Updated with latest from mchmmer branch

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

diff --git a/test/jalview/ext/ensembl/EnsemblGeneTest.java b/test/jalview/ext/ensembl/EnsemblGeneTest.java
index a8c491c..217742d 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblGeneTest.java
+++ b/test/jalview/ext/ensembl/EnsemblGeneTest.java
@@ -25,6 +25,7 @@ import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Cache;
 import jalview.datamodel.SequenceDummy;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
@@ -53,6 +54,7 @@ public class EnsemblGeneTest
   @BeforeClass(alwaysRun = true)
   public void setUp()
   {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
   }
 
@@ -173,7 +175,8 @@ public class EnsemblGeneTest
     // NMD_transcript_variant treated like transcript in Ensembl
     SequenceFeature sf3 = new SequenceFeature("NMD_transcript_variant", "",
             22000, 22500, 0f, null);
-    sf3.setValue("Parent", "gene:" + geneId);
+    // id matching should not be case-sensitive
+    sf3.setValue("Parent", "gene:" + geneId.toLowerCase());
     sf3.setValue("transcript_id", "transcript3");
     genomic.addSequenceFeature(sf3);
 
@@ -259,6 +262,9 @@ public class EnsemblGeneTest
     sf.setValue("ID", "gene:" + accId);
     assertTrue(testee.identifiesSequence(sf, accId));
 
+    // test is not case-sensitive
+    assertTrue(testee.identifiesSequence(sf, accId.toLowerCase()));
+
     // transcript not valid:
     sf = new SequenceFeature("transcript", "", 1, 2, 0f, null);
     sf.setValue("ID", "gene:" + accId);
@@ -296,4 +302,28 @@ public class EnsemblGeneTest
     assertEquals(-1, fc.compare("coding_exon", "feature_variant"));
     assertEquals(1f, fc.getTransparency());
   }
+
+  @Test(groups = "Network")
+  public void testGetGeneIds()
+  {
+    /*
+     * ENSG00000158828 gene id PINK1 human
+     * ENST00000321556 transcript for the same gene - should not be duplicated
+     * P30419 Uniprot identifier for ENSG00000136448
+     * ENST00000592782 transcript for Uniprot gene - should not be duplicated
+     * BRAF - gene name resolvabe (at time of writing) for 6 model species
+     */
+    String ids = "ENSG00000158828 ENST00000321556 P30419 ENST00000592782 BRAF";
+    EnsemblGene testee = new EnsemblGene();
+    List<String> geneIds = testee.getGeneIds(ids);
+    assertEquals(8, geneIds.size());
+    assertTrue(geneIds.contains("ENSG00000158828"));
+    assertTrue(geneIds.contains("ENSG00000136448"));
+    assertTrue(geneIds.contains("ENSG00000157764")); // BRAF human
+    assertTrue(geneIds.contains("ENSMUSG00000002413")); // mouse
+    assertTrue(geneIds.contains("ENSRNOG00000010957")); // rat
+    assertTrue(geneIds.contains("ENSXETG00000004845")); // xenopus
+    assertTrue(geneIds.contains("ENSDARG00000017661")); // zebrafish
+    assertTrue(geneIds.contains("ENSGALG00000012865")); // chicken
+  }
 }