X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FFeaturesFileTest.java;fp=test%2Fjalview%2Fio%2FFeaturesFileTest.java;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=04ddeb08802d9260daeb950247cfdbfc84b12388;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java deleted file mode 100644 index 04ddeb0..0000000 --- a/test/jalview/io/FeaturesFileTest.java +++ /dev/null @@ -1,924 +0,0 @@ -/* - * 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.io; - -import static org.testng.AssertJUnit.assertEquals; -import static org.testng.AssertJUnit.assertFalse; -import static org.testng.AssertJUnit.assertNotNull; -import static org.testng.AssertJUnit.assertSame; -import static org.testng.AssertJUnit.assertTrue; -import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals; - -import jalview.api.FeatureColourI; -import jalview.api.FeatureRenderer; -import jalview.datamodel.Alignment; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.SequenceDummy; -import jalview.datamodel.SequenceFeature; -import jalview.datamodel.SequenceI; -import jalview.datamodel.features.FeatureMatcher; -import jalview.datamodel.features.FeatureMatcherI; -import jalview.datamodel.features.FeatureMatcherSet; -import jalview.datamodel.features.FeatureMatcherSetI; -import jalview.datamodel.features.SequenceFeatures; -import jalview.gui.AlignFrame; -import jalview.gui.Desktop; -import jalview.gui.JvOptionPane; -import jalview.schemes.FeatureColour; -import jalview.util.matcher.Condition; -import jalview.viewmodel.seqfeatures.FeatureRendererModel; -import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean; - -import java.awt.Color; -import java.io.File; -import java.io.IOException; -import java.util.HashMap; -import java.util.Iterator; -import java.util.List; -import java.util.Map; - -import org.testng.annotations.AfterClass; -import org.testng.annotations.BeforeClass; -import org.testng.annotations.Test; - -public class FeaturesFileTest -{ - private static final String LINE_SEPARATOR = System.getProperty("line.separator"); - private static String simpleGffFile = "examples/testdata/simpleGff3.gff"; - - @AfterClass(alwaysRun = true) - public void tearDownAfterClass() - { - /* - * remove any sequence mappings created so they don't pollute other tests - */ - Desktop.getStructureSelectionManager().resetAll(); - } - - @BeforeClass(alwaysRun = true) - public void setUpJvOptionPane() - { - JvOptionPane.setInteractiveMode(false); - JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); - } - - @Test(groups = { "Functional" }) - public void testParse() throws Exception - { - File f = new File("examples/uniref50.fa"); - AlignmentI al = readAlignmentFile(f); - AlignFrame af = new AlignFrame(al, 500, 500); - Map colours = af.getFeatureRenderer() - .getFeatureColours(); - FeaturesFile featuresFile = new FeaturesFile( - "examples/exampleFeatures.txt", DataSourceType.FILE); - assertTrue("Test " + "Features file test" - + "\nFailed to parse features file.", - featuresFile.parse(al.getDataset(), colours, true)); - - /* - * Refetch the colour map from the FeatureRenderer (to confirm it has been - * updated - JAL-1904), and verify (some) feature group colours - */ - colours = af.getFeatureRenderer().getFeatureColours(); - assertEquals("27 feature group colours not found", 27, colours.size()); - assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1)); - assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb)); - FeatureColourI kdColour = colours.get("kdHydrophobicity"); - assertTrue(kdColour.isGraduatedColour()); - assertTrue(kdColour.isAboveThreshold()); - assertEquals(-2f, kdColour.getThreshold()); - - /* - * verify (some) features on sequences - */ - List sfs = al.getSequenceAt(0).getDatasetSequence() - .getSequenceFeatures(); // FER_CAPAA - SequenceFeatures.sortFeatures(sfs, true); - assertEquals(8, sfs.size()); - - /* - * verify (in ascending start position order) - */ - SequenceFeature sf = sfs.get(0); - assertEquals("Pfam family%LINK%", sf.description); - assertEquals(0, sf.begin); - assertEquals(0, sf.end); - assertEquals("uniprot", sf.featureGroup); - assertEquals("Pfam", sf.type); - assertEquals(1, sf.links.size()); - assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111", - sf.links.get(0)); - - sf = sfs.get(1); - assertEquals("Ferredoxin_fold Status: True Positive ", sf.description); - assertEquals(3, sf.begin); - assertEquals(93, sf.end); - assertEquals("uniprot", sf.featureGroup); - assertEquals("Cath", sf.type); - - sf = sfs.get(2); - assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%", - sf.description); - assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111", - sf.links.get(0)); - assertEquals(8, sf.begin); - assertEquals(83, sf.end); - assertEquals("uniprot", sf.featureGroup); - assertEquals("Pfam", sf.type); - - sf = sfs.get(3); - assertEquals("Iron-sulfur (2Fe-2S)", sf.description); - assertEquals(39, sf.begin); - assertEquals(39, sf.end); - assertEquals("uniprot", sf.featureGroup); - assertEquals("METAL", sf.type); - - sf = sfs.get(4); - assertEquals("Iron-sulfur (2Fe-2S)", sf.description); - assertEquals(44, sf.begin); - assertEquals(44, sf.end); - assertEquals("uniprot", sf.featureGroup); - assertEquals("METAL", sf.type); - - sf = sfs.get(5); - assertEquals("Iron-sulfur (2Fe-2S)", sf.description); - assertEquals(47, sf.begin); - assertEquals(47, sf.end); - assertEquals("uniprot", sf.featureGroup); - assertEquals("METAL", sf.type); - - sf = sfs.get(6); - assertEquals("Iron-sulfur (2Fe-2S)", sf.description); - assertEquals(77, sf.begin); - assertEquals(77, sf.end); - assertEquals("uniprot", sf.featureGroup); - assertEquals("METAL", sf.type); - - sf = sfs.get(7); - assertEquals( - "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%", - sf.description); - assertEquals( - "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&service=NetPhos-2.0", - sf.links.get(0)); - assertEquals(89, sf.begin); - assertEquals(89, sf.end); - assertEquals("netphos", sf.featureGroup); - assertEquals("PHOSPHORYLATION (T)", sf.type); - } - - /** - * Test parsing a features file with a mix of Jalview and GFF formatted - * content - * - * @throws Exception - */ - @Test(groups = { "Functional" }) - public void testParse_mixedJalviewGff() throws Exception - { - File f = new File("examples/uniref50.fa"); - AlignmentI al = readAlignmentFile(f); - AlignFrame af = new AlignFrame(al, 500, 500); - Map colours = af.getFeatureRenderer() - .getFeatureColours(); - // GFF2 uses space as name/value separator in column 9 - String gffData = "METAL\tcc9900\n" - + "GFF\n" - + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n" - + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t."; - FeaturesFile featuresFile = new FeaturesFile(gffData, - DataSourceType.PASTE); - assertTrue("Failed to parse features file", - featuresFile.parse(al.getDataset(), colours, true)); - - // verify colours read or synthesized - colours = af.getFeatureRenderer().getFeatureColours(); - assertEquals("1 feature group colours not found", 1, colours.size()); - assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900)); - - // verify feature on FER_CAPAA - List sfs = al.getSequenceAt(0).getDatasetSequence() - .getSequenceFeatures(); - assertEquals(1, sfs.size()); - SequenceFeature sf = sfs.get(0); - assertEquals("Iron-sulfur,2Fe-2S", sf.description); - assertEquals(44, sf.begin); - assertEquals(45, sf.end); - assertEquals("uniprot", sf.featureGroup); - assertEquals("METAL", sf.type); - assertEquals(4f, sf.getScore(), 0.001f); - - // verify feature on FER1_SOLLC - sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures(); - assertEquals(1, sfs.size()); - sf = sfs.get(0); - assertEquals("uniprot", sf.description); - assertEquals(55, sf.begin); - assertEquals(130, sf.end); - assertEquals("uniprot", sf.featureGroup); - assertEquals("Pfam", sf.type); - assertEquals(2f, sf.getScore(), 0.001f); - } - - public static AlignmentI readAlignmentFile(File f) throws IOException - { - System.out.println("Reading file: " + f); - String ff = f.getPath(); - FormatAdapter rf = new FormatAdapter(); - - AlignmentI al = rf.readFile(ff, DataSourceType.FILE, - new IdentifyFile().identify(ff, DataSourceType.FILE)); - - al.setDataset(null); // creates dataset sequences - assertNotNull("Couldn't read supplied alignment data.", al); - return al; - } - - /** - * Test parsing a features file with GFF formatted content only - * - * @throws Exception - */ - @Test(groups = { "Functional" }) - public void testParse_pureGff3() throws Exception - { - File f = new File("examples/uniref50.fa"); - AlignmentI al = readAlignmentFile(f); - AlignFrame af = new AlignFrame(al, 500, 500); - Map colours = af.getFeatureRenderer() - .getFeatureColours(); - // GFF3 uses '=' separator for name/value pairs in colum 9 - String gffData = "##gff-version 3\n" - + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t" - + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465\n" - + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23"; - FeaturesFile