X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FFeaturesFileTest.java;h=b753e94d612138ea9aec1088ede28d2eb101db3b;hb=refs%2Fheads%2Fpatch%2FJAL-3584_cherrypickto-JAL-3676_2.11.1.1;hp=ab0728943d3d6ba26ea12d7558a6042fb93da532;hpb=84ed42e8d0aa07b03441b045d240ebb51f94c53c;p=jalview.git diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java index ab07289..b753e94 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 { @@ -268,10 +269,12 @@ 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); @@ -284,14 +287,25 @@ 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(); @@ -476,18 +490,20 @@ 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); /* - * include non-positional features + * include non-positional features, but still no positional features */ fr.setGroupVisibility("uniprot", true); exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, - true); - expected = "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n" - + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n" + 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); @@ -497,12 +513,12 @@ 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(expected, exported); @@ -511,21 +527,48 @@ public class FeaturesFileTest */ fr.setVisible("Pfam"); exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, - false); + 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\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); } @@ -544,11 +587,11 @@ 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); + true, false); assertEquals(gffHeader, exported); /* @@ -564,9 +607,14 @@ 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); /* @@ -585,7 +633,7 @@ public class FeaturesFileTest * with no features displayed, exclude non-positional features */ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, - false); + false, false); assertEquals(gffHeader, exported); /* @@ -594,7 +642,7 @@ 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(expected, exported); @@ -606,7 +654,7 @@ 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); @@ -616,7 +664,7 @@ 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"; @@ -627,12 +675,16 @@ 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\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); } @@ -674,7 +726,7 @@ 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()); } @@ -741,23 +793,24 @@ 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); /* * now threshold to Score > 1.1 - should exclude sf2 */ - FeatureColourI fc = new FeatureColour(Color.white, Color.BLACK, + 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"; + false, false); + expected = gffHeader + + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n"; assertEquals(expected, exported); /* @@ -765,9 +818,10 @@ 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); /* @@ -778,8 +832,9 @@ 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); } @@ -814,7 +869,7 @@ 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" @@ -826,13 +881,13 @@ public class FeaturesFileTest * now threshold to Score > 1.1 - should exclude sf2 * (and there should be no empty STARTGROUP/ENDGROUP output) */ - FeatureColourI fc = new FeatureColour(Color.white, Color.BLACK, + 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, 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" @@ -844,7 +899,7 @@ public class FeaturesFileTest */ 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" @@ -861,7 +916,7 @@ 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"