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.util.matcher.Condition;
47 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
48 import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
50 import java.awt.Color;
52 import java.io.IOException;
53 import java.util.HashMap;
54 import java.util.Iterator;
55 import java.util.List;
58 import org.testng.annotations.AfterClass;
59 import org.testng.annotations.BeforeClass;
60 import org.testng.annotations.Test;
62 public class FeaturesFileTest
64 private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
66 @AfterClass(alwaysRun = true)
67 public void tearDownAfterClass()
70 * remove any sequence mappings created so they don't pollute other tests
72 Desktop.getInstance().getStructureSelectionManager().resetAll();
75 @BeforeClass(alwaysRun = true)
76 public void setUpJvOptionPane()
78 JvOptionPane.setInteractiveMode(false);
79 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
82 @Test(groups = { "Functional" })
83 public void testParse() throws Exception
85 File f = new File("examples/uniref50.fa");
86 AlignmentI al = readAlignmentFile(f);
87 AlignFrame af = new AlignFrame(al, 500, 500);
88 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
90 FeaturesFile featuresFile = new FeaturesFile(
91 "examples/exampleFeatures.txt", DataSourceType.FILE);
92 assertTrue("Test " + "Features file test"
93 + "\nFailed to parse features file.",
94 featuresFile.parse(al.getDataset(), colours, true));
97 * Refetch the colour map from the FeatureRenderer (to confirm it has been
98 * updated - JAL-1904), and verify (some) feature group colours
100 colours = af.getFeatureRenderer().getFeatureColours();
101 assertEquals("27 feature group colours not found", 27, colours.size());
102 assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
103 assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
104 FeatureColourI kdColour = colours.get("kdHydrophobicity");
105 assertTrue(kdColour.isGraduatedColour());
106 assertTrue(kdColour.isAboveThreshold());
107 assertEquals(-2f, kdColour.getThreshold());
110 * verify (some) features on sequences
112 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
113 .getSequenceFeatures(); // FER_CAPAA
114 SequenceFeatures.sortFeatures(sfs, true);
115 assertEquals(8, sfs.size());
118 * verify (in ascending start position order)
120 SequenceFeature sf = sfs.get(0);
121 assertEquals("Pfam family%LINK%", sf.description);
122 assertEquals(0, sf.begin);
123 assertEquals(0, sf.end);
124 assertEquals("uniprot", sf.featureGroup);
125 assertEquals("Pfam", sf.type);
126 assertEquals(1, sf.links.size());
127 assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
131 assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
132 assertEquals(3, sf.begin);
133 assertEquals(93, sf.end);
134 assertEquals("uniprot", sf.featureGroup);
135 assertEquals("Cath", sf.type);
138 assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
140 assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
142 assertEquals(8, sf.begin);
143 assertEquals(83, sf.end);
144 assertEquals("uniprot", sf.featureGroup);
145 assertEquals("Pfam", sf.type);
148 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
149 assertEquals(39, sf.begin);
150 assertEquals(39, sf.end);
151 assertEquals("uniprot", sf.featureGroup);
152 assertEquals("METAL", sf.type);
155 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
156 assertEquals(44, sf.begin);
157 assertEquals(44, sf.end);
158 assertEquals("uniprot", sf.featureGroup);
159 assertEquals("METAL", sf.type);
162 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
163 assertEquals(47, sf.begin);
164 assertEquals(47, sf.end);
165 assertEquals("uniprot", sf.featureGroup);
166 assertEquals("METAL", sf.type);
169 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
170 assertEquals(77, sf.begin);
171 assertEquals(77, sf.end);
172 assertEquals("uniprot", sf.featureGroup);
173 assertEquals("METAL", sf.type);
177 "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
180 "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&service=NetPhos-2.0",
182 assertEquals(89, sf.begin);
183 assertEquals(89, sf.end);
184 assertEquals("netphos", sf.featureGroup);
185 assertEquals("PHOSPHORYLATION (T)", sf.type);
189 * Test parsing a features file with a mix of Jalview and GFF formatted
194 @Test(groups = { "Functional" })
195 public void testParse_mixedJalviewGff() throws Exception
197 File f = new File("examples/uniref50.fa");
198 AlignmentI al = readAlignmentFile(f);
199 AlignFrame af = new AlignFrame(al, 500, 500);
200 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
201 .getFeatureColours();
202 // GFF2 uses space as name/value separator in column 9
203 String gffData = "METAL\tcc9900\n"
205 + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
