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 final String LINE_SEPARATOR = System.getProperty("line.separator");
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 Desktop.getStructureSelectionManager().resetAll();
76 @BeforeClass(alwaysRun = true)
77 public void setUpJvOptionPane()
79 JvOptionPane.setInteractiveMode(false);
80 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
83 @Test(groups = { "Functional" })
84 public void testParse() throws Exception
86 File f = new File("examples/uniref50.fa");
87 AlignmentI al = readAlignmentFile(f);
88 AlignFrame af = new AlignFrame(al, 500, 500);
89 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
91 FeaturesFile featuresFile = new FeaturesFile(
92 "examples/exampleFeatures.txt", DataSourceType.FILE);
93 assertTrue("Test " + "Features file test"
94 + "\nFailed to parse features file.",
95 featuresFile.parse(al.getDataset(), colours, true));
98 * Refetch the colour map from the FeatureRenderer (to confirm it has been
99 * updated - JAL-1904), and verify (some) feature group colours
101 colours = af.getFeatureRenderer().getFeatureColours();
102 assertEquals("27 feature group colours not found", 27, colours.size());
103 assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
104 assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
105 FeatureColourI kdColour = colours.get("kdHydrophobicity");
106 assertTrue(kdColour.isGraduatedColour());
107 assertTrue(kdColour.isAboveThreshold());
108 assertEquals(-2f, kdColour.getThreshold());
111 * verify (some) features on sequences
113 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
114 .getSequenceFeatures(); // FER_CAPAA
115 SequenceFeatures.sortFeatures(sfs, true);
116 assertEquals(8, sfs.size());
119 * verify (in ascending start position order)
121 SequenceFeature sf = sfs.get(0);
122 assertEquals("Pfam family%LINK%", sf.description);
123 assertEquals(0, sf.begin);
124 assertEquals(0, sf.end);
125 assertEquals("uniprot", sf.featureGroup);
126 assertEquals("Pfam", sf.type);
127 assertEquals(1, sf.links.size());
128 assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
132 assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
133 assertEquals(3, sf.begin);
134 assertEquals(93, sf.end);
135 assertEquals("uniprot", sf.featureGroup);
136 assertEquals("Cath", sf.type);
139 assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
141 assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
143 assertEquals(8, sf.begin);
144 assertEquals(83, sf.end);
145 assertEquals("uniprot", sf.featureGroup);
146 assertEquals("Pfam", sf.type);
149 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
150 assertEquals(39, sf.begin);
151 assertEquals(39, sf.end);
152 assertEquals("uniprot", sf.featureGroup);
153 assertEquals("METAL", sf.type);
156 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
157 assertEquals(44, sf.begin);
158 assertEquals(44, sf.end);
159 assertEquals("uniprot", sf.featureGroup);
160 assertEquals("METAL", sf.type);
163 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
164 assertEquals(47, sf.begin);
165 assertEquals(47, sf.end);
166 assertEquals("uniprot", sf.featureGroup);
167 assertEquals("METAL", sf.type);
170 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
171 assertEquals(77, sf.begin);
172 assertEquals(77, sf.end);
173 assertEquals("uniprot", sf.featureGroup);
174 assertEquals("METAL", sf.type);
178 "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
181 "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&service=NetPhos-2.0",
183 assertEquals(89, sf.begin);
184 assertEquals(89, sf.end);
185 assertEquals("netphos", sf.featureGroup);
186 assertEquals("PHOSPHORYLATION (T)", sf.type);
190 * Test parsing a features file with a mix of Jalview and GFF formatted
195 @Test(groups = { "Functional" })
196 public void testParse_mixedJalviewGff() throws Exception
198 File f = new File("examples/uniref50.fa");
199 AlignmentI al = readAlignmentFile(f);
200 AlignFrame af = new AlignFrame(al, 500, 500);
201 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
202 .getFeatureColours();
203 // GFF2 uses space as name/value separator in column 9
204 String gffData = "METAL\tcc9900\n"
206 + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
207 + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
208 FeaturesFile featuresFile = new FeaturesFile(gffData,
209 DataSourceType.PASTE);
210 assertTrue("Failed to parse features file",
211 featuresFile.parse(al.getDataset(), colours, true));
213 // verify colours read or synthesized
214 colours = af.getFeatureRenderer().getFeatureColours();
