X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fgff%2FSequenceOntologyLite.java;h=2cbec369e9e345945c6c31e3b1bc5942b0370751;hb=6a05eb3f55d97e685f0c723822384633d5636778;hp=670d8874fd42cb1563b41c2d4a1bdf38e15f56c4;hpb=cd61435e058e0bf9b60292149c20299be7b4cf1f;p=jalview.git

diff --git a/src/jalview/io/gff/SequenceOntologyLite.java b/src/jalview/io/gff/SequenceOntologyLite.java
index 670d887..2cbec36 100644
--- 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...
@@ -253,4 +254,70 @@ public class SequenceOntologyLite extends OntologyBase
       return termsNotFound;
     }
   }
+
+  @Override
+  public List<String> getRootParents(final String term)
+  {
+    /*
+     * check in cache first
+     */
+    if (rootParents.containsKey(term))
+    {
+      return rootParents.get(term);
+    }
+
+    List<String> top = new ArrayList<>();
+    List<String> query = new ArrayList<>();
+    query.add(term);
+
+    while (!query.isEmpty())
+    {
+      List<String> nextQuery = new ArrayList<>();
+      for (String q : query)
+      {
+        List<String> theParents = parents.get(q);
+        if (theParents != null)
+        {
+          if (theParents.size() == 1 && theParents.get(0).equals(q))
+          {
+            /*
+             * top-level term
+             */
+            if (!top.contains(q))
+            {
+              top.add(q);
+            }
+          }
+          else
+          {
+            for (String p : theParents)
+            {
+              if (!p.equals(q))
+              {
+                nextQuery.add(p);
+              }
+            }
+          }
+        }
+      }
+      query = nextQuery;
+    }
+
+    rootParents.put(term, top);
+
+    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);
+  }
 }