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  1. Project Clover database Mon Nov 18 2024 09:38:20 GMT
  2. Package jalview.analysis

File AlignmentUtilsTests.java

 

Code metrics

14
1,290
54
1
2,963
1,914
61
0.05
23.89
54
1.13

Classes

Class Line # Actions
AlignmentUtilsTests 76 1,290 61
0.9351988493.5%
 

Contributing tests

This file is covered by 44 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.analysis;
22   
23    import static org.testng.Assert.assertNotEquals;
24    import static org.testng.AssertJUnit.assertEquals;
25    import static org.testng.AssertJUnit.assertFalse;
26    import static org.testng.AssertJUnit.assertNotNull;
27    import static org.testng.AssertJUnit.assertNull;
28    import static org.testng.AssertJUnit.assertSame;
29    import static org.testng.AssertJUnit.assertTrue;
30   
31    import java.awt.Color;
32    import java.io.IOException;
33    import java.util.ArrayList;
34    import java.util.Arrays;
35    import java.util.HashMap;
36    import java.util.LinkedHashMap;
37    import java.util.List;
38    import java.util.Map;
39    import java.util.Set;
40    import java.util.SortedMap;
41    import java.util.TreeMap;
42   
43    import org.testng.Assert;
44    import org.testng.annotations.BeforeClass;
45    import org.testng.annotations.DataProvider;
46    import org.testng.annotations.Test;
47   
48    import jalview.datamodel.AlignedCodonFrame;
49    import jalview.datamodel.Alignment;
50    import jalview.datamodel.AlignmentAnnotation;
51    import jalview.datamodel.AlignmentI;
52    import jalview.datamodel.Annotation;
53    import jalview.datamodel.ContactListI;
54    import jalview.datamodel.ContactMatrixI;
55    import jalview.datamodel.DBRefEntry;
56    import jalview.datamodel.GeneLociI;
57    import jalview.datamodel.Mapping;
58    import jalview.datamodel.SearchResultMatchI;
59    import jalview.datamodel.SearchResultsI;
60    import jalview.datamodel.SeqDistanceContactMatrix;
61    import jalview.datamodel.Sequence;
62    import jalview.datamodel.SequenceFeature;
63    import jalview.datamodel.SequenceGroup;
64    import jalview.datamodel.SequenceI;
65    import jalview.gui.JvOptionPane;
66    import jalview.io.AppletFormatAdapter;
67    import jalview.io.DataSourceType;
68    import jalview.io.FileFormat;
69    import jalview.io.FileFormatI;
70    import jalview.io.FormatAdapter;
71    import jalview.io.gff.SequenceOntologyI;
72    import jalview.util.Comparison;
73    import jalview.util.MapList;
74    import jalview.util.MappingUtils;
75   
 
76    public class AlignmentUtilsTests
77    {
78    private static Sequence ts = new Sequence("short",
79    "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
80   
 
81  1 toggle @BeforeClass(alwaysRun = true)
82    public void setUpJvOptionPane()
83    {
84  1 JvOptionPane.setInteractiveMode(false);
85  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
86   
87  1 AlignmentAnnotation ann1 = new AlignmentAnnotation(
88    "Secondary Structure", "Secondary Structure",
89    new Annotation[] {});
90  1 AlignmentAnnotation ann2 = new AlignmentAnnotation("jnetpred",
91    "jnetpred", new Annotation[] {});
92  1 AlignmentAnnotation ann3 = new AlignmentAnnotation("Temp", "Temp",
93    new Annotation[] {});
94  1 AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "Temp",
95    new Annotation[] {});
96   
97  1 AlignmentAnnotation[] anns1 = new AlignmentAnnotation[] { ann1, ann3,
98    ann4 };
99   
100  1 AlignmentAnnotation[] anns2 = new AlignmentAnnotation[] { ann2, ann3,
101    ann4 };
102   
103  1 AlignmentAnnotation[] anns3 = new AlignmentAnnotation[] { ann3, ann4 };
104   
105  1 AlignmentAnnotation[] anns4 = new AlignmentAnnotation[0];
106   
107  1 AlignmentAnnotation[] anns5 = new AlignmentAnnotation[] { ann1, ann2,
108    ann3, ann4 };
109    }
110   
 
