merge from 2_4_Release branch

[jalview.git] / src / jalview / gui / PairwiseAlignPanel.java

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 190dcb0..15c8c70 100755 (executable)
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
@@ -28,21 +28,22 @@ import jalview.jbgui.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class PairwiseAlignPanel
-    extends GPairwiseAlignPanel
+public class PairwiseAlignPanel extends GPairwiseAlignPanel
 {
 
   AlignViewport av;
+
   Vector sequences;
 
   /**
    * Creates a new PairwiseAlignPanel object.
-   *
-   * @param av DOCUMENT ME!
+   * 
+   * @param av
+   *                DOCUMENT ME!
    */
   public PairwiseAlignPanel(AlignViewport av)
   {
@@ -63,7 +64,8 @@ public class PairwiseAlignPanel
       seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
     }
 
-    String type = (av.alignment.isNucleotide()) ? AlignSeq.DNA : AlignSeq.PEP;
+    String type = (av.alignment.isNucleotide()) ? AlignSeq.DNA
+            : AlignSeq.PEP;
 
     float[][] scores = new float[seqs.length][seqs.length];
     double totscore = 0;
@@ -76,8 +78,8 @@ public class PairwiseAlignPanel
       for (int j = 0; j < i; j++)
       {
 
-        AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],
-                                   seqs[j], seqStrings[j], type);
+        AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j],
+                seqStrings[j], type);
 
         if (as.s1str.length() == 0 || as.s2str.length() == 0)
         {
@@ -88,35 +90,30 @@ public class PairwiseAlignPanel
         as.traceAlignment();
 
         as.printAlignment(System.out);
-        scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;
+        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()
-            );
+        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());
+        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");
+      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());
+        jalview.util.Format.print(System.out, "%s \n", ("" + i) + " "
+                + seqs[i].getName());
       }
 
       System.out.println("\n");
@@ -125,8 +122,8 @@ public class PairwiseAlignPanel
       {
         for (int j = 0; j < i; j++)
         {
-          jalview.util.Format.print(System.out, "%7.3f",
-                                    scores[i][j] / totscore);
+          jalview.util.Format.print(System.out, "%7.3f", scores[i][j]
+                  / totscore);
         }
       }
 
@@ -136,8 +133,9 @@ public class PairwiseAlignPanel
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void viewInEditorButton_actionPerformed(ActionEvent e)
   {
@@ -149,11 +147,9 @@ public class PairwiseAlignPanel
     }
 
     AlignFrame af = new AlignFrame(new Alignment(seq),
-                                   AlignFrame.DEFAULT_WIDTH,
-                                   AlignFrame.DEFAULT_HEIGHT);
+            AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
 
     Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",
-                             AlignFrame.DEFAULT_WIDTH,
-                             AlignFrame.DEFAULT_HEIGHT);
+            AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
   }
 }