JAL-2189 apply license

[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..c0570e0 100644 (file)
--- a/src/jalview/io/gff/SequenceOntologyI.java
+++ b/src/jalview/io/gff/SequenceOntologyI.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 java.util.List;
@@ -7,10 +27,13 @@ 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 +48,9 @@ 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";