111  1 toggle @Test(groups = { "Functional" })
112    public void testExpandContext()
113    {
114  1 AlignmentI al = new Alignment(new Sequence[] {});
115  6 for (int i = 4; i < 14; i += 2)
116    {
117  5 SequenceI s1 = ts.deriveSequence().getSubSequence(i, i + 7);
118  5 al.addSequence(s1);
119    }
120  1 System.out.println(new AppletFormatAdapter()
121    .formatSequences(FileFormat.Clustal, al, true));
122  27 for (int flnk = -1; flnk < 25; flnk++)
123    {
124  26 AlignmentI exp = AlignmentUtils.expandContext(al, flnk);
125  26 System.out.println("\nFlank size: " + flnk);
126  26 System.out.println(new AppletFormatAdapter()
127    .formatSequences(FileFormat.Clustal, exp, true));
128  26 if (flnk == -1)
129    {
130    /*
131    * Full expansion to complete sequences
132    */
133  1 for (SequenceI sq : exp.getSequences())
134    {
135  5 String ung = sq.getSequenceAsString().replaceAll("-+", "");
136  5 final String errorMsg = "Flanking sequence not the same as original dataset sequence.\n"
137    + ung + "\n"
138    + sq.getDatasetSequence().getSequenceAsString();
139  5 assertTrue(errorMsg, ung.equalsIgnoreCase(
140    sq.getDatasetSequence().getSequenceAsString()));
141    }
142    }
143  25 else if (flnk == 24)
144    {
145    /*
146    * Last sequence is fully expanded, others have leading gaps to match
147    */
148  1 assertTrue(exp.getSequenceAt(4).getSequenceAsString()
149    .startsWith("abc"));
150  1 assertTrue(exp.getSequenceAt(3).getSequenceAsString()
151    .startsWith("--abc"));
152  1 assertTrue(exp.getSequenceAt(2).getSequenceAsString()
153    .startsWith("----abc"));
154  1 assertTrue(exp.getSequenceAt(1).getSequenceAsString()
155    .startsWith("------abc"));
156  1 assertTrue(exp.getSequenceAt(0).getSequenceAsString()
157    .startsWith("--------abc"));
158    }
159    }
160    }
161   
162    /**
163    * Test that annotations are correctly adjusted by expandContext
164    */
 
