JAL-1988 JAL-3130 New jlinked JRE in jalview_java2 with modules. Still needs jaxws...
[jalview.git] / test / jalview / io / FeaturesFileTest.java
1 /*
2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
4  * 
5  * This file is part of Jalview.
6  * 
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.
11  *  
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.
16  * 
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.
20  */
21 package jalview.io;
22
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.assertSame;
27 import static org.testng.AssertJUnit.assertTrue;
28 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
29
30 import jalview.api.FeatureColourI;
31 import jalview.api.FeatureRenderer;
32 import jalview.datamodel.Alignment;
33 import jalview.datamodel.AlignmentI;
34 import jalview.datamodel.SequenceDummy;
35 import jalview.datamodel.SequenceFeature;
36 import jalview.datamodel.SequenceI;
37 import jalview.datamodel.features.FeatureMatcher;
38 import jalview.datamodel.features.FeatureMatcherI;
39 import jalview.datamodel.features.FeatureMatcherSet;
40 import jalview.datamodel.features.FeatureMatcherSetI;
41 import jalview.datamodel.features.SequenceFeatures;
42 import jalview.gui.AlignFrame;
43 import jalview.gui.Desktop;
44 import jalview.gui.JvOptionPane;
45 import jalview.schemes.FeatureColour;
46 import jalview.structure.StructureSelectionManager;
47 import jalview.util.matcher.Condition;
48
49 import java.awt.Color;
50 import java.io.File;
51 import java.io.IOException;
52 import java.util.ArrayList;
53 import java.util.Arrays;
54 import java.util.HashMap;
55 import java.util.Iterator;
56 import java.util.List;
57 import java.util.Map;
58
59 import org.testng.annotations.AfterClass;
60 import org.testng.annotations.BeforeClass;
61 import org.testng.annotations.Test;
62
63 public class FeaturesFileTest
64 {
65   private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
66
67   @AfterClass(alwaysRun = true)
68   public void tearDownAfterClass()
69   {
70     /*
71      * remove any sequence mappings created so they don't pollute other tests
72      */
73     StructureSelectionManager ssm = StructureSelectionManager
74             .getStructureSelectionManager(Desktop.instance);
75     ssm.resetAll();
76   }
77
78   @BeforeClass(alwaysRun = true)
79   public void setUpJvOptionPane()
80   {
81     JvOptionPane.setInteractiveMode(false);
82     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
83   }
84
85   @Test(groups = { "Functional" })
86   public void testParse() throws Exception
87   {
88     File f = new File("examples/uniref50.fa");
89     AlignmentI al = readAlignmentFile(f);
90     AlignFrame af = new AlignFrame(al, 500, 500);
91     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
92             .getFeatureColours();
93     FeaturesFile featuresFile = new FeaturesFile(
94             "examples/exampleFeatures.txt", DataSourceType.FILE);
95     assertTrue("Test " + "Features file test"
96             + "\nFailed to parse features file.",
97             featuresFile.parse(al.getDataset(), colours, true));
98
99     /*
100      * Refetch the colour map from the FeatureRenderer (to confirm it has been
101      * updated - JAL-1904), and verify (some) feature group colours
102      */
103     colours = af.getFeatureRenderer().getFeatureColours();
104     assertEquals("27 feature group colours not found", 27, colours.size());
105     assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
106     assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
107     FeatureColourI kdColour = colours.get("kdHydrophobicity");
108     assertTrue(kdColour.isGraduatedColour());
109     assertTrue(kdColour.isAboveThreshold());
110     assertEquals(-2f, kdColour.getThreshold());
111
112     /*
113      * verify (some) features on sequences
114      */
115     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
116             .getSequenceFeatures(); // FER_CAPAA
117     SequenceFeatures.sortFeatures(sfs, true);
118     assertEquals(8, sfs.size());
119
120     /*
121      * verify (in ascending start position order)
122      */
123     SequenceFeature sf = sfs.get(0);
124     assertEquals("Pfam family%LINK%", sf.description);
125     assertEquals(0, sf.begin);
126     assertEquals(0, sf.end);
127     assertEquals("uniprot", sf.featureGroup);
128     assertEquals("Pfam", sf.type);
129     assertEquals(1, sf.links.size());
130     assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
131             sf.links.get(0));
132
133     sf = sfs.get(1);
134     assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
135     assertEquals(3, sf.begin);
136     assertEquals(93, sf.end);
137     assertEquals("uniprot", sf.featureGroup);
138     assertEquals("Cath", sf.type);
