2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertFalse;
25 import static org.testng.AssertJUnit.assertNotNull;
26 import static org.testng.AssertJUnit.assertSame;
27 import static org.testng.AssertJUnit.assertTrue;
28 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
30 import jalview.api.FeatureColourI;
31 import jalview.api.FeatureRenderer;
32 import jalview.datamodel.Alignment;
33 import jalview.datamodel.AlignmentI;
34 import jalview.datamodel.SequenceDummy;
35 import jalview.datamodel.SequenceFeature;
36 import jalview.datamodel.SequenceI;
37 import jalview.datamodel.features.FeatureMatcher;
38 import jalview.datamodel.features.FeatureMatcherI;
39 import jalview.datamodel.features.FeatureMatcherSet;
40 import jalview.datamodel.features.FeatureMatcherSetI;
41 import jalview.datamodel.features.SequenceFeatures;
42 import jalview.gui.AlignFrame;
43 import jalview.gui.Desktop;
44 import jalview.gui.JvOptionPane;
45 import jalview.schemes.FeatureColour;
46 import jalview.structure.StructureSelectionManager;
47 import jalview.util.matcher.Condition;
48 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
49 import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
51 import java.awt.Color;
53 import java.io.IOException;
54 import java.util.HashMap;
55 import java.util.Iterator;
56 import java.util.List;
59 import org.testng.annotations.AfterClass;
60 import org.testng.annotations.BeforeClass;
61 import org.testng.annotations.Test;
63 public class FeaturesFileTest
65 private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
67 @AfterClass(alwaysRun = true)
68 public void tearDownAfterClass()
71 * remove any sequence mappings created so they don't pollute other tests
73 StructureSelectionManager ssm = StructureSelectionManager
74 .getStructureSelectionManager(Desktop.instance);
78 @BeforeClass(alwaysRun = true)
79 public void setUpJvOptionPane()
81 JvOptionPane.setInteractiveMode(false);
82 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
85 @Test(groups = { "Functional" })
86 public void testParse() throws Exception
88 File f = new File("examples/uniref50.fa");
89 AlignmentI al = readAlignmentFile(f);
90 AlignFrame af = new AlignFrame(al, 500, 500);
91 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
93 FeaturesFile featuresFile = new FeaturesFile(
94 "examples/exampleFeatures.txt", DataSourceType.FILE);
95 assertTrue("Test " + "Features file test"
96 + "\nFailed to parse features file.",
97 featuresFile.parse(al.getDataset(), colours, true));
100 * Refetch the colour map from the FeatureRenderer (to confirm it has been
101 * updated - JAL-1904), and verify (some) feature group colours
103 colours = af.getFeatureRenderer().getFeatureColours();
104 assertEquals("27 feature group colours not found", 27, colours.size());
105 assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
106 assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
107 FeatureColourI kdColour = colours.get("kdHydrophobicity");
108 assertTrue(kdColour.isGraduatedColour());
109 assertTrue(kdColour.isAboveThreshold());
110 assertEquals(-2f, kdColour.getThreshold());
113 * verify (some) features on sequences
115 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
116 .getSequenceFeatures(); // FER_CAPAA
117 SequenceFeatures.sortFeatures(sfs, true);
118 assertEquals(8, sfs.size());
121 * verify (in ascending start position order)
123 SequenceFeature sf = sfs.get(0);
124 assertEquals("Pfam family%LINK%", sf.description);
125 assertEquals(0, sf.begin);
126 assertEquals(0, sf.end);
127 assertEquals("uniprot", sf.featureGroup);
128 assertEquals("Pfam", sf.type);
129 assertEquals(1, sf.links.size());
130 assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
134 assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
135 assertEquals(3, sf.begin);
136 assertEquals(93, sf.end);
137 assertEquals("uniprot", sf.featureGroup);
138 assertEquals("Cath", sf.type);
141 assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
143 assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
145 assertEquals(8, sf.begin);
146 assertEquals(83, sf.end);
147 assertEquals("uniprot", sf.featureGroup);
148 assertEquals("Pfam", sf.type);
151 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
