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  1. Project Clover database Mon Sep 2 2024 17:57:51 BST
  2. Package jalview.io

File FeaturesFileTest.java

 

Code metrics

2
402
18
1
919
676
19
0.05
22.33
18
1.06

Classes

Class Line # Actions
FeaturesFileTest 64 402 19
0.9976303699.8%
 

Contributing tests

This file is covered by 14 tests. .

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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 java.awt.Color;
31    import java.io.File;
32    import java.io.IOException;
33    import java.util.HashMap;
34    import java.util.Iterator;
35    import java.util.List;
36    import java.util.Map;
37   
38    import org.testng.annotations.AfterClass;
39    import org.testng.annotations.BeforeClass;
40    import org.testng.annotations.Test;
41   
42    import jalview.api.FeatureColourI;
43    import jalview.api.FeatureRenderer;
44    import jalview.datamodel.Alignment;
45    import jalview.datamodel.AlignmentI;
46    import jalview.datamodel.SequenceDummy;
47    import jalview.datamodel.SequenceFeature;
48    import jalview.datamodel.SequenceI;
49    import jalview.datamodel.features.FeatureMatcher;
50    import jalview.datamodel.features.FeatureMatcherI;
51    import jalview.datamodel.features.FeatureMatcherSet;
52    import jalview.datamodel.features.FeatureMatcherSetI;
53    import jalview.datamodel.features.SequenceFeatures;
54    import jalview.gui.AlignFrame;
55    import jalview.gui.Desktop;
56    import jalview.gui.JvOptionPane;
57    import jalview.schemes.FeatureColour;
58    import jalview.structure.StructureSelectionManager;
59    import jalview.util.matcher.Condition;
60    import jalview.viewmodel.seqfeatures.FeatureRendererModel;
61    import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
62    import junit.extensions.PA;
63   
 
64    public class FeaturesFileTest
65    {
66    private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
67   
 
68  1 toggle @AfterClass(alwaysRun = true)
69    public void tearDownAfterClass()
70    {
71    /*
72    * remove any sequence mappings created so they don't pollute other tests
73    */
74  1 StructureSelectionManager ssm = StructureSelectionManager
75    .getStructureSelectionManager(Desktop.instance);
76  1 ssm.resetAll();
77    }
78   
 
79  1 toggle @BeforeClass(alwaysRun = true)
80    public void setUpJvOptionPane()
81    {
82  1 JvOptionPane.setInteractiveMode(false);
83  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
84    }
85   
 
