X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fgff%2FInterProScanHelper.java;h=948cdd2d4065eb5555a22b50164f25f613e46555;hb=bed0c230be450b16213e30ee1dcaf3e76ddfc669;hp=e1334e1df0a8b16c4178b2517e968d7c1b4dbf09;hpb=604cbee405a837565ba1a74aa9bddd62aed685ab;p=jalview.git
diff --git a/src/jalview/io/gff/InterProScanHelper.java b/src/jalview/io/gff/InterProScanHelper.java
index e1334e1..948cdd2 100644
--- 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
+ *
+ * - uses Source (column 2) as feature type instead of the default column 3
+ * - sets "InterProScan" as the feature group
+ * - extracts "signature_desc" attribute as the feature description
+ *
+ */
@Override
protected SequenceFeature buildSequenceFeature(String[] gff,
Map> 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
@@ -91,13 +97,6 @@ public class InterProScanHelper extends Gff3Helper
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;
}
@@ -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)
- || (".".equals(columns[SOURCE_COL]) && so.isA(type,
- SequenceOntologyI.POLYPEPTIDE)))
+ || (".".equals(columns[SOURCE_COL])
+ && so.isA(type, SequenceOntologyI.POLYPEPTIDE)))
{
return true;
}
@@ -125,7 +124,8 @@ public class InterProScanHelper extends Gff3Helper
* GFF field 'ID' rather than the usual 'Target' :-O
*/
@Override
- protected String findTargetId(String target, Map> set)
+ protected String findTargetId(String target,
+ Map> set)
{
List ids = set.get(ID);
if (ids == null || ids.size() != 1)