2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertFalse;
25 import static org.testng.AssertJUnit.assertNotNull;
26 import static org.testng.AssertJUnit.assertSame;
27 import static org.testng.AssertJUnit.assertTrue;
28 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
30 import java.awt.Color;
32 import java.io.IOException;
33 import java.util.HashMap;
34 import java.util.Iterator;
35 import java.util.List;
38 import org.testng.annotations.AfterClass;
39 import org.testng.annotations.BeforeClass;
40 import org.testng.annotations.Test;
42 import jalview.api.FeatureColourI;
43 import jalview.api.FeatureRenderer;
44 import jalview.datamodel.Alignment;
45 import jalview.datamodel.AlignmentI;
46 import jalview.datamodel.SequenceDummy;
47 import jalview.datamodel.SequenceFeature;
48 import jalview.datamodel.SequenceI;
49 import jalview.datamodel.features.FeatureMatcher;
50 import jalview.datamodel.features.FeatureMatcherI;
51 import jalview.datamodel.features.FeatureMatcherSet;
52 import jalview.datamodel.features.FeatureMatcherSetI;
53 import jalview.datamodel.features.SequenceFeatures;
54 import jalview.gui.AlignFrame;
55 import jalview.gui.Desktop;
56 import jalview.gui.JvOptionPane;
57 import jalview.schemes.FeatureColour;
58 import jalview.structure.StructureSelectionManager;
59 import jalview.util.matcher.Condition;
60 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
61 import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
62 import junit.extensions.PA;
64 public class FeaturesFileTest
66 private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
68 @AfterClass(alwaysRun = true)
69 public void tearDownAfterClass()
72 * remove any sequence mappings created so they don't pollute other tests
74 StructureSelectionManager ssm = StructureSelectionManager
75 .getStructureSelectionManager(Desktop.instance);
79 @BeforeClass(alwaysRun = true)
80 public void setUpJvOptionPane()
82 JvOptionPane.setInteractiveMode(false);
83 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
86 @Test(groups = { "Functional" })
87 public void testParse() throws Exception
89 File f = new File("examples/uniref50.fa");
90 AlignmentI al = readAlignmentFile(f);
91 AlignFrame af = new AlignFrame(al, 500, 500);
92 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
94 FeaturesFile featuresFile = new FeaturesFile(
95 "examples/exampleFeatures.txt", DataSourceType.FILE);
97 "Test " + "Features file test"
98 + "\nFailed to parse features file.",
99 featuresFile.parse(al.getDataset(), colours, true));
102 * Refetch the colour map from the FeatureRenderer (to confirm it has been
103 * updated - JAL-1904), and verify (some) feature group colours
105 colours = af.getFeatureRenderer().getFeatureColours();
106 assertEquals("27 feature group colours not found", 27, colours.size());
107 assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
108 assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
109 FeatureColourI kdColour = colours.get("kdHydrophobicity");
110 assertTrue(kdColour.isGraduatedColour());
111 assertTrue(kdColour.isAboveThreshold());
112 assertEquals(-2f, kdColour.getThreshold());
115 * verify (some) features on sequences
117 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
118 .getSequenceFeatures(); // FER_CAPAA
119 SequenceFeatures.sortFeatures(sfs, true);
120 assertEquals(8, sfs.size());
123 * verify (in ascending start position order)
125 SequenceFeature sf = sfs.get(0);
126 assertEquals("Pfam family%LINK%", sf.description);
127 assertEquals(0, sf.begin);
128 assertEquals(0, sf.end);
129 assertEquals("uniprot", sf.featureGroup);
130 assertEquals("Pfam", sf.type);
131 assertEquals(1, sf.links.size());
132 assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
136 assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
137 assertEquals(3, sf.begin);
138 assertEquals(93, sf.end);
139 assertEquals("uniprot", sf.featureGroup);
140 assertEquals("Cath", sf.type);
143 assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
145 assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
147 assertEquals(8, sf.begin);
148 assertEquals(83, sf.end);
149 assertEquals("uniprot", sf.featureGroup);
150 assertEquals("Pfam", sf.type);
153 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
154 assertEquals(39, sf.begin);