86  1 toggle @Test(groups = { "Functional" })
87    public void testParse() throws Exception
88    {
89  1 File f = new File("examples/uniref50.fa");
90  1 AlignmentI al = readAlignmentFile(f);
91  1 AlignFrame af = new AlignFrame(al, 500, 500);
92  1 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
93    .getFeatureColours();
94  1 FeaturesFile featuresFile = new FeaturesFile(
95    "examples/exampleFeatures.txt", DataSourceType.FILE);
96  1 assertTrue(
97    "Test " + "Features file test"
98    + "\nFailed to parse features file.",
99    featuresFile.parse(al.getDataset(), colours, true));
100   
101    /*
102    * Refetch the colour map from the FeatureRenderer (to confirm it has been
103    * updated - JAL-1904), and verify (some) feature group colours
104    */
105  1 colours = af.getFeatureRenderer().getFeatureColours();
106  1 assertEquals("27 feature group colours not found", 27, colours.size());
107  1 assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
108  1 assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
109  1 FeatureColourI kdColour = colours.get("kdHydrophobicity");
110  1 assertTrue(kdColour.isGraduatedColour());
111  1 assertTrue(kdColour.isAboveThreshold());
112  1 assertEquals(-2f, kdColour.getThreshold());
113   
114    /*
115    * verify (some) features on sequences
116    */
117  1 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
118    .getSequenceFeatures(); // FER_CAPAA
119  1 SequenceFeatures.sortFeatures(sfs, true);
120  1 assertEquals(8, sfs.size());
121   
122    /*
123    * verify (in ascending start position order)
124    */
125  1 SequenceFeature sf = sfs.get(0);
126  1 assertEquals("Pfam family%LINK%", sf.description);
127  1 assertEquals(0, sf.begin);
128  1 assertEquals(0, sf.end);
129  1 assertEquals("uniprot", sf.featureGroup);
130  1 assertEquals("Pfam", sf.type);
131  1 assertEquals(1, sf.links.size());
132  1 assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
133    sf.links.get(0));
134   
135  1 sf = sfs.get(1);
136  1 assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
137  1 assertEquals(3, sf.begin);
138  1 assertEquals(93, sf.end);
139  1 assertEquals("uniprot", sf.featureGroup);
140  1 assertEquals("Cath", sf.type);
141   
142  1 sf = sfs.get(2);
143  1 assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
144    sf.description);
145  1 assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
146    sf.links.get(0));
147  1 assertEquals(8, sf.begin);
148  1 assertEquals(83, sf.end);
149  1 assertEquals("uniprot", sf.featureGroup);
150  1 assertEquals("Pfam", sf.type);
151   
152  1 sf = sfs.get(3);
153  1 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
154  1 assertEquals(39, sf.begin);
155  1 assertEquals(39, sf.end);
156  1 assertEquals("uniprot", sf.featureGroup);
157  1 assertEquals("METAL", sf.type);
158   
159  1 sf = sfs.get(4);
160  1 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
161  1 assertEquals(44, sf.begin);
162  1 assertEquals(44, sf.end);
163  1 assertEquals("uniprot", sf.featureGroup);
164  1 assertEquals("METAL", sf.type);
165   
166  1 sf = sfs.get(5);
167  1 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
168  1 assertEquals(47, sf.begin);
169  1 assertEquals(47, sf.end);
170  1 assertEquals("uniprot", sf.featureGroup);
171  1 assertEquals("METAL", sf.type);
172   
173  1 sf = sfs.get(6);
174  1 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
175  1 assertEquals(77, sf.begin);
176  1 assertEquals(77, sf.end);
177  1 assertEquals("uniprot", sf.featureGroup);
178  1 assertEquals("METAL", sf.type);
179   
180  1 sf = sfs.get(7);
181  1 assertEquals(
182    "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
183    sf.description);
184  1 assertEquals(
185    "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&amp;service=NetPhos-2.0",
186    sf.links.get(0));
187  1 assertEquals(89, sf.begin);
188  1 assertEquals(89, sf.end);
189  1 assertEquals("netphos", sf.featureGroup);
190  1 assertEquals("PHOSPHORYLATION (T)", sf.type);
191    }
192   
193    /**
194    * Test parsing a features file with a mix of Jalview and GFF formatted
195    * content
196    *
197    * @throws Exception
198    */
 
199  1 toggle @Test(groups = { "Functional" })
200    public void testParse_mixedJalviewGff() throws Exception
201    {
202  1 File f = new File("examples/uniref50.fa");
203  1 AlignmentI al = readAlignmentFile(f);
204  1 AlignFrame af = new AlignFrame(al, 500, 500);
205  1 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
206    .getFeatureColours();
207    // GFF2 uses space as name/value separator in column 9
208  1 String gffData = "METAL\tcc9900\n" + "GFF\n"
209    + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
210    + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
211  1 FeaturesFile featuresFile = new FeaturesFile(gffData,
212    DataSourceType.PASTE);
213  1 assertTrue("Failed to parse features file",
214    featuresFile.parse(al.getDataset(), colours, true));
215   
216    // verify colours read or synthesized
217  1 colours = af.getFeatureRenderer().getFeatureColours();
218  1 assertEquals("1 feature group colours not found", 1, colours.size());
219  1 assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
220   
221    // verify feature on FER_CAPAA
222  1 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
223    .getSequenceFeatures();
224  1 assertEquals(1, sfs.size());
225  1 SequenceFeature sf = sfs.get(0);
226  1 assertEquals("Iron-sulfur,2Fe-2S", sf.description);
227  1 assertEquals(44, sf.begin);
228  1 assertEquals(45, sf.end);
229  1 assertEquals("uniprot", sf.featureGroup);
230  1 assertEquals("METAL", sf.type);
231  1 assertEquals(4f, sf.getScore(), 0.001f);
232   
233    // verify feature on FER1_SOLLC
234  1 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
235  1 assertEquals(1, sfs.size());
236  1 sf = sfs.get(0);
237  1 assertEquals("uniprot", sf.description);
238  1 assertEquals(55, sf.begin);
239  1 assertEquals(130, sf.end);
240  1 assertEquals("uniprot", sf.featureGroup);
241  1 assertEquals("Pfam", sf.type);
242  1 assertEquals(2f, sf.getScore(), 0.001f);
243    }
244   
 
