2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertFalse;
25 import static org.testng.AssertJUnit.assertNotNull;
26 import static org.testng.AssertJUnit.assertSame;
27 import static org.testng.AssertJUnit.assertTrue;
28 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
30 import jalview.api.FeatureColourI;
31 import jalview.api.FeatureRenderer;
32 import jalview.datamodel.Alignment;
33 import jalview.datamodel.AlignmentI;
34 import jalview.datamodel.SequenceDummy;
35 import jalview.datamodel.SequenceFeature;
36 import jalview.datamodel.SequenceI;
37 import jalview.datamodel.features.FeatureMatcher;
38 import jalview.datamodel.features.FeatureMatcherI;
39 import jalview.datamodel.features.FeatureMatcherSet;
40 import jalview.datamodel.features.FeatureMatcherSetI;
41 import jalview.datamodel.features.SequenceFeatures;
42 import jalview.gui.AlignFrame;
43 import jalview.gui.Desktop;
44 import jalview.gui.JvOptionPane;
45 import jalview.schemes.FeatureColour;
46 import jalview.structure.StructureSelectionManager;
47 import jalview.util.matcher.Condition;
48 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
49 import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
51 import java.awt.Color;
53 import java.io.IOException;
54 import java.util.HashMap;
55 import java.util.Iterator;
56 import java.util.List;
59 import org.testng.annotations.AfterClass;
60 import org.testng.annotations.BeforeClass;
61 import org.testng.annotations.Test;
63 public class FeaturesFileTest
65 private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
67 @AfterClass(alwaysRun = true)
68 public void tearDownAfterClass()
71 * remove any sequence mappings created so they don't pollute other tests
73 StructureSelectionManager ssm = StructureSelectionManager
74 .getStructureSelectionManager(Desktop.instance);
78 @BeforeClass(alwaysRun = true)
79 public void setUpJvOptionPane()
81 JvOptionPane.setInteractiveMode(false);
82 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
85 @Test(groups = { "Functional" })
86 public void testParse() throws Exception
88 File f = new File("examples/uniref50.fa");
89 AlignmentI al = readAlignmentFile(f);
90 AlignFrame af = new AlignFrame(al, 500, 500);
91 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
93 FeaturesFile featuresFile = new FeaturesFile(
94 "examples/exampleFeatures.txt", DataSourceType.FILE);
95 assertTrue("Test " + "Features file test"
96 + "\nFailed to parse features file.",
97 featuresFile.parse(al.getDataset(), colours, true));
100 * Refetch the colour map from the FeatureRenderer (to confirm it has been
101 * updated - JAL-1904), and verify (some) feature group colours
103 colours = af.getFeatureRenderer().getFeatureColours();
104 assertEquals("27 feature group colours not found", 27, colours.size());
105 assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
106 assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
107 FeatureColourI kdColour = colours.get("kdHydrophobicity");
108 assertTrue(kdColour.isGraduatedColour());
109 assertTrue(kdColour.isAboveThreshold());
110 assertEquals(-2f, kdColour.getThreshold());
113 * verify (some) features on sequences
115 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
116 .getSequenceFeatures(); // FER_CAPAA
117 SequenceFeatures.sortFeatures(sfs, true);
118 assertEquals(8, sfs.size());
121 * verify (in ascending start position order)
123 SequenceFeature sf = sfs.get(0);
124 assertEquals("Pfam family%LINK%", sf.description);
125 assertEquals(0, sf.begin);
126 assertEquals(0, sf.end);
127 assertEquals("uniprot", sf.featureGroup);
128 assertEquals("Pfam", sf.type);
129 assertEquals(1, sf.links.size());
130 assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
134 assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
135 assertEquals(3, sf.begin);
136 assertEquals(93, sf.end);
137 assertEquals("uniprot", sf.featureGroup);
138 assertEquals("Cath", sf.type);
141 assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
143 assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
145 assertEquals(8, sf.begin);
146 assertEquals(83, sf.end);
147 assertEquals("uniprot", sf.featureGroup);
148 assertEquals("Pfam", sf.type);
151 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
152 assertEquals(39, sf.begin);
153 assertEquals(39, sf.end);
154 assertEquals("uniprot", sf.featureGroup);
155 assertEquals("METAL", sf.type);
158 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
159 assertEquals(44, sf.begin);