206 + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
207 FeaturesFile featuresFile = new FeaturesFile(gffData,
208 DataSourceType.PASTE);
209 assertTrue("Failed to parse features file",
210 featuresFile.parse(al.getDataset(), colours, true));
212 // verify colours read or synthesized
213 colours = af.getFeatureRenderer().getFeatureColours();
214 assertEquals("1 feature group colours not found", 1, colours.size());
215 assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
217 // verify feature on FER_CAPAA
218 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
219 .getSequenceFeatures();
220 assertEquals(1, sfs.size());
221 SequenceFeature sf = sfs.get(0);
222 assertEquals("Iron-sulfur,2Fe-2S", sf.description);
223 assertEquals(44, sf.begin);
224 assertEquals(45, sf.end);
225 assertEquals("uniprot", sf.featureGroup);
226 assertEquals("METAL", sf.type);
227 assertEquals(4f, sf.getScore(), 0.001f);
229 // verify feature on FER1_SOLLC
230 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
231 assertEquals(1, sfs.size());
233 assertEquals("uniprot", sf.description);
234 assertEquals(55, sf.begin);
235 assertEquals(130, sf.end);
236 assertEquals("uniprot", sf.featureGroup);
237 assertEquals("Pfam", sf.type);
238 assertEquals(2f, sf.getScore(), 0.001f);
241 public static AlignmentI readAlignmentFile(File f) throws IOException
243 System.out.println("Reading file: " + f);
244 String ff = f.getPath();
245 FormatAdapter rf = new FormatAdapter();
247 AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
248 new IdentifyFile().identify(ff, DataSourceType.FILE));
250 al.setDataset(null); // creates dataset sequences
251 assertNotNull("Couldn't read supplied alignment data.", al);
256 * Test parsing a features file with GFF formatted content only
260 @Test(groups = { "Functional" })
261 public void testParse_pureGff3() throws Exception
263 File f = new File("examples/uniref50.fa");
264 AlignmentI al = readAlignmentFile(f);
265 AlignFrame af = new AlignFrame(al, 500, 500);
266 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
267 .getFeatureColours();
268 // GFF3 uses '=' separator for name/value pairs in colum 9
269 String gffData = "##gff-version 3\n"
270 + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
271 + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465\n"
272 + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
273 FeaturesFile featuresFile = new FeaturesFile(gffData,
274 DataSourceType.PASTE);
275 assertTrue("Failed to parse features file",
276 featuresFile.parse(al.getDataset(), colours, true));
278 // verify feature on FER_CAPAA
279 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
280 .getSequenceFeatures();
281 assertEquals(1, sfs.size());
282 SequenceFeature sf = sfs.get(0);
283 // description parsed from Note attribute
284 assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description);
285 assertEquals(39, sf.begin);
286 assertEquals(39, sf.end);
287 assertEquals("uniprot", sf.featureGroup);
288 assertEquals("METAL", sf.type);
290 "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465",
291 sf.getValue("ATTRIBUTES"));
293 // verify feature on FER1_SOLLC1
294 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
295 assertEquals(1, sfs.size());
297 // ID used for description if available
298 assertEquals("$23", sf.description);
299 assertEquals(55, sf.begin);
300 assertEquals(130, sf.end);
301 assertEquals("uniprot", sf.featureGroup);
302 assertEquals("Pfam", sf.type);
303 assertEquals(3f, sf.getScore(), 0.001f);
307 * Test parsing a features file with Jalview format features (but no colour
308 * descriptors or startgroup to give the hint not to parse as GFF)
312 @Test(groups = { "Functional" })
313 public void testParse_jalviewFeaturesOnly() throws Exception
315 File f = new File("examples/uniref50.fa");
316 AlignmentI al = readAlignmentFile(f);
317 AlignFrame af = new AlignFrame(al, 500, 500);
318 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
319 .getFeatureColours();
322 * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
324 String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
325 + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
326 FeaturesFile featuresFile = new FeaturesFile(featureData,
327 DataSourceType.PASTE);
328 assertTrue("Failed to parse features file",
329 featuresFile.parse(al.getDataset(), colours, true));
331 // verify FER_CAPAA feature
332 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
333 .getSequenceFeatures();
334 assertEquals(1, sfs.size());
335 SequenceFeature sf = sfs.get(0);
336 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
337 assertEquals(39, sf.begin);
338 assertEquals(39, sf.end);
339 assertEquals("METAL", sf.type);
341 // verify FER1_SOLLC feature
