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.assertTrue;
28 import jalview.api.FeatureColourI;
29 import jalview.api.FeatureRenderer;
30 import jalview.datamodel.Alignment;
31 import jalview.datamodel.AlignmentI;
32 import jalview.datamodel.SequenceDummy;
33 import jalview.datamodel.SequenceFeature;
34 import jalview.datamodel.SequenceI;
35 import jalview.datamodel.features.SequenceFeatures;
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("27 feature group colours not found", 27, colours.size());
83 assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
84 assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
85 FeatureColourI kdColour = colours.get("kdHydrophobicity");
86 assertTrue(kdColour.isGraduatedColour());
87 assertTrue(kdColour.isAboveThreshold());
88 assertEquals(-2f, kdColour.getThreshold());
91 * verify (some) features on sequences
93 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
94 .getSequenceFeatures(); // FER_CAPAA
95 SequenceFeatures.sortFeatures(sfs, true);
96 assertEquals(8, sfs.size());
99 * verify (in ascending start position order)
101 SequenceFeature sf = sfs.get(0);
102 assertEquals("Pfam family%LINK%", sf.description);
103 assertEquals(0, sf.begin);
104 assertEquals(0, sf.end);
105 assertEquals("uniprot", sf.featureGroup);
106 assertEquals("Pfam", sf.type);
107 assertEquals(1, sf.links.size());
108 assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
112 assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
113 assertEquals(3, sf.begin);
114 assertEquals(93, sf.end);
115 assertEquals("uniprot", sf.featureGroup);
116 assertEquals("Cath", sf.type);
119 assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
121 assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
123 assertEquals(8, sf.begin);
124 assertEquals(83, sf.end);
125 assertEquals("uniprot", sf.featureGroup);
126 assertEquals("Pfam", sf.type);
129 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
130 assertEquals(39, sf.begin);
131 assertEquals(39, sf.end);
132 assertEquals("uniprot", sf.featureGroup);
133 assertEquals("METAL", sf.type);
136 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
137 assertEquals(44, sf.begin);
138 assertEquals(44, sf.end);
139 assertEquals("uniprot", sf.featureGroup);
140 assertEquals("METAL", sf.type);
143 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
144 assertEquals(47, sf.begin);
145 assertEquals(47, sf.end);
146 assertEquals("uniprot", sf.featureGroup);
147 assertEquals("METAL", sf.type);
150 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
151 assertEquals(77, sf.begin);
152 assertEquals(77, sf.end);
153 assertEquals("uniprot", sf.featureGroup);
154 assertEquals("METAL", sf.type);
158 "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
161 "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&service=NetPhos-2.0",
163 assertEquals(89, sf.begin);
164 assertEquals(89, sf.end);
165 assertEquals("netphos", sf.featureGroup);
166 assertEquals("PHOSPHORYLATION (T)", sf.type);
170 * Test parsing a features file with a mix of Jalview and GFF formatted
175 @Test(groups = { "Functional" })
176 public void testParse_mixedJalviewGff() throws Exception
178 File f = new File("examples/uniref50.fa");
179 AlignmentI al = readAlignmentFile(f);
180 AlignFrame af = new AlignFrame(al, 500, 500);
181 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
182 .getFeatureColours();
183 // GFF2 uses space as name/value separator in column 9
184 String gffData = "METAL\tcc9900\n"
186 + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
187 + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
188 FeaturesFile featuresFile = new FeaturesFile(gffData,
189 DataSourceType.PASTE);
190 assertTrue("Failed to parse features file",
191 featuresFile.parse(al.getDataset(), colours, true));
193 // verify colours read or synthesized
194 colours = af.getFeatureRenderer().getFeatureColours();
195 assertEquals("1 feature group colours not found", 1, colours.size());
196 assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
198 // verify feature on FER_CAPAA
199 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
200 .getSequenceFeatures();
201 assertEquals(1, sfs.size());
202 SequenceFeature sf = sfs.get(0);
203 assertEquals("Iron-sulfur,2Fe-2S", sf.description);
204 assertEquals(44, sf.begin);
205 assertEquals(45, sf.end);
206 assertEquals("uniprot", sf.featureGroup);
207 assertEquals("METAL", sf.type);
208 assertEquals(4f, sf.getScore(), 0.001f);
210 // verify feature on FER1_SOLLC