featuresFile = new FeaturesFile(gffData, - DataSourceType.PASTE); - assertTrue("Failed to parse features file", - featuresFile.parse(al.getDataset(), colours, true)); - - // verify feature on FER_CAPAA - List sfs = al.getSequenceAt(0).getDatasetSequence() - .getSequenceFeatures(); - assertEquals(1, sfs.size()); - SequenceFeature sf = sfs.get(0); - // description parsed from Note attribute - assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description); - assertEquals(39, sf.begin); - assertEquals(39, sf.end); - assertEquals("uniprot", sf.featureGroup); - assertEquals("METAL", sf.type); - assertEquals( - "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465", - sf.getValue("ATTRIBUTES")); - - // verify feature on FER1_SOLLC1 - sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures(); - assertEquals(1, sfs.size()); - sf = sfs.get(0); - // ID used for description if available - assertEquals("$23", sf.description); - assertEquals(55, sf.begin); - assertEquals(130, sf.end); - assertEquals("uniprot", sf.featureGroup); - assertEquals("Pfam", sf.type); - assertEquals(3f, sf.getScore(), 0.001f); - } - - /** - * Test parsing a features file with Jalview format features (but no colour - * descriptors or startgroup to give the hint not to parse as GFF) - * - * @throws Exception - */ - @Test(groups = { "Functional" }) - public void testParse_jalviewFeaturesOnly() throws Exception - { - File f = new File("examples/uniref50.fa"); - AlignmentI al = readAlignmentFile(f); - AlignFrame af = new AlignFrame(al, 500, 500); - Map colours = af.getFeatureRenderer() - .getFeatureColours(); - - /* - * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC - */ - String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n" - + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n"; - FeaturesFile featuresFile = new FeaturesFile(featureData, - DataSourceType.PASTE); - assertTrue("Failed to parse features file", - featuresFile.parse(al.getDataset(), colours, true)); - - // verify FER_CAPAA feature - List sfs = al.getSequenceAt(0).getDatasetSequence() - .getSequenceFeatures(); - assertEquals(1, sfs.size()); - SequenceFeature sf = sfs.get(0); - assertEquals("Iron-sulfur (2Fe-2S)", sf.description); - assertEquals(39, sf.begin); - assertEquals(39, sf.end); - assertEquals("METAL", sf.type); - - // verify FER1_SOLLC feature - sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures(); - assertEquals(1, sfs.size()); - sf = sfs.get(0); - assertEquals("Iron-phosphorus (2Fe-P)", sf.description); - assertEquals(86, sf.begin); - assertEquals(87, sf.end); - assertEquals("METALLIC", sf.type); - } - - private void checkDatasetfromSimpleGff3(AlignmentI dataset) - { - assertEquals("no sequences extracted from GFF3 file", 2, - dataset.getHeight()); - - SequenceI seq1 = dataset.findName("seq1"); - SequenceI seq2 = dataset.findName("seq2"); - assertNotNull(seq1); - assertNotNull(seq2); - assertFalse( - "Failed to replace dummy seq1 with real sequence", - seq1 instanceof SequenceDummy - && ((SequenceDummy) seq1).isDummy()); - assertFalse( - "Failed to replace dummy seq2 with real sequence", - seq2 instanceof SequenceDummy - && ((SequenceDummy) seq2).isDummy()); - String placeholderseq = new SequenceDummy("foo").getSequenceAsString(); - assertFalse("dummy replacement buggy for seq1", - placeholderseq.equals(seq1.getSequenceAsString())); - assertFalse("dummy replacement buggy for seq2", - placeholderseq.equals(seq2.getSequenceAsString())); - assertNotNull("No features added to seq1", seq1.getSequenceFeatures()); - assertEquals("Wrong number of features", 3, seq1.getSequenceFeatures() - .size()); - assertTrue(seq2.getSequenceFeatures().isEmpty()); - assertEquals( - "Wrong number of features", - 0, - seq2.getSequenceFeatures() == null ? 