160 assertEquals(44, sf.end);
161 assertEquals("uniprot", sf.featureGroup);
162 assertEquals("METAL", sf.type);
165 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
166 assertEquals(47, sf.begin);
167 assertEquals(47, sf.end);
168 assertEquals("uniprot", sf.featureGroup);
169 assertEquals("METAL", sf.type);
172 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
173 assertEquals(77, sf.begin);
174 assertEquals(77, sf.end);
175 assertEquals("uniprot", sf.featureGroup);
176 assertEquals("METAL", sf.type);
180 "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
183 "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&service=NetPhos-2.0",
185 assertEquals(89, sf.begin);
186 assertEquals(89, sf.end);
187 assertEquals("netphos", sf.featureGroup);
188 assertEquals("PHOSPHORYLATION (T)", sf.type);
192 * Test parsing a features file with a mix of Jalview and GFF formatted
197 @Test(groups = { "Functional" })
198 public void testParse_mixedJalviewGff() throws Exception
200 File f = new File("examples/uniref50.fa");
201 AlignmentI al = readAlignmentFile(f);
202 AlignFrame af = new AlignFrame(al, 500, 500);
203 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
204 .getFeatureColours();
205 // GFF2 uses space as name/value separator in column 9
206 String gffData = "METAL\tcc9900\n"
208 + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
209 + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
210 FeaturesFile featuresFile = new FeaturesFile(gffData,
211 DataSourceType.PASTE);
212 assertTrue("Failed to parse features file",
213 featuresFile.parse(al.getDataset(), colours, true));
215 // verify colours read or synthesized
216 colours = af.getFeatureRenderer().getFeatureColours();
217 assertEquals("1 feature group colours not found", 1, colours.size());
218 assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
220 // verify feature on FER_CAPAA
221 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
222 .getSequenceFeatures();
223 assertEquals(1, sfs.size());
224 SequenceFeature sf = sfs.get(0);
225 assertEquals("Iron-sulfur,2Fe-2S", sf.description);
226 assertEquals(44, sf.begin);
227 assertEquals(45, sf.end);
228 assertEquals("uniprot", sf.featureGroup);
229 assertEquals("METAL", sf.type);
230 assertEquals(4f, sf.getScore(), 0.001f);
232 // verify feature on FER1_SOLLC
233 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
234 assertEquals(1, sfs.size());
236 assertEquals("uniprot", sf.description);
237 assertEquals(55, sf.begin);
238 assertEquals(130, sf.end);
239 assertEquals("uniprot", sf.featureGroup);
240 assertEquals("Pfam", sf.type);
241 assertEquals(2f, sf.getScore(), 0.001f);
244 public static AlignmentI readAlignmentFile(File f) throws IOException
246 System.out.println("Reading file: " + f);
247 String ff = f.getPath();
248 FormatAdapter rf = new FormatAdapter();
250 AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
251 new IdentifyFile().identify(ff, DataSourceType.FILE));
253 al.setDataset(null); // creates dataset sequences
254 assertNotNull("Couldn't read supplied alignment data.", al);
259 * Test parsing a features file with GFF formatted content only
263 @Test(groups = { "Functional" })
264 public void testParse_pureGff3() throws Exception
266 File f = new File("examples/uniref50.fa");
267 AlignmentI al = readAlignmentFile(f);
268 AlignFrame af = new AlignFrame(al, 500, 500);
269 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
270 .getFeatureColours();
271 // GFF3 uses '=' separator for name/value pairs in colum 9
272 String gffData = "##gff-version 3\n"
273 + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
274 + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465\n"
275 + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
276 FeaturesFile featuresFile = new FeaturesFile(gffData,
277 DataSourceType.PASTE);
278 assertTrue("Failed to parse features file",
279 featuresFile.parse(al.getDataset(), colours, true));
281 // verify feature on FER_CAPAA
282 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
283 .getSequenceFeatures();
284 assertEquals(1, sfs.size());
285 SequenceFeature sf = sfs.get(0);
286 // description parsed from Note attribute
287 assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description);
288 assertEquals(39, sf.begin);
289 assertEquals(39, sf.end);
290 assertEquals("uniprot", sf.featureGroup);
291 assertEquals("METAL", sf.type);
293 "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465",
294 sf.getValue("ATTRIBUTES"));
296 // verify feature on FER1_SOLLC1