245  8 toggle public static AlignmentI readAlignmentFile(File f) throws IOException
246    {
247  8 System.out.println("Reading file: " + f);
248  8 String ff = f.getPath();
249  8 FormatAdapter rf = new FormatAdapter();
250   
251  8 AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
252    new IdentifyFile().identify(ff, DataSourceType.FILE));
253   
254  8 al.setDataset(null); // creates dataset sequences
255  8 assertNotNull("Couldn't read supplied alignment data.", al);
256  8 return al;
257    }
258   
259    /**
260    * Test parsing a features file with GFF formatted content only
261    *
262    * @throws Exception
263    */
 
264  1 toggle @Test(groups = { "Functional" })
265    public void testParse_pureGff3() throws Exception
266    {
267  1 File f = new File("examples/uniref50.fa");
268  1 AlignmentI al = readAlignmentFile(f);
269  1 AlignFrame af = new AlignFrame(al, 500, 500);
270  1 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
271    .getFeatureColours();
272    // GFF3 uses '=' separator for name/value pairs in column 9
273    // comma (%2C) equals (%3D) or semi-colon (%3B) should be url-escaped in
274    // values
275  1 String gffData = "##gff-version 3\n"
276    + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
277    + "Note=Iron-sulfur (2Fe-2S);Note=another note,and another;evidence=ECO%3B0000255%2CPROSITE%3DProRule:PRU00465;"
278    + "CSQ=AF=21,POLYPHEN=benign,possibly_damaging,clin_sig=Benign%3Dgood\n"
279    + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
280  1 FeaturesFile featuresFile = new FeaturesFile(gffData,
281    DataSourceType.PASTE);
282  1 assertTrue("Failed to parse features file",
283    featuresFile.parse(al.getDataset(), colours, true));
284   
285    // verify feature on FER_CAPAA
286  1 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
287    .getSequenceFeatures();
288  1 assertEquals(1, sfs.size());
289  1 SequenceFeature sf = sfs.get(0);
290    // description parsed from Note attribute
291  1 assertEquals("Iron-sulfur (2Fe-2S),another note,and another",
292    sf.description);
293  1 assertEquals(39, sf.begin);
294  1 assertEquals(39, sf.end);
295  1 assertEquals("uniprot", sf.featureGroup);
296  1 assertEquals("METAL", sf.type);
297  1 assertEquals(5, sf.otherDetails.size());
298  1 assertEquals("ECO;0000255,PROSITE=ProRule:PRU00465", // url decoded
299    sf.getValue("evidence"));
300  1 assertEquals("Iron-sulfur (2Fe-2S),another note,and another",
301    sf.getValue("Note"));
302  1 assertEquals("21", sf.getValueAsString("CSQ", "AF"));
303  1 assertEquals("benign,possibly_damaging",
304    sf.getValueAsString("CSQ", "POLYPHEN"));
305  1 assertEquals("Benign=good", sf.getValueAsString("CSQ", "clin_sig")); // url
306    // decoded
307    // todo change STRAND and !Phase into fields of SequenceFeature instead
308  1 assertEquals(".", sf.otherDetails.get("STRAND"));
309  1 assertEquals(0, sf.getStrand());
310  1 assertEquals(".", sf.getPhase());
311   
312    // verify feature on FER1_SOLLC1
313  1 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
314  1 assertEquals(1, sfs.size());
315  1 sf = sfs.get(0);
316    // ID used for description if available
317  1 assertEquals("$23", sf.description);
318  1 assertEquals(55, sf.begin);
319  1 assertEquals(130, sf.end);
320  1 assertEquals("uniprot", sf.featureGroup);
321  1 assertEquals("Pfam", sf.type);
322  1 assertEquals(3f, sf.getScore(), 0.001f);
323    }
324   
325    /**
326    * Test parsing a features file with Jalview format features (but no colour
327    * descriptors or startgroup to give the hint not to parse as GFF)
328    *
329    * @throws Exception
330    */
 
