X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=f48701169722061cb3d6f82f3792f12deb75676d;hb=ccc53e88e3260886f5d3bdacc619c0f374be9b8f;hp=cbbcf700c9b6309ef1aae1218ef2d99ab6224c55;hpb=7dc7fb2a35c435d825bc91c5ae60ec6073419a69;p=jalview.git

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index cbbcf70..f487011 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -20,15 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.analysis.AlignSeq;
-import jalview.commands.CommandI;
-import jalview.commands.EditCommand;
-import jalview.commands.EditCommand.Action;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.jbgui.GSliderPanel;
-import jalview.util.MessageManager;
-
 import java.awt.event.ActionEvent;
 import java.util.ArrayList;
 import java.util.List;
@@ -42,6 +33,15 @@ import javax.swing.event.ChangeListener;
 import javax.swing.event.InternalFrameAdapter;
 import javax.swing.event.InternalFrameEvent;
 
+import jalview.analysis.AlignSeq;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GSliderPanel;
+import jalview.util.MessageManager;
+
 /**
  * DOCUMENT ME!
  * 
@@ -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.
 
@@ -100,10 +100,12 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     worker.start();
 
     frame = new JInternalFrame();
+    frame.setFrameIcon(null);
     frame.setContentPane(this);
-    Desktop.addInternalFrame(frame, MessageManager
-            .getString("label.redundancy_threshold_selection"), 400, 100,
-            false);
+    Desktop.addInternalFrame(frame,
+            MessageManager
+                    .getString("label.redundancy_threshold_selection"),
+            true, FRAME_WIDTH, FRAME_HEIGHT, false, true);
     frame.addInternalFrameListener(new InternalFrameAdapter()
     {
       @Override
@@ -174,15 +176,15 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     progress.setVisible(false);
     progress = null;
 
-    label.setText(MessageManager
-            .getString("label.enter_redundancy_threshold"));
+    label.setText(
+            MessageManager.getString("label.enter_redundancy_threshold"));
     slider.setVisible(true);
     applyButton.setEnabled(true);
     valueField.setVisible(true);
 
     validate();
     sliderValueChanged();
-    // System.out.println((System.currentTimeMillis()-start));
+    // jalview.bin.Console.outPrintln((System.currentTimeMillis()-start));
   }
 
   void sliderValueChanged()
@@ -193,7 +195,7 @@ 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])
@@ -213,7 +215,7 @@ 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);
 
@@ -224,13 +226,12 @@ 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()];
@@ -238,7 +239,7 @@ 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();
@@ -263,8 +264,8 @@ 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.firePropertyChange("alignment", null,
+              ap.av.getAlignment().getSequences());
     }
 
   }
@@ -289,12 +290,12 @@ 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.firePropertyChange("alignment", null,
+              ap.av.getAlignment().getSequences());
       af.updateEditMenuBar();
     }
 
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, true);
 
     if (historyList.size() == 0)
     {