From a04fb81ff7a088f544e0aed9c2d49be4c7a26e4b Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 27 Apr 2005 10:43:15 +0000
Subject: [PATCH] gff
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@2430 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/io/GFFDocumentEntry.java | 36 ++++++++++++-------
1 file changed, 24 insertions(+), 12 deletions(-)
diff --git a/uk/ac/sanger/artemis/io/GFFDocumentEntry.java b/uk/ac/sanger/artemis/io/GFFDocumentEntry.java
index fd84eaf80..98470fcc5 100644
--- a/uk/ac/sanger/artemis/io/GFFDocumentEntry.java
+++ b/uk/ac/sanger/artemis/io/GFFDocumentEntry.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/GFFDocumentEntry.java,v 1.11 2005-04-27 08:26:58 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/GFFDocumentEntry.java,v 1.12 2005-04-27 10:43:15 tjc Exp $
*/
package uk.ac.sanger.artemis.io;
@@ -36,7 +36,7 @@ import java.util.Vector;
* A DocumentEntry that can read an GFF entry from a Document.
*
* @author Kim Rutherford
- * @version $Id: GFFDocumentEntry.java,v 1.11 2005-04-27 08:26:58 tjc Exp $
+ * @version $Id: GFFDocumentEntry.java,v 1.12 2005-04-27 10:43:15 tjc Exp $
**/
public class GFFDocumentEntry extends SimpleDocumentEntry
@@ -176,18 +176,21 @@ public class GFFDocumentEntry extends SimpleDocumentEntry
try
{
- if(this_feature.getKey().getKeyString().equals("CDS"))
+ String key = this_feature.getKey().getKeyString();
+ if(key.equals("CDS") || key.equals("polypeptide_domain"))
{
- if(this_feature.getQualifierByName("ID") != null)
+ if(this_feature.getQualifierByName("Parent") != null)
{
final StringVector values =
- this_feature.getQualifierByName("ID").getValues();
+ this_feature.getQualifierByName("Parent").getValues();
group_name = values.elementAt(0);
// check the parent is a gene
// if(!genes.contains(group_name))
// continue;
}
+ else
+ continue;
}
else
continue;
@@ -203,15 +206,24 @@ public class GFFDocumentEntry extends SimpleDocumentEntry
}
else
{
- StringVector values =
- this_feature.getQualifierByName("Parent").getValues();
- String parent = values.elementAt(0);
+ String parent1 = null;
+ String parent2 = null;
+
+ try
+ {
+ StringVector values =
+ this_feature.getQualifierByName("ID").getValues();
+ parent1 = values.elementAt(0);
- Feature stored_feature = other_features.featureAt(0);
- values = stored_feature.getQualifierByName("Parent").getValues();
-
+ Feature stored_feature = other_features.featureAt(0);
+ values = stored_feature.getQualifierByName("ID").getValues();
+ parent2 = values.elementAt(0);
+ }
+ catch(NullPointerException e){}
+
// same ID with same Parent
- if(parent.equals(values.elementAt(0)))
+ if((parent1 == null && parent2 == null) ||
+ parent1.equals(parent2))
other_features.add(this_feature);
}
--
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