297 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
298 assertEquals(1, sfs.size());
300 // ID used for description if available
301 assertEquals("$23", sf.description);
302 assertEquals(55, sf.begin);
303 assertEquals(130, sf.end);
304 assertEquals("uniprot", sf.featureGroup);
305 assertEquals("Pfam", sf.type);
306 assertEquals(3f, sf.getScore(), 0.001f);
310 * Test parsing a features file with Jalview format features (but no colour
311 * descriptors or startgroup to give the hint not to parse as GFF)
315 @Test(groups = { "Functional" })
316 public void testParse_jalviewFeaturesOnly() throws Exception
318 File f = new File("examples/uniref50.fa");
319 AlignmentI al = readAlignmentFile(f);
320 AlignFrame af = new AlignFrame(al, 500, 500);
321 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
322 .getFeatureColours();
325 * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
327 String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
328 + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
329 FeaturesFile featuresFile = new FeaturesFile(featureData,
330 DataSourceType.PASTE);
331 assertTrue("Failed to parse features file",
332 featuresFile.parse(al.getDataset(), colours, true));
334 // verify FER_CAPAA feature
335 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
336 .getSequenceFeatures();
337 assertEquals(1, sfs.size());
338 SequenceFeature sf = sfs.get(0);
339 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
340 assertEquals(39, sf.begin);
341 assertEquals(39, sf.end);
342 assertEquals("METAL", sf.type);
344 // verify FER1_SOLLC feature
345 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
346 assertEquals(1, sfs.size());
348 assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
349 assertEquals(86, sf.begin);
350 assertEquals(87, sf.end);
351 assertEquals("METALLIC", sf.type);
354 private void checkDatasetfromSimpleGff3(AlignmentI dataset)
356 assertEquals("no sequences extracted from GFF3 file", 2,
357 dataset.getHeight());
359 SequenceI seq1 = dataset.findName("seq1");
360 SequenceI seq2 = dataset.findName("seq2");
364 "Failed to replace dummy seq1 with real sequence",
365 seq1 instanceof SequenceDummy
366 && ((SequenceDummy) seq1).isDummy());
368 "Failed to replace dummy seq2 with real sequence",
369 seq2 instanceof SequenceDummy
370 && ((SequenceDummy) seq2).isDummy());
371 String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
372 assertFalse("dummy replacement buggy for seq1",
373 placeholderseq.equals(seq1.getSequenceAsString()));
374 assertFalse("dummy replacement buggy for seq2",
375 placeholderseq.equals(seq2.getSequenceAsString()));
376 assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
377 assertEquals("Wrong number of features", 3, seq1.getSequenceFeatures()
379 assertTrue(seq2.getSequenceFeatures().isEmpty());
381 "Wrong number of features",
383 seq2.getSequenceFeatures() == null ? 0 : seq2
384 .getSequenceFeatures().size());
386 "Expected at least one CDNA/Protein mapping for seq1",
387 dataset.getCodonFrame(seq1) != null
388 && dataset.getCodonFrame(seq1).size() > 0);
392 @Test(groups = { "Functional" })
393 public void readGff3File() throws IOException
395 FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
396 DataSourceType.FILE);
397 Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
398 gffreader.addProperties(dataset);
399 checkDatasetfromSimpleGff3(dataset);
402 @Test(groups = { "Functional" })
403 public void simpleGff3FileClass() throws IOException
405 AlignmentI dataset = new Alignment(new SequenceI[] {});
406 FeaturesFile ffile = new FeaturesFile(simpleGffFile,
407 DataSourceType.FILE);
409 boolean parseResult = ffile.parse(dataset, null, false, false);
410 assertTrue("return result should be true", parseResult);
411 checkDatasetfromSimpleGff3(dataset);
414 @Test(groups = { "Functional" })
415 public void simpleGff3FileLoader() throws IOException
417 AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
418 simpleGffFile, DataSourceType.FILE);
420 "Didn't read the alignment into an alignframe from Gff3 File",
422 checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
425 @Test(groups = { "Functional" })
426 public void simpleGff3RelaxedIdMatching() throws IOException
428 AlignmentI dataset = new Alignment(new SequenceI[] {});
429 FeaturesFile ffile = new FeaturesFile(simpleGffFile,
430 DataSourceType.FILE);
432 boolean parseResult = ffile.parse(dataset, null, false, true);
433 assertTrue("return result (relaxedID matching) should be true",
