X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblCdnaTest.java;h=c9d8deb93308f43981f0c7b2d26fed6efdbc7e94;hb=b9bde68b87a581a1f21e47cb19839791a192134a;hp=fb0204b438fb892532e169de7487027b16a21a2e;hpb=5f4e1e4c330b045e9c8bce28ee132a0fca3834d8;p=jalview.git

diff --git a/test/jalview/ext/ensembl/EnsemblCdnaTest.java b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
index fb0204b..c9d8deb 100644
--- a/test/jalview/ext/ensembl/EnsemblCdnaTest.java
+++ b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
@@ -25,6 +25,7 @@ import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceDummy;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
@@ -212,20 +213,25 @@ public class EnsemblCdnaTest
             20500, 0f, null);
     assertFalse(testee.retainFeature(sf, accId));
 
-    sf.setType("aberrant_processed_transcript");
+    sf = new SequenceFeature("aberrant_processed_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 retained
-    sf.setType("sequence_variant");
+    sf = new SequenceFeature("sequence_variant", "", 20000, 20500, 0f, null);
     assertTrue(testee.retainFeature(sf, accId));
 
     // other feature with desired parent is retained
     sf.setValue("Parent", "transcript:" + accId);
     assertTrue(testee.retainFeature(sf, accId));
 
+    // test is not case-sensitive
+    assertTrue(testee.retainFeature(sf, accId.toLowerCase()));
+
     // feature with wrong parent is not retained
     sf.setValue("Parent", "transcript:XYZ");
     assertFalse(testee.retainFeature(sf, accId));
@@ -236,34 +242,51 @@ public class EnsemblCdnaTest
    * accession id as parent
    */
   @Test(groups = "Functional")
-  public void testIdentifiesSequence()
+  public void testGetIdentifyingFeatures()
   {
     String accId = "ABC123";
-    EnsemblCdna testee = new EnsemblCdna();
+    SequenceI seq = new Sequence(accId, "MKLNFRQIE");
 
-    // exon with no parent not valid
-    SequenceFeature sf = new SequenceFeature("exon", "", 1, 2, 0f, null);
-    assertFalse(testee.identifiesSequence(sf, accId));
+    // exon with no parent: not valid
+    SequenceFeature sf1 = new SequenceFeature("exon", "", 1, 2, 0f, null);
+    seq.addSequenceFeature(sf1);
 
-    // exon with wrong parent not valid
-    sf.setValue("Parent", "transcript:XYZ");
-    assertFalse(testee.identifiesSequence(sf, accId));
+    // exon with wrong parent: not valid
+    SequenceFeature sf2 = new SequenceFeature("exon", "", 1, 2, 0f, null);
+    sf2.setValue("Parent", "transcript:XYZ");
+    seq.addSequenceFeature(sf2);
 
     // exon with right parent is valid
-    sf.setValue("Parent", "transcript:" + accId);
-    assertTrue(testee.identifiesSequence(sf, accId));
+    SequenceFeature sf3 = new SequenceFeature("exon", "", 1, 2, 0f, null);
+    sf3.setValue("Parent", "transcript:" + accId);
+    seq.addSequenceFeature(sf3);
 
     // exon sub-type with right parent is valid
-    sf.setType("coding_exon");
-    assertTrue(testee.identifiesSequence(sf, accId));
+    SequenceFeature sf4 = new SequenceFeature("coding_exon", "", 1, 2, 0f,
+            null);
+    sf4.setValue("Parent", "transcript:" + accId);
+    seq.addSequenceFeature(sf4);
 
     // transcript not valid:
-    sf.setType("transcript");
-    assertFalse(testee.identifiesSequence(sf, accId));
+    SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f,
+            null);
+    sf5.setValue("Parent", "transcript:" + accId);
+    seq.addSequenceFeature(sf5);
 
     // CDS not valid:
-    sf.setType("CDS");
-    assertFalse(testee.identifiesSequence(sf, accId));
+    SequenceFeature sf6 = new SequenceFeature("transcript", "", 1, 2, 0f,
+            null);
+    sf6.setValue("Parent", "transcript:" + accId);
+    seq.addSequenceFeature(sf6);
+
+    List<SequenceFeature> sfs = new EnsemblCdna()
+            .getIdentifyingFeatures(seq, accId);
+    assertFalse(sfs.contains(sf1));
+    assertFalse(sfs.contains(sf2));
+    assertTrue(sfs.contains(sf3));
+    assertTrue(sfs.contains(sf4));
+    assertFalse(sfs.contains(sf5));
+    assertFalse(sfs.contains(sf6));
   }
 
   @Test(groups = "Functional")