X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPairwiseAlignPanel.java;h=d0b0c986e7bae3c1c8f2b1df8b8a3380830f0d55;hb=23d3cb8d0e4c227224587135f41132d436dc1178;hp=d5243e314ec08646b5f560e984e6401bbfe05b1d;hpb=f24dacb1da56fccf05d684e2f4899facec2aecf7;p=jalview.git

diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index d5243e3..d0b0c98 100755
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -25,24 +25,32 @@ import java.awt.event.*;
 
 import jalview.analysis.*;
 import jalview.datamodel.*;
-import jalview.jbappletgui.*;
+import java.awt.*;
 
 public class PairwiseAlignPanel
-    extends GPairwiseAlignPanel
+    extends Panel implements ActionListener
 {
   Vector sequences = new Vector();
   AlignmentPanel ap;
 
   public PairwiseAlignPanel(AlignmentPanel ap)
   {
-    super();
+    try
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+  }
     this.ap = ap;
     float scores[][] = new float[ap.av.alignment.getHeight()][ap.av.alignment.
         getHeight()];
     double totscore = 0;
-    int count = ap.av.getSelectionGroup().getSize();
+    int count = ap.av.getSelectionGroup().getSize(false);
 
     int acount = 0;
+    Sequence seq;
     for (int i = 1; i < count; i++)
     {
       for (int j = 0; j < i; j++)
@@ -54,14 +62,24 @@ public class PairwiseAlignPanel
 
         as.calcScoreMatrix();
         as.traceAlignment();
-        as.printAlignment();
+        as.printAlignment(System.out);
         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()));
 
+        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()
+            );
+
+        sequences.addElement(seq);
       }
     }
 
@@ -78,7 +96,13 @@ public class PairwiseAlignPanel
     }
   }
 
-  protected void viewInEditorButton_actionPerformed(ActionEvent e)
+  public void actionPerformed(ActionEvent evt)
+  {
+    if(evt.getSource()==viewInEditorButton)
+      viewInEditorButton_actionPerformed();
+  }
+
+  protected void viewInEditorButton_actionPerformed()
   {
 
     Sequence[] seq = new Sequence[sequences.size()];
@@ -90,8 +114,27 @@ public class PairwiseAlignPanel
 
     new AlignFrame(new Alignment(seq),
                                    ap.alignFrame.applet,
-                                   "Pairwise Aligned Sequences");
+                                   "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 {
+      this.setLayout(borderLayout1);
+      textarea.setFont(new java.awt.Font("Monospaced", 0, 12));
+      textarea.setText("");
+      viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));
+      viewInEditorButton.setLabel("View in alignment editor");
+      viewInEditorButton.addActionListener(this);
+      this.add(scrollPane, BorderLayout.CENTER);
+      scrollPane.add(textarea);
+      this.add(jPanel1, BorderLayout.SOUTH);
+      jPanel1.add(viewInEditorButton, null);
+  }
 
 }