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 3323e27..948cdd2 100644 (file)
--- 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 <http://www.gnu.org/licenses/>.
+ * 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
+   * <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
@@ -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<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)