X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FRedundancyPanel.java;h=d2d4384e1f9ccbd40afd1d73d0db3aeb737900b7;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=2e8811a9d3d06d73a0c8318124ac0be2ba1d9003;hpb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;p=jalview.git

diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index 2e8811a..d2d4384 100755
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -21,21 +21,20 @@ package jalview.appletgui;
 
 import java.util.*;
 
-import java.awt.event.*;
-
 import java.awt.*;
+import java.awt.event.*;
 
-import jalview.datamodel.*;
-import jalview.appletgui.PaintRefresher;
 import jalview.commands.*;
+import jalview.datamodel.*;
 
-public class RedundancyPanel extends SliderPanel implements Runnable, WindowListener
+public class RedundancyPanel
+    extends SliderPanel implements Runnable, WindowListener
 {
   AlignmentPanel ap;
 
   Stack historyList = new Stack(); // simpler than synching with alignFrame.
-  float [] redundancy;
-  SequenceI [] originalSequences;
+  float[] redundancy;
+  SequenceI[] originalSequences;
   Frame frame;
   Vector redundantSeqs;
 
@@ -54,7 +53,7 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
 
     slider.setVisibleAmount(1);
     slider.setMinimum(0);
-    slider.setMaximum(100+slider.getVisibleAmount());
+    slider.setMaximum(100 + slider.getVisibleAmount());
     slider.setValue(100);
 
     slider.addAdjustmentListener(new AdjustmentListener()
@@ -76,6 +75,7 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
     Thread worker = new Thread(this);
     worker.start();
   }
+
   /**
    * This is a copy of remove redundancy in jalivew.datamodel.Alignment
    * except we dont want to remove redundancy, just calculate once
@@ -88,103 +88,113 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
    */
   public void run()
   {
-      label.setText("Calculating....");
+    label.setText("Calculating....");
 
-      slider.setVisible(false);
-      applyButton.setEnabled(false);
-      valueField.setVisible(false);
+    slider.setVisible(false);
+    applyButton.setEnabled(false);
+    valueField.setVisible(false);
 
-      validate();
+    validate();
 
-      String[] omitHidden = null;
+    String[] omitHidden = null;
 
-      SequenceGroup sg = ap.av.getSelectionGroup();
-      int height;
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    int height;
 
-      int start, end;
+    int start, end;
 
-      if ( (sg != null) && (sg.getSize() >= 1))
-      {
-         originalSequences = sg.getSequencesInOrder(ap.av.alignment);
-         start = sg.getStartRes();
-         end = sg.getEndRes();
-      }
-      else
-      {
-        originalSequences = ap.av.alignment.getSequencesArray();
-        start = 0;
-        end = ap.av.alignment.getWidth();
-      }
+    if ( (sg != null) && (sg.getSize() >= 1))
+    {
+      originalSequences = sg.getSequencesInOrder(ap.av.alignment);
+      start = sg.getStartRes();
+      end = sg.getEndRes();
+    }
+    else
+    {
+      originalSequences = ap.av.alignment.getSequencesArray();
+      start = 0;
+      end = ap.av.alignment.getWidth();
+    }
 
-      height = originalSequences.length;
+    height = originalSequences.length;
 
-      redundancy = new float[height];
-      for (int i = 0; i < height; i++)
-      {
-        redundancy[i] = 0f;
-      }
+    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;
+    String seqi, seqj;
+    for (int i = 0; i < height; i++)
+    {
+      for (int j = 0; j < i; j++)
       {
-     //   omitHidden = ap.av.getSelectionAsString();
-      }
+        if (i == j)
+        {
+          continue;
+        }
 
+        if (omitHidden == null)
+        {
+          seqi = originalSequences[i].getSequenceAsString(start, end);
+          seqj = originalSequences[j].getSequenceAsString(start, end);
+        }
+        else
+        {
+          seqi = omitHidden[i];
+          seqj = omitHidden[j];
+        }
 
-     // long start = System.currentTimeMillis();
+        pid = jalview.util.Comparison.PID(seqi, seqj);
 
-      float pid;
-      String seqi, seqj;
-      for (int i = 0; i < height; i++)
-      {
-          for (int j = 0; j < i; j++)
-          {
-            if(i==j)
-              continue;
-
-            if(omitHidden==null)
-            {
-              seqi = originalSequences[i].getSequenceAsString(start, end);
-              seqj = originalSequences[j].getSequenceAsString(start, end);
-            }
-            else
-            {
-              seqi = omitHidden[i];
-              seqj = omitHidden[j];
-            }
-
-            pid = jalview.util.Comparison.PID( seqi,  seqj );
-
-            if(seqj.length() < seqi.length())
-              redundancy[j] = Math.max(pid, redundancy[j]);
-            else
-              redundancy[i] = Math.max(pid, redundancy[i]);
-
-          }
-      }
+        if (seqj.length() < seqi.length())
+        {
+          redundancy[j] = Math.max(pid, redundancy[j]);
+        }
+        else
+        {
+          redundancy[i] = Math.max(pid, redundancy[i]);
+        }
 