139
140     sf = sfs.get(2);
141     assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
142             sf.description);
143     assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
144             sf.links.get(0));
145     assertEquals(8, sf.begin);
146     assertEquals(83, sf.end);
147     assertEquals("uniprot", sf.featureGroup);
148     assertEquals("Pfam", sf.type);
149
150     sf = sfs.get(3);
151     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
152     assertEquals(39, sf.begin);
153     assertEquals(39, sf.end);
154     assertEquals("uniprot", sf.featureGroup);
155     assertEquals("METAL", sf.type);
156
157     sf = sfs.get(4);
158     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
159     assertEquals(44, sf.begin);
160     assertEquals(44, sf.end);
161     assertEquals("uniprot", sf.featureGroup);
162     assertEquals("METAL", sf.type);
163
164     sf = sfs.get(5);
165     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
166     assertEquals(47, sf.begin);
167     assertEquals(47, sf.end);
168     assertEquals("uniprot", sf.featureGroup);
169     assertEquals("METAL", sf.type);
170
171     sf = sfs.get(6);
172     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
173     assertEquals(77, sf.begin);
174     assertEquals(77, sf.end);
175     assertEquals("uniprot", sf.featureGroup);
176     assertEquals("METAL", sf.type);
177
178     sf = sfs.get(7);
179     assertEquals(
180             "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
181             sf.description);
182     assertEquals(
183             "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&amp;service=NetPhos-2.0",
184             sf.links.get(0));
185     assertEquals(89, sf.begin);
186     assertEquals(89, sf.end);
187     assertEquals("netphos", sf.featureGroup);
188     assertEquals("PHOSPHORYLATION (T)", sf.type);
189   }
190
191   /**
192    * Test parsing a features file with a mix of Jalview and GFF formatted
193    * content
194    * 
195    * @throws Exception
196    */
197   @Test(groups = { "Functional" })
198   public void testParse_mixedJalviewGff() throws Exception
199   {
200     File f = new File("examples/uniref50.fa");
201     AlignmentI al = readAlignmentFile(f);
202     AlignFrame af = new AlignFrame(al, 500, 500);
203     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
204             .getFeatureColours();
205     // GFF2 uses space as name/value separator in column 9
206     String gffData = "METAL\tcc9900\n"
207             + "GFF\n"
208             + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
209             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
210     FeaturesFile featuresFile = new FeaturesFile(gffData,
211             DataSourceType.PASTE);
212     assertTrue("Failed to parse features file",
213             featuresFile.parse(al.getDataset(), colours, true));
214
215     // verify colours read or synthesized
216     colours = af.getFeatureRenderer().getFeatureColours();
217     assertEquals("1 feature group colours not found", 1, colours.size());
218     assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
219
220     // verify feature on FER_CAPAA
221     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
222             .getSequenceFeatures();
223     assertEquals(1, sfs.size());
224     SequenceFeature sf = sfs.get(0);
225     assertEquals("Iron-sulfur,2Fe-2S", sf.description);
226     assertEquals(44, sf.begin);
227     assertEquals(45, sf.end);
228     assertEquals("uniprot", sf.featureGroup);
229     assertEquals("METAL", sf.type);
230     assertEquals(4f, sf.getScore(), 0.001f);
231
232     // verify feature on FER1_SOLLC
233     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
234     assertEquals(1, sfs.size());
235     sf = sfs.get(0);
236     assertEquals("uniprot", sf.description);
237     assertEquals(55, sf.begin);
238     assertEquals(130, sf.end);
239     assertEquals("uniprot", sf.featureGroup);
240     assertEquals("Pfam", sf.type);
241     assertEquals(2f, sf.getScore(), 0.001f);
242   }
243
244   public static AlignmentI readAlignmentFile(File f) throws IOException
245   {
246     System.out.println("Reading file: " + f);
247     String ff = f.getPath();
248     FormatAdapter rf = new FormatAdapter();
249
250     AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
251             new IdentifyFile().identify(ff, DataSourceType.FILE));
252
253     al.setDataset(null); // creates dataset sequences
254     assertNotNull("Couldn't read supplied alignment data.", al);
255     return al;
256   }
257
258   /**
259    * Test parsing a features file with GFF formatted content only
260    * 
261    * @throws Exception
262    */
263   @Test(groups = { "Functional" })
