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 java.awt.Color;
32 import java.io.IOException;
33 import java.util.HashMap;
34 import java.util.Iterator;
35 import java.util.List;
38 import org.testng.annotations.AfterClass;
39 import org.testng.annotations.BeforeClass;
40 import org.testng.annotations.Test;
42 import jalview.api.FeatureColourI;
43 import jalview.api.FeatureRenderer;
44 import jalview.datamodel.Alignment;
45 import jalview.datamodel.AlignmentI;
46 import jalview.datamodel.SequenceDummy;
47 import jalview.datamodel.SequenceFeature;
48 import jalview.datamodel.SequenceI;
49 import jalview.datamodel.features.FeatureMatcher;
50 import jalview.datamodel.features.FeatureMatcherI;
51 import jalview.datamodel.features.FeatureMatcherSet;
52 import jalview.datamodel.features.FeatureMatcherSetI;
53 import jalview.datamodel.features.SequenceFeatures;
54 import jalview.gui.AlignFrame;
55 import jalview.gui.Desktop;
56 import jalview.gui.JvOptionPane;
57 import jalview.schemes.FeatureColour;
58 import jalview.structure.StructureSelectionManager;
59 import jalview.util.matcher.Condition;
60 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
61 import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
62 import junit.extensions.PA;
64 public class FeaturesFileTest
66 private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
68 @AfterClass(alwaysRun = true)
69 public void tearDownAfterClass()
72 * remove any sequence mappings created so they don't pollute other tests
74 StructureSelectionManager ssm = StructureSelectionManager
75 .getStructureSelectionManager(Desktop.instance);
79 @BeforeClass(alwaysRun = true)
80 public void setUpJvOptionPane()
82 JvOptionPane.setInteractiveMode(false);
83 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
86 @Test(groups = { "Functional" })
87 public void testParse() throws Exception
89 File f = new File("examples/uniref50.fa");
90 AlignmentI al = readAlignmentFile(f);
91 AlignFrame af = new AlignFrame(al, 500, 500);
92 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
94 FeaturesFile featuresFile = new FeaturesFile(
95 "examples/exampleFeatures.txt", DataSourceType.FILE);
96 assertTrue("Test " + "Features file test"
97 + "\nFailed to parse features file.",
98 featuresFile.parse(al.getDataset(), colours, true));
101 * Refetch the colour map from the FeatureRenderer (to confirm it has been
102 * updated - JAL-1904), and verify (some) feature group colours
104 colours = af.getFeatureRenderer().getFeatureColours();
105 assertEquals("27 feature group colours not found", 27, colours.size());
106 assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
107 assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
108 FeatureColourI kdColour = colours.get("kdHydrophobicity");
109 assertTrue(kdColour.isGraduatedColour());
110 assertTrue(kdColour.isAboveThreshold());
111 assertEquals(-2f, kdColour.getThreshold());
114 * verify (some) features on sequences
116 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
117 .getSequenceFeatures(); // FER_CAPAA
118 SequenceFeatures.sortFeatures(sfs, true);
119 assertEquals(8, sfs.size());
122 * verify (in ascending start position order)
124 SequenceFeature sf = sfs.get(0);
125 assertEquals("Pfam family%LINK%", sf.description);
126 assertEquals(0, sf.begin);
127 assertEquals(0, sf.end);
128 assertEquals("uniprot", sf.featureGroup);
129 assertEquals("Pfam", sf.type);
130 assertEquals(1, sf.links.size());
131 assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
135 assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
136 assertEquals(3, sf.begin);
137 assertEquals(93, sf.end);
138 assertEquals("uniprot", sf.featureGroup);
139 assertEquals("Cath", sf.type);
142 assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
144 assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
146 assertEquals(8, sf.begin);
147 assertEquals(83, sf.end);
148 assertEquals("uniprot", sf.featureGroup);
149 assertEquals("Pfam", sf.type);
152 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
153 assertEquals(39, sf.begin);
154 assertEquals(39, sf.end);
155 assertEquals("uniprot", sf.featureGroup);
156 assertEquals("METAL", sf.type);
