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 column 9
272 // comma (%2C) equals (%3D) or semi-colon (%3B) should be url-escaped in values
273 String gffData = "##gff-version 3\n"
274 + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
275 + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO%3B0000255%2CPROSITE%3DProRule:PRU00465;"
276 + "jvmap_CSQ={AF=21,clin_sig=Benign%3Dgood}\n"
277 + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
278 FeaturesFile featuresFile = new FeaturesFile(gffData,
279 DataSourceType.PASTE);
280 assertTrue("Failed to parse features file",
281 featuresFile.parse(al.getDataset(), colours, true));
283 // verify feature on FER_CAPAA
284 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
285 .getSequenceFeatures();
286 assertEquals(1, sfs.size());
287 SequenceFeature sf = sfs.get(0);
288 // description parsed from Note attribute
289 assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description);
290 assertEquals(39, sf.begin);
291 assertEquals(39, sf.end);
292 assertEquals("uniprot", sf.featureGroup);
293 assertEquals("METAL", sf.type);
294 assertEquals(5, sf.otherDetails.size());
295 assertEquals("ECO;0000255,PROSITE=ProRule:PRU00465", // url decoded
296 sf.getValue("evidence"));
297 assertEquals("Iron-sulfur (2Fe-2S),another note",
298 sf.getValue("Note"));
299 assertEquals("21", sf.getValueAsString("CSQ", "AF"));
300 assertEquals("Benign=good", sf.getValueAsString("CSQ", "clin_sig")); // url decoded
301 // todo change STRAND and !Phase into fields of SequenceFeature instead
302 assertEquals(".", sf.otherDetails.get("STRAND"));
303 assertEquals(0, sf.getStrand());
304 assertEquals(".", sf.getPhase());
306 // verify feature on FER1_SOLLC1
307 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
308 assertEquals(1, sfs.size());
310 // ID used for description if available
311 assertEquals("$23", sf.description);
312 assertEquals(55, sf.begin);
313 assertEquals(130, sf.end);
314 assertEquals("uniprot", sf.featureGroup);
315 assertEquals("Pfam", sf.type);
316 assertEquals(3f, sf.getScore(), 0.001f);
320 * Test parsing a features file with Jalview format features (but no colour
321 * descriptors or startgroup to give the hint not to parse as GFF)
325 @Test(groups = { "Functional" })
326 public void testParse_jalviewFeaturesOnly() throws Exception
328 File f = new File("examples/uniref50.fa");
329 AlignmentI al = readAlignmentFile(f);
330 AlignFrame af = new AlignFrame(al, 500, 500);
331 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
332 .getFeatureColours();
335 * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
337 String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
338 + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
339 FeaturesFile featuresFile = new FeaturesFile(featureData,
340 DataSourceType.PASTE);
341 assertTrue("Failed to parse features file",
342 featuresFile.parse(al.getDataset(), colours, true));
344 // verify FER_CAPAA feature
345 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
346 .getSequenceFeatures();
347 assertEquals(1, sfs.size());
348 SequenceFeature sf = sfs.get(0);
349 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
350 assertEquals(39, sf.begin);
351 assertEquals(39, sf.end);
352 assertEquals("METAL", sf.type);
354 // verify FER1_SOLLC feature
355 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
356 assertEquals(1, sfs.size());
358 assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
359 assertEquals(86, sf.begin);
360 assertEquals(87, sf.end);
361 assertEquals("METALLIC", sf.type);
364 private void checkDatasetfromSimpleGff3(AlignmentI dataset)
366 assertEquals("no sequences extracted from GFF3 file", 2,
367 dataset.getHeight());
369 SequenceI seq1 = dataset.findName("seq1");
370 SequenceI seq2 = dataset.findName("seq2");
374 "Failed to replace dummy seq1 with real sequence",
375 seq1 instanceof SequenceDummy
376 && ((SequenceDummy) seq1).isDummy());
378 "Failed to replace dummy seq2 with real sequence",
379 seq2 instanceof SequenceDummy
380 && ((SequenceDummy) seq2).isDummy());
381 String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
382 assertFalse("dummy replacement buggy for seq1",
383 placeholderseq.equals(seq1.getSequenceAsString()));
384 assertFalse("dummy replacement buggy for seq2",
385 placeholderseq.equals(seq2.getSequenceAsString()));
386 assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
387 assertEquals("Wrong number of features", 3, seq1.getSequenceFeatures()
389 assertTrue(seq2.getSequenceFeatures().isEmpty());
391 "Wrong number of features",
393 seq2.getSequenceFeatures() == null ? 0 : seq2
394 .getSequenceFeatures().size());
396 "Expected at least one CDNA/Protein mapping for seq1",
397 dataset.getCodonFrame(seq1) != null
398 && dataset.getCodonFrame(seq1).size() > 0);
402 @Test(groups = { "Functional" })
403 public void readGff3File() throws IOException
405 FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
406 DataSourceType.FILE);
407 Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
408 gffreader.addProperties(dataset);
409 checkDatasetfromSimpleGff3(dataset);
412 @Test(groups = { "Functional" })
413 public void simpleGff3FileClass() throws IOException
415 AlignmentI dataset = new Alignment(new SequenceI[] {});
416 FeaturesFile ffile = new FeaturesFile(simpleGffFile,
417 DataSourceType.FILE);
419 boolean parseResult = ffile.parse(dataset, null, false, false);
