Merge branch 'kjvdh/features/PhylogenyViewer_tabbedsupport' into merge/2_11_2/kjvdh...

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

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 8bf2fba..b248ec4 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.
 
@@ -96,7 +96,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     slider.setMaximum(100);
     slider.setValue(100);
 
-    Thread worker = new Thread(this);
+    Thread worker = new Thread(this, "CreateRedundancyPanelThread");
     worker.start();
 
     frame = new JInternalFrame();
@@ -104,7 +104,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     Desktop.addInternalFrame(frame,
             MessageManager
                     .getString("label.redundancy_threshold_selection"),
-            400, 100, false);
+            true, FRAME_WIDTH, FRAME_HEIGHT, false, true);
     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();
@@ -295,7 +294,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
       af.updateEditMenuBar();
     }
 
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, true);
 
     if (historyList.size() == 0)
     {