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.assertNull;
27 import static org.testng.AssertJUnit.assertTrue;
29 import jalview.api.FeatureColourI;
30 import jalview.api.FeatureRenderer;
31 import jalview.datamodel.Alignment;
32 import jalview.datamodel.AlignmentI;
33 import jalview.datamodel.SequenceDummy;
34 import jalview.datamodel.SequenceFeature;
35 import jalview.datamodel.SequenceI;
36 import jalview.gui.AlignFrame;
37 import jalview.gui.JvOptionPane;
39 import java.awt.Color;
41 import java.io.IOException;
42 import java.util.ArrayList;
43 import java.util.Arrays;
44 import java.util.HashMap;
45 import java.util.List;
48 import org.testng.annotations.BeforeClass;
49 import org.testng.annotations.Test;
51 public class FeaturesFileTest
54 @BeforeClass(alwaysRun = true)
55 public void setUpJvOptionPane()
57 JvOptionPane.setInteractiveMode(false);
58 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
61 private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
63 @Test(groups = { "Functional" })
64 public void testParse() throws Exception
66 File f = new File("examples/uniref50.fa");
67 AlignmentI al = readAlignmentFile(f);
68 AlignFrame af = new AlignFrame(al, 500, 500);
69 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
71 FeaturesFile featuresFile = new FeaturesFile(
72 "examples/exampleFeatures.txt", DataSourceType.FILE);
73 assertTrue("Test " + "Features file test"
74 + "\nFailed to parse features file.",
75 featuresFile.parse(al.getDataset(), colours, true));
78 * Refetch the colour map from the FeatureRenderer (to confirm it has been
79 * updated - JAL-1904), and verify (some) feature group colours
81 colours = af.getFeatureRenderer().getFeatureColours();
82 assertEquals("26 feature group colours not found", 26, colours.size());
83 assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
84 assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
87 * verify (some) features on sequences
89 SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
90 .getSequenceFeatures(); // FER_CAPAA
91 assertEquals(8, sfs.length);
92 SequenceFeature sf = sfs[0];
93 assertEquals("Pfam family%LINK%", sf.description);
94 assertEquals(0, sf.begin);
95 assertEquals(0, sf.end);
96 assertEquals("uniprot", sf.featureGroup);
97 assertEquals("Pfam", sf.type);
98 assertEquals(1, sf.links.size());
99 assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
103 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
104 assertEquals(39, sf.begin);
105 assertEquals(39, sf.end);
106 assertEquals("uniprot", sf.featureGroup);
107 assertEquals("METAL", sf.type);
109 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
110 assertEquals(44, sf.begin);
111 assertEquals(44, sf.end);
112 assertEquals("uniprot", sf.featureGroup);
113 assertEquals("METAL", sf.type);
115 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
116 assertEquals(47, sf.begin);
117 assertEquals(47, sf.end);
118 assertEquals("uniprot", sf.featureGroup);
119 assertEquals("METAL", sf.type);
121 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
122 assertEquals(77, sf.begin);
123 assertEquals(77, sf.end);
124 assertEquals("uniprot", sf.featureGroup);
125 assertEquals("METAL", sf.type);
127 assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
129 assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
131 assertEquals(8, sf.begin);
132 assertEquals(83, sf.end);
133 assertEquals("uniprot", sf.featureGroup);
134 assertEquals("Pfam", sf.type);
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 "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
146 "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&service=NetPhos-2.0",
148 assertEquals(89, sf.begin);
149 assertEquals(89, sf.end);
150 assertEquals("netphos", sf.featureGroup);
151 assertEquals("PHOSPHORYLATION (T)", sf.type);
155 * Test parsing a features file with a mix of Jalview and GFF formatted
160 @Test(groups = { "Functional" })
161 public void testParse_mixedJalviewGff() throws Exception
163 File f = new File("examples/uniref50.fa");
164 AlignmentI al = readAlignmentFile(f);
165 AlignFrame af = new AlignFrame(al, 500, 500);
166 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
167 .getFeatureColours();
168 // GFF2 uses space as name/value separator in column 9
169 String gffData = "METAL\tcc9900\n"
171 + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
172 + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
173 FeaturesFile featuresFile = new FeaturesFile(gffData,
