X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblGeneTest.java;h=4a6036fe1ce2c183e1ff315cb6a8cb828666feb2;hb=5504c1347eb582d05ae9086608223209ecb8c13d;hp=446b4f766e463fad94af2b56ef1e932948c8e25a;hpb=a4f2a7f356b8edab17a9a5bb6f2e71a1419792a9;p=jalview.git diff --git a/test/jalview/ext/ensembl/EnsemblGeneTest.java b/test/jalview/ext/ensembl/EnsemblGeneTest.java index 446b4f7..4a6036f 100644 --- a/test/jalview/ext/ensembl/EnsemblGeneTest.java +++ b/test/jalview/ext/ensembl/EnsemblGeneTest.java @@ -20,6 +20,8 @@ */ 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; @@ -81,7 +83,7 @@ public class EnsemblGeneTest // gene at (start + 10500) length 101 SequenceFeature sf = new SequenceFeature("gene", "", 10500, 10600, 0f, null); - sf.setValue("ID", "gene:" + geneId); + sf.setValue("id", geneId); sf.setStrand("+"); genomic.addSequenceFeature(sf); @@ -113,7 +115,7 @@ public class EnsemblGeneTest // gene at (start + 10500) length 101 SequenceFeature sf = new SequenceFeature("gene", "", 10500, 10600, 0f, null); - sf.setValue("ID", "gene:" + geneId); + sf.setValue("id", geneId); sf.setStrand("+"); genomic.addSequenceFeature(sf); @@ -146,30 +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"); + SequenceFeature sf2 = new SequenceFeature("snRNA", "", 21000, 21500, 0f, + null); + 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"); + SequenceFeature sf4 = new SequenceFeature("snRNA", "", 23000, 23500, 0f, + null); + sf4.setValue("Parent", "XYZ"); + sf4.setValue("id", "transcript4"); genomic.addSequenceFeature(sf4); EnsemblGene testee = new EnsemblGene(); @@ -196,24 +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 = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500, 0f, + null); + 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); @@ -235,30 +237,32 @@ public class EnsemblGeneTest seq.addSequenceFeature(sf1); // gene with wrong ID not valid - SequenceFeature sf2 = new SequenceFeature("gene", "", 1, 2, 0f, null); - sf2.setValue("ID", "gene:XYZ"); + SequenceFeature sf2 = new SequenceFeature("gene", "a", 1, 2, 0f, null); + sf2.setValue("id", "XYZ"); seq.addSequenceFeature(sf2); // gene with right ID is valid - SequenceFeature sf3 = new SequenceFeature("gene", "", 1, 2, 0f, null); - sf3.setValue("ID", "gene:" + 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 - SequenceFeature sf4 = new SequenceFeature("snRNA_gene", "", 1, 2, 0f, null); - sf4.setValue("ID", "gene:" + accId); + SequenceFeature sf4 = new SequenceFeature("snRNA_gene", "", 1, 2, 0f, + null); + sf4.setValue("id", accId); seq.addSequenceFeature(sf4); // transcript not valid: - SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f, null); - sf5.setValue("ID", "gene:" + accId); + SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f, + null); + sf5.setValue("id", accId); seq.addSequenceFeature(sf5); // exon not valid: SequenceFeature sf6 = new SequenceFeature("exon", "", 1, 2, 0f, null); - sf6.setValue("ID", "gene:" + accId); + sf6.setValue("id", accId); seq.addSequenceFeature(sf6); - + List sfs = new EnsemblGene() .getIdentifyingFeatures(seq, accId); assertFalse(sfs.contains(sf1)); @@ -271,22 +275,28 @@ public class EnsemblGeneTest /** * 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")); - assertEquals(Color.RED, fc.getFeatureColour("sequence_variant") - .getColour()); - assertEquals(Color.RED, fc.getFeatureColour("feature_variant") - .getColour()); + 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").getColour()); assertTrue(fc.getFeatureColour("exon").isColourByLabel()); assertTrue(fc.getFeatureColour("coding_exon").isColourByLabel()); assertEquals(1, fc.compare("sequence_variant", "exon")); @@ -309,7 +319,6 @@ public class EnsemblGeneTest String ids = "ENSG00000158828 ENST00000321556 P30419 ENST00000592782 BRAF"; EnsemblGene testee = new EnsemblGene(); List geneIds = testee.getGeneIds(ids); - assertEquals(8, geneIds.size()); assertTrue(geneIds.contains("ENSG00000158828")); assertTrue(geneIds.contains("ENSG00000136448")); assertTrue(geneIds.contains("ENSG00000157764")); // BRAF human @@ -318,5 +327,7 @@ public class EnsemblGeneTest assertTrue(geneIds.contains("ENSXETG00000004845")); // xenopus assertTrue(geneIds.contains("ENSDARG00000017661")); // zebrafish assertTrue(geneIds.contains("ENSGALG00000012865")); // chicken + assertEquals(8, geneIds.size()); + } }