X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=ad07497063ecac8694a9f4639a74bde173d2dcfc;hb=4a3def9f59cefe629c9a33d87483283aee085928;hp=8ba1feb1669313f10c8b6f6dfc4396419fa57592;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 8ba1feb..ad07497 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -1,35 +1,47 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
-import java.util.*;
-
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
-
 import jalview.analysis.AlignSeq;
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.jbgui.*;
+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;
+import java.util.Stack;
+import java.util.Vector;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JProgressBar;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
 /**
  * DOCUMENT ME!
  * 
@@ -42,7 +54,9 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 
   AlignmentPanel ap;
 
-  Stack historyList = new Stack(); // simpler than synching with alignFrame.
+  Stack<CommandI> historyList = new Stack<>();
+
+  // simpler than synching with alignFrame.
 
   float[] redundancy;
 
@@ -68,6 +82,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 
     slider.addChangeListener(new ChangeListener()
     {
+      @Override
       public void stateChanged(ChangeEvent evt)
       {
         valueField.setText(slider.getValue() + "");
@@ -81,18 +96,21 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     slider.setMaximum(100);
     slider.setValue(100);
 
-    Thread worker = new Thread(this);
+    Thread worker = new Thread(this, "CreateRedundancyPanel");
     worker.start();
 
     frame = new JInternalFrame();
     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
       public void internalFrameClosing(InternalFrameEvent evt)
       {
-        ap.idPanel.idCanvas.setHighlighted(null);
+        ap.getIdPanel().getIdCanvas().setHighlighted(null);
       }
     });
 
@@ -110,6 +128,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public void run()
   {
     JProgressBar progress = new JProgressBar();
@@ -156,7 +175,8 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     progress.setVisible(false);
     progress = null;
 
-    label.setText("Enter the redundancy threshold");
+    label.setText(
+            MessageManager.getString("label.enter_redundancy_threshold"));
     slider.setVisible(true);
     applyButton.setEnabled(true);
     valueField.setVisible(true);
@@ -174,7 +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])
@@ -182,7 +202,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
         redundantSequences.add(originalSequences[i]);
       }
     }
-    ap.idPanel.idCanvas.setHighlighted(redundantSequences);
+    ap.getIdPanel().getIdCanvas().setHighlighted(redundantSequences);
   }
 
   /**
@@ -191,9 +211,10 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void applyButton_actionPerformed(ActionEvent e)
   {
-    Vector del = new Vector();
+    List<SequenceI> del = new ArrayList<>();
 
     undoButton.setEnabled(true);
 
@@ -204,13 +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()];
@@ -218,15 +238,16 @@ 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();
         }
       }
 
-      EditCommand cut = new EditCommand("Remove Redundancy",
-              EditCommand.CUT, deleted, 0, width, ap.av.getAlignment());
+      EditCommand cut = new EditCommand(
+              MessageManager.getString("action.remove_redundancy"),
+              Action.CUT, deleted, 0, width, ap.av.getAlignment());
 
       for (int i = 0; i < del.size(); i++)
       {
@@ -242,8 +263,8 @@ 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());
     }
 
   }
@@ -254,18 +275,26 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void undoButton_actionPerformed(ActionEvent e)
   {
-    CommandI command = (CommandI) historyList.pop();
-    command.undoCommand(af.getViewAlignments());
+    if (historyList == null || historyList.isEmpty())
+    {
+      undoButton.setEnabled(false);
+      return;
+    }
 
-    if (ap.av.historyList.contains(command))
+    CommandI command = historyList.pop();
+    if (ap.av.getHistoryList().contains(command))
     {
-      ap.av.historyList.remove(command);
+      command.undoCommand(af.getViewAlignments());
+      ap.av.getHistoryList().remove(command);
+      ap.av.firePropertyChange("alignment", null,
+              ap.av.getAlignment().getSequences());
       af.updateEditMenuBar();
     }
 
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, true);
 
     if (historyList.size() == 0)
     {
@@ -273,22 +302,4 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     }
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  public void valueField_actionPerformed(ActionEvent e)
-  {
-    try
-    {
-      int i = Integer.parseInt(valueField.getText());
-      slider.setValue(i);
-    } catch (Exception ex)
-    {
-      valueField.setText(slider.getValue() + "");
-    }
-  }
-
 }