155 assertEquals(39, sf.end);
156 assertEquals("uniprot", sf.featureGroup);
157 assertEquals("METAL", sf.type);
160 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
161 assertEquals(44, sf.begin);
162 assertEquals(44, sf.end);
163 assertEquals("uniprot", sf.featureGroup);
164 assertEquals("METAL", sf.type);
167 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
168 assertEquals(47, sf.begin);
169 assertEquals(47, sf.end);
170 assertEquals("uniprot", sf.featureGroup);
171 assertEquals("METAL", sf.type);
174 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
175 assertEquals(77, sf.begin);
176 assertEquals(77, sf.end);
177 assertEquals("uniprot", sf.featureGroup);
178 assertEquals("METAL", sf.type);
182 "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
185 "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&service=NetPhos-2.0",
187 assertEquals(89, sf.begin);
188 assertEquals(89, sf.end);
189 assertEquals("netphos", sf.featureGroup);
190 assertEquals("PHOSPHORYLATION (T)", sf.type);
194 * Test parsing a features file with a mix of Jalview and GFF formatted
199 @Test(groups = { "Functional" })
200 public void testParse_mixedJalviewGff() throws Exception
202 File f = new File("examples/uniref50.fa");
203 AlignmentI al = readAlignmentFile(f);
204 AlignFrame af = new AlignFrame(al, 500, 500);
205 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
206 .getFeatureColours();
207 // GFF2 uses space as name/value separator in column 9
208 String gffData = "METAL\tcc9900\n" + "GFF\n"
209 + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
210 + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
211 FeaturesFile featuresFile = new FeaturesFile(gffData,
212 DataSourceType.PASTE);
213 assertTrue("Failed to parse features file",
214 featuresFile.parse(al.getDataset(), colours, true));
216 // verify colours read or synthesized
217 colours = af.getFeatureRenderer().getFeatureColours();
218 assertEquals("1 feature group colours not found", 1, colours.size());
219 assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
221 // verify feature on FER_CAPAA
222 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
223 .getSequenceFeatures();
224 assertEquals(1, sfs.size());
225 SequenceFeature sf = sfs.get(0);
226 assertEquals("Iron-sulfur,2Fe-2S", sf.description);
227 assertEquals(44, sf.begin);
228 assertEquals(45, sf.end);
229 assertEquals("uniprot", sf.featureGroup);
230 assertEquals("METAL", sf.type);
231 assertEquals(4f, sf.getScore(), 0.001f);
233 // verify feature on FER1_SOLLC
234 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
235 assertEquals(1, sfs.size());
237 assertEquals("uniprot", sf.description);
238 assertEquals(55, sf.begin);
239 assertEquals(130, sf.end);
240 assertEquals("uniprot", sf.featureGroup);
241 assertEquals("Pfam", sf.type);
242 assertEquals(2f, sf.getScore(), 0.001f);
245 public static AlignmentI readAlignmentFile(File f) throws IOException
247 System.out.println("Reading file: " + f);
248 String ff = f.getPath();
249 FormatAdapter rf = new FormatAdapter();
251 AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
252 new IdentifyFile().identify(ff, DataSourceType.FILE));
254 al.setDataset(null); // creates dataset sequences
255 assertNotNull("Couldn't read supplied alignment data.", al);
260 * Test parsing a features file with GFF formatted content only
264 @Test(groups = { "Functional" })
265 public void testParse_pureGff3() throws Exception
267 File f = new File("examples/uniref50.fa");
268 AlignmentI al = readAlignmentFile(f);
269 AlignFrame af = new AlignFrame(al, 500, 500);
270 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
271 .getFeatureColours();
272 // GFF3 uses '=' separator for name/value pairs in column 9
273 // comma (%2C) equals (%3D) or semi-colon (%3B) should be url-escaped in
275 String gffData = "##gff-version 3\n"
276 + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
277 + "Note=Iron-sulfur (2Fe-2S);Note=another note,and another;evidence=ECO%3B0000255%2CPROSITE%3DProRule:PRU00465;"
278 + "CSQ=AF=21,POLYPHEN=benign,possibly_damaging,clin_sig=Benign%3Dgood\n"
279 + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
280 FeaturesFile featuresFile = new FeaturesFile(gffData,
281 DataSourceType.PASTE);
