removed Iterator usage.

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index 5da89b0..50077e3 100644 (file)
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -45,27 +45,25 @@ public class MapList
       return true;
     if (obj!=null && obj.fromRatio==fromRatio && obj.toRatio==toRatio
         && obj.fromShifts!=null && obj.toShifts!=null) {
-      Iterator i,j;
-      for (i=fromShifts.iterator(),j=obj.fromShifts.iterator(); i.hasNext();) {
-        int[] mi=(int[]) i.next();
-        if (!j.hasNext())
-          return false;
-        int[] mj=(int[]) j.next();
+      int i,iSize=fromShifts.size(),j,jSize=obj.fromShifts.size();
+      if (iSize!=jSize)
+        return false;
+      for (i=0,iSize=fromShifts.size(),j=0, jSize=obj.fromShifts.size(); i<iSize;) {
+        int[] mi=(int[]) fromShifts.elementAt(i++);
+        int[] mj=(int[]) obj.fromShifts.elementAt(j++);
         if (mi[0]!=mj[0] || mi[1]!=mj[1])
           return false;
       }
-      if (j.hasNext())
+      iSize=toShifts.size();
+      jSize=obj.toShifts.size();
+      if (iSize!=jSize)
         return false;
-      for (i=toShifts.iterator(),j=obj.toShifts.iterator(); i.hasNext();) {
-        int[] mi=(int[]) i.next();
-        if (!j.hasNext())
-          return false;
-        int[] mj=(int[]) j.next();
+      for (i=0,j=0; i<iSize;) {
+        int[] mi=(int[]) toShifts.elementAt(i++);
+        int[] mj=(int[]) obj.toShifts.elementAt(j++);
         if (mi[0]!=mj[0] || mi[1]!=mj[1])
           return false;
       }
-      if (j.hasNext())
-        return false;
       return true;
     }
     return false;
@@ -157,21 +155,21 @@ public class MapList
   private int[][] posMap(Vector intVals, int ratio, Vector toIntVals,
       int toRatio)
   {
-    Iterator iv = intVals.iterator();
-    if (!iv.hasNext())
+    int iv=0,ivSize = intVals.size();
+    if (iv>=ivSize)
     {
       return null;
     }
-    int[] intv=(int[]) iv.next();
+    int[] intv=(int[]) intVals.elementAt(iv++);
     int from=intv[0],to=intv[1];
     if (from > to)
     {
       from = intv[1];
       to=intv[0];
     }
-    while (iv.hasNext())
+    while (iv<ivSize)
     {
-      intv = (int[]) iv.next();
+      intv = (int[]) intVals.elementAt(iv++);
       if (intv[0]<from)
       {
         from=intv[0];
@@ -284,14 +282,14 @@ public class MapList
   private int[] shift(int pos, Vector fromShifts, int fromRatio,
       Vector toShifts, int toRatio)
   {
-    int[] fromCount = countPos(fromShifts.iterator(), pos);
+    int[] fromCount = countPos(fromShifts, pos);
     if (fromCount==null)
     {
       return null;
     }
     int fromRemainder=(fromCount[0]-1) % fromRatio;
     int toCount = 1+(((fromCount[0]-1) / fromRatio) * toRatio);
-    int[] toPos = countToPos(toShifts.iterator(), toCount);
+    int[] toPos = countToPos(toShifts, toCount);
     if (toPos==null)
     {
       return null; // throw new Error("Bad Mapping!");
@@ -307,12 +305,12 @@ public class MapList
    * @param pos
    * @return number of positions or null if pos is not within intervals
    */
-  private int[] countPos(Iterator intVals, int pos)
+  private int[] countPos(Vector intVals, int pos)
   {
-    int count=0,intv[];
-    while (intVals.hasNext())
+    int count=0,intv[],iv=0,ivSize=intVals.size();
+    while (iv<ivSize)
     {
-      intv = (int[])intVals.next();
+      intv = (int[])intVals.elementAt(iv++);
       if (intv[0] <= intv[1])
       {
         if (pos >= intv[0] && pos <= intv[1])
@@ -348,14 +346,14 @@ public class MapList
    * @param pos
    * @return position pos in interval set
    */
-  private int[] countToPos(Iterator intVals, int pos)
+  private int[] countToPos(Vector intVals, int pos)
   {
-    int count = 0, diff = 0, intv[] =
+    int count = 0, diff = 0, iv=0,ivSize=intVals.size(), intv[] =
     {
         0, 0};
-    while (intVals.hasNext())
+    while (iv<ivSize)
     {
-      intv = (int[])intVals.next();
+      intv = (int[])intVals.elementAt(iv++);
       diff = intv[1]-intv[0];
       if (diff >= 0)
       {
@@ -431,10 +429,10 @@ public class MapList
     // correct for word direction for start and end
     int startpos = fromStart[0]+fromStart[2]*(fromRatio2-1);
     int endpos = fromEnd[0]+fromEnd[2]*(fromRatio2-1);
-    Iterator intv = fromShifts2.iterator();
+    int intv=0,intvSize= fromShifts2.size();
     int iv[],i=0,fs=-1,fe=-1; // containing intervals
-    while (intv.hasNext() && (fs==-1 || fe==-1)) {
-      iv = (int[]) intv.next();
+    while (intv<intvSize && (fs==-1 || fe==-1)) {
+      iv = (int[]) fromShifts2.elementAt(intv++);
       if (iv[0]<=iv[1]) {
         if (fs==-1 && startpos>=iv[0] && startpos<=iv[1]) {
           fs = i; 
@@ -456,20 +454,16 @@ public class MapList
       return null;
     Vector ranges=new Vector();
     if (fs<=fe) {
-      intv = fromShifts2.iterator();
-      i=0;
-      while (i<fs) {
-        intv.next();
-        i++;
-      }
+      intv = fs;
+      i=fs;
       // truncate initial interval
-      iv = (int[]) intv.next();
+      iv = (int[]) fromShifts2.elementAt(intv++);
       iv = new int[] { iv[0], iv[1]};// clone
       if (i==fs)
         iv[0] = startpos;
       while (i!=fe) {
         ranges.addElement(iv); // add initial range
-        iv = (int[]) intv.next(); // get next interval
+        iv = (int[]) fromShifts2.elementAt(intv++); // get next interval
         iv = new int[] { iv[0], iv[1]};// clone
         i++;
       }
@@ -505,14 +499,15 @@ public class MapList
     if (ranges!=null && ranges.size()>0) 
     {
       range = new int[ranges.size()*2];
-      intv = ranges.iterator();
+      intv = 0;
+      intvSize=ranges.size();
       i=0; 
-      while (intv.hasNext()) 
+      while (intv<intvSize) 
       {
-        iv = (int[]) intv.next();
+        iv = (int[]) ranges.elementAt(intv);
         range[i++] = iv[0];
         range[i++] = iv[1];
-        intv.remove();
+        ranges.setElementAt(null, intv++); // remove
       }
     }
     return range;