331  1 toggle @Test(groups = { "Functional" })
332    public void testParse_jalviewFeaturesOnly() throws Exception
333    {
334  1 File f = new File("examples/uniref50.fa");
335  1 AlignmentI al = readAlignmentFile(f);
336  1 AlignFrame af = new AlignFrame(al, 500, 500);
337  1 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
338    .getFeatureColours();
339   
340    /*
341    * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
342    */
343  1 String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
344    + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
345  1 FeaturesFile featuresFile = new FeaturesFile(featureData,
346    DataSourceType.PASTE);
347  1 assertTrue("Failed to parse features file",
348    featuresFile.parse(al.getDataset(), colours, true));
349   
350    // verify FER_CAPAA feature
351  1 List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
352    .getSequenceFeatures();
353  1 assertEquals(1, sfs.size());
354  1 SequenceFeature sf = sfs.get(0);
355  1 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
356  1 assertEquals(39, sf.begin);
357  1 assertEquals(39, sf.end);
358  1 assertEquals("METAL", sf.type);
359   
360    // verify FER1_SOLLC feature
361  1 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
362  1 assertEquals(1, sfs.size());
363  1 sf = sfs.get(0);
364  1 assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
365  1 assertEquals(86, sf.begin);
366  1 assertEquals(87, sf.end);
367  1 assertEquals("METALLIC", sf.type);
368    }
369   
 
370  4 toggle private void checkDatasetfromSimpleGff3(AlignmentI dataset)
371    {
372  4 assertEquals("no sequences extracted from GFF3 file", 2,
373    dataset.getHeight());
374   
375  4 SequenceI seq1 = dataset.findName("seq1");
376  4 SequenceI seq2 = dataset.findName("seq2");
377  4 assertNotNull(seq1);
378  4 assertNotNull(seq2);
379  4 assertFalse("Failed to replace dummy seq1 with real sequence",
380    seq1 instanceof SequenceDummy
381    && ((SequenceDummy) seq1).isDummy());
382  4 assertFalse("Failed to replace dummy seq2 with real sequence",
383    seq2 instanceof SequenceDummy
384    && ((SequenceDummy) seq2).isDummy());
385  4 String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
386  4 assertFalse("dummy replacement buggy for seq1",
387    placeholderseq.equals(seq1.getSequenceAsString()));
388  4 assertFalse("dummy replacement buggy for seq2",
389    placeholderseq.equals(seq2.getSequenceAsString()));
390  4 assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
391  4 assertEquals("Wrong number of features", 3,
392    seq1.getSequenceFeatures().size());
393  4 assertTrue(seq2.getSequenceFeatures().isEmpty());
394  4 assertEquals("Wrong number of features", 0,
395  4 seq2.getSequenceFeatures() == null ? 0
396    : seq2.getSequenceFeatures().size());
397  4 assertTrue("Expected at least one CDNA/Protein mapping for seq1",
398    dataset.getCodonFrame(seq1) != null
399    && dataset.getCodonFrame(seq1).size() > 0);
400   
401    }
402   
 
403  1 toggle @Test(groups = { "Functional" })
404    public void readGff3File() throws IOException
405    {
406  1 FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
407    DataSourceType.FILE);
408  1 Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
409  1 gffreader.addProperties(dataset);
410  1 checkDatasetfromSimpleGff3(dataset);
411    }
412   
 
413  1 toggle @Test(groups = { "Functional" })
414    public void simpleGff3FileClass() throws IOException
415    {
416  1 AlignmentI dataset = new Alignment(new SequenceI[] {});
417  1 FeaturesFile ffile = new FeaturesFile(simpleGffFile,
418    DataSourceType.FILE);
419   
420  1 boolean parseResult = ffile.parse(dataset, null, false, false);
421  1 assertTrue("return result should be true", parseResult);
422  1 checkDatasetfromSimpleGff3(dataset);
423    }
424   
 
425  1 toggle @Test(groups = { "Functional" })
426    public void simpleGff3FileLoader() throws IOException
427    {
428  1 AlignFrame af = new FileLoader(false)
429    .LoadFileWaitTillLoaded(simpleGffFile, DataSourceType.FILE);
430  1 assertTrue(
431    "Didn't read the alignment into an alignframe from Gff3 File",
432    af != null);
433  1 checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
434    }
435   
 
436  1 toggle @Test(groups = { "Functional" })
437    public void simpleGff3RelaxedIdMatching() throws IOException
438    {
439  1 AlignmentI dataset = new Alignment(new SequenceI[] {});
440  1 FeaturesFile ffile = new FeaturesFile(simpleGffFile,
441    DataSourceType.FILE);
442   
443  1 boolean parseResult = ffile.parse(dataset, null, false, true);
444  1 assertTrue("return result (relaxedID matching) should be true",
445    parseResult);
446  1 checkDatasetfromSimpleGff3(dataset);
447    }
448   
 
