X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=a9d26908a1cac6d286d066e2aaceea292bb1b16f;hb=fd18e2c73cd015d4e38ad91da0e5d7532ff0ef42;hp=18a1edda4af9f22456e5c08b5dae7ad826407843;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 18a1edd..09ea57e 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -29,8 +29,10 @@ import jalview.datamodel.SequenceI;
 import jalview.jbgui.GSliderPanel;
 import jalview.util.MessageManager;
 
+import java.awt.Color;
 import java.awt.event.ActionEvent;
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Stack;
 import java.util.Vector;
@@ -66,6 +68,8 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 
   Vector redundantSeqs;
 
+  private SequenceI[] redreps;
+
   /**
    * Creates a new RedundancyPanel object.
    * 
@@ -82,6 +86,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 
     slider.addChangeListener(new ChangeListener()
     {
+      @Override
       public void stateChanged(ChangeEvent evt)
       {
         valueField.setText(slider.getValue() + "");
@@ -89,7 +94,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
       }
     });
 
-    applyButton.setText(MessageManager.getString("action.remove"));
+    applyButton.setText(MessageManager.getString("action.hide"));
     allGroupsCheck.setVisible(false);
     slider.setMinimum(0);
     slider.setMaximum(100);
@@ -105,6 +110,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
             false);
     frame.addInternalFrameListener(new InternalFrameAdapter()
     {
+      @Override
       public void internalFrameClosing(InternalFrameEvent evt)
       {
         ap.getIdPanel().getIdCanvas().setHighlighted(null);
@@ -125,6 +131,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public void run()
   {
     JProgressBar progress = new JProgressBar();
@@ -164,15 +171,19 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     {
       omitHidden = ap.av.getViewAsString(sg != null);
     }
-    redundancy = AlignSeq.computeRedundancyMatrix(originalSequences,
+    Object rr[] = AlignSeq.computeRedundancyMatrixWithRep(
+            originalSequences,
             omitHidden, start, end, false);
 
+    redundancy = (float[]) rr[0];
+    redreps = (SequenceI[]) rr[1];
+
     progress.setIndeterminate(false);
     progress.setVisible(false);
     progress = null;
 
     label.setText(MessageManager
-            .getString("label.enter_redundancy_thereshold"));
+            .getString("label.enter_redundancy_threshold"));
     slider.setVisible(true);
     applyButton.setEnabled(true);
     valueField.setVisible(true);
@@ -207,23 +218,106 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void applyButton_actionPerformed(ActionEvent e)
   {
-    Vector del = new Vector();
 
     undoButton.setEnabled(true);
 
     float value = slider.getValue();
     SequenceGroup sg = ap.av.getSelectionGroup();
-
+    // delete_seqs(value, sg);
+    hide_seqs(value, sg);
+  }
+  private void hide_seqs(float value, SequenceGroup sg)
+  {
+    /**
+     * hash to look up the representative for a sequence
+     */
+    HashMap<SequenceI, SequenceI> rep = new HashMap<SequenceI, SequenceI>();
+    /**
+     * hash to collect lists of sequences represented by a sequence
+     */
+    HashMap<SequenceI, SequenceGroup> reps = new HashMap<SequenceI, SequenceGroup>();
     for (int i = 0; i < redundancy.length; i++)
     {
       if (value <= redundancy[i])
       {
-        del.addElement(originalSequences[i]);
+        // does this sequence represent other sequences ?
+        SequenceGroup repset;
+        // is the representative also redundant ?
+        SequenceI repForI = rep.get(redreps[i]);
+        if (repForI==null) {
+          // the representative is still in the alignment. 
+          // is it representing anything already ? 
+          repset = reps.get(redreps[i]);
+          if (repset==null)
+          {
+            repset = new SequenceGroup();
+          }
+          repset.addSequence(originalSequences[i], false);
+          rep.put(originalSequences[i], redreps[i]);
+          reps.put(redreps[i], repset);
+          // and save the representative sequence for originalSeq
+          repForI = redreps[i];
+        } else {
+          // already hidden the representative for this sequence, so look up its redundant peers
+          repset = reps.get(repForI);
+          if (repset==null)
+          {
+            throw new Error("Implementation failure for redundancy set creation");
+          }
+          // add the sequence to the peerset, and mark sequence's representative in hash
+          repset.addSequence(originalSequences[i], false);
+          rep.put(originalSequences[i], repForI);
+        }
+        // merge any sequences represented by this with its new containing group
+        SequenceGroup existingreps = reps.remove(originalSequences[i]);
+        if (existingreps!=null)
+        {
+          for (SequenceI sq:existingreps.getSequences())
+          {
+            rep.put(sq, repForI);
+            repset.addSequence(sq, false);
+          }
+        }
       }
     }
+    int s = 0, e = ap.av.getAlignment().getWidth();
+    if (sg != null)
+    {
+      s = sg.getStartRes();
+      e = sg.getEndRes();
+    }
+    List<SequenceGroup> sgs = new ArrayList<SequenceGroup>();
+    for (SequenceI repseq: reps.keySet())
+    {
+      sg = reps.get(repseq);
+      sg.addSequence(repseq, false);
+      sg.setSeqrep(repseq);
+      sg.setStartRes(s);
+      sg.setEndRes(e);
+      sgs.add(sg);
+    }
+    ap.alignFrame.avc.showRandomColoursForGroups(sgs);
+    for (SequenceI repseq : reps.keySet())
+    {
+      sg = reps.get(repseq);
+      ap.av.hideRepSequences(repseq, sg);
+    }
+  }
 
+  private void delete_seqs(float value, SequenceGroup sg)
+  {
+    ArrayList<SequenceI> del = new ArrayList<SequenceI>();
+
+    for (int i = 0; i < redundancy.length; i++)
+    {
+      if (value <= redundancy[i])
+      {
+        del.add(originalSequences[i]);
+      }
+    }
     // This has to be done before the restoreHistoryItem method of alignFrame
     // will
     // actually restore these sequences.
@@ -234,7 +328,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
       int width = 0;
       for (int i = 0; i < del.size(); i++)
       {
-        deleted[i] = (SequenceI) del.elementAt(i);
+        deleted[i] = del.get(i);
         if (deleted[i].getLength() > width)
         {
           width = deleted[i].getLength();
@@ -271,6 +365,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void undoButton_actionPerformed(ActionEvent e)
   {
     if (historyList == null || historyList.isEmpty())
@@ -303,6 +398,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void valueField_actionPerformed(ActionEvent e)
   {
     try