165  1 toggle @Test(groups = { "Functional" })
166    public void testExpandContext_annotation()
167    {
168  1 AlignmentI al = new Alignment(new Sequence[] {});
169  1 SequenceI ds = new Sequence("Seq1", "ABCDEFGHI");
170    // subsequence DEF:
171  1 SequenceI seq1 = ds.deriveSequence().getSubSequence(3, 6);
172  1 al.addSequence(seq1);
173   
174    /*
175    * Annotate DEF with 4/5/6 respectively
176    */
177  1 Annotation[] anns = new Annotation[] { new Annotation(4),
178    new Annotation(5), new Annotation(6) };
179  1 AlignmentAnnotation ann = new AlignmentAnnotation("SS",
180    "secondary structure", anns);
181  1 seq1.addAlignmentAnnotation(ann);
182   
183    /*
184    * The annotations array should match aligned positions
185    */
186  1 assertEquals(3, ann.annotations.length);
187  1 assertEquals(4, ann.annotations[0].value, 0.001);
188  1 assertEquals(5, ann.annotations[1].value, 0.001);
189  1 assertEquals(6, ann.annotations[2].value, 0.001);
190   
191    /*
192    * Check annotation to sequence position mappings before expanding the
193    * sequence; these are set up in Sequence.addAlignmentAnnotation ->
194    * Annotation.setSequenceRef -> createSequenceMappings
195    */
196  1 assertNull(ann.getAnnotationForPosition(1));
197  1 assertNull(ann.getAnnotationForPosition(2));
198  1 assertNull(ann.getAnnotationForPosition(3));
199  1 assertEquals(4, ann.getAnnotationForPosition(4).value, 0.001);
200  1 assertEquals(5, ann.getAnnotationForPosition(5).value, 0.001);
201  1 assertEquals(6, ann.getAnnotationForPosition(6).value, 0.001);
202  1 assertNull(ann.getAnnotationForPosition(7));
203  1 assertNull(ann.getAnnotationForPosition(8));
204  1 assertNull(ann.getAnnotationForPosition(9));
205   
206    /*
207    * Expand the subsequence to the full sequence abcDEFghi
208    */
209  1 AlignmentI expanded = AlignmentUtils.expandContext(al, -1);
210  1 assertEquals("abcDEFghi",
211    expanded.getSequenceAt(0).getSequenceAsString());
212   
213    /*
214    * Confirm the alignment and sequence have the same SS annotation,
215    * referencing the expanded sequence
216    */
217  1 ann = expanded.getSequenceAt(0).getAnnotation()[0];
218  1 assertSame(ann, expanded.getAlignmentAnnotation()[0]);
219  1 assertSame(expanded.getSequenceAt(0), ann.sequenceRef);
220   
221    /*
222    * The annotations array should have null values except for annotated
223    * positions
224    */
225  1 assertNull(ann.annotations[0]);
226  1 assertNull(ann.annotations[1]);
227  1 assertNull(ann.annotations[2]);
228  1 assertEquals(4, ann.annotations[3].value, 0.001);
229  1 assertEquals(5, ann.annotations[4].value, 0.001);
230  1 assertEquals(6, ann.annotations[5].value, 0.001);
231  1 assertNull(ann.annotations[6]);
232  1 assertNull(ann.annotations[7]);
233  1 assertNull(ann.annotations[8]);
234   
235    /*
236    * sequence position mappings should be unchanged
237    */
238  1 assertNull(ann.getAnnotationForPosition(1));
239  1 assertNull(ann.getAnnotationForPosition(2));
240  1 assertNull(ann.getAnnotationForPosition(3));
241  1 assertEquals(4, ann.getAnnotationForPosition(4).value, 0.001);
242  1 assertEquals(5, ann.getAnnotationForPosition(5).value, 0.001);
243  1 assertEquals(6, ann.getAnnotationForPosition(6).value, 0.001);
244  1 assertNull(ann.getAnnotationForPosition(7));
245  1 assertNull(ann.getAnnotationForPosition(8));
246  1 assertNull(ann.getAnnotationForPosition(9));
247    }
248   
249    /**
250    * Test method that returns a map of lists of sequences by sequence name.
251    *
252    * @throws IOException
253    */
 
254  1 toggle @Test(groups = { "Functional" })
255    public void testGetSequencesByName() throws IOException
256    {
257  1 final String data = ">Seq1Name\nKQYL\n" + ">Seq2Name\nRFPW\n"
258    + ">Seq1Name\nABCD\n";
259  1 AlignmentI al = loadAlignment(data, FileFormat.Fasta);
260  1 Map<String, List<SequenceI>> map = AlignmentUtils
261    .getSequencesByName(al);
262  1 assertEquals(2, map.keySet().size());
263  1 assertEquals(2, map.get("Seq1Name").size());
264  1 assertEquals("KQYL", map.get("Seq1Name").get(0).getSequenceAsString());
265  1 assertEquals("ABCD", map.get("Seq1Name").get(1).getSequenceAsString());
266  1 assertEquals(1, map.get("Seq2Name").size());
267  1 assertEquals("RFPW", map.get("Seq2Name").get(0).getSequenceAsString());
268    }
269   
270    /**
271    * Helper method to load an alignment and ensure dataset sequences are set up.
272    *
273    * @param data
274    * @param format
275    * TODO
276    * @return
277    * @throws IOException
278    */
 
