JAL-1705 tests added

diff --git a/test/jalview/ext/ensembl/EnsemblCdnaTest.java b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
new file mode 100644 (file)
index 0000000..30bc81b
--- /dev/null
+++ b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
@@ -0,0 +1,160 @@
+package jalview.ext.ensembl;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
+
+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.Test;
+
+public class EnsemblCdnaTest
+{
+  /**
+   * 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()
+  {
+    EnsemblCdna testee = new EnsemblCdna();
+    SequenceI genomic = new SequenceDummy("chr7");
+    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);
+    genomic.addSequenceFeature(sf);
+
+    SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
+
+    MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
+            transcriptId, 23);
+    List<int[]> fromRanges = ranges.getFromRanges();
+    assertEquals(2, fromRanges.size());
+
+    /*
+     * from ranges should be sorted by start order descending
+     * and hold mappings from reverse strand sense
+     */
+    assertEquals(20500, fromRanges.get(0)[0]);
+    assertEquals(20000, fromRanges.get(0)[1]);
+    assertEquals(10600, fromRanges.get(1)[0]);
+    assertEquals(10500, fromRanges.get(1)[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(624, toRanges.get(0)[1]);
+  }
+
+  /**
+   * Test that the cdna part of genomic sequence is correctly identified by
+   * 'exon' features (or subtypes).
+   */
+  @Test(groups = "Functional")
+  public void getGenomicRangesFromFeatures()
+  {
+    EnsemblCdna testee = new EnsemblCdna();
+    SequenceI genomic = new SequenceDummy("chr7");
+    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);
+  
+    SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
+  
+    MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
+            transcriptId, 23);
+    List<int[]> fromRanges = ranges.getFromRanges();
+    assertEquals(2, fromRanges.size());
+    // from ranges should be sorted by start order
+    assertEquals(10500, fromRanges.get(0)[0]);
+    assertEquals(10600, fromRanges.get(0)[1]);
+    assertEquals(20000, fromRanges.get(1)[0]);
+    assertEquals(20500, fromRanges.get(1)[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(624, toRanges.get(0)[1]);
+  }
+
+  /**
+   * The method under test should give up and return null if both forward and
+   * reverse strands are present in the features of interest
+   */
+  @Test(groups = "Functional")
+  public void getGenomicRangesFromFeatures_mixedStrand()
+  {
+    EnsemblCdna testee = new EnsemblCdna();
+    SequenceI genomic = new SequenceDummy("chr7");
+    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);
+  
+    SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
+  
+    MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
+            transcriptId, 23);
+    assertNull(ranges);
+  }
+}

diff --git a/test/jalview/ext/ensembl/EnsemblSeqProxyAdapter.java b/test/jalview/ext/ensembl/EnsemblSeqProxyAdapter.java
new file mode 100644 (file)
index 0000000..7077eac
--- /dev/null
+++ b/test/jalview/ext/ensembl/EnsemblSeqProxyAdapter.java
@@ -0,0 +1,36 @@
+package jalview.ext.ensembl;
+
+import jalview.datamodel.SequenceFeature;
+
+/**
+ * A convenience class to simplify writing unit tests (pending Mockito or
+ * similar?)
+ */
+public class EnsemblSeqProxyAdapter extends EnsemblSeqProxy
+{
+
+  @Override
+  public String getDbName()
+  {
+    return null;
+  }
+
+  @Override
+  protected EnsemblFeatureType[] getFeaturesToFetch()
+  {
+    return null;
+  }
+
+  @Override
+  protected EnsemblSeqType getSourceEnsemblType()
+  {
+    return null;
+  }
+
+  @Override
+  protected boolean identifiesSequence(SequenceFeature sf, String accId)
+  {
+    return false;
+  }
+
+}