X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FFeaturesFileTest.java;h=32ca8412fb61d7fb173f54f5cd48a3b900bdfa0a;hb=c9b3c9348544a95ee1fc8b28abf117f5d49cbb82;hp=56305dabe8c5567d0a6cdb85ec982dc81cb9624d;hpb=bf0d052fef43e9809b7170dbfd372b3ea116391b;p=jalview.git diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java index 56305da..32ca841 100644 --- a/test/jalview/io/FeaturesFileTest.java +++ b/test/jalview/io/FeaturesFileTest.java @@ -23,8 +23,9 @@ 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.assertNull; +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; @@ -33,20 +34,54 @@ 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 java.awt.Color; import java.io.File; import java.io.IOException; +import java.util.ArrayList; +import java.util.Arrays; +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"; + @AfterClass(alwaysRun = true) + public void tearDownAfterClass() + { + /* + * remove any sequence mappings created so they don't pollute other tests + */ + StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + ssm.resetAll(); + } + + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + @Test(groups = { "Functional" }) public void testParse() throws Exception { @@ -56,7 +91,7 @@ public class FeaturesFileTest Map colours = af.getFeatureRenderer() .getFeatureColours(); FeaturesFile featuresFile = new FeaturesFile( - "examples/exampleFeatures.txt", FormatAdapter.FILE); + "examples/exampleFeatures.txt", DataSourceType.FILE); assertTrue("Test " + "Features file test" + "\nFailed to parse features file.", featuresFile.parse(al.getDataset(), colours, true)); @@ -66,62 +101,87 @@ 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); @@ -143,11 +203,12 @@ public class FeaturesFileTest Map colours = af.getFeatureRenderer() .getFeatureColours(); // GFF2 uses space as name/value separator in column 9 - String gffData = "METAL\tcc9900\n" + "GFF\n" + 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, - FormatAdapter.PASTE); + DataSourceType.PASTE); assertTrue("Failed to parse features file", featuresFile.parse(al.getDataset(), colours, true)); @@ -157,10 +218,10 @@ public class FeaturesFileTest assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900)); // verify feature on FER_CAPAA - SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence() + List sfs = al.getSequenceAt(0).getDatasetSequence() .getSequenceFeatures(); - assertEquals(1, sfs.length); - SequenceFeature sf = sfs[0]; + assertEquals(1, sfs.size()); + SequenceFeature sf = sfs.get(0); assertEquals("Iron-sulfur,2Fe-2S", sf.description); assertEquals(44, sf.begin); assertEquals(45, sf.end); @@ -170,8 +231,8 @@ public class FeaturesFileTest // verify feature on FER1_SOLLC sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures(); - assertEquals(1, sfs.length); - sf = sfs[0]; + assertEquals(1, sfs.size()); + sf = sfs.get(0); assertEquals("uniprot", sf.description); assertEquals(55, sf.begin); assertEquals(130, sf.end); @@ -186,8 +247,8 @@ public class FeaturesFileTest String ff = f.getPath(); FormatAdapter rf = new FormatAdapter(); - AlignmentI al = rf.readFile(ff, FormatAdapter.FILE, - new IdentifyFile().identify(ff, FormatAdapter.FILE)); + 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); @@ -213,15 +274,15 @@ public class FeaturesFileTest + "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, - FormatAdapter.PASTE); + DataSourceType.PASTE); assertTrue("Failed to parse features file", featuresFile.parse(al.getDataset(), colours, true)); // verify feature on FER_CAPAA - SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence() + List sfs = al.getSequenceAt(0).getDatasetSequence() .getSequenceFeatures(); - assertEquals(1, sfs.length); - SequenceFeature sf = sfs[0]; + 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); @@ -234,8 +295,8 @@ public class FeaturesFileTest // verify feature on FER1_SOLLC1 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures(); - assertEquals(1, sfs.length); - sf = sfs[0]; + assertEquals(1, sfs.size()); + sf = sfs.get(0); // ID used for description if available assertEquals("$23", sf.description); assertEquals(55, sf.begin); @@ -266,15 +327,15 @@ public class FeaturesFileTest 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, - FormatAdapter.PASTE); + DataSourceType.PASTE); assertTrue("Failed to parse features file", featuresFile.parse(al.getDataset(), colours, true)); // verify FER_CAPAA feature - SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence() + List sfs = al.getSequenceAt(0).getDatasetSequence() .getSequenceFeatures(); - assertEquals(1, sfs.length); - SequenceFeature sf = sfs[0]; + assertEquals(1, sfs.size()); + SequenceFeature sf = sfs.get(0); assertEquals("Iron-sulfur (2Fe-2S)", sf.description); assertEquals(39, sf.begin); assertEquals(39, sf.end); @@ -282,8 +343,8 @@ public class FeaturesFileTest // verify FER1_SOLLC feature sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures(); - assertEquals(1, sfs.length); - sf = sfs[0]; + assertEquals(1, sfs.size()); + sf = sfs.get(0); assertEquals("Iron-phosphorus (2Fe-P)", sf.description); assertEquals(86, sf.begin); assertEquals(87, sf.end); @@ -294,7 +355,7 @@ public class FeaturesFileTest { assertEquals("no sequences extracted from GFF3 file", 2, dataset.getHeight()); - + SequenceI seq1 = dataset.findName("seq1"); SequenceI seq2 = dataset.findName("seq2"); assertNotNull(seq1); @@ -313,26 +374,26 @@ public class FeaturesFileTest 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().length); - assertNull(seq2.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().length); + .