279  1 toggle protected AlignmentI loadAlignment(final String data, FileFormatI format)
280    throws IOException
281    {
282  1 AlignmentI a = new FormatAdapter().readFile(data, DataSourceType.PASTE,
283    format);
284  1 a.setDataset(null);
285  1 return a;
286    }
287   
288    /**
289    * Test mapping of protein to cDNA, for the case where we have no sequence
290    * cross-references, so mappings are made first-served 1-1 where sequences
291    * translate.
292    *
293    * @throws IOException
294    */
 
295  1 toggle @Test(groups = { "Functional" })
296    public void testMapProteinAlignmentToCdna_noXrefs() throws IOException
297    {
298  1 List<SequenceI> protseqs = new ArrayList<>();
299  1 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
300  1 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
301  1 protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
302  1 AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
303  1 protein.setDataset(null);
304   
305  1 List<SequenceI> dnaseqs = new ArrayList<>();
306  1 dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR
307  1 dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAA")); // = EIQ
308  1 dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ
309  1 dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG")); // = EIQ
310  1 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
311  1 cdna.setDataset(null);
312   
313  1 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
314   
315    // 3 mappings made, each from 1 to 1 sequence
316  1 assertEquals(3, protein.getCodonFrames().size());
317  1 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
318  1 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
319  1 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
320   
321    // V12345 mapped to A22222
322  1 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
323    .get(0);
324  1 assertEquals(1, acf.getdnaSeqs().length);
325  1 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
326    acf.getdnaSeqs()[0]);
327  1 Mapping[] protMappings = acf.getProtMappings();
328  1 assertEquals(1, protMappings.length);
329  1 MapList mapList = protMappings[0].getMap();
330  1 assertEquals(3, mapList.getFromRatio());
331  1 assertEquals(1, mapList.getToRatio());
332  1 assertTrue(
333    Arrays.equals(new int[]
334    { 1, 9 }, mapList.getFromRanges().get(0)));
335  1 assertEquals(1, mapList.getFromRanges().size());
336  1 assertTrue(
337    Arrays.equals(new int[]
338    { 1, 3 }, mapList.getToRanges().get(0)));
339  1 assertEquals(1, mapList.getToRanges().size());
340   
341    // V12346 mapped to A33333
342  1 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
343  1 assertEquals(1, acf.getdnaSeqs().length);
344  1 assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
345    acf.getdnaSeqs()[0]);
346   
347    // V12347 mapped to A11111
348  1 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
349  1 assertEquals(1, acf.getdnaSeqs().length);
350  1 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
351    acf.getdnaSeqs()[0]);
352   
353    // no mapping involving the 'extra' A44444
354  1 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(3)).isEmpty());
355    }
356   
357    /**
358    * Test for the alignSequenceAs method that takes two sequences and a mapping.
359    */
 
360  1 toggle @Test(groups = { "Functional" })
361    public void testAlignSequenceAs_withMapping_noIntrons()
362    {
363  1 MapList map = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 }, 3, 1);
364   
365    /*
366    * No existing gaps in dna:
367    */
368  1 checkAlignSequenceAs("GGGAAA", "-A-L-", false, false, map,
369    "---GGG---AAA");
370   
371    /*
372    * Now introduce gaps in dna but ignore them when realigning.
373    */
374  1 checkAlignSequenceAs("-G-G-G-A-A-A-", "-A-L-", false, false, map,
375    "---GGG---AAA");
376   
377    /*
378    * Now include gaps in dna when realigning. First retaining 'mapped' gaps
379    * only, i.e. those within the exon region.
380    */
381  1 checkAlignSequenceAs("-G-G--G-A--A-A-", "-A-L-", true, false, map,
382    "---G-G--G---A--A-A");
383   
384    /*
385    * Include all gaps in dna when realigning (within and without the exon
386    * region). The leading gap, and the gaps between codons, are subsumed by
387    * the protein alignment gap.
388    */
389  1 checkAlignSequenceAs("-G-GG--AA-A---", "-A-L-", true, true, map,
390    "---G-GG---AA-A---");
391   
392    /*
393    * Include only unmapped gaps in dna when realigning (outside the exon
394    * region). The leading gap, and the gaps between codons, are subsumed by
395    * the protein alignment gap.
396    */
397  1 checkAlignSequenceAs("-G-GG--AA-A-", "-A-L-", false, true, map,
398    "---GGG---AAA---");
399    }
400   
401    /**
402    * Test for the alignSequenceAs method that takes two sequences and a mapping.
403    */
 
