X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPairwiseAlignPanel.java;h=26836cdcf294610733210facd185e6cdd506679a;hb=de468b0bf50850a89c6a8a7acfa4ff5b689ffed1;hp=55cf2ccb95004792c97b9677d850cbf326143d0c;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index 55cf2cc..26836cd 100755
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -25,22 +25,29 @@ 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();
-  AlignViewport av;
+  AlignmentPanel ap;
 
-  public PairwiseAlignPanel(AlignViewport av)
+  public PairwiseAlignPanel(AlignmentPanel ap)
   {
-    super();
-    this.av = av;
-    float scores[][] = new float[av.getAlignment().getHeight()][av.getAlignment().
+    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 = av.getSelectionGroup().getSize();
+    int count = ap.av.getSelectionGroup().getSize();
 
     int acount = 0;
     for (int i = 1; i < count; i++)
@@ -48,13 +55,13 @@ public class PairwiseAlignPanel
       for (int j = 0; j < i; j++)
       {
         acount++;
-        AlignSeq as = new AlignSeq(av.getSelectionGroup().getSequenceAt(i),
-                                   av.getSelectionGroup().getSequenceAt(j),
+        AlignSeq as = new AlignSeq(ap.av.getSelectionGroup().getSequenceAt(i),
+                                   ap.av.getSelectionGroup().getSequenceAt(j),
                                    "pep");
 
         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];
 
@@ -78,7 +85,13 @@ 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()];
@@ -88,11 +101,28 @@ public class PairwiseAlignPanel
       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);
+    new AlignFrame(new Alignment(seq),
+                                   ap.alignFrame.applet,
+                                   "Pairwise Aligned Sequences");
 
   }
+  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);
+  }
 
 }