X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=ba3c9ac04001fc31a55d8b7947b1228436f56f6e;hb=32c056ffe34e60a1fde83bf4061af6e82d41f958;hp=76f4eb50469f95179424ccea4054fa1605106bf2;hpb=c521a798765bb3672e89ea8cda3241a97d6c6e73;p=jalview.git

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 76f4eb5..ba3c9ac 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -1,79 +1,157 @@
+/*
+ * 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;
+    Vector sequences;
 
+    /**
+     * Creates a new PairwiseAlignPanel object.
+     *
+     * @param av DOCUMENT ME!
+     */
     public PairwiseAlignPanel(AlignViewport av)
     {
-      super();
-      this.av = av;
-      Vector selsubset = new Vector();
-      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));
-      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++)
+        super();
+        this.av = av;
+
+        sequences = new Vector();
+
+        SequenceI [] seqs;
+        String []  seqStrings = av.getViewAsString(true);
+
+        if(av.getSelectionGroup()==null)
         {
-          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()));
+          seqs = av.alignment.getSequencesArray();
+        }
+        else
+        {
+          seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
         }
-      }
-      if (count > 2)
-      {
-        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)
-  {
+        float[][] scores = new float[seqs.length][seqs.length];
+        double totscore = 0;
+        int count = seqs.length;
+
+        Sequence seq;
+
+        for (int i = 1; i < count; i++)
+        {
+            for (int j = 0; j < i; j++)
+            {
+
+                AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],
+                        seqs[j], seqStrings[j], "pep");
 
-      Sequence [] seq = new Sequence[sequences.size()];
+                if(as.s1str.length()==0 || as.s2str.length()==0)
+                {
+                  continue;
+                }
 
-      for (int i=0;i<sequences.size();i++)
-       seq[i] = (Sequence) sequences.elementAt(i);
+                as.calcScoreMatrix();
+                as.traceAlignment();
 
 
-      AlignFrame af = new AlignFrame(new Alignment(seq));
-      Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",
-                               AlignFrame.NEW_WINDOW_WIDTH,
-                               AlignFrame.NEW_WINDOW_HEIGHT);
+                as.printAlignment(System.out);
+                scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;
+                totscore = totscore + scores[i][j];
 
-  }
+                textarea.append(as.getOutput());
+                seq = new Sequence(as.getS1().getName(),
+                                   as.getAStr1(),
+                                   as.getS1().getStart(),
+                                   as.getS1().getEnd()
+                );
+                sequences.add(seq);
 
+                seq = new Sequence(as.getS2().getName(),
+                                   as.getAStr2(),
+                                   as.getS2().getStart(),
+                                   as.getS2().getEnd() );
+                sequences.add(seq);
+            }
+        }
+
+        if (count > 2)
+        {
+            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) + " " +
+                    seqs[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");
+        }
+    }
+
+    /**
+     * 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);
+    }
 }