From cf207870d6c0bcd0175b59e71171df45a5f7f12c Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Tue, 10 Sep 2013 12:25:32 +0100
Subject: [PATCH] fix for adjusting coordinate offset in multiple sequence GFF
---
uk/ac/sanger/artemis/io/GFFDocumentEntry.java | 10 ++++++----
1 file changed, 6 insertions(+), 4 deletions(-)
diff --git a/uk/ac/sanger/artemis/io/GFFDocumentEntry.java b/uk/ac/sanger/artemis/io/GFFDocumentEntry.java
index bf2e8af75..3ef88f24a 100644
--- a/uk/ac/sanger/artemis/io/GFFDocumentEntry.java
+++ b/uk/ac/sanger/artemis/io/GFFDocumentEntry.java
@@ -959,11 +959,11 @@ public class GFFDocumentEntry extends SimpleDocumentEntry
if(contig_ranges != null)
{
final FeatureVector gff_regions = getAllFeatures();
- final Enumeration gff_features = gff_regions.elements();
-
+ final Enumeration<Feature> gff_features = gff_regions.elements();
+
while(gff_features.hasMoreElements())
{
- final Feature f = (Feature) gff_features.nextElement();
+ final Feature f = gff_features.nextElement();
if( !(f instanceof GFFStreamFeature) )
continue;
@@ -986,7 +986,9 @@ public class GFFDocumentEntry extends SimpleDocumentEntry
r.getEnd()+new_range.getStart()-1));
}
- f.setLocation(new Location(new_ranges, f.getLocation().isComplement()));
+ Location l = new Location(new_ranges, f.getLocation().isComplement());
+ f.setLocation(l);
+ ((uk.ac.sanger.artemis.Feature)f.getUserData()).setLocation(l);
}
catch(OutOfRangeException e)
{
--
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