JAL-1705 take feature ID for description if nothing better found

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

diff --git a/src/jalview/io/gff/SequenceOntologyLite.java b/src/jalview/io/gff/SequenceOntologyLite.java
index 173dea6..c0ae971 100644 (file)
--- a/src/jalview/io/gff/SequenceOntologyLite.java
+++ b/src/jalview/io/gff/SequenceOntologyLite.java
@@ -55,10 +55,24 @@ public class SequenceOntologyLite implements SequenceOntologyI
     { "structural_variant", "sequence_variant" },
     
     /*
-     * no sub-types of exon or CDS yet encountered; add if needed
+     * no sub-types of exon or CDS encountered in Ensembl
+     * a few added here for testing purposes
      */
     { "exon", "exon" },
-    { "CDS", "CDS" }
+    { "coding_exon", "exon" },
+    { "CDS", "CDS" },
+    { "CDS_predicted", "CDS" },
+    
+    /*
+     * used in exonerate GFF
+     */
+    { "protein_match", "protein_match"},
+    { "nucleotide_match", "nucleotide_match"},
+    
+    /*
+     * used in InterProScan GFF
+     */
+    { "polypeptide", "polypeptide" }
   };
   // @formatter:on