JAL-1705 JAL-1191 SequenceOntologyLite added as hard-coded alternative

[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 2e98e4e..d29645b 100644 (file)
--- a/src/jalview/io/gff/Gff3Helper.java
+++ b/src/jalview/io/gff/Gff3Helper.java
@@ -70,12 +70,13 @@ public class Gff3Helper extends GffHelperBase
       String atts = gff[ATTRIBUTES_COL];
       Map<String, List<String>> attributes = parseNameValuePairs(atts);
 
-      if (SequenceOntology.getInstance().isProteinMatch(soTerm))
+      SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+      if (so.isA(soTerm, SequenceOntologyI.PROTEIN_MATCH))
       {
-        sf = processProteinMatch(attributes, seq, gff, align,
-                newseqs, relaxedIdMatching);
+        sf = processProteinMatch(attributes, seq, gff, align, newseqs,
+                relaxedIdMatching);
       }
-      else if (SequenceOntology.getInstance().isNucleotideMatch(soTerm))
+      else if (so.isA(soTerm, SequenceOntologyI.NUCLEOTIDE_MATCH))
       {
         sf = processNucleotideMatch(attributes, seq, gff, align,
                 newseqs, relaxedIdMatching);
@@ -372,9 +373,9 @@ public class Gff3Helper extends GffHelperBase
       desc = target.split(" ")[0];
     }
 
-    SequenceOntology so = SequenceOntology.getInstance();
+    SequenceOntologyI so = SequenceOntologyFactory.getInstance();
     String type = sf.getType();
-    if (so.isSequenceVariant(type))
+    if (so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT))
     {
       /*
        * Ensembl returns dna variants as 'alleles'