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JAL-3829 JAL-3865 test structure chooser queries to mocked 3D Beacons FTS
[jalview.git]
/
src
/
jalview
/
io
/
gff
/
InterProScanHelper.java
diff --git
a/src/jalview/io/gff/InterProScanHelper.java
b/src/jalview/io/gff/InterProScanHelper.java
index
e1334e1
..
948cdd2
100644
(file)
--- a/
src/jalview/io/gff/InterProScanHelper.java
+++ b/
src/jalview/io/gff/InterProScanHelper.java
@@
-73,13
+73,19
@@
public class InterProScanHelper extends Gff3Helper
}
/**
}
/**
- *
- */
+ * An override that
+ * <ul>
+ * <li>uses Source (column 2) as feature type instead of the default column 3</li>
+ * <li>sets "InterProScan" as the feature group</li>
+ * <li>extracts "signature_desc" attribute as the feature description</li>
+ * </ul>
+ */
@Override
protected SequenceFeature buildSequenceFeature(String[] gff,
Map<String, List<String>> attributes)
{
@Override
protected SequenceFeature buildSequenceFeature(String[] gff,
Map<String, List<String>> attributes)
{
- SequenceFeature sf = super.buildSequenceFeature(gff, attributes);
+ SequenceFeature sf = super.buildSequenceFeature(gff, SOURCE_COL,
+ INTER_PRO_SCAN, attributes);
/*
* signature_desc is a more informative source of description
/*
* signature_desc is a more informative source of description
@@
-91,13
+97,6
@@
public class InterProScanHelper extends Gff3Helper
sf.setDescription(description);
}
sf.setDescription(description);
}
- /*
- * Set sequence feature group as 'InterProScan', and type as the source
- * database for this match (e.g. 'Pfam')
- */
- sf.setType(gff[SOURCE_COL]);
- sf.setFeatureGroup(INTER_PRO_SCAN);
-
return sf;
}
return sf;
}
@@
-112,8
+111,8
@@
public class InterProScanHelper extends Gff3Helper
SequenceOntologyI so = SequenceOntologyFactory.getInstance();
String type = columns[TYPE_COL];
if (so.isA(type, SequenceOntologyI.PROTEIN_MATCH)
SequenceOntologyI so = SequenceOntologyFactory.getInstance();
String type = columns[TYPE_COL];
if (so.isA(type, SequenceOntologyI.PROTEIN_MATCH)
- || (".".equals(columns[SOURCE_COL]) && so.isA(type,
- SequenceOntologyI.POLYPEPTIDE)))
+ || (".".equals(columns[SOURCE_COL])
+ && so.isA(type, SequenceOntologyI.POLYPEPTIDE)))
{
return true;
}
{
return true;
}
@@
-125,7
+124,8
@@
public class InterProScanHelper extends Gff3Helper
* GFF field 'ID' rather than the usual 'Target' :-O
*/
@Override
* GFF field 'ID' rather than the usual 'Target' :-O
*/
@Override
- protected String findTargetId(String target, Map<String, List<String>> set)
+ protected String findTargetId(String target,
+ Map<String, List<String>> set)
{
List<String> ids = set.get(ID);
if (ids == null || ids.size() != 1)
{
List<String> ids = set.get(ID);
if (ids == null || ids.size() != 1)