X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblGeneTest.java;h=8b1e8404f7bb01e9f66cdc198d423df0d47e9bd5;hb=7e00183505bd4c58d1ce62ee121ed372c3b058f2;hp=5920b89e85af17c1d94fc0257f5873f2c2c7c664;hpb=3eb959d7f16b64260b8bec08d49b28ffc9670517;p=jalview.git diff --git a/test/jalview/ext/ensembl/EnsemblGeneTest.java b/test/jalview/ext/ensembl/EnsemblGeneTest.java index 5920b89..8b1e840 100644 --- a/test/jalview/ext/ensembl/EnsemblGeneTest.java +++ b/test/jalview/ext/ensembl/EnsemblGeneTest.java @@ -25,6 +25,8 @@ import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertTrue; import jalview.api.FeatureSettingsModelI; +import jalview.bin.Cache; +import jalview.datamodel.Sequence; import jalview.datamodel.SequenceDummy; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; @@ -53,6 +55,7 @@ public class EnsemblGeneTest @BeforeClass(alwaysRun = true) public void setUp() { + Cache.loadProperties("test/jalview/io/testProps.jvprops"); SequenceOntologyFactory.setInstance(new SequenceOntologyLite()); } @@ -75,18 +78,10 @@ public class EnsemblGeneTest genomic.setEnd(50000); String geneId = "ABC123"; - // gene at (start+20000) length 501 - // should be ignored - the first 'gene' found defines the whole range - // (note features are found in position order, not addition order) - SequenceFeature sf = new SequenceFeature("gene", "", 20000, 20500, 0f, - null); - sf.setValue("ID", "gene:" + geneId); - sf.setStrand("+"); - genomic.addSequenceFeature(sf); - // gene at (start + 10500) length 101 - sf = new SequenceFeature("gene", "", 10500, 10600, 0f, null); - sf.setValue("ID", "gene:" + geneId); + SequenceFeature sf = new SequenceFeature("gene", "", 10500, 10600, 0f, + null); + sf.setValue("id", geneId); sf.setStrand("+"); genomic.addSequenceFeature(sf); @@ -115,18 +110,10 @@ public class EnsemblGeneTest genomic.setEnd(50000); String geneId = "ABC123"; - // gene at (start+20000) length 501 - // should be ignored - the first 'gene' found defines the whole range - // (real data would only have one such feature) - SequenceFeature sf = new SequenceFeature("ncRNA_gene", "", 20000, - 20500, 0f, null); - sf.setValue("ID", "gene:" + geneId); - sf.setStrand("-"); - genomic.addSequenceFeature(sf); - // gene at (start + 10500) length 101 - sf = new SequenceFeature("gene", "", 10500, 10600, 0f, null); - sf.setValue("ID", "gene:" + geneId); + SequenceFeature sf = new SequenceFeature("gene", "", 10500, 10600, 0f, + null); + sf.setValue("id", geneId); sf.setStrand("+"); genomic.addSequenceFeature(sf); @@ -159,29 +146,30 @@ public class EnsemblGeneTest // transcript feature SequenceFeature sf1 = new SequenceFeature("transcript", "", 20000, 20500, 0f, null); - sf1.setValue("Parent", "gene:" + geneId); - sf1.setValue("transcript_id", "transcript1"); + sf1.setValue("Parent", geneId); + sf1.setValue("id", "transcript1"); genomic.addSequenceFeature(sf1); // transcript sub-type feature SequenceFeature sf2 = new SequenceFeature("snRNA", "", 21000, 21500, 0f, null); - sf2.setValue("Parent", "gene:" + geneId); - sf2.setValue("transcript_id", "transcript2"); + sf2.setValue("Parent", geneId); + sf2.setValue("id", "transcript2"); genomic.addSequenceFeature(sf2); // NMD_transcript_variant treated like transcript in Ensembl SequenceFeature sf3 = new SequenceFeature("NMD_transcript_variant", "", 22000, 22500, 0f, null); - sf3.setValue("Parent", "gene:" + geneId); - sf3.setValue("transcript_id", "transcript3"); + // id matching should not be case-sensitive + sf3.setValue("Parent", geneId.toLowerCase()); + sf3.setValue("id", "transcript3"); genomic.addSequenceFeature(sf3); // transcript for a different gene - ignored