X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FFeaturesFileTest.java;h=95ac67991e0a21bb985366e2fe17fbdead47f728;hb=4a3def9f59cefe629c9a33d87483283aee085928;hp=6429e16f9d566cf4e046c74a6632f2dd6c1045d3;hpb=c05b2da460c1e6ba38e2c0a0d3e8399e0b847d60;p=jalview.git diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java index 6429e16..95ac679 100644 --- a/test/jalview/io/FeaturesFileTest.java +++ b/test/jalview/io/FeaturesFileTest.java @@ -23,8 +23,21 @@ 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 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; import jalview.api.FeatureColourI; import jalview.api.FeatureRenderer; @@ -33,20 +46,35 @@ 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 java.awt.Color; -import java.io.File; -import java.io.IOException; -import java.util.HashMap; -import java.util.Map; - -import org.testng.annotations.BeforeClass; -import org.testng.annotations.Test; +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 junit.extensions.PA; 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() @@ -55,8 +83,6 @@ public class FeaturesFileTest JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); } - private static String simpleGffFile = "examples/testdata/simpleGff3.gff"; - @Test(groups = { "Functional" }) public void testParse() throws Exception { @@ -67,8 +93,9 @@ public class FeaturesFileTest .getFeatureColours(); FeaturesFile featuresFile = new FeaturesFile( "examples/exampleFeatures.txt", DataSourceType.FILE); - assertTrue("Test " + "Features file test" - + "\nFailed to parse features file.", + assertTrue( + "Test " + "Features file test" + + "\nFailed to parse features file.", featuresFile.parse(al.getDataset(), colours, true)); /* @@ -76,17 +103,26 @@ 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(8, 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); @@ -96,46 +132,52 @@ public class FeaturesFileTest assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111", sf.links.get(0)); - sf = sfs[1]; + 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[2]; + + 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[3]; + + 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[4]; + + 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[5]; - 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[6]; - 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[7]; + + sf = sfs.get(7); assertEquals( "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%", sf.description); @@ -163,8 +205,7 @@ 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, @@ -178,10 +219,10 @@ 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); @@ -191,8 +232,8 @@ 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); @@ -228,10 +269,13 @@ public class FeaturesFileTest AlignFrame af = new AlignFrame(al, 500, 500); Map colours = af.getFeatureRenderer() .getFeatureColours(); - // GFF3 uses '=' separator for name/value pairs in colum 9 + // GFF3 uses '=' separator for name/value pairs in column 9 + // comma (%2C) equals (%3D) or semi-colon (%3B) should be url-escaped in + // values 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" + + "Note=Iron-sulfur (2Fe-2S);Note=another note,and another;evidence=ECO%3B0000255%2CPROSITE%3DProRule:PRU00465;" + + "CSQ=AF=21,POLYPHEN=benign,possibly_damaging,clin_sig=Benign%3Dgood\n" + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23"; FeaturesFile featuresFile = new FeaturesFile(gffData, DataSourceType.PASTE); @@ -239,24 +283,36 @@ public class FeaturesFileTest 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("Iron-sulfur (2Fe-2S),another note,and another", + 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")); + assertEquals(5, sf.otherDetails.size()); + assertEquals("ECO;0000255,PROSITE=ProRule:PRU00465", // url decoded + sf.getValue("evidence")); + assertEquals("Iron-sulfur (2Fe-2S),another note,and another", + sf.getValue("Note")); + assertEquals("21", sf.getValueAsString("CSQ", "AF")); + assertEquals("benign,possibly_damaging", + sf.getValueAsString("CSQ", "POLYPHEN")); + assertEquals("Benign=good", sf.getValueAsString("CSQ", "clin_sig")); // url + // decoded + // todo change STRAND and !Phase into fields of SequenceFeature instead + assertEquals(".", sf.otherDetails.get("STRAND")); + assertEquals(0, sf.getStrand()); + assertEquals(".", sf.getPhase()); // 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); @@ -292,10 +348,10 @@ public class FeaturesFileTest 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); @@ -303,8 +359,8 @@ 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); @@ -320,12 +376,10 @@ public class FeaturesFileTest SequenceI seq2 = dataset.findName("seq2"); assertNotNull(seq1); assertNotNull(seq2); - assertFalse( - "Failed to replace dummy seq1 with real sequence", + assertFalse("Failed to replace dummy seq1 with real sequence", seq1 instanceof SequenceDummy && ((SequenceDummy) seq1).isDummy()); - assertFalse( - "Failed to replace dummy seq2 with real sequence", + assertFalse("Failed to replace dummy seq2 with real sequence", seq2 instanceof SequenceDummy && ((SequenceDummy) seq2).isDummy()); String placeholderseq = new SequenceDummy("foo").getSequenceAsString(); @@ -335,15 +389,12 @@ public class FeaturesFileTest 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", - 0, - seq2.getSequenceFeatures() == null ? 0 : seq2 - .getSequenceFeatures().length); - assertTrue( - "Expected at least one CDNA/Protein mapping for seq1", + 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); @@ -365,7 +416,7 @@ public class FeaturesFileTest 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); @@ -374,8 +425,8 @@ public class FeaturesFileTest @Test(groups = { "Functional" }) public void simpleGff3FileLoader() throws IOException { - AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded( - simpleGffFile, DataSourceType.FILE); + AlignFrame af = new FileLoader(false) + .LoadFileWaitTillLoaded(simpleGffFile, DataSourceType.FILE); assertTrue( "Didn't read the alignment into an alignframe from Gff3 File", af != null); @@ -388,7 +439,7 @@ public class FeaturesFileTest 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); @@ -405,8 +456,7 @@ public class FeaturesFileTest .