X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FFeaturesFileTest.java;h=36b4edfc44eb6bc31085451d59eb7286bd5c8f1d;hb=6200addf078b7f7ace90597dc056dafc7fc602c1;hp=fd4cad73709e7c612ed91200db90b3f917c99191;hpb=19b1c75919e4d2f255cbaf811dc15d26850490e6;p=jalview.git diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java index fd4cad7..36b4edf 100644 --- a/test/jalview/io/FeaturesFileTest.java +++ b/test/jalview/io/FeaturesFileTest.java @@ -34,20 +34,23 @@ 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.ArrayList; -import java.util.Arrays; import java.util.HashMap; import java.util.Iterator; import java.util.List; @@ -68,7 +71,7 @@ public class FeaturesFileTest * remove any sequence mappings created so they don't pollute other tests */ StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); + .getStructureSelectionManager(Desktop.getInstance()); ssm.resetAll(); } @@ -265,10 +268,12 @@ 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); @@ -281,14 +286,25 @@ public class FeaturesFileTest 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(); @@ -472,24 +488,22 @@ public class FeaturesFileTest * first with no features displayed, exclude non-positional features */ FeatureRenderer fr = af.alignPanel.getFeatureRenderer(); - Map visible = fr.getDisplayedFeatureCols(); - List visibleGroups = new ArrayList<>( - Arrays.asList(new String[] {})); - String exported = featuresFile.printJalviewFormat( - al.getSequencesArray(), visible, null, visibleGroups, 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 */ - 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"; + 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); /* @@ -497,14 +511,13 @@ public class FeaturesFileTest */ fr.setVisible("METAL"); fr.setVisible("GAMMA-TURN"); - visible = fr.getDisplayedFeatureCols(); - exported = featuresFile.printJalviewFormat(al.getSequencesArray(), - visible, null, visibleGroups, 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); @@ -512,23 +525,49 @@ public class FeaturesFileTest * now set Pfam visible */ fr.setVisible("Pfam"); - visible = fr.getDisplayedFeatureCols(); - exported = featuresFile.printJalviewFormat(al.getSequencesArray(), - visible, null, visibleGroups, 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" + + "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" + + "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" - // null / empty group features output after features in named - // groups: + + "\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); } @@ -544,16 +583,14 @@ public class FeaturesFileTest * no features */ FeaturesFile featuresFile = new FeaturesFile(); - FeatureRenderer fr = af.alignPanel.getFeatureRenderer(); - Map visible = new HashMap<>(); - List visibleGroups = new ArrayList<>( - Arrays.asList(new String[] {})); + FeatureRendererModel fr = (FeatureRendererModel) af.alignPanel + .getFeatureRenderer(); String exported = featuresFile.printGffFormat(al.getSequencesArray(), - visible, visibleGroups, false); + fr, false, false); String gffHeader = "##gff-version 2\n"; assertEquals(gffHeader, exported); - exported = featuresFile.printGffFormat(al.getSequencesArray(), visible, - visibleGroups, true); + exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, + true, false); assertEquals(gffHeader, exported); /* @@ -569,24 +606,42 @@ public class FeaturesFileTest "s3dm")); SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f, "Uniprot"); - sf.setAttributes("x=y;black=white"); 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, - visibleGroups, false); + exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, + false, false); assertEquals(gffHeader, exported); /* * include non-positional features */ - visibleGroups.add("Uniprot"); - exported = featuresFile.printGffFormat(al.getSequencesArray(), visible, - visibleGroups, 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); @@ -597,9 +652,8 @@ public class FeaturesFileTest */ fr.setVisible("METAL"); fr.setVisible("GAMMA-TURN"); - visible = fr.getDisplayedFeatureCols(); - exported = featuresFile.printGffFormat(al.getSequencesArray(), visible, - visibleGroups, 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); @@ -607,9 +661,9 @@ public class FeaturesFileTest /* * set s3dm group visible */ - visibleGroups.add("s3dm"); - exported = featuresFile.printGffFormat(al.getSequencesArray(), visible, - visibleGroups, false); + 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"; @@ -619,14 +673,17 @@ public class FeaturesFileTest * now set Pfam visible */ fr.setVisible("Pfam"); - visible = fr.getDisplayedFeatureCols(); - exported = featuresFile.printGffFormat(al.getSequencesArray(), visible, - visibleGroups, 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); } @@ -672,4 +729,199 @@ public class FeaturesFileTest 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); + } }