264   public void testParse_pureGff3() throws Exception
265   {
266     File f = new File("examples/uniref50.fa");
267     AlignmentI al = readAlignmentFile(f);
268     AlignFrame af = new AlignFrame(al, 500, 500);
269     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
270             .getFeatureColours();
271     // GFF3 uses '=' separator for name/value pairs in colum 9
272     String gffData = "##gff-version 3\n"
273             + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
274             + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465\n"
275             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
276     FeaturesFile featuresFile = new FeaturesFile(gffData,
277             DataSourceType.PASTE);
278     assertTrue("Failed to parse features file",
279             featuresFile.parse(al.getDataset(), colours, true));
280
281     // verify feature on FER_CAPAA
282     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
283             .getSequenceFeatures();
284     assertEquals(1, sfs.size());
285     SequenceFeature sf = sfs.get(0);
286     // description parsed from Note attribute
287     assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description);
288     assertEquals(39, sf.begin);
289     assertEquals(39, sf.end);
290     assertEquals("uniprot", sf.featureGroup);
291     assertEquals("METAL", sf.type);
292     assertEquals(
293             "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465",
294             sf.getValue("ATTRIBUTES"));
295
296     // verify feature on FER1_SOLLC1
297     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
298     assertEquals(1, sfs.size());
299     sf = sfs.get(0);
300     // ID used for description if available
301     assertEquals("$23", sf.description);
302     assertEquals(55, sf.begin);
303     assertEquals(130, sf.end);
304     assertEquals("uniprot", sf.featureGroup);
305     assertEquals("Pfam", sf.type);
306     assertEquals(3f, sf.getScore(), 0.001f);
307   }
308
309   /**
310    * Test parsing a features file with Jalview format features (but no colour
311    * descriptors or startgroup to give the hint not to parse as GFF)
312    * 
313    * @throws Exception
314    */
315   @Test(groups = { "Functional" })
316   public void testParse_jalviewFeaturesOnly() throws Exception
317   {
318     File f = new File("examples/uniref50.fa");
319     AlignmentI al = readAlignmentFile(f);
320     AlignFrame af = new AlignFrame(al, 500, 500);
321     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
322             .getFeatureColours();
323
324     /*
325      * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
326      */
327     String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
328             + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
329     FeaturesFile featuresFile = new FeaturesFile(featureData,
330             DataSourceType.PASTE);
331     assertTrue("Failed to parse features file",
332             featuresFile.parse(al.getDataset(), colours, true));
333
334     // verify FER_CAPAA feature
335     List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
336             .getSequenceFeatures();
337     assertEquals(1, sfs.size());
338     SequenceFeature sf = sfs.get(0);
339     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
340     assertEquals(39, sf.begin);
341     assertEquals(39, sf.end);
342     assertEquals("METAL", sf.type);
343
344     // verify FER1_SOLLC feature
345     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
346     assertEquals(1, sfs.size());
347     sf = sfs.get(0);
348     assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
349     assertEquals(86, sf.begin);
350     assertEquals(87, sf.end);
351     assertEquals("METALLIC", sf.type);
352   }
353
354   private void checkDatasetfromSimpleGff3(AlignmentI dataset)
355   {
356     assertEquals("no sequences extracted from GFF3 file", 2,
357             dataset.getHeight());
358
359     SequenceI seq1 = dataset.findName("seq1");
360     SequenceI seq2 = dataset.findName("seq2");
361     assertNotNull(seq1);
362     assertNotNull(seq2);
363     assertFalse(
364             "Failed to replace dummy seq1 with real sequence",
365             seq1 instanceof SequenceDummy
366                     && ((SequenceDummy) seq1).isDummy());
367     assertFalse(
368             "Failed to replace dummy seq2 with real sequence",
369             seq2 instanceof SequenceDummy
370                     && ((SequenceDummy) seq2).isDummy());
371     String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
372     assertFalse("dummy replacement buggy for seq1",
373             placeholderseq.equals(seq1.getSequenceAsString()));
374     assertFalse("dummy replacement buggy for seq2",
375             placeholderseq.equals(seq2.getSequenceAsString()));
