Multiple Views

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

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 5dd2fc4..50183eb 100755 (executable)
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -43,9 +43,9 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     AlignmentPanel ap;\r
     Stack historyList = new Stack(); // simpler than synching with alignFrame.\r
     float [] redundancy;\r
-    Vector originalSequences;\r
-    Hashtable originalColours;\r
+    SequenceI [] originalSequences;\r
     JInternalFrame frame;\r
+    Vector redundantSeqs;\r
 \r
     /**\r
      * Creates a new RedundancyPanel object.\r
@@ -53,10 +53,11 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
      * @param ap DOCUMENT ME!\r
      * @param af DOCUMENT ME!\r
      */\r
-    public RedundancyPanel(AlignmentPanel ap, AlignFrame af)\r
+    public RedundancyPanel(final AlignmentPanel ap, AlignFrame af)\r
     {\r
         this.ap = ap;\r
         this.af = af;\r
+        redundantSeqs = new Vector();\r
 \r
         slider.addChangeListener(new ChangeListener()\r
             {\r
@@ -69,7 +70,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 \r
         applyButton.setText("Remove");\r
         allGroupsCheck.setVisible(false);\r
-        slider.setMinimum(60);\r
+        slider.setMinimum(0);\r
         slider.setMaximum(100);\r
         slider.setValue(100);\r
 \r
@@ -84,7 +85,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
             {\r
               public void internalFrameClosing(InternalFrameEvent evt)\r
               {\r
-                resetColours();\r
+               ap.idPanel.idCanvas.setHighlighted(null);\r
               }\r
             }\r
             );\r
@@ -116,63 +117,66 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 \r
         validate();\r
 \r
-        Vector sel = new Vector();\r
+        String[] omitHidden = null;\r
+\r
         SequenceGroup sg = ap.av.getSelectionGroup();\r
         int height;\r
-        originalSequences = new Vector();\r
-        originalColours = new Hashtable();\r
 \r
-        if ( (sg != null) && (sg.getSize() >= 1))\r
+        int start, end;\r
+\r
+        if ( (sg != null) && (sg.getSize(false) >= 1))\r
         {\r
-           height = sg.getSize();\r
-          for (int i = 0; i < sg.getSize(); i++)\r
-          {\r
-            sel.addElement(sg.getSequenceAt(i));\r
-          }\r
+           originalSequences = sg.getSequencesInOrder(ap.av.alignment);\r
+           start = sg.getStartRes();\r
+           end = sg.getEndRes();\r
         }\r
         else\r
         {\r
-          height = ap.av.alignment.getHeight();\r
-          for (int i = 0; i < ap.av.alignment.getHeight(); i++)\r
-          {\r
-            sel.addElement(ap.av.alignment.getSequenceAt(i));\r
-          }\r
+          originalSequences = ap.av.alignment.getSequencesArray();\r
+          start = 0;\r
+          end = ap.av.alignment.getWidth();\r
         }\r
 \r
+        height = originalSequences.length;\r
+\r
         redundancy = new float[height];\r
         for (int i = 0; i < height; i++)\r
         {\r
           redundancy[i] = 0f;\r
         }\r
 \r
+        if (ap.av.hasHiddenColumns)\r
+        {\r
+          omitHidden = ap.av.getViewAsString(sg!=null);\r
+        }\r
+\r
 \r
        // long start = System.currentTimeMillis();\r
 \r
         float pid;\r
-        SequenceI seqi, seqj;\r
-        for (int i = 0; i < sel.size(); i++)\r
+        String seqi, seqj;\r
+        for (int i = 0; i < height; i++)\r
         {\r
-            originalSequences.addElement(sel.elementAt(i));\r
-            originalColours.put(sel.elementAt(i),\r
-                               ((SequenceI) sel.elementAt(i)).getColor());\r
 \r
             for (int j = 0; j < i; j++)\r
             {\r
               if(i==j)\r
                 continue;\r
 \r
-              seqi = (SequenceI) sel.elementAt(i);\r
-              seqj = (SequenceI) sel.elementAt(j);\r
-\r
-              if (sg != null)\r
-                pid = Comparison.PID( seqi,\r
-                                     seqj,\r
-                                     sg.getStartRes(), sg.getEndRes());\r
+              if(omitHidden==null)\r
+              {\r
+                seqi = originalSequences[i].getSequence(start, end);\r
+                seqj = originalSequences[j].getSequence(start, end);\r
+              }\r
               else\r
-                pid = Comparison.PID( seqi,  seqj );\r
+              {\r
+                seqi = omitHidden[i];\r
+                seqj = omitHidden[j];\r
+              }\r
 \r
+              pid = Comparison.PID( seqi,  seqj );\r
 \r
-              if(seqj.getLength() < seqi.getLength())\r
+              if(seqj.length() < seqi.length())\r
                 redundancy[j] = Math.max(pid, redundancy[j]);\r
               else\r
                 redundancy[i] = Math.max(pid, redundancy[i]);\r
@@ -180,7 +184,6 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
             }\r
         }\r
 \r
-\r
         progress.setIndeterminate(false);\r
         progress.setVisible(false);\r
         progress = null;\r
@@ -191,7 +194,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
         valueField.setVisible(true);\r
 \r
         validate();\r
-       // System.out.println("blob done "+ (System.currentTimeMillis()-start));\r
+       // System.out.println((System.currentTimeMillis()-start));\r
     }\r
 \r
     void sliderValueChanged()\r
@@ -204,13 +207,13 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
       for(int i=0; i<redundancy.length; i++)\r
       {\r
         if (value > redundancy[i])\r
-           ((SequenceI)originalSequences.elementAt(i)).setColor(java.awt.Color.white);\r
-        else\r
-           ((SequenceI)originalSequences.elementAt(i)).setColor(java.awt.Color.red);\r
-      }\r
+          redundantSeqs.remove(originalSequences[i]);\r
+        else if(!redundantSeqs.contains(originalSequences[i]))\r
+          redundantSeqs.add(originalSequences[i]);\r
 \r
-      PaintRefresher.Refresh(null,ap.av.alignment);\r
+      }\r
 \r
+      ap.idPanel.idCanvas.setHighlighted(redundantSeqs);\r
     }\r
 \r
     /**\r
@@ -241,8 +244,9 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
         {\r
           if (value <= redundancy[i])\r
           {\r
-            SequenceI seq = (SequenceI) originalSequences.elementAt(i);\r
+            SequenceI seq = originalSequences[i];\r
             ap.av.alignment.deleteSequence(seq);\r
+            PaintRefresher.Refresh(this,ap.av.getSequenceSetId(),seq,null);\r
             del.add(seq);\r
             if (sg != null)\r
             {\r
@@ -267,16 +271,6 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
         af.updateEditMenuBar();\r
     }\r
 \r
-    void resetColours()\r
-    {\r
-      for(int i=0; i<originalSequences.size(); i++)\r
-      {\r
-        SequenceI seq = (SequenceI)originalSequences.elementAt(i);\r
-        seq.setColor( (java.awt.Color)originalColours.get(seq));\r
-      }\r
-\r
-      PaintRefresher.Refresh(ap.av.alignment);\r
-    }\r
 \r
     /**\r
      * DOCUMENT ME!\r