Sequence numbering maintained

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

diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index fc2bfb7..0dd3253 100755 (executable)
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -50,6 +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
@@ -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