From d64e2f3ffad3343d800917db02af73e12a9cd51e Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 16 Apr 2009 08:28:21 +0000
Subject: [PATCH] strip sequence ID from fasta header for gff sequence
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10491 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/io/SimpleDocumentEntry.java | 13 ++++++++-----
1 file changed, 8 insertions(+), 5 deletions(-)
diff --git a/uk/ac/sanger/artemis/io/SimpleDocumentEntry.java b/uk/ac/sanger/artemis/io/SimpleDocumentEntry.java
index 5bb1f5cd4..6249225b0 100644
--- a/uk/ac/sanger/artemis/io/SimpleDocumentEntry.java
+++ b/uk/ac/sanger/artemis/io/SimpleDocumentEntry.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/SimpleDocumentEntry.java,v 1.26 2008-11-20 16:39:49 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/SimpleDocumentEntry.java,v 1.27 2009-04-16 08:28:21 tjc Exp $
*/
package uk.ac.sanger.artemis.io;
@@ -40,7 +40,7 @@ import javax.swing.JOptionPane;
* This class contains the methods common to all DocumentEntry objects.
*
* @author Kim Rutherford <kmr@sanger.ac.uk>
- * @version $Id: SimpleDocumentEntry.java,v 1.26 2008-11-20 16:39:49 tjc Exp $
+ * @version $Id: SimpleDocumentEntry.java,v 1.27 2009-04-16 08:28:21 tjc Exp $
**/
abstract public class SimpleDocumentEntry
@@ -228,12 +228,15 @@ abstract public class SimpleDocumentEntry
fake_fasta_features.add(new_feature);
- // record coordinates to adjust feature coordinateds
+ // record coordinates to adjust feature coordinates
if(isGFF)
{
if(contig_ranges == null)
- contig_ranges = new Hashtable();
- contig_ranges.put(header_strings[i], new_range);
+ contig_ranges = new Hashtable();
+
+ // find the sequence id from the header
+ String thisHeader[] = header_strings[i].split("\\s");
+ contig_ranges.put(thisHeader[0], new_range);
}
}
catch(InvalidRelationException e)
--
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