0 : seq2 - .getSequenceFeatures().size()); - assertTrue( - "Expected at least one CDNA/Protein mapping for seq1", - dataset.getCodonFrame(seq1) != null - && dataset.getCodonFrame(seq1).size() > 0); - - } - - @Test(groups = { "Functional" }) - public void readGff3File() throws IOException - { - FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile, - DataSourceType.FILE); - Alignment dataset = new Alignment(gffreader.getSeqsAsArray()); - gffreader.addProperties(dataset); - checkDatasetfromSimpleGff3(dataset); - } - - @Test(groups = { "Functional" }) - public void simpleGff3FileClass() throws IOException - { - AlignmentI dataset = new Alignment(new SequenceI[] {}); - FeaturesFile ffile = new FeaturesFile(simpleGffFile, - DataSourceType.FILE); - - boolean parseResult = ffile.parse(dataset, null, false, false); - assertTrue("return result should be true", parseResult); - checkDatasetfromSimpleGff3(dataset); - } - - @Test(groups = { "Functional" }) - public void simpleGff3FileLoader() throws IOException - { - AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded( - simpleGffFile, DataSourceType.FILE); - assertTrue( - "Didn't read the alignment into an alignframe from Gff3 File", - af != null); - checkDatasetfromSimpleGff3(af.getViewport().getAlignment()); - } - - @Test(groups = { "Functional" }) - public void simpleGff3RelaxedIdMatching() throws IOException - { - AlignmentI dataset = new Alignment(new SequenceI[] {}); - FeaturesFile ffile = new FeaturesFile(simpleGffFile, - DataSourceType.FILE); - - boolean parseResult = ffile.parse(dataset, null, false, true); - assertTrue("return result (relaxedID matching) should be true", - parseResult); - checkDatasetfromSimpleGff3(dataset); - } - - @Test(groups = { "Functional" }) - public void testPrintJalviewFormat() throws Exception - { - File f = new File("examples/uniref50.fa"); - AlignmentI al = readAlignmentFile(f); - AlignFrame af = new AlignFrame(al, 500, 500); - Map colours = af.getFeatureRenderer() - .getFeatureColours(); - String features = "METAL\tcc9900\n" - + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n" - + "Pfam\tred\n" - + "STARTGROUP\tuniprot\n" - + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\n" // non-positional feature - + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n" - + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n" - + "Pfam domainPfam_3_4\tFER_CAPAA\t-1\t20\t20\tPfam\n" - + "ENDGROUP\tuniprot\n"; - FeaturesFile featuresFile = new FeaturesFile(features, - DataSourceType.PASTE); - featuresFile.parse(al.getDataset(), colours, false); - - /* - * add positional and non-positional features with null and - * empty feature group to check handled correctly - */ - SequenceI seq = al.getSequenceAt(1); // FER_CAPAN - seq.addSequenceFeature(new SequenceFeature("Pfam", "desc1", 0, 0, 1.3f, - null)); - seq.addSequenceFeature(new SequenceFeature("Pfam", "desc2", 4, 9, - Float.NaN, null)); - seq = al.getSequenceAt(2); // FER1_SOLLC - seq.addSequenceFeature(new SequenceFeature("Pfam", "desc3", 0, 0, - Float.NaN, "")); - seq.addSequenceFeature(new SequenceFeature("Pfam", "desc4", 5, 8, - -2.6f, "")); - - /* - * first with no features displayed, exclude non-positional features - */ - FeatureRenderer fr = af.alignPanel.getFeatureRenderer(); - String exported = featuresFile - .printJalviewFormat(al.getSequencesArray(), fr, false); - String expected = "No Features Visible"; - assertEquals(expected, exported); - - /* - * include non-positional features, but still no positional features - */ - fr.setGroupVisibility("uniprot", true); - exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, - true); - expected = "\nSTARTGROUP\tuniprot\n" - + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n" - + "ENDGROUP\tuniprot\n\n" - + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n\n" - + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"; // NaN is not output - assertEquals( - expected.replace("\n", LINE_SEPARATOR), - exported); - - /* - * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam - */ - fr.setVisible("METAL"); - fr.setVisible("GAMMA-TURN"); - exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, - false); - expected = "METAL\tcc9900\n" - + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n" - + "\nSTARTGROUP\tuniprot\n" - + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n" - + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n" - + "ENDGROUP\tuniprot\n"; - assertEquals(fixLineEnd(expected), exported); - - /* - * now set Pfam visible - */ - fr.setVisible("Pfam"); - exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, - false); - /* - * features are output within group, ordered by sequence and type - */ - expected = "METAL\tcc9900\n" - + "Pfam\tff0000\n" - + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n" - + "\nSTARTGROUP\tuniprot\n" - + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n" - + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n" - + "Pfam domainPfam_3_4\tFER_CAPAA\t-1\t20\t20\tPfam\t0.0\n" - + "ENDGROUP\tuniprot\n" - // null / empty group features are output after named groups - + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n" - + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n"; - assertEquals(fixLineEnd(expected), exported); - - /* - * hide uniprot group - */ - fr.setGroupVisibility("uniprot", false); - expected = "METAL\tcc9900\n" + "Pfam\tff0000\n" - + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n" - + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n" - + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n"; - exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, - false); - assertEquals(fixLineEnd(expected), exported); - - /* - * include non-positional (overrides group not shown) - */ - exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, - true); - expected = "METAL\tcc9900\n" + "Pfam\tff0000\n" - + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n" - + "\nSTARTGROUP\tuniprot\n" - + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n" - + "ENDGROUP\tuniprot\n" - + "\ndesc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n" - + "desc2\tFER_CAPAN\t-1\t4\t9\tPfam\n" - + "\ndesc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n" - + "desc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n"; - assertEquals(fixLineEnd(expected), exported); - } - - @Test(groups = { "Functional" }) - public void testPrintGffFormat() throws Exception - { - File f = new File("examples/uniref50.fa"); - AlignmentI al = readAlignmentFile(f); - AlignFrame af = new AlignFrame(al, 500, 500); - - /* - * no features - */ - FeaturesFile featuresFile = new FeaturesFile(); - FeatureRendererModel fr = (FeatureRendererModel) af.alignPanel - .getFeatureRenderer(); - String exported = featuresFile.printGffFormat(al.getSequencesArray(), - fr, false); - String gffHeader = "##gff-version 2\n"; - assertEquals( - fixLineEnd(gffHeader), - exported); - exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, - true); - assertEquals( - fixLineEnd(gffHeader), - exported); - - /* - * add some features - */ - al.getSequenceAt(0).addSequenceFeature( - new SequenceFeature("Domain", "Cath", 0, 0, 0f, "Uniprot")); - al.getSequenceAt(0).addSequenceFeature( - new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, null)); - al.getSequenceAt(1) - .addSequenceFeature( - new SequenceFeature("GAMMA-TURN", "Turn", 36, 38, 2.1f, - "s3dm")); - SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f, - "Uniprot"); - sf.setAttributes("x=y;black=white"); - sf.setStrand("+"); - sf.setPhase("2"); - al.getSequenceAt(1).addSequenceFeature(sf); - - /* - * 'discover' features then hide all feature types - */ - fr.findAllFeatures(true); - FeatureSettingsBean[] data = new FeatureSettingsBean[4]; - FeatureColourI fc = new FeatureColour(Color.PINK); - data[0] = new FeatureSettingsBean("Domain", fc, null, false); - data[1] = new FeatureSettingsBean("METAL", fc, null, false); - data[2] = new FeatureSettingsBean("GAMMA-TURN", fc, null, false); - data[3] = new FeatureSettingsBean("Pfam", fc, null, false); - fr.setFeaturePriority(data); - - /* - * with no features displayed, exclude non-positional features - */ - exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, - false); - assertEquals( - fixLineEnd(gffHeader), - exported); - - /* - * include non-positional features - */ - fr.setGroupVisibility("Uniprot", true); - fr.setGroupVisibility("s3dm", false); - exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, - true); - String expected = gffHeader - + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n"; - assertEquals( - fixLineEnd(expected), - exported); - - /* - * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam - * only Uniprot group visible here... - */ - fr.setVisible("METAL"); - fr.setVisible("GAMMA-TURN"); - exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, - false); - // METAL feature has null group: description used for column 2 - expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"; - assertEquals( - expected.replace("\n", LINE_SEPARATOR), - exported); - - /* - * set s3dm group visible - */ - fr.setGroupVisibility("s3dm", true); - exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, - false); - // METAL feature has null group: description used for column 2 - expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n" - + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n"; - assertEquals( - expected.replace("\n", LINE_SEPARATOR), - exported); - - /* - * now set Pfam visible - */ - fr.setVisible("Pfam"); - exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, - false); - // Pfam feature