Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

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

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index c4390c0..f487011 100755 (executable)
--- 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!
  * 
@@ -100,11 +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);
+            true, FRAME_WIDTH, FRAME_HEIGHT, false, true);
     frame.addInternalFrameListener(new InternalFrameAdapter()
     {
       @Override
@@ -183,7 +184,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 
     validate();
     sliderValueChanged();
-    // System.out.println((System.currentTimeMillis()-start));
+    // jalview.bin.Console.outPrintln((System.currentTimeMillis()-start));
   }
 
   void sliderValueChanged()
@@ -214,7 +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);
 
@@ -225,13 +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()];
@@ -239,7 +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();