JAL-1114 - refactor methods handling Vectors and Hashtables to Lists and Maps, and...

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index fe96419..76001a5 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1559,10 +1559,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   synchronized void slideSequences(boolean right, int size)
   {
-    Vector sg = new Vector();
+    List<SequenceI> sg = new Vector();
     if (viewport.cursorMode)
     {
-      sg.addElement(viewport.getAlignment().getSequenceAt(
+      sg.add(viewport.getAlignment().getSequenceAt(
               alignPanel.seqPanel.seqCanvas.cursorY));
     }
     else if (viewport.getSelectionGroup() != null
@@ -1586,10 +1586,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         invertGroup.add(viewport.getAlignment().getSequenceAt(i));
     }
 
-    SequenceI[] seqs1 = new SequenceI[sg.size()];
-    for (int i = 0; i < sg.size(); i++)
-      seqs1[i] = (SequenceI) sg.elementAt(i);
-
+    SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
+            
     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
     for (int i = 0; i < invertGroup.size(); i++)
       seqs2[i] = (SequenceI) invertGroup.elementAt(i);
@@ -2237,12 +2235,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       addHistoryItem(trimRegion);
 
-      Vector groups = viewport.getAlignment().getGroups();
-
-      for (int i = 0; i < groups.size(); i++)
+      for (SequenceGroup sg :viewport.getAlignment().getGroups())
       {
-        SequenceGroup sg = (SequenceGroup) groups.get(i);
-
         if ((trimLeft && !sg.adjustForRemoveLeft(column))
                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
         {
@@ -2925,8 +2919,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   public void clustalColour_actionPerformed(ActionEvent e)
   {
-    changeColour(new ClustalxColourScheme(viewport.getAlignment()
-            .getSequences(), viewport.getAlignment().getWidth()));
+    changeColour(new ClustalxColourScheme(viewport.getAlignment(), viewport.getHiddenRepSequences()));
   }
 
   /**
@@ -3104,12 +3097,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (viewport.getColourAppliesToAllGroups())
     {
-      Vector groups = viewport.getAlignment().getGroups();
 
-      for (int i = 0; i < groups.size(); i++)
-      {
-        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
 
+      for (SequenceGroup sg:viewport.getAlignment().getGroups())
+      {
         if (cs == null)
         {
           sg.cs = null;
@@ -3118,8 +3109,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
         if (cs instanceof ClustalxColourScheme)
         {
-          sg.cs = new ClustalxColourScheme(sg.getSequences(viewport
-                  .getHiddenRepSequences()), sg.getWidth());
+          sg.cs = new ClustalxColourScheme(sg, viewport
+                  .getHiddenRepSequences());
         }
         else if (cs instanceof UserColourScheme)
         {
@@ -3571,13 +3562,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         return;
       }
 
-      int s = 0;
       SequenceGroup sg = viewport.getSelectionGroup();
 
       /* Decide if the selection is a column region */
-      while (s < sg.getSize())
+      for (SequenceI _s:sg.getSequences())
       {
-        if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg
+        if (_s.getLength() < sg
                 .getEndRes())
         {
           JOptionPane
@@ -5292,9 +5282,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         Color col = new Color((int) (Math.random() * 255),
                 (int) (Math.random() * 255), (int) (Math.random() * 255));
         col = col.brighter();
-        for (Enumeration sq = gps[g].getSequences(null).elements(); sq
-                .hasMoreElements(); viewport.setSequenceColour(
-                (SequenceI) sq.nextElement(), col))
+        for (SequenceI s:gps[g].getSequences())
+          viewport.setSequenceColour(
+                s, col)
           ;
       }
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());