159 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
160 assertEquals(44, sf.begin);
161 assertEquals(44, sf.end);
162 assertEquals("uniprot", sf.featureGroup);
163 assertEquals("METAL", sf.type);
166 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
167 assertEquals(47, sf.begin);
168 assertEquals(47, sf.end);
169 assertEquals("uniprot", sf.featureGroup);
170 assertEquals("METAL", sf.type);
173 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
174 assertEquals(77, sf.begin);
175 assertEquals(77, sf.end);
176 assertEquals("uniprot", sf.featureGroup);
177 assertEquals("METAL", sf.type);
181 "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
184 "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&service=NetPhos-2.0",
186 assertEquals(89, sf.begin);
187 assertEquals(89, sf.end);
188 assertEquals("netphos", sf.featureGroup);
189 assertEquals("PHOSPHORYLATION (T)", sf.type);
193 * Test parsing a features file with a mix of Jalview and GFF formatted
198 @Test(groups = { "Functional" })
199 public void testParse_mixedJalviewGff() throws Exception
201 File f = new File("examples/uniref50.fa");
202 AlignmentI al = readAlignmentFile(f);
203 AlignFrame af = new AlignFrame(al, 500, 500);
204 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
205 .getFeatureColours();
206 // GFF2 uses space as name/value separator in column 9
207 String gffData = "METAL\tcc9900\n"
209 + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
210 + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
211 FeaturesFile featuresFile = new FeaturesFile(gffData,
212 DataSourceType.PASTE);
213 assertTrue("Failed to parse features file",
214 featuresFile.parse(al.getDataset(), colours, true));
216 // verify colours read or synthesized
217 colours = af.getFeatureRenderer().getFeatureColours();
218 assertEquals("1 feature group colours not found", 1, colours.size());
219 assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
221 // verify feature on FER_CAPAA
222 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
223 .getSequenceFeatures();
224 assertEquals(1, sfs.size());
225 SequenceFeature sf = sfs.get(0);
226 assertEquals("Iron-sulfur,2Fe-2S", sf.description);
227 assertEquals(44, sf.begin);
228 assertEquals(45, sf.end);
229 assertEquals("uniprot", sf.featureGroup);
230 assertEquals("METAL", sf.type);
231 assertEquals(4f, sf.getScore(), 0.001f);
233 // verify feature on FER1_SOLLC
234 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
235 assertEquals(1, sfs.size());
237 assertEquals("uniprot", sf.description);
238 assertEquals(55, sf.begin);
239 assertEquals(130, sf.end);
240 assertEquals("uniprot", sf.featureGroup);
241 assertEquals("Pfam", sf.type);
242 assertEquals(2f, sf.getScore(), 0.001f);
245 public static AlignmentI readAlignmentFile(File f) throws IOException
247 System.out.println("Reading file: " + f);
248 String ff = f.getPath();
249 FormatAdapter rf = new FormatAdapter();
251 AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
252 new IdentifyFile().identify(ff, DataSourceType.FILE));
254 al.setDataset(null); // creates dataset sequences
255 assertNotNull("Couldn't read supplied alignment data.", al);
260 * Test parsing a features file with GFF formatted content only
264 @Test(groups = { "Functional" })
265 public void testParse_pureGff3() throws Exception
267 File f = new File("examples/uniref50.fa");
268 AlignmentI al = readAlignmentFile(f);
269 AlignFrame af = new AlignFrame(al, 500, 500);
270 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
271 .getFeatureColours();
272 // GFF3 uses '=' separator for name/value pairs in column 9
273 // comma (%2C) equals (%3D) or semi-colon (%3B) should be url-escaped in values
274 String gffData = "##gff-version 3\n"
275 + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
276 + "Note=Iron-sulfur (2Fe-2S);Note=another note,and another;evidence=ECO%3B0000255%2CPROSITE%3DProRule:PRU00465;"
277 + "CSQ=AF=21,POLYPHEN=benign,possibly_damaging,clin_sig=Benign%3Dgood\n"
278 + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
279 FeaturesFile featuresFile = new FeaturesFile(gffData,
280 DataSourceType.PASTE);
281 assertTrue("Failed to parse features file",
