/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNotNull;
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;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.FeatureMatcher;
import jalview.datamodel.features.FeatureMatcherI;
import jalview.datamodel.features.FeatureMatcherSet;
import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.datamodel.features.SequenceFeatures;
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;
import junit.extensions.PA;
public class FeaturesFileTest
{
private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
@AfterClass(alwaysRun = true)
public void tearDownAfterClass()
{
/*
* remove any sequence mappings created so they don't pollute other tests
*/
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
ssm.resetAll();
}
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
JvOptionPane.setInteractiveMode(false);
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
@Test(groups = { "Functional" })
public void testParse() throws Exception
{
File f = new File("examples/uniref50.fa");
AlignmentI al = readAlignmentFile(f);
AlignFrame af = new AlignFrame(al, 500, 500);
Map colours = af.getFeatureRenderer()
.getFeatureColours();
FeaturesFile featuresFile = new FeaturesFile(
"examples/exampleFeatures.txt", DataSourceType.FILE);
assertTrue(
"Test " + "Features file test"
+ "\nFailed to parse features file.",
featuresFile.parse(al.getDataset(), colours, true));
/*
* Refetch the colour map from the FeatureRenderer (to confirm it has been
* updated - JAL-1904), and verify (some) feature group colours
*/
colours = af.getFeatureRenderer().getFeatureColours();
assertEquals("27 feature group colours not found", 27, colours.size());
assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
FeatureColourI kdColour = colours.get("kdHydrophobicity");
assertTrue(kdColour.isGraduatedColour());
assertTrue(kdColour.isAboveThreshold());
assertEquals(-2f, kdColour.getThreshold());
/*
* verify (some) features on sequences
*/
List sfs = al.getSequenceAt(0).getDatasetSequence()
.getSequenceFeatures(); // FER_CAPAA
SequenceFeatures.sortFeatures(sfs, true);
assertEquals(8, sfs.size());
/*
* verify (in ascending start position order)
*/
SequenceFeature sf = sfs.get(0);
assertEquals("Pfam family%LINK%", sf.description);
assertEquals(0, sf.begin);
assertEquals(0, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("Pfam", sf.type);
assertEquals(1, sf.links.size());
assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
sf.links.get(0));
sf = sfs.get(1);
assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
assertEquals(3, sf.begin);
assertEquals(93, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("Cath", sf.type);
sf = sfs.get(2);
assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
sf.description);
assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
sf.links.get(0));
assertEquals(8, sf.begin);
assertEquals(83, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("Pfam", sf.type);
sf = sfs.get(3);
assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
assertEquals(39, sf.begin);
assertEquals(39, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("METAL", sf.type);
sf = sfs.get(4);
assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
assertEquals(44, sf.begin);
assertEquals(44, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("METAL", sf.type);
sf = sfs.get(5);
assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
assertEquals(47, sf.begin);
assertEquals(47, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("METAL", sf.type);
sf = sfs.get(6);
assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
assertEquals(77, sf.begin);
assertEquals(77, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("METAL", sf.type);
sf = sfs.get(7);
assertEquals(
"High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
sf.description);
assertEquals(
"PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&service=NetPhos-2.0",
sf.links.get(0));
assertEquals(89, sf.begin);
assertEquals(89, sf.end);
assertEquals("netphos", sf.featureGroup);
assertEquals("PHOSPHORYLATION (T)", sf.type);
}
/**
* Test parsing a features file with a mix of Jalview and GFF formatted
* content
*
* @throws Exception
*/
@Test(groups = { "Functional" })
public void testParse_mixedJalviewGff() throws Exception
{
File f = new File("examples/uniref50.fa");
AlignmentI al = readAlignmentFile(f);
AlignFrame af = new AlignFrame(al, 500, 500);
Map colours = af.getFeatureRenderer()
.getFeatureColours();
// GFF2 uses space as name/value separator in column 9
