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Commit f1c4ee0f authored by tcarver's avatar tcarver
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fix for CDS IDs in multi-sequence GFF files

parent b96b5e34
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......@@ -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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