Merge branch 'develop' into features/JAL-3010ontologyFeatureSettings

[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 d4c2278..2cbec36 100644 (file)
--- a/src/jalview/io/gff/SequenceOntologyLite.java
+++ b/src/jalview/io/gff/SequenceOntologyLite.java
@@ -73,6 +73,7 @@ public class SequenceOntologyLite extends OntologyBase
     { "snRNA", "transcript" },
     { "miRNA", "transcript" },
     { "lincRNA", "transcript" },
+    { "lnc_RNA", "transcript" },
     { "rRNA", "transcript" },
     { "mRNA", "transcript" },
     // there are many more sub-types of ncRNA...
@@ -306,4 +307,17 @@ public class SequenceOntologyLite extends OntologyBase
 
     return top.isEmpty() ? null : top;
   }
+
+  @Override
+  public List<String> getParents(String term)
+  {
+    List<String> result = parents.get(term);
+    return result == null ? new ArrayList<>() : result;
+  }
+
+  @Override
+  public boolean isValidTerm(String term)
+  {
+    return parents.containsKey(term);
+  }
 }