211 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
212 assertEquals(1, sfs.size());
214 assertEquals("uniprot", sf.description);
215 assertEquals(55, sf.begin);
216 assertEquals(130, sf.end);
217 assertEquals("uniprot", sf.featureGroup);
218 assertEquals("Pfam", sf.type);
219 assertEquals(2f, sf.getScore(), 0.001f);
222 public static AlignmentI readAlignmentFile(File f) throws IOException
224 System.out.println("Reading file: " + f);
225 String ff = f.getPath();
226 FormatAdapter rf = new FormatAdapter();
228 AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
229 new IdentifyFile().identify(ff, DataSourceType.FILE));
231 al.setDataset(null); // creates dataset sequences
232 assertNotNull("Couldn't read supplied alignment data.", al);
237 * Test parsing a features file with GFF formatted content only
241 @Test(groups = { "Functional" })
242 public void testParse_pureGff3() throws Exception
244 File f = new File("examples/uniref50.fa");
245 AlignmentI al = readAlignmentFile(f);
246 AlignFrame af = new AlignFrame(al, 500, 500);
247 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
248 .getFeatureColours();
249 // GFF3 uses '=' separator for name/value pairs in colum 9
250 String gffData = "##gff-version 3\n"
251 + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
252 + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465\n"
253 + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
254 FeaturesFile featuresFile = new FeaturesFile(gffData,
255 DataSourceType.PASTE);
256 assertTrue("Failed to parse features file",
257 featuresFile.parse(al.getDataset(), colours, true));
259 // verify feature on FER_CAPAA
260 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
261 .getSequenceFeatures();
262 assertEquals(1, sfs.size());
263 SequenceFeature sf = sfs.get(0);
264 // description parsed from Note attribute
265 assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description);
266 assertEquals(39, sf.begin);
267 assertEquals(39, sf.end);
268 assertEquals("uniprot", sf.featureGroup);
269 assertEquals("METAL", sf.type);
271 "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465",
272 sf.getValue("ATTRIBUTES"));
274 // verify feature on FER1_SOLLC1
275 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
276 assertEquals(1, sfs.size());
278 // ID used for description if available
279 assertEquals("$23", sf.description);
280 assertEquals(55, sf.begin);
281 assertEquals(130, sf.end);
282 assertEquals("uniprot", sf.featureGroup);
283 assertEquals("Pfam", sf.type);
284 assertEquals(3f, sf.getScore(), 0.001f);
288 * Test parsing a features file with Jalview format features (but no colour
289 * descriptors or startgroup to give the hint not to parse as GFF)
293 @Test(groups = { "Functional" })
294 public void testParse_jalviewFeaturesOnly() throws Exception
296 File f = new File("examples/uniref50.fa");
297 AlignmentI al = readAlignmentFile(f);
298 AlignFrame af = new AlignFrame(al, 500, 500);
299 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
300 .getFeatureColours();
303 * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
305 String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
306 + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
307 FeaturesFile featuresFile = new FeaturesFile(featureData,
308 DataSourceType.PASTE);
309 assertTrue("Failed to parse features file",
310 featuresFile.parse(al.getDataset(), colours, true));
312 // verify FER_CAPAA feature
313 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
314 .getSequenceFeatures();
315 assertEquals(1, sfs.size());
316 SequenceFeature sf = sfs.get(0);
317 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
318 assertEquals(39, sf.begin);
319 assertEquals(39, sf.end);
320 assertEquals("METAL", sf.type);
322 // verify FER1_SOLLC feature
323 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
324 assertEquals(1, sfs.size());
326 assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
327 assertEquals(86, sf.begin);
328 assertEquals(87, sf.end);
329 assertEquals("METALLIC", sf.type);
332 private void checkDatasetfromSimpleGff3(AlignmentI dataset)
334 assertEquals("no sequences extracted from GFF3 file", 2,
335 dataset.getHeight());
337 SequenceI seq1 = dataset.findName("seq1");
338 SequenceI seq2 = dataset.findName("seq2");
342 "Failed to replace dummy seq1 with real sequence",
343 seq1 instanceof SequenceDummy
344 && ((SequenceDummy) seq1).isDummy());
346 "Failed to replace dummy seq2 with real sequence",
347 seq2 instanceof SequenceDummy
