Merge branch 'develop' into features/JAL-2446NCList

[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)
   {
-    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<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)