merge from 2_4_Release branch

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

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 1e51879..2355b47 100755 (executable)
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program 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 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program 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 this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -31,26 +31,33 @@ import jalview.util.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class RedundancyPanel
-    extends GSliderPanel implements Runnable
+public class RedundancyPanel extends GSliderPanel implements Runnable
 {
   AlignFrame af;
+
   AlignmentPanel ap;
+
   Stack historyList = new Stack(); // simpler than synching with alignFrame.
+
   float[] redundancy;
+
   SequenceI[] originalSequences;
+
   JInternalFrame frame;
+
   Vector redundantSeqs;
 
   /**
    * Creates a new RedundancyPanel object.
-   *
-   * @param ap DOCUMENT ME!
-   * @param af DOCUMENT ME!
+   * 
+   * @param ap
+   *                DOCUMENT ME!
+   * @param af
+   *                DOCUMENT ME!
    */
   public RedundancyPanel(final AlignmentPanel ap, AlignFrame af)
   {
@@ -79,26 +86,27 @@ public class RedundancyPanel
     frame = new JInternalFrame();
     frame.setContentPane(this);
     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
-                             100, false);
+            100, false);
     frame.addInternalFrameListener(new InternalFrameAdapter()
     {
       public void internalFrameClosing(InternalFrameEvent evt)
       {
         ap.idPanel.idCanvas.setHighlighted(null);
       }
-    }
-    );
+    });
 
   }
 
   /**
-   * This is a copy of remove redundancy in jalivew.datamodel.Alignment
-   * except we dont want to remove redundancy, just calculate once
-   * so we can use the slider to dynamically hide redundant sequences
-   *
-   * @param threshold DOCUMENT ME!
-   * @param sel DOCUMENT ME!
-   *
+   * This is a copy of remove redundancy in jalivew.datamodel.Alignment except
+   * we dont want to remove redundancy, just calculate once so we can use the
+   * slider to dynamically hide redundant sequences
+   * 
+   * @param threshold
+   *                DOCUMENT ME!
+   * @param sel
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public void run()
@@ -122,7 +130,7 @@ public class RedundancyPanel
 
     int start, end;
 
-    if ( (sg != null) && (sg.getSize() >= 1))
+    if ((sg != null) && (sg.getSize() >= 1))
     {
       originalSequences = sg.getSequencesInOrder(ap.av.alignment);
       start = sg.getStartRes();
@@ -227,8 +235,9 @@ public class RedundancyPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void applyButton_actionPerformed(ActionEvent e)
   {
@@ -247,7 +256,8 @@ public class RedundancyPanel
       }
     }
 
-    // This has to be done before the restoreHistoryItem method of alignFrame will
+    // This has to be done before the restoreHistoryItem method of alignFrame
+    // will
     // actually restore these sequences.
     if (del.size() > 0)
     {
@@ -264,16 +274,12 @@ public class RedundancyPanel
       }
 
       EditCommand cut = new EditCommand("Remove Redundancy",
-                                        EditCommand.CUT, deleted, 0, width,
-                                        ap.av.alignment);
+              EditCommand.CUT, deleted, 0, width, ap.av.alignment);
 
       for (int i = 0; i < del.size(); i++)
       {
         ap.av.alignment.deleteSequence(deleted[i]);
-        PaintRefresher.Refresh(this,
-                               ap.av.getSequenceSetId(),
-                               true,
-                               true);
+        PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
         if (sg != null)
         {
           sg.deleteSequence(deleted[i], false);
@@ -284,16 +290,17 @@ public class RedundancyPanel
 
       ap.alignFrame.addHistoryItem(cut);
 
-      ap.av.firePropertyChange("alignment", null,
-                               ap.av.getAlignment().getSequences());
+      ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+              .getSequences());
     }
 
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void undoButton_actionPerformed(ActionEvent e)
   {
@@ -316,8 +323,9 @@ public class RedundancyPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void valueField_actionPerformed(ActionEvent e)
   {
@@ -325,8 +333,7 @@ public class RedundancyPanel
     {
       int i = Integer.parseInt(valueField.getText());
       slider.setValue(i);
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       valueField.setText(slider.getValue() + "");
     }