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.HashMap;
45 import org.testng.annotations.BeforeClass;
46 import org.testng.annotations.Test;
48 public class FeaturesFileTest
51 @BeforeClass(alwaysRun = true)
52 public void setUpJvOptionPane()
54 JvOptionPane.setInteractiveMode(false);
55 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
58 private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
60 @Test(groups = { "Functional" })
61 public void testParse() throws Exception
63 File f = new File("examples/uniref50.fa");
64 AlignmentI al = readAlignmentFile(f);
65 AlignFrame af = new AlignFrame(al, 500, 500);
66 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
68 FeaturesFile featuresFile = new FeaturesFile(
69 "examples/exampleFeatures.txt", DataSourceType.FILE);
70 assertTrue("Test " + "Features file test"
71 + "\nFailed to parse features file.",
72 featuresFile.parse(al.getDataset(), colours, true));
75 * Refetch the colour map from the FeatureRenderer (to confirm it has been
76 * updated - JAL-1904), and verify (some) feature group colours
78 colours = af.getFeatureRenderer().getFeatureColours();
79 assertEquals("26 feature group colours not found", 26, colours.size());
80 assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
81 assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
84 * verify (some) features on sequences
86 SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
87 .getSequenceFeatures(); // FER_CAPAA
88 assertEquals(8, sfs.length);
89 SequenceFeature sf = sfs[0];
90 assertEquals("Pfam family%LINK%", sf.description);
91 assertEquals(0, sf.begin);
92 assertEquals(0, sf.end);
93 assertEquals("uniprot", sf.featureGroup);
94 assertEquals("Pfam", sf.type);
95 assertEquals(1, sf.links.size());
96 assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
100 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
101 assertEquals(39, sf.begin);
102 assertEquals(39, sf.end);
103 assertEquals("uniprot", sf.featureGroup);
104 assertEquals("METAL", sf.type);
106 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
107 assertEquals(44, sf.begin);
108 assertEquals(44, sf.end);
109 assertEquals("uniprot", sf.featureGroup);
110 assertEquals("METAL", sf.type);
112 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
113 assertEquals(47, sf.begin);
114 assertEquals(47, sf.end);
115 assertEquals("uniprot", sf.featureGroup);
116 assertEquals("METAL", sf.type);
118 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
119 assertEquals(77, sf.begin);
120 assertEquals(77, sf.end);
121 assertEquals("uniprot", sf.featureGroup);
122 assertEquals("METAL", sf.type);
124 assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
126 assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
128 assertEquals(8, sf.begin);
129 assertEquals(83, sf.end);
130 assertEquals("uniprot", sf.featureGroup);
131 assertEquals("Pfam", sf.type);
133 assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
134 assertEquals(3, sf.begin);
135 assertEquals(93, sf.end);
136 assertEquals("uniprot", sf.featureGroup);
137 assertEquals("Cath", sf.type);
140 "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
143 "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&service=NetPhos-2.0",
145 assertEquals(89, sf.begin);
146 assertEquals(89, sf.end);
147 assertEquals("netphos", sf.featureGroup);
148 assertEquals("PHOSPHORYLATION (T)", sf.type);
152 * Test parsing a features file with a mix of Jalview and GFF formatted
157 @Test(groups = { "Functional" })
158 public void testParse_mixedJalviewGff() throws Exception
160 File f = new File("examples/uniref50.fa");
161 AlignmentI al = readAlignmentFile(f);
162 AlignFrame af = new AlignFrame(al, 500, 500);
163 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
164 .getFeatureColours();
165 // GFF2 uses space as name/value separator in column 9
166 String gffData = "METAL\tcc9900\n"
168 + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
169 + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
170 FeaturesFile featuresFile = new FeaturesFile(gffData,
171 DataSourceType.PASTE);
172 assertTrue("Failed to parse features file",
173 featuresFile.parse(al.getDataset(), colours, true));
175 // verify colours read or synthesized
176 colours = af.getFeatureRenderer().getFeatureColours();
177 assertEquals("1 feature group colours not found", 1, colours.size());
178 assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
180 // verify feature on FER_CAPAA
181 SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
182 .getSequenceFeatures();
183 assertEquals(1, sfs.length);
184 SequenceFeature sf = sfs[0];
185 assertEquals("Iron-sulfur,2Fe-2S", sf.description);
186 assertEquals(44, sf.begin);
187 assertEquals(45, sf.end);
188 assertEquals("uniprot", sf.featureGroup);
189 assertEquals("METAL", sf.type);
190 assertEquals(4f, sf.getScore(), 0.001f);
192 // verify feature on FER1_SOLLC
193 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
194 assertEquals(1, sfs.length);
196 assertEquals("uniprot", sf.description);
197 assertEquals(55, sf.begin);
198 assertEquals(130, sf.end);
199 assertEquals("uniprot", sf.featureGroup);
200 assertEquals("Pfam", sf.type);
201 assertEquals(2f, sf.getScore(), 0.001f);
204 public static AlignmentI readAlignmentFile(File f) throws IOException
206 System.out.println("Reading file: " + f);
207 String ff = f.getPath();
208 FormatAdapter rf = new FormatAdapter();
210 AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
211 new IdentifyFile().identify(ff, DataSourceType.FILE));
213 al.setDataset(null); // creates dataset sequences