342 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
343 assertEquals(1, sfs.size());
345 assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
346 assertEquals(86, sf.begin);
347 assertEquals(87, sf.end);
348 assertEquals("METALLIC", sf.type);
351 private void checkDatasetfromSimpleGff3(AlignmentI dataset)
353 assertEquals("no sequences extracted from GFF3 file", 2,
354 dataset.getHeight());
356 SequenceI seq1 = dataset.findName("seq1");
357 SequenceI seq2 = dataset.findName("seq2");
361 "Failed to replace dummy seq1 with real sequence",
362 seq1 instanceof SequenceDummy
363 && ((SequenceDummy) seq1).isDummy());
365 "Failed to replace dummy seq2 with real sequence",
366 seq2 instanceof SequenceDummy
367 && ((SequenceDummy) seq2).isDummy());
368 String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
369 assertFalse("dummy replacement buggy for seq1",
370 placeholderseq.equals(seq1.getSequenceAsString()));
371 assertFalse("dummy replacement buggy for seq2",
372 placeholderseq.equals(seq2.getSequenceAsString()));
373 assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
374 assertEquals("Wrong number of features", 3, seq1.getSequenceFeatures()
376 assertTrue(seq2.getSequenceFeatures().isEmpty());
378 "Wrong number of features",
380 seq2.getSequenceFeatures() == null ? 0 : seq2
381 .getSequenceFeatures().size());
383 "Expected at least one CDNA/Protein mapping for seq1",
384 dataset.getCodonFrame(seq1) != null
385 && dataset.getCodonFrame(seq1).size() > 0);
389 @Test(groups = { "Functional" })
390 public void readGff3File() throws IOException
392 FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
393 DataSourceType.FILE);
394 Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
395 gffreader.addProperties(dataset);
396 checkDatasetfromSimpleGff3(dataset);
399 @Test(groups = { "Functional" })
400 public void simpleGff3FileClass() throws IOException
402 AlignmentI dataset = new Alignment(new SequenceI[] {});
403 FeaturesFile ffile = new FeaturesFile(simpleGffFile,
404 DataSourceType.FILE);
406 boolean parseResult = ffile.parse(dataset, null, false, false);
407 assertTrue("return result should be true", parseResult);
408 checkDatasetfromSimpleGff3(dataset);
411 @Test(groups = { "Functional" })
412 public void simpleGff3FileLoader() throws IOException
414 AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
415 simpleGffFile, DataSourceType.FILE);
417 "Didn't read the alignment into an alignframe from Gff3 File",
419 checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
422 @Test(groups = { "Functional" })
423 public void simpleGff3RelaxedIdMatching() throws IOException
425 AlignmentI dataset = new Alignment(new SequenceI[] {});
426 FeaturesFile ffile = new FeaturesFile(simpleGffFile,
427 DataSourceType.FILE);
429 boolean parseResult = ffile.parse(dataset, null, false, true);
430 assertTrue("return result (relaxedID matching) should be true",
432 checkDatasetfromSimpleGff3(dataset);
435 @Test(groups = { "Functional" })
436 public void testPrintJalviewFormat() throws Exception
438 File f = new File("examples/uniref50.fa");
439 AlignmentI al = readAlignmentFile(f);
440 AlignFrame af = new AlignFrame(al, 500, 500);
441 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
442 .getFeatureColours();
443 String features = "METAL\tcc9900\n"
444 + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
446 + "STARTGROUP\tuniprot\n"
447 + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\n" // non-positional feature
448 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
449 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
450 + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
451 + "ENDGROUP\tuniprot\n";
452 FeaturesFile featuresFile = new FeaturesFile(features,
453 DataSourceType.PASTE);
454 featuresFile.parse(al.getDataset(), colours, false);
457 * add positional and non-positional features with null and
458 * empty feature group to check handled correctly
460 SequenceI seq = al.getSequenceAt(1); // FER_CAPAN
461 seq.addSequenceFeature(new SequenceFeature("Pfam", "desc1", 0, 0, 1.3f,
463 seq.addSequenceFeature(new SequenceFeature("Pfam", "desc2", 4, 9,
465 seq = al.getSequenceAt(2); // FER1_SOLLC
466 seq.addSequenceFeature(new SequenceFeature("Pfam", "desc3", 0, 0,
468 seq.addSequenceFeature(new SequenceFeature("Pfam", "desc4", 5, 8,
472 * first with no features displayed, exclude non-positional features
474 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
475 String exported = featuresFile
476 .printJalviewFormat(al.getSequencesArray(), fr, false);
477 String expected = "No Features Visible";
478 assertEquals(expected, exported);
481 * include non-positional features, but still no positional features
483 fr.setGroupVisibility("uniprot", true);
