X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=824a33b869a6a8b3aeebd3ed9ceb885481e89428;hb=7e129811d6ff01074428462284dffc2a6c2395a4;hp=34c1cd917f6f0fb252de743de48435710db7bfae;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 34c1cd9..824a33b 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -18,8 +18,6 @@
 */
 package jalview.datamodel;
 
-import MCview.*;
-
 import jalview.analysis.*;
 
 import java.awt.*;
@@ -57,10 +55,30 @@ public class Sequence implements SequenceI
      */
     public Sequence(String name, String sequence, int start, int end)
     {
-        this.name = name;
-        this.sequence = sequence;
-        this.start = start;
-        this.end = end;
+      this.name = name;
+      this.sequence = sequence;
+      this.start = start;
+      this.end = end;
+
+      if (end < 1)
+      {
+        int endRes = 0;
+        char ch;
+        for (int j = 0; j < sequence.length(); j++)
+        {
+          ch = sequence.charAt(j);
+          if (!jalview.util.Comparison.isGap( (ch)))
+          {
+            endRes++;
+          }
+        }
+        if (endRes > 0)
+        {
+          endRes += start - 1;
+        }
+
+        this.end = endRes;
+      }
 
         setDisplayId();
     }