404  1 toggle @Test(groups = { "Functional" })
405    public void testAlignSequenceAs_withMapping_withIntrons()
406    {
407    /*
408    * Exons at codon 2 (AAA) and 4 (TTT)
409    */
410  1 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
411    new int[]
412    { 1, 2 }, 3, 1);
413   
414    /*
415    * Simple case: no gaps in dna
416    */
417  1 checkAlignSequenceAs("GGGAAACCCTTTGGG", "--A-L-", false, false, map,
418    "GGG---AAACCCTTTGGG");
419   
420    /*
421    * Add gaps to dna - but ignore when realigning.
422    */
423  1 checkAlignSequenceAs("-G-G-G--A--A---AC-CC-T-TT-GG-G-", "--A-L-", false,
424    false, map, "GGG---AAACCCTTTGGG");
425   
426    /*
427    * Add gaps to dna - include within exons only when realigning.
428    */
429  1 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-", true,
430    false, map, "GGG---A--A---ACCCT-TTGGG");
431   
432    /*
433    * Include gaps outside exons only when realigning.
434    */
435  1 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
436    false, true, map, "-G-G-GAAAC-CCTTT-GG-G-");
437   
438    /*
439    * Include gaps following first intron if we are 'preserving mapped gaps'
440    */
441  1 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-", true,
442    true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
443   
444    /*
445    * Include all gaps in dna when realigning.
446    */
447  1 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-", true,
448    true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
449    }
450   
451    /**
452    * Test for the case where not all of the protein sequence is mapped to cDNA.
453    */
 
454  1 toggle @Test(groups = { "Functional" })
455    public void testAlignSequenceAs_withMapping_withUnmappedProtein()
456    {
457    /*
458    * Exons at codon 2 (AAA) and 4 (TTT) mapped to A and P
459    */
460  1 final MapList map = new MapList(new int[] { 4, 6, 10, 12 },
461    new int[]
462    { 1, 1, 3, 3 }, 3, 1);
463   
464    /*
465    * -L- 'aligns' ccc------
466    */
467  1 checkAlignSequenceAs("gggAAAcccTTTggg", "-A-L-P-", false, false, map,
468    "gggAAAccc------TTTggg");
469    }
470   
471    /**
472    * Helper method that performs and verifies the method under test.
473    *
474    * @param alignee
475    * the sequence to be realigned
476    * @param alignModel
477    * the sequence whose alignment is to be copied
478    * @param preserveMappedGaps
479    * @param preserveUnmappedGaps
480    * @param map
481    * @param expected
482    */
 
483  14 toggle protected void checkAlignSequenceAs(final String alignee,
484    final String alignModel, final boolean preserveMappedGaps,
485    final boolean preserveUnmappedGaps, MapList map,
486    final String expected)
487    {
488  14 SequenceI alignMe = new Sequence("Seq1", alignee);
489  14 alignMe.createDatasetSequence();
490  14 SequenceI alignFrom = new Sequence("Seq2", alignModel);
491  14 alignFrom.createDatasetSequence();
492  14 AlignedCodonFrame acf = new AlignedCodonFrame();
493  14 acf.addMap(alignMe.getDatasetSequence(), alignFrom.getDatasetSequence(),
494    map);
495   
496  14 AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "---", '-',
497    preserveMappedGaps, preserveUnmappedGaps);
498  14 assertEquals(expected, alignMe.getSequenceAsString());
499    }
500   
501    /**
502    * Test for the alignSequenceAs method where we preserve gaps in introns only.
503    */
 
