JAL-2189 format tests

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

diff --git a/test/jalview/ext/ensembl/EnsemblCdnaTest.java b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
index 2d99a52..973ef3d 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblCdnaTest.java
+++ b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
@@ -14,23 +14,25 @@ import jalview.util.MapList;
 
 import java.util.List;
 
+import org.testng.Assert;
 import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class EnsemblCdnaTest
 {
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public void setUp()
   {
     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
   }
 
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public void tearDown()
   {
     SequenceOntologyFactory.setInstance(null);
   }
+
   /**
    * Test that the cdna part of genomic sequence is correctly identified by
    * 'exon' features (or subtypes) - reverse strand case.
@@ -98,30 +100,30 @@ public class EnsemblCdnaTest
     genomic.setStart(10000);
     genomic.setEnd(50000);
     String transcriptId = "ABC123";
-  
+
     // exon at (start+10000) length 501
     SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
             null);
     sf.setValue("Parent", "transcript:" + transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
-  
+
     // exon (sub-type) at (start + exon_variant) length 101
     sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
     sf.setValue("Parent", "transcript:" + transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
-  
+
     // exon belonging to a different transcript doesn't count
     sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null);
     sf.setValue("Parent", "transcript:anotherOne");
     genomic.addSequenceFeature(sf);
-  
+
     // transcript feature doesn't count
     sf = new SequenceFeature("transcript", "", 10000, 50000, 0f, null);
     sf.setStrand("-"); // weird but ignored
     genomic.addSequenceFeature(sf);
-  
+
     MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
             transcriptId, 23);
     List<int[]> fromRanges = ranges.getFromRanges();
@@ -150,18 +152,18 @@ public class EnsemblCdnaTest
     genomic.setStart(10000);
     genomic.setEnd(50000);
     String transcriptId = "ABC123";
-  
+
     SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
             null);
     sf.setValue("Parent", "transcript:" + transcriptId);
     sf.setStrand("-");
     genomic.addSequenceFeature(sf);
-  
+
     sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
     sf.setValue("Parent", "transcript:" + transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
-  
+
     MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
             transcriptId, 23);
     assertNull(ranges);
@@ -234,4 +236,17 @@ public class EnsemblCdnaTest
     sf.setType("CDS");
     assertFalse(testee.identifiesSequence(sf, accId));
   }
+
+  @Test(groups = "Functional")
+  public void testIsValidReference() throws Exception
+  {
+    EnsemblSequenceFetcher esq = new EnsemblCdna();
+    Assert.assertTrue(esq.isValidReference("CCDS5863.1"));
+    Assert.assertTrue(esq.isValidReference("ENST00000288602"));
+    Assert.assertTrue(esq.isValidReference("ENSG00000288602"));
+    Assert.assertFalse(esq.isValidReference("ENSP00000288602"));
+    Assert.assertFalse(esq.isValidReference("ENST0000288602"));
+    // non-human species having a 3 character identifier included:
+    Assert.assertTrue(esq.isValidReference("ENSMUSG00000099398"));
+  }
 }