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;
public class FeaturesFileTest
{
- private static final String LINE_SEPARATOR = System.getProperty("line.separator");
private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
@AfterClass(alwaysRun = true)
/*
* 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)
AlignFrame af = new AlignFrame(al, 500, 500);
Map<String, FeatureColourI> 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);
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();
*/
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);
*/
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
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
*/
+ "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"
+ "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\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
+ "\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"
+ "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" })
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
"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<String, String> 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);
/*
* 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
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
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);
}
/**
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());
}
/**
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
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
"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);
}
/**
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
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
"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);
}
}
git://source.jalview.org / jalview.git / blobdiff