From f1c4ee0fcfae5c7c1d2bde27e89b44939720d9bd Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Mon, 22 Apr 2013 10:39:05 +0100
Subject: [PATCH] fix for CDS IDs in multi-sequence GFF files
---
uk/ac/sanger/artemis/io/GFFStreamFeature.java | 13 +++++++++++--
1 file changed, 11 insertions(+), 2 deletions(-)
diff --git a/uk/ac/sanger/artemis/io/GFFStreamFeature.java b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
index a8508516f..74f1c4c70 100644
--- a/uk/ac/sanger/artemis/io/GFFStreamFeature.java
+++ b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
@@ -479,13 +479,22 @@ public class GFFStreamFeature extends SimpleDocumentFeature
{
if(id_range_store != null)
{
+ int offset = 0;
+ if(getGffSeqName() != null && contig_ranges != null &&
+ contig_ranges.containsKey(getGffSeqName()))
+ {
+ // adjust for coordinates in multi-sequence GFF
+ Range offset_range = contig_ranges.get(getGffSeqName());
+ offset = offset_range.getStart()-1;
+ }
+
Enumeration<String> enum_ranges = id_range_store.keys();
while(enum_ranges.hasMoreElements())
{
String key = enum_ranges.nextElement();
Range range = id_range_store.get(key);
- if(range.getStart() == r.getStart() &&
- range.getEnd() == r.getEnd())
+ if(range.getStart() == r.getStart()-offset &&
+ range.getEnd() == r.getEnd()-offset)
return key;
}
}
--
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