From ce63216585308bf40dd3f8370c3af13e098a7a3b Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 7 Jul 2006 13:30:38 +0000
Subject: [PATCH] Sequence numbering maintained

---
 src/jalview/analysis/AlignSeq.java            |    4 ++--
 src/jalview/appletgui/PairwiseAlignPanel.java |   15 +++++++++++++--
 src/jalview/gui/PairwiseAlignPanel.java       |   14 ++++++++++++--
 3 files changed, 27 insertions(+), 6 deletions(-)

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 401ad01..d3dfc9b 100755
--- 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");
         output.append("Sequence ");
         output.append(new Format("%" + maxid + "s").form(s1.getName()));
-        output.append(" :  " + seq1start + " - " + seq1end + " (Sequence length = " +
+        output.append(" :  " + s1.getStart() + " - " + s1.getEnd() + " (Sequence length = " +
             s1str.length() + ")\n");
         output .append("Sequence ");
         output.append(new Format("%" + maxid + "s").form(s2.getName()));
-        output .append(" :  " + seq2start + " - " + seq2end + " (Sequence length = " +
+        output.append(" :  " + s2.getStart() + " - " + s2.getEnd() + " (Sequence length = " +
             s2str.length() + ")\n\n");
 
         for (int j = 0; j < nochunks; j++)
diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index fc2bfb7..0dd3253 100755
--- 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();
 
     int acount = 0;
+    Sequence seq;
     for (int i = 1; i < count; i++)
     {
       for (int j = 0; j < i; j++)
@@ -66,9 +67,19 @@ public class PairwiseAlignPanel
         totscore = totscore + scores[i][j];
 
         textarea.append(as.getOutput());
-        sequences.addElement(new Sequence(as.getS1().getName(), as.getAStr1()));
-        sequences.addElement(new Sequence(as.getS2().getName(), as.getAStr2()));
 
+        seq = new Sequence(as.getS1().getName(),
+                           as.getAStr1(),
+                           as.getS1().getStart(), as.getS1().getEnd()
+            );
+        sequences.addElement(seq);
+
+        seq = new Sequence(as.getS2().getName(),
+                           as.getAStr2(),
+                           as.getS2().getStart(), as.getS2().getEnd()
+            );
+
+        sequences.addElement(seq);
       }
     }
 
diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 31efd84..76c75cb 100755
--- 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();
 
         int acount = 0;
+        Sequence seq;
 
         for (int i = 1; i < count; i++)
         {
@@ -82,8 +83,17 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
                 totscore = totscore + scores[i][j];
 
                 textarea.append(as.getOutput());
-                sequences.add(new Sequence(as.getS1().getName(), as.getAStr1()));
-                sequences.add(new Sequence(as.getS2().getName(), as.getAStr2()));
+                seq = new Sequence(as.getS1().getName(),
+                                   as.getAStr1(),
+                    as.getS1().getStart(), as.getS1().getEnd()
+                );
+                sequences.add(seq);
+
+                seq = new Sequence(as.getS2().getName(),
+                                   as.getAStr2(),
+                                   as.getS2().getStart(), as.getS2().getEnd()
+                    );
+                sequences.add(seq);
             }
         }
 
-- 
1.7.10.2