282 assertTrue("Failed to parse features file",
283 featuresFile.parse(al.getDataset(), colours, true));
285 // verify feature on FER_CAPAA
286 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
287 .getSequenceFeatures();
288 assertEquals(1, sfs.size());
289 SequenceFeature sf = sfs.get(0);
290 // description parsed from Note attribute
291 assertEquals("Iron-sulfur (2Fe-2S),another note,and another",
293 assertEquals(39, sf.begin);
294 assertEquals(39, sf.end);
295 assertEquals("uniprot", sf.featureGroup);
296 assertEquals("METAL", sf.type);
297 assertEquals(5, sf.otherDetails.size());
298 assertEquals("ECO;0000255,PROSITE=ProRule:PRU00465", // url decoded
299 sf.getValue("evidence"));
300 assertEquals("Iron-sulfur (2Fe-2S),another note,and another",
301 sf.getValue("Note"));
302 assertEquals("21", sf.getValueAsString("CSQ", "AF"));
303 assertEquals("benign,possibly_damaging",
304 sf.getValueAsString("CSQ", "POLYPHEN"));
305 assertEquals("Benign=good", sf.getValueAsString("CSQ", "clin_sig")); // url
307 // todo change STRAND and !Phase into fields of SequenceFeature instead
308 assertEquals(".", sf.otherDetails.get("STRAND"));
309 assertEquals(0, sf.getStrand());
310 assertEquals(".", sf.getPhase());
312 // verify feature on FER1_SOLLC1
313 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
314 assertEquals(1, sfs.size());
316 // ID used for description if available
317 assertEquals("$23", sf.description);
318 assertEquals(55, sf.begin);
319 assertEquals(130, sf.end);
320 assertEquals("uniprot", sf.featureGroup);
321 assertEquals("Pfam", sf.type);
322 assertEquals(3f, sf.getScore(), 0.001f);
326 * Test parsing a features file with Jalview format features (but no colour
327 * descriptors or startgroup to give the hint not to parse as GFF)
331 @Test(groups = { "Functional" })
332 public void testParse_jalviewFeaturesOnly() throws Exception
334 File f = new File("examples/uniref50.fa");
335 AlignmentI al = readAlignmentFile(f);
336 AlignFrame af = new AlignFrame(al, 500, 500);
337 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
338 .getFeatureColours();
341 * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
343 String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
344 + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
345 FeaturesFile featuresFile = new FeaturesFile(featureData,
346 DataSourceType.PASTE);
347 assertTrue("Failed to parse features file",
348 featuresFile.parse(al.getDataset(), colours, true));
350 // verify FER_CAPAA feature
351 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
352 .getSequenceFeatures();
353 assertEquals(1, sfs.size());
354 SequenceFeature sf = sfs.get(0);
355 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
356 assertEquals(39, sf.begin);
357 assertEquals(39, sf.end);
358 assertEquals("METAL", sf.type);
360 // verify FER1_SOLLC feature
361 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
362 assertEquals(1, sfs.size());
364 assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
365 assertEquals(86, sf.begin);
366 assertEquals(87, sf.end);
367 assertEquals("METALLIC", sf.type);
370 private void checkDatasetfromSimpleGff3(AlignmentI dataset)
372 assertEquals("no sequences extracted from GFF3 file", 2,
373 dataset.getHeight());
375 SequenceI seq1 = dataset.findName("seq1");
376 SequenceI seq2 = dataset.findName("seq2");
379 assertFalse("Failed to replace dummy seq1 with real sequence",
380 seq1 instanceof SequenceDummy
381 && ((SequenceDummy) seq1).isDummy());
382 assertFalse("Failed to replace dummy seq2 with real sequence",
383 seq2 instanceof SequenceDummy
384 && ((SequenceDummy) seq2).isDummy());
385 String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
386 assertFalse("dummy replacement buggy for seq1",
387 placeholderseq.equals(seq1.getSequenceAsString()));
388 assertFalse("dummy replacement buggy for seq2",
389 placeholderseq.equals(seq2.getSequenceAsString()));
390 assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
391 assertEquals("Wrong number of features", 3,
392 seq1.getSequenceFeatures().size());
393 assertTrue(seq2.getSequenceFeatures().isEmpty());
394 assertEquals("Wrong number of features", 0,
395 seq2.getSequenceFeatures() == null ? 0
396 : seq2.getSequenceFeatures().size());
397 assertTrue("Expected at least one CDNA/Protein mapping for seq1",