152 assertEquals(39, sf.begin);
153 assertEquals(39, sf.end);
154 assertEquals("uniprot", sf.featureGroup);
155 assertEquals("METAL", sf.type);
158 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
159 assertEquals(44, sf.begin);
160 assertEquals(44, sf.end);
161 assertEquals("uniprot", sf.featureGroup);
162 assertEquals("METAL", sf.type);
165 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
166 assertEquals(47, sf.begin);
167 assertEquals(47, sf.end);
168 assertEquals("uniprot", sf.featureGroup);
169 assertEquals("METAL", sf.type);
172 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
173 assertEquals(77, sf.begin);
174 assertEquals(77, sf.end);
175 assertEquals("uniprot", sf.featureGroup);
176 assertEquals("METAL", sf.type);
180 "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
183 "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&service=NetPhos-2.0",
185 assertEquals(89, sf.begin);
186 assertEquals(89, sf.end);
187 assertEquals("netphos", sf.featureGroup);
188 assertEquals("PHOSPHORYLATION (T)", sf.type);
192 * Test parsing a features file with a mix of Jalview and GFF formatted
197 @Test(groups = { "Functional" })
198 public void testParse_mixedJalviewGff() throws Exception
200 File f = new File("examples/uniref50.fa");
201 AlignmentI al = readAlignmentFile(f);
202 AlignFrame af = new AlignFrame(al, 500, 500);
203 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
204 .getFeatureColours();
205 // GFF2 uses space as name/value separator in column 9
206 String gffData = "METAL\tcc9900\n"
208 + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
209 + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
210 FeaturesFile featuresFile = new FeaturesFile(gffData,
211 DataSourceType.PASTE);
212 assertTrue("Failed to parse features file",
213 featuresFile.parse(al.getDataset(), colours, true));
215 // verify colours read or synthesized
216 colours = af.getFeatureRenderer().getFeatureColours();
217 assertEquals("1 feature group colours not found", 1, colours.size());
218 assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
220 // verify feature on FER_CAPAA
221 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
222 .getSequenceFeatures();
223 assertEquals(1, sfs.size());
224 SequenceFeature sf = sfs.get(0);
225 assertEquals("Iron-sulfur,2Fe-2S", sf.description);
226 assertEquals(44, sf.begin);
227 assertEquals(45, sf.end);
228 assertEquals("uniprot", sf.featureGroup);
229 assertEquals("METAL", sf.type);
230 assertEquals(4f, sf.getScore(), 0.001f);
232 // verify feature on FER1_SOLLC
233 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
234 assertEquals(1, sfs.size());
236 assertEquals("uniprot", sf.description);
237 assertEquals(55, sf.begin);
238 assertEquals(130, sf.end);
239 assertEquals("uniprot", sf.featureGroup);
240 assertEquals("Pfam", sf.type);
241 assertEquals(2f, sf.getScore(), 0.001f);
244 public static AlignmentI readAlignmentFile(File f) throws IOException
246 System.out.println("Reading file: " + f);
247 String ff = f.getPath();
248 FormatAdapter rf = new FormatAdapter();
250 AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
251 new IdentifyFile().identify(ff, DataSourceType.FILE));
253 al.setDataset(null); // creates dataset sequences
254 assertNotNull("Couldn't read supplied alignment data.", al);
259 * Test parsing a features file with GFF formatted content only
263 @Test(groups = { "Functional" })
264 public void testParse_pureGff3() throws Exception
266 File f = new File("examples/uniref50.fa");
267 AlignmentI al = readAlignmentFile(f);
268 AlignFrame af = new AlignFrame(al, 500, 500);
269 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
270 .getFeatureColours();
271 // GFF3 uses '=' separator for name/value pairs in column 9
272 // comma (%2C) equals (%3D) or semi-colon (%3B) should be url-escaped in values
273 String gffData = "##gff-version 3\n"
274 + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
275 + "Note=Iron-sulfur (2Fe-2S);Note=another note,and another;evidence=ECO%3B0000255%2CPROSITE%3DProRule:PRU00465;"
276 + "CSQ=AF=21,POLYPHEN=benign,possibly_damaging,clin_sig=Benign%3Dgood\n"
277 + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
