JAL-1705 further unit tests

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

diff --git a/src/jalview/io/gff/SequenceOntologyI.java b/src/jalview/io/gff/SequenceOntologyI.java
index 8128177..c7a5baa 100644 (file)
--- a/src/jalview/io/gff/SequenceOntologyI.java
+++ b/src/jalview/io/gff/SequenceOntologyI.java
@@ -7,10 +7,13 @@ public interface SequenceOntologyI
   /*
    * selected commonly used values for quick reference
    */
+  // SO:0000104
   public static final String POLYPEPTIDE = "polypeptide";
 
+  // SO:0000349
   public static final String PROTEIN_MATCH = "protein_match";
 
+  // SO:0000347
   public static final String NUCLEOTIDE_MATCH = "nucleotide_match";
 
   // SO:0000316
@@ -25,6 +28,9 @@ public interface SequenceOntologyI
   // SO:0000673
   public static final String TRANSCRIPT = "transcript";
 
+  // SO:0001621 isA sequence_variant but used in Ensembl as a transcript
+  public static final String NMD_TRANSCRIPT_VARIANT = "NMD_transcript_variant";
+
   // SO:0000704
   public static final String GENE = "gene";