398 dataset.getCodonFrame(seq1) != null
399 && dataset.getCodonFrame(seq1).size() > 0);
403 @Test(groups = { "Functional" })
404 public void readGff3File() throws IOException
406 FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
407 DataSourceType.FILE);
408 Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
409 gffreader.addProperties(dataset);
410 checkDatasetfromSimpleGff3(dataset);
413 @Test(groups = { "Functional" })
414 public void simpleGff3FileClass() throws IOException
416 AlignmentI dataset = new Alignment(new SequenceI[] {});
417 FeaturesFile ffile = new FeaturesFile(simpleGffFile,
418 DataSourceType.FILE);
420 boolean parseResult = ffile.parse(dataset, null, false, false);
421 assertTrue("return result should be true", parseResult);
422 checkDatasetfromSimpleGff3(dataset);
425 @Test(groups = { "Functional" })
426 public void simpleGff3FileLoader() throws IOException
428 AlignFrame af = new FileLoader(false)
429 .LoadFileWaitTillLoaded(simpleGffFile, DataSourceType.FILE);
431 "Didn't read the alignment into an alignframe from Gff3 File",
433 checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
436 @Test(groups = { "Functional" })
437 public void simpleGff3RelaxedIdMatching() throws IOException
439 AlignmentI dataset = new Alignment(new SequenceI[] {});
440 FeaturesFile ffile = new FeaturesFile(simpleGffFile,
441 DataSourceType.FILE);
443 boolean parseResult = ffile.parse(dataset, null, false, true);
444 assertTrue("return result (relaxedID matching) should be true",
446 checkDatasetfromSimpleGff3(dataset);
449 @Test(groups = { "Functional" })
450 public void testPrintJalviewFormat() throws Exception
452 File f = new File("examples/uniref50.fa");
453 AlignmentI al = readAlignmentFile(f);
454 AlignFrame af = new AlignFrame(al, 500, 500);
455 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
456 .getFeatureColours();
457 String features = "METAL\tcc9900\n"
458 + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
459 + "Pfam\tred\n" + "STARTGROUP\tuniprot\n"
460 + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\n" // non-positional feature
461 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
462 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
463 + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
464 + "ENDGROUP\tuniprot\n";
465 FeaturesFile featuresFile = new FeaturesFile(features,
466 DataSourceType.PASTE);
467 featuresFile.parse(al.getDataset(), colours, false);
470 * add positional and non-positional features with null and
471 * empty feature group to check handled correctly
473 SequenceI seq = al.getSequenceAt(1); // FER_CAPAN
474 seq.addSequenceFeature(
475 new SequenceFeature("Pfam", "desc1", 0, 0, 1.3f, null));
476 seq.addSequenceFeature(
477 new SequenceFeature("Pfam", "desc2", 4, 9, Float.NaN, null));
478 seq = al.getSequenceAt(2); // FER1_SOLLC
479 seq.addSequenceFeature(
480 new SequenceFeature("Pfam", "desc3", 0, 0, Float.NaN, ""));
481 seq.addSequenceFeature(
482 new SequenceFeature("Pfam", "desc4", 5, 8, -2.6f, ""));
485 * first with no features displayed, exclude non-positional features
487 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
488 String exported = featuresFile
489 .printJalviewFormat(al.getSequencesArray(), fr, false, false);
490 String expected = "No Features Visible";
491 assertEquals(expected, exported);
494 * include non-positional features, but still no positional features
496 fr.setGroupVisibility("uniprot", true);
497 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
499 expected = "\nSTARTGROUP\tuniprot\n"
500 + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
501 + "ENDGROUP\tuniprot\n\n"
502 + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n\n"
503 + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"; // NaN is not output
504 assertEquals(expected, exported);
507 * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
509 fr.setVisible("METAL");
510 fr.setVisible("GAMMA-TURN");
511 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
513 expected = "METAL\tcc9900\n"
514 + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
515 + "\nSTARTGROUP\tuniprot\n"
516 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
517 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