215 assertEquals("1 feature group colours not found", 1, colours.size());
216 assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
218 // verify feature on FER_CAPAA
219 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
220 .getSequenceFeatures();
221 assertEquals(1, sfs.size());
222 SequenceFeature sf = sfs.get(0);
223 assertEquals("Iron-sulfur,2Fe-2S", sf.description);
224 assertEquals(44, sf.begin);
225 assertEquals(45, sf.end);
226 assertEquals("uniprot", sf.featureGroup);
227 assertEquals("METAL", sf.type);
228 assertEquals(4f, sf.getScore(), 0.001f);
230 // verify feature on FER1_SOLLC
231 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
232 assertEquals(1, sfs.size());
234 assertEquals("uniprot", sf.description);
235 assertEquals(55, sf.begin);
236 assertEquals(130, sf.end);
237 assertEquals("uniprot", sf.featureGroup);
238 assertEquals("Pfam", sf.type);
239 assertEquals(2f, sf.getScore(), 0.001f);
242 public static AlignmentI readAlignmentFile(File f) throws IOException
244 System.out.println("Reading file: " + f);
245 String ff = f.getPath();
246 FormatAdapter rf = new FormatAdapter();
248 AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
249 new IdentifyFile().identify(ff, DataSourceType.FILE));
251 al.setDataset(null); // creates dataset sequences
252 assertNotNull("Couldn't read supplied alignment data.", al);
257 * Test parsing a features file with GFF formatted content only
261 @Test(groups = { "Functional" })
262 public void testParse_pureGff3() throws Exception
264 File f = new File("examples/uniref50.fa");
265 AlignmentI al = readAlignmentFile(f);
266 AlignFrame af = new AlignFrame(al, 500, 500);
267 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
268 .getFeatureColours();
269 // GFF3 uses '=' separator for name/value pairs in colum 9
270 String gffData = "##gff-version 3\n"
271 + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
272 + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465\n"
273 + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
274 FeaturesFile featuresFile = new FeaturesFile(gffData,
275 DataSourceType.PASTE);
276 assertTrue("Failed to parse features file",
277 featuresFile.parse(al.getDataset(), colours, true));
279 // verify feature on FER_CAPAA
280 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
281 .getSequenceFeatures();
282 assertEquals(1, sfs.size());
283 SequenceFeature sf = sfs.get(0);
284 // description parsed from Note attribute
285 assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description);
286 assertEquals(39, sf.begin);
287 assertEquals(39, sf.end);
288 assertEquals("uniprot", sf.featureGroup);
289 assertEquals("METAL", sf.type);
291 "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465",
292 sf.getValue("ATTRIBUTES"));
294 // verify feature on FER1_SOLLC1
295 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
296 assertEquals(1, sfs.size());
298 // ID used for description if available
299 assertEquals("$23", sf.description);
300 assertEquals(55, sf.begin);
301 assertEquals(130, sf.end);
302 assertEquals("uniprot", sf.featureGroup);
303 assertEquals("Pfam", sf.type);
304 assertEquals(3f, sf.getScore(), 0.001f);
308 * Test parsing a features file with Jalview format features (but no colour
309 * descriptors or startgroup to give the hint not to parse as GFF)
313 @Test(groups = { "Functional" })
314 public void testParse_jalviewFeaturesOnly() throws Exception
316 File f = new File("examples/uniref50.fa");
317 AlignmentI al = readAlignmentFile(f);
318 AlignFrame af = new AlignFrame(al, 500, 500);
319 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
320 .getFeatureColours();
323 * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
325 String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
326 + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
327 FeaturesFile featuresFile = new FeaturesFile(featureData,
328 DataSourceType.PASTE);
329 assertTrue("Failed to parse features file",
330 featuresFile.parse(al.getDataset(), colours, true));
332 // verify FER_CAPAA feature
333 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
334 .getSequenceFeatures();
335 assertEquals(1, sfs.size());
336 SequenceFeature sf = sfs.get(0);
337 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
338 assertEquals(39, sf.begin);
339 assertEquals(39, sf.end);
340 assertEquals("METAL", sf.type);
342 // verify FER1_SOLLC feature
343 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
344 assertEquals(1, sfs.size());
346 assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
347 assertEquals(86, sf.begin);
348 assertEquals(87, sf.end);
349 assertEquals("METALLIC", sf.type);