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,
DataSourceType.PASTE);
assertTrue("Failed to parse features file",
featuresFile.parse(al.getDataset(), colours, true));
// verify colours read or synthesized
colours = af.getFeatureRenderer().getFeatureColours();
assertEquals("1 feature group colours not found", 1, colours.size());
assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
// verify feature on FER_CAPAA
List sfs = al.getSequenceAt(0).getDatasetSequence()
.getSequenceFeatures();
assertEquals(1, sfs.size());
SequenceFeature sf = sfs.get(0);
assertEquals("Iron-sulfur,2Fe-2S", sf.description);
assertEquals(44, sf.begin);
assertEquals(45, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("METAL", sf.type);
assertEquals(4f, sf.getScore(), 0.001f);
// verify feature on FER1_SOLLC
sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
assertEquals(1, sfs.size());
sf = sfs.get(0);
assertEquals("uniprot", sf.description);
assertEquals(55, sf.begin);
assertEquals(130, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("Pfam", sf.type);
assertEquals(2f, sf.getScore(), 0.001f);
}
public static AlignmentI readAlignmentFile(File f) throws IOException
{
System.out.println("Reading file: " + f);
String ff = f.getPath();
FormatAdapter rf = new FormatAdapter();
AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
new IdentifyFile().identify(ff, DataSourceType.FILE));
al.setDataset(null); // creates dataset sequences
assertNotNull("Couldn't read supplied alignment data.", al);
return al;
}
/**
* Test parsing a features file with GFF formatted content only
*
* @throws Exception
*/
@Test(groups = { "Functional" })
public void testParse_pureGff3() throws Exception
{
File f = new File("examples/uniref50.fa");
AlignmentI al = readAlignmentFile(f);
AlignFrame af = new AlignFrame(al, 500, 500);
Map colours = af.getFeatureRenderer()
.getFeatureColours();
// 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,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);
assertTrue("Failed to parse features file",
featuresFile.parse(al.getDataset(), colours, true));
// verify feature on FER_CAPAA
List sfs = al.getSequenceAt(0).getDatasetSequence()
.getSequenceFeatures();
assertEquals(1, sfs.size());
SequenceFeature sf = sfs.get(0);
// description parsed from Note attribute
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(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();
assertEquals(1, sfs.size());
sf = sfs.get(0);
// ID used for description if available
assertEquals("$23", sf.description);
assertEquals(55, sf.begin);
assertEquals(130, sf.end);
assertEquals("uniprot", sf.featureGroup);
assertEquals("Pfam", sf.type);
assertEquals(3f, sf.getScore(), 0.001f);
}
/**
* Test parsing a features file with Jalview format features (but no colour
* descriptors or startgroup to give the hint not to parse as GFF)
*
* @throws Exception
*/
@Test(groups = { "Functional" })
public void testParse_jalviewFeaturesOnly() throws Exception
{
File f = new File("examples/uniref50.fa");
AlignmentI al = readAlignmentFile(f);
AlignFrame af = new AlignFrame(al, 500, 500);
Map colours = af.getFeatureRenderer()
.getFeatureColours();
/*
* one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
*/
String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
+ "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
FeaturesFile featuresFile = new FeaturesFile(featureData,
DataSourceType.PASTE);
assertTrue("Failed to parse features file",
featuresFile.parse(al.getDataset(), colours, true));
// verify FER_CAPAA feature
List sfs = al.getSequenceAt(0).getDatasetSequence()
.getSequenceFeatures();
assertEquals(1, sfs.size());
SequenceFeature sf = sfs.get(0);
assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
assertEquals(39, sf.begin);
assertEquals(39, sf.end);
assertEquals("METAL", sf.type);
// verify FER1_SOLLC feature
sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
assertEquals(1, sfs.size());
sf = sfs.get(0);
assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
assertEquals(86, sf.begin);
assertEquals(87, sf.end);
assertEquals("METALLIC", sf.type);
}
private void checkDatasetfromSimpleGff3(AlignmentI dataset)
{
assertEquals("no sequences extracted from GFF3 file", 2,
dataset.getHeight());
SequenceI seq1 = dataset.findName("seq1");
SequenceI seq2 = dataset.findName("seq2");
assertNotNull(seq1);
assertNotNull(seq2);
assertFalse("Failed to replace dummy seq1 with real sequence",
seq1 instanceof SequenceDummy
&& ((SequenceDummy) seq1).isDummy());