420 assertTrue("return result should be true", parseResult);
421 checkDatasetfromSimpleGff3(dataset);
424 @Test(groups = { "Functional" })
425 public void simpleGff3FileLoader() throws IOException
427 AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
428 simpleGffFile, DataSourceType.FILE);
430 "Didn't read the alignment into an alignframe from Gff3 File",
432 checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
435 @Test(groups = { "Functional" })
436 public void simpleGff3RelaxedIdMatching() throws IOException
438 AlignmentI dataset = new Alignment(new SequenceI[] {});
439 FeaturesFile ffile = new FeaturesFile(simpleGffFile,
440 DataSourceType.FILE);
442 boolean parseResult = ffile.parse(dataset, null, false, true);
443 assertTrue("return result (relaxedID matching) should be true",
445 checkDatasetfromSimpleGff3(dataset);
448 @Test(groups = { "Functional" })
449 public void testPrintJalviewFormat() throws Exception
451 File f = new File("examples/uniref50.fa");
452 AlignmentI al = readAlignmentFile(f);
453 AlignFrame af = new AlignFrame(al, 500, 500);
454 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
455 .getFeatureColours();
456 String features = "METAL\tcc9900\n"
457 + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
459 + "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(new SequenceFeature("Pfam", "desc1", 0, 0, 1.3f,
476 seq.addSequenceFeature(new SequenceFeature("Pfam", "desc2", 4, 9,
478 seq = al.getSequenceAt(2); // FER1_SOLLC
479 seq.addSequenceFeature(new SequenceFeature("Pfam", "desc3", 0, 0,
481 seq.addSequenceFeature(new SequenceFeature("Pfam", "desc4", 5, 8,
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"
532 + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
533 + "\nSTARTGROUP\tuniprot\n"
534 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
535 + "<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"
536 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
537 + "ENDGROUP\tuniprot\n"
538 // null / empty group features are output after named groups
539 + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
540 + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
541 assertEquals(expected, exported);
546 fr.setGroupVisibility("uniprot", false);
547 expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
548 + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
549 + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
550 + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
551 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
553 assertEquals(expected, exported);
556 * include non-positional (overrides group not shown)
558 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
560 expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
561 + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
562 + "\nSTARTGROUP\tuniprot\n"
563 + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
564 + "ENDGROUP\tuniprot\n"
565 + "\ndesc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n"
566 + "desc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
567 + "\ndesc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"
568 + "desc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
569 assertEquals(expected, exported);
572 @Test(groups = { "Functional" })
573 public void testPrintGffFormat() throws Exception
575 File f = new File("examples/uniref50.fa");
576 AlignmentI al = readAlignmentFile(f);
577 AlignFrame af = new AlignFrame(al, 500, 500);
582 FeaturesFile featuresFile = new FeaturesFile();
583 FeatureRendererModel fr = (FeatureRendererModel) af.alignPanel
584 .getFeatureRenderer();
585 String exported = featuresFile.printGffFormat(al.getSequencesArray(),
587 String gffHeader = "##gff-version 2\n";
588 assertEquals(gffHeader, exported);
589 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
591 assertEquals(gffHeader, exported);
596 al.getSequenceAt(0).addSequenceFeature(
597 new SequenceFeature("Domain", "Cath", 0, 0, 0f, "Uniprot"));
598 al.getSequenceAt(0).addSequenceFeature(
599 new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, null));
602 new SequenceFeature("GAMMA-TURN", "Turn", 36, 38, 2.1f,
604 SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f,
608 sf.setValue("x", "y");
609 sf.setValue("black", "white");
610 al.getSequenceAt(1).addSequenceFeature(sf);
613 * 'discover' features then hide all feature types
615 fr.findAllFeatures(true);
616 FeatureSettingsBean[] data = new FeatureSettingsBean[4];
617 FeatureColourI fc = new FeatureColour(Color.PINK);
618 data[0] = new FeatureSettingsBean("Domain", fc, null, false);
619 data[1] = new FeatureSettingsBean("METAL", fc, null, false);
620 data[2] = new FeatureSettingsBean("GAMMA-TURN", fc, null, false);
621 data[3] = new FeatureSettingsBean("Pfam", fc, null, false);
622 fr.setFeaturePriority(data);
625 * with no features displayed, exclude non-positional features
627 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
629 assertEquals(gffHeader, exported);
632 * include non-positional features
634 fr.setGroupVisibility("Uniprot", true);
635 fr.setGroupVisibility("s3dm", false);
636 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
638 String expected = gffHeader
639 + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
640 assertEquals(expected, exported);
643 * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
644 * only Uniprot group visible here...