352 private void checkDatasetfromSimpleGff3(AlignmentI dataset)
354 assertEquals("no sequences extracted from GFF3 file", 2,
355 dataset.getHeight());
357 SequenceI seq1 = dataset.findName("seq1");
358 SequenceI seq2 = dataset.findName("seq2");
362 "Failed to replace dummy seq1 with real sequence",
363 seq1 instanceof SequenceDummy
364 && ((SequenceDummy) seq1).isDummy());
366 "Failed to replace dummy seq2 with real sequence",
367 seq2 instanceof SequenceDummy
368 && ((SequenceDummy) seq2).isDummy());
369 String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
370 assertFalse("dummy replacement buggy for seq1",
371 placeholderseq.equals(seq1.getSequenceAsString()));
372 assertFalse("dummy replacement buggy for seq2",
373 placeholderseq.equals(seq2.getSequenceAsString()));
374 assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
375 assertEquals("Wrong number of features", 3, seq1.getSequenceFeatures()
377 assertTrue(seq2.getSequenceFeatures().isEmpty());
379 "Wrong number of features",
381 seq2.getSequenceFeatures() == null ? 0 : seq2
382 .getSequenceFeatures().size());
384 "Expected at least one CDNA/Protein mapping for seq1",
385 dataset.getCodonFrame(seq1) != null
386 && dataset.getCodonFrame(seq1).size() > 0);
390 @Test(groups = { "Functional" })
391 public void readGff3File() throws IOException
393 FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
394 DataSourceType.FILE);
395 Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
396 gffreader.addProperties(dataset);
397 checkDatasetfromSimpleGff3(dataset);
400 @Test(groups = { "Functional" })
401 public void simpleGff3FileClass() throws IOException
403 AlignmentI dataset = new Alignment(new SequenceI[] {});
404 FeaturesFile ffile = new FeaturesFile(simpleGffFile,
405 DataSourceType.FILE);
407 boolean parseResult = ffile.parse(dataset, null, false, false);
408 assertTrue("return result should be true", parseResult);
409 checkDatasetfromSimpleGff3(dataset);
412 @Test(groups = { "Functional" })
413 public void simpleGff3FileLoader() throws IOException
415 AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
416 simpleGffFile, DataSourceType.FILE);
418 "Didn't read the alignment into an alignframe from Gff3 File",
420 checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
423 @Test(groups = { "Functional" })
424 public void simpleGff3RelaxedIdMatching() throws IOException
426 AlignmentI dataset = new Alignment(new SequenceI[] {});
427 FeaturesFile ffile = new FeaturesFile(simpleGffFile,
428 DataSourceType.FILE);
430 boolean parseResult = ffile.parse(dataset, null, false, true);
431 assertTrue("return result (relaxedID matching) should be true",
433 checkDatasetfromSimpleGff3(dataset);
436 @Test(groups = { "Functional" })
437 public void testPrintJalviewFormat() throws Exception
439 File f = new File("examples/uniref50.fa");
440 AlignmentI al = readAlignmentFile(f);
441 AlignFrame af = new AlignFrame(al, 500, 500);
442 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
443 .getFeatureColours();
444 String features = "METAL\tcc9900\n"
445 + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
447 + "STARTGROUP\tuniprot\n"
448 + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\n" // non-positional feature
449 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
450 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
451 + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
452 + "ENDGROUP\tuniprot\n";
453 FeaturesFile featuresFile = new FeaturesFile(features,
454 DataSourceType.PASTE);
455 featuresFile.parse(al.getDataset(), colours, false);
458 * add positional and non-positional features with null and
459 * empty feature group to check handled correctly
461 SequenceI seq = al.getSequenceAt(1); // FER_CAPAN
462 seq.addSequenceFeature(new SequenceFeature("Pfam", "desc1", 0, 0, 1.3f,
464 seq.addSequenceFeature(new SequenceFeature("Pfam", "desc2", 4, 9,
466 seq = al.getSequenceAt(2); // FER1_SOLLC
467 seq.addSequenceFeature(new SequenceFeature("Pfam", "desc3", 0, 0,
469 seq.addSequenceFeature(new SequenceFeature("Pfam", "desc4", 5, 8,
473 * first with no features displayed, exclude non-positional features
475 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
476 String exported = featuresFile
477 .printJalviewFormat(al.getSequencesArray(), fr, false);
478 String expected = "No Features Visible";
479 assertEquals(expected, exported);
482 * include non-positional features, but still no positional features
484 fr.setGroupVisibility("uniprot", true);
485 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
487 expected = "\nSTARTGROUP\tuniprot\n"
488 + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