SequenceFeature sf4 = new SequenceFeature("snRNA", "", 23000, 23500, 0f, null); - sf4.setValue("Parent", "gene:XYZ"); - sf4.setValue("transcript_id", "transcript4"); + sf4.setValue("Parent", "XYZ"); + sf4.setValue("id", "transcript4"); genomic.addSequenceFeature(sf4); EnsemblGene testee = new EnsemblGene(); @@ -208,24 +196,24 @@ public class EnsemblGeneTest EnsemblGene testee = new EnsemblGene(); SequenceFeature sf = new SequenceFeature("gene", "", 20000, 20500, 0f, null); - sf.setValue("ID", "gene:" + geneId); + sf.setValue("id", geneId); assertFalse(testee.retainFeature(sf, geneId)); sf = new SequenceFeature("transcript", "", 20000, 20500, 0f, null); - sf.setValue("Parent", "gene:" + geneId); + sf.setValue("Parent", geneId); assertTrue(testee.retainFeature(sf, geneId)); sf = new SequenceFeature("mature_transcript", "", 20000, 20500, 0f, null); - sf.setValue("Parent", "gene:" + geneId); + sf.setValue("Parent", geneId); assertTrue(testee.retainFeature(sf, geneId)); sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500, 0f, null); - sf.setValue("Parent", "gene:" + geneId); + sf.setValue("Parent", geneId); assertTrue(testee.retainFeature(sf, geneId)); - sf.setValue("Parent", "gene:XYZ"); + sf.setValue("Parent", "ßXYZ"); assertFalse(testee.retainFeature(sf, geneId)); sf = new SequenceFeature("anything", "", 20000, 20500, 0f, null); @@ -237,37 +225,48 @@ public class EnsemblGeneTest * accession id as ID */ @Test(groups = "Functional") - public void testIdentifiesSequence() + public void testGetIdentifyingFeatures() { String accId = "ABC123"; - EnsemblGene testee = new EnsemblGene(); + SequenceI seq = new Sequence(accId, "HIBEES"); // gene with no ID not valid - SequenceFeature sf = new SequenceFeature("gene", "", 1, 2, 0f, null); - assertFalse(testee.identifiesSequence(sf, accId)); + SequenceFeature sf1 = new SequenceFeature("gene", "", 1, 2, 0f, null); + seq.addSequenceFeature(sf1); // gene with wrong ID not valid - sf.setValue("ID", "gene:XYZ"); - assertFalse(testee.identifiesSequence(sf, accId)); + SequenceFeature sf2 = new SequenceFeature("gene", "a", 1, 2, 0f, null); + sf2.setValue("id", "XYZ"); + seq.addSequenceFeature(sf2); // gene with right ID is valid - sf.setValue("ID", "gene:" + accId); - assertTrue(testee.identifiesSequence(sf, accId)); + SequenceFeature sf3 = new SequenceFeature("gene", "b", 1, 2, 0f, null); + sf3.setValue("id", accId); + seq.addSequenceFeature(sf3); // gene sub-type with right ID is valid - sf = new SequenceFeature("snRNA_gene", "", 1, 2, 0f, null); - sf.setValue("ID", "gene:" + accId); - assertTrue(testee.identifiesSequence(sf, accId)); + SequenceFeature sf4 = new SequenceFeature("snRNA_gene", "", 1, 2, 0f, null); + sf4.setValue("id", accId); + seq.addSequenceFeature(sf4); // transcript not valid: - sf = new SequenceFeature("transcript", "", 1, 2, 0f, null); - sf.setValue("ID", "gene:" + accId); - assertFalse(testee.identifiesSequence(sf, accId)); + SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f, null); + sf5.setValue("id", accId); + seq.addSequenceFeature(sf5); // exon not valid: - sf = new SequenceFeature("exon", "", 1, 2, 0f, null); - sf.setValue("ID", "gene:" + accId); - assertFalse(testee.identifiesSequence(sf, accId)); + SequenceFeature sf6 = new SequenceFeature("exon", "", 1, 2, 0f, null); + sf6.setValue("id", accId); + seq.addSequenceFeature(sf6); + + List sfs = new EnsemblGene() + .getIdentifyingFeatures(seq, accId); + assertFalse(sfs.contains(sf1)); + assertFalse(sfs.contains(sf2)); + assertTrue(sfs.contains(sf3)); + assertTrue(sfs.contains(sf4)); + assertFalse(sfs.contains(sf5)); + assertFalse(sfs.contains(sf6)); } /**