518 + "ENDGROUP\tuniprot\n";
519 assertEquals(expected, exported);
522 * now set Pfam visible
524 fr.setVisible("Pfam");
525 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
528 * features are output within group, ordered by sequence and type
530 expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
531 + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
532 + "\nSTARTGROUP\tuniprot\n"
533 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
534 + "<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"
535 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
536 + "ENDGROUP\tuniprot\n"
537 // null / empty group features are output after named groups
538 + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
539 + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
540 assertEquals(expected, exported);
545 fr.setGroupVisibility("uniprot", false);
546 expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
547 + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
548 + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
549 + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
550 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
552 assertEquals(expected, exported);
555 * include non-positional (overrides group not shown)
557 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
559 expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
560 + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
561 + "\nSTARTGROUP\tuniprot\n"
562 + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
563 + "ENDGROUP\tuniprot\n"
564 + "\ndesc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n"
565 + "desc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
566 + "\ndesc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"
567 + "desc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
568 assertEquals(expected, exported);
571 @Test(groups = { "Functional" })
572 public void testPrintGffFormat() throws Exception
574 File f = new File("examples/uniref50.fa");
575 AlignmentI al = readAlignmentFile(f);
576 AlignFrame af = new AlignFrame(al, 500, 500);
581 FeaturesFile featuresFile = new FeaturesFile();
582 FeatureRendererModel fr = (FeatureRendererModel) af.alignPanel
583 .getFeatureRenderer();
584 String exported = featuresFile.printGffFormat(al.getSequencesArray(),
586 String gffHeader = "##gff-version 2\n";
587 assertEquals(gffHeader, exported);
588 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, true,
590 assertEquals(gffHeader, exported);
595 al.getSequenceAt(0).addSequenceFeature(
596 new SequenceFeature("Domain", "Cath", 0, 0, 0f, "Uniprot"));
597 al.getSequenceAt(0).addSequenceFeature(
598 new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, null));
599 al.getSequenceAt(1).addSequenceFeature(new SequenceFeature("GAMMA-TURN",
600 "Turn", 36, 38, 2.1f, "s3dm"));
601 SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f,
605 sf.setValue("x", "y");
606 sf.setValue("black", "white");
607 Map<String, String> csq = new HashMap<>();
608 csq.put("SIFT", "benign,mostly benign,cloudy, with meatballs");
609 csq.put("consequence", "missense_variant");
610 sf.setValue("CSQ", csq);
611 al.getSequenceAt(1).addSequenceFeature(sf);
614 * 'discover' features then hide all feature types
616 fr.findAllFeatures(true);
617 FeatureSettingsBean[] data = new FeatureSettingsBean[4];
618 FeatureColourI fc = new FeatureColour(Color.PINK);
619 data[0] = new FeatureSettingsBean("Domain", fc, null, false);
620 data[1] = new FeatureSettingsBean("METAL", fc, null, false);
621 data[2] = new FeatureSettingsBean("GAMMA-TURN", fc, null, false);
622 data[3] = new FeatureSettingsBean("Pfam", fc, null, false);
623 fr.setFeaturePriority(data);
626 * with no features displayed, exclude non-positional features
628 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
630 assertEquals(gffHeader, exported);
633 * include non-positional features
635 fr.setGroupVisibility("Uniprot", true);
636 fr.setGroupVisibility("s3dm", false);
637 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, true,
639 String expected = gffHeader
640 + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
641 assertEquals(expected, exported);
644 * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
645 * only Uniprot group visible here...