484 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
486 expected = "\nSTARTGROUP\tuniprot\n"
487 + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
488 + "ENDGROUP\tuniprot\n\n"
489 + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n\n"
490 + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"; // NaN is not output
492 expected.replace("\n", System.getProperty("line.separator")),
496 * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
498 fr.setVisible("METAL");
499 fr.setVisible("GAMMA-TURN");
500 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
502 expected = "METAL\tcc9900\n"
503 + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
504 + "\nSTARTGROUP\tuniprot\n"
505 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
506 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
507 + "ENDGROUP\tuniprot\n";
508 assertEquals(fixLineEnd(expected), exported);
511 * now set Pfam visible
513 fr.setVisible("Pfam");
514 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
517 * features are output within group, ordered by sequence and type
519 expected = "METAL\tcc9900\n"
521 + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
522 + "\nSTARTGROUP\tuniprot\n"
523 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
524 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
525 + "<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"
526 + "ENDGROUP\tuniprot\n"
527 // null / empty group features are output after named groups
528 + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
529 + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
530 assertEquals(fixLineEnd(expected), exported);
535 fr.setGroupVisibility("uniprot", false);
536 expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
537 + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
538 + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
539 + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
540 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
542 assertEquals(fixLineEnd(expected), exported);
545 * include non-positional (overrides group not shown)
547 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
549 expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
550 + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
551 + "\nSTARTGROUP\tuniprot\n"
552 + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
553 + "ENDGROUP\tuniprot\n"
554 + "\ndesc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n"
555 + "desc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
556 + "\ndesc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"
557 + "desc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
558 assertEquals(fixLineEnd(expected), exported);
561 @Test(groups = { "Functional" })
562 public void testPrintGffFormat() throws Exception
564 File f = new File("examples/uniref50.fa");
565 AlignmentI al = readAlignmentFile(f);
566 AlignFrame af = new AlignFrame(al, 500, 500);
571 FeaturesFile featuresFile = new FeaturesFile();
572 FeatureRendererModel fr = (FeatureRendererModel) af.alignPanel
573 .getFeatureRenderer();
574 String exported = featuresFile.printGffFormat(al.getSequencesArray(),
576 String gffHeader = "##gff-version 2\n";
578 fixLineEnd(gffHeader),
580 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
583 fixLineEnd(gffHeader),
589 al.getSequenceAt(0).addSequenceFeature(
590 new SequenceFeature("Domain", "Cath", 0, 0, 0f, "Uniprot"));
591 al.getSequenceAt(0).addSequenceFeature(
592 new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, null));
595 new SequenceFeature("GAMMA-TURN", "Turn", 36, 38, 2.1f,
597 SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f,
599 sf.setAttributes("x=y;black=white");
602 al.getSequenceAt(1).addSequenceFeature(sf);
605 * 'discover' features then hide all feature types
607 fr.findAllFeatures(true);
608 FeatureSettingsBean[] data = new FeatureSettingsBean[4];
609 FeatureColourI fc = new FeatureColour(Color.PINK);
610 data[0] = new FeatureSettingsBean("Domain", fc, null, false);
611 data[1] = new FeatureSettingsBean("METAL", fc, null, false);
612 data[2] = new FeatureSettingsBean("GAMMA-TURN", fc, null, false);
613 data[3] = new FeatureSettingsBean("Pfam", fc, null, false);
614 fr.setFeaturePriority(data);
617 * with no features displayed, exclude non-positional features
619 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
622 fixLineEnd(gffHeader),
626 * include non-positional features
628 fr.setGroupVisibility("Uniprot", true);
629 fr.setGroupVisibility("s3dm", false);
630 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
632 String expected = gffHeader
633 + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
635 fixLineEnd(expected),
639 * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
640 * only Uniprot group visible here...
