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;
38 import java.awt.Color;
40 import java.io.IOException;
43 import org.testng.annotations.Test;
45 public class FeaturesFileTest
48 private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
50 @Test(groups = { "Functional" })
51 public void testParse() throws Exception
53 File f = new File("examples/uniref50.fa");
54 AlignmentI al = readAlignmentFile(f);
55 AlignFrame af = new AlignFrame(al, 500, 500);
56 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
58 FeaturesFile featuresFile = new FeaturesFile(
59 "examples/exampleFeatures.txt", FormatAdapter.FILE);
60 assertTrue("Test " + "Features file test"
61 + "\nFailed to parse features file.",
62 featuresFile.parse(al.getDataset(), colours, true));
65 * Refetch the colour map from the FeatureRenderer (to confirm it has been
66 * updated - JAL-1904), and verify (some) feature group colours
68 colours = af.getFeatureRenderer().getFeatureColours();
69 assertEquals("26 feature group colours not found", 26, colours.size());
70 assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
71 assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
74 * verify (some) features on sequences
76 SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
77 .getSequenceFeatures(); // FER_CAPAA
78 assertEquals(7, sfs.length);
79 SequenceFeature sf = sfs[0];
80 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
81 assertEquals(39, sf.begin);
82 assertEquals(39, sf.end);
83 assertEquals("uniprot", sf.featureGroup);
84 assertEquals("METAL", sf.type);
86 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
87 assertEquals(44, sf.begin);
88 assertEquals(44, sf.end);
89 assertEquals("uniprot", sf.featureGroup);
90 assertEquals("METAL", sf.type);
92 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
93 assertEquals(47, sf.begin);
94 assertEquals(47, sf.end);
95 assertEquals("uniprot", sf.featureGroup);
96 assertEquals("METAL", sf.type);
98 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
99 assertEquals(77, sf.begin);
100 assertEquals(77, sf.end);
101 assertEquals("uniprot", sf.featureGroup);
102 assertEquals("METAL", sf.type);
104 assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
106 assertEquals("Pfam 8_8|http://pfam.sanger.ac.uk/family/PF00111",
107 sf.links.get(0).toString());
108 assertEquals(8, sf.begin);
109 assertEquals(83, sf.end);
110 assertEquals("uniprot", sf.featureGroup);
111 assertEquals("Pfam", sf.type);
113 assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
114 assertEquals(3, sf.begin);
115 assertEquals(93, sf.end);
116 assertEquals("uniprot", sf.featureGroup);
117 assertEquals("Cath", sf.type);
120 "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
123 "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&service=NetPhos-2.0",
124 sf.links.get(0).toString());
125 assertEquals(89, sf.begin);
126 assertEquals(89, sf.end);
127 assertEquals("netphos", sf.featureGroup);
128 assertEquals("PHOSPHORYLATION (T)", sf.type);
132 * Test parsing a features file with a mix of Jalview and GFF formatted
137 @Test(groups = { "Functional" })
138 public void testParse_mixedJalviewGff() throws Exception
140 File f = new File("examples/uniref50.fa");
141 AlignmentI al = readAlignmentFile(f);
142 AlignFrame af = new AlignFrame(al, 500, 500);
143 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
144 .getFeatureColours();
145 // GFF2 uses space as name/value separator in column 9
146 String gffData = "METAL\tcc9900\n" + "GFF\n"
147 + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
148 + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
149 FeaturesFile featuresFile = new FeaturesFile(gffData,
150 FormatAdapter.PASTE);
151 assertTrue("Failed to parse features file",
152 featuresFile.parse(al.getDataset(), colours, true));
154 // verify colours read or synthesized
155 colours = af.getFeatureRenderer().getFeatureColours();
156 assertEquals("1 feature group colours not found", 1, colours.size());
157 assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
159 // verify feature on FER_CAPAA
160 SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
161 .getSequenceFeatures();
162 assertEquals(1, sfs.length);
163 SequenceFeature sf = sfs[0];
164 assertEquals("Iron-sulfur,2Fe-2S", sf.description);
165 assertEquals(44, sf.begin);
166 assertEquals(45, sf.end);
167 assertEquals("uniprot", sf.featureGroup);
168 assertEquals("METAL", sf.type);
169 assertEquals(4f, sf.getScore(), 0.001f);
171 // verify feature on FER1_SOLLC