columns include strand(+), phase(2), attributes - expected = gffHeader - + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n" - + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n" - + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n"; - assertEquals(fixLineEnd(expected), exported); - } - - private String fixLineEnd(String s) - { - return s.replace("\n", LINE_SEPARATOR); - } - - /** - * Test for parsing of feature filters as represented in a Jalview features - * file - * - * @throws Exception - */ - @Test(groups = { "Functional" }) - public void testParseFilters() throws Exception - { - Map filters = new HashMap<>(); - String text = "sequence_variant\tCSQ:PolyPhen NotContains 'damaging'\n" - + "missense_variant\t(label contains foobar) and (Score lt 1.3)"; - FeaturesFile featuresFile = new FeaturesFile(text, - DataSourceType.PASTE); - featuresFile.parseFilters(filters); - assertEquals(filters.size(), 2); - - FeatureMatcherSetI fm = filters.get("sequence_variant"); - assertNotNull(fm); - Iterator matchers = fm.getMatchers().iterator(); - FeatureMatcherI matcher = matchers.next(); - assertFalse(matchers.hasNext()); - String[] attributes = matcher.getAttribute(); - assertArrayEquals(attributes, new String[] { "CSQ", "PolyPhen" }); - assertSame(matcher.getMatcher().getCondition(), Condition.NotContains); - assertEquals(matcher.getMatcher().getPattern(), "damaging"); - - fm = filters.get("missense_variant"); - assertNotNull(fm); - matchers = fm.getMatchers().iterator(); - matcher = matchers.next(); - assertTrue(matcher.isByLabel()); - assertSame(matcher.getMatcher().getCondition(), Condition.Contains); - assertEquals(matcher.getMatcher().getPattern(), "foobar"); - matcher = matchers.next(); - assertTrue(matcher.isByScore()); - assertSame(matcher.getMatcher().getCondition(), Condition.LT); - assertEquals(matcher.getMatcher().getPattern(), "1.3"); - assertEquals(matcher.getMatcher().getFloatValue(), 1.3f); - - assertFalse(matchers.hasNext()); - } - - @Test(groups = { "Functional" }) - public void testOutputFeatureFilters() - { - FeaturesFile ff = new FeaturesFile(); - StringBuilder sb = new StringBuilder(); - Map visible = new HashMap<>(); - visible.put("pfam", new FeatureColour(Color.red)); - Map featureFilters = new HashMap<>(); - - // with no filters, nothing is output - ff.outputFeatureFilters(sb, visible, featureFilters); - assertEquals("", sb.toString()); - - // with filter for not visible features only, nothing is output - FeatureMatcherSet filter = new FeatureMatcherSet(); - filter.and(FeatureMatcher.byLabel(Condition.Present, null)); - featureFilters.put("foobar", filter); - ff.outputFeatureFilters(sb, visible, featureFilters); - assertEquals("", sb.toString()); - - // with filters for visible feature types - FeatureMatcherSet filter2 = new FeatureMatcherSet(); - filter2.and(FeatureMatcher.byAttribute(Condition.Present, null, "CSQ", - "PolyPhen")); - filter2.and(FeatureMatcher.byScore(Condition.LE, "-2.4")); - featureFilters.put("pfam", filter2); - visible.put("foobar", new FeatureColour(Color.blue)); - ff.outputFeatureFilters(sb, visible, featureFilters); - String expected = "\nSTARTFILTERS\nfoobar\tLabel Present\npfam\t(CSQ:PolyPhen Present) AND (Score LE -2.4)\nENDFILTERS\n"; - assertEquals(fixLineEnd(expected), sb.toString()); - } - - /** - * Output as GFF should not include features which are not visible due to - * colour threshold or feature filter settings - * - * @throws Exception - */ - @Test(groups = { "Functional" }) - public void testPrintGffFormat_withFilters() throws Exception - { - File f = new File("examples/uniref50.fa"); - AlignmentI al = readAlignmentFile(f); - AlignFrame af = new AlignFrame(al, 500, 500); - SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, - null); - sf1.setValue("clin_sig", "Likely Pathogenic"); - sf1.setValue("AF", "24"); - al.getSequenceAt(0).addSequenceFeature(sf1); - SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f, - null); - sf2.setValue("clin_sig", "Benign"); - sf2.setValue("AF", "46"); - al.getSequenceAt(0).addSequenceFeature(sf2); - - FeaturesFile featuresFile = new FeaturesFile(); - FeatureRenderer fr = af.alignPanel.getFeatureRenderer(); - final String gffHeader = "##gff-version 2\n"; - - fr.setVisible("METAL"); - fr.setColour("METAL", new FeatureColour(Color.PINK)); - String exported = featuresFile.printGffFormat(al.getSequencesArray(), - fr, false); - String expected = gffHeader - + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n" - + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n"; - assertEquals( - fixLineEnd(expected), exported); - - /* - * now threshold to Score > 1.1 - should exclude sf2 - */ - FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK, - Color.white, 0f, 2f); - fc.setAboveThreshold(true); - fc.setThreshold(1.1f); - fr.setColour("METAL", fc); - exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, - false); - expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"; - assertEquals(fixLineEnd(expected), exported); - - /* - * remove threshold and check sf2 is exported - */ - fc.setAboveThreshold(false); - exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, - false); - expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n" - + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n"; - assertEquals(fixLineEnd(expected), exported); - - /* - * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1 - */ - FeatureMatcherSetI filter = new FeatureMatcherSet(); - filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign", - "clin_sig")); - fr.setFeatureFilter("METAL", filter); - exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, - false); - expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n"; - assertEquals(fixLineEnd(expected), exported); - } - - /** - * Output as Jalview should not include features which are not visible due to - * colour threshold or feature filter settings - * - * @throws Exception - */ - @Test(groups = { "Functional" }) - public void testPrintJalviewFormat_withFilters() throws Exception - { - File f = new File("examples/uniref50.fa"); - AlignmentI al = readAlignmentFile(f); - AlignFrame af = new AlignFrame(al, 500, 500); - SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, - "grp1"); - sf1.setValue("clin_sig", "Likely Pathogenic"); - sf1.setValue("AF", "24"); - al.getSequenceAt(0).addSequenceFeature(sf1); - SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f, - "grp2"); - sf2.setValue("clin_sig", "Benign"); - sf2.setValue("AF", "46"); - al.getSequenceAt(0).addSequenceFeature(sf2); - - FeaturesFile featuresFile = new FeaturesFile(); - FeatureRenderer fr = af.alignPanel.getFeatureRenderer(); - fr.findAllFeatures(true); - - fr.setVisible("METAL"); - fr.setColour("METAL", new FeatureColour(Color.PINK)); - String exported = featuresFile.printJalviewFormat( - al.getSequencesArray(), - fr, false); - String expected = "METAL\tffafaf\n\nSTARTGROUP\tgrp1\n" - + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n" - + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n" - + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n" - + "ENDGROUP\tgrp2\n"; - assertEquals( - fixLineEnd(expected), - exported); - - /* - * now threshold to Score > 1.1 - should exclude sf2 - * (and there should be no empty STARTGROUP/ENDGROUP output) - */ - FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK, - Color.white, 0f, 2f); - fc.setAboveThreshold(true); - fc.setThreshold(1.1f); - fr.setColour("METAL", fc); - exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, - false); - expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|above|1.1\n\n" - + "STARTGROUP\tgrp1\n" - + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n" - + "ENDGROUP\tgrp1\n"; - assertEquals( - expected.replace("\n", LINE_SEPARATOR), - exported); - - /* - * remove threshold and check sf2 is exported - */ - fc.setAboveThreshold(false); - exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, - false); - expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n" - + "STARTGROUP\tgrp1\n" - + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n" - + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n" - + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n" - + "ENDGROUP\tgrp2\n"; - assertEquals(fixLineEnd(expected), exported); - - /* - * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1 - */ - FeatureMatcherSetI filter = new FeatureMatcherSet(); - filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign", - "clin_sig")); - fr.setFeatureFilter("METAL", filter); - exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, - false); - expected = "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n"; - expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n" - + "STARTFILTERS\nMETAL\tclin_sig Contains benign\nENDFILTERS\n\n" - + "STARTGROUP\tgrp2\n" - + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n" - + "ENDGROUP\tgrp2\n"; - assertEquals(fixLineEnd(expected), exported); - } -}