JAL-1432 updated copyright notices

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

diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index c9fc0b7..5712390 100755 (executable)
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -1,20 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
- * 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 file is part of Jalview.
  * 
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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.appletgui;
 
@@ -23,14 +23,13 @@ import java.util.*;
 import java.awt.*;
 import java.awt.event.*;
 
+import jalview.analysis.AlignSeq;
 import jalview.commands.*;
 import jalview.datamodel.*;
 
 public class RedundancyPanel extends SliderPanel implements Runnable,
         WindowListener
 {
-  AlignmentPanel ap;
-
   Stack historyList = new Stack(); // simpler than synching with alignFrame.
 
   float[] redundancy;
@@ -85,9 +84,9 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
    * slider to dynamically hide redundant sequences
    * 
    * @param threshold
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param sel
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -110,68 +109,21 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
 
     if ((sg != null) && (sg.getSize() >= 1))
     {
-      originalSequences = sg.getSequencesInOrder(ap.av.alignment);
+      originalSequences = sg.getSequencesInOrder(ap.av.getAlignment());
       start = sg.getStartRes();
       end = sg.getEndRes();
     }
     else
     {
-      originalSequences = ap.av.alignment.getSequencesArray();
+      originalSequences = ap.av.getAlignment().getSequencesArray();
       start = 0;
-      end = ap.av.alignment.getWidth();
+      end = ap.av.getAlignment().getWidth();
     }
 
     height = originalSequences.length;
 
-    redundancy = new float[height];
-    for (int i = 0; i < height; i++)
-    {
-      redundancy[i] = 0f;
-    }
-
-    // if (ap.av.hasHiddenColumns)
-    {
-      // omitHidden = ap.av.getSelectionAsString();
-    }
-
-    // long start = System.currentTimeMillis();
-
-    float pid;
-    String seqi, seqj;
-    for (int i = 0; i < height; i++)
-    {
-      for (int j = 0; j < i; j++)
-      {
-        if (i == j)
-        {
-          continue;
-        }
-
-        if (omitHidden == null)
-        {
-          seqi = originalSequences[i].getSequenceAsString(start, end);
-          seqj = originalSequences[j].getSequenceAsString(start, end);
-        }
-        else
-        {
-          seqi = omitHidden[i];
-          seqj = omitHidden[j];
-        }
-
-        pid = jalview.util.Comparison.PID(seqi, seqj);
-
-        if (seqj.length() < seqi.length())
-        {
-          redundancy[j] = Math.max(pid, redundancy[j]);
-        }
-        else
-        {
-          redundancy[i] = Math.max(pid, redundancy[i]);
-        }
-
-      }
-    }
-
+    redundancy = AlignSeq.computeRedundancyMatrix(originalSequences,
+            omitHidden, start, end, false);
     label.setText("Enter the redundancy threshold");
     slider.setVisible(true);
     applyButton.setEnabled(true);
@@ -242,12 +194,11 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
       }
 
       EditCommand cut = new EditCommand("Remove Redundancy",
-              EditCommand.CUT, deleted, 0, width, ap.av.alignment);
-
+              EditCommand.CUT, deleted, 0, width, ap.av.getAlignment());
+      AlignmentI alignment = ap.av.getAlignment();
       for (int i = 0; i < del.size(); i++)
       {
-        ap.av.alignment.deleteSequence(deleted[i]);
-        PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
+        alignment.deleteSequence(deleted[i]);
         if (sg != null)
         {
           sg.deleteSequence(deleted[i], false);
@@ -258,8 +209,9 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
 
       ap.alignFrame.addHistoryItem(cut);
 
-      ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
-              .getSequences());
+      PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
+      // ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+      // .getSequences());
     }
 
   }