278 FeaturesFile featuresFile = new FeaturesFile(gffData,
279 DataSourceType.PASTE);
280 assertTrue("Failed to parse features file",
281 featuresFile.parse(al.getDataset(), colours, true));
283 // verify feature on FER_CAPAA
284 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
285 .getSequenceFeatures();
286 assertEquals(1, sfs.size());
287 SequenceFeature sf = sfs.get(0);
288 // description parsed from Note attribute
289 assertEquals("Iron-sulfur (2Fe-2S),another note,and another",
291 assertEquals(39, sf.begin);
292 assertEquals(39, sf.end);
293 assertEquals("uniprot", sf.featureGroup);
294 assertEquals("METAL", sf.type);
295 assertEquals(5, sf.otherDetails.size());
296 assertEquals("ECO;0000255,PROSITE=ProRule:PRU00465", // url decoded
297 sf.getValue("evidence"));
298 assertEquals("Iron-sulfur (2Fe-2S),another note,and another",
299 sf.getValue("Note"));
300 assertEquals("21", sf.getValueAsString("CSQ", "AF"));
301 assertEquals("benign,possibly_damaging",
302 sf.getValueAsString("CSQ", "POLYPHEN"));
303 assertEquals("Benign=good", sf.getValueAsString("CSQ", "clin_sig")); // url decoded
304 // todo change STRAND and !Phase into fields of SequenceFeature instead
305 assertEquals(".", sf.otherDetails.get("STRAND"));
306 assertEquals(0, sf.getStrand());
307 assertEquals(".", sf.getPhase());
309 // verify feature on FER1_SOLLC1
310 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
311 assertEquals(1, sfs.size());
313 // ID used for description if available
314 assertEquals("$23", sf.description);
315 assertEquals(55, sf.begin);
316 assertEquals(130, sf.end);
317 assertEquals("uniprot", sf.featureGroup);
318 assertEquals("Pfam", sf.type);
319 assertEquals(3f, sf.getScore(), 0.001f);
323 * Test parsing a features file with Jalview format features (but no colour
324 * descriptors or startgroup to give the hint not to parse as GFF)
328 @Test(groups = { "Functional" })
329 public void testParse_jalviewFeaturesOnly() throws Exception
331 File f = new File("examples/uniref50.fa");
332 AlignmentI al = readAlignmentFile(f);
333 AlignFrame af = new AlignFrame(al, 500, 500);
334 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
335 .getFeatureColours();
338 * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
340 String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
341 + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
342 FeaturesFile featuresFile = new FeaturesFile(featureData,
343 DataSourceType.PASTE);
344 assertTrue("Failed to parse features file",
345 featuresFile.parse(al.getDataset(), colours, true));
347 // verify FER_CAPAA feature
348 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
349 .getSequenceFeatures();
350 assertEquals(1, sfs.size());
351 SequenceFeature sf = sfs.get(0);
352 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
353 assertEquals(39, sf.begin);
354 assertEquals(39, sf.end);
355 assertEquals("METAL", sf.type);
357 // verify FER1_SOLLC feature
358 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
359 assertEquals(1, sfs.size());
361 assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
362 assertEquals(86, sf.begin);
363 assertEquals(87, sf.end);
364 assertEquals("METALLIC", sf.type);
367 private void checkDatasetfromSimpleGff3(AlignmentI dataset)
369 assertEquals("no sequences extracted from GFF3 file", 2,
370 dataset.getHeight());
372 SequenceI seq1 = dataset.findName("seq1");
373 SequenceI seq2 = dataset.findName("seq2");
377 "Failed to replace dummy seq1 with real sequence",
378 seq1 instanceof SequenceDummy
379 && ((SequenceDummy) seq1).isDummy());
381 "Failed to replace dummy seq2 with real sequence",
382 seq2 instanceof SequenceDummy
383 && ((SequenceDummy) seq2).isDummy());
384 String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
385 assertFalse("dummy replacement buggy for seq1",
386 placeholderseq.equals(seq1.getSequenceAsString()));
387 assertFalse("dummy replacement buggy for seq2",
388 placeholderseq.equals(seq2.getSequenceAsString()));
389 assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
390 assertEquals("Wrong number of features", 3, seq1.getSequenceFeatures()
392 assertTrue(seq2.getSequenceFeatures().isEmpty());
394 "Wrong number of features",
396 seq2.getSequenceFeatures() == null ? 0 : seq2
