X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FFeaturesFileTest.java;h=77c18dbd054cf19f2367ca9f241026d6bac8a854;hb=3c8a25936a2d805e7e3d7ab82f83b13135406d18;hp=d65f9dfac3914d91349c78a049d1c284abface45;hpb=0b1c761dfaa8242f122cf868e8897a06ec6eb727;p=jalview.git diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java index d65f9df..77c18db 100644 --- a/test/jalview/io/FeaturesFileTest.java +++ b/test/jalview/io/FeaturesFileTest.java @@ -21,58 +21,69 @@ 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.structure.StructureSelectionManager; +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 String simpleGffFile = "examples/testdata/simpleGff3.gff"; - static String TestFiles[][] = { { "Test example features import/export", - "examples/uniref50.fa", "examples/exampleFeatures.txt" } }; - - @Test(groups = { "Functional" }) - public void testParse() throws Exception + @AfterClass(alwaysRun = true) + public void tearDownAfterClass() { - testFeaturesFileIO("Features file test"); + /* + * remove any sequence mappings created so they don't pollute other tests + */ + StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + ssm.resetAll(); } - public static AlignmentI readAlignmentFile(File f) throws IOException + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() { - System.out.println("Reading file: " + f); - String ff = f.getPath(); - FormatAdapter rf = new FormatAdapter(); - - AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE, - new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE)); - - al.setDataset(null); // creates dataset sequences - assertNotNull("Couldn't read supplied alignment data.", al); - return al; + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); } - /** - * Helper method for testing - * - * @param testname - * @param f - * alignment file - * @param featFile - * features file to load on to the alignment - * @throws IOException - */ - public static void testFeaturesFileIO(String testname) throws IOException + @Test(groups = { "Functional" }) + public void testParse() throws Exception { File f = new File("examples/uniref50.fa"); AlignmentI al = readAlignmentFile(f); @@ -80,8 +91,9 @@ public class FeaturesFileTest Map colours = af.getFeatureRenderer() .getFeatureColours(); FeaturesFile featuresFile = new FeaturesFile( - "examples/exampleFeatures.txt", FormatAdapter.FILE); - assertTrue("Test " + testname + "\nFailed to parse features file.", + "examples/exampleFeatures.txt", DataSourceType.FILE); + assertTrue("Test " + "Features file test" + + "\nFailed to parse features file.", featuresFile.parse(al.getDataset(), colours, true)); /* @@ -89,65 +101,802 @@ public class FeaturesFileTest * updated - JAL-1904), and verify (some) feature group colours */ colours = af.getFeatureRenderer().getFeatureColours(); - assertEquals("26 feature group colours not found", 26, colours.size()); + 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 */ - SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence() + List sfs = al.getSequenceAt(0).getDatasetSequence() .getSequenceFeatures(); // FER_CAPAA - assertEquals(7, sfs.length); - SequenceFeature sf = sfs[0]; + 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[1]; + + 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[2]; + + 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[3]; + + 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[4]; - assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%", - sf.description); - assertEquals("Pfam 8_8|http://pfam.sanger.ac.uk/family/PF00111", - sf.links.get(0).toString()); - assertEquals(8, sf.begin); - assertEquals(83, sf.end); - assertEquals("uniprot", sf.featureGroup); - assertEquals("Pfam", sf.type); - sf = sfs[5]; - 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[6]; + + 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).toString()); + 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, 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(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(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(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(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(gffHeader, exported); + exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, + true); + assertEquals(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(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(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, 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, 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(expected, exported); + } + + /** + * 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(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(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(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(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(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(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, 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(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(expected, exported); + } }