282 featuresFile.parse(al.getDataset(), colours, true));
284 // verify feature on FER_CAPAA
285 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
286 .getSequenceFeatures();
287 assertEquals(1, sfs.size());
288 SequenceFeature sf = sfs.get(0);
289 // description parsed from Note attribute
290 assertEquals("Iron-sulfur (2Fe-2S),another note,and another",
292 assertEquals(39, sf.begin);
293 assertEquals(39, sf.end);
294 assertEquals("uniprot", sf.featureGroup);
295 assertEquals("METAL", sf.type);
296 assertEquals(5, sf.otherDetails.size());
297 assertEquals("ECO;0000255,PROSITE=ProRule:PRU00465", // url decoded
298 sf.getValue("evidence"));
299 assertEquals("Iron-sulfur (2Fe-2S),another note,and another",
300 sf.getValue("Note"));
301 assertEquals("21", sf.getValueAsString("CSQ", "AF"));
302 assertEquals("benign,possibly_damaging",
303 sf.getValueAsString("CSQ", "POLYPHEN"));
304 assertEquals("Benign=good", sf.getValueAsString("CSQ", "clin_sig")); // url decoded
305 // todo change STRAND and !Phase into fields of SequenceFeature instead
306 assertEquals(".", sf.otherDetails.get("STRAND"));
307 assertEquals(0, sf.getStrand());
308 assertEquals(".", sf.getPhase());
310 // verify feature on FER1_SOLLC1
311 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
312 assertEquals(1, sfs.size());
314 // ID used for description if available
315 assertEquals("$23", sf.description);
316 assertEquals(55, sf.begin);
317 assertEquals(130, sf.end);
318 assertEquals("uniprot", sf.featureGroup);
319 assertEquals("Pfam", sf.type);
320 assertEquals(3f, sf.getScore(), 0.001f);
324 * Test parsing a features file with Jalview format features (but no colour
325 * descriptors or startgroup to give the hint not to parse as GFF)
329 @Test(groups = { "Functional" })
330 public void testParse_jalviewFeaturesOnly() throws Exception
332 File f = new File("examples/uniref50.fa");
333 AlignmentI al = readAlignmentFile(f);
334 AlignFrame af = new AlignFrame(al, 500, 500);
335 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
336 .getFeatureColours();
339 * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
341 String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
342 + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
343 FeaturesFile featuresFile = new FeaturesFile(featureData,
344 DataSourceType.PASTE);
345 assertTrue("Failed to parse features file",
346 featuresFile.parse(al.getDataset(), colours, true));
348 // verify FER_CAPAA feature
349 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
350 .getSequenceFeatures();
351 assertEquals(1, sfs.size());
352 SequenceFeature sf = sfs.get(0);
353 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
354 assertEquals(39, sf.begin);
355 assertEquals(39, sf.end);
356 assertEquals("METAL", sf.type);
358 // verify FER1_SOLLC feature
359 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
360 assertEquals(1, sfs.size());
362 assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
363 assertEquals(86, sf.begin);
364 assertEquals(87, sf.end);
365 assertEquals("METALLIC", sf.type);
368 private void checkDatasetfromSimpleGff3(AlignmentI dataset)
370 assertEquals("no sequences extracted from GFF3 file", 2,
371 dataset.getHeight());
373 SequenceI seq1 = dataset.findName("seq1");
374 SequenceI seq2 = dataset.findName("seq2");
378 "Failed to replace dummy seq1 with real sequence",
379 seq1 instanceof SequenceDummy
380 && ((SequenceDummy) seq1).isDummy());
382 "Failed to replace dummy seq2 with real sequence",
383 seq2 instanceof SequenceDummy
384 && ((SequenceDummy) seq2).isDummy());
385 String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
386 assertFalse("dummy replacement buggy for seq1",
387 placeholderseq.equals(seq1.getSequenceAsString()));
388 assertFalse("dummy replacement buggy for seq2",
389 placeholderseq.equals(seq2.getSequenceAsString()));
390 assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
391 assertEquals("Wrong number of features", 3, seq1.getSequenceFeatures()
393 assertTrue(seq2.getSequenceFeatures().isEmpty());
395 "Wrong number of features",
397 seq2.getSequenceFeatures() == null ? 0 : seq2
398 .getSequenceFeatures().size());