397 .getSequenceFeatures().size());
399 "Expected at least one CDNA/Protein mapping for seq1",
400 dataset.getCodonFrame(seq1) != null
401 && dataset.getCodonFrame(seq1).size() > 0);
405 @Test(groups = { "Functional" })
406 public void readGff3File() throws IOException
408 FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
409 DataSourceType.FILE);
410 Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
411 gffreader.addProperties(dataset);
412 checkDatasetfromSimpleGff3(dataset);
415 @Test(groups = { "Functional" })
416 public void simpleGff3FileClass() throws IOException
418 AlignmentI dataset = new Alignment(new SequenceI[] {});
419 FeaturesFile ffile = new FeaturesFile(simpleGffFile,
420 DataSourceType.FILE);
422 boolean parseResult = ffile.parse(dataset, null, false, false);
423 assertTrue("return result should be true", parseResult);
424 checkDatasetfromSimpleGff3(dataset);
427 @Test(groups = { "Functional" })
428 public void simpleGff3FileLoader() throws IOException
430 AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
431 simpleGffFile, DataSourceType.FILE);
433 "Didn't read the alignment into an alignframe from Gff3 File",
435 checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
438 @Test(groups = { "Functional" })
439 public void simpleGff3RelaxedIdMatching() throws IOException
441 AlignmentI dataset = new Alignment(new SequenceI[] {});
442 FeaturesFile ffile = new FeaturesFile(simpleGffFile,
443 DataSourceType.FILE);
445 boolean parseResult = ffile.parse(dataset, null, false, true);
446 assertTrue("return result (relaxedID matching) should be true",
448 checkDatasetfromSimpleGff3(dataset);
451 @Test(groups = { "Functional" })
452 public void testPrintJalviewFormat() throws Exception
454 File f = new File("examples/uniref50.fa");
455 AlignmentI al = readAlignmentFile(f);
456 AlignFrame af = new AlignFrame(al, 500, 500);
457 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
458 .getFeatureColours();
459 String features = "METAL\tcc9900\n"
460 + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
462 + "STARTGROUP\tuniprot\n"
463 + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\n" // non-positional feature
464 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
465 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
466 + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
467 + "ENDGROUP\tuniprot\n";
468 FeaturesFile featuresFile = new FeaturesFile(features,
469 DataSourceType.PASTE);
470 featuresFile.parse(al.getDataset(), colours, false);
473 * add positional and non-positional features with null and
474 * empty feature group to check handled correctly
476 SequenceI seq = al.getSequenceAt(1); // FER_CAPAN
477 seq.addSequenceFeature(new SequenceFeature("Pfam", "desc1", 0, 0, 1.3f,
479 seq.addSequenceFeature(new SequenceFeature("Pfam", "desc2", 4, 9,
481 seq = al.getSequenceAt(2); // FER1_SOLLC
482 seq.addSequenceFeature(new SequenceFeature("Pfam", "desc3", 0, 0,
484 seq.addSequenceFeature(new SequenceFeature("Pfam", "desc4", 5, 8,
488 * first with no features displayed, exclude non-positional features
490 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
491 String exported = featuresFile
492 .printJalviewFormat(al.getSequencesArray(), fr, false, false);
493 String expected = "No Features Visible";
494 assertEquals(expected, exported);
497 * include non-positional features, but still no positional features
499 fr.setGroupVisibility("uniprot", true);
500 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
502 expected = "\nSTARTGROUP\tuniprot\n"
503 + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
504 + "ENDGROUP\tuniprot\n\n"
505 + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n\n"
506 + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"; // NaN is not output
507 assertEquals(expected, exported);
510 * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
512 fr.setVisible("METAL");
513 fr.setVisible("GAMMA-TURN");
514 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
516 expected = "METAL\tcc9900\n"
517 + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
518 + "\nSTARTGROUP\tuniprot\n"
519 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
