Sequence numbering maintained

[jalview.git] / src / jalview / analysis / AlignSeq.java

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 401ad01..d3dfc9b 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -424,11 +424,11 @@ public class AlignSeq
         output.append("Length of alignment = " + (aseq1.length - count) + "\n");\r
         output.append("Sequence ");\r
         output.append(new Format("%" + maxid + "s").form(s1.getName()));\r
-        output.append(" :  " + seq1start + " - " + seq1end + " (Sequence length = " +\r
+        output.append(" :  " + s1.getStart() + " - " + s1.getEnd() + " (Sequence length = " +\r
             s1str.length() + ")\n");\r
         output .append("Sequence ");\r
         output.append(new Format("%" + maxid + "s").form(s2.getName()));\r
-        output .append(" :  " + seq2start + " - " + seq2end + " (Sequence length = " +\r
+        output.append(" :  " + s2.getStart() + " - " + s2.getEnd() + " (Sequence length = " +\r
             s2str.length() + ")\n\n");\r
 \r
         for (int j = 0; j < nochunks; j++)\r