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" + + "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" @@ -417,21 +467,40 @@ public class FeaturesFileTest 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(); - Map visible = fr.getDisplayedFeatureCols(); - String exported = featuresFile.printJalviewFormat( - al.getSequencesArray(), visible, false); + String exported = featuresFile + .printJalviewFormat(al.getSequencesArray(), fr, false, false); String expected = "No Features Visible"; assertEquals(expected, exported); /* - * include non-positional features + * include non-positional features, but still no positional features */ - exported = featuresFile.printJalviewFormat(al.getSequencesArray(), - visible, true); - expected = "\nSTARTGROUP\tuniprot\nCath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\nENDGROUP\tuniprot\n"; + fr.setGroupVisibility("uniprot", true); + exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, + true, false); + 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); /* @@ -439,14 +508,13 @@ public class FeaturesFileTest */ fr.setVisible("METAL"); fr.setVisible("GAMMA-TURN"); - visible = fr.getDisplayedFeatureCols(); - exported = featuresFile.printJalviewFormat(al.getSequencesArray(), - visible, false); + exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, + false, 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" - + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n" + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n" + + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n" + "ENDGROUP\tuniprot\n"; assertEquals(expected, exported); @@ -454,20 +522,49 @@ public class FeaturesFileTest * now set Pfam visible */ fr.setVisible("Pfam"); - visible = fr.getDisplayedFeatureCols(); - exported = featuresFile.printJalviewFormat(al.getSequencesArray(), - visible, false); + exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, + false, false); /* - * features are output within group, ordered by sequence and by type + * features are output within group, ordered by sequence and type */ - expected = "METAL\tcc9900\n" - + "Pfam\tff0000\n" - + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n" + 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"; + + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\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, false); + assertEquals(expected, exported); + + /* + * include non-positional (overrides group not shown) + */ + exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, + true, false); + 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); } @@ -482,14 +579,14 @@ public class FeaturesFileTest * no features */ FeaturesFile featuresFile = new FeaturesFile(); - FeatureRenderer fr = af.alignPanel.getFeatureRenderer(); - Map visible = new HashMap(); - String exported = featuresFile.printGffFormat( - al.getSequencesArray(), visible, false); + FeatureRendererModel fr = (FeatureRendererModel) af.alignPanel + .getFeatureRenderer(); + String exported = featuresFile.printGffFormat(al.getSequencesArray(), + fr, false, false); String gffHeader = "##gff-version 2\n"; assertEquals(gffHeader, exported); - exported = featuresFile.printGffFormat(al.getSequencesArray(), visible, - true); + exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, true, + false); assertEquals(gffHeader, exported); /* @@ -499,56 +596,324 @@ public class FeaturesFileTest 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"); + al.getSequenceAt(1).addSequenceFeature(new SequenceFeature("GAMMA-TURN", + "Turn", 36, 38, 2.1f, "s3dm")); + SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f, + "Uniprot"); sf.setStrand("+"); sf.setPhase("2"); + sf.setValue("x", "y"); + sf.setValue("black", "white"); + Map csq = new HashMap<>(); + csq.put("SIFT", "benign,mostly benign,cloudy, with meatballs"); + csq.put("consequence", "missense_variant"); + sf.setValue("CSQ", csq); 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(), visible, - false); + exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, + false, false); assertEquals(gffHeader, exported); - + /* * include non-positional features */ - exported = featuresFile.printGffFormat(al.getSequencesArray(), - visible, true); + fr.setGroupVisibility("Uniprot", true); + fr.setGroupVisibility("s3dm", false); + exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, true, + false); 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, false); + exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, + false, 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, 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, false); + exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, + false, 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"; + // CSQ output as CSQ=att1=value1,att2=value2 + // note all commas are encoded here which is wrong - it should be + // SIFT=benign,mostly benign,cloudy%2C with meatballs + + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white;" + + "CSQ=SIFT=benign%2Cmostly benign%2Ccloudy%2C with meatballs,consequence=missense_variant\n" + + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\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(PA.getValue(matcher.getMatcher(), "floatValue"), 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, false); + String expected = gffHeader + + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n" + + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\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, false); + expected = gffHeader + + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n"; + assertEquals(expected, exported); + + /* + * remove threshold and check sf2 is exported + */ + fc.setAboveThreshold(false); + exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, + false, false); + expected = gffHeader + + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n" + + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\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, false); + expected = gffHeader + + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\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, 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, 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, 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, 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); } }