647 fr.setVisible("METAL");
648 fr.setVisible("GAMMA-TURN");
649 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
651 // METAL feature has null group: description used for column 2
652 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
653 assertEquals(expected, exported);
656 * set s3dm group visible
658 fr.setGroupVisibility("s3dm", true);
659 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
661 // METAL feature has null group: description used for column 2
662 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
663 + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
664 assertEquals(expected, exported);
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
673 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
674 // CSQ output as CSQ=att1=value1,att2=value2
675 // note all commas are encoded here which is wrong - it should be
676 // SIFT=benign,mostly benign,cloudy%2C with meatballs
677 + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white;"
678 + "CSQ=SIFT=benign%2Cmostly benign%2Ccloudy%2C with meatballs,consequence=missense_variant\n"
679 + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
680 assertEquals(expected, exported);
684 * Test for parsing of feature filters as represented in a Jalview features
689 @Test(groups = { "Functional" })
690 public void testParseFilters() throws Exception
692 Map<String, FeatureMatcherSetI> filters = new HashMap<>();
693 String text = "sequence_variant\tCSQ:PolyPhen NotContains 'damaging'\n"
694 + "missense_variant\t(label contains foobar) and (Score lt 1.3)";
695 FeaturesFile featuresFile = new FeaturesFile(text,
696 DataSourceType.PASTE);
697 featuresFile.parseFilters(filters);
698 assertEquals(filters.size(), 2);
700 FeatureMatcherSetI fm = filters.get("sequence_variant");
702 Iterator<FeatureMatcherI> matchers = fm.getMatchers().iterator();
703 FeatureMatcherI matcher = matchers.next();
704 assertFalse(matchers.hasNext());
705 String[] attributes = matcher.getAttribute();
706 assertArrayEquals(attributes, new String[] { "CSQ", "PolyPhen" });
707 assertSame(matcher.getMatcher().getCondition(), Condition.NotContains);
708 assertEquals(matcher.getMatcher().getPattern(), "damaging");
710 fm = filters.get("missense_variant");
712 matchers = fm.getMatchers().iterator();
713 matcher = matchers.next();
714 assertTrue(matcher.isByLabel());
715 assertSame(matcher.getMatcher().getCondition(), Condition.Contains);
716 assertEquals(matcher.getMatcher().getPattern(), "foobar");
717 matcher = matchers.next();
718 assertTrue(matcher.isByScore());
719 assertSame(matcher.getMatcher().getCondition(), Condition.LT);
720 assertEquals(matcher.getMatcher().getPattern(), "1.3");
721 assertEquals(PA.getValue(matcher.getMatcher(), "floatValue"), 1.3f);
723 assertFalse(matchers.hasNext());
726 @Test(groups = { "Functional" })
727 public void testOutputFeatureFilters()
729 FeaturesFile ff = new FeaturesFile();
730 StringBuilder sb = new StringBuilder();
731 Map<String, FeatureColourI> visible = new HashMap<>();
732 visible.put("pfam", new FeatureColour(Color.red));
733 Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
735 // with no filters, nothing is output
736 ff.outputFeatureFilters(sb, visible, featureFilters);
737 assertEquals("", sb.toString());
739 // with filter for not visible features only, nothing is output
740 FeatureMatcherSet filter = new FeatureMatcherSet();
741 filter.and(FeatureMatcher.byLabel(Condition.Present, null));
742 featureFilters.put("foobar", filter);
743 ff.outputFeatureFilters(sb, visible, featureFilters);
744 assertEquals("", sb.toString());
746 // with filters for visible feature types
747 FeatureMatcherSet filter2 = new FeatureMatcherSet();
748 filter2.and(FeatureMatcher.byAttribute(Condition.Present, null, "CSQ",
750 filter2.and(FeatureMatcher.byScore(Condition.LE, "-2.4"));
751 featureFilters.put("pfam", filter2);
752 visible.put("foobar", new FeatureColour(Color.blue));
753 ff.outputFeatureFilters(sb, visible, featureFilters);
754 String expected = "\nSTARTFILTERS\nfoobar\tLabel Present\npfam\t(CSQ:PolyPhen Present) AND (Score LE -2.4)\nENDFILTERS\n";
755 assertEquals(expected, sb.toString());
759 * Output as GFF should not include features which are not visible due to
760 * colour threshold or feature filter settings