assertFalse("Failed to replace dummy seq2 with real sequence",
seq2 instanceof SequenceDummy
&& ((SequenceDummy) seq2).isDummy());
String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
assertFalse("dummy replacement buggy for seq1",
placeholderseq.equals(seq1.getSequenceAsString()));
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());
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",
dataset.getCodonFrame(seq1) != null
&& dataset.getCodonFrame(seq1).size() > 0);
}
@Test(groups = { "Functional" })
public void readGff3File() throws IOException
{
FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
DataSourceType.FILE);
Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
gffreader.addProperties(dataset);
checkDatasetfromSimpleGff3(dataset);
}
@Test(groups = { "Functional" })
public void simpleGff3FileClass() throws IOException
{
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);
}
@Test(groups = { "Functional" })
public void simpleGff3FileLoader() throws IOException
{
AlignFrame af = new FileLoader(false)
.LoadFileWaitTillLoaded(simpleGffFile, DataSourceType.FILE);
assertTrue(
"Didn't read the alignment into an alignframe from Gff3 File",
af != null);
checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
}
@Test(groups = { "Functional" })
public void simpleGff3RelaxedIdMatching() throws IOException
{
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);
checkDatasetfromSimpleGff3(dataset);
}
@Test(groups = { "Functional" })
public void testPrintJalviewFormat() throws Exception
{
File f = new File("examples/uniref50.fa");
AlignmentI al = readAlignmentFile(f);
AlignFrame af = new AlignFrame(al, 500, 500);
Map colours = af.getFeatureRenderer()
.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"
+ "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"
+ "Pfam domainPfam_3_4\tFER_CAPAA\t-1\t20\t20\tPfam\n"
+ "ENDGROUP\tuniprot\n";
FeaturesFile featuresFile = new FeaturesFile(features,
DataSourceType.PASTE);
featuresFile.parse(al.getDataset(), colours, false);
/*
* add positional and non-positional features with null and
* 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 = 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, ""));
/*
* first with no features displayed, exclude non-positional features
*/
FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
String exported = featuresFile
.printJalviewFormat(al.getSequencesArray(), fr, false, false);
String expected = "No Features Visible";
assertEquals(expected, exported);
/*
* include non-positional features, but still no positional features
*/
fr.setGroupVisibility("uniprot", true);
exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
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);
/*
* 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);
expected = "METAL\tcc9900\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"
+ "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
+ "ENDGROUP\tuniprot\n";
assertEquals(expected, exported);
/*
* now set Pfam visible
*/
fr.setVisible("Pfam");
exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
false, false);
/*
* 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"
+ "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"
+ "\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);
}
@Test(groups = { "Functional" })
public void testPrintGffFormat() throws Exception
{
File f = new File("examples/uniref50.fa");
AlignmentI al = readAlignmentFile(f);
AlignFrame af = new AlignFrame(al, 500, 500);
/*
* no features
*/
FeaturesFile featuresFile = new FeaturesFile();
FeatureRendererModel fr = (FeatureRendererModel) af.alignPanel
.getFeatureRenderer();
String exported = featuresFile.printGffFormat(al.getSequencesArray(),
fr, false, false);
String gffHeader = "##gff-version 2\n";
assertEquals(gffHeader, exported);
exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, true,
false);
assertEquals(gffHeader, exported);
/*
* add some features
*/
al.getSequenceAt(0).addSequenceFeature(
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"));
SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f,
"Uniprot");
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);
/*
* '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(), fr,
false, false);
assertEquals(gffHeader, exported);
/*
* include non-positional features
*/
fr.setGroupVisibility("Uniprot", true);
fr.setGroupVisibility("s3dm", false);
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);
/*
* set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
* only Uniprot group visible here...