172 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
173 assertEquals(1, sfs.length);
175 assertEquals("uniprot", sf.description);
176 assertEquals(55, sf.begin);
177 assertEquals(130, sf.end);
178 assertEquals("uniprot", sf.featureGroup);
179 assertEquals("Pfam", sf.type);
180 assertEquals(2f, sf.getScore(), 0.001f);
183 public static AlignmentI readAlignmentFile(File f) throws IOException
185 System.out.println("Reading file: " + f);
186 String ff = f.getPath();
187 FormatAdapter rf = new FormatAdapter();
189 AlignmentI al = rf.readFile(ff, FormatAdapter.FILE,
190 new IdentifyFile().identify(ff, FormatAdapter.FILE));
192 al.setDataset(null); // creates dataset sequences
193 assertNotNull("Couldn't read supplied alignment data.", al);
198 * Test parsing a features file with GFF formatted content only
202 @Test(groups = { "Functional" })
203 public void testParse_pureGff3() throws Exception
205 File f = new File("examples/uniref50.fa");
206 AlignmentI al = readAlignmentFile(f);
207 AlignFrame af = new AlignFrame(al, 500, 500);
208 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
209 .getFeatureColours();
210 // GFF3 uses '=' separator for name/value pairs in colum 9
211 String gffData = "##gff-version 3\n"
212 + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
213 + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465\n"
214 + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
215 FeaturesFile featuresFile = new FeaturesFile(gffData,
216 FormatAdapter.PASTE);
217 assertTrue("Failed to parse features file",
218 featuresFile.parse(al.getDataset(), colours, true));
220 // verify feature on FER_CAPAA
221 SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
222 .getSequenceFeatures();
223 assertEquals(1, sfs.length);
224 SequenceFeature sf = sfs[0];
225 // description parsed from Note attribute
226 assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description);
227 assertEquals(39, sf.begin);
228 assertEquals(39, sf.end);
229 assertEquals("uniprot", sf.featureGroup);
230 assertEquals("METAL", sf.type);
232 "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465",
233 sf.getValue("ATTRIBUTES"));
235 // verify feature on FER1_SOLLC1
236 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
237 assertEquals(1, sfs.length);
239 // ID used for description if available
240 assertEquals("$23", sf.description);
241 assertEquals(55, sf.begin);
242 assertEquals(130, sf.end);
243 assertEquals("uniprot", sf.featureGroup);
244 assertEquals("Pfam", sf.type);
245 assertEquals(3f, sf.getScore(), 0.001f);
249 * Test parsing a features file with Jalview format features (but no colour
250 * descriptors or startgroup to give the hint not to parse as GFF)
254 @Test(groups = { "Functional" })
255 public void testParse_jalviewFeaturesOnly() throws Exception
257 File f = new File("examples/uniref50.fa");
258 AlignmentI al = readAlignmentFile(f);
259 AlignFrame af = new AlignFrame(al, 500, 500);
260 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
261 .getFeatureColours();
264 * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
266 String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
267 + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
268 FeaturesFile featuresFile = new FeaturesFile(featureData,
269 FormatAdapter.PASTE);
270 assertTrue("Failed to parse features file",
271 featuresFile.parse(al.getDataset(), colours, true));
273 // verify FER_CAPAA feature
274 SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
275 .getSequenceFeatures();
276 assertEquals(1, sfs.length);
277 SequenceFeature sf = sfs[0];
278 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
279 assertEquals(39, sf.begin);
280 assertEquals(39, sf.end);
281 assertEquals("METAL", sf.type);
283 // verify FER1_SOLLC feature
284 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
285 assertEquals(1, sfs.length);
287 assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
288 assertEquals(86, sf.begin);
289 assertEquals(87, sf.end);
290 assertEquals("METALLIC", sf.type);
293 private void checkDatasetfromSimpleGff3(AlignmentI dataset)
295 assertEquals("no sequences extracted from GFF3 file", 2,
296 dataset.getHeight());
298 SequenceI seq1 = dataset.findName("seq1");
299 SequenceI seq2 = dataset.findName("seq2");
303 "Failed to replace dummy seq1 with real sequence",
304 seq1 instanceof SequenceDummy
305 && ((SequenceDummy) seq1).isDummy());
307 "Failed to replace dummy seq2 with real sequence",
308 seq2 instanceof SequenceDummy
309 && ((SequenceDummy) seq2).isDummy());
