temp push

[jalview.git] / src / jalview / io / gff / Gff3Helper.java

diff --git a/src/jalview/io/gff/Gff3Helper.java b/src/jalview/io/gff/Gff3Helper.java
index a25a014..e422ed4 100644 (file)
--- a/src/jalview/io/gff/Gff3Helper.java
+++ b/src/jalview/io/gff/Gff3Helper.java
@@ -91,7 +91,7 @@ public class Gff3Helper extends GffHelperBase
       String atts = gff[ATTRIBUTES_COL];
       Map<String, List<String>> attributes = parseNameValuePairs(atts);
 
-      SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+      SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
       if (so.isA(soTerm, SequenceOntologyI.PROTEIN_MATCH))
       {
         sf = processProteinMatch(attributes, seq, gff, align, newseqs,
@@ -350,15 +350,6 @@ public class Gff3Helper extends GffHelperBase
   }
 
   /**
-   * Return '=' as the name-value separator used in column 9 attributes.
-   */
-  @Override
-  protected char getNameValueSeparator()
-  {
-    return '=';
-  }
-
-  /**
    * Modifies the default SequenceFeature in order to set the Target sequence id
    * as the description
    */
@@ -394,7 +385,7 @@ public class Gff3Helper extends GffHelperBase
       desc = target.split(" ")[0];
     }
 
-    SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+    SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
     String type = sf.getType();
     if (so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT))
     {
@@ -424,6 +415,11 @@ public class Gff3Helper extends GffHelperBase
       desc = (String) sf.getValue(ID);
     }
 
+    /*
+     * and decode comma, equals, semi-colon as required by GFF3 spec
+     */
+    desc = StringUtils.urlDecode(desc, GFF_ENCODABLE);
+
     return desc;
   }
 }