400 "Expected at least one CDNA/Protein mapping for seq1",
401 dataset.getCodonFrame(seq1) != null
402 && dataset.getCodonFrame(seq1).size() > 0);
406 @Test(groups = { "Functional" })
407 public void readGff3File() throws IOException
409 FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
410 DataSourceType.FILE);
411 Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
412 gffreader.addProperties(dataset);
413 checkDatasetfromSimpleGff3(dataset);
416 @Test(groups = { "Functional" })
417 public void simpleGff3FileClass() throws IOException
419 AlignmentI dataset = new Alignment(new SequenceI[] {});
420 FeaturesFile ffile = new FeaturesFile(simpleGffFile,
421 DataSourceType.FILE);
423 boolean parseResult = ffile.parse(dataset, null, false, false);
424 assertTrue("return result should be true", parseResult);
425 checkDatasetfromSimpleGff3(dataset);
428 @Test(groups = { "Functional" })
429 public void simpleGff3FileLoader() throws IOException
431 AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
432 simpleGffFile, DataSourceType.FILE);
434 "Didn't read the alignment into an alignframe from Gff3 File",
436 checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
439 @Test(groups = { "Functional" })
440 public void simpleGff3RelaxedIdMatching() throws IOException
442 AlignmentI dataset = new Alignment(new SequenceI[] {});
443 FeaturesFile ffile = new FeaturesFile(simpleGffFile,
444 DataSourceType.FILE);
446 boolean parseResult = ffile.parse(dataset, null, false, true);
447 assertTrue("return result (relaxedID matching) should be true",
449 checkDatasetfromSimpleGff3(dataset);
452 @Test(groups = { "Functional" })
453 public void testPrintJalviewFormat() throws Exception
455 File f = new File("examples/uniref50.fa");
456 AlignmentI al = readAlignmentFile(f);
457 AlignFrame af = new AlignFrame(al, 500, 500);
458 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
459 .getFeatureColours();
460 String features = "METAL\tcc9900\n"
461 + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
463 + "STARTGROUP\tuniprot\n"
464 + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\n" // non-positional feature
465 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
466 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
467 + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
468 + "ENDGROUP\tuniprot\n";
469 FeaturesFile featuresFile = new FeaturesFile(features,
470 DataSourceType.PASTE);
471 featuresFile.parse(al.getDataset(), colours, false);
474 * add positional and non-positional features with null and
475 * empty feature group to check handled correctly
477 SequenceI seq = al.getSequenceAt(1); // FER_CAPAN
478 seq.addSequenceFeature(new SequenceFeature("Pfam", "desc1", 0, 0, 1.3f,
480 seq.addSequenceFeature(new SequenceFeature("Pfam", "desc2", 4, 9,
482 seq = al.getSequenceAt(2); // FER1_SOLLC
483 seq.addSequenceFeature(new SequenceFeature("Pfam", "desc3", 0, 0,
485 seq.addSequenceFeature(new SequenceFeature("Pfam", "desc4", 5, 8,
489 * first with no features displayed, exclude non-positional features
491 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
492 String exported = featuresFile
493 .printJalviewFormat(al.getSequencesArray(), fr, false, false);
494 String expected = "No Features Visible";
495 assertEquals(expected, exported);
498 * include non-positional features, but still no positional features
500 fr.setGroupVisibility("uniprot", true);
501 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
503 expected = "\nSTARTGROUP\tuniprot\n"
504 + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
505 + "ENDGROUP\tuniprot\n\n"
506 + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n\n"
507 + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"; // NaN is not output
508 assertEquals(expected, exported);
511 * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
513 fr.setVisible("METAL");
514 fr.setVisible("GAMMA-TURN");
515 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
517 expected = "METAL\tcc9900\n"
518 + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
519 + "\nSTARTGROUP\tuniprot\n"
520 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
521 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
