X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblGeneTest.java;h=e16197a34f49c17ce795bbb78140584a23d449af;hb=61ff8fb4efa315c35149c9d11850d99e3d00c441;hp=1b1a2b4499d69374869dbe3e20ad786599c7cdad;hpb=2779b461347e684414f9e98e607e138b1e43db84;p=jalview.git diff --git a/test/jalview/ext/ensembl/EnsemblGeneTest.java b/test/jalview/ext/ensembl/EnsemblGeneTest.java index 1b1a2b4..e16197a 100644 --- a/test/jalview/ext/ensembl/EnsemblGeneTest.java +++ b/test/jalview/ext/ensembl/EnsemblGeneTest.java @@ -20,11 +20,15 @@ */ package jalview.ext.ensembl; +import java.util.Locale; + import static org.testng.AssertJUnit.assertEquals; 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 +57,7 @@ public class EnsemblGeneTest @BeforeClass(alwaysRun = true) public void setUp() { + Cache.loadProperties("test/jalview/io/testProps.jvprops"); SequenceOntologyFactory.setInstance(new SequenceOntologyLite()); } @@ -75,18 +80,10 @@ 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 +112,10 @@ 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); @@ -159,30 +148,30 @@ 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); // id matching should not be case-sensitive - sf3.setValue("Parent", "gene:" + geneId.toLowerCase()); - sf3.setValue("transcript_id", "transcript3"); + sf3.setValue("Parent", geneId.toLowerCase(Locale.ROOT)); + 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(); @@ -209,24 +198,24 @@ 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); @@ -238,56 +227,70 @@ 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)); - - // test is not case-sensitive - assertTrue(testee.identifiesSequence(sf, accId.toLowerCase())); + 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)); } /** * Check behaviour of feature colour scheme for EnsemblGene sequences. - * Currently coded to display exon and sequence_variant (or sub-types) only, - * with sequence_variant in red above exon coloured by label. + * Currently coded to hide all except exon and sequence_variant (or sub-types) + * only, with sequence_variant in red above exon coloured by label. */ @Test(groups = "Functional") public void testGetFeatureColourScheme() { FeatureSettingsModelI fc = new EnsemblGene().getFeatureColourScheme(); - assertTrue(fc.isFeatureDisplayed("exon")); - assertTrue(fc.isFeatureDisplayed("coding_exon")); // subtype of exon - assertTrue(fc.isFeatureDisplayed("sequence_variant")); - assertTrue(fc.isFeatureDisplayed("feature_variant")); // subtype - assertFalse(fc.isFeatureDisplayed("transcript")); + assertFalse(fc.isFeatureDisplayed("exon")); + assertFalse(fc.isFeatureHidden("exon")); + assertFalse(fc.isFeatureDisplayed("coding_exon")); // subtype of exon + assertFalse(fc.isFeatureHidden("coding_exon")); // subtype of exon + assertFalse(fc.isFeatureDisplayed("sequence_variant")); + assertFalse(fc.isFeatureHidden("sequence_variant")); + assertFalse(fc.isFeatureDisplayed("feature_variant")); // subtype + assertFalse(fc.isFeatureHidden("feature_variant")); // subtype + assertTrue(fc.isFeatureHidden("transcript")); + assertTrue(fc.isFeatureHidden("CDS")); + assertEquals(Color.RED, fc.getFeatureColour("sequence_variant") .getColour()); assertEquals(Color.RED, fc.getFeatureColour("feature_variant")