X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FFeaturesFileTest.java;h=95ac67991e0a21bb985366e2fe17fbdead47f728;hb=5d003f492184b893aa4c2f437c6021626b573c45;hp=6f7bebe9f7025b160e17405758fb3053b724cad1;hpb=74393b51f368cb9f58589472d432a433d9c4386d;p=jalview.git diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java index 6f7bebe..95ac679 100644 --- a/test/jalview/io/FeaturesFileTest.java +++ b/test/jalview/io/FeaturesFileTest.java @@ -27,6 +27,18 @@ 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; import jalview.datamodel.Alignment; @@ -47,18 +59,7 @@ 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; +import junit.extensions.PA; public class FeaturesFileTest { @@ -92,8 +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)); /* @@ -203,8 +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, @@ -268,10 +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); @@ -284,14 +288,26 @@ 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(); @@ -360,12 +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(); @@ -374,16 +388,13 @@ 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() - .size()); + 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().size()); - assertTrue( - "Expected at least one CDNA/Protein mapping for seq1", + 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); @@ -405,7 +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); @@ -414,8 +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); @@ -428,7 +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); @@ -445,8 +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" @@ -461,22 +471,22 @@ public class FeaturesFileTest * 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.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, "")); + 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(); String exported = featuresFile - .printJalviewFormat(al.getSequencesArray(), fr, false); + .printJalviewFormat(al.getSequencesArray(), fr, false, false); String expected = "No Features Visible"; assertEquals(expected, exported); @@ -485,7 +495,7 @@ public class FeaturesFileTest */ fr.setGroupVisibility("uniprot", true); exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, - true); + true, false); expected = "\nSTARTGROUP\tuniprot\n" + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n" + "ENDGROUP\tuniprot\n\n" @@ -499,7 +509,7 @@ public class FeaturesFileTest fr.setVisible("METAL"); fr.setVisible("GAMMA-TURN"); exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, - false); + false, false); expected = "METAL\tcc9900\n" + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n" + "\nSTARTGROUP\tuniprot\n" @@ -513,12 +523,11 @@ public class FeaturesFileTest */ fr.setVisible("Pfam"); exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, - false); + false, false); /* * features are output within group, ordered by sequence and type */ - expected = "METAL\tcc9900\n" - + "Pfam\tff0000\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" + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n" @@ -539,14 +548,14 @@ public class FeaturesFileTest + "\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, false); assertEquals(expected, exported); /* * include non-positional (overrides group not shown) */ exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, - true); + 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" @@ -573,11 +582,11 @@ public class FeaturesFileTest FeatureRendererModel fr = (FeatureRendererModel) af.alignPanel .getFeatureRenderer(); String exported = featuresFile.printGffFormat(al.getSequencesArray(), - fr, false); + fr, false, false); String gffHeader = "##gff-version 2\n"; assertEquals(gffHeader, exported); - exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, - true); + exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, true, + false); assertEquals(gffHeader, exported); /* @@ -587,15 +596,18 @@ 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")); + 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"); + 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); /* @@ -614,7 +626,7 @@ public class FeaturesFileTest * with no features displayed, exclude non-positional features */ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, - false); + false, false); assertEquals(gffHeader, exported); /* @@ -622,8 +634,8 @@ public class FeaturesFileTest */ fr.setGroupVisibility("Uniprot", true); fr.setGroupVisibility("s3dm", false); - exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, - true); + 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); @@ -635,7 +647,7 @@ public class FeaturesFileTest fr.setVisible("METAL"); fr.setVisible("GAMMA-TURN"); exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, - false); + 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); @@ -645,7 +657,7 @@ public class FeaturesFileTest */ fr.setGroupVisibility("s3dm", true); exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, - false); + 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"; @@ -656,11 +668,14 @@ public class FeaturesFileTest */ fr.setVisible("Pfam"); exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, - false); + 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\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n" + expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\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); } @@ -703,7 +718,7 @@ public class FeaturesFileTest assertTrue(matcher.isByScore()); assertSame(matcher.getMatcher().getCondition(), Condition.LT); assertEquals(matcher.getMatcher().getPattern(), "1.3"); - assertEquals(matcher.getMatcher().getFloatValue(), 1.3f); + assertEquals(PA.getValue(matcher.getMatcher(), "floatValue"), 1.3f); assertFalse(matchers.hasNext()); } @@ -762,7 +777,7 @@ public class FeaturesFileTest 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"; @@ -770,10 +785,10 @@ public class FeaturesFileTest fr.setVisible("METAL"); fr.setColour("METAL", new FeatureColour(Color.PINK)); String exported = featuresFile.printGffFormat(al.getSequencesArray(), - fr, false); + fr, false, 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"; + + "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); /* @@ -785,8 +800,9 @@ public class FeaturesFileTest 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"; + false, false); + expected = gffHeader + + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n"; assertEquals(expected, exported); /* @@ -794,9 +810,10 @@ public class FeaturesFileTest */ 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"; + 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); /* @@ -807,8 +824,9 @@ public class FeaturesFileTest "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"; + false, false); + expected = gffHeader + + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n"; assertEquals(expected, exported); } @@ -834,23 +852,22 @@ public class FeaturesFileTest 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 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) @@ -861,19 +878,19 @@ public class FeaturesFileTest fc.setThreshold(1.1f); fr.setColour("METAL", fc); exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, - false); + 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, 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" @@ -881,7 +898,7 @@ public class FeaturesFileTest + "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 */ @@ -890,7 +907,7 @@ public class FeaturesFileTest "clin_sig")); fr.setFeatureFilter("METAL", filter); exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, - false); + 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"