after merge

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

diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index d5243e3..910a206 100755 (executable)
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -25,17 +25,24 @@ import java.awt.event.*;
 \r
 import jalview.analysis.*;\r
 import jalview.datamodel.*;\r
-import jalview.jbappletgui.*;\r
+import java.awt.*;\r
 \r
 public class PairwiseAlignPanel\r
-    extends GPairwiseAlignPanel\r
+    extends Panel\r
 {\r
   Vector sequences = new Vector();\r
   AlignmentPanel ap;\r
 \r
   public PairwiseAlignPanel(AlignmentPanel ap)\r
   {\r
-    super();\r
+    try\r
+    {\r
+      jbInit();\r
+    }\r
+    catch (Exception e)\r
+    {\r
+      e.printStackTrace();\r
+  }\r
     this.ap = ap;\r
     float scores[][] = new float[ap.av.alignment.getHeight()][ap.av.alignment.\r
         getHeight()];\r
@@ -54,7 +61,7 @@ public class PairwiseAlignPanel
 \r
         as.calcScoreMatrix();\r
         as.traceAlignment();\r
-        as.printAlignment();\r
+        as.printAlignment(System.out);\r
         scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;\r
         totscore = totscore + scores[i][j];\r
 \r
@@ -93,5 +100,27 @@ public class PairwiseAlignPanel
                                    "Pairwise Aligned Sequences");\r
 \r
   }\r
+  protected ScrollPane scrollPane = new ScrollPane();\r
+  protected TextArea textarea = new TextArea();\r
+  protected Button viewInEditorButton = new Button();\r
+  Panel jPanel1 = new Panel();\r
+  BorderLayout borderLayout1 = new BorderLayout();\r
+\r
+  private void jbInit() throws Exception {\r
+      this.setLayout(borderLayout1);\r
+      textarea.setFont(new java.awt.Font("Monospaced", 0, 12));\r
+      textarea.setText("");\r
+      viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));\r
+      viewInEditorButton.setLabel("View in alignment editor");\r
+      viewInEditorButton.addActionListener(new java.awt.event.ActionListener() {\r
+              public void actionPerformed(ActionEvent e) {\r
+                  viewInEditorButton_actionPerformed(e);\r
+              }\r
+          });\r
+      this.add(scrollPane, BorderLayout.CENTER);\r
+      scrollPane.add(textarea);\r
+      this.add(jPanel1, BorderLayout.SOUTH);\r
+      jPanel1.add(viewInEditorButton, null);\r
+  }\r
 \r
 }\r