X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblCdnaTest.java;h=90c38d4a4d070adf8155b80fc766f1c9a77b610d;hb=a064561d8665ee9db217b17cda826fceac90cbbc;hp=30bc81ba709a740ee774214349dd9b892f2e0d52;hpb=e7a5ac489e89d1c97ba55c817015945ed208f495;p=jalview.git

diff --git a/test/jalview/ext/ensembl/EnsemblCdnaTest.java b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
index 30bc81b..90c38d4 100644
--- a/test/jalview/ext/ensembl/EnsemblCdnaTest.java
+++ b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
@@ -1,7 +1,9 @@
 package jalview.ext.ensembl;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.datamodel.SequenceDummy;
 import jalview.datamodel.SequenceFeature;
@@ -12,16 +14,30 @@ 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
+  public void setUp()
+  {
+    SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
+  }
+
+  @AfterClass
+  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.
    */
   @Test(groups = "Functional")
-  public void getGenomicRangesFromFeatures_reverseStrand()
+  public void testGetGenomicRangesFromFeatures_reverseStrand()
   {
     EnsemblCdna testee = new EnsemblCdna();
     SequenceI genomic = new SequenceDummy("chr7");
@@ -51,8 +67,6 @@ public class EnsemblCdnaTest
     sf = new SequenceFeature("transcript", "", 10000, 50000, 0f, null);
     genomic.addSequenceFeature(sf);
 
-    SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
-
     MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
             transcriptId, 23);
     List<int[]> fromRanges = ranges.getFromRanges();
@@ -75,10 +89,10 @@ public class EnsemblCdnaTest
 
   /**
    * Test that the cdna part of genomic sequence is correctly identified by
-   * 'exon' features (or subtypes).
+   * 'exon' features (or subtypes) with the desired transcript as parent
    */
   @Test(groups = "Functional")
-  public void getGenomicRangesFromFeatures()
+  public void testGetGenomicRangesFromFeatures()
   {
     EnsemblCdna testee = new EnsemblCdna();
     SequenceI genomic = new SequenceDummy("chr7");
@@ -109,8 +123,6 @@ public class EnsemblCdnaTest
     sf.setStrand("-"); // weird but ignored
     genomic.addSequenceFeature(sf);
   
-    SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
-  
     MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
             transcriptId, 23);
     List<int[]> fromRanges = ranges.getFromRanges();
@@ -132,7 +144,7 @@ public class EnsemblCdnaTest
    * reverse strands are present in the features of interest
    */
   @Test(groups = "Functional")
-  public void getGenomicRangesFromFeatures_mixedStrand()
+  public void testGetGenomicRangesFromFeatures_mixedStrand()
   {
     EnsemblCdna testee = new EnsemblCdna();
     SequenceI genomic = new SequenceDummy("chr7");
@@ -151,10 +163,89 @@ public class EnsemblCdnaTest
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
   
-    SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
-  
     MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
             transcriptId, 23);
     assertNull(ranges);
   }
+
+  /**
+   * Test the method that retains features except for 'transcript' (or
+   * subtypes), or features with parent other than the given id
+   */
+  @Test(groups = "Functional")
+  public void testRetainFeature()
+  {
+    String accId = "ABC123";
+    EnsemblCdna testee = new EnsemblCdna();
+
+    SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
+            20500, 0f, null);
+    assertFalse(testee.retainFeature(sf, accId));
+
+    sf.setType("aberrant_processed_transcript");
+    assertFalse(testee.retainFeature(sf, accId));
+
+    sf.setType("NMD_transcript_variant");
+    assertFalse(testee.retainFeature(sf, accId));
+
+    // other feature with no parent is retained
+    sf.setType("sequence_variant");
+    assertTrue(testee.retainFeature(sf, accId));
+
+    // other feature with desired parent is retained
+    sf.setValue("Parent", "transcript:" + accId);
+    assertTrue(testee.retainFeature(sf, accId));
+
+    // feature with wrong parent is not retained
+    sf.setValue("Parent", "transcript:XYZ");
+    assertFalse(testee.retainFeature(sf, accId));
+  }
+
+  /**
+   * Test the method that picks out 'exon' (or subtype) features with the
+   * accession id as parent
+   */
+  @Test(groups = "Functional")
+  public void testIdentifiesSequence()
+  {
+    String accId = "ABC123";
+    EnsemblCdna testee = new EnsemblCdna();
+
+    // exon with no parent not valid
+    SequenceFeature sf = new SequenceFeature("exon", "", 1, 2, 0f, null);
+    assertFalse(testee.identifiesSequence(sf, accId));
+
+    // exon with wrong parent not valid
+    sf.setValue("Parent", "transcript:XYZ");
+    assertFalse(testee.identifiesSequence(sf, accId));
+
+    // exon with right parent is valid
+    sf.setValue("Parent", "transcript:" + accId);
+    assertTrue(testee.identifiesSequence(sf, accId));
+
+    // exon sub-type with right parent is valid
+    sf.setType("coding_exon");
+    assertTrue(testee.identifiesSequence(sf, accId));
+
+    // transcript not valid:
+    sf.setType("transcript");
+    assertFalse(testee.identifiesSequence(sf, accId));
+
+    // CDS not valid:
+    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"));
+  }
 }