X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=190dcb059c3afbe04efb6927fc9fbc594fc0dcc9;hb=9ca31f2261760b6fad088295feb701e400e7150f;hp=30effb79fdb3779ca9055a14d8efc181744883fe;hpb=a442f71fc61f1b8b41cedd2c2fd78a5c5323bafb;p=jalview.git

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 30effb7..190dcb0 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.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
@@ -18,16 +18,13 @@
  */
 package jalview.gui;
 
-import jalview.analysis.*;
-
-import jalview.datamodel.*;
-
-import jalview.jbgui.*;
+import java.util.*;
 
 import java.awt.event.*;
 
-import java.util.*;
-
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.jbgui.*;
 
 /**
  * DOCUMENT ME!
@@ -35,127 +32,128 @@ import java.util.*;
  * @author $author$
  * @version $Revision$
  */
-public class PairwiseAlignPanel extends GPairwiseAlignPanel
+public class PairwiseAlignPanel
+    extends GPairwiseAlignPanel
 {
 
-    AlignViewport av;
-    Vector sequences;
+  AlignViewport av;
+  Vector sequences;
+
+  /**
+   * Creates a new PairwiseAlignPanel object.
+   *
+   * @param av DOCUMENT ME!
+   */
+  public PairwiseAlignPanel(AlignViewport av)
+  {
+    super();
+    this.av = av;
 
-    /**
-     * Creates a new PairwiseAlignPanel object.
-     *
-     * @param av DOCUMENT ME!
-     */
-    public PairwiseAlignPanel(AlignViewport av)
+    sequences = new Vector();
+
+    SequenceI[] seqs;
+    String[] seqStrings = av.getViewAsString(true);
+
+    if (av.getSelectionGroup() == null)
+    {
+      seqs = av.alignment.getSequencesArray();
+    }
+    else
     {
-        super();
-        this.av = av;
+      seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+    }
 
-        sequences = new Vector();
+    String type = (av.alignment.isNucleotide()) ? AlignSeq.DNA : AlignSeq.PEP;
 
-        SequenceI [] seqs;
-        String []  seqStrings = av.getViewAsString(true);
+    float[][] scores = new float[seqs.length][seqs.length];
+    double totscore = 0;
+    int count = seqs.length;
 
-        if(av.getSelectionGroup()==null)
-        {
-          seqs = av.alignment.getSequencesArray();
-        }
-        else
-        {
-          seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
-        }
+    Sequence seq;
 
-        String type=(av.alignment.isNucleotide()) ? AlignSeq.DNA : AlignSeq.PEP;
-        
-        float[][] scores = new float[seqs.length][seqs.length];
-        double totscore = 0;
-        int count = seqs.length;
+    for (int i = 1; i < count; i++)
+    {
+      for (int j = 0; j < i; j++)
+      {
 
-        Sequence seq;
+        AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],
+                                   seqs[j], seqStrings[j], type);
 
-        for (int i = 1; i < count; i++)
+        if (as.s1str.length() == 0 || as.s2str.length() == 0)
         {
-            for (int j = 0; j < i; j++)
-            {
-
-                AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],
-                        seqs[j], seqStrings[j], type);
-
-                if(as.s1str.length()==0 || as.s2str.length()==0)
-                {
-                  continue;
-                }
-
-                as.calcScoreMatrix();
-                as.traceAlignment();
-
-
-                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);
-            }
+          continue;
         }
 
-        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");
-        }
+        as.calcScoreMatrix();
+        as.traceAlignment();
+
+        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);
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void viewInEditorButton_actionPerformed(ActionEvent e)
+    if (count > 2)
     {
-        Sequence[] seq = new Sequence[sequences.size()];
+      System.out.println(
+          "Pairwise alignment scaled similarity score matrix\n");
 
-        for (int i = 0; i < sequences.size(); i++)
+      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++)
         {
-            seq[i] = (Sequence) sequences.elementAt(i);
+          jalview.util.Format.print(System.out, "%7.3f",
+                                    scores[i][j] / totscore);
         }
+      }
 
-        AlignFrame af = new AlignFrame(new Alignment(seq),
-                                           AlignFrame.DEFAULT_WIDTH,
-                                           AlignFrame.DEFAULT_HEIGHT);
-
-        Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",
-            AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+      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),
+                                   AlignFrame.DEFAULT_WIDTH,
+                                   AlignFrame.DEFAULT_HEIGHT);
+
+    Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",
+                             AlignFrame.DEFAULT_WIDTH,
+                             AlignFrame.DEFAULT_HEIGHT);
+  }
 }