214 assertNotNull("Couldn't read supplied alignment data.", al);
219 * Test parsing a features file with GFF formatted content only
223 @Test(groups = { "Functional" })
224 public void testParse_pureGff3() throws Exception
226 File f = new File("examples/uniref50.fa");
227 AlignmentI al = readAlignmentFile(f);
228 AlignFrame af = new AlignFrame(al, 500, 500);
229 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
230 .getFeatureColours();
231 // GFF3 uses '=' separator for name/value pairs in colum 9
232 String gffData = "##gff-version 3\n"
233 + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
234 + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465\n"
235 + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
236 FeaturesFile featuresFile = new FeaturesFile(gffData,
237 DataSourceType.PASTE);
238 assertTrue("Failed to parse features file",
239 featuresFile.parse(al.getDataset(), colours, true));
241 // verify feature on FER_CAPAA
242 SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
243 .getSequenceFeatures();
244 assertEquals(1, sfs.length);
245 SequenceFeature sf = sfs[0];
246 // description parsed from Note attribute
247 assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description);
248 assertEquals(39, sf.begin);
249 assertEquals(39, sf.end);
250 assertEquals("uniprot", sf.featureGroup);
251 assertEquals("METAL", sf.type);
253 "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465",
254 sf.getValue("ATTRIBUTES"));
256 // verify feature on FER1_SOLLC1
257 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
258 assertEquals(1, sfs.length);
260 // ID used for description if available
261 assertEquals("$23", sf.description);
262 assertEquals(55, sf.begin);
263 assertEquals(130, sf.end);
264 assertEquals("uniprot", sf.featureGroup);
265 assertEquals("Pfam", sf.type);
266 assertEquals(3f, sf.getScore(), 0.001f);
270 * Test parsing a features file with Jalview format features (but no colour
271 * descriptors or startgroup to give the hint not to parse as GFF)
275 @Test(groups = { "Functional" })
276 public void testParse_jalviewFeaturesOnly() throws Exception
278 File f = new File("examples/uniref50.fa");
279 AlignmentI al = readAlignmentFile(f);
280 AlignFrame af = new AlignFrame(al, 500, 500);
281 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
282 .getFeatureColours();
285 * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
287 String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
288 + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
289 FeaturesFile featuresFile = new FeaturesFile(featureData,
290 DataSourceType.PASTE);
291 assertTrue("Failed to parse features file",
292 featuresFile.parse(al.getDataset(), colours, true));
294 // verify FER_CAPAA feature
295 SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
296 .getSequenceFeatures();
297 assertEquals(1, sfs.length);
298 SequenceFeature sf = sfs[0];
299 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
300 assertEquals(39, sf.begin);
301 assertEquals(39, sf.end);
302 assertEquals("METAL", sf.type);
304 // verify FER1_SOLLC feature
305 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
306 assertEquals(1, sfs.length);
308 assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
309 assertEquals(86, sf.begin);
310 assertEquals(87, sf.end);
311 assertEquals("METALLIC", sf.type);
314 private void checkDatasetfromSimpleGff3(AlignmentI dataset)
316 assertEquals("no sequences extracted from GFF3 file", 2,
317 dataset.getHeight());
319 SequenceI seq1 = dataset.findName("seq1");
320 SequenceI seq2 = dataset.findName("seq2");
324 "Failed to replace dummy seq1 with real sequence",
325 seq1 instanceof SequenceDummy
326 && ((SequenceDummy) seq1).isDummy());
328 "Failed to replace dummy seq2 with real sequence",
329 seq2 instanceof SequenceDummy
330 && ((SequenceDummy) seq2).isDummy());
331 String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
332 assertFalse("dummy replacement buggy for seq1",
333 placeholderseq.equals(seq1.getSequenceAsString()));
334 assertFalse("dummy replacement buggy for seq2",
335 placeholderseq.equals(seq2.getSequenceAsString()));
336 assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
337 assertEquals("Wrong number of features", 3,
338 seq1.getSequenceFeatures().length);
339 assertNull(seq2.getSequenceFeatures());
341 "Wrong number of features",
343 seq2.getSequenceFeatures() == null ? 0 : seq2
344 .getSequenceFeatures().length);
346 "Expected at least one CDNA/Protein mapping for seq1",
347 dataset.getCodonFrame(seq1) != null
348 && dataset.getCodonFrame(seq1).size() > 0);
352 @Test(groups = { "Functional" })
353 public void readGff3File() throws IOException
355 FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
356 DataSourceType.FILE);
357 Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
358 gffreader.addProperties(dataset);
359 checkDatasetfromSimpleGff3(dataset);
362 @Test(groups = { "Functional" })
363 public void simpleGff3FileClass() throws IOException
365 AlignmentI dataset = new Alignment(new SequenceI[] {});
366 FeaturesFile ffile = new FeaturesFile(simpleGffFile,
367 DataSourceType.FILE);
369 boolean parseResult = ffile.parse(dataset, null, false, false);
370 assertTrue("return result should be true", parseResult);
371 checkDatasetfromSimpleGff3(dataset);
374 @Test(groups = { "Functional" })
375 public void simpleGff3FileLoader() throws IOException
377 AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
378 simpleGffFile, DataSourceType.FILE);
380 "Didn't read the alignment into an alignframe from Gff3 File",