174 DataSourceType.PASTE);
175 assertTrue("Failed to parse features file",
176 featuresFile.parse(al.getDataset(), colours, true));
178 // verify colours read or synthesized
179 colours = af.getFeatureRenderer().getFeatureColours();
180 assertEquals("1 feature group colours not found", 1, colours.size());
181 assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
183 // verify feature on FER_CAPAA
184 SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
185 .getSequenceFeatures();
186 assertEquals(1, sfs.length);
187 SequenceFeature sf = sfs[0];
188 assertEquals("Iron-sulfur,2Fe-2S", sf.description);
189 assertEquals(44, sf.begin);
190 assertEquals(45, sf.end);
191 assertEquals("uniprot", sf.featureGroup);
192 assertEquals("METAL", sf.type);
193 assertEquals(4f, sf.getScore(), 0.001f);
195 // verify feature on FER1_SOLLC
196 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
197 assertEquals(1, sfs.length);
199 assertEquals("uniprot", sf.description);
200 assertEquals(55, sf.begin);
201 assertEquals(130, sf.end);
202 assertEquals("uniprot", sf.featureGroup);
203 assertEquals("Pfam", sf.type);
204 assertEquals(2f, sf.getScore(), 0.001f);
207 public static AlignmentI readAlignmentFile(File f) throws IOException
209 System.out.println("Reading file: " + f);
210 String ff = f.getPath();
211 FormatAdapter rf = new FormatAdapter();
213 AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
214 new IdentifyFile().identify(ff, DataSourceType.FILE));
216 al.setDataset(null); // creates dataset sequences
217 assertNotNull("Couldn't read supplied alignment data.", al);
222 * Test parsing a features file with GFF formatted content only
226 @Test(groups = { "Functional" })
227 public void testParse_pureGff3() throws Exception
229 File f = new File("examples/uniref50.fa");
230 AlignmentI al = readAlignmentFile(f);
231 AlignFrame af = new AlignFrame(al, 500, 500);
232 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
233 .getFeatureColours();
234 // GFF3 uses '=' separator for name/value pairs in colum 9
235 String gffData = "##gff-version 3\n"
236 + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
237 + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465\n"
238 + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
239 FeaturesFile featuresFile = new FeaturesFile(gffData,
240 DataSourceType.PASTE);
241 assertTrue("Failed to parse features file",
242 featuresFile.parse(al.getDataset(), colours, true));
244 // verify feature on FER_CAPAA
245 SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
246 .getSequenceFeatures();
247 assertEquals(1, sfs.length);
248 SequenceFeature sf = sfs[0];
249 // description parsed from Note attribute
250 assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description);
251 assertEquals(39, sf.begin);
252 assertEquals(39, sf.end);
253 assertEquals("uniprot", sf.featureGroup);
254 assertEquals("METAL", sf.type);
256 "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465",
257 sf.getValue("ATTRIBUTES"));
259 // verify feature on FER1_SOLLC1
260 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
261 assertEquals(1, sfs.length);
263 // ID used for description if available
264 assertEquals("$23", sf.description);
265 assertEquals(55, sf.begin);
266 assertEquals(130, sf.end);
267 assertEquals("uniprot", sf.featureGroup);
268 assertEquals("Pfam", sf.type);
269 assertEquals(3f, sf.getScore(), 0.001f);
273 * Test parsing a features file with Jalview format features (but no colour
274 * descriptors or startgroup to give the hint not to parse as GFF)
278 @Test(groups = { "Functional" })
279 public void testParse_jalviewFeaturesOnly() throws Exception
281 File f = new File("examples/uniref50.fa");
282 AlignmentI al = readAlignmentFile(f);
283 AlignFrame af = new AlignFrame(al, 500, 500);
284 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
285 .getFeatureColours();
288 * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
290 String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
291 + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
292 FeaturesFile featuresFile = new FeaturesFile(featureData,
293 DataSourceType.PASTE);
294 assertTrue("Failed to parse features file",
295 featuresFile.parse(al.getDataset(), colours, true));
297 // verify FER_CAPAA feature
298 SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
299 .getSequenceFeatures();
300 assertEquals(1, sfs.length);
301 SequenceFeature sf = sfs[0];
302 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
303 assertEquals(39, sf.begin);