489 + "ENDGROUP\tuniprot\n\n"
490 + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n\n"
491 + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"; // NaN is not output
493 expected.replace("\n", LINE_SEPARATOR),
497 * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
499 fr.setVisible("METAL");
500 fr.setVisible("GAMMA-TURN");
501 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
503 expected = "METAL\tcc9900\n"
504 + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
505 + "\nSTARTGROUP\tuniprot\n"
506 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
507 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
508 + "ENDGROUP\tuniprot\n";
509 assertEquals(fixLineEnd(expected), exported);
512 * now set Pfam visible
514 fr.setVisible("Pfam");
515 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
518 * features are output within group, ordered by sequence and type
520 expected = "METAL\tcc9900\n"
522 + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
523 + "\nSTARTGROUP\tuniprot\n"
524 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
525 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
526 + "<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"
527 + "ENDGROUP\tuniprot\n"
528 // null / empty group features are output after named groups
529 + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
530 + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
531 assertEquals(fixLineEnd(expected), exported);
536 fr.setGroupVisibility("uniprot", false);
537 expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
538 + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
539 + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
540 + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
541 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
543 assertEquals(fixLineEnd(expected), exported);
546 * include non-positional (overrides group not shown)
548 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
550 expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
551 + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
552 + "\nSTARTGROUP\tuniprot\n"
553 + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
554 + "ENDGROUP\tuniprot\n"
555 + "\ndesc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n"
556 + "desc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
557 + "\ndesc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"
558 + "desc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
559 assertEquals(fixLineEnd(expected), exported);
562 @Test(groups = { "Functional" })
563 public void testPrintGffFormat() throws Exception
565 File f = new File("examples/uniref50.fa");
566 AlignmentI al = readAlignmentFile(f);
567 AlignFrame af = new AlignFrame(al, 500, 500);
572 FeaturesFile featuresFile = new FeaturesFile();
573 FeatureRendererModel fr = (FeatureRendererModel) af.alignPanel
574 .getFeatureRenderer();
575 String exported = featuresFile.printGffFormat(al.getSequencesArray(),
577 String gffHeader = "##gff-version 2\n";
579 fixLineEnd(gffHeader),
581 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
584 fixLineEnd(gffHeader),
590 al.getSequenceAt(0).addSequenceFeature(
591 new SequenceFeature("Domain", "Cath", 0, 0, 0f, "Uniprot"));
592 al.getSequenceAt(0).addSequenceFeature(
593 new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, null));
596 new SequenceFeature("GAMMA-TURN", "Turn", 36, 38, 2.1f,
598 SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f,
600 sf.setAttributes("x=y;black=white");
603 al.getSequenceAt(1).addSequenceFeature(sf);
606 * 'discover' features then hide all feature types
608 fr.findAllFeatures(true);
609 FeatureSettingsBean[] data = new FeatureSettingsBean[4];
610 FeatureColourI fc = new FeatureColour(Color.PINK);
611 data[0] = new FeatureSettingsBean("Domain", fc, null, false);
612 data[1] = new FeatureSettingsBean("METAL", fc, null, false);
613 data[2] = new FeatureSettingsBean("GAMMA-TURN", fc, null, false);
614 data[3] = new FeatureSettingsBean("Pfam", fc, null, false);
615 fr.setFeaturePriority(data);
618 * with no features displayed, exclude non-positional features
620 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
623 fixLineEnd(gffHeader),
627 * include non-positional features
629 fr.setGroupVisibility("Uniprot", true);
630 fr.setGroupVisibility("s3dm", false);
631 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
633 String expected = gffHeader
634 + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
636 fixLineEnd(expected),
640 * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
641 * only Uniprot group visible here...