310 String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
311 assertFalse("dummy replacement buggy for seq1",
312 placeholderseq.equals(seq1.getSequenceAsString()));
313 assertFalse("dummy replacement buggy for seq2",
314 placeholderseq.equals(seq2.getSequenceAsString()));
315 assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
316 assertEquals("Wrong number of features", 3,
317 seq1.getSequenceFeatures().length);
318 assertNull(seq2.getSequenceFeatures());
320 "Wrong number of features",
322 seq2.getSequenceFeatures() == null ? 0 : seq2
323 .getSequenceFeatures().length);
325 "Expected at least one CDNA/Protein mapping for seq1",
326 dataset.getCodonFrame(seq1) != null
327 && dataset.getCodonFrame(seq1).size() > 0);
331 @Test(groups = { "Functional" })
332 public void readGff3File() throws IOException
334 FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
336 Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
337 gffreader.addProperties(dataset);
338 checkDatasetfromSimpleGff3(dataset);
341 @Test(groups = { "Functional" })
342 public void simpleGff3FileClass() throws IOException
344 AlignmentI dataset = new Alignment(new SequenceI[] {});
345 FeaturesFile ffile = new FeaturesFile(simpleGffFile,
348 boolean parseResult = ffile.parse(dataset, null, false, false);
349 assertTrue("return result should be true", parseResult);
350 checkDatasetfromSimpleGff3(dataset);
353 @Test(groups = { "Functional" })
354 public void simpleGff3FileLoader() throws IOException
356 AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
357 simpleGffFile, FormatAdapter.FILE);
359 "Didn't read the alignment into an alignframe from Gff3 File",
361 checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
364 @Test(groups = { "Functional" })
365 public void simpleGff3RelaxedIdMatching() throws IOException
367 AlignmentI dataset = new Alignment(new SequenceI[] {});
368 FeaturesFile ffile = new FeaturesFile(simpleGffFile,
371 boolean parseResult = ffile.parse(dataset, null, false, true);
372 assertTrue("return result (relaxedID matching) should be true",
374 checkDatasetfromSimpleGff3(dataset);
377 @Test(groups = { "Functional" })
378 public void testPrintJalviewFormat() throws Exception
380 File f = new File("examples/uniref50.fa");
381 AlignmentI al = readAlignmentFile(f);
382 AlignFrame af = new AlignFrame(al, 500, 500);
383 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
384 .getFeatureColours();
385 String features = "METAL\tcc9900\n"
386 + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
388 + "STARTGROUP\tuniprot\n"
389 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
390 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
391 + "<html>Pfam domain<a href=\"http://pfam.sanger.ac.uk/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
392 + "ENDGROUP\tuniprot\n";
393 FeaturesFile featuresFile = new FeaturesFile(features,
394 FormatAdapter.PASTE);
395 featuresFile.parse(al.getDataset(), colours, false);
398 * first with no features displayed
400 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
401 Map<String, FeatureColourI> visible = fr
402 .getDisplayedFeatureCols();
403 String exported = featuresFile.printJalviewFormat(
404 al.getSequencesArray(), visible);
405 String expected = "No Features Visible";
406 assertEquals(expected, exported);
409 * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
411 fr.setVisible("METAL");
412 fr.setVisible("GAMMA-TURN");
413 visible = fr.getDisplayedFeatureCols();
414 exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
416 expected = "METAL\tcc9900\n"
417 + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
418 + "\nSTARTGROUP\tuniprot\n"
419 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
420 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
421 + "ENDGROUP\tuniprot\n";
422 assertEquals(expected, exported);
425 * now set Pfam visible
427 fr.setVisible("Pfam");
428 visible = fr.getDisplayedFeatureCols();
429 exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
432 * note the order of feature types is uncontrolled - derives from
433 * FeaturesDisplayed.featuresDisplayed which is a HashSet
435 expected = "METAL\tcc9900\n"
437 + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
438 + "\nSTARTGROUP\tuniprot\n"
439 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
440 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
441 + "<html>Pfam domain<a href=\"http://pfam.sanger.ac.uk/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\t0.0\n"
442 + "ENDGROUP\tuniprot\n";
443 assertEquals(expected, exported);