304 assertEquals(39, sf.end);
305 assertEquals("METAL", sf.type);
307 // verify FER1_SOLLC feature
308 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
309 assertEquals(1, sfs.length);
311 assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
312 assertEquals(86, sf.begin);
313 assertEquals(87, sf.end);
314 assertEquals("METALLIC", sf.type);
317 private void checkDatasetfromSimpleGff3(AlignmentI dataset)
319 assertEquals("no sequences extracted from GFF3 file", 2,
320 dataset.getHeight());
322 SequenceI seq1 = dataset.findName("seq1");
323 SequenceI seq2 = dataset.findName("seq2");
327 "Failed to replace dummy seq1 with real sequence",
328 seq1 instanceof SequenceDummy
329 && ((SequenceDummy) seq1).isDummy());
331 "Failed to replace dummy seq2 with real sequence",
332 seq2 instanceof SequenceDummy
333 && ((SequenceDummy) seq2).isDummy());
334 String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
335 assertFalse("dummy replacement buggy for seq1",
336 placeholderseq.equals(seq1.getSequenceAsString()));
337 assertFalse("dummy replacement buggy for seq2",
338 placeholderseq.equals(seq2.getSequenceAsString()));
339 assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
340 assertEquals("Wrong number of features", 3,
341 seq1.getSequenceFeatures().length);
342 assertNull(seq2.getSequenceFeatures());
344 "Wrong number of features",
346 seq2.getSequenceFeatures() == null ? 0 : seq2
347 .getSequenceFeatures().length);
349 "Expected at least one CDNA/Protein mapping for seq1",
350 dataset.getCodonFrame(seq1) != null
351 && dataset.getCodonFrame(seq1).size() > 0);
355 @Test(groups = { "Functional" })
356 public void readGff3File() throws IOException
358 FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
359 DataSourceType.FILE);
360 Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
361 gffreader.addProperties(dataset);
362 checkDatasetfromSimpleGff3(dataset);
365 @Test(groups = { "Functional" })
366 public void simpleGff3FileClass() throws IOException
368 AlignmentI dataset = new Alignment(new SequenceI[] {});
369 FeaturesFile ffile = new FeaturesFile(simpleGffFile,
370 DataSourceType.FILE);
372 boolean parseResult = ffile.parse(dataset, null, false, false);
373 assertTrue("return result should be true", parseResult);
374 checkDatasetfromSimpleGff3(dataset);
377 @Test(groups = { "Functional" })
378 public void simpleGff3FileLoader() throws IOException
380 AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
381 simpleGffFile, DataSourceType.FILE);
383 "Didn't read the alignment into an alignframe from Gff3 File",
385 checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
388 @Test(groups = { "Functional" })
389 public void simpleGff3RelaxedIdMatching() throws IOException
391 AlignmentI dataset = new Alignment(new SequenceI[] {});
392 FeaturesFile ffile = new FeaturesFile(simpleGffFile,
393 DataSourceType.FILE);
395 boolean parseResult = ffile.parse(dataset, null, false, true);
396 assertTrue("return result (relaxedID matching) should be true",
398 checkDatasetfromSimpleGff3(dataset);
401 @Test(groups = { "Functional" })
402 public void testPrintJalviewFormat() throws Exception
404 File f = new File("examples/uniref50.fa");
405 AlignmentI al = readAlignmentFile(f);
406 AlignFrame af = new AlignFrame(al, 500, 500);
407 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
408 .getFeatureColours();
409 String features = "METAL\tcc9900\n"
410 + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
412 + "STARTGROUP\tuniprot\n"
413 + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\n" // non-positional feature
414 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
415 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
416 + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
417 + "ENDGROUP\tuniprot\n";
418 FeaturesFile featuresFile = new FeaturesFile(features,
419 DataSourceType.PASTE);
420 featuresFile.parse(al.getDataset(), colours, false);
423 * first with no features displayed, exclude non-positional features
425 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
426 Map<String, FeatureColourI> visible = fr.getDisplayedFeatureCols();
427 List<String> visibleGroups = new ArrayList<String>(
428 Arrays.asList(new String[] {}));
429 String exported = featuresFile.printJalviewFormat(
430 al.getSequencesArray(), visible, visibleGroups, false);
431 String expected = "No Features Visible";
432 assertEquals(expected, exported);
435 * include non-positional features
437 visibleGroups.add("uniprot");