504  1 toggle @Test(groups = { "Functional" })
505    public void testAlignSequenceAs_keepIntronGapsOnly()
506    {
507   
508    /*
509    * Intron GGGAAA followed by exon CCCTTT
510    */
511  1 MapList map = new MapList(new int[] { 7, 12 }, new int[] { 1, 2 }, 3,
512    1);
513   
514  1 checkAlignSequenceAs("GG-G-AA-A-C-CC-T-TT", "AL", false, true, map,
515    "GG-G-AA-ACCCTTT");
516    }
517   
518    /**
519    * Test the method that realigns protein to match mapped codon alignment.
520    */
 
521  1 toggle @Test(groups = { "Functional" })
522    public void testAlignProteinAsDna()
523    {
524    // seq1 codons are [1,2,3] [4,5,6] [7,8,9] [10,11,12]
525  1 SequenceI dna1 = new Sequence("Seq1", "TGCCATTACCAG-");
526    // seq2 codons are [1,3,4] [5,6,7] [8,9,10] [11,12,13]
527  1 SequenceI dna2 = new Sequence("Seq2", "T-GCCATTACCAG");
528    // seq3 codons are [1,2,3] [4,5,7] [8,9,10] [11,12,13]
529  1 SequenceI dna3 = new Sequence("Seq3", "TGCCA-TTACCAG");
530  1 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
531  1 dna.setDataset(null);
532   
533    // protein alignment will be realigned like dna
534  1 SequenceI prot1 = new Sequence("Seq1", "CHYQ");
535  1 SequenceI prot2 = new Sequence("Seq2", "CHYQ");
536  1 SequenceI prot3 = new Sequence("Seq3", "CHYQ");
537  1 SequenceI prot4 = new Sequence("Seq4", "R-QSV"); // unmapped, unchanged
538  1 AlignmentI protein = new Alignment(
539    new SequenceI[]
540    { prot1, prot2, prot3, prot4 });
541  1 protein.setDataset(null);
542   
543  1 MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3,
544    1);
545  1 AlignedCodonFrame acf = new AlignedCodonFrame();
546  1 acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
547  1 acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map);
548  1 acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map);
549  1 ArrayList<AlignedCodonFrame> acfs = new ArrayList<>();
550  1 acfs.add(acf);
551  1 protein.setCodonFrames(acfs);
552   
553    /*
554    * Translated codon order is [1,2,3] [1,3,4] [4,5,6] [4,5,7] [5,6,7] [7,8,9]
555    * [8,9,10] [10,11,12] [11,12,13]
556    */
557  1 AlignmentUtils.alignProteinAsDna(protein, dna);
558  1 assertEquals("C-H--Y-Q-", prot1.getSequenceAsString());
559  1 assertEquals("-C--H-Y-Q", prot2.getSequenceAsString());
560  1 assertEquals("C--H--Y-Q", prot3.getSequenceAsString());
561  1 assertEquals("R-QSV", prot4.getSequenceAsString());
562    }
563   
564    /**
565    * Test the method that tests whether a CDNA sequence translates to a protein
566    * sequence
567    */
 
