From 71a5df9830e7ea6a5092f1fe2162d93e6341e18c Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 12 Feb 2016 16:53:14 +0000
Subject: [PATCH] JAL-1191 additions to SOLite, tweak to test

---
 src/jalview/io/gff/SequenceOntologyLite.java  |   20 +++++++++++++++-----
 test/jalview/io/gff/SequenceOntologyTest.java |   14 +++++++++++---
 2 files changed, 26 insertions(+), 8 deletions(-)

diff --git a/src/jalview/io/gff/SequenceOntologyLite.java b/src/jalview/io/gff/SequenceOntologyLite.java
index c0ae971..d2e6654 100644
--- a/src/jalview/io/gff/SequenceOntologyLite.java
+++ b/src/jalview/io/gff/SequenceOntologyLite.java
@@ -22,6 +22,9 @@ public class SequenceOntologyLite implements SequenceOntologyI
 {
   /*
    * initial selection of types of interest when processing Ensembl features
+   * NB unlike the full SequenceOntology we don't traverse indirect
+   * child-parent relationships here so e.g. need to list every sub-type
+   * of gene (direct or indirect) that is of interest
    */
   // @formatter:off
   private final String[][] TERMS = new String[][] {
@@ -32,15 +35,21 @@ public class SequenceOntologyLite implements SequenceOntologyI
     { "gene", "gene" }, 
     { "ncRNA_gene", "gene" }, 
     { "snRNA_gene", "gene" },
+    { "miRNA_gene", "gene" },
+    { "lincRNA_gene", "gene" },
     
     /*
      * transcript sub-types:
      */
     { "transcript", "transcript" }, 
     { "mature_transcript", "transcript" }, 
+    { "processed_transcript", "transcript" }, 
+    { "aberrant_processed_transcript", "transcript" },
     { "ncRNA", "transcript" },
     { "snRNA", "transcript" },
-    { "aberrant_processed_transcript", "transcript" },
+    { "miRNA", "transcript" },
+    { "lincRNA", "transcript" },
+    // there are many more sub-types of ncRNA...
     
     /*
      * sequence_variant sub-types:
@@ -55,8 +64,8 @@ public class SequenceOntologyLite implements SequenceOntologyI
     { "structural_variant", "sequence_variant" },
     
     /*
-     * no sub-types of exon or CDS encountered in Ensembl
-     * a few added here for testing purposes
+     * no sub-types of exon or CDS yet seen in Ensembl
+     * some added here for testing purposes
      */
     { "exon", "exon" },
     { "coding_exon", "exon" },
@@ -64,10 +73,11 @@ public class SequenceOntologyLite implements SequenceOntologyI
     { "CDS_predicted", "CDS" },
     
     /*
-     * used in exonerate GFF
+     * terms used in exonerate or PASA GFF
      */
     { "protein_match", "protein_match"},
     { "nucleotide_match", "nucleotide_match"},
+    { "cDNA_match", "nucleotide_match"},
     
     /*
      * used in InterProScan GFF
@@ -169,7 +179,7 @@ public class SequenceOntologyLite implements SequenceOntologyI
       if (!termsNotFound.contains(term))
       {
         System.out.println("SO term " + term
-                + " not known - either invalid or needs modelled in "
+                + " not known - may be invalid, or model if needed in "
                 + getClass().getName());
         termsNotFound.add(term);
       }
diff --git a/test/jalview/io/gff/SequenceOntologyTest.java b/test/jalview/io/gff/SequenceOntologyTest.java
index f791a1e..0b72515 100644
--- a/test/jalview/io/gff/SequenceOntologyTest.java
+++ b/test/jalview/io/gff/SequenceOntologyTest.java
@@ -3,20 +3,28 @@ package jalview.io.gff;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
 
-import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class SequenceOntologyTest
 {
   private SequenceOntologyI so;
 
-  @BeforeMethod
+  @BeforeClass
   public void setUp() {
     long now = System.currentTimeMillis();
-    so = SequenceOntologyFactory.getInstance();
+    SequenceOntologyFactory.setInstance(new SequenceOntology());
     long elapsed = System.currentTimeMillis() - now;
     System.out.println("Load and cache of Sequence Ontology took "
             + elapsed + "ms");
+    so = SequenceOntologyFactory.getInstance();
+  }
+
+  @AfterClass
+  public void tearDown()
+  {
+    SequenceOntologyFactory.setInstance(null);
   }
 
   @Test(groups = "Functional")
-- 
1.7.10.2