X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=5423dc96e02598a42b843b47256bee816224958c;hb=76b6b31c53b099a3034e0622ec78d4c2b455a309;hp=78d842450b161d11cacf8f114cc20de3b1d49764;hpb=df9b85c1cf39894039018499fe802406cc37f209;p=jalview.git

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 78d8424..5423dc9 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -43,9 +43,9 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     AlignmentPanel ap;
     Stack historyList = new Stack(); // simpler than synching with alignFrame.
     float [] redundancy;
-    Vector originalSequences;
-    Hashtable originalColours;
+    SequenceI [] originalSequences;
     JInternalFrame frame;
+    Vector redundantSeqs;
 
     /**
      * Creates a new RedundancyPanel object.
@@ -53,10 +53,11 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
      * @param ap DOCUMENT ME!
      * @param af DOCUMENT ME!
      */
-    public RedundancyPanel(AlignmentPanel ap, AlignFrame af)
+    public RedundancyPanel(final AlignmentPanel ap, AlignFrame af)
     {
         this.ap = ap;
         this.af = af;
+        redundantSeqs = new Vector();
 
         slider.addChangeListener(new ChangeListener()
             {
@@ -69,7 +70,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 
         applyButton.setText("Remove");
         allGroupsCheck.setVisible(false);
-        slider.setMinimum(60);
+        slider.setMinimum(0);
         slider.setMaximum(100);
         slider.setValue(100);
 
@@ -84,7 +85,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
             {
               public void internalFrameClosing(InternalFrameEvent evt)
               {
-                resetColours();
+               ap.idPanel.idCanvas.setHighlighted(null);
               }
             }
             );
@@ -116,63 +117,66 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 
         validate();
 
-        Vector sel = new Vector();
+        String[] omitHidden = null;
+
         SequenceGroup sg = ap.av.getSelectionGroup();
         int height;
-        originalSequences = new Vector();
-        originalColours = new Hashtable();
+
+        int start, end;
 
         if ( (sg != null) && (sg.getSize(false) >= 1))
         {
-           height = sg.getSize(false);
-          for (int i = 0; i < sg.getSize(false); i++)
-          {
-            sel.addElement(sg.getSequenceAt(i));
-          }
+           originalSequences = sg.getSequencesInOrder(ap.av.alignment);
+           start = sg.getStartRes();
+           end = sg.getEndRes();
         }
         else
         {
-          height = ap.av.alignment.getHeight();
-          for (int i = 0; i < ap.av.alignment.getHeight(); i++)
-          {
-            sel.addElement(ap.av.alignment.getSequenceAt(i));
-          }
+          originalSequences = ap.av.alignment.getSequencesArray();
+          start = 0;
+          end = ap.av.alignment.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.getViewAsString(sg!=null);
+        }
+
 
        // long start = System.currentTimeMillis();
 
         float pid;
-        SequenceI seqi, seqj;
-        for (int i = 0; i < sel.size(); i++)
+        String seqi, seqj;
+        for (int i = 0; i < height; i++)
         {
-            originalSequences.addElement(sel.elementAt(i));
-            originalColours.put(sel.elementAt(i),
-                               ((SequenceI) sel.elementAt(i)).getColor());
 
             for (int j = 0; j < i; j++)
             {
               if(i==j)
                 continue;
 
-              seqi = (SequenceI) sel.elementAt(i);
-              seqj = (SequenceI) sel.elementAt(j);
-
-              if (sg != null)
-                pid = Comparison.PID( seqi,
-                                     seqj,
-                                     sg.getStartRes(), sg.getEndRes());
+              if(omitHidden==null)
+              {
+                seqi = originalSequences[i].getSequence(start, end);
+                seqj = originalSequences[j].getSequence(start, end);
+              }
               else
-                pid = Comparison.PID( seqi,  seqj );
+              {
+                seqi = omitHidden[i];
+                seqj = omitHidden[j];
+              }
 
+              pid = Comparison.PID( seqi,  seqj );
 
-              if(seqj.getLength() < seqi.getLength())
+              if(seqj.length() < seqi.length())
                 redundancy[j] = Math.max(pid, redundancy[j]);
               else
                 redundancy[i] = Math.max(pid, redundancy[i]);
@@ -180,7 +184,6 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
             }
         }
 
-
         progress.setIndeterminate(false);
         progress.setVisible(false);
         progress = null;
@@ -191,7 +194,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
         valueField.setVisible(true);
 
         validate();
-       // System.out.println("blob done "+ (System.currentTimeMillis()-start));
+       // System.out.println((System.currentTimeMillis()-start));
     }
 
     void sliderValueChanged()
@@ -204,13 +207,13 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
       for(int i=0; i<redundancy.length; i++)
       {
         if (value > redundancy[i])
-           ((SequenceI)originalSequences.elementAt(i)).setColor(java.awt.Color.white);
-        else
-           ((SequenceI)originalSequences.elementAt(i)).setColor(java.awt.Color.red);
-      }
+          redundantSeqs.remove(originalSequences[i]);
+        else if(!redundantSeqs.contains(originalSequences[i]))
+          redundantSeqs.add(originalSequences[i]);
 
-      PaintRefresher.Refresh(null,ap.av.alignment);
+      }
 
+      ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
     }
 
     /**
@@ -241,7 +244,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
         {
           if (value <= redundancy[i])
           {
-            SequenceI seq = (SequenceI) originalSequences.elementAt(i);
+            SequenceI seq = originalSequences[i];
             ap.av.alignment.deleteSequence(seq);
             del.add(seq);
             if (sg != null)
@@ -267,16 +270,6 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
         af.updateEditMenuBar();
     }
 
-    void resetColours()
-    {
-      for(int i=0; i<originalSequences.size(); i++)
-      {
-        SequenceI seq = (SequenceI)originalSequences.elementAt(i);
-        seq.setColor( (java.awt.Color)originalColours.get(seq));
-      }
-
-      PaintRefresher.Refresh(ap.av.alignment);
-    }
 
     /**
      * DOCUMENT ME!