438 exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
439 visible, visibleGroups, true);
440 expected = "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n\nSTARTGROUP\tuniprot\nENDGROUP\tuniprot\n";
441 assertEquals(expected, exported);
444 * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
446 fr.setVisible("METAL");
447 fr.setVisible("GAMMA-TURN");
448 visible = fr.getDisplayedFeatureCols();
449 exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
450 visible, visibleGroups, false);
451 expected = "METAL\tcc9900\n"
452 + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
453 + "\nSTARTGROUP\tuniprot\n"
454 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
455 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
456 + "ENDGROUP\tuniprot\n";
457 assertEquals(expected, exported);
460 * now set Pfam visible
462 fr.setVisible("Pfam");
463 visible = fr.getDisplayedFeatureCols();
464 exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
465 visible, visibleGroups, false);
467 * features are output within group, ordered by sequence and by type
469 expected = "METAL\tcc9900\n"
471 + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
472 + "\nSTARTGROUP\tuniprot\n"
473 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
474 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
475 + "<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"
476 + "ENDGROUP\tuniprot\n";
477 assertEquals(expected, exported);
480 @Test(groups = { "Functional" })
481 public void testPrintGffFormat() throws Exception
483 File f = new File("examples/uniref50.fa");
484 AlignmentI al = readAlignmentFile(f);
485 AlignFrame af = new AlignFrame(al, 500, 500);
490 FeaturesFile featuresFile = new FeaturesFile();
491 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
492 Map<String, FeatureColourI> visible = new HashMap<String, FeatureColourI>();
493 List<String> visibleGroups = new ArrayList<String>(
494 Arrays.asList(new String[] {}));
495 String exported = featuresFile.printGffFormat(al.getSequencesArray(),
496 visible, visibleGroups, false);
497 String gffHeader = "##gff-version 2\n";
498 assertEquals(gffHeader, exported);
499 exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
500 visibleGroups, true);
501 assertEquals(gffHeader, exported);
506 al.getSequenceAt(0).addSequenceFeature(
507 new SequenceFeature("Domain", "Cath", 0, 0, 0f, "Uniprot"));
508 al.getSequenceAt(0).addSequenceFeature(
509 new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, null));
512 new SequenceFeature("GAMMA-TURN", "Turn", 36, 38, 2.1f,
514 SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f,
516 sf.setAttributes("x=y;black=white");
519 al.getSequenceAt(1).addSequenceFeature(sf);
522 * with no features displayed, exclude non-positional features
524 exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
525 visibleGroups, false);
526 assertEquals(gffHeader, exported);
529 * include non-positional features
531 visibleGroups.add("Uniprot");
532 exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
533 visibleGroups, true);
534 String expected = gffHeader
535 + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
536 assertEquals(expected, exported);
539 * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
540 * only Uniprot group visible here...
542 fr.setVisible("METAL");
543 fr.setVisible("GAMMA-TURN");
544 visible = fr.getDisplayedFeatureCols();
545 exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
546 visibleGroups, false);
547 // METAL feature has null group: description used for column 2
548 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
549 assertEquals(expected, exported);
552 * set s3dm group visible
554 visibleGroups.add("s3dm");
555 exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
556 visibleGroups, false);
557 // METAL feature has null group: description used for column 2
558 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
559 + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
560 assertEquals(expected, exported);
563 * now set Pfam visible
565 fr.setVisible("Pfam");
566 visible = fr.getDisplayedFeatureCols();
567 exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
568 visibleGroups, false);
569 // Pfam feature columns include strand(+), phase(2), attributes
571 + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
572 + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n"
573 + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n";
574 assertEquals(expected, exported);