522 + "ENDGROUP\tuniprot\n";
523 assertEquals(expected, exported);
526 * now set Pfam visible
528 fr.setVisible("Pfam");
529 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
532 * features are output within group, ordered by sequence and type
534 expected = "METAL\tcc9900\n"
536 + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
537 + "\nSTARTGROUP\tuniprot\n"
538 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
539 + "<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"
540 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
541 + "ENDGROUP\tuniprot\n"
542 // null / empty group features are output after named groups
543 + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
544 + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
545 assertEquals(expected, exported);
550 fr.setGroupVisibility("uniprot", false);
551 expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
552 + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
553 + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
554 + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
555 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
557 assertEquals(expected, exported);
560 * include non-positional (overrides group not shown)
562 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
564 expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
565 + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
566 + "\nSTARTGROUP\tuniprot\n"
567 + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
568 + "ENDGROUP\tuniprot\n"
569 + "\ndesc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n"
570 + "desc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
571 + "\ndesc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"
572 + "desc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
573 assertEquals(expected, exported);
576 @Test(groups = { "Functional" })
577 public void testPrintGffFormat() throws Exception
579 File f = new File("examples/uniref50.fa");
580 AlignmentI al = readAlignmentFile(f);
581 AlignFrame af = new AlignFrame(al, 500, 500);
586 FeaturesFile featuresFile = new FeaturesFile();
587 FeatureRendererModel fr = (FeatureRendererModel) af.alignPanel
588 .getFeatureRenderer();
589 String exported = featuresFile.printGffFormat(al.getSequencesArray(),
591 String gffHeader = "##gff-version 2\n";
592 assertEquals(gffHeader, exported);
593 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
595 assertEquals(gffHeader, exported);
600 al.getSequenceAt(0).addSequenceFeature(
601 new SequenceFeature("Domain", "Cath", 0, 0, 0f, "Uniprot"));
602 al.getSequenceAt(0).addSequenceFeature(
603 new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, null));
606 new SequenceFeature("GAMMA-TURN", "Turn", 36, 38, 2.1f,
608 SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f,
612 sf.setValue("x", "y");
613 sf.setValue("black", "white");
614 Map<String, String> csq = new HashMap<>();
615 csq.put("SIFT", "benign,mostly benign,cloudy, with meatballs");
616 csq.put("consequence", "missense_variant");
617 sf.setValue("CSQ", csq);
618 al.getSequenceAt(1).addSequenceFeature(sf);
621 * 'discover' features then hide all feature types
623 fr.findAllFeatures(true);
624 FeatureSettingsBean[] data = new FeatureSettingsBean[4];
625 FeatureColourI fc = new FeatureColour(Color.PINK);
626 data[0] = new FeatureSettingsBean("Domain", fc, null, false);
627 data[1] = new FeatureSettingsBean("METAL", fc, null, false);
628 data[2] = new FeatureSettingsBean("GAMMA-TURN", fc, null, false);
629 data[3] = new FeatureSettingsBean("Pfam", fc, null, false);
630 fr.setFeaturePriority(data);
633 * with no features displayed, exclude non-positional features
635 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
637 assertEquals(gffHeader, exported);
640 * include non-positional features
642 fr.setGroupVisibility("Uniprot", true);
643 fr.setGroupVisibility("s3dm", false);
644 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
646 String expected = gffHeader
647 + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
648 assertEquals(expected, exported);
651 * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
652 * only Uniprot group visible here...
