X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FFeaturesFileTest.java;h=6f7bebe9f7025b160e17405758fb3053b724cad1;hb=74393b51f368cb9f58589472d432a433d9c4386d;hp=a00c3a25d8705343b615e5b35850d207560d86cf;hpb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;p=jalview.git diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java index a00c3a2..6f7bebe 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 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"; + @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 { @@ -66,17 +101,26 @@ 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); @@ -86,46 +130,52 @@ 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); @@ -168,10 +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); @@ -181,8 +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); @@ -229,10 +279,10 @@ 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(39, sf.begin); @@ -245,8 +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); @@ -282,10 +332,10 @@ 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); @@ -293,8 +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); @@ -324,14 +374,14 @@ 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 @@ -397,6 +447,7 @@ 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" @@ -406,25 +457,51 @@ public class FeaturesFileTest 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(); - String exported = featuresFile.printJalviewFormat( - al.getSequencesArray(), visible); + 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"); - visible = fr.getDisplayedFeatureCols(); - exported = featuresFile.printJalviewFormat(al.getSequencesArray(), - visible); + exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, + 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" @@ -435,21 +512,391 @@ public class FeaturesFileTest * now set Pfam visible */ fr.setVisible("Pfam"); - visible = fr.getDisplayedFeatureCols(); - exported = featuresFile.printJalviewFormat(al.getSequencesArray(), - visible); + exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, + 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 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"; + + "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); + 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\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\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(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); } }