X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSeqCigar.java;h=84da27877cbb7fdb0684c4c9d3c15b09324a4361;hb=6d1bf1ef4e1af507f9e6f2393cf35cde82a1314a;hp=0203383cba18c117d2171b01d3ce196b094a20ce;hpb=108d9a136d1794445f2169c04d80b7662085390d;p=jalview.git

diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index 0203383..84da278 100644
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel;
 
 import jalview.analysis.*;
@@ -62,10 +80,11 @@ public class SeqCigar
       throw new Error(
           "Implementation Error - unexpected null from getSequenceAndDeletions");
     }
-
+    int bounds[] = (int[]) edit_result[1];
     seq = new Sequence(refseq.getName(), (String) edit_result[0],
-                       refseq.getStart() + start+( (int[]) edit_result[1])[0],
-                       refseq.getStart() + start+( (int[]) edit_result[1])[2]);
+                       refseq.getStart() + start+bounds[0],
+                       refseq.getStart() + start+((bounds[2]==0) ? -1 : bounds[2]));
+    // seq.checkValidRange(); probably not needed
     seq.setDatasetSequence(refseq);
     return seq;
   }
@@ -416,16 +435,14 @@ public class SeqCigar
       SequenceI ref = alseqs[i].getRefSeq();
       seqs[i] = new Sequence(ref.getName(), g_seqs[i].toString(),
                              ref.getStart() + alseqs[i].start+bounds[0],
-                             ref.getStart() + alseqs[i].start+bounds[2]);
+                             ref.getStart() + alseqs[i].start+(bounds[2]==0 ? -1 : bounds[2]));
       seqs[i].setDatasetSequence(ref);
     }
     if (segments!=null) {
-      int delshift=0; // need to shift the segments to their absolute positions in the sequence cigar frame.
       for (int i=0; i<segments.length; i+=3) {
         //int start=shifts.shift(segments[i]-1)+1;
         //int end=shifts.shift(segments[i]+segments[i+1]-1)-1;
-        colsel.hideColumns(delshift+segments[i], delshift+segments[i]+segments[i+2]-1);
-        delshift+=segments[i+2];
+        colsel.hideColumns(segments[i+1], segments[i+1]+segments[i+2]-1);
       }
     }
     return seqs;