568  1 toggle @Test(groups = { "Functional" })
569    public void testTranslatesAs()
570    {
571    // null arguments check
572  1 assertFalse(AlignmentUtils.translatesAs(null, 0, null));
573  1 assertFalse(AlignmentUtils.translatesAs(new char[] { 't' }, 0, null));
574  1 assertFalse(AlignmentUtils.translatesAs(null, 0, new char[] { 'a' }));
575   
576    // straight translation
577  1 assertTrue(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
578    "FPKG".toCharArray()));
579    // with extra start codon (not in protein)
580  1 assertTrue(AlignmentUtils.translatesAs("atgtttcccaaaggg".toCharArray(),
581    3, "FPKG".toCharArray()));
582    // with stop codon1 (not in protein)
583  1 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtaa".toCharArray(),
584    0, "FPKG".toCharArray()));
585    // with stop codon1 (in protein as *)
586  1 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtaa".toCharArray(),
587    0, "FPKG*".toCharArray()));
588    // with stop codon2 (not in protein)
589  1 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtag".toCharArray(),
590    0, "FPKG".toCharArray()));
591    // with stop codon3 (not in protein)
592  1 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtga".toCharArray(),
593    0, "FPKG".toCharArray()));
594    // with start and stop codon1
595  1 assertTrue(AlignmentUtils.translatesAs(
596    "atgtttcccaaagggtaa".toCharArray(), 3, "FPKG".toCharArray()));
597    // with start and stop codon1 (in protein as *)
598  1 assertTrue(AlignmentUtils.translatesAs(
599    "atgtttcccaaagggtaa".toCharArray(), 3, "FPKG*".toCharArray()));
600    // with start and stop codon2
601  1 assertTrue(AlignmentUtils.translatesAs(
602    "atgtttcccaaagggtag".toCharArray(), 3, "FPKG".toCharArray()));
603    // with start and stop codon3
604  1 assertTrue(AlignmentUtils.translatesAs(
605    "atgtttcccaaagggtga".toCharArray(), 3, "FPKG".toCharArray()));
606   
607    // with embedded stop codons
608  1 assertTrue(AlignmentUtils.translatesAs(
609    "atgtttTAGcccaaaTAAgggtga".toCharArray(), 3,
610    "F*PK*G".toCharArray()));
611   
612    // wrong protein
613  1 assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
614    "FPMG".toCharArray()));
615   
616    // truncated dna
617  1 assertFalse(AlignmentUtils.translatesAs("tttcccaaagg".toCharArray(), 0,
618    "FPKG".toCharArray()));
619   
620    // truncated protein
621  1 assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
622    "FPK".toCharArray()));
623   
624    // overlong dna (doesn't end in stop codon)
625  1 assertFalse(AlignmentUtils.translatesAs("tttcccaaagggttt".toCharArray(),
626    0, "FPKG".toCharArray()));
627   
628    // dna + stop codon + more
629  1 assertFalse(AlignmentUtils.translatesAs(
630    "tttcccaaagggttaga".toCharArray(), 0, "FPKG".toCharArray()));
631   
632    // overlong protein
633  1 assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
634    "FPKGQ".toCharArray()));
635    }
636   
637    /**
638    * Test mapping of protein to cDNA, for cases where the cDNA has start and/or
639    * stop codons in addition to the protein coding sequence.
640    *
641    * @throws IOException
642    */
 
