Append start and end

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

diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index c9285dd..0dd3253 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 implements ActionListener\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
@@ -43,6 +50,7 @@ public class PairwiseAlignPanel
     int count = ap.av.getSelectionGroup().getSize();\r
 \r
     int acount = 0;\r
+    Sequence seq;\r
     for (int i = 1; i < count; i++)\r
     {\r
       for (int j = 0; j < i; j++)\r
@@ -54,14 +62,24 @@ 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
         textarea.append(as.getOutput());\r
-        sequences.addElement(new Sequence(as.getS1().getName(), as.getAStr1()));\r
-        sequences.addElement(new Sequence(as.getS2().getName(), as.getAStr2()));\r
 \r
+        seq = new Sequence(as.getS1().getName(),\r
+                           as.getAStr1(),\r
+                           as.getS1().getStart(), as.getS1().getEnd()\r
+            );\r
+        sequences.addElement(seq);\r
+\r
+        seq = new Sequence(as.getS2().getName(),\r
+                           as.getAStr2(),\r
+                           as.getS2().getStart(), as.getS2().getEnd()\r
+            );\r
+\r
+        sequences.addElement(seq);\r
       }\r
     }\r
 \r
@@ -78,7 +96,13 @@ public class PairwiseAlignPanel
     }\r
   }\r
 \r
-  protected void viewInEditorButton_actionPerformed(ActionEvent e)\r
+  public void actionPerformed(ActionEvent evt)\r
+  {\r
+    if(evt.getSource()==viewInEditorButton)\r
+      viewInEditorButton_actionPerformed();\r
+  }\r
+\r
+  protected void viewInEditorButton_actionPerformed()\r
   {\r
 \r
     Sequence[] seq = new Sequence[sequences.size()];\r
@@ -88,10 +112,29 @@ public class PairwiseAlignPanel
       seq[i] = (Sequence) sequences.elementAt(i);\r
     }\r
 \r
-    AlignFrame af = new AlignFrame(new Alignment(seq),\r
+    new AlignFrame(new Alignment(seq),\r
                                    ap.alignFrame.applet,\r
-                                   "Pairwise Aligned Sequences");\r
+                                   "Pairwise Aligned Sequences",\r
+                                   false);\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(this);\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