update author list in license for (JAL-826)

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

diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index 05372a4..354d8bf 100755 (executable)
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -1,22 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * 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
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
-
 package jalview.appletgui;
 
 import java.util.*;
@@ -27,10 +25,10 @@ import java.awt.event.*;
 import jalview.analysis.*;
 import jalview.datamodel.*;
 
-public class PairwiseAlignPanel
-    extends Panel implements ActionListener
+public class PairwiseAlignPanel extends Panel implements ActionListener
 {
   Vector sequences = new Vector();
+
   AlignmentPanel ap;
 
   public PairwiseAlignPanel(AlignmentPanel ap)
@@ -38,8 +36,7 @@ public class PairwiseAlignPanel
     try
     {
       jbInit();
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
       e.printStackTrace();
     }
@@ -61,8 +58,8 @@ public class PairwiseAlignPanel
     float scores[][] = new float[seqs.length][seqs.length];
     double totscore = 0;
     int count = ap.av.getSelectionGroup().getSize();
-    String type = (ap.av.alignment.isNucleotide()) ? AlignSeq.DNA :
-        AlignSeq.PEP;
+    String type = (ap.av.alignment.isNucleotide()) ? AlignSeq.DNA
+            : AlignSeq.PEP;
     Sequence seq;
 
     for (int i = 1; i < count; i++)
@@ -70,8 +67,8 @@ 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)
         {
@@ -82,35 +79,30 @@ 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.addElement(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.addElement(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");
@@ -119,8 +111,8 @@ 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);
         }
       }
 
@@ -146,21 +138,22 @@ public class PairwiseAlignPanel
       seq[i] = (Sequence) sequences.elementAt(i);
     }
 
-    new AlignFrame(new Alignment(seq),
-                   ap.av.applet,
-                   "Pairwise Aligned Sequences",
-                   false);
+    new AlignFrame(new Alignment(seq), ap.av.applet,
+            "Pairwise Aligned Sequences", false);
 
   }
 
   protected ScrollPane scrollPane = new ScrollPane();
+
   protected TextArea textarea = new TextArea();
+
   protected Button viewInEditorButton = new Button();
+
   Panel jPanel1 = new Panel();
+
   BorderLayout borderLayout1 = new BorderLayout();
 
-  private void jbInit()
-      throws Exception
+  private void jbInit() throws Exception
   {
     this.setLayout(borderLayout1);
     textarea.setFont(new java.awt.Font("Monospaced", 0, 12));