JAL-2679 case-insensitive comparison of query and retrieved accession

[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 edecc23..1b1a2b4 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblGeneTest.java
+++ b/test/jalview/ext/ensembl/EnsemblGeneTest.java
@@ -173,7 +173,8 @@ 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);
 
@@ -211,22 +212,24 @@ public class EnsemblGeneTest
     sf.setValue("ID", "gene:" + geneId);
     assertFalse(testee.retainFeature(sf, geneId));
 
-    sf.setType("transcript");
+    sf = new SequenceFeature("transcript", "", 20000, 20500, 0f, null);
     sf.setValue("Parent", "gene:" + geneId);
     assertTrue(testee.retainFeature(sf, geneId));
 
-    sf.setType("mature_transcript");
+    sf = new SequenceFeature("mature_transcript", "", 20000, 20500, 0f,
+            null);
     sf.setValue("Parent", "gene:" + geneId);
     assertTrue(testee.retainFeature(sf, geneId));
 
-    sf.setType("NMD_transcript_variant");
+    sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
+            0f, null);
     sf.setValue("Parent", "gene:" + geneId);
     assertTrue(testee.retainFeature(sf, geneId));
 
     sf.setValue("Parent", "gene:XYZ");
     assertFalse(testee.retainFeature(sf, geneId));
 
-    sf.setType("anything");
+    sf = new SequenceFeature("anything", "", 20000, 20500, 0f, null);
     assertTrue(testee.retainFeature(sf, geneId));
   }
 
@@ -253,15 +256,21 @@ public class EnsemblGeneTest
     assertTrue(testee.identifiesSequence(sf, accId));
 
     // gene sub-type with right ID is valid
-    sf.setType("snRNA_gene");
+    sf = new SequenceFeature("snRNA_gene", "", 1, 2, 0f, null);
+    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.setType("transcript");
+    sf = new SequenceFeature("transcript", "", 1, 2, 0f, null);
+    sf.setValue("ID", "gene:" + accId);
     assertFalse(testee.identifiesSequence(sf, accId));
 
     // exon not valid:
-    sf.setType("exon");
+    sf = new SequenceFeature("exon", "", 1, 2, 0f, null);
+    sf.setValue("ID", "gene:" + accId);
     assertFalse(testee.identifiesSequence(sf, accId));
   }
 
@@ -291,4 +300,28 @@ 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
+  }
 }