435 checkDatasetfromSimpleGff3(dataset);
438 @Test(groups = { "Functional" })
439 public void testPrintJalviewFormat() throws Exception
441 File f = new File("examples/uniref50.fa");
442 AlignmentI al = readAlignmentFile(f);
443 AlignFrame af = new AlignFrame(al, 500, 500);
444 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
445 .getFeatureColours();
446 String features = "METAL\tcc9900\n"
447 + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
449 + "STARTGROUP\tuniprot\n"
450 + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\n" // non-positional feature
451 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
452 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
453 + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
454 + "ENDGROUP\tuniprot\n";
455 FeaturesFile featuresFile = new FeaturesFile(features,
456 DataSourceType.PASTE);
457 featuresFile.parse(al.getDataset(), colours, false);
460 * add positional and non-positional features with null and
461 * empty feature group to check handled correctly
463 SequenceI seq = al.getSequenceAt(1); // FER_CAPAN
464 seq.addSequenceFeature(new SequenceFeature("Pfam", "desc1", 0, 0, 1.3f,
466 seq.addSequenceFeature(new SequenceFeature("Pfam", "desc2", 4, 9,
468 seq = al.getSequenceAt(2); // FER1_SOLLC
469 seq.addSequenceFeature(new SequenceFeature("Pfam", "desc3", 0, 0,
471 seq.addSequenceFeature(new SequenceFeature("Pfam", "desc4", 5, 8,
475 * first with no features displayed, exclude non-positional features
477 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
478 String exported = featuresFile
479 .printJalviewFormat(al.getSequencesArray(), fr, false, false);
480 String expected = "No Features Visible";
481 assertEquals(expected, exported);
484 * include non-positional features, but still no positional features
486 fr.setGroupVisibility("uniprot", true);
487 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
489 expected = "\nSTARTGROUP\tuniprot\n"
490 + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
491 + "ENDGROUP\tuniprot\n\n"
492 + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n\n"
493 + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"; // NaN is not output
494 assertEquals(expected, exported);
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 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
507 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
508 + "ENDGROUP\tuniprot\n";
509 assertEquals(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 + "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 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\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(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(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(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";
578 assertEquals(gffHeader, exported);
579 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
581 assertEquals(gffHeader, exported);
586 al.getSequenceAt(0).addSequenceFeature(
587 new SequenceFeature("Domain", "Cath", 0, 0, 0f, "Uniprot"));
588 al.getSequenceAt(0).addSequenceFeature(
589 new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, null));
592 new SequenceFeature("GAMMA-TURN", "Turn", 36, 38, 2.1f,
594 SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f,
596 sf.setAttributes("x=y;black=white");
599 al.getSequenceAt(1).addSequenceFeature(sf);
602 * 'discover' features then hide all feature types
604 fr.findAllFeatures(true);
605 FeatureSettingsBean[] data = new FeatureSettingsBean[4];
606 FeatureColourI fc = new FeatureColour(Color.PINK);
607 data[0] = new FeatureSettingsBean("Domain", fc, null, false);
608 data[1] = new FeatureSettingsBean("METAL", fc, null, false);
609 data[2] = new FeatureSettingsBean("GAMMA-TURN", fc, null, false);
610 data[3] = new FeatureSettingsBean("Pfam", fc, null, false);
611 fr.setFeaturePriority(data);
614 * with no features displayed, exclude non-positional features
616 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
618 assertEquals(gffHeader, exported);
621 * include non-positional features
623 fr.setGroupVisibility("Uniprot", true);
624 fr.setGroupVisibility("s3dm", false);
625 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
627 String expected = gffHeader
628 + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
629 assertEquals(expected, exported);
632 * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
633 * only Uniprot group visible here...
