Sequence numbering maintained

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

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

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