*/
fr.setVisible("METAL");
fr.setVisible("GAMMA-TURN");
exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
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);
/*
* set s3dm group visible
*/
fr.setGroupVisibility("s3dm", true);
exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
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, exported);
/*
* now set Pfam visible
*/
fr.setVisible("Pfam");
exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
false, false);
// Pfam feature columns include strand(+), phase(2), attributes
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);
}
/**
* Test for parsing of feature filters as represented in a Jalview features
* file
*
* @throws Exception
*/
@Test(groups = { "Functional" })
public void testParseFilters() throws Exception
{
Map filters = new HashMap<>();
String text = "sequence_variant\tCSQ:PolyPhen NotContains 'damaging'\n"
+ "missense_variant\t(label contains foobar) and (Score lt 1.3)";
FeaturesFile featuresFile = new FeaturesFile(text,
DataSourceType.PASTE);
featuresFile.parseFilters(filters);
assertEquals(filters.size(), 2);
FeatureMatcherSetI fm = filters.get("sequence_variant");
assertNotNull(fm);
Iterator matchers = fm.getMatchers().iterator();
FeatureMatcherI matcher = matchers.next();
assertFalse(matchers.hasNext());
String[] attributes = matcher.getAttribute();
assertArrayEquals(attributes, new String[] { "CSQ", "PolyPhen" });
assertSame(matcher.getMatcher().getCondition(), Condition.NotContains);
assertEquals(matcher.getMatcher().getPattern(), "damaging");
fm = filters.get("missense_variant");
assertNotNull(fm);
matchers = fm.getMatchers().iterator();
matcher = matchers.next();
assertTrue(matcher.isByLabel());
assertSame(matcher.getMatcher().getCondition(), Condition.Contains);
assertEquals(matcher.getMatcher().getPattern(), "foobar");
matcher = matchers.next();
assertTrue(matcher.isByScore());
assertSame(matcher.getMatcher().getCondition(), Condition.LT);
assertEquals(matcher.getMatcher().getPattern(), "1.3");
assertEquals(PA.getValue(matcher.getMatcher(), "floatValue"), 1.3f);
assertFalse(matchers.hasNext());
}
@Test(groups = { "Functional" })
public void testOutputFeatureFilters()
{
FeaturesFile ff = new FeaturesFile();
StringBuilder sb = new StringBuilder();
Map visible = new HashMap<>();
visible.put("pfam", new FeatureColour(Color.red));
Map featureFilters = new HashMap<>();
// with no filters, nothing is output
ff.outputFeatureFilters(sb, visible, featureFilters);
assertEquals("", sb.toString());
// with filter for not visible features only, nothing is output
FeatureMatcherSet filter = new FeatureMatcherSet();
filter.and(FeatureMatcher.byLabel(Condition.Present, null));
featureFilters.put("foobar", filter);
ff.outputFeatureFilters(sb, visible, featureFilters);
assertEquals("", sb.toString());
// with filters for visible feature types
FeatureMatcherSet filter2 = new FeatureMatcherSet();
filter2.and(FeatureMatcher.byAttribute(Condition.Present, null, "CSQ",
"PolyPhen"));
filter2.and(FeatureMatcher.byScore(Condition.LE, "-2.4"));
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";
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, false);
String 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);
/*
* 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, 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, 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
*/
FeatureMatcherSetI filter = new FeatureMatcherSet();
filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
"clin_sig"));
fr.setFeatureFilter("METAL", filter);
exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
false, false);
expected = gffHeader
+ "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\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, 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, 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);
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, 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);
}
}