first patch for JAL-774 - ensure end is a valid bound to limit search for last sequen...

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 13f928c..22929f5 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -116,7 +116,7 @@ public class Sequence implements SequenceI
 
   void checkValidRange()
   {
-    if (end < 1)
+    // Note: JAL-774 : http://issues.jalview.org/browse/JAL-774?focusedCommentId=11239&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-11239
     {
       int endRes = 0;
       for (int j = 0; j < sequence.length; j++)
@@ -131,7 +131,9 @@ public class Sequence implements SequenceI
         endRes += start - 1;
       }
 
-      this.end = endRes;
+      if (end<endRes) { 
+        end = endRes;
+      }
     }
 
   }
@@ -582,7 +584,7 @@ public class Sequence implements SequenceI
     // returns the alignment position for a residue
     int j = start;
     int i = 0;
-
+    // Rely on end being at least as long as the length of the sequence.
     while ((i < sequence.length) && (j <= end) && (j <= pos))
     {
       if (!jalview.util.Comparison.isGap(sequence[i]))