove(SequenceGroup sg)
@@ -62,7 +62,7 @@ public class SuperGroup
 
   public void deleteGroup(SequenceGroup sg)
   {
-    sequenceGroups.remove(sg);
+    sequenceGroups.removeElement(sg);
   }
 
   public void setSuperGroupProperties(SequenceGroup sg)
@@ -74,7 +74,7 @@ public class SuperGroup
 
     for(int i=0; i<sequenceGroups.size(); i++)
     {
-      SequenceGroup temp = (SequenceGroup)sequenceGroups.get(i);
+      SequenceGroup temp = (SequenceGroup)sequenceGroups.elementAt(i);
       temp.cs = sg.cs;
       temp.colourText = sg.colourText;
       temp.displayText = sg.displayText;
@@ -90,6 +90,6 @@ public class SuperGroup
 
   public SequenceGroup getGroupeAt(int i)
   {
-    return (SequenceGroup) sequenceGroups.get(i);
+    return (SequenceGroup) sequenceGroups.elementAt(i);
   }
 }
-- 
1.7.10.2