646 fr.setVisible("METAL");
647 fr.setVisible("GAMMA-TURN");
648 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
650 // METAL feature has null group: description used for column 2
651 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
652 assertEquals(expected, exported);
655 * set s3dm group visible
657 fr.setGroupVisibility("s3dm", true);
658 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
660 // METAL feature has null group: description used for column 2
661 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
662 + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
663 assertEquals(expected, exported);
666 * now set Pfam visible
668 fr.setVisible("Pfam");
669 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
671 // Pfam feature columns include strand(+), phase(2), attributes
673 + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
674 + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n"
675 + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
676 assertEquals(expected, exported);
680 * Test for parsing of feature filters as represented in a Jalview features
685 @Test(groups = { "Functional" })
686 public void testParseFilters() throws Exception
688 Map<String, FeatureMatcherSetI> filters = new HashMap<>();
689 String text = "sequence_variant\tCSQ:PolyPhen NotContains 'damaging'\n"
690 + "missense_variant\t(label contains foobar) and (Score lt 1.3)";
691 FeaturesFile featuresFile = new FeaturesFile(text,
692 DataSourceType.PASTE);
693 featuresFile.parseFilters(filters);
694 assertEquals(filters.size(), 2);
696 FeatureMatcherSetI fm = filters.get("sequence_variant");
698 Iterator<FeatureMatcherI> matchers = fm.getMatchers().iterator();
699 FeatureMatcherI matcher = matchers.next();
700 assertFalse(matchers.hasNext());
701 String[] attributes = matcher.getAttribute();
702 assertArrayEquals(attributes, new String[] { "CSQ", "PolyPhen" });
703 assertSame(matcher.getMatcher().getCondition(), Condition.NotContains);
704 assertEquals(matcher.getMatcher().getPattern(), "damaging");
706 fm = filters.get("missense_variant");
708 matchers = fm.getMatchers().iterator();
709 matcher = matchers.next();
710 assertTrue(matcher.isByLabel());
711 assertSame(matcher.getMatcher().getCondition(), Condition.Contains);
712 assertEquals(matcher.getMatcher().getPattern(), "foobar");
713 matcher = matchers.next();
714 assertTrue(matcher.isByScore());
715 assertSame(matcher.getMatcher().getCondition(), Condition.LT);
716 assertEquals(matcher.getMatcher().getPattern(), "1.3");
717 assertEquals(matcher.getMatcher().getFloatValue(), 1.3f);
719 assertFalse(matchers.hasNext());
722 @Test(groups = { "Functional" })
723 public void testOutputFeatureFilters()
725 FeaturesFile ff = new FeaturesFile();
726 StringBuilder sb = new StringBuilder();
727 Map<String, FeatureColourI> visible = new HashMap<>();
728 visible.put("pfam", new FeatureColour(Color.red));
729 Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
731 // with no filters, nothing is output
732 ff.outputFeatureFilters(sb, visible, featureFilters);
733 assertEquals("", sb.toString());
735 // with filter for not visible features only, nothing is output
736 FeatureMatcherSet filter = new FeatureMatcherSet();
737 filter.and(FeatureMatcher.byLabel(Condition.Present, null));
738 featureFilters.put("foobar", filter);
739 ff.outputFeatureFilters(sb, visible, featureFilters);
740 assertEquals("", sb.toString());
742 // with filters for visible feature types
743 FeatureMatcherSet filter2 = new FeatureMatcherSet();
744 filter2.and(FeatureMatcher.byAttribute(Condition.Present, null, "CSQ",
746 filter2.and(FeatureMatcher.byScore(Condition.LE, "-2.4"));
747 featureFilters.put("pfam", filter2);
748 visible.put("foobar", new FeatureColour(Color.blue));
749 ff.outputFeatureFilters(sb, visible, featureFilters);
750 String expected = "\nSTARTFILTERS\nfoobar\tLabel Present\npfam\t(CSQ:PolyPhen Present) AND (Score LE -2.4)\nENDFILTERS\n";
751 assertEquals(expected, sb.toString());
755 * Output as GFF should not include features which are not visible due to
756 * colour threshold or feature filter settings
760 @Test(groups = { "Functional" })
761 public void testPrintGffFormat_withFilters() throws Exception
763 File f = new File("examples/uniref50.fa");
764 AlignmentI al = readAlignmentFile(f);
765 AlignFrame af = new AlignFrame(al, 500, 500);
766 SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
768 sf1.setValue("clin_sig", "Likely Pathogenic");
769 sf1.setValue("AF", "24");
770 al.getSequenceAt(0).addSequenceFeature(sf1);
771 SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
773 sf2.setValue("clin_sig", "Benign");