520 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
521 + "ENDGROUP\tuniprot\n";
522 assertEquals(expected, exported);
525 * now set Pfam visible
527 fr.setVisible("Pfam");
528 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
531 * features are output within group, ordered by sequence and type
533 expected = "METAL\tcc9900\n"
535 + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
536 + "\nSTARTGROUP\tuniprot\n"
537 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
538 + "<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"
539 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
540 + "ENDGROUP\tuniprot\n"
541 // null / empty group features are output after named groups
542 + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
543 + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
544 assertEquals(expected, exported);
549 fr.setGroupVisibility("uniprot", false);
550 expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
551 + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
552 + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
553 + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
554 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
556 assertEquals(expected, exported);
559 * include non-positional (overrides group not shown)
561 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
563 expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
564 + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
565 + "\nSTARTGROUP\tuniprot\n"
566 + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
567 + "ENDGROUP\tuniprot\n"
568 + "\ndesc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n"
569 + "desc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
570 + "\ndesc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"
571 + "desc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
572 assertEquals(expected, exported);
575 @Test(groups = { "Functional" })
576 public void testPrintGffFormat() throws Exception
578 File f = new File("examples/uniref50.fa");
579 AlignmentI al = readAlignmentFile(f);
580 AlignFrame af = new AlignFrame(al, 500, 500);
585 FeaturesFile featuresFile = new FeaturesFile();
586 FeatureRendererModel fr = (FeatureRendererModel) af.alignPanel
587 .getFeatureRenderer();
588 String exported = featuresFile.printGffFormat(al.getSequencesArray(),
590 String gffHeader = "##gff-version 2\n";
591 assertEquals(gffHeader, exported);
592 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
594 assertEquals(gffHeader, exported);
599 al.getSequenceAt(0).addSequenceFeature(
600 new SequenceFeature("Domain", "Cath", 0, 0, 0f, "Uniprot"));
601 al.getSequenceAt(0).addSequenceFeature(
602 new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, null));
605 new SequenceFeature("GAMMA-TURN", "Turn", 36, 38, 2.1f,
607 SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f,
611 sf.setValue("x", "y");
612 sf.setValue("black", "white");
613 Map<String, String> csq = new HashMap<>();
614 csq.put("SIFT", "benign,mostly benign,cloudy, with meatballs");
615 csq.put("consequence", "missense_variant");
616 sf.setValue("CSQ", csq);
617 al.getSequenceAt(1).addSequenceFeature(sf);
620 * 'discover' features then hide all feature types
622 fr.findAllFeatures(true);
623 FeatureSettingsBean[] data = new FeatureSettingsBean[4];
624 FeatureColourI fc = new FeatureColour(Color.PINK);
625 data[0] = new FeatureSettingsBean("Domain", fc, null, false);
626 data[1] = new FeatureSettingsBean("METAL", fc, null, false);
627 data[2] = new FeatureSettingsBean("GAMMA-TURN", fc, null, false);
628 data[3] = new FeatureSettingsBean("Pfam", fc, null, false);
629 fr.setFeaturePriority(data);
632 * with no features displayed, exclude non-positional features
634 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
636 assertEquals(gffHeader, exported);
639 * include non-positional features
641 fr.setGroupVisibility("Uniprot", true);
642 fr.setGroupVisibility("s3dm", false);
643 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
645 String expected = gffHeader
646 + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
647 assertEquals(expected, exported);
650 * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
651 * only Uniprot group visible here...
