+++ /dev/null
-/*
- * 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 <http://www.gnu.org/licenses/>.
- * 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 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.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;
-
-public class FeaturesFileTest
-{
- private static final String LINE_SEPARATOR = System.getProperty("line.separator");
- 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
- */
- Desktop.getStructureSelectionManager().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<String, FeatureColourI> 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<SequenceFeature> 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<String, FeatureColourI> 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<SequenceFeature> 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<String, FeatureColourI> colours = af.getFeatureRenderer()
- .getFeatureColours();
- // GFF3 uses '=' separator for name/value pairs in colum 9
- 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"
- + "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<SequenceFeature> 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", 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"));
-
- // 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<String, FeatureColourI> 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<SequenceFeature> 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<String, FeatureColourI> 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"
- + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\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);
- 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);
- 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);
-
- /*
- * 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);
- 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"
- + "ENDGROUP\tuniprot\n";
- assertEquals(fixLineEnd(expected), exported);
-
- /*
- * now set Pfam visible
- */
- fr.setVisible("Pfam");
- exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
- 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"
- + "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"
- + "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);
-
- /*
- * 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);
- assertEquals(fixLineEnd(expected), exported);
-
- /*
- * include non-positional (overrides group not shown)
- */
- exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
- true);
- 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(fixLineEnd(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);
- String gffHeader = "##gff-version 2\n";
- assertEquals(
- fixLineEnd(gffHeader),
- exported);
- exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
- true);
- assertEquals(
- fixLineEnd(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.setAttributes("x=y;black=white");
- sf.setStrand("+");
- sf.setPhase("2");
- 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);
- assertEquals(
- fixLineEnd(gffHeader),
- exported);
-
- /*
- * include non-positional features
- */
- fr.setGroupVisibility("Uniprot", true);
- fr.setGroupVisibility("s3dm", false);
- exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
- true);
- String expected = gffHeader
- + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
- assertEquals(
- fixLineEnd(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);
- // 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);
-
- /*
- * set s3dm group visible
- */
- fr.setGroupVisibility("s3dm", true);
- exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
- 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);
-
- /*
- * now set Pfam visible
- */
- fr.setVisible("Pfam");
- exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
- 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);
- }
-
- /**
- * Test for parsing of feature filters as represented in a Jalview features
- * file
- *
- * @throws Exception
- */
- @Test(groups = { "Functional" })
- public void testParseFilters() throws Exception
- {
- Map<String, FeatureMatcherSetI> 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<FeatureMatcherI> 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(matcher.getMatcher().getFloatValue(), 1.3f);
-
- assertFalse(matchers.hasNext());
- }
-
- @Test(groups = { "Functional" })
- public void testOutputFeatureFilters()
- {
- FeaturesFile ff = new FeaturesFile();
- StringBuilder sb = new StringBuilder();
- Map<String, FeatureColourI> visible = new HashMap<>();
- visible.put("pfam", new FeatureColour(Color.red));
- Map<String, FeatureMatcherSetI> 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(fixLineEnd(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);
- 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);
-
- /*
- * 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);
- expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
- assertEquals(fixLineEnd(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);
-
- /*
- * 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);
- expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
- assertEquals(fixLineEnd(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);
- 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);
-
- /*
- * 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);
- 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);
-
- /*
- * remove threshold and check sf2 is exported
- */
- fc.setAboveThreshold(false);
- exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
- 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);
-
- /*
- * 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);
- 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);
- }
-}
git://source.jalview.org / jalview.git / blobdiff