449  1 toggle @Test(groups = { "Functional" })
450    public void testPrintJalviewFormat() throws Exception
451    {
452  1 File f = new File("examples/uniref50.fa");
453  1 AlignmentI al = readAlignmentFile(f);
454  1 AlignFrame af = new AlignFrame(al, 500, 500);
455  1 Map<String, FeatureColourI> colours = af.getFeatureRenderer()
456    .getFeatureColours();
457  1 String features = "METAL\tcc9900\n"
458    + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
459    + "Pfam\tred\n" + "STARTGROUP\tuniprot\n"
460    + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\n" // non-positional feature
461    + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
462    + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
463    + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
464    + "ENDGROUP\tuniprot\n";
465  1 FeaturesFile featuresFile = new FeaturesFile(features,
466    DataSourceType.PASTE);
467  1 featuresFile.parse(al.getDataset(), colours, false);
468   
469    /*
470    * add positional and non-positional features with null and
471    * empty feature group to check handled correctly
472    */
473  1 SequenceI seq = al.getSequenceAt(1); // FER_CAPAN
474  1 seq.addSequenceFeature(
475    new SequenceFeature("Pfam", "desc1", 0, 0, 1.3f, null));
476  1 seq.addSequenceFeature(
477    new SequenceFeature("Pfam", "desc2", 4, 9, Float.NaN, null));
478  1 seq = al.getSequenceAt(2); // FER1_SOLLC
479  1 seq.addSequenceFeature(
480    new SequenceFeature("Pfam", "desc3", 0, 0, Float.NaN, ""));
481  1 seq.addSequenceFeature(
482    new SequenceFeature("Pfam", "desc4", 5, 8, -2.6f, ""));
483   
484    /*
485    * first with no features displayed, exclude non-positional features
486    */
487  1 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
488  1 String exported = featuresFile
489    .printJalviewFormat(al.getSequencesArray(), fr, false, false);
490  1 String expected = "No Features Visible";
491  1 assertEquals(expected, exported);
492   
493    /*
494    * include non-positional features, but still no positional features
495    */
496  1 fr.setGroupVisibility("uniprot", true);
497  1 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
498    true, false);
499  1 expected = "\nSTARTGROUP\tuniprot\n"
500    + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
501    + "ENDGROUP\tuniprot\n\n"
502    + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n\n"
503    + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"; // NaN is not output
504  1 assertEquals(expected, exported);
505   
506    /*
507    * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
508    */
509  1 fr.setVisible("METAL");
510  1 fr.setVisible("GAMMA-TURN");
511  1 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
512    false, false);
513  1 expected = "METAL\tcc9900\n"
514    + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
515    + "\nSTARTGROUP\tuniprot\n"
516    + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
517    + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
518    + "ENDGROUP\tuniprot\n";
519  1 assertEquals(expected, exported);
520   
521    /*
522    * now set Pfam visible
523    */
524  1 fr.setVisible("Pfam");
525  1 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
526    false, false);
527    /*
528    * features are output within group, ordered by sequence and type
529    */
530  1 expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
531    + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
532    + "\nSTARTGROUP\tuniprot\n"
533    + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
534    + "<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"
535    + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
536    + "ENDGROUP\tuniprot\n"
537    // null / empty group features are output after named groups
538    + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
539    + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
540  1 assertEquals(expected, exported);
541   
542    /*
543    * hide uniprot group
544    */
545  1 fr.setGroupVisibility("uniprot", false);
546  1 expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
547    + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
548    + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
549    + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
550  1 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
551    false, false);
552  1 assertEquals(expected, exported);
553   
554    /*
555    * include non-positional (overrides group not shown)
556    */
557  1 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
558    true, false);
559  1 expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
560    + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
561    + "\nSTARTGROUP\tuniprot\n"
562    + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
563    + "ENDGROUP\tuniprot\n"
564    + "\ndesc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n"
565    + "desc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
566    + "\ndesc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"
567    + "desc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
568  1 assertEquals(expected, exported);
569    }
570   
 