653 fr.setVisible("METAL");
654 fr.setVisible("GAMMA-TURN");
655 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
657 // METAL feature has null group: description used for column 2
658 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
659 assertEquals(expected, exported);
662 * set s3dm group visible
664 fr.setGroupVisibility("s3dm", true);
665 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
667 // METAL feature has null group: description used for column 2
668 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
669 + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
670 assertEquals(expected, exported);
673 * now set Pfam visible
675 fr.setVisible("Pfam");
676 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
678 // Pfam feature columns include strand(+), phase(2), attributes
680 + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
681 // CSQ output as CSQ=att1=value1,att2=value2
682 // note all commas are encoded here which is wrong - it should be
683 // SIFT=benign,mostly benign,cloudy%2C with meatballs
684 + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white;"
685 + "CSQ=SIFT=benign%2Cmostly benign%2Ccloudy%2C with meatballs,consequence=missense_variant\n"
686 + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
687 assertEquals(expected, exported);
691 * Test for parsing of feature filters as represented in a Jalview features
696 @Test(groups = { "Functional" })
697 public void testParseFilters() throws Exception
699 Map<String, FeatureMatcherSetI> filters = new HashMap<>();
700 String text = "sequence_variant\tCSQ:PolyPhen NotContains 'damaging'\n"
701 + "missense_variant\t(label contains foobar) and (Score lt 1.3)";
702 FeaturesFile featuresFile = new FeaturesFile(text,
703 DataSourceType.PASTE);
704 featuresFile.parseFilters(filters);
705 assertEquals(filters.size(), 2);
707 FeatureMatcherSetI fm = filters.get("sequence_variant");
709 Iterator<FeatureMatcherI> matchers = fm.getMatchers().iterator();
710 FeatureMatcherI matcher = matchers.next();
711 assertFalse(matchers.hasNext());
712 String[] attributes = matcher.getAttribute();
713 assertArrayEquals(attributes, new String[] { "CSQ", "PolyPhen" });
714 assertSame(matcher.getMatcher().getCondition(), Condition.NotContains);
715 assertEquals(matcher.getMatcher().getPattern(), "damaging");
717 fm = filters.get("missense_variant");
719 matchers = fm.getMatchers().iterator();
720 matcher = matchers.next();
721 assertTrue(matcher.isByLabel());
722 assertSame(matcher.getMatcher().getCondition(), Condition.Contains);
723 assertEquals(matcher.getMatcher().getPattern(), "foobar");
724 matcher = matchers.next();
725 assertTrue(matcher.isByScore());
726 assertSame(matcher.getMatcher().getCondition(), Condition.LT);
727 assertEquals(matcher.getMatcher().getPattern(), "1.3");
728 assertEquals(matcher.getMatcher().getFloatValue(), 1.3f);
730 assertFalse(matchers.hasNext());
733 @Test(groups = { "Functional" })
734 public void testOutputFeatureFilters()
736 FeaturesFile ff = new FeaturesFile();
737 StringBuilder sb = new StringBuilder();
738 Map<String, FeatureColourI> visible = new HashMap<>();
739 visible.put("pfam", new FeatureColour(Color.red));
740 Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
742 // with no filters, nothing is output
743 ff.outputFeatureFilters(sb, visible, featureFilters);
744 assertEquals("", sb.toString());
746 // with filter for not visible features only, nothing is output
747 FeatureMatcherSet filter = new FeatureMatcherSet();
748 filter.and(FeatureMatcher.byLabel(Condition.Present, null));
749 featureFilters.put("foobar", filter);
750 ff.outputFeatureFilters(sb, visible, featureFilters);
751 assertEquals("", sb.toString());
753 // with filters for visible feature types
754 FeatureMatcherSet filter2 = new FeatureMatcherSet();
755 filter2.and(FeatureMatcher.byAttribute(Condition.Present, null, "CSQ",
757 filter2.and(FeatureMatcher.byScore(Condition.LE, "-2.4"));
758 featureFilters.put("pfam", filter2);
759 visible.put("foobar", new FeatureColour(Color.blue));
760 ff.outputFeatureFilters(sb, visible, featureFilters);
761 String expected = "\nSTARTFILTERS\nfoobar\tLabel Present\npfam\t(CSQ:PolyPhen Present) AND (Score LE -2.4)\nENDFILTERS\n";
762 assertEquals(expected, sb.toString());
766 * Output as GFF should not include features which are not visible due to
767 * colour threshold or feature filter settings
771 @Test(groups = { "Functional" })
772 public void testPrintGffFormat_withFilters() throws Exception
774 File f = new File("examples/uniref50.fa");
775 AlignmentI al = readAlignmentFile(f);
776 AlignFrame af = new AlignFrame(al, 500, 500);
777 SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
779 sf1.setValue("clin_sig", "Likely Pathogenic");
780 sf1.setValue("AF", "24");