382 checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
385 @Test(groups = { "Functional" })
386 public void simpleGff3RelaxedIdMatching() throws IOException
388 AlignmentI dataset = new Alignment(new SequenceI[] {});
389 FeaturesFile ffile = new FeaturesFile(simpleGffFile,
390 DataSourceType.FILE);
392 boolean parseResult = ffile.parse(dataset, null, false, true);
393 assertTrue("return result (relaxedID matching) should be true",
395 checkDatasetfromSimpleGff3(dataset);
398 @Test(groups = { "Functional" })
399 public void testPrintJalviewFormat() throws Exception
401 File f = new File("examples/uniref50.fa");
402 AlignmentI al = readAlignmentFile(f);
403 AlignFrame af = new AlignFrame(al, 500, 500);
404 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
405 .getFeatureColours();
406 String features = "METAL\tcc9900\n"
407 + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
409 + "STARTGROUP\tuniprot\n"
410 + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\n" // non-positional feature
411 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
412 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
413 + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
414 + "ENDGROUP\tuniprot\n";
415 FeaturesFile featuresFile = new FeaturesFile(features,
416 DataSourceType.PASTE);
417 featuresFile.parse(al.getDataset(), colours, false);
420 * first with no features displayed, exclude non-positional features
422 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
423 Map<String, FeatureColourI> visible = fr.getDisplayedFeatureCols();
424 String exported = featuresFile.printJalviewFormat(
425 al.getSequencesArray(), visible, false);
426 String expected = "No Features Visible";
427 assertEquals(expected, exported);
430 * include non-positional features
432 exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
434 expected = "\nSTARTGROUP\tuniprot\nCath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\nENDGROUP\tuniprot\n";
435 assertEquals(expected, exported);
438 * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
440 fr.setVisible("METAL");
441 fr.setVisible("GAMMA-TURN");
442 visible = fr.getDisplayedFeatureCols();
443 exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
445 expected = "METAL\tcc9900\n"
446 + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
447 + "\nSTARTGROUP\tuniprot\n"
448 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
449 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
450 + "ENDGROUP\tuniprot\n";
451 assertEquals(expected, exported);
454 * now set Pfam visible
456 fr.setVisible("Pfam");
457 visible = fr.getDisplayedFeatureCols();
458 exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
461 * features are output within group, ordered by sequence and by type
463 expected = "METAL\tcc9900\n"
465 + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
466 + "\nSTARTGROUP\tuniprot\n"
467 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
468 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
469 + "<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"
470 + "ENDGROUP\tuniprot\n";
471 assertEquals(expected, exported);
474 @Test(groups = { "Functional" })
475 public void testPrintGffFormat() throws Exception
477 File f = new File("examples/uniref50.fa");
478 AlignmentI al = readAlignmentFile(f);
479 AlignFrame af = new AlignFrame(al, 500, 500);
484 FeaturesFile featuresFile = new FeaturesFile();
485 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
486 Map<String, FeatureColourI> visible = new HashMap<String, FeatureColourI>();
487 String exported = featuresFile.printGffFormat(
488 al.getSequencesArray(), visible, false);
489 String gffHeader = "##gff-version 2\n";
490 assertEquals(gffHeader, exported);
491 exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
493 assertEquals(gffHeader, exported);
498 al.getSequenceAt(0).addSequenceFeature(
499 new SequenceFeature("Domain", "Cath", 0, 0, 0f, "Uniprot"));
500 al.getSequenceAt(0).addSequenceFeature(
501 new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, null));
504 new SequenceFeature("GAMMA-TURN", "Turn", 36, 38, 2.1f,
506 SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f, "Uniprot");
507 sf.setAttributes("x=y;black=white");
510 al.getSequenceAt(1).addSequenceFeature(sf);
513 * with no features displayed, exclude non-positional features
515 exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
517 assertEquals(gffHeader, exported);
520 * include non-positional features
522 exported = featuresFile.printGffFormat(al.getSequencesArray(),
524 String expected = gffHeader
525 + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
526 assertEquals(expected, exported);
529 * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
531 fr.setVisible("METAL");
532 fr.setVisible("GAMMA-TURN");
533 visible = fr.getDisplayedFeatureCols();
534 exported = featuresFile.printGffFormat(al.getSequencesArray(),
536 // METAL feature has null group: description used for column 2
537 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
538 + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
539 assertEquals(expected, exported);
542 * now set Pfam visible
544 fr.setVisible("Pfam");
545 visible = fr.getDisplayedFeatureCols();
546 exported = featuresFile.printGffFormat(al.getSequencesArray(),
548 // Pfam feature columns include strand(+), phase(2), attributes
549 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
550 + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n"
551 + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n";
552 assertEquals(expected, exported);