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, - FormatAdapter.FILE); + DataSourceType.FILE); Alignment dataset = new Alignment(gffreader.getSeqsAsArray()); gffreader.addProperties(dataset); checkDatasetfromSimpleGff3(dataset); @@ -343,7 +404,7 @@ public class FeaturesFileTest { AlignmentI dataset = new Alignment(new SequenceI[] {}); FeaturesFile ffile = new FeaturesFile(simpleGffFile, - FormatAdapter.FILE); + DataSourceType.FILE); boolean parseResult = ffile.parse(dataset, null, false, false); assertTrue("return result should be true", parseResult); @@ -354,7 +415,7 @@ public class FeaturesFileTest public void simpleGff3FileLoader() throws IOException { AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded( - simpleGffFile, FormatAdapter.FILE); + simpleGffFile, DataSourceType.FILE); assertTrue( "Didn't read the alignment into an alignframe from Gff3 File", af != null); @@ -366,7 +427,7 @@ public class FeaturesFileTest { AlignmentI dataset = new Alignment(new SequenceI[] {}); FeaturesFile ffile = new FeaturesFile(simpleGffFile, - FormatAdapter.FILE); + DataSourceType.FILE); boolean parseResult = ffile.parse(dataset, null, false, true); assertTrue("return result (relaxedID matching) should be true", @@ -386,38 +447,67 @@ public class FeaturesFileTest + "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" + + "Pfam domainPfam_3_4\tFER_CAPAA\t-1\t20\t20\tPfam\n" + "ENDGROUP\tuniprot\n"; FeaturesFile featuresFile = new FeaturesFile(features, - FormatAdapter.PASTE); + DataSourceType.PASTE); featuresFile.parse(al.getDataset(), colours, false); /* - * first with no features displayed + * 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(); - Map visible = fr - .getDisplayedFeatureCols(); + Map visible = fr.getDisplayedFeatureCols(); + List visibleGroups = new ArrayList<>( + Arrays.asList(new String[] {})); String exported = featuresFile.printJalviewFormat( - al.getSequencesArray(), visible); + al.getSequencesArray(), visible, null, visibleGroups, false); String expected = "No Features Visible"; assertEquals(expected, exported); /* + * include non-positional features + */ + visibleGroups.add("uniprot"); + exported = featuresFile.printJalviewFormat(al.getSequencesArray(), + visible, null, visibleGroups, true); + expected = "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n" + + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n" + + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n" // NaN is not output + + "\nSTARTGROUP\tuniprot\nENDGROUP\tuniprot\n"; + assertEquals(expected, exported); + + /* * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam */ fr.setVisible("METAL"); fr.setVisible("GAMMA-TURN"); visible = fr.getDisplayedFeatureCols(); exported = featuresFile.printJalviewFormat(al.getSequencesArray(), - visible); + visible, null, visibleGroups, false); expected = "METAL\tcc9900\n" - + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n" + + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n" + "\nSTARTGROUP\tuniprot\n" - + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\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); @@ -427,19 +517,194 @@ public class FeaturesFileTest fr.setVisible("Pfam"); visible = fr.getDisplayedFeatureCols(); exported = featuresFile.printJalviewFormat(al.getSequencesArray(), - visible); + visible, null, visibleGroups, false); /* - * note the order of feature types is uncontrolled - derives from - * FeaturesDisplayed.featuresDisplayed which is a HashSet + * features are output within group, ordered by sequence and by type */ expected = "METAL\tcc9900\n" + "Pfam\tff0000\n" - + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n" + + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n" + "\nSTARTGROUP\tuniprot\n" - + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n" + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n" - + "Pfam domainPfam_3_4\tFER_CAPAA\t-1\t20\t20\tPfam\t0.0\n" - + "ENDGROUP\tuniprot\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 output after features in named + // groups: + + "desc2\tFER_CAPAN\t-1\t4\t9\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(); + FeatureRenderer fr = af.alignPanel.getFeatureRenderer(); + Map visible = new HashMap<>(); + List visibleGroups = new ArrayList<>( + Arrays.asList(new String[] {})); + String exported = featuresFile.printGffFormat(al.getSequencesArray(), + visible, visibleGroups, false); + String gffHeader = "##gff-version 2\n"; + assertEquals(gffHeader, exported); + exported = featuresFile.printGffFormat(al.getSequencesArray(), visible, + visibleGroups, 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); + + /* + * with no features displayed, exclude non-positional features + */ + exported = featuresFile.printGffFormat(al.getSequencesArray(), visible, + visibleGroups, false); + assertEquals(gffHeader, exported); + + /* + * include non-positional features + */ + visibleGroups.add("Uniprot"); + exported = featuresFile.printGffFormat(al.getSequencesArray(), visible, + visibleGroups, 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"); + visible = fr.getDisplayedFeatureCols(); + exported = featuresFile.printGffFormat(al.getSequencesArray(), visible, + visibleGroups, 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 + */ + visibleGroups.add("s3dm"); + exported = featuresFile.printGffFormat(al.getSequencesArray(), visible, + visibleGroups, 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"); + visible = fr.getDisplayedFeatureCols(); + exported = featuresFile.printGffFormat(al.getSequencesArray(), visible, + visibleGroups, 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\n"; + assertEquals(expected, sb.toString()); + } }