781 al.getSequenceAt(0).addSequenceFeature(sf1);
782 SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
784 sf2.setValue("clin_sig", "Benign");
785 sf2.setValue("AF", "46");
786 al.getSequenceAt(0).addSequenceFeature(sf2);
788 FeaturesFile featuresFile = new FeaturesFile();
789 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
790 final String gffHeader = "##gff-version 2\n";
792 fr.setVisible("METAL");
793 fr.setColour("METAL", new FeatureColour(Color.PINK));
794 String exported = featuresFile.printGffFormat(al.getSequencesArray(),
796 String expected = gffHeader
797 + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n"
798 + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
799 assertEquals(expected, exported);
802 * now threshold to Score > 1.1 - should exclude sf2
804 FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
805 Color.white, 0f, 2f);
806 fc.setAboveThreshold(true);
807 fc.setThreshold(1.1f);
808 fr.setColour("METAL", fc);
809 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
812 + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n";
813 assertEquals(expected, exported);
816 * remove threshold and check sf2 is exported
818 fc.setAboveThreshold(false);
819 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
822 + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n"
823 + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
824 assertEquals(expected, exported);
827 * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
829 FeatureMatcherSetI filter = new FeatureMatcherSet();
830 filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
832 fr.setFeatureFilter("METAL", filter);
833 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
836 + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
837 assertEquals(expected, exported);
841 * Output as Jalview should not include features which are not visible due to
842 * colour threshold or feature filter settings
846 @Test(groups = { "Functional" })
847 public void testPrintJalviewFormat_withFilters() throws Exception
849 File f = new File("examples/uniref50.fa");
850 AlignmentI al = readAlignmentFile(f);
851 AlignFrame af = new AlignFrame(al, 500, 500);
852 SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
854 sf1.setValue("clin_sig", "Likely Pathogenic");
855 sf1.setValue("AF", "24");
856 al.getSequenceAt(0).addSequenceFeature(sf1);
857 SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
859 sf2.setValue("clin_sig", "Benign");
860 sf2.setValue("AF", "46");
861 al.getSequenceAt(0).addSequenceFeature(sf2);
863 FeaturesFile featuresFile = new FeaturesFile();
864 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
865 fr.findAllFeatures(true);
867 fr.setVisible("METAL");
868 fr.setColour("METAL", new FeatureColour(Color.PINK));
869 String exported = featuresFile.printJalviewFormat(
870 al.getSequencesArray(),
872 String expected = "METAL\tffafaf\n\nSTARTGROUP\tgrp1\n"
873 + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
874 + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
875 + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
876 + "ENDGROUP\tgrp2\n";
877 assertEquals(expected, exported);
880 * now threshold to Score > 1.1 - should exclude sf2
881 * (and there should be no empty STARTGROUP/ENDGROUP output)
883 FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
884 Color.white, 0f, 2f);
885 fc.setAboveThreshold(true);
886 fc.setThreshold(1.1f);
887 fr.setColour("METAL", fc);
888 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
890 expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|above|1.1\n\n"
891 + "STARTGROUP\tgrp1\n"
892 + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
893 + "ENDGROUP\tgrp1\n";
894 assertEquals(expected, exported);
897 * remove threshold and check sf2 is exported
899 fc.setAboveThreshold(false);
900 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
902 expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
903 + "STARTGROUP\tgrp1\n"
904 + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
905 + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
906 + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
907 + "ENDGROUP\tgrp2\n";
908 assertEquals(expected, exported);
911 * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
913 FeatureMatcherSetI filter = new FeatureMatcherSet();
914 filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
916 fr.setFeatureFilter("METAL", filter);
917 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
919 expected = "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
920 expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
921 + "STARTFILTERS\nMETAL\tclin_sig Contains benign\nENDFILTERS\n\n"
922 + "STARTGROUP\tgrp2\n"
923 + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
924 + "ENDGROUP\tgrp2\n";
925 assertEquals(expected, exported);