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;
44 import org.testng.annotations.BeforeClass;
45 import org.testng.annotations.Test;
47 public class FeaturesFileTest
50 @BeforeClass(alwaysRun = true)
51 public void setUpJvOptionPane()
53 JvOptionPane.setInteractiveMode(false);
54 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
57 private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
59 @Test(groups = { "Functional" })
60 public void testParse() throws Exception
62 File f = new File("examples/uniref50.fa");
63 AlignmentI al = readAlignmentFile(f);
64 AlignFrame af = new AlignFrame(al, 500, 500);
65 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
67 FeaturesFile featuresFile = new FeaturesFile(
68 "examples/exampleFeatures.txt", DataSourceType.FILE);
69 assertTrue("Test " + "Features file test"
70 + "\nFailed to parse features file.",
71 featuresFile.parse(al.getDataset(), colours, true));
74 * Refetch the colour map from the FeatureRenderer (to confirm it has been
75 * updated - JAL-1904), and verify (some) feature group colours
77 colours = af.getFeatureRenderer().getFeatureColours();
78 assertEquals("26 feature group colours not found", 26, colours.size());
79 assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
80 assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
83 * verify (some) features on sequences
85 SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
86 .getSequenceFeatures(); // FER_CAPAA
87 assertEquals(8, sfs.length);
88 SequenceFeature sf = sfs[0];
89 assertEquals("Pfam family%LINK%", sf.description);
90 assertEquals(0, sf.begin);
91 assertEquals(0, sf.end);
92 assertEquals("uniprot", sf.featureGroup);
93 assertEquals("Pfam", sf.type);
94 assertEquals(1, sf.links.size());
95 assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
99 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
100 assertEquals(39, sf.begin);
101 assertEquals(39, sf.end);
102 assertEquals("uniprot", sf.featureGroup);
103 assertEquals("METAL", sf.type);
105 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
106 assertEquals(44, sf.begin);
107 assertEquals(44, sf.end);
108 assertEquals("uniprot", sf.featureGroup);
109 assertEquals("METAL", sf.type);
111 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
112 assertEquals(47, sf.begin);
113 assertEquals(47, sf.end);
114 assertEquals("uniprot", sf.featureGroup);
115 assertEquals("METAL", sf.type);
117 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
118 assertEquals(77, sf.begin);
119 assertEquals(77, sf.end);
120 assertEquals("uniprot", sf.featureGroup);
121 assertEquals("METAL", sf.type);
123 assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
125 assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
127 assertEquals(8, sf.begin);
128 assertEquals(83, sf.end);
129 assertEquals("uniprot", sf.featureGroup);
130 assertEquals("Pfam", sf.type);
132 assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
133 assertEquals(3, sf.begin);
134 assertEquals(93, sf.end);
135 assertEquals("uniprot", sf.featureGroup);
136 assertEquals("Cath", sf.type);
139 "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
142 "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&service=NetPhos-2.0",
144 assertEquals(89, sf.begin);
145 assertEquals(89, sf.end);
146 assertEquals("netphos", sf.featureGroup);
147 assertEquals("PHOSPHORYLATION (T)", sf.type);
151 * Test parsing a features file with a mix of Jalview and GFF formatted
156 @Test(groups = { "Functional" })
157 public void testParse_mixedJalviewGff() throws Exception
159 File f = new File("examples/uniref50.fa");
160 AlignmentI al = readAlignmentFile(f);
161 AlignFrame af = new AlignFrame(al, 500, 500);
162 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
163 .getFeatureColours();
164 // GFF2 uses space as name/value separator in column 9
165 String gffData = "METAL\tcc9900\n"
167 + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
168 + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
169 FeaturesFile featuresFile = new FeaturesFile(gffData,
170 DataSourceType.PASTE);
171 assertTrue("Failed to parse features file",
172 featuresFile.parse(al.getDataset(), colours, true));
174 // verify colours read or synthesized
175 colours = af.getFeatureRenderer().getFeatureColours();
176 assertEquals("1 feature group colours not found", 1, colours.size());
177 assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
179 // verify feature on FER_CAPAA
180 SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
181 .getSequenceFeatures();
182 assertEquals(1, sfs.length);
183 SequenceFeature sf = sfs[0];
184 assertEquals("Iron-sulfur,2Fe-2S", sf.description);
