X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=08481d01c88b5dd3ccb2d9fc6321bd999ace6786;hb=ad20cd92225f2ee8c251d39b00b90555d382a616;hp=adbbfc36f521552ee130fa5ef3fcb769f7c15989;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index adbbfc3..08481d0 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 
@@ -23,10 +23,10 @@ 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.util.*;
 
 /**
  * DOCUMENT ME!
@@ -131,68 +131,24 @@ public class RedundancyPanel extends GSliderPanel 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)
+    if (ap.av.hasHiddenColumns())
     {
       omitHidden = ap.av.getViewAsString(sg != null);
     }
-
-    // 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 = 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);
 
     progress.setIndeterminate(false);
     progress.setVisible(false);
@@ -273,12 +229,11 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
       }
 
       EditCommand cut = new EditCommand("Remove Redundancy",
-              EditCommand.CUT, deleted, 0, width, ap.av.alignment);
+              EditCommand.CUT, deleted, 0, width, 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);
+        ap.av.getAlignment().deleteSequence(deleted[i]);
         if (sg != null)
         {
           sg.deleteSequence(deleted[i], false);
@@ -289,8 +244,9 @@ public class RedundancyPanel extends GSliderPanel 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());
     }
 
   }