571  1 toggle @Test(groups = { "Functional" })
572    public void testPrintGffFormat() throws Exception
573    {
574  1 File f = new File("examples/uniref50.fa");
575  1 AlignmentI al = readAlignmentFile(f);
576  1 AlignFrame af = new AlignFrame(al, 500, 500);
577   
578    /*
579    * no features
580    */
581  1 FeaturesFile featuresFile = new FeaturesFile();
582  1 FeatureRendererModel fr = (FeatureRendererModel) af.alignPanel
583    .getFeatureRenderer();
584  1 String exported = featuresFile.printGffFormat(al.getSequencesArray(),
585    fr, false, false);
586  1 String gffHeader = "##gff-version 2\n";
587  1 assertEquals(gffHeader, exported);
588  1 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, true,
589    false);
590  1 assertEquals(gffHeader, exported);
591   
592    /*
593    * add some features
594    */
595  1 al.getSequenceAt(0).addSequenceFeature(
596    new SequenceFeature("Domain", "Cath", 0, 0, 0f, "Uniprot"));
597  1 al.getSequenceAt(0).addSequenceFeature(
598    new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, null));
599  1 al.getSequenceAt(1).addSequenceFeature(new SequenceFeature("GAMMA-TURN",
600    "Turn", 36, 38, 2.1f, "s3dm"));
601  1 SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f,
602    "Uniprot");
603  1 sf.setStrand("+");
604  1 sf.setPhase("2");
605  1 sf.setValue("x", "y");
606  1 sf.setValue("black", "white");
607  1 Map<String, String> csq = new HashMap<>();
608  1 csq.put("SIFT", "benign,mostly benign,cloudy, with meatballs");
609  1 csq.put("consequence", "missense_variant");
610  1 sf.setValue("CSQ", csq);
611  1 al.getSequenceAt(1).addSequenceFeature(sf);
612   
613    /*
614    * 'discover' features then hide all feature types
615    */
616  1 fr.findAllFeatures(true);
617  1 FeatureSettingsBean[] data = new FeatureSettingsBean[4];
618  1 FeatureColourI fc = new FeatureColour(Color.PINK);
619  1 data[0] = new FeatureSettingsBean("Domain", fc, null, false);
620  1 data[1] = new FeatureSettingsBean("METAL", fc, null, false);
621  1 data[2] = new FeatureSettingsBean("GAMMA-TURN", fc, null, false);
622  1 data[3] = new FeatureSettingsBean("Pfam", fc, null, false);
623  1 fr.setFeaturePriority(data);
624   
625    /*
626    * with no features displayed, exclude non-positional features
627    */
628  1 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
629    false, false);
630  1 assertEquals(gffHeader, exported);
631   
632    /*
633    * include non-positional features
634    */
635  1 fr.setGroupVisibility("Uniprot", true);
636  1 fr.setGroupVisibility("s3dm", false);
637  1 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, true,
638    false);
639  1 String expected = gffHeader
640    + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
641  1 assertEquals(expected, exported);
642   
643    /*
644    * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
645    * only Uniprot group visible here...
646    */
647  1 fr.setVisible("METAL");
648  1 fr.setVisible("GAMMA-TURN");
649  1 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
650    false, false);
651    // METAL feature has null group: description used for column 2
652  1 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
653  1 assertEquals(expected, exported);
654   
655    /*
656    * set s3dm group visible
657    */
658  1 fr.setGroupVisibility("s3dm", true);
659  1 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
660    false, false);
661    // METAL feature has null group: description used for column 2
662  1 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
663    + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
664  1 assertEquals(expected, exported);
665   
666    /*
667    * now set Pfam visible
668    */
669  1 fr.setVisible("Pfam");
670  1 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
671    false, false);
672    // Pfam feature columns include strand(+), phase(2), attributes
673  1 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
674    // CSQ output as CSQ=att1=value1,att2=value2
675    // note all commas are encoded here which is wrong - it should be
676    // SIFT=benign,mostly benign,cloudy%2C with meatballs
677    + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white;"
678    + "CSQ=SIFT=benign%2Cmostly benign%2Ccloudy%2C with meatballs,consequence=missense_variant\n"
679    + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
680  1 assertEquals(expected, exported);
681    }
682   
683    /**
684    * Test for parsing of feature filters as represented in a Jalview features
685    * file
686    *
687    * @throws Exception
688    */
 