635 fr.setVisible("METAL");
636 fr.setVisible("GAMMA-TURN");
637 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
639 // METAL feature has null group: description used for column 2
640 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
641 assertEquals(expected, exported);
644 * set s3dm group visible
646 fr.setGroupVisibility("s3dm", true);
647 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
649 // METAL feature has null group: description used for column 2
650 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
651 + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
652 assertEquals(expected, exported);
655 * now set Pfam visible
657 fr.setVisible("Pfam");
658 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
660 // Pfam feature columns include strand(+), phase(2), attributes
662 + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
663 + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n"
664 + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
665 assertEquals(expected, exported);
669 * Test for parsing of feature filters as represented in a Jalview features
674 @Test(groups = { "Functional" })
675 public void testParseFilters() throws Exception
677 Map<String, FeatureMatcherSetI> filters = new HashMap<>();
678 String text = "sequence_variant\tCSQ:PolyPhen NotContains 'damaging'\n"
679 + "missense_variant\t(label contains foobar) and (Score lt 1.3)";
680 FeaturesFile featuresFile = new FeaturesFile(text,
681 DataSourceType.PASTE);
682 featuresFile.parseFilters(filters);
683 assertEquals(filters.size(), 2);
685 FeatureMatcherSetI fm = filters.get("sequence_variant");
687 Iterator<FeatureMatcherI> matchers = fm.getMatchers().iterator();
688 FeatureMatcherI matcher = matchers.next();
689 assertFalse(matchers.hasNext());
690 String[] attributes = matcher.getAttribute();
691 assertArrayEquals(attributes, new String[] { "CSQ", "PolyPhen" });
692 assertSame(matcher.getMatcher().getCondition(), Condition.NotContains);
693 assertEquals(matcher.getMatcher().getPattern(), "damaging");
695 fm = filters.get("missense_variant");
697 matchers = fm.getMatchers().iterator();
698 matcher = matchers.next();
699 assertTrue(matcher.isByLabel());
700 assertSame(matcher.getMatcher().getCondition(), Condition.Contains);
701 assertEquals(matcher.getMatcher().getPattern(), "foobar");
702 matcher = matchers.next();
703 assertTrue(matcher.isByScore());
704 assertSame(matcher.getMatcher().getCondition(), Condition.LT);
705 assertEquals(matcher.getMatcher().getPattern(), "1.3");
706 assertEquals(matcher.getMatcher().getFloatValue(), 1.3f);
708 assertFalse(matchers.hasNext());
711 @Test(groups = { "Functional" })
712 public void testOutputFeatureFilters()
714 FeaturesFile ff = new FeaturesFile();
715 StringBuilder sb = new StringBuilder();
716 Map<String, FeatureColourI> visible = new HashMap<>();
717 visible.put("pfam", new FeatureColour(Color.red));
718 Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
720 // with no filters, nothing is output
721 ff.outputFeatureFilters(sb, visible, featureFilters);
722 assertEquals("", sb.toString());
724 // with filter for not visible features only, nothing is output
725 FeatureMatcherSet filter = new FeatureMatcherSet();
726 filter.and(FeatureMatcher.byLabel(Condition.Present, null));
727 featureFilters.put("foobar", filter);
728 ff.outputFeatureFilters(sb, visible, featureFilters);
729 assertEquals("", sb.toString());
731 // with filters for visible feature types
732 FeatureMatcherSet filter2 = new FeatureMatcherSet();
733 filter2.and(FeatureMatcher.byAttribute(Condition.Present, null, "CSQ",
735 filter2.and(FeatureMatcher.byScore(Condition.LE, "-2.4"));
736 featureFilters.put("pfam", filter2);
737 visible.put("foobar", new FeatureColour(Color.blue));
738 ff.outputFeatureFilters(sb, visible, featureFilters);
739 String expected = "\nSTARTFILTERS\nfoobar\tLabel Present\npfam\t(CSQ:PolyPhen Present) AND (Score LE -2.4)\nENDFILTERS\n";
740 assertEquals(expected, sb.toString());
744 * Output as GFF should not include features which are not visible due to
745 * colour threshold or feature filter settings
749 @Test(groups = { "Functional" })
750 public void testPrintGffFormat_withFilters() throws Exception
752 File f = new File("examples/uniref50.fa");
753 AlignmentI al = readAlignmentFile(f);
754 AlignFrame af = new AlignFrame(al, 500, 500);
755 SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
757 sf1.setValue("clin_sig", "Likely Pathogenic");
758 sf1.setValue("AF", "24");
759 al.getSequenceAt(0).addSequenceFeature(sf1);
760 SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
762 sf2.setValue("clin_sig", "Benign");