654 fr.setVisible("METAL");
655 fr.setVisible("GAMMA-TURN");
656 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
658 // METAL feature has null group: description used for column 2
659 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
660 assertEquals(expected, exported);
663 * set s3dm group visible
665 fr.setGroupVisibility("s3dm", true);
666 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
668 // METAL feature has null group: description used for column 2
669 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
670 + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
671 assertEquals(expected, exported);
674 * now set Pfam visible
676 fr.setVisible("Pfam");
677 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
679 // Pfam feature columns include strand(+), phase(2), attributes
681 + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
682 // CSQ output as CSQ=att1=value1,att2=value2
683 // note all commas are encoded here which is wrong - it should be
684 // SIFT=benign,mostly benign,cloudy%2C with meatballs
685 + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white;"
686 + "CSQ=SIFT=benign%2Cmostly benign%2Ccloudy%2C with meatballs,consequence=missense_variant\n"
687 + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
688 assertEquals(expected, exported);
692 * Test for parsing of feature filters as represented in a Jalview features
697 @Test(groups = { "Functional" })
698 public void testParseFilters() throws Exception
700 Map<String, FeatureMatcherSetI> filters = new HashMap<>();
701 String text = "sequence_variant\tCSQ:PolyPhen NotContains 'damaging'\n"
702 + "missense_variant\t(label contains foobar) and (Score lt 1.3)";
703 FeaturesFile featuresFile = new FeaturesFile(text,
704 DataSourceType.PASTE);
705 featuresFile.parseFilters(filters);
706 assertEquals(filters.size(), 2);
708 FeatureMatcherSetI fm = filters.get("sequence_variant");
710 Iterator<FeatureMatcherI> matchers = fm.getMatchers().iterator();
711 FeatureMatcherI matcher = matchers.next();
712 assertFalse(matchers.hasNext());
713 String[] attributes = matcher.getAttribute();
714 assertArrayEquals(attributes, new String[] { "CSQ", "PolyPhen" });
715 assertSame(matcher.getMatcher().getCondition(), Condition.NotContains);
716 assertEquals(matcher.getMatcher().getPattern(), "damaging");
718 fm = filters.get("missense_variant");
720 matchers = fm.getMatchers().iterator();
721 matcher = matchers.next();
722 assertTrue(matcher.isByLabel());
723 assertSame(matcher.getMatcher().getCondition(), Condition.Contains);
724 assertEquals(matcher.getMatcher().getPattern(), "foobar");
725 matcher = matchers.next();
726 assertTrue(matcher.isByScore());
727 assertSame(matcher.getMatcher().getCondition(), Condition.LT);
728 assertEquals(matcher.getMatcher().getPattern(), "1.3");
729 assertEquals(PA.getValue(matcher.getMatcher(), "floatValue"), 1.3f);
731 assertFalse(matchers.hasNext());
734 @Test(groups = { "Functional" })
735 public void testOutputFeatureFilters()
737 FeaturesFile ff = new FeaturesFile();
738 StringBuilder sb = new StringBuilder();
739 Map<String, FeatureColourI> visible = new HashMap<>();
740 visible.put("pfam", new FeatureColour(Color.red));
741 Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
743 // with no filters, nothing is output
744 ff.outputFeatureFilters(sb, visible, featureFilters);
745 assertEquals("", sb.toString());
747 // with filter for not visible features only, nothing is output
748 FeatureMatcherSet filter = new FeatureMatcherSet();
749 filter.and(FeatureMatcher.byLabel(Condition.Present, null));
750 featureFilters.put("foobar", filter);
751 ff.outputFeatureFilters(sb, visible, featureFilters);
752 assertEquals("", sb.toString());
754 // with filters for visible feature types
755 FeatureMatcherSet filter2 = new FeatureMatcherSet();
756 filter2.and(FeatureMatcher.byAttribute(Condition.Present, null, "CSQ",
758 filter2.and(FeatureMatcher.byScore(Condition.LE, "-2.4"));
759 featureFilters.put("pfam", filter2);
760 visible.put("foobar", new FeatureColour(Color.blue));
761 ff.outputFeatureFilters(sb, visible, featureFilters);
762 String expected = "\nSTARTFILTERS\nfoobar\tLabel Present\npfam\t(CSQ:PolyPhen Present) AND (Score LE -2.4)\nENDFILTERS\n";
763 assertEquals(expected, sb.toString());
767 * Output as GFF should not include features which are not visible due to
768 * colour threshold or feature filter settings
772 @Test(groups = { "Functional" })
773 public void testPrintGffFormat_withFilters() throws Exception
775 File f = new File("examples/uniref50.fa");
776 AlignmentI al = readAlignmentFile(f);
777 AlignFrame af = new AlignFrame(al, 500, 500);
778 SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
780 sf1.setValue("clin_sig", "Likely Pathogenic");
781 sf1.setValue("AF", "24");
