merge from 2_4_Release branch

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

diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index 9881b64..9682000 100755 (executable)
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -1,22 +1,21 @@
 /*
- * 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
  */
-
 package jalview.appletgui;
 
 import java.util.*;
@@ -27,15 +26,19 @@ import java.awt.event.*;
 import jalview.commands.*;
 import jalview.datamodel.*;
 
-public class RedundancyPanel
-    extends SliderPanel implements Runnable, WindowListener
+public class RedundancyPanel extends SliderPanel implements Runnable,
+        WindowListener
 {
   AlignmentPanel ap;
 
   Stack historyList = new Stack(); // simpler than synching with alignFrame.
+
   float[] redundancy;
+
   SequenceI[] originalSequences;
+
   Frame frame;
+
   Vector redundantSeqs;
 
   public RedundancyPanel(AlignmentPanel ap)
@@ -67,8 +70,8 @@ public class RedundancyPanel
 
     frame = new Frame();
     frame.add(this);
-    jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
-                                     400, 100);
+    jalview.bin.JalviewLite.addFrame(frame,
+            "Redundancy threshold selection", 400, 100);
 
     frame.addWindowListener(this);
 
@@ -77,13 +80,15 @@ public class RedundancyPanel
   }
 
   /**
-   * 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()
@@ -103,7 +108,7 @@ 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();
@@ -124,9 +129,9 @@ public class RedundancyPanel
       redundancy[i] = 0f;
     }
 
-    //  if (ap.av.hasHiddenColumns)
+    // if (ap.av.hasHiddenColumns)
     {
-      //   omitHidden = ap.av.getSelectionAsString();
+      // omitHidden = ap.av.getSelectionAsString();
     }
 
     // long start = System.currentTimeMillis();
@@ -198,10 +203,7 @@ public class RedundancyPanel
     }
 
     ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
-    PaintRefresher.Refresh(this,
-                           ap.av.getSequenceSetId(),
-                           true,
-                           true);
+    PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
 
   }
 
@@ -222,7 +224,8 @@ 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)
     {
@@ -239,16 +242,12 @@ 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);
@@ -259,8 +258,8 @@ 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());
     }
 
   }
@@ -290,15 +289,15 @@ public class RedundancyPanel
     {
       int i = Integer.parseInt(valueField.getText());
       slider.setValue(i);
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       valueField.setText(slider.getValue() + "");
     }
   }
 
   public void windowOpened(WindowEvent evt)
-  {}
+  {
+  }
 
   public void windowClosing(WindowEvent evt)
   {
@@ -306,17 +305,22 @@ public class RedundancyPanel
   }
 
   public void windowClosed(WindowEvent evt)
-  {}
+  {
+  }
 
   public void windowActivated(WindowEvent evt)
-  {}
+  {
+  }
 
   public void windowDeactivated(WindowEvent evt)
-  {}
+  {
+  }
 
   public void windowIconified(WindowEvent evt)
-  {}
+  {
+  }
 
   public void windowDeiconified(WindowEvent evt)
-  {}
+  {
+  }
 }