376     assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
377     assertEquals("Wrong number of features", 3, seq1.getSequenceFeatures()
378             .size());
379     assertTrue(seq2.getSequenceFeatures().isEmpty());
380     assertEquals(
381             "Wrong number of features",
382             0,
383             seq2.getSequenceFeatures() == null ? 0 : seq2
384                     .getSequenceFeatures().size());
385     assertTrue(
386             "Expected at least one CDNA/Protein mapping for seq1",
387             dataset.getCodonFrame(seq1) != null
388                     && dataset.getCodonFrame(seq1).size() > 0);
389
390   }
391
392   @Test(groups = { "Functional" })
393   public void readGff3File() throws IOException
394   {
395     FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
396             DataSourceType.FILE);
397     Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
398     gffreader.addProperties(dataset);
399     checkDatasetfromSimpleGff3(dataset);
400   }
401
402   @Test(groups = { "Functional" })
403   public void simpleGff3FileClass() throws IOException
404   {
405     AlignmentI dataset = new Alignment(new SequenceI[] {});
406     FeaturesFile ffile = new FeaturesFile(simpleGffFile,
407             DataSourceType.FILE);
408   
409     boolean parseResult = ffile.parse(dataset, null, false, false);
410     assertTrue("return result should be true", parseResult);
411     checkDatasetfromSimpleGff3(dataset);
412   }
413
414   @Test(groups = { "Functional" })
415   public void simpleGff3FileLoader() throws IOException
416   {
417     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
418             simpleGffFile, DataSourceType.FILE);
419     assertTrue(
420             "Didn't read the alignment into an alignframe from Gff3 File",
421             af != null);
422     checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
423   }
424
425   @Test(groups = { "Functional" })
426   public void simpleGff3RelaxedIdMatching() throws IOException
427   {
428     AlignmentI dataset = new Alignment(new SequenceI[] {});
429     FeaturesFile ffile = new FeaturesFile(simpleGffFile,
430             DataSourceType.FILE);
431   
432     boolean parseResult = ffile.parse(dataset, null, false, true);
433     assertTrue("return result (relaxedID matching) should be true",
434             parseResult);
435     checkDatasetfromSimpleGff3(dataset);
436   }
437
438   @Test(groups = { "Functional" })
439   public void testPrintJalviewFormat() throws Exception
440   {
441     File f = new File("examples/uniref50.fa");
442     AlignmentI al = readAlignmentFile(f);
443     AlignFrame af = new AlignFrame(al, 500, 500);
444     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
445             .getFeatureColours();
446     String features = "METAL\tcc9900\n"
447             + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
448             + "Pfam\tred\n"
449             + "STARTGROUP\tuniprot\n"
450             + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\n" // non-positional feature
451             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
452             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
453             + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
454             + "ENDGROUP\tuniprot\n";
455     FeaturesFile featuresFile = new FeaturesFile(features,
456             DataSourceType.PASTE);
457     featuresFile.parse(al.getDataset(), colours, false);
458
459     /*
460      * add positional and non-positional features with null and
461      * empty feature group to check handled correctly
462      */
463     SequenceI seq = al.getSequenceAt(1); // FER_CAPAN
464     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc1", 0, 0, 1.3f,
465             null));
466     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc2", 4, 9,
467             Float.NaN, null));
468     seq = al.getSequenceAt(2); // FER1_SOLLC
469     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc3", 0, 0,
470             Float.NaN, ""));
471     seq.addSequenceFeature(new SequenceFeature("Pfam", "desc4", 5, 8,
472             -2.6f, ""));
473
474     /*
475      * first with no features displayed, exclude non-positional features
476      */
477     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
478     Map<String, FeatureColourI> visible = fr.getDisplayedFeatureCols();
479     List<String> visibleGroups = new ArrayList<>(
480             Arrays.asList(new String[] {}));
481     String exported = featuresFile.printJalviewFormat(
482             al.getSequencesArray(), visible, null, visibleGroups, false);
483     String expected = "No Features Visible";
484     assertEquals(expected, exported);
485
486     /*
