X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=65090633a7106c72f9949972e99913fc339258e9;hb=da18eb63c94018e134fb60d70e6de43e99bbff50;hp=0d3b0f3ce8232be8ca4477f5caef038b12b11921;hpb=577f505f54fe343e89f581461e780ea8308c20ec;p=jalview.git

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 0d3b0f3..6509063 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -1,74 +1,135 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.gui;
 
-import jalview.datamodel.*;
-import jalview.jbgui.GPairwiseAlignPanel;
 import jalview.analysis.*;
+
+import jalview.datamodel.*;
+
+import jalview.jbgui.*;
+
 import java.awt.event.*;
-import javax.swing.*;
+
 import java.util.*;
 
 
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class PairwiseAlignPanel extends GPairwiseAlignPanel
 {
     Vector sequences = new Vector();
     AlignViewport av;
 
+    /**
+     * Creates a new PairwiseAlignPanel object.
+     *
+     * @param av DOCUMENT ME!
+     */
     public PairwiseAlignPanel(AlignViewport av)
     {
-      super();
-      this.av = av;
-      float scores[][] = new float[av.getAlignment().getHeight()][av.getAlignment().getHeight()];
-      double totscore = 0;
-      int count = av.getSelectionGroup().getSize();
+        super();
+        this.av = av;
 
-      int acount = 0;
-        for (int i = 1; i < count; i++)
-        {
-          for (int j = 0; j < i; j++)
-          {
-            acount++;
-            AlignSeq as = new AlignSeq(av.getSelectionGroup().getSequenceAt(i),
-                                       av.getSelectionGroup().getSequenceAt(j),"pep");
+        Vector selsubset = new Vector();
 
-            as.calcScoreMatrix();
-            as.traceAlignment();
-            as.printAlignment();
-            scores[i][j] = (float)as.getMaxScore()/(float)as.getASeq1().length;
-            totscore = totscore + scores[i][j];
+        for (int i = 0, j = av.getSelectionGroup().getSize(); i < j; i++)
+        {
+            if (av.getAlignment().getSequences().contains(av.getSelectionGroup()
+                                                                .getSequenceAt(i)))
+            {
+                selsubset.add(av.getSelectionGroup().getSequenceAt(i));
+            }
+        }
 
-            textarea.append(as.getOutput());
-            sequences.add( new Sequence( as.getS1().getName(), as.getAStr1()) );
-            sequences.add( new Sequence( as.getS2().getName(), as.getAStr2()) );
+        float[][] scores = new float[selsubset.size()][selsubset.size()];
+        double totscore = 0;
+        int count = selsubset.size();
 
+        int acount = 0;
 
-          }
+        for (int i = 1; i < count; i++)
+        {
+            for (int j = 0; j < i; j++)
+            {
+                acount++;
+
+                AlignSeq as = new AlignSeq((SequenceI) selsubset.elementAt(i),
+                        (SequenceI) selsubset.elementAt(j), "pep");
+                as.calcScoreMatrix();
+                as.traceAlignment();
+                as.printAlignment();
+                scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;
+                totscore = totscore + scores[i][j];
+
+                textarea.append(as.getOutput());
+                sequences.add(new Sequence(as.getS1().getName(), as.getAStr1()));
+                sequences.add(new Sequence(as.getS2().getName(), as.getAStr2()));
+            }
         }
 
         if (count > 2)
         {
-          for (int i = 0; i < count;i++)
-            for (int j = 0; j < i; j++)
-              jalview.util.Format.print(System.out,"%7.3f",scores[i][j]/totscore);
+            System.out.println(
+                "Pairwise alignment scaled similarity score matrix\n");
+
+            for (int i = 0; i < count; i++)
+            {
+                jalview.util.Format.print(System.out, "%s \n",
+                    ("" + i) + " " +
+                    ((SequenceI) selsubset.elementAt(i)).getName());
+            }
+
+            System.out.println("\n");
+
+            for (int i = 0; i < count; i++)
+            {
+                for (int j = 0; j < i; j++)
+                {
+                    jalview.util.Format.print(System.out, "%7.3f",
+                        scores[i][j] / totscore);
+                }
+            }
+
+            System.out.println("\n");
         }
-      }
-
-
-  protected void viewInEditorButton_actionPerformed(ActionEvent e)
-  {
-
-      Sequence [] seq = new Sequence[sequences.size()];
-
-      for (int i=0;i<sequences.size();i++)
-       seq[i] = (Sequence) sequences.elementAt(i);
-
-
-      AlignFrame af = new AlignFrame(new Alignment(seq));
-      int newHeight = seq.length * af.viewport.getCharHeight() + 200;
-      if(newHeight>500)
-        newHeight=500;
-
-      Desktop.addInternalFrame(af, "Pairwise Aligned Sequences", 700,newHeight);
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void viewInEditorButton_actionPerformed(ActionEvent e)
+    {
+        Sequence[] seq = new Sequence[sequences.size()];
 
-  }
+        for (int i = 0; i < sequences.size(); i++)
+        {
+            seq[i] = (Sequence) sequences.elementAt(i);
+        }
 
+        AlignFrame af = new AlignFrame(new Alignment(seq));
+        Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",
+            AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);
+    }
 }