X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FFeaturesFileTest.java;h=36b4edfc44eb6bc31085451d59eb7286bd5c8f1d;hb=6200addf078b7f7ace90597dc056dafc7fc602c1;hp=04ddeb08802d9260daeb950247cfdbfc84b12388;hpb=4b1c969e87feaefd4fb9c49ba3d6b828b3ce1a9c;p=jalview.git diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java index 04ddeb0..36b4edf 100644 --- a/test/jalview/io/FeaturesFileTest.java +++ b/test/jalview/io/FeaturesFileTest.java @@ -43,6 +43,7 @@ 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; @@ -61,7 +62,6 @@ import org.testng.annotations.Test; public class FeaturesFileTest { - private static final String LINE_SEPARATOR = System.getProperty("line.separator"); private static String simpleGffFile = "examples/testdata/simpleGff3.gff"; @AfterClass(alwaysRun = true) @@ -70,7 +70,9 @@ public class FeaturesFileTest /* * remove any sequence mappings created so they don't pollute other tests */ - Desktop.getStructureSelectionManager().resetAll(); + StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.getInstance()); + ssm.resetAll(); } @BeforeClass(alwaysRun = true) @@ -266,10 +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); @@ -282,14 +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(); @@ -474,7 +489,7 @@ public class FeaturesFileTest */ 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); @@ -483,15 +498,13 @@ 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" + "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.replace("\n", LINE_SEPARATOR), - exported); + assertEquals(expected, exported); /* * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam @@ -499,21 +512,21 @@ 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" - + "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(fixLineEnd(expected), exported); + assertEquals(expected, exported); /* * now set Pfam visible */ fr.setVisible("Pfam"); exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, - false); + false, false); /* * features are output within group, ordered by sequence and type */ @@ -521,14 +534,14 @@ public class FeaturesFileTest + "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" + + "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(fixLineEnd(expected), exported); + assertEquals(expected, exported); /* * hide uniprot group @@ -539,14 +552,14 @@ 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); - assertEquals(fixLineEnd(expected), exported); + 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" @@ -556,7 +569,7 @@ public class FeaturesFileTest + "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(fixLineEnd(expected), exported); + assertEquals(expected, exported); } @Test(groups = { "Functional" }) @@ -573,16 +586,12 @@ 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( - fixLineEnd(gffHeader), - exported); + assertEquals(gffHeader, exported); exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, - true); - assertEquals( - fixLineEnd(gffHeader), - exported); + true, false); + assertEquals(gffHeader, exported); /* * add some features @@ -597,9 +606,14 @@ 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); /* @@ -618,10 +632,8 @@ public class FeaturesFileTest * with no features displayed, exclude non-positional features */ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, - false); - assertEquals( - fixLineEnd(gffHeader), - exported); + false, false); + assertEquals(gffHeader, exported); /* * include non-positional features @@ -629,12 +641,10 @@ public class FeaturesFileTest fr.setGroupVisibility("Uniprot", true); fr.setGroupVisibility("s3dm", false); exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, - true); + true, false); String expected = gffHeader + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n"; - assertEquals( - fixLineEnd(expected), - exported); + assertEquals(expected, exported); /* * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam @@ -643,43 +653,38 @@ 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.replace("\n", LINE_SEPARATOR), - exported); + assertEquals(expected, exported); /* * set s3dm group visible */ 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"; - assertEquals( - expected.replace("\n", LINE_SEPARATOR), - exported); + assertEquals(expected, exported); /* * now set Pfam visible */ 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\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"; - assertEquals(fixLineEnd(expected), exported); - } - - private String fixLineEnd(String s) - { - return s.replace("\n", LINE_SEPARATOR); + // 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); } /** @@ -754,7 +759,7 @@ public class FeaturesFileTest 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(fixLineEnd(expected), sb.toString()); + assertEquals(expected, sb.toString()); } /** @@ -787,12 +792,11 @@ 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"; - assertEquals( - fixLineEnd(expected), exported); + + "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 @@ -803,19 +807,21 @@ 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"; - assertEquals(fixLineEnd(expected), exported); + 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); - 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(fixLineEnd(expected), exported); + 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 @@ -825,9 +831,10 @@ 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"; - assertEquals(fixLineEnd(expected), exported); + false, false); + expected = gffHeader + + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n"; + assertEquals(expected, exported); } /** @@ -861,15 +868,13 @@ public class FeaturesFileTest fr.setColour("METAL", new FeatureColour(Color.PINK)); String exported = featuresFile.printJalviewFormat( al.getSequencesArray(), - fr, false); + 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( - fixLineEnd(expected), - exported); + assertEquals(expected, exported); /* * now threshold to Score > 1.1 - should exclude sf2 @@ -881,28 +886,26 @@ 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.replace("\n", LINE_SEPARATOR), - exported); + 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" + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n" + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n" + "ENDGROUP\tgrp2\n"; - assertEquals(fixLineEnd(expected), exported); + assertEquals(expected, exported); /* * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1 @@ -912,13 +915,13 @@ 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" + "STARTGROUP\tgrp2\n" + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n" + "ENDGROUP\tgrp2\n"; - assertEquals(fixLineEnd(expected), exported); + assertEquals(expected, exported); } }