Merge branch 'docs/2_8_1_Release' into Release_2_8_1_Branch

[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 5712390..3d7c80f
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -19,13 +19,14 @@
 package jalview.appletgui;
 
 import java.util.*;
-
+import java.util.List;
 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
@@ -50,7 +51,7 @@ 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 +71,7 @@ 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 +93,7 @@ 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);
@@ -124,12 +125,13 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
 
     redundancy = AlignSeq.computeRedundancyMatrix(originalSequences,
             omitHidden, start, end, false);
-    label.setText("Enter the redundancy threshold");
+    label.setText(MessageManager.getString("label.enter_redundancy_threshold"));
     slider.setVisible(true);
     applyButton.setEnabled(true);
     valueField.setVisible(true);
 
     validate();
+    sliderValueChanged();
     // System.out.println("blob done "+ (System.currentTimeMillis()-start));
   }
 
@@ -142,19 +144,16 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
 
     float value = slider.getValue();
 
+    List<SequenceI> redundantSequences = new ArrayList<SequenceI>();
     for (int i = 0; i < redundancy.length; i++)
     {
-      if (value > redundancy[i])
-      {
-        redundantSeqs.removeElement(originalSequences[i]);
-      }
-      else if (!redundantSeqs.contains(originalSequences[i]))
+      if (value <= redundancy[i])
       {
-        redundantSeqs.addElement(originalSequences[i]);
+        redundantSequences.add(originalSequences[i]);
       }
     }
 
-    ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
+    ap.idPanel.idCanvas.setHighlighted(redundantSequences);
     PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
 
   }