487      * include non-positional features
488      */
489     visibleGroups.add("uniprot");
490     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
491             visible, null, visibleGroups, true);
492     expected = "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
493             + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n"
494             + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n" // NaN is not output
495             + "\nSTARTGROUP\tuniprot\nENDGROUP\tuniprot\n";
496     assertEquals(expected, exported);
497
498     /*
499      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
500      */
501     fr.setVisible("METAL");
502     fr.setVisible("GAMMA-TURN");
503     visible = fr.getDisplayedFeatureCols();
504     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
505             visible, null, visibleGroups, false);
506     expected = "METAL\tcc9900\n"
507             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
508             + "\nSTARTGROUP\tuniprot\n"
509             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
510             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
511             + "ENDGROUP\tuniprot\n";
512     assertEquals(expected, exported);
513
514     /*
515      * now set Pfam visible
516      */
517     fr.setVisible("Pfam");
518     visible = fr.getDisplayedFeatureCols();
519     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
520             visible, null, visibleGroups, false);
521     /*
522      * features are output within group, ordered by sequence and by type
523      */
524     expected = "METAL\tcc9900\n"
525             + "Pfam\tff0000\n"
526             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
527             + "\nSTARTGROUP\tuniprot\n"
528             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
529             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
530             + "<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"
531             + "ENDGROUP\tuniprot\n"
532             // null / empty group features output after features in named
533             // groups:
534             + "desc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
535             + "desc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
536     assertEquals(expected, exported);
537   }
538
539   @Test(groups = { "Functional" })
540   public void testPrintGffFormat() throws Exception
541   {
542     File f = new File("examples/uniref50.fa");
543     AlignmentI al = readAlignmentFile(f);
544     AlignFrame af = new AlignFrame(al, 500, 500);
545
546     /*
547      * no features
548      */
549     FeaturesFile featuresFile = new FeaturesFile();
550     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
551     Map<String, FeatureColourI> visible = new HashMap<>();
552     List<String> visibleGroups = new ArrayList<>(
553             Arrays.asList(new String[] {}));
554     String exported = featuresFile.printGffFormat(al.getSequencesArray(),
555             visible, visibleGroups, false);
556     String gffHeader = "##gff-version 2\n";
557     assertEquals(gffHeader, exported);
558     exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
559             visibleGroups, true);
560     assertEquals(gffHeader, exported);
561
562     /*
563      * add some features
564      */
565     al.getSequenceAt(0).addSequenceFeature(
566             new SequenceFeature("Domain", "Cath", 0, 0, 0f, "Uniprot"));
567     al.getSequenceAt(0).addSequenceFeature(
568             new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, null));
569     al.getSequenceAt(1)
570             .addSequenceFeature(
571                     new SequenceFeature("GAMMA-TURN", "Turn", 36, 38, 2.1f,
572                             "s3dm"));
573     SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f,
574             "Uniprot");
575     sf.setAttributes("x=y;black=white");
576     sf.setStrand("+");
577     sf.setPhase("2");
578     al.getSequenceAt(1).addSequenceFeature(sf);
579
580     /*
581      * with no features displayed, exclude non-positional features
582      */
583     exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
584             visibleGroups, false);
585     assertEquals(gffHeader, exported);
586
587     /*
588      * include non-positional features
589      */
590     visibleGroups.add("Uniprot");
591     exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
592             visibleGroups, true);
593     String expected = gffHeader
594             + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
595     assertEquals(expected, exported);
596
597     /*
598      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
599      * only Uniprot group visible here...
