JAL-3954 Register AlignFrame as web service change listener and add menus

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

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 8bf2fba..c7e2b8e 100755 (executable)
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -54,7 +54,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 
   AlignmentPanel ap;
 
-  Stack<CommandI> historyList = new Stack<CommandI>();
+  Stack<CommandI> historyList = new Stack<>();
 
   // simpler than synching with alignFrame.
 
@@ -103,8 +103,8 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     frame.setContentPane(this);
     Desktop.addInternalFrame(frame,
             MessageManager
-                    .getString("label.redundancy_threshold_selection"),
-            400, 100, false);
+                    .getString("label.redundancy_threshold_selection"), Desktop.FRAME_MAKE_VISIBLE,
+            FRAME_WIDTH, FRAME_HEIGHT, Desktop.FRAME_NOT_RESIZABLE, Desktop.FRAME_ALLOW_ANY_SIZE);
     frame.addInternalFrameListener(new InternalFrameAdapter()
     {
       @Override
@@ -194,7 +194,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     }
 
     float value = slider.getValue();
-    List<SequenceI> redundantSequences = new ArrayList<SequenceI>();
+    List<SequenceI> redundantSequences = new ArrayList<>();
     for (int i = 0; i < redundancy.length; i++)
     {
       if (value <= redundancy[i])
@@ -214,7 +214,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
   @Override
   public void applyButton_actionPerformed(ActionEvent e)
   {
-    Vector del = new Vector();
+    List<SequenceI> del = new ArrayList<>();
 
     undoButton.setEnabled(true);
 
@@ -225,13 +225,12 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     {
       if (value <= redundancy[i])
       {
-        del.addElement(originalSequences[i]);
+        del.add(originalSequences[i]);
       }
     }
 
     // This has to be done before the restoreHistoryItem method of alignFrame
-    // will
-    // actually restore these sequences.
+    // will actually restore these sequences.
     if (del.size() > 0)
     {
       SequenceI[] deleted = new SequenceI[del.size()];
@@ -239,7 +238,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
       int width = 0;
       for (int i = 0; i < del.size(); i++)
       {
-        deleted[i] = (SequenceI) del.elementAt(i);
+        deleted[i] = del.get(i);
         if (deleted[i].getLength() > width)
         {
           width = deleted[i].getLength();
@@ -264,8 +263,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
       ap.alignFrame.addHistoryItem(cut);
 
       PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
-      ap.av.firePropertyChange("alignment", null,
-              ap.av.getAlignment().getSequences());
+      ap.av.notifyAlignment();
     }
 
   }
@@ -290,12 +288,11 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     {
       command.undoCommand(af.getViewAlignments());
       ap.av.getHistoryList().remove(command);
-      ap.av.firePropertyChange("alignment", null,
-              ap.av.getAlignment().getSequences());
+      ap.av.notifyAlignment();
       af.updateEditMenuBar();
     }
 
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, true);
 
     if (historyList.size() == 0)
     {