+      }
+    }
 
-      label.setText("Enter the redundancy threshold");
-      slider.setVisible(true);
-      applyButton.setEnabled(true);
-      valueField.setVisible(true);
+    label.setText("Enter the redundancy threshold");
+    slider.setVisible(true);
+    applyButton.setEnabled(true);
+    valueField.setVisible(true);
 
-      validate();
-     // System.out.println("blob done "+ (System.currentTimeMillis()-start));
+    validate();
+    // System.out.println("blob done "+ (System.currentTimeMillis()-start));
   }
 
   void sliderValueChanged()
   {
-    if(redundancy==null)
+    if (redundancy == null)
+    {
       return;
+    }
 
     float value = slider.getValue();
 
-    for(int i=0; i<redundancy.length; i++)
+    for (int i = 0; i < redundancy.length; i++)
     {
       if (value > redundancy[i])
-         redundantSeqs.removeElement(originalSequences[i]);
-      else if(!redundantSeqs.contains(originalSequences[i]))
-         redundantSeqs.addElement(originalSequences[i]);
+      {
+        redundantSeqs.removeElement(originalSequences[i]);
+      }
+      else if (!redundantSeqs.contains(originalSequences[i]))
+      {
+        redundantSeqs.addElement(originalSequences[i]);
+      }
     }
 
     ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
@@ -193,59 +203,65 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
                            true,
                            true);
 
-    }
+  }
+
   public void applyButton_actionPerformed()
-  {        Vector del = new Vector();
+  {
+    Vector del = new Vector();
+
+    undoButton.setEnabled(true);
 
-        undoButton.setEnabled(true);
+    float value = slider.getValue();
+    SequenceGroup sg = ap.av.getSelectionGroup();
+
+    for (int i = 0; i < redundancy.length; i++)
+    {
+      if (value <= redundancy[i])
+      {
+        del.addElement(originalSequences[i]);
+      }
+    }
 
-        float value = slider.getValue();
-        SequenceGroup sg = ap.av.getSelectionGroup();
+    // This has to be done before the restoreHistoryItem method of alignFrame will
+    // actually restore these sequences.
+    if (del.size() > 0)
+    {
+      SequenceI[] deleted = new SequenceI[del.size()];
 
-        for (int i = 0; i < redundancy.length; i++)
+      int width = 0;
+      for (int i = 0; i < del.size(); i++)
+      {
+        deleted[i] = (SequenceI) del.elementAt(i);
+        if (deleted[i].getLength() > width)
         {
-          if (value <= redundancy[i])
-          {
-            del.addElement(originalSequences[i]);
-          }
+          width = deleted[i].getLength();
         }
+      }
 
-        // This has to be done before the restoreHistoryItem method of alignFrame will
-        // actually restore these sequences.
-        if (del.size() > 0)
+      EditCommand cut = new EditCommand("Remove Redundancy",
+                                        EditCommand.CUT, deleted, 0, width,
+                                        ap.av.alignment);
+
+      for (int i = 0; i < del.size(); i++)
+      {
+        ap.av.alignment.deleteSequence(deleted[i]);
+        PaintRefresher.Refresh(this,
+                               ap.av.getSequenceSetId(),
+                               true,
+                               true);
+        if (sg != null)
         {
-          SequenceI [] deleted = new SequenceI[del.size()];
-
-          int width = 0;
-          for (int i = 0; i < del.size(); i++)
-          {
-            deleted[i] = (SequenceI)del.elementAt(i);
-            if(deleted[i].getLength()>width)
-              width = deleted[i].getLength();
-          }
-
-          EditCommand cut = new EditCommand("Remove Redundancy",
-              EditCommand.CUT, deleted,0,width,ap.av.alignment);
-
-          for (int i = 0; i < del.size(); i++)
-          {
-            ap.av.alignment.deleteSequence( deleted[i] );
-            PaintRefresher.Refresh(this,
-                                   ap.av.getSequenceSetId(),
-                                   true,
-                                   true);
-            if (sg != null)
-            {
-              sg.deleteSequence(deleted[i], false);
-            }
-          }
-
-          historyList.push(cut);
-
-          ap.alignFrame.addHistoryItem(cut);
-
-          ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
+          sg.deleteSequence(deleted[i], false);
         }
+      }
+
+      historyList.push(cut);
+
+      ap.alignFrame.addHistoryItem(cut);
+
+      ap.av.firePropertyChange("alignment", null,
+                               ap.av.getAlignment().getSequences());
+    }
 
   }
 
@@ -265,7 +281,7 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
     if (historyList.size() == 0)
     {
       undoButton.setEnabled(false);
-      }
+    }
   }
 
   public void valueField_actionPerformed(ActionEvent e)
@@ -281,7 +297,6 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
     }
   }
 
-
   public void windowOpened(WindowEvent evt)
   {}
 
@@ -295,10 +310,13 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
 
   public void windowActivated(WindowEvent evt)
   {}
+
   public void windowDeactivated(WindowEvent evt)
   {}
+
   public void windowIconified(WindowEvent evt)
   {}
+
   public void windowDeiconified(WindowEvent evt)
   {}
 }