600      */
601     fr.setVisible("METAL");
602     fr.setVisible("GAMMA-TURN");
603     visible = fr.getDisplayedFeatureCols();
604     exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
605             visibleGroups, false);
606     // METAL feature has null group: description used for column 2
607     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
608     assertEquals(expected, exported);
609
610     /*
611      * set s3dm group visible
612      */
613     visibleGroups.add("s3dm");
614     exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
615             visibleGroups, false);
616     // METAL feature has null group: description used for column 2
617     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
618             + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
619     assertEquals(expected, exported);
620
621     /*
622      * now set Pfam visible
623      */
624     fr.setVisible("Pfam");
625     visible = fr.getDisplayedFeatureCols();
626     exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
627             visibleGroups, false);
628     // Pfam feature columns include strand(+), phase(2), attributes
629     expected = gffHeader
630             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
631             + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n"
632             + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n";
633     assertEquals(expected, exported);
634   }
635
636   /**
637    * Test for parsing of feature filters as represented in a Jalview features
638    * file
639    * 
640    * @throws Exception
641    */
642   @Test(groups = { "Functional" })
643   public void testParseFilters() throws Exception
644   {
645     Map<String, FeatureMatcherSetI> filters = new HashMap<>();
646     String text = "sequence_variant\tCSQ:PolyPhen NotContains 'damaging'\n"
647             + "missense_variant\t(label contains foobar) and (Score lt 1.3)";
648     FeaturesFile featuresFile = new FeaturesFile(text,
649             DataSourceType.PASTE);
650     featuresFile.parseFilters(filters);
651     assertEquals(filters.size(), 2);
652
653     FeatureMatcherSetI fm = filters.get("sequence_variant");
654     assertNotNull(fm);
655     Iterator<FeatureMatcherI> matchers = fm.getMatchers().iterator();
656     FeatureMatcherI matcher = matchers.next();
657     assertFalse(matchers.hasNext());
658     String[] attributes = matcher.getAttribute();
659     assertArrayEquals(attributes, new String[] { "CSQ", "PolyPhen" });
660     assertSame(matcher.getMatcher().getCondition(), Condition.NotContains);
661     assertEquals(matcher.getMatcher().getPattern(), "damaging");
662
663     fm = filters.get("missense_variant");
664     assertNotNull(fm);
665     matchers = fm.getMatchers().iterator();
666     matcher = matchers.next();
667     assertTrue(matcher.isByLabel());
668     assertSame(matcher.getMatcher().getCondition(), Condition.Contains);
669     assertEquals(matcher.getMatcher().getPattern(), "foobar");
670     matcher = matchers.next();
671     assertTrue(matcher.isByScore());
672     assertSame(matcher.getMatcher().getCondition(), Condition.LT);
673     assertEquals(matcher.getMatcher().getPattern(), "1.3");
674     assertEquals(matcher.getMatcher().getFloatValue(), 1.3f);
675
676     assertFalse(matchers.hasNext());
677   }
678
679   @Test(groups = { "Functional" })
680   public void testOutputFeatureFilters()
681   {
682     FeaturesFile ff = new FeaturesFile();
683     StringBuilder sb = new StringBuilder();
684     Map<String, FeatureColourI> visible = new HashMap<>();
685     visible.put("pfam", new FeatureColour(Color.red));
686     Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
687
688     // with no filters, nothing is output
689     ff.outputFeatureFilters(sb, visible, featureFilters);
690     assertEquals("", sb.toString());
691
692     // with filter for not visible features only, nothing is output
693     FeatureMatcherSet filter = new FeatureMatcherSet();
694     filter.and(FeatureMatcher.byLabel(Condition.Present, null));
695     featureFilters.put("foobar", filter);
696     ff.outputFeatureFilters(sb, visible, featureFilters);
697     assertEquals("", sb.toString());
698
699     // with filters for visible feature types
700     FeatureMatcherSet filter2 = new FeatureMatcherSet();
701     filter2.and(FeatureMatcher.byAttribute(Condition.Present, null, "CSQ",
702             "PolyPhen"));
703     filter2.and(FeatureMatcher.byScore(Condition.LE, "-2.4"));
704     featureFilters.put("pfam", filter2);
705     visible.put("foobar", new FeatureColour(Color.blue));
706     ff.outputFeatureFilters(sb, visible, featureFilters);
707     String expected = "\nSTARTFILTERS\nfoobar\tLabel Present\npfam\t(CSQ:PolyPhen Present) AND (Score LE -2.4)\nENDFILTERS\n\n";
708     assertEquals(expected, sb.toString());
709   }
710 }