i18n

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

diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
old mode 100755 (executable)
new mode 100644 (file)
index 634c82e..d91e53b
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/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 
@@ -22,14 +22,14 @@ import java.util.*;
 import java.awt.*;
 import java.awt.event.*;
 
+import jalview.analysis.AlignSeq;
 import jalview.commands.*;
 import jalview.datamodel.*;
+import jalview.util.MessageManager;
 
 public class RedundancyPanel extends SliderPanel implements Runnable,
         WindowListener
 {
-  AlignmentPanel ap;
-
   Stack historyList = new Stack(); // simpler than synching with alignFrame.
 
   float[] redundancy;
@@ -50,7 +50,7 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
     applyButton.setVisible(true);
     allGroupsCheck.setVisible(false);
 
-    label.setText("Enter the redundancy threshold");
+    label.setText(MessageManager.getString("label.enter_redundancy_threshold"));
     valueField.setText("100");
 
     slider.setVisibleAmount(1);
@@ -70,7 +70,7 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
     frame = new Frame();
     frame.add(this);
     jalview.bin.JalviewLite.addFrame(frame,
-            "Redundancy threshold selection", 400, 100);
+            MessageManager.getString("label.redundancy_threshold_selection"), 400, 100);
 
     frame.addWindowListener(this);
 
@@ -92,7 +92,7 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
    */
   public void run()
   {
-    label.setText("Calculating....");
+    label.setText(MessageManager.getString("label.calculating"));
 
     slider.setVisible(false);
     applyButton.setEnabled(false);
@@ -109,69 +109,22 @@ 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]);
-        }
-
-      }
-    }
-
-    label.setText("Enter the redundancy threshold");
+    redundancy = AlignSeq.computeRedundancyMatrix(originalSequences,
+            omitHidden, start, end, false);
+    label.setText(MessageManager.getString("label.enter_redundancy_threshold"));
     slider.setVisible(true);
     applyButton.setEnabled(true);
     valueField.setVisible(true);
@@ -241,12 +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);
@@ -257,8 +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());
     }
 
   }