782 al.getSequenceAt(0).addSequenceFeature(sf1);
783 SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
785 sf2.setValue("clin_sig", "Benign");
786 sf2.setValue("AF", "46");
787 al.getSequenceAt(0).addSequenceFeature(sf2);
789 FeaturesFile featuresFile = new FeaturesFile();
790 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
791 final String gffHeader = "##gff-version 2\n";
793 fr.setVisible("METAL");
794 fr.setColour("METAL", new FeatureColour(Color.PINK));
795 String exported = featuresFile.printGffFormat(al.getSequencesArray(),
797 String expected = gffHeader
798 + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n"
799 + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
800 assertEquals(expected, exported);
803 * now threshold to Score > 1.1 - should exclude sf2
805 FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
806 Color.white, 0f, 2f);
807 fc.setAboveThreshold(true);
808 fc.setThreshold(1.1f);
809 fr.setColour("METAL", fc);
810 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
813 + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n";
814 assertEquals(expected, exported);
817 * remove threshold and check sf2 is exported
819 fc.setAboveThreshold(false);
820 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
823 + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n"
824 + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
825 assertEquals(expected, exported);
828 * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
830 FeatureMatcherSetI filter = new FeatureMatcherSet();
831 filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
833 fr.setFeatureFilter("METAL", filter);
834 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
837 + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
838 assertEquals(expected, exported);
842 * Output as Jalview should not include features which are not visible due to
843 * colour threshold or feature filter settings
847 @Test(groups = { "Functional" })
848 public void testPrintJalviewFormat_withFilters() throws Exception
850 File f = new File("examples/uniref50.fa");
851 AlignmentI al = readAlignmentFile(f);
852 AlignFrame af = new AlignFrame(al, 500, 500);
853 SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
855 sf1.setValue("clin_sig", "Likely Pathogenic");
856 sf1.setValue("AF", "24");
857 al.getSequenceAt(0).addSequenceFeature(sf1);
858 SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
860 sf2.setValue("clin_sig", "Benign");
861 sf2.setValue("AF", "46");
862 al.getSequenceAt(0).addSequenceFeature(sf2);
864 FeaturesFile featuresFile = new FeaturesFile();
865 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
866 fr.findAllFeatures(true);
868 fr.setVisible("METAL");
869 fr.setColour("METAL", new FeatureColour(Color.PINK));
870 String exported = featuresFile.printJalviewFormat(
871 al.getSequencesArray(),
873 String expected = "METAL\tffafaf\n\nSTARTGROUP\tgrp1\n"
874 + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
875 + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
876 + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
877 + "ENDGROUP\tgrp2\n";
878 assertEquals(expected, exported);
881 * now threshold to Score > 1.1 - should exclude sf2
882 * (and there should be no empty STARTGROUP/ENDGROUP output)
884 FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
885 Color.white, 0f, 2f);
886 fc.setAboveThreshold(true);
887 fc.setThreshold(1.1f);
888 fr.setColour("METAL", fc);
889 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
891 expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|above|1.1\n\n"
892 + "STARTGROUP\tgrp1\n"
893 + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
894 + "ENDGROUP\tgrp1\n";
895 assertEquals(expected, exported);
898 * remove threshold and check sf2 is exported
900 fc.setAboveThreshold(false);
901 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
903 expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
904 + "STARTGROUP\tgrp1\n"
905 + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
906 + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
907 + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
908 + "ENDGROUP\tgrp2\n";
909 assertEquals(expected, exported);
912 * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
914 FeatureMatcherSetI filter = new FeatureMatcherSet();
915 filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
917 fr.setFeatureFilter("METAL", filter);
918 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
920 expected = "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
921 expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
922 + "STARTFILTERS\nMETAL\tclin_sig Contains benign\nENDFILTERS\n\n"
923 + "STARTGROUP\tgrp2\n"
924 + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
925 + "ENDGROUP\tgrp2\n";
926 assertEquals(expected, exported);