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JAL-1191 isolated SequenceOntology (BioJava wrapper) to /ext/so folder
[jalview.git]
/
src
/
jalview
/
io
/
gff
/
Gff3Helper.java
diff --git
a/src/jalview/io/gff/Gff3Helper.java
b/src/jalview/io/gff/Gff3Helper.java
index
bd34d3c
..
031900d
100644
(file)
--- a/
src/jalview/io/gff/Gff3Helper.java
+++ b/
src/jalview/io/gff/Gff3Helper.java
@@
-5,7
+5,6
@@
import jalview.datamodel.AlignmentI;
import jalview.datamodel.MappingType;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.MappingType;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.ext.ensembl.EnsemblSeqProxy;
import jalview.util.MapList;
import jalview.util.StringUtils;
import jalview.util.MapList;
import jalview.util.StringUtils;
@@
-388,8
+387,9
@@
public class Gff3Helper extends GffHelperBase
* extract 'Name' for a transcript (to show gene name)
* or an exon (so 'colour by label' shows exon boundaries)
*/
* extract 'Name' for a transcript (to show gene name)
* or an exon (so 'colour by label' shows exon boundaries)
*/
- if (EnsemblSeqProxy.isTranscript(type)
- || so.isA(type, SequenceOntology.EXON))
+ if (SequenceOntologyI.NMD_TRANSCRIPT_VARIANT.equals(type)
+ || so.isA(type, SequenceOntologyI.TRANSCRIPT)
+ || so.isA(type, SequenceOntologyI.EXON))
{
desc = StringUtils.listToDelimitedString(attributes.get("Name"), ",");
}
{
desc = StringUtils.listToDelimitedString(attributes.get("Name"), ",");
}