diff --git a/uk/ac/sanger/artemis/Feature.java b/uk/ac/sanger/artemis/Feature.java
index 58f7d42c657ac98f6bee3454ae37d5dd5d1f65c1..781dad435f7fbfff7aa36b8b0e639b48204dcc38 100644
--- a/uk/ac/sanger/artemis/Feature.java
+++ b/uk/ac/sanger/artemis/Feature.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/Feature.java,v 1.29 2007-10-02 14:17:39 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/Feature.java,v 1.30 2007-10-08 09:44:29 tjc Exp $
*/
package uk.ac.sanger.artemis;
@@ -60,7 +60,7 @@ import java.util.Date;
* embl.Feature and embl.Entry objects.
*
* @author Kim Rutherford
- * @version $Id: Feature.java,v 1.29 2007-10-02 14:17:39 tjc Exp $
+ * @version $Id: Feature.java,v 1.30 2007-10-08 09:44:29 tjc Exp $
**/
public class Feature
@@ -2628,7 +2628,7 @@ CHANGED_END:
else
return entry.getBases().getReverseStrand();
}
-
+
/**
* Return the reference of a new copy of this Feature. This method will
* update the underlying embl.Entry and the new Feature will be installed
@@ -2636,12 +2636,26 @@ CHANGED_END:
* @return The reference of the new feature.
**/
public Feature duplicate()
+ throws ReadOnlyException
+ {
+ return duplicate(false);
+ }
+
+ /**
+ * Return the reference of a new copy of this Feature. This method will
+ * update the underlying embl.Entry and the new Feature will be installed
+ * in the same Entry object as this one.
+ * @param isDuplicatedInChado if true then create new ID and update in chado
+ * @return
+ * @throws ReadOnlyException
+ */
+ public Feature duplicate(final boolean isDuplicatedInChado)
throws ReadOnlyException
{
uk.ac.sanger.artemis.io.Feature new_embl_feature;
if(getEmblFeature() instanceof GFFStreamFeature)
- new_embl_feature = new GFFStreamFeature(getEmblFeature());
+ new_embl_feature = new GFFStreamFeature(getEmblFeature(), isDuplicatedInChado);
else
new_embl_feature = new EmblStreamFeature(getEmblFeature());
@@ -2649,7 +2663,7 @@ CHANGED_END:
try
{
- getEntry().add(return_feature, true, false);
+ getEntry().add(return_feature, !isDuplicatedInChado, false);
}
catch(EntryInformationException e)
{
diff --git a/uk/ac/sanger/artemis/io/GFFStreamFeature.java b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
index aba7c3495395dcbfe27f3457e14ce8d9e45e9641..b1a28cc4d6bc741a7ae354e4b1c9c15111c8980b 100644
--- a/uk/ac/sanger/artemis/io/GFFStreamFeature.java
+++ b/uk/ac/sanger/artemis/io/GFFStreamFeature.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/GFFStreamFeature.java,v 1.56 2007-07-30 09:57:16 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/GFFStreamFeature.java,v 1.57 2007-10-08 09:43:12 tjc Exp $
*/
package uk.ac.sanger.artemis.io;
@@ -49,7 +49,7 @@ import uk.ac.sanger.artemis.util.StringVector;
* A StreamFeature that thinks it is a GFF feature.
*
* @author Kim Rutherford
- * @version $Id: GFFStreamFeature.java,v 1.56 2007-07-30 09:57:16 tjc Exp $
+ * @version $Id: GFFStreamFeature.java,v 1.57 2007-10-08 09:43:12 tjc Exp $
**/
public class GFFStreamFeature extends SimpleDocumentFeature
@@ -149,13 +149,18 @@ public class GFFStreamFeature extends SimpleDocumentFeature
}
}
+ public GFFStreamFeature(final Feature feature)
+ {
+ this(feature, false);
+ }
+
/**
* Create a new GFFStreamFeature with the same key, location and
* qualifiers as the given feature. The feature should be added to an
* Entry (with Entry.add()).
* @param feature The feature to copy.
**/
- public GFFStreamFeature(final Feature feature)
+ public GFFStreamFeature(final Feature feature, final boolean isDuplicatedInChado)
{
this(feature.getKey(), feature.getLocation(), feature.getQualifiers());
@@ -171,6 +176,52 @@ public class GFFStreamFeature extends SimpleDocumentFeature
this.setGffSeqName(((GFFStreamFeature)feature).getGffSeqName());
this.setGffSource(((GFFStreamFeature)feature).getGffSource());
+
+
+ if(isDuplicatedInChado)
+ {
+ try
+ {
+ final String uniquename;
+ if(id_range_store != null)
+ {
+ final Hashtable new_id_range_store = new Hashtable(id_range_store.size());
+ final Enumeration enumIdRangeStore = id_range_store.keys();
+ while(enumIdRangeStore.hasMoreElements())
+ {
+ final String keyId = (String)enumIdRangeStore.nextElement();
+ final Range range = (Range)id_range_store.get(keyId);
+ new_id_range_store.put(keyId+":DUP", range);
+ }
+ id_range_store.clear();
+ this.id_range_store = (Hashtable) new_id_range_store.clone();
+
+ uniquename = getSegmentID(getLocation().getRanges());
+ }
+ else
+ uniquename = (String) getQualifierByName("ID").getValues().get(0)+":DUP";
+ setQualifier(new Qualifier("ID", uniquename));
+
+ if(getQualifierByName("Parent") != null)
+ {
+ final String parent =
+ (String) getQualifierByName("Parent").getValues().get(0);
+ setQualifier(new Qualifier("Parent", parent+":DUP"));
+ }
+
+ if(getQualifierByName("Derives_from") != null)
+ {
+ final String derives_from =
+ (String) getQualifierByName("Derives_from").getValues().get(0);
+ setQualifier(new Qualifier("Derives_from", derives_from+":DUP"));
+ }
+ removeQualifierByName("feature_id");
+ removeQualifierByName("timelastmodified");
+ removeQualifierByName("feature_relationship_rank");
+ }
+ catch(ReadOnlyException e){}
+ catch(EntryInformationException e){}
+ }
}
}