X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPairwiseAlignPanel.java;h=55cf2ccb95004792c97b9677d850cbf326143d0c;hb=3ca1aeccca8d3adfd55d1ff8bd447f8bf0d4ac2f;hp=65f40c351ca2fd4ba72ddc375feb5a4e3f733bac;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index 65f40c3..55cf2cc 100755
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -1,89 +1,97 @@
 /*
-* 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
-*/
+ * 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.appletgui;
 
-import jalview.datamodel.*;
-import jalview.jbappletgui.GPairwiseAlignPanel;
-import jalview.analysis.*;
-import java.awt.event.*;
 import java.util.*;
 
+import java.awt.event.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.jbappletgui.*;
 
-public class PairwiseAlignPanel extends GPairwiseAlignPanel
+public class PairwiseAlignPanel
+    extends GPairwiseAlignPanel
 {
-    Vector sequences = new Vector();
-    AlignViewport av;
+  Vector sequences = new Vector();
+  AlignViewport av;
 
-    public PairwiseAlignPanel(AlignViewport av)
+  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();
+
+    int acount = 0;
+    for (int i = 1; i < count; i++)
     {
-      super();
-      this.av = av;
-      float scores[][] = new float[av.getAlignment().getHeight()][av.getAlignment().getHeight()];
-      double totscore = 0;
-      int count = av.getSelectionGroup().getSize();
-
-      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");
-
-            as.calcScoreMatrix();
-            as.traceAlignment();
-            as.printAlignment();
-            scores[i][j] = (float)as.getMaxScore()/(float)as.getASeq1().length;
-            totscore = totscore + scores[i][j];
+      for (int j = 0; j < i; j++)
+      {
+        acount++;
+        AlignSeq as = new AlignSeq(av.getSelectionGroup().getSequenceAt(i),
+                                   av.getSelectionGroup().getSequenceAt(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.addElement(new Sequence(as.getS1().getName(), as.getAStr1()));
+        sequences.addElement(new Sequence(as.getS2().getName(), as.getAStr2()));
 
-            textarea.append(as.getOutput());
-            sequences.addElement( new Sequence( as.getS1().getName(), as.getAStr1()) );
-            sequences.addElement( new Sequence( as.getS2().getName(), as.getAStr2()) );
-
-
-          }
-        }
+      }
+    }
 
-        if (count > 2)
+    if (count > 2)
+    {
+      for (int i = 0; i < count; i++)
+      {
+        for (int j = 0; j < i; j++)
         {
-          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);
+          jalview.util.Format.print(System.out, "%7.3f",
+                                    scores[i][j] / totscore);
         }
       }
-
+    }
+  }
 
   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);
+    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));
-      jalview.bin.JalviewLite.addFrame(af, "Pairwise Aligned Sequences",
-                               AlignFrame.NEW_WINDOW_WIDTH,
-                               AlignFrame.NEW_WINDOW_HEIGHT);
+    AlignFrame af = new AlignFrame(new Alignment(seq));
+    jalview.bin.JalviewLite.addFrame(af, "Pairwise Aligned Sequences",
+                                     AlignFrame.NEW_WINDOW_WIDTH,
+                                     AlignFrame.NEW_WINDOW_HEIGHT);
 
   }