643 fr.setVisible("METAL");
644 fr.setVisible("GAMMA-TURN");
645 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
647 // METAL feature has null group: description used for column 2
648 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
650 expected.replace("\n", LINE_SEPARATOR),
654 * set s3dm group visible
656 fr.setGroupVisibility("s3dm", true);
657 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
659 // METAL feature has null group: description used for column 2
660 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
661 + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
663 expected.replace("\n", LINE_SEPARATOR),
667 * now set Pfam visible
669 fr.setVisible("Pfam");
670 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
672 // Pfam feature columns include strand(+), phase(2), attributes
674 + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
675 + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n"
676 + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n";
677 assertEquals(fixLineEnd(expected), exported);
680 private String fixLineEnd(String s)
682 return s.replace("\n", LINE_SEPARATOR);
686 * Test for parsing of feature filters as represented in a Jalview features
691 @Test(groups = { "Functional" })
692 public void testParseFilters() throws Exception
694 Map<String, FeatureMatcherSetI> filters = new HashMap<>();
695 String text = "sequence_variant\tCSQ:PolyPhen NotContains 'damaging'\n"
696 + "missense_variant\t(label contains foobar) and (Score lt 1.3)";
697 FeaturesFile featuresFile = new FeaturesFile(text,
698 DataSourceType.PASTE);
699 featuresFile.parseFilters(filters);
700 assertEquals(filters.size(), 2);
702 FeatureMatcherSetI fm = filters.get("sequence_variant");
704 Iterator<FeatureMatcherI> matchers = fm.getMatchers().iterator();
705 FeatureMatcherI matcher = matchers.next();
706 assertFalse(matchers.hasNext());
707 String[] attributes = matcher.getAttribute();
708 assertArrayEquals(attributes, new String[] { "CSQ", "PolyPhen" });
709 assertSame(matcher.getMatcher().getCondition(), Condition.NotContains);
710 assertEquals(matcher.getMatcher().getPattern(), "damaging");
712 fm = filters.get("missense_variant");
714 matchers = fm.getMatchers().iterator();
715 matcher = matchers.next();
716 assertTrue(matcher.isByLabel());
717 assertSame(matcher.getMatcher().getCondition(), Condition.Contains);
718 assertEquals(matcher.getMatcher().getPattern(), "foobar");
719 matcher = matchers.next();
720 assertTrue(matcher.isByScore());
721 assertSame(matcher.getMatcher().getCondition(), Condition.LT);
722 assertEquals(matcher.getMatcher().getPattern(), "1.3");
723 assertEquals(matcher.getMatcher().getFloatValue(), 1.3f);
725 assertFalse(matchers.hasNext());
728 @Test(groups = { "Functional" })
729 public void testOutputFeatureFilters()
731 FeaturesFile ff = new FeaturesFile();
732 StringBuilder sb = new StringBuilder();
733 Map<String, FeatureColourI> visible = new HashMap<>();
734 visible.put("pfam", new FeatureColour(Color.red));
735 Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
737 // with no filters, nothing is output
738 ff.outputFeatureFilters(sb, visible, featureFilters);
739 assertEquals("", sb.toString());
741 // with filter for not visible features only, nothing is output
742 FeatureMatcherSet filter = new FeatureMatcherSet();
743 filter.and(FeatureMatcher.byLabel(Condition.Present, null));
744 featureFilters.put("foobar", filter);
745 ff.outputFeatureFilters(sb, visible, featureFilters);
746 assertEquals("", sb.toString());
748 // with filters for visible feature types
749 FeatureMatcherSet filter2 = new FeatureMatcherSet();
750 filter2.and(FeatureMatcher.byAttribute(Condition.Present, null, "CSQ",
752 filter2.and(FeatureMatcher.byScore(Condition.LE, "-2.4"));
753 featureFilters.put("pfam", filter2);
754 visible.put("foobar", new FeatureColour(Color.blue));
755 ff.outputFeatureFilters(sb, visible, featureFilters);
756 String expected = "\nSTARTFILTERS\nfoobar\tLabel Present\npfam\t(CSQ:PolyPhen Present) AND (Score LE -2.4)\nENDFILTERS\n";
757 assertEquals(fixLineEnd(expected), sb.toString());
761 * Output as GFF should not include features which are not visible due to
762 * colour threshold or feature filter settings
766 @Test(groups = { "Functional" })
767 public void testPrintGffFormat_withFilters() throws Exception
769 File f = new File("examples/uniref50.fa");
770 AlignmentI al = readAlignmentFile(f);
771 AlignFrame af = new AlignFrame(al, 500, 500);
772 SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
774 sf1.setValue("clin_sig", "Likely Pathogenic");
775 sf1.setValue("AF", "24");
776 al.getSequenceAt(0).addSequenceFeature(sf1);
777 SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
