X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=a14578a8b762bd59c617bc9978566171579d5028;hb=fa129d373443b56d8a59fdec3a87f6f14b1771f3;hp=1e51879561a099ea8171a69e428d2354e4b5f61a;hpb=fa93bb578999b13c0364a712ae368ca8841012a1;p=jalview.git

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 1e51879..a14578a 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * 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.
+ * 
+ * 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/>.
  */
 package jalview.gui;
 
@@ -31,26 +30,33 @@ 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 +85,27 @@ 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 +129,7 @@ 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 +234,9 @@ public class RedundancyPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
    */
   public void applyButton_actionPerformed(ActionEvent e)
   {
@@ -247,7 +255,8 @@ 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 +273,12 @@ 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 +289,17 @@ 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 +322,9 @@ public class RedundancyPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
    */
   public void valueField_actionPerformed(ActionEvent e)
   {
@@ -325,8 +332,7 @@ public class RedundancyPanel
     {
       int i = Integer.parseInt(valueField.getText());
       slider.setValue(i);
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       valueField.setText(slider.getValue() + "");
     }