Takes string[] instead of seq[]

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

diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index 910a206..d0b0c98 100755 (executable)
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -28,7 +28,7 @@ import jalview.datamodel.*;
 import java.awt.*;\r
 \r
 public class PairwiseAlignPanel\r
-    extends Panel\r
+    extends Panel implements ActionListener\r
 {\r
   Vector sequences = new Vector();\r
   AlignmentPanel ap;\r
@@ -47,9 +47,10 @@ public class PairwiseAlignPanel
     float scores[][] = new float[ap.av.alignment.getHeight()][ap.av.alignment.\r
         getHeight()];\r
     double totscore = 0;\r
-    int count = ap.av.getSelectionGroup().getSize();\r
+    int count = ap.av.getSelectionGroup().getSize(false);\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
@@ -66,9 +67,19 @@ public class PairwiseAlignPanel
         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
@@ -85,7 +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
@@ -97,7 +114,8 @@ public class PairwiseAlignPanel
 \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
@@ -112,11 +130,7 @@ public class PairwiseAlignPanel
       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
+      viewInEditorButton.addActionListener(this);\r
       this.add(scrollPane, BorderLayout.CENTER);\r
       scrollPane.add(textarea);\r
       this.add(jPanel1, BorderLayout.SOUTH);\r