779 sf2.setValue("clin_sig", "Benign");
780 sf2.setValue("AF", "46");
781 al.getSequenceAt(0).addSequenceFeature(sf2);
783 FeaturesFile featuresFile = new FeaturesFile();
784 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
785 final String gffHeader = "##gff-version 2\n";
787 fr.setVisible("METAL");
788 fr.setColour("METAL", new FeatureColour(Color.PINK));
789 String exported = featuresFile.printGffFormat(al.getSequencesArray(),
791 String expected = gffHeader
792 + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
793 + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
795 fixLineEnd(expected), exported);
798 * now threshold to Score > 1.1 - should exclude sf2
800 FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
801 Color.white, 0f, 2f);
802 fc.setAboveThreshold(true);
803 fc.setThreshold(1.1f);
804 fr.setColour("METAL", fc);
805 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
807 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
808 assertEquals(fixLineEnd(expected), exported);
811 * remove threshold and check sf2 is exported
813 fc.setAboveThreshold(false);
814 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
816 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
817 + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
818 assertEquals(fixLineEnd(expected), exported);
821 * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
823 FeatureMatcherSetI filter = new FeatureMatcherSet();
824 filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
826 fr.setFeatureFilter("METAL", filter);
827 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
829 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
830 assertEquals(fixLineEnd(expected), exported);
834 * Output as Jalview should not include features which are not visible due to
835 * colour threshold or feature filter settings
839 @Test(groups = { "Functional" })
840 public void testPrintJalviewFormat_withFilters() throws Exception
842 File f = new File("examples/uniref50.fa");
843 AlignmentI al = readAlignmentFile(f);
844 AlignFrame af = new AlignFrame(al, 500, 500);
845 SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
847 sf1.setValue("clin_sig", "Likely Pathogenic");
848 sf1.setValue("AF", "24");
849 al.getSequenceAt(0).addSequenceFeature(sf1);
850 SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
852 sf2.setValue("clin_sig", "Benign");
853 sf2.setValue("AF", "46");
854 al.getSequenceAt(0).addSequenceFeature(sf2);
856 FeaturesFile featuresFile = new FeaturesFile();
857 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
858 fr.findAllFeatures(true);
860 fr.setVisible("METAL");
861 fr.setColour("METAL", new FeatureColour(Color.PINK));
862 String exported = featuresFile.printJalviewFormat(
863 al.getSequencesArray(),
865 String expected = "METAL\tffafaf\n\nSTARTGROUP\tgrp1\n"
866 + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
867 + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
868 + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
869 + "ENDGROUP\tgrp2\n";
871 fixLineEnd(expected),
875 * now threshold to Score > 1.1 - should exclude sf2
876 * (and there should be no empty STARTGROUP/ENDGROUP output)
878 FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
879 Color.white, 0f, 2f);
880 fc.setAboveThreshold(true);
881 fc.setThreshold(1.1f);
882 fr.setColour("METAL", fc);
883 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
885 expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|above|1.1\n\n"
886 + "STARTGROUP\tgrp1\n"
887 + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
888 + "ENDGROUP\tgrp1\n";
890 expected.replace("\n", LINE_SEPARATOR),
894 * remove threshold and check sf2 is exported
896 fc.setAboveThreshold(false);
897 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
899 expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
900 + "STARTGROUP\tgrp1\n"
901 + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
902 + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
903 + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
904 + "ENDGROUP\tgrp2\n";
905 assertEquals(fixLineEnd(expected), exported);
908 * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
910 FeatureMatcherSetI filter = new FeatureMatcherSet();
911 filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
913 fr.setFeatureFilter("METAL", filter);
914 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
916 expected = "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
917 expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
918 + "STARTFILTERS\nMETAL\tclin_sig Contains benign\nENDFILTERS\n\n"
919 + "STARTGROUP\tgrp2\n"
920 + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
921 + "ENDGROUP\tgrp2\n";
922 assertEquals(fixLineEnd(expected), exported);