348 && ((SequenceDummy) seq2).isDummy());
349 String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
350 assertFalse("dummy replacement buggy for seq1",
351 placeholderseq.equals(seq1.getSequenceAsString()));
352 assertFalse("dummy replacement buggy for seq2",
353 placeholderseq.equals(seq2.getSequenceAsString()));
354 assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
355 assertEquals("Wrong number of features", 3, seq1.getSequenceFeatures()
357 assertTrue(seq2.getSequenceFeatures().isEmpty());
359 "Wrong number of features",
361 seq2.getSequenceFeatures() == null ? 0 : seq2
362 .getSequenceFeatures().size());
364 "Expected at least one CDNA/Protein mapping for seq1",
365 dataset.getCodonFrame(seq1) != null
366 && dataset.getCodonFrame(seq1).size() > 0);
370 @Test(groups = { "Functional" })
371 public void readGff3File() throws IOException
373 FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
374 DataSourceType.FILE);
375 Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
376 gffreader.addProperties(dataset);
377 checkDatasetfromSimpleGff3(dataset);
380 @Test(groups = { "Functional" })
381 public void simpleGff3FileClass() throws IOException
383 AlignmentI dataset = new Alignment(new SequenceI[] {});
384 FeaturesFile ffile = new FeaturesFile(simpleGffFile,
385 DataSourceType.FILE);
387 boolean parseResult = ffile.parse(dataset, null, false, false);
388 assertTrue("return result should be true", parseResult);
389 checkDatasetfromSimpleGff3(dataset);
392 @Test(groups = { "Functional" })
393 public void simpleGff3FileLoader() throws IOException
395 AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
396 simpleGffFile, DataSourceType.FILE);
398 "Didn't read the alignment into an alignframe from Gff3 File",
400 checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
403 @Test(groups = { "Functional" })
404 public void simpleGff3RelaxedIdMatching() throws IOException
406 AlignmentI dataset = new Alignment(new SequenceI[] {});
407 FeaturesFile ffile = new FeaturesFile(simpleGffFile,
408 DataSourceType.FILE);
410 boolean parseResult = ffile.parse(dataset, null, false, true);
411 assertTrue("return result (relaxedID matching) should be true",
413 checkDatasetfromSimpleGff3(dataset);
416 @Test(groups = { "Functional" })
417 public void testPrintJalviewFormat() throws Exception
419 File f = new File("examples/uniref50.fa");
420 AlignmentI al = readAlignmentFile(f);
421 AlignFrame af = new AlignFrame(al, 500, 500);
422 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
423 .getFeatureColours();
424 String features = "METAL\tcc9900\n"
425 + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
427 + "STARTGROUP\tuniprot\n"
428 + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\n" // non-positional feature
429 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
430 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
431 + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
432 + "ENDGROUP\tuniprot\n";
433 FeaturesFile featuresFile = new FeaturesFile(features,
434 DataSourceType.PASTE);
435 featuresFile.parse(al.getDataset(), colours, false);
438 * add positional and non-positional features with null and
439 * empty feature group to check handled correctly
441 SequenceI seq = al.getSequenceAt(1); // FER_CAPAN
442 seq.addSequenceFeature(new SequenceFeature("Pfam", "desc1", 0, 0, 1.3f,
444 seq.addSequenceFeature(new SequenceFeature("Pfam", "desc2", 4, 9,
446 seq = al.getSequenceAt(2); // FER1_SOLLC
447 seq.addSequenceFeature(new SequenceFeature("Pfam", "desc3", 0, 0,
449 seq.addSequenceFeature(new SequenceFeature("Pfam", "desc4", 5, 8,
453 * first with no features displayed, exclude non-positional features
455 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
456 Map<String, FeatureColourI> visible = fr.getDisplayedFeatureCols();
457 List<String> visibleGroups = new ArrayList<String>(
458 Arrays.asList(new String[] {}));
459 String exported = featuresFile.printJalviewFormat(
460 al.getSequencesArray(), visible, visibleGroups, false);
461 String expected = "No Features Visible";
462 assertEquals(expected, exported);
465 * include non-positional features
467 visibleGroups.add("uniprot");
468 exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
469 visible, visibleGroups, true);
470 expected = "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
471 + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n"
472 + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n" // NaN is not output
