X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FFeaturesFileTest.java;h=77c18dbd054cf19f2367ca9f241026d6bac8a854;hb=3c8a25936a2d805e7e3d7ab82f83b13135406d18;hp=32ca8412fb61d7fb173f54f5cd48a3b900bdfa0a;hpb=c9b3c9348544a95ee1fc8b28abf117f5d49cbb82;p=jalview.git diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java index 32ca841..77c18db 100644 --- a/test/jalview/io/FeaturesFileTest.java +++ b/test/jalview/io/FeaturesFileTest.java @@ -45,12 +45,12 @@ 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; @@ -475,24 +475,22 @@ 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); 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); + 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); /* @@ -500,9 +498,8 @@ 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); expected = "METAL\tcc9900\n" + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n" + "\nSTARTGROUP\tuniprot\n" @@ -515,11 +512,10 @@ 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); /* - * 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" @@ -529,9 +525,36 @@ public class FeaturesFileTest + "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: + // 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); } @@ -547,16 +570,14 @@ 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); String gffHeader = "##gff-version 2\n"; assertEquals(gffHeader, exported); - exported = featuresFile.printGffFormat(al.getSequencesArray(), visible, - visibleGroups, true); + exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, + true); assertEquals(gffHeader, exported); /* @@ -578,18 +599,31 @@ public class FeaturesFileTest 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); 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); String expected = gffHeader + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n"; assertEquals(expected, exported); @@ -600,9 +634,8 @@ 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); // 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); @@ -610,9 +643,9 @@ 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); // 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"; @@ -622,9 +655,8 @@ 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); // Pfam feature columns include strand(+), phase(2), attributes expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n" @@ -704,7 +736,167 @@ public class FeaturesFileTest 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"; + 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); + } }