185 assertEquals(44, sf.begin);
186 assertEquals(45, sf.end);
187 assertEquals("uniprot", sf.featureGroup);
188 assertEquals("METAL", sf.type);
189 assertEquals(4f, sf.getScore(), 0.001f);
191 // verify feature on FER1_SOLLC
192 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
193 assertEquals(1, sfs.length);
195 assertEquals("uniprot", sf.description);
196 assertEquals(55, sf.begin);
197 assertEquals(130, sf.end);
198 assertEquals("uniprot", sf.featureGroup);
199 assertEquals("Pfam", sf.type);
200 assertEquals(2f, sf.getScore(), 0.001f);
203 public static AlignmentI readAlignmentFile(File f) throws IOException
205 System.out.println("Reading file: " + f);
206 String ff = f.getPath();
207 FormatAdapter rf = new FormatAdapter();
209 AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
210 new IdentifyFile().identify(ff, DataSourceType.FILE));
212 al.setDataset(null); // creates dataset sequences
213 assertNotNull("Couldn't read supplied alignment data.", al);
218 * Test parsing a features file with GFF formatted content only
222 @Test(groups = { "Functional" })
223 public void testParse_pureGff3() throws Exception
225 File f = new File("examples/uniref50.fa");
226 AlignmentI al = readAlignmentFile(f);
227 AlignFrame af = new AlignFrame(al, 500, 500);
228 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
229 .getFeatureColours();
230 // GFF3 uses '=' separator for name/value pairs in colum 9
231 String gffData = "##gff-version 3\n"
232 + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
233 + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465\n"
234 + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
235 FeaturesFile featuresFile = new FeaturesFile(gffData,
236 DataSourceType.PASTE);
237 assertTrue("Failed to parse features file",
238 featuresFile.parse(al.getDataset(), colours, true));
240 // verify feature on FER_CAPAA
241 SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
242 .getSequenceFeatures();
243 assertEquals(1, sfs.length);
244 SequenceFeature sf = sfs[0];
245 // description parsed from Note attribute
246 assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description);
247 assertEquals(39, sf.begin);
248 assertEquals(39, sf.end);
249 assertEquals("uniprot", sf.featureGroup);
250 assertEquals("METAL", sf.type);
252 "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465",
253 sf.getValue("ATTRIBUTES"));
255 // verify feature on FER1_SOLLC1
256 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
257 assertEquals(1, sfs.length);
259 // ID used for description if available
260 assertEquals("$23", sf.description);
261 assertEquals(55, sf.begin);
262 assertEquals(130, sf.end);
263 assertEquals("uniprot", sf.featureGroup);
264 assertEquals("Pfam", sf.type);
265 assertEquals(3f, sf.getScore(), 0.001f);
269 * Test parsing a features file with Jalview format features (but no colour
270 * descriptors or startgroup to give the hint not to parse as GFF)
274 @Test(groups = { "Functional" })
275 public void testParse_jalviewFeaturesOnly() throws Exception
277 File f = new File("examples/uniref50.fa");
278 AlignmentI al = readAlignmentFile(f);
279 AlignFrame af = new AlignFrame(al, 500, 500);
280 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
281 .getFeatureColours();
284 * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
286 String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
287 + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
288 FeaturesFile featuresFile = new FeaturesFile(featureData,
289 DataSourceType.PASTE);
290 assertTrue("Failed to parse features file",
291 featuresFile.parse(al.getDataset(), colours, true));
293 // verify FER_CAPAA feature
294 SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
295 .getSequenceFeatures();
296 assertEquals(1, sfs.length);
297 SequenceFeature sf = sfs[0];
298 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
299 assertEquals(39, sf.begin);
300 assertEquals(39, sf.end);
301 assertEquals("METAL", sf.type);
303 // verify FER1_SOLLC feature
304 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
305 assertEquals(1, sfs.length);
307 assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
308 assertEquals(86, sf.begin);
309 assertEquals(87, sf.end);
310 assertEquals("METALLIC", sf.type);
313 private void checkDatasetfromSimpleGff3(AlignmentI dataset)
315 assertEquals("no sequences extracted from GFF3 file", 2,
316 dataset.getHeight());
318 SequenceI seq1 = dataset.findName("seq1");
319 SequenceI seq2 = dataset.findName("seq2");
323 "Failed to replace dummy seq1 with real sequence",
324 seq1 instanceof SequenceDummy
325 && ((SequenceDummy) seq1).isDummy());
