X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FRedundancyPanel.java;h=7608cb9bbdeac91a8c7c6f6027d1b0b6196aadad;hb=7bc213bae5828287329a3490faba291706599b03;hp=273261243a5caf061ee9bf527e6fb64859b1945c;hpb=7928c1a7fab123e9e8baa935f37ab08a965341e7;p=jalview.git

diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index 2732612..7608cb9 100755
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -33,10 +33,9 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
   AlignmentPanel ap;
 
   Stack historyList = new Stack(); // simpler than synching with alignFrame.
-  Vector originalSequences;
-  Hashtable originalColours;
-  SequenceI[] oldAlignment;
   float [] redundancy;
+  SequenceI [] originalSequences;
+  Hashtable originalColours;
   Frame frame;
 
   public RedundancyPanel(AlignmentPanel ap)
@@ -95,65 +94,69 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
 
       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() >= 1))
+      if ( (sg != null) && (sg.getSize(false) >= 1))
       {
-         height = sg.getSize();
-        for (int i = 0; i < sg.getSize(); 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.getSelectionAsString();
+      }
+
 
      // 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());
+          originalColours.put(originalSequences[i],
+                             originalSequences[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)
+            if(omitHidden==null)
             {
-              pid = jalview.util.Comparison.PID(seqi,
-                                                seqj,
-                                                sg.getStartRes(), sg.getEndRes());
+              seqi = originalSequences[i].getSequence(start, end);
+              seqj = originalSequences[j].getSequence(start, end);
             }
             else
-              pid = jalview.util.Comparison.PID( seqi,  seqj );
+            {
+              seqi = omitHidden[i];
+              seqj = omitHidden[j];
+            }
 
+            pid = jalview.util.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]);
@@ -181,9 +184,9 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
     for(int i=0; i<redundancy.length; i++)
     {
       if (value > redundancy[i])
-         ((SequenceI)originalSequences.elementAt(i)).setColor(java.awt.Color.white);
+         originalSequences[i].setColor(java.awt.Color.white);
       else
-         ((SequenceI)originalSequences.elementAt(i)).setColor(java.awt.Color.red);
+         originalSequences[i].setColor(java.awt.Color.red);
     }
 
     PaintRefresher.Refresh(null,ap.av.alignment);
@@ -212,7 +215,7 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
             {
               if (value <= redundancy[i])
               {
-                SequenceI seq = (SequenceI) originalSequences.elementAt(i);
+                SequenceI seq = originalSequences[i];
                 ap.av.alignment.deleteSequence(seq);
                 del.addElement(seq);
                 if (sg != null)
@@ -270,9 +273,9 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
 
   public void windowClosing(WindowEvent evt)
   {
-    for(int i=0; i<originalSequences.size(); i++)
+    for(int i=0; i<originalSequences.length; i++)
     {
-      SequenceI seq = (SequenceI)originalSequences.elementAt(i);
+      SequenceI seq = originalSequences[i];
       seq.setColor( (java.awt.Color)originalColours.get(seq));
     }