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

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

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 3cf869c..13527d0 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -18,6 +18,7 @@
 package jalview.gui;
 
 import java.util.*;
+import java.util.List;
 
 import java.awt.*;
 import java.awt.event.*;
@@ -1163,12 +1164,12 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (groupEditing)
     {
-      Vector vseqs = sg.getSequences(av.getHiddenRepSequences());
+      List<SequenceI> vseqs = sg.getSequences(av.getHiddenRepSequences());
       int g, groupSize = vseqs.size();
       SequenceI[] groupSeqs = new SequenceI[groupSize];
       for (g = 0; g < groupSeqs.length; g++)
       {
-        groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
+        groupSeqs[g] = (SequenceI) vseqs.get(g);
       }
 
       // drag to right
@@ -1673,9 +1674,8 @@ public class SeqPanel extends JPanel implements MouseListener,
     {
       if (stretchGroup.cs instanceof ClustalxColourScheme)
       {
-        ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(
-                stretchGroup.getSequences(av.getHiddenRepSequences()),
-                stretchGroup.getWidth());
+        ((ClustalxColourScheme) stretchGroup.cs).alignmentChanged(
+                stretchGroup,av.getHiddenRepSequences());
       }
 
       if (stretchGroup.cs.conservationApplied())