774 sf2.setValue("AF", "46");
775 al.getSequenceAt(0).addSequenceFeature(sf2);
777 FeaturesFile featuresFile = new FeaturesFile();
778 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
779 final String gffHeader = "##gff-version 2\n";
781 fr.setVisible("METAL");
782 fr.setColour("METAL", new FeatureColour(Color.PINK));
783 String exported = featuresFile.printGffFormat(al.getSequencesArray(),
785 String expected = gffHeader
786 + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n"
787 + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
788 assertEquals(expected, exported);
791 * now threshold to Score > 1.1 - should exclude sf2
793 FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
794 Color.white, 0f, 2f);
795 fc.setAboveThreshold(true);
796 fc.setThreshold(1.1f);
797 fr.setColour("METAL", fc);
798 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
801 + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n";
802 assertEquals(expected, exported);
805 * remove threshold and check sf2 is exported
807 fc.setAboveThreshold(false);
808 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
811 + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n"
812 + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
813 assertEquals(expected, exported);
816 * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
818 FeatureMatcherSetI filter = new FeatureMatcherSet();
819 filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
821 fr.setFeatureFilter("METAL", filter);
822 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
825 + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
826 assertEquals(expected, exported);
830 * Output as Jalview should not include features which are not visible due to
831 * colour threshold or feature filter settings
835 @Test(groups = { "Functional" })
836 public void testPrintJalviewFormat_withFilters() throws Exception
838 File f = new File("examples/uniref50.fa");
839 AlignmentI al = readAlignmentFile(f);
840 AlignFrame af = new AlignFrame(al, 500, 500);
841 SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
843 sf1.setValue("clin_sig", "Likely Pathogenic");
844 sf1.setValue("AF", "24");
845 al.getSequenceAt(0).addSequenceFeature(sf1);
846 SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
848 sf2.setValue("clin_sig", "Benign");
849 sf2.setValue("AF", "46");
850 al.getSequenceAt(0).addSequenceFeature(sf2);
852 FeaturesFile featuresFile = new FeaturesFile();
853 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
854 fr.findAllFeatures(true);
856 fr.setVisible("METAL");
857 fr.setColour("METAL", new FeatureColour(Color.PINK));
858 String exported = featuresFile.printJalviewFormat(
859 al.getSequencesArray(),
861 String expected = "METAL\tffafaf\n\nSTARTGROUP\tgrp1\n"
862 + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
863 + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
864 + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
865 + "ENDGROUP\tgrp2\n";
866 assertEquals(expected, exported);
869 * now threshold to Score > 1.1 - should exclude sf2
870 * (and there should be no empty STARTGROUP/ENDGROUP output)
872 FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
873 Color.white, 0f, 2f);
874 fc.setAboveThreshold(true);
875 fc.setThreshold(1.1f);
876 fr.setColour("METAL", fc);
877 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
879 expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|above|1.1\n\n"
880 + "STARTGROUP\tgrp1\n"
881 + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
882 + "ENDGROUP\tgrp1\n";
883 assertEquals(expected, exported);
886 * remove threshold and check sf2 is exported
888 fc.setAboveThreshold(false);
889 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
891 expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
892 + "STARTGROUP\tgrp1\n"
893 + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
894 + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
895 + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
896 + "ENDGROUP\tgrp2\n";
897 assertEquals(expected, exported);
900 * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
902 FeatureMatcherSetI filter = new FeatureMatcherSet();
903 filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
905 fr.setFeatureFilter("METAL", filter);
906 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
908 expected = "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
909 expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
910 + "STARTFILTERS\nMETAL\tclin_sig Contains benign\nENDFILTERS\n\n"
911 + "STARTGROUP\tgrp2\n"
912 + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
913 + "ENDGROUP\tgrp2\n";
914 assertEquals(expected, exported);