X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblGenomeTest.java;h=11140f9f86eaddbe668e2b739397bbb2fcf1c6dd;hb=61ff8fb4efa315c35149c9d11850d99e3d00c441;hp=654797c5c87a5fcd52d7d5013d6a6be06c243408;hpb=5f4e1e4c330b045e9c8bce28ee132a0fca3834d8;p=jalview.git

diff --git a/test/jalview/ext/ensembl/EnsemblGenomeTest.java b/test/jalview/ext/ensembl/EnsemblGenomeTest.java
index 654797c..11140f9 100644
--- a/test/jalview/ext/ensembl/EnsemblGenomeTest.java
+++ b/test/jalview/ext/ensembl/EnsemblGenomeTest.java
@@ -24,6 +24,7 @@ import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceDummy;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
@@ -76,13 +77,13 @@ public class EnsemblGenomeTest
     // transcript at (start+10000) length 501
     SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
             20500, 0f, null);
-    sf.setValue("ID", "transcript:" + transcriptId);
+    sf.setValue("id", transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
 
     // transcript (sub-type) at (start + 10500) length 101
     sf = new SequenceFeature("ncRNA", "", 10500, 10600, 0f, null);
-    sf.setValue("ID", "transcript:" + transcriptId);
+    sf.setValue("id", transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
 
@@ -90,13 +91,13 @@ public class EnsemblGenomeTest
     // although strictly it is a sequence_variant in SO
     sf = new SequenceFeature("NMD_transcript_variant", "", 11000, 12000,
             0f, null);
-    sf.setValue("ID", "transcript:" + transcriptId);
+    sf.setValue("id", transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
 
     // transcript with a different ID doesn't count
     sf = new SequenceFeature("transcript", "", 11500, 12600, 0f, null);
-    sf.setValue("ID", "transcript:anotherOne");
+    sf.setValue("id", "anotherOne");
     genomic.addSequenceFeature(sf);
 
     // parent of transcript feature doesn't count
@@ -136,22 +137,24 @@ public class EnsemblGenomeTest
             20500, 0f, null);
     assertFalse(testee.retainFeature(sf, accId));
 
-    sf.setType("mature_transcript");
+    sf = new SequenceFeature("mature_transcript", "", 20000, 20500, 0f,
+            null);
     assertFalse(testee.retainFeature(sf, accId));
 
-    sf.setType("NMD_transcript_variant");
+    sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
+            0f, null);
     assertFalse(testee.retainFeature(sf, accId));
 
     // other feature with no parent is kept
-    sf.setType("anything");
+    sf = new SequenceFeature("anything", "", 20000, 20500, 0f, null);
     assertTrue(testee.retainFeature(sf, accId));
 
     // other feature with correct parent is kept
-    sf.setValue("Parent", "transcript:" + accId);
+    sf.setValue("Parent", accId);
     assertTrue(testee.retainFeature(sf, accId));
 
     // other feature with wrong parent is not kept
-    sf.setValue("Parent", "transcript:XYZ");
+    sf.setValue("Parent", "XYZ");
     assertFalse(testee.retainFeature(sf, accId));
   }
 
@@ -160,39 +163,59 @@ public class EnsemblGenomeTest
    * accession id as ID
    */
   @Test(groups = "Functional")
-  public void testIdentifiesSequence()
+  public void testGetIdentifyingFeatures()
   {
     String accId = "ABC123";
-    EnsemblGenome testee = new EnsemblGenome();
+    SequenceI seq = new Sequence(accId, "HEARTS");
 
     // transcript with no ID not valid
-    SequenceFeature sf = new SequenceFeature("transcript", "", 1, 2, 0f,
+    SequenceFeature sf1 = new SequenceFeature("transcript", "", 1, 2, 0f,
             null);
-    assertFalse(testee.identifiesSequence(sf, accId));
+    seq.addSequenceFeature(sf1);
 
     // transcript with wrong ID not valid
-    sf.setValue("ID", "transcript");
-    assertFalse(testee.identifiesSequence(sf, accId));
+    // NB change desc to avoid rejection of duplicate feature!
+    SequenceFeature sf2 = new SequenceFeature("transcript", "a", 1, 2, 0f,
+            null);
+    sf2.setValue("id", "transcript");
+    seq.addSequenceFeature(sf2);
 
     // transcript with right ID is valid
-    sf.setValue("ID", "transcript:" + accId);
-    assertTrue(testee.identifiesSequence(sf, accId));
+    SequenceFeature sf3 = new SequenceFeature("transcript", "b", 1, 2, 0f,
+            null);
+    sf3.setValue("id", accId);
+    seq.addSequenceFeature(sf3);
 
     // transcript sub-type with right ID is valid
-    sf.setType("ncRNA");
-    assertTrue(testee.identifiesSequence(sf, accId));
+    SequenceFeature sf4 = new SequenceFeature("ncRNA", "", 1, 2, 0f, null);
+    sf4.setValue("id", accId);
+    seq.addSequenceFeature(sf4);
 
     // Ensembl treats NMD_transcript_variant as if a transcript
-    sf.setType("NMD_transcript_variant");
-    assertTrue(testee.identifiesSequence(sf, accId));
+    SequenceFeature sf5 = new SequenceFeature("NMD_transcript_variant", "",
+            1, 2, 0f, null);
+    sf5.setValue("id", accId);
+    seq.addSequenceFeature(sf5);
 
     // gene not valid:
-    sf.setType("gene");
-    assertFalse(testee.identifiesSequence(sf, accId));
+    SequenceFeature sf6 = new SequenceFeature("gene", "", 1, 2, 0f, null);
+    sf6.setValue("id", accId);
+    seq.addSequenceFeature(sf6);
 
     // exon not valid:
-    sf.setType("exon");
-    assertFalse(testee.identifiesSequence(sf, accId));
+    SequenceFeature sf7 = new SequenceFeature("exon", "", 1, 2, 0f, null);
+    sf7.setValue("id", accId);
+    seq.addSequenceFeature(sf7);
+
+    List<SequenceFeature> sfs = new EnsemblGenome()
+            .getIdentifyingFeatures(seq, accId);
+    assertFalse(sfs.contains(sf1));
+    assertFalse(sfs.contains(sf2));
+    assertTrue(sfs.contains(sf3));
+    assertTrue(sfs.contains(sf4));
+    assertTrue(sfs.contains(sf5));
+    assertFalse(sfs.contains(sf6));
+    assertFalse(sfs.contains(sf7));
   }
 
 }