689  1 toggle @Test(groups = { "Functional" })
690    public void testParseFilters() throws Exception
691    {
692  1 Map<String, FeatureMatcherSetI> filters = new HashMap<>();
693  1 String text = "sequence_variant\tCSQ:PolyPhen NotContains 'damaging'\n"
694    + "missense_variant\t(label contains foobar) and (Score lt 1.3)";
695  1 FeaturesFile featuresFile = new FeaturesFile(text,
696    DataSourceType.PASTE);
697  1 featuresFile.parseFilters(filters);
698  1 assertEquals(filters.size(), 2);
699   
700  1 FeatureMatcherSetI fm = filters.get("sequence_variant");
701  1 assertNotNull(fm);
702  1 Iterator<FeatureMatcherI> matchers = fm.getMatchers().iterator();
703  1 FeatureMatcherI matcher = matchers.next();
704  1 assertFalse(matchers.hasNext());
705  1 String[] attributes = matcher.getAttribute();
706  1 assertArrayEquals(attributes, new String[] { "CSQ", "PolyPhen" });
707  1 assertSame(matcher.getMatcher().getCondition(), Condition.NotContains);
708  1 assertEquals(matcher.getMatcher().getPattern(), "damaging");
709   
710  1 fm = filters.get("missense_variant");
711  1 assertNotNull(fm);
712  1 matchers = fm.getMatchers().iterator();
713  1 matcher = matchers.next();
714  1 assertTrue(matcher.isByLabel());
715  1 assertSame(matcher.getMatcher().getCondition(), Condition.Contains);
716  1 assertEquals(matcher.getMatcher().getPattern(), "foobar");
717  1 matcher = matchers.next();
718  1 assertTrue(matcher.isByScore());
719  1 assertSame(matcher.getMatcher().getCondition(), Condition.LT);
720  1 assertEquals(matcher.getMatcher().getPattern(), "1.3");
721  1 assertEquals(PA.getValue(matcher.getMatcher(), "floatValue"), 1.3f);
722   
723  1 assertFalse(matchers.hasNext());
724    }
725   
 
726  1 toggle @Test(groups = { "Functional" })
727    public void testOutputFeatureFilters()
728    {
729  1 FeaturesFile ff = new FeaturesFile();
730  1 StringBuilder sb = new StringBuilder();
731  1 Map<String, FeatureColourI> visible = new HashMap<>();
732  1 visible.put("pfam", new FeatureColour(Color.red));
733  1 Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
734   
735    // with no filters, nothing is output
736  1 ff.outputFeatureFilters(sb, visible, featureFilters);
737  1 assertEquals("", sb.toString());
738   
739    // with filter for not visible features only, nothing is output
740  1 FeatureMatcherSet filter = new FeatureMatcherSet();
741  1 filter.and(FeatureMatcher.byLabel(Condition.Present, null));
742  1 featureFilters.put("foobar", filter);
743  1 ff.outputFeatureFilters(sb, visible, featureFilters);
744  1 assertEquals("", sb.toString());
745   
746    // with filters for visible feature types
747  1 FeatureMatcherSet filter2 = new FeatureMatcherSet();
748  1 filter2.and(FeatureMatcher.byAttribute(Condition.Present, null, "CSQ",
749    "PolyPhen"));
750  1 filter2.and(FeatureMatcher.byScore(Condition.LE, "-2.4"));
751  1 featureFilters.put("pfam", filter2);
752  1 visible.put("foobar", new FeatureColour(Color.blue));
753  1 ff.outputFeatureFilters(sb, visible, featureFilters);
754  1 String expected = "\nSTARTFILTERS\nfoobar\tLabel Present\npfam\t(CSQ:PolyPhen Present) AND (Score LE -2.4)\nENDFILTERS\n";
755  1 assertEquals(expected, sb.toString());
756    }
757   
758    /**
759    * Output as GFF should not include features which are not visible due to
760    * colour threshold or feature filter settings
761    *
762    * @throws Exception
763    */
 
