From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Sun, 2 Sep 2012 13:30:12 +0000 (+0100)
Subject: JAL-1062 JAL-659 correct start position for retrieved sequence
X-Git-Tag: Jalview_2_9~358
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6316d355ff3e86cad23a834a737c68a394819ec9;p=jalview.git

JAL-1062 JAL-659 correct start position for retrieved sequence
---

diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
index ebe0134..269baf1 100644
--- a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
+++ b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
@@ -93,7 +93,7 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
     }
     this.source = source;
     this.dbname = dbname;
-    this.dbrefname = dbrefname;
+    this.dbrefname = dbrefname.toUpperCase();
     if (coordsys!=null ) {
       this.coordsys = coordsys;
     }
@@ -253,6 +253,7 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
               // in the XML
               Sequence sq = new Sequence(lbl, e.getContent().replaceAll(
                       "\\s+", ""));
+              sq.setStart(e.getStart().intValue());
               sq.addDBRef(new DBRefEntry(getDbSource(), getDbVersion()
                       + ":" + e.getVersion(), lbl));
               seqs.addElement(sq);