JAL-3076 refactor for more efficient scan of 'gene' features

[jalview.git] / test / jalview / ext / ensembl / EnsemblGenomeTest.java

diff --git a/test/jalview/ext/ensembl/EnsemblGenomeTest.java b/test/jalview/ext/ensembl/EnsemblGenomeTest.java
index 8687da9..72ee492 100644 (file)
--- 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;
@@ -162,43 +163,58 @@ 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));
+    SequenceFeature sf2 = new SequenceFeature("transcript", "", 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", "", 1, 2, 0f,
+            null);
+    sf3.setValue("ID", "transcript:" + accId);
+    seq.addSequenceFeature(sf3);
 
     // transcript sub-type with right ID is valid
-    sf = new SequenceFeature("ncRNA", "", 1, 2, 0f, null);
-    sf.setValue("ID", "transcript:" + accId);
-    assertTrue(testee.identifiesSequence(sf, accId));
+    SequenceFeature sf4 = new SequenceFeature("ncRNA", "", 1, 2, 0f, null);
+    sf4.setValue("ID", "transcript:" + accId);
+    seq.addSequenceFeature(sf4);
 
     // Ensembl treats NMD_transcript_variant as if a transcript
-    sf = new SequenceFeature("NMD_transcript_variant", "", 1, 2, 0f, null);
-    sf.setValue("ID", "transcript:" + accId);
-    assertTrue(testee.identifiesSequence(sf, accId));
+    SequenceFeature sf5 = new SequenceFeature("NMD_transcript_variant", "",
+            1, 2, 0f, null);
+    sf5.setValue("ID", "transcript:" + accId);
+    seq.addSequenceFeature(sf5);
 
     // gene not valid:
-    sf = new SequenceFeature("gene", "", 1, 2, 0f, null);
-    sf.setValue("ID", "transcript:" + accId);
-    assertFalse(testee.identifiesSequence(sf, accId));
+    SequenceFeature sf6 = new SequenceFeature("gene", "", 1, 2, 0f, null);
+    sf6.setValue("ID", "transcript:" + accId);
+    seq.addSequenceFeature(sf6);
 
     // exon not valid:
-    sf = new SequenceFeature("exon", "", 1, 2, 0f, null);
-    sf.setValue("ID", "transcript:" + accId);
-    assertFalse(testee.identifiesSequence(sf, accId));
+    SequenceFeature sf7 = new SequenceFeature("exon", "", 1, 2, 0f, null);
+    sf7.setValue("ID", "transcript:" + 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));
   }
 
 }