327 "Failed to replace dummy seq2 with real sequence",
328 seq2 instanceof SequenceDummy
329 && ((SequenceDummy) seq2).isDummy());
330 String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
331 assertFalse("dummy replacement buggy for seq1",
332 placeholderseq.equals(seq1.getSequenceAsString()));
333 assertFalse("dummy replacement buggy for seq2",
334 placeholderseq.equals(seq2.getSequenceAsString()));
335 assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
336 assertEquals("Wrong number of features", 3,
337 seq1.getSequenceFeatures().length);
338 assertNull(seq2.getSequenceFeatures());
340 "Wrong number of features",
342 seq2.getSequenceFeatures() == null ? 0 : seq2
343 .getSequenceFeatures().length);
345 "Expected at least one CDNA/Protein mapping for seq1",
346 dataset.getCodonFrame(seq1) != null
347 && dataset.getCodonFrame(seq1).size() > 0);
351 @Test(groups = { "Functional" })
352 public void readGff3File() throws IOException
354 FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
355 DataSourceType.FILE);
356 Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
357 gffreader.addProperties(dataset);
358 checkDatasetfromSimpleGff3(dataset);
361 @Test(groups = { "Functional" })
362 public void simpleGff3FileClass() throws IOException
364 AlignmentI dataset = new Alignment(new SequenceI[] {});
365 FeaturesFile ffile = new FeaturesFile(simpleGffFile,
366 DataSourceType.FILE);
368 boolean parseResult = ffile.parse(dataset, null, false, false);
369 assertTrue("return result should be true", parseResult);
370 checkDatasetfromSimpleGff3(dataset);
373 @Test(groups = { "Functional" })
374 public void simpleGff3FileLoader() throws IOException
376 AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
377 simpleGffFile, DataSourceType.FILE);
379 "Didn't read the alignment into an alignframe from Gff3 File",
381 checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
384 @Test(groups = { "Functional" })
385 public void simpleGff3RelaxedIdMatching() throws IOException
387 AlignmentI dataset = new Alignment(new SequenceI[] {});
388 FeaturesFile ffile = new FeaturesFile(simpleGffFile,
389 DataSourceType.FILE);
391 boolean parseResult = ffile.parse(dataset, null, false, true);
392 assertTrue("return result (relaxedID matching) should be true",
394 checkDatasetfromSimpleGff3(dataset);
397 @Test(groups = { "Functional" })
398 public void testPrintJalviewFormat() throws Exception
400 File f = new File("examples/uniref50.fa");
401 AlignmentI al = readAlignmentFile(f);
402 AlignFrame af = new AlignFrame(al, 500, 500);
403 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
404 .getFeatureColours();
405 String features = "METAL\tcc9900\n"
406 + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
408 + "STARTGROUP\tuniprot\n"
409 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
410 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
411 + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
412 + "ENDGROUP\tuniprot\n";
413 FeaturesFile featuresFile = new FeaturesFile(features,
414 DataSourceType.PASTE);
415 featuresFile.parse(al.getDataset(), colours, false);
418 * first with no features displayed
420 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
421 Map<String, FeatureColourI> visible = fr.getDisplayedFeatureCols();
422 String exported = featuresFile.printJalviewFormat(
423 al.getSequencesArray(), visible);
424 String expected = "No Features Visible";
425 assertEquals(expected, exported);
428 * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
430 fr.setVisible("METAL");
431 fr.setVisible("GAMMA-TURN");
432 visible = fr.getDisplayedFeatureCols();
433 exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
435 expected = "METAL\tcc9900\n"
436 + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
437 + "\nSTARTGROUP\tuniprot\n"
438 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
439 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
440 + "ENDGROUP\tuniprot\n";
441 assertEquals(expected, exported);
444 * now set Pfam visible
446 fr.setVisible("Pfam");
447 visible = fr.getDisplayedFeatureCols();
448 exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
451 * note the order of feature types is uncontrolled - derives from
452 * FeaturesDisplayed.featuresDisplayed which is a HashSet
454 expected = "METAL\tcc9900\n"
456 + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
457 + "\nSTARTGROUP\tuniprot\n"
458 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
459 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
460 + "<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"
461 + "ENDGROUP\tuniprot\n";
462 assertEquals(expected, exported);