X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblGeneTest.java;h=2de08f582a98bd2a5d0cb44f8c56420116c08642;hb=ca74027f55fb1f8af9fef0d77348449a07a1b5d5;hp=1f1a84e3f1302eb691159d6ec666106d47b1e10d;hpb=e96f5e8ce137e879dd4b4f37fb5c4d134e2778e2;p=jalview.git diff --git a/test/jalview/ext/ensembl/EnsemblGeneTest.java b/test/jalview/ext/ensembl/EnsemblGeneTest.java index 1f1a84e..2de08f5 100644 --- a/test/jalview/ext/ensembl/EnsemblGeneTest.java +++ b/test/jalview/ext/ensembl/EnsemblGeneTest.java @@ -1,17 +1,43 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ 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.assertSame; 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; +import jalview.gui.JvOptionPane; import jalview.io.gff.SequenceOntologyFactory; import jalview.io.gff.SequenceOntologyLite; import jalview.util.MapList; +import java.awt.Color; import java.util.List; import org.testng.annotations.AfterClass; @@ -20,13 +46,22 @@ import org.testng.annotations.Test; public class EnsemblGeneTest { - @BeforeClass + + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + + @BeforeClass(alwaysRun = true) public void setUp() { + Cache.loadProperties("test/jalview/io/testProps.jvprops"); SequenceOntologyFactory.setInstance(new SequenceOntologyLite()); } - @AfterClass + @AfterClass(alwaysRun = true) public void tearDown() { SequenceOntologyFactory.setInstance(null); @@ -45,17 +80,10 @@ public class EnsemblGeneTest genomic.setEnd(50000); String geneId = "ABC123"; - // gene at (start+10000) length 501 - 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 - // should be ignored - the first 'gene' found defines the whole range - 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); @@ -63,13 +91,13 @@ public class EnsemblGeneTest 23); List fromRanges = ranges.getFromRanges(); assertEquals(1, fromRanges.size()); - assertEquals(20000, fromRanges.get(0)[0]); - assertEquals(20500, fromRanges.get(0)[1]); + assertEquals(10500, fromRanges.get(0)[0]); + assertEquals(10600, fromRanges.get(0)[1]); // to range should start from given start numbering List toRanges = ranges.getToRanges(); assertEquals(1, toRanges.size()); assertEquals(23, toRanges.get(0)[0]); - assertEquals(523, toRanges.get(0)[1]); + assertEquals(123, toRanges.get(0)[1]); } /** @@ -84,18 +112,10 @@ public class EnsemblGeneTest genomic.setEnd(50000); String geneId = "ABC123"; - // gene at (start+10000) length 501 - 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 - // should be ignored - the first 'gene' found defines the whole range - // (real data would only have one such feature) - 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); @@ -104,13 +124,13 @@ public class EnsemblGeneTest List fromRanges = ranges.getFromRanges(); assertEquals(1, fromRanges.size()); // from range on reverse strand: - assertEquals(20500, fromRanges.get(0)[0]); - assertEquals(20000, fromRanges.get(0)[1]); + assertEquals(10500, fromRanges.get(0)[0]); + assertEquals(10600, fromRanges.get(0)[1]); // to range should start from given start numbering List toRanges = ranges.getToRanges(); assertEquals(1, toRanges.size()); assertEquals(23, toRanges.get(0)[0]); - assertEquals(523, toRanges.get(0)[1]); + assertEquals(123, toRanges.get(0)[1]); } /** @@ -128,34 +148,43 @@ public class EnsemblGeneTest // transcript feature SequenceFeature sf1 = new SequenceFeature("transcript", "", 20000, 20500, 0f, null); - sf1.setValue("Parent", "gene:" + geneId); + sf1.setValue("Parent", geneId); + sf1.setValue("id", "transcript1"); genomic.addSequenceFeature(sf1); // transcript sub-type feature - SequenceFeature sf2 = new SequenceFeature("snRNA", "", 20000, - 20500, 0f, null); - sf2.setValue("Parent", "gene:" + geneId); + 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", "", - 20000, 20500, 0f, null); - sf3.setValue("Parent", "gene:" + geneId); + 22000, 22500, 0f, null); + // id matching should not be case-sensitive + 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", "", 20000, 20500, + SequenceFeature sf4 = new SequenceFeature("snRNA", "", 23000, 23500, 0f, null); - sf4.setValue("Parent", "gene:XYZ"); + sf4.setValue("Parent", "XYZ"); + sf4.setValue("id", "transcript4"); genomic.addSequenceFeature(sf4); EnsemblGene testee = new EnsemblGene(); + + /* + * with no filter + */ List features = testee.getTranscriptFeatures(geneId, genomic); assertEquals(3, features.size()); - assertSame(sf1, features.get(0)); - assertSame(sf2, features.get(1)); - assertSame(sf3, features.get(2)); + assertTrue(features.contains(sf1)); + assertTrue(features.contains(sf2)); + assertTrue(features.contains(sf3)); } /** @@ -167,27 +196,29 @@ public class EnsemblGeneTest { String geneId = "ABC123"; EnsemblGene testee = new EnsemblGene(); - SequenceFeature sf = new SequenceFeature("gene", "", 20000, - 20500, 0f, null); - sf.setValue("ID", "gene:" + geneId); + SequenceFeature sf = new SequenceFeature("gene", "", 20000, 20500, 0f, + null); + sf.setValue("id", geneId); assertFalse(testee.retainFeature(sf, geneId)); - sf.setType("transcript"); - sf.setValue("Parent", "gene:" + geneId); + sf = new SequenceFeature("transcript", "", 20000, 20500, 0f, null); + sf.setValue("Parent", geneId); assertTrue(testee.retainFeature(sf, geneId)); - sf.setType("mature_transcript"); - sf.setValue("Parent", "gene:" + geneId); + sf = new SequenceFeature("mature_transcript", "", 20000, 20500, 0f, + null); + sf.setValue("Parent", geneId); assertTrue(testee.retainFeature(sf, geneId)); - sf.setType("NMD_transcript_variant"); - 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.setType("anything"); + sf = new SequenceFeature("anything", "", 20000, 20500, 0f, null); assertTrue(testee.retainFeature(sf, geneId)); } @@ -196,33 +227,105 @@ 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.setType("snRNA_gene"); - 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.setType("transcript"); - 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.setType("exon"); - 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 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(); + 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")); + assertEquals(-1, fc.compare("exon", "sequence_variant")); + assertEquals(1, fc.compare("feature_variant", "coding_exon")); + 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 geneIds = testee.getGeneIds(ids); + 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 + assertEquals(8, geneIds.size()); + } }