763 sf2.setValue("AF", "46");
764 al.getSequenceAt(0).addSequenceFeature(sf2);
766 FeaturesFile featuresFile = new FeaturesFile();
767 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
768 final String gffHeader = "##gff-version 2\n";
770 fr.setVisible("METAL");
771 fr.setColour("METAL", new FeatureColour(Color.PINK));
772 String exported = featuresFile.printGffFormat(al.getSequencesArray(),
774 String expected = gffHeader
775 + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
776 + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
777 assertEquals(expected, exported);
780 * now threshold to Score > 1.1 - should exclude sf2
782 FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
783 Color.white, 0f, 2f);
784 fc.setAboveThreshold(true);
785 fc.setThreshold(1.1f);
786 fr.setColour("METAL", fc);
787 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
789 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
790 assertEquals(expected, exported);
793 * remove threshold and check sf2 is exported
795 fc.setAboveThreshold(false);
796 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
798 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
799 + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
800 assertEquals(expected, exported);
803 * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
805 FeatureMatcherSetI filter = new FeatureMatcherSet();
806 filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
808 fr.setFeatureFilter("METAL", filter);
809 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
811 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
812 assertEquals(expected, exported);
816 * Output as Jalview should not include features which are not visible due to
817 * colour threshold or feature filter settings
821 @Test(groups = { "Functional" })
822 public void testPrintJalviewFormat_withFilters() throws Exception
824 File f = new File("examples/uniref50.fa");
825 AlignmentI al = readAlignmentFile(f);
826 AlignFrame af = new AlignFrame(al, 500, 500);
827 SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
829 sf1.setValue("clin_sig", "Likely Pathogenic");
830 sf1.setValue("AF", "24");
831 al.getSequenceAt(0).addSequenceFeature(sf1);
832 SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
834 sf2.setValue("clin_sig", "Benign");
835 sf2.setValue("AF", "46");
836 al.getSequenceAt(0).addSequenceFeature(sf2);
838 FeaturesFile featuresFile = new FeaturesFile();
839 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
840 fr.findAllFeatures(true);
842 fr.setVisible("METAL");
843 fr.setColour("METAL", new FeatureColour(Color.PINK));
844 String exported = featuresFile.printJalviewFormat(
845 al.getSequencesArray(),
847 String expected = "METAL\tffafaf\n\nSTARTGROUP\tgrp1\n"
848 + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
849 + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
850 + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
851 + "ENDGROUP\tgrp2\n";
852 assertEquals(expected, exported);
855 * now threshold to Score > 1.1 - should exclude sf2
856 * (and there should be no empty STARTGROUP/ENDGROUP output)
858 FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
859 Color.white, 0f, 2f);
860 fc.setAboveThreshold(true);
861 fc.setThreshold(1.1f);
862 fr.setColour("METAL", fc);
863 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
865 expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|above|1.1\n\n"
866 + "STARTGROUP\tgrp1\n"
867 + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
868 + "ENDGROUP\tgrp1\n";
869 assertEquals(expected, exported);
872 * remove threshold and check sf2 is exported
874 fc.setAboveThreshold(false);
875 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
877 expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
878 + "STARTGROUP\tgrp1\n"
879 + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
880 + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
881 + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
882 + "ENDGROUP\tgrp2\n";
883 assertEquals(expected, exported);
886 * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
888 FeatureMatcherSetI filter = new FeatureMatcherSet();
889 filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
891 fr.setFeatureFilter("METAL", filter);
892 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
894 expected = "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
895 expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
896 + "STARTFILTERS\nMETAL\tclin_sig Contains benign\nENDFILTERS\n\n"
897 + "STARTGROUP\tgrp2\n"
898 + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
899 + "ENDGROUP\tgrp2\n";
900 assertEquals(expected, exported);