642 fr.setVisible("METAL");
643 fr.setVisible("GAMMA-TURN");
644 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
646 // METAL feature has null group: description used for column 2
647 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
649 expected.replace("\n", System.getProperty("line.separator")),
653 * set s3dm group visible
655 fr.setGroupVisibility("s3dm", true);
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 + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
662 expected.replace("\n", System.getProperty("line.separator")),
666 * now set Pfam visible
668 fr.setVisible("Pfam");
669 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
671 // Pfam feature columns include strand(+), phase(2), attributes
673 + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
674 + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n"
675 + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n";
677 expected.replace("\n", System.getProperty("line.separator")),
681 private String fixLineEnd(String s)
683 return s.replace("\n", System.getProperty("line.separator"));
687 * Test for parsing of feature filters as represented in a Jalview features
692 @Test(groups = { "Functional" })
693 public void testParseFilters() throws Exception
695 Map<String, FeatureMatcherSetI> filters = new HashMap<>();
696 String text = "sequence_variant\tCSQ:PolyPhen NotContains 'damaging'\n"
697 + "missense_variant\t(label contains foobar) and (Score lt 1.3)";
698 FeaturesFile featuresFile = new FeaturesFile(text,
699 DataSourceType.PASTE);
700 featuresFile.parseFilters(filters);
701 assertEquals(filters.size(), 2);
703 FeatureMatcherSetI fm = filters.get("sequence_variant");
705 Iterator<FeatureMatcherI> matchers = fm.getMatchers().iterator();
706 FeatureMatcherI matcher = matchers.next();
707 assertFalse(matchers.hasNext());
708 String[] attributes = matcher.getAttribute();
709 assertArrayEquals(attributes, new String[] { "CSQ", "PolyPhen" });
710 assertSame(matcher.getMatcher().getCondition(), Condition.NotContains);
711 assertEquals(matcher.getMatcher().getPattern(), "damaging");
713 fm = filters.get("missense_variant");
715 matchers = fm.getMatchers().iterator();
716 matcher = matchers.next();
717 assertTrue(matcher.isByLabel());
718 assertSame(matcher.getMatcher().getCondition(), Condition.Contains);
719 assertEquals(matcher.getMatcher().getPattern(), "foobar");
720 matcher = matchers.next();
721 assertTrue(matcher.isByScore());
722 assertSame(matcher.getMatcher().getCondition(), Condition.LT);
723 assertEquals(matcher.getMatcher().getPattern(), "1.3");
724 assertEquals(matcher.getMatcher().getFloatValue(), 1.3f);
726 assertFalse(matchers.hasNext());
729 @Test(groups = { "Functional" })
730 public void testOutputFeatureFilters()
732 FeaturesFile ff = new FeaturesFile();
733 StringBuilder sb = new StringBuilder();
734 Map<String, FeatureColourI> visible = new HashMap<>();
735 visible.put("pfam", new FeatureColour(Color.red));
736 Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
738 // with no filters, nothing is output
739 ff.outputFeatureFilters(sb, visible, featureFilters);
740 assertEquals("", sb.toString());
742 // with filter for not visible features only, nothing is output
743 FeatureMatcherSet filter = new FeatureMatcherSet();
744 filter.and(FeatureMatcher.byLabel(Condition.Present, null));
745 featureFilters.put("foobar", filter);
746 ff.outputFeatureFilters(sb, visible, featureFilters);
747 assertEquals("", sb.toString());
749 // with filters for visible feature types
750 FeatureMatcherSet filter2 = new FeatureMatcherSet();
751 filter2.and(FeatureMatcher.byAttribute(Condition.Present, null, "CSQ",
753 filter2.and(FeatureMatcher.byScore(Condition.LE, "-2.4"));
754 featureFilters.put("pfam", filter2);
755 visible.put("foobar", new FeatureColour(Color.blue));
756 ff.outputFeatureFilters(sb, visible, featureFilters);
757 String expected = "\nSTARTFILTERS\nfoobar\tLabel Present\npfam\t(CSQ:PolyPhen Present) AND (Score LE -2.4)\nENDFILTERS\n";
758 assertEquals(fixLineEnd(expected), sb.toString());
762 * Output as GFF should not include features which are not visible due to
763 * colour threshold or feature filter settings
767 @Test(groups = { "Functional" })
768 public void testPrintGffFormat_withFilters() throws Exception
770 File f = new File("examples/uniref50.fa");
771 AlignmentI al = readAlignmentFile(f);
772 AlignFrame af = new AlignFrame(al, 500, 500);
773 SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
775 sf1.setValue("clin_sig", "Likely Pathogenic");
776 sf1.setValue("AF", "24");
777 al.getSequenceAt(0).addSequenceFeature(sf1);
778 SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
780 sf2.setValue("clin_sig", "Benign");
