end position not correctly set.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@408 be28352e-c001-0410-b1a7-c7978e42abec

diff --git a/src/uk/ac/vamsas/objects/utils/Seq.java b/src/uk/ac/vamsas/objects/utils/Seq.java
index ec279a1..7c82d82 100644 (file)
--- a/src/uk/ac/vamsas/objects/utils/Seq.java
+++ b/src/uk/ac/vamsas/objects/utils/Seq.java
@@ -95,12 +95,12 @@ public class Seq {
       asq.setName(name);
       asq.setSequence(alSequence);
       asq.setRefid(refseq);
+      if (end>refseq.getEnd() || end<start || end==-1)
+        end = refseq.getEnd();
+      asq.setEnd(end);
       if (start<refseq.getStart())
         start = refseq.getStart();
       asq.setStart(start);
-      if (end>refseq.getEnd())
-        end = refseq.getEnd();
-      asq.setEnd(end);
       return asq;
     }
     return null;