764 @Test(groups = { "Functional" })
765 public void testPrintGffFormat_withFilters() throws Exception
767 File f = new File("examples/uniref50.fa");
768 AlignmentI al = readAlignmentFile(f);
769 AlignFrame af = new AlignFrame(al, 500, 500);
770 SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
772 sf1.setValue("clin_sig", "Likely Pathogenic");
773 sf1.setValue("AF", "24");
774 al.getSequenceAt(0).addSequenceFeature(sf1);
775 SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
777 sf2.setValue("clin_sig", "Benign");
778 sf2.setValue("AF", "46");
779 al.getSequenceAt(0).addSequenceFeature(sf2);
781 FeaturesFile featuresFile = new FeaturesFile();
782 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
783 final String gffHeader = "##gff-version 2\n";
785 fr.setVisible("METAL");
786 fr.setColour("METAL", new FeatureColour(Color.PINK));
787 String exported = featuresFile.printGffFormat(al.getSequencesArray(),
789 String expected = gffHeader
790 + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n"
791 + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
792 assertEquals(expected, exported);
795 * now threshold to Score > 1.1 - should exclude sf2
797 FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
798 Color.white, 0f, 2f);
799 fc.setAboveThreshold(true);
800 fc.setThreshold(1.1f);
801 fr.setColour("METAL", fc);
802 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
805 + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n";
806 assertEquals(expected, exported);
809 * remove threshold and check sf2 is exported
811 fc.setAboveThreshold(false);
812 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
815 + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n"
816 + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
817 assertEquals(expected, exported);
820 * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
822 FeatureMatcherSetI filter = new FeatureMatcherSet();
823 filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
825 fr.setFeatureFilter("METAL", filter);
826 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
829 + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
830 assertEquals(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
863 .printJalviewFormat(al.getSequencesArray(), fr, false, false);
864 String expected = "METAL\tffafaf\n\nSTARTGROUP\tgrp1\n"
865 + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
866 + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
867 + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
868 + "ENDGROUP\tgrp2\n";
869 assertEquals(expected, exported);
872 * now threshold to Score > 1.1 - should exclude sf2
873 * (and there should be no empty STARTGROUP/ENDGROUP output)
875 FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
876 Color.white, 0f, 2f);
877 fc.setAboveThreshold(true);
878 fc.setThreshold(1.1f);
879 fr.setColour("METAL", fc);
880 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
882 expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|above|1.1\n\n"
883 + "STARTGROUP\tgrp1\n"
884 + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
885 + "ENDGROUP\tgrp1\n";
886 assertEquals(expected, exported);
889 * remove threshold and check sf2 is exported
891 fc.setAboveThreshold(false);
892 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
894 expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
895 + "STARTGROUP\tgrp1\n"
896 + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
897 + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
898 + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
899 + "ENDGROUP\tgrp2\n";
900 assertEquals(expected, exported);
903 * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
905 FeatureMatcherSetI filter = new FeatureMatcherSet();
906 filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
908 fr.setFeatureFilter("METAL", filter);
909 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
911 expected = "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
912 expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
913 + "STARTFILTERS\nMETAL\tclin_sig Contains benign\nENDFILTERS\n\n"
914 + "STARTGROUP\tgrp2\n"
915 + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
916 + "ENDGROUP\tgrp2\n";
917 assertEquals(expected, exported);