781 sf2.setValue("AF", "46");
782 al.getSequenceAt(0).addSequenceFeature(sf2);
784 FeaturesFile featuresFile = new FeaturesFile();
785 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
786 final String gffHeader = "##gff-version 2\n";
788 fr.setVisible("METAL");
789 fr.setColour("METAL", new FeatureColour(Color.PINK));
790 String exported = featuresFile.printGffFormat(al.getSequencesArray(),
792 String expected = gffHeader
793 + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
794 + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
796 fixLineEnd(expected), exported);
799 * now threshold to Score > 1.1 - should exclude sf2
801 FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
802 Color.white, 0f, 2f);
803 fc.setAboveThreshold(true);
804 fc.setThreshold(1.1f);
805 fr.setColour("METAL", fc);
806 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
808 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
809 assertEquals(fixLineEnd(expected), exported);
812 * remove threshold and check sf2 is exported
814 fc.setAboveThreshold(false);
815 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
817 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
818 + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
819 assertEquals(fixLineEnd(expected), exported);
822 * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
824 FeatureMatcherSetI filter = new FeatureMatcherSet();
825 filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
827 fr.setFeatureFilter("METAL", filter);
828 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
830 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
831 assertEquals(fixLineEnd(expected), exported);
835 * Output as Jalview should not include features which are not visible due to
836 * colour threshold or feature filter settings
840 @Test(groups = { "Functional" })
841 public void testPrintJalviewFormat_withFilters() throws Exception
843 File f = new File("examples/uniref50.fa");
844 AlignmentI al = readAlignmentFile(f);
845 AlignFrame af = new AlignFrame(al, 500, 500);
846 SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
848 sf1.setValue("clin_sig", "Likely Pathogenic");
849 sf1.setValue("AF", "24");
850 al.getSequenceAt(0).addSequenceFeature(sf1);
851 SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
853 sf2.setValue("clin_sig", "Benign");
854 sf2.setValue("AF", "46");
855 al.getSequenceAt(0).addSequenceFeature(sf2);
857 FeaturesFile featuresFile = new FeaturesFile();
858 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
859 fr.findAllFeatures(true);
861 fr.setVisible("METAL");
862 fr.setColour("METAL", new FeatureColour(Color.PINK));
863 String exported = featuresFile.printJalviewFormat(
864 al.getSequencesArray(),
866 String expected = "METAL\tffafaf\n\nSTARTGROUP\tgrp1\n"
867 + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
868 + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
869 + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
870 + "ENDGROUP\tgrp2\n";
872 fixLineEnd(expected),
876 * now threshold to Score > 1.1 - should exclude sf2
877 * (and there should be no empty STARTGROUP/ENDGROUP output)
879 FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
880 Color.white, 0f, 2f);
881 fc.setAboveThreshold(true);
882 fc.setThreshold(1.1f);
883 fr.setColour("METAL", fc);
884 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
886 expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|above|1.1\n\n"
887 + "STARTGROUP\tgrp1\n"
888 + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
889 + "ENDGROUP\tgrp1\n";
891 expected.replace("\n", System.getProperty("line.separator")),
895 * remove threshold and check sf2 is exported
897 fc.setAboveThreshold(false);
898 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
900 expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
901 + "STARTGROUP\tgrp1\n"
902 + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
903 + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
904 + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
905 + "ENDGROUP\tgrp2\n";
906 assertEquals(fixLineEnd(expected), exported);
909 * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
911 FeatureMatcherSetI filter = new FeatureMatcherSet();
912 filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
914 fr.setFeatureFilter("METAL", filter);
915 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
917 expected = "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
918 expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
919 + "STARTFILTERS\nMETAL\tclin_sig Contains benign\nENDFILTERS\n\n"
920 + "STARTGROUP\tgrp2\n"
921 + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
922 + "ENDGROUP\tgrp2\n";
923 assertEquals(fixLineEnd(expected), exported);