473 + "\nSTARTGROUP\tuniprot\nENDGROUP\tuniprot\n";
474 assertEquals(expected, exported);
477 * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
479 fr.setVisible("METAL");
480 fr.setVisible("GAMMA-TURN");
481 visible = fr.getDisplayedFeatureCols();
482 exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
483 visible, visibleGroups, false);
484 expected = "METAL\tcc9900\n"
485 + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
486 + "\nSTARTGROUP\tuniprot\n"
487 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
488 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
489 + "ENDGROUP\tuniprot\n";
490 assertEquals(expected, exported);
493 * now set Pfam visible
495 fr.setVisible("Pfam");
496 visible = fr.getDisplayedFeatureCols();
497 exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
498 visible, visibleGroups, false);
500 * features are output within group, ordered by sequence and by type
502 expected = "METAL\tcc9900\n"
504 + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
505 + "\nSTARTGROUP\tuniprot\n"
506 + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
507 + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
508 + "<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"
509 + "ENDGROUP\tuniprot\n"
510 // null / empty group features output after features in named
512 + "desc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
513 + "desc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
514 assertEquals(expected, exported);
517 @Test(groups = { "Functional" })
518 public void testPrintGffFormat() throws Exception
520 File f = new File("examples/uniref50.fa");
521 AlignmentI al = readAlignmentFile(f);
522 AlignFrame af = new AlignFrame(al, 500, 500);
527 FeaturesFile featuresFile = new FeaturesFile();
528 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
529 Map<String, FeatureColourI> visible = new HashMap<String, FeatureColourI>();
530 List<String> visibleGroups = new ArrayList<String>(
531 Arrays.asList(new String[] {}));
532 String exported = featuresFile.printGffFormat(al.getSequencesArray(),
533 visible, visibleGroups, false);
534 String gffHeader = "##gff-version 2\n";
535 assertEquals(gffHeader, exported);
536 exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
537 visibleGroups, true);
538 assertEquals(gffHeader, exported);
543 al.getSequenceAt(0).addSequenceFeature(
544 new SequenceFeature("Domain", "Cath", 0, 0, 0f, "Uniprot"));
545 al.getSequenceAt(0).addSequenceFeature(
546 new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, null));
549 new SequenceFeature("GAMMA-TURN", "Turn", 36, 38, 2.1f,
551 SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f,
553 sf.setAttributes("x=y;black=white");
556 al.getSequenceAt(1).addSequenceFeature(sf);
559 * with no features displayed, exclude non-positional features
561 exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
562 visibleGroups, false);
563 assertEquals(gffHeader, exported);
566 * include non-positional features
568 visibleGroups.add("Uniprot");
569 exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
570 visibleGroups, true);
571 String expected = gffHeader
572 + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
573 assertEquals(expected, exported);
576 * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
577 * only Uniprot group visible here...
579 fr.setVisible("METAL");
580 fr.setVisible("GAMMA-TURN");
581 visible = fr.getDisplayedFeatureCols();
582 exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
583 visibleGroups, false);
584 // METAL feature has null group: description used for column 2
585 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
586 assertEquals(expected, exported);
589 * set s3dm group visible
591 visibleGroups.add("s3dm");
592 exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
593 visibleGroups, false);
594 // METAL feature has null group: description used for column 2
595 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
596 + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
597 assertEquals(expected, exported);
600 * now set Pfam visible
602 fr.setVisible("Pfam");
603 visible = fr.getDisplayedFeatureCols();
604 exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
605 visibleGroups, false);
606 // Pfam feature columns include strand(+), phase(2), attributes
608 + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
609 + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n"
610 + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n";
611 assertEquals(expected, exported);