764  1 toggle @Test(groups = { "Functional" })
765    public void testPrintGffFormat_withFilters() throws Exception
766    {
767  1 File f = new File("examples/uniref50.fa");
768  1 AlignmentI al = readAlignmentFile(f);
769  1 AlignFrame af = new AlignFrame(al, 500, 500);
770  1 SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
771    null);
772  1 sf1.setValue("clin_sig", "Likely Pathogenic");
773  1 sf1.setValue("AF", "24");
774  1 al.getSequenceAt(0).addSequenceFeature(sf1);
775  1 SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
776    null);
777  1 sf2.setValue("clin_sig", "Benign");
778  1 sf2.setValue("AF", "46");
779  1 al.getSequenceAt(0).addSequenceFeature(sf2);
780   
781  1 FeaturesFile featuresFile = new FeaturesFile();
782  1 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
783  1 final String gffHeader = "##gff-version 2\n";
784   
785  1 fr.setVisible("METAL");
786  1 fr.setColour("METAL", new FeatureColour(Color.PINK));
787  1 String exported = featuresFile.printGffFormat(al.getSequencesArray(),
788    fr, false, false);
789  1 String expected = gffHeader
790    + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n"
791    + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
792  1 assertEquals(expected, exported);
793   
794    /*
795    * now threshold to Score > 1.1 - should exclude sf2
796    */
797  1 FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
798    Color.white, 0f, 2f);
799  1 fc.setAboveThreshold(true);
800  1 fc.setThreshold(1.1f);
801  1 fr.setColour("METAL", fc);
802  1 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
803    false, false);
804  1 expected = gffHeader
805    + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n";
806  1 assertEquals(expected, exported);
807   
808    /*
809    * remove threshold and check sf2 is exported
810    */
811  1 fc.setAboveThreshold(false);
812  1 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
813    false, false);
814  1 expected = gffHeader
815    + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n"
816    + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
817  1 assertEquals(expected, exported);
818   
819    /*
820    * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
821    */
822  1 FeatureMatcherSetI filter = new FeatureMatcherSet();
823  1 filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
824    "clin_sig"));
825  1 fr.setFeatureFilter("METAL", filter);
826  1 exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
827    false, false);
828  1 expected = gffHeader
829    + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
830  1 assertEquals(expected, exported);
831    }
832   
833    /**
834    * Output as Jalview should not include features which are not visible due to
835    * colour threshold or feature filter settings
836    *
837    * @throws Exception
838    */
 
839  1 toggle @Test(groups = { "Functional" })
840    public void testPrintJalviewFormat_withFilters() throws Exception
841    {
842  1 File f = new File("examples/uniref50.fa");
843  1 AlignmentI al = readAlignmentFile(f);
844  1 AlignFrame af = new AlignFrame(al, 500, 500);
845  1 SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
846    "grp1");
847  1 sf1.setValue("clin_sig", "Likely Pathogenic");
848  1 sf1.setValue("AF", "24");
849  1 al.getSequenceAt(0).addSequenceFeature(sf1);
850  1 SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
851    "grp2");
852  1 sf2.setValue("clin_sig", "Benign");
853  1 sf2.setValue("AF", "46");
854  1 al.getSequenceAt(0).addSequenceFeature(sf2);
855   
856  1 FeaturesFile featuresFile = new FeaturesFile();
857  1 FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
858  1 fr.findAllFeatures(true);
859   
860  1 fr.setVisible("METAL");
861  1 fr.setColour("METAL", new FeatureColour(Color.PINK));
862  1 String exported = featuresFile
863    .printJalviewFormat(al.getSequencesArray(), fr, false, false);
864  1 String expected = "METAL\tffafaf\n\nSTARTGROUP\tgrp1\n"
865    + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
866    + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
867    + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
868    + "ENDGROUP\tgrp2\n";
869  1 assertEquals(expected, exported);
870   
871    /*
872    * now threshold to Score > 1.1 - should exclude sf2
873    * (and there should be no empty STARTGROUP/ENDGROUP output)
874    */
875  1 FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
876    Color.white, 0f, 2f);
877  1 fc.setAboveThreshold(true);
878  1 fc.setThreshold(1.1f);
879  1 fr.setColour("METAL", fc);
880  1 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
881    false, false);
882  1 expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|above|1.1\n\n"
883    + "STARTGROUP\tgrp1\n"
884    + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
885    + "ENDGROUP\tgrp1\n";
886  1 assertEquals(expected, exported);
887   
888    /*
889    * remove threshold and check sf2 is exported
890    */
891  1 fc.setAboveThreshold(false);
892  1 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
893    false, false);
894  1 expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
895    + "STARTGROUP\tgrp1\n"
896    + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
897    + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
898    + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
899    + "ENDGROUP\tgrp2\n";
900  1 assertEquals(expected, exported);
901   
902    /*
903    * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
904    */
905  1 FeatureMatcherSetI filter = new FeatureMatcherSet();
906  1 filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
907    "clin_sig"));
908  1 fr.setFeatureFilter("METAL", filter);
909  1 exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
910    false, false);
911  1 expected = "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
912  1 expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
913    + "STARTFILTERS\nMETAL\tclin_sig Contains benign\nENDFILTERS\n\n"
914    + "STARTGROUP\tgrp2\n"
915    + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
916    + "ENDGROUP\tgrp2\n";
917  1 assertEquals(expected, exported);
918    }
919    }
  • Report generated by OpenClover v 4.4.1 on Mon Sep 2 2024 18:05:00 BST using coverage data from Mon Sep 2 2024 18:04:45 BST.
  • OpenClover is free and open-source software.