X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Futils%2FSeq.java;h=7c82d82418dae1cc99872454a5981d8e423cc59f;hb=4aeaba257ad7e3206158565b356da7e4b15bf0a2;hp=8ec3f9c088d3895ff55782c27f04fc53922d43ee;hpb=a9e0b2497cae20cee8ec0d8c66d51e0d819b8581;p=vamsas.git

diff --git a/src/uk/ac/vamsas/objects/utils/Seq.java b/src/uk/ac/vamsas/objects/utils/Seq.java
index 8ec3f9c..7c82d82 100644
--- a/src/uk/ac/vamsas/objects/utils/Seq.java
+++ b/src/uk/ac/vamsas/objects/utils/Seq.java
@@ -89,18 +89,18 @@ public class Seq {
      }
      return seq;
   }
-  public static AlignmentSequence newAlignmentSequence(String name, String alSequence, Sequence refseq, int start, int end) {
+  public static AlignmentSequence newAlignmentSequence(String name, String alSequence, Sequence refseq, long start, long end) {
     if (refseq!=null) {
       AlignmentSequence asq = new AlignmentSequence();
       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;