mungo merge

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

diff --git a/test/jalview/ext/ensembl/EnsemblGenomeTest.java b/test/jalview/ext/ensembl/EnsemblGenomeTest.java
new file mode 100644 (file)
index 0000000..daad8b1
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+++ b/test/jalview/ext/ensembl/EnsemblGenomeTest.java
@@ -0,0 +1,170 @@
+package jalview.ext.ensembl;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.datamodel.SequenceDummy;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyLite;
+import jalview.util.MapList;
+
+import java.util.List;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class EnsemblGenomeTest
+{
+  @BeforeClass
+  public void setUp()
+  {
+    SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
+  }
+
+  @AfterClass
+  public void tearDown()
+  {
+    SequenceOntologyFactory.setInstance(null);
+  }
+
+  /**
+   * Test that the genomic sequence part of genomic sequence is correctly
+   * identified by 'transcript' features (or subtypes) with the correct gene ID
+   */
+  @Test(groups = "Functional")
+  public void testGetGenomicRangesFromFeatures()
+  {
+    EnsemblGenome testee = new EnsemblGenome();
+    SequenceI genomic = new SequenceDummy("chr7");
+    genomic.setStart(10000);
+    genomic.setEnd(50000);
+    String transcriptId = "ABC123";
+  
+    // transcript at (start+10000) length 501
+    SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
+            20500, 0f,
+            null);
+    sf.setValue("ID", "transcript:" + 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.setStrand("+");
+    genomic.addSequenceFeature(sf);
+
+    // Ensembl treats NMD_transcript_variant as if transcript
+    // 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.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");
+    genomic.addSequenceFeature(sf);
+  
+    // parent of transcript feature doesn't count
+    sf = new SequenceFeature("gene_member_region", "", 10000, 50000, 0f,
+            null);
+    genomic.addSequenceFeature(sf);
+
+    MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
+            transcriptId, 23);
+    List<int[]> fromRanges = ranges.getFromRanges();
+    assertEquals(3, fromRanges.size());
+    // from ranges should be sorted by start order
+    assertEquals(10500, fromRanges.get(0)[0]);
+    assertEquals(10600, fromRanges.get(0)[1]);
+    assertEquals(11000, fromRanges.get(1)[0]);
+    assertEquals(12000, fromRanges.get(1)[1]);
+    assertEquals(20000, fromRanges.get(2)[0]);
+    assertEquals(20500, fromRanges.get(2)[1]);
+    // to range should start from given start numbering
+    List<int[]> toRanges = ranges.getToRanges();
+    assertEquals(1, toRanges.size());
+    assertEquals(23, toRanges.get(0)[0]);
+    assertEquals(1625, toRanges.get(0)[1]);
+  }
+
+  /**
+   * Test the method that retains features except for 'transcript' (or
+   * sub-type), or those with parent other than the given id
+   */
+  @Test(groups = "Functional")
+  public void testRetainFeature()
+  {
+    String accId = "ABC123";
+    EnsemblGenome testee = new EnsemblGenome();
+
+    SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
+            20500, 0f, null);
+    assertFalse(testee.retainFeature(sf, accId));
+  
+    sf.setType("mature_transcript");
+    assertFalse(testee.retainFeature(sf, accId));
+  
+    sf.setType("NMD_transcript_variant");
+    assertFalse(testee.retainFeature(sf, accId));
+  
+    // other feature with no parent is kept
+    sf.setType("anything");
+    assertTrue(testee.retainFeature(sf, accId));
+
+    // other feature with correct parent is kept
+    sf.setValue("Parent", "transcript:" + accId);
+    assertTrue(testee.retainFeature(sf, accId));
+
+    // other feature with wrong parent is not kept
+    sf.setValue("Parent", "transcript:XYZ");
+    assertFalse(testee.retainFeature(sf, accId));
+  }
+
+  /**
+   * Test the method that picks out 'transcript' (or subtype) features with the
+   * accession id as ID
+   */
+  @Test(groups = "Functional")
+  public void testIdentifiesSequence()
+  {
+    String accId = "ABC123";
+    EnsemblGenome testee = new EnsemblGenome();
+  
+    // transcript with no ID not valid
+    SequenceFeature sf = new SequenceFeature("transcript", "", 1, 2, 0f,
+            null);
+    assertFalse(testee.identifiesSequence(sf, accId));
+  
+    // transcript with wrong ID not valid
+    sf.setValue("ID", "transcript");
+    assertFalse(testee.identifiesSequence(sf, accId));
+  
+    // transcript with right ID is valid
+    sf.setValue("ID", "transcript:" + accId);
+    assertTrue(testee.identifiesSequence(sf, accId));
+  
+    // transcript sub-type with right ID is valid
+    sf.setType("ncRNA");
+    assertTrue(testee.identifiesSequence(sf, accId));
+
+    // Ensembl treats NMD_transcript_variant as if a transcript
+    sf.setType("NMD_transcript_variant");
+    assertTrue(testee.identifiesSequence(sf, accId));
+  
+    // gene not valid:
+    sf.setType("gene");
+    assertFalse(testee.identifiesSequence(sf, accId));
+  
+    // exon not valid:
+    sf.setType("exon");
+    assertFalse(testee.identifiesSequence(sf, accId));
+  }
+
+}