X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fgff%2FInterProScanHelper.java;h=948cdd2d4065eb5555a22b50164f25f613e46555;hb=bed0c230be450b16213e30ee1dcaf3e76ddfc669;hp=3323e27370c465eecac02e0586b65f95a50455a4;hpb=8f920d337154e092f5f9056ffde3cdf2735eca43;p=jalview.git
diff --git a/src/jalview/io/gff/InterProScanHelper.java b/src/jalview/io/gff/InterProScanHelper.java
index 3323e27..948cdd2 100644
--- a/src/jalview/io/gff/InterProScanHelper.java
+++ b/src/jalview/io/gff/InterProScanHelper.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.io.gff;
import jalview.datamodel.AlignmentI;
@@ -53,13 +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
@@ -71,13 +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;
}
@@ -89,10 +108,11 @@ public class InterProScanHelper extends Gff3Helper
*/
public static boolean recognises(String[] columns)
{
- SequenceOntology so = SequenceOntology.getInstance();
+ SequenceOntologyI so = SequenceOntologyFactory.getInstance();
String type = columns[TYPE_COL];
- if (so.isProteinMatch(type)
- || (".".equals(columns[SOURCE_COL]) && so.isPolypeptide(type)))
+ if (so.isA(type, SequenceOntologyI.PROTEIN_MATCH)
+ || (".".equals(columns[SOURCE_COL])
+ && so.isA(type, SequenceOntologyI.POLYPEPTIDE)))
{
return true;
}
@@ -104,7 +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)