Sequence numbering maintained

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

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 31efd84..76c75cb 100755 (executable)
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -66,6 +66,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         int count = selsubset.size();\r
 \r
         int acount = 0;\r
+        Sequence seq;\r
 \r
         for (int i = 1; i < count; i++)\r
         {\r
@@ -82,8 +83,17 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
                 totscore = totscore + scores[i][j];\r
 \r
                 textarea.append(as.getOutput());\r
-                sequences.add(new Sequence(as.getS1().getName(), as.getAStr1()));\r
-                sequences.add(new Sequence(as.getS2().getName(), as.getAStr2()));\r
+                seq = new Sequence(as.getS1().getName(),\r
+                                   as.getAStr1(),\r
+                    as.getS1().getStart(), as.getS1().getEnd()\r
+                );\r
+                sequences.add(seq);\r
+\r
+                seq = new Sequence(as.getS2().getName(),\r
+                                   as.getAStr2(),\r
+                                   as.getS2().getStart(), as.getS2().getEnd()\r
+                    );\r
+                sequences.add(seq);\r
             }\r
         }\r
 \r