643  1 toggle @Test(groups = { "Functional" })
644    public void testMapProteinAlignmentToCdna_withStartAndStopCodons()
645    throws IOException
646    {
647  1 List<SequenceI> protseqs = new ArrayList<>();
648  1 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
649  1 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
650  1 protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
651  1 AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
652  1 protein.setDataset(null);
653   
654  1 List<SequenceI> dnaseqs = new ArrayList<>();
655    // start + SAR:
656  1 dnaseqs.add(new Sequence("EMBL|A11111", "ATGTCAGCACGC"));
657    // = EIQ + stop
658  1 dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAATAA"));
659    // = start +EIQ + stop
660  1 dnaseqs.add(new Sequence("EMBL|A33333", "ATGGAAATCCAGTAG"));
661  1 dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG"));
662  1 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
663  1 cdna.setDataset(null);
664   
665  1 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
666   
667    // 3 mappings made, each from 1 to 1 sequence
668  1 assertEquals(3, protein.getCodonFrames().size());
669  1 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
670  1 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
671  1 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
672   
673    // V12345 mapped from A22222
674  1 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
675    .get(0);
676  1 assertEquals(1, acf.getdnaSeqs().length);
677  1 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
678    acf.getdnaSeqs()[0]);
679  1 Mapping[] protMappings = acf.getProtMappings();
680  1 assertEquals(1, protMappings.length);
681  1 MapList mapList = protMappings[0].getMap();
682  1 assertEquals(3, mapList.getFromRatio());
683  1 assertEquals(1, mapList.getToRatio());
684  1 assertTrue(
685    Arrays.equals(new int[]
686    { 1, 9 }, mapList.getFromRanges().get(0)));
687  1 assertEquals(1, mapList.getFromRanges().size());
688  1 assertTrue(
689    Arrays.equals(new int[]
690    { 1, 3 }, mapList.getToRanges().get(0)));
691  1 assertEquals(1, mapList.getToRanges().size());
692   
693    // V12346 mapped from A33333 starting position 4
694  1 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
695  1 assertEquals(1, acf.getdnaSeqs().length);
696  1 assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
697    acf.getdnaSeqs()[0]);
698  1 protMappings = acf.getProtMappings();
699  1 assertEquals(1, protMappings.length);
700  1 mapList = protMappings[0].getMap();
701  1 assertEquals(3, mapList.getFromRatio());
702  1 assertEquals(1, mapList.getToRatio());
703  1 assertTrue(
704    Arrays.equals(new int[]
705    { 4, 12 }, mapList.getFromRanges().get(0)));
706  1 assertEquals(1, mapList.getFromRanges().size());
707  1 assertTrue(
708    Arrays.equals(new int[]
709    { 1, 3 }, mapList.getToRanges().get(0)));
710  1 assertEquals(1, mapList.getToRanges().size());
711   
712    // V12347 mapped to A11111 starting position 4
713  1 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
714  1 assertEquals(1, acf.getdnaSeqs().length);
715  1 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
716    acf.getdnaSeqs()[0]);
717  1 protMappings = acf.getProtMappings();
718  1 assertEquals(1, protMappings.length);
719  1 mapList = protMappings[0].getMap();
720  1 assertEquals(3, mapList.getFromRatio());
721  1 assertEquals(1, mapList.getToRatio());
722  1 assertTrue(
723    Arrays.equals(new int[]
724    { 4, 12 }, mapList.getFromRanges().get(0)));
725  1 assertEquals(1, mapList.getFromRanges().size());
726  1 assertTrue(
727    Arrays.equals(new int[]
728    { 1, 3 }, mapList.getToRanges().get(0)));
729  1 assertEquals(1, mapList.getToRanges().size());
730   
731    // no mapping involving the 'extra' A44444
732  1 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(3)).isEmpty());
733    }
734   
735    /**
736    * Test mapping of protein to cDNA, for the case where we have some sequence
737    * cross-references. Verify that 1-to-many mappings are made where
738    * cross-references exist and sequences are mappable.
739    *
740    * @throws IOException
741    */
 
742  1 toggle @Test(groups = { "Functional" })
743    public void testMapProteinAlignmentToCdna_withXrefs() throws IOException
744    {
745  1 List<SequenceI> protseqs = new ArrayList<>();
746  1 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
747  1 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
748  1 protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
749  1 AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
750  1 protein.setDataset(null);
751   
752  1 List<SequenceI> dnaseqs = new ArrayList<>();
753  1 dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR
754  1 dnaseqs.add(new Sequence("EMBL|A22222", "ATGGAGATACAA")); // = start + EIQ
755  1 dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ
756  1 dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG")); // = EIQ
757  1 dnaseqs.add(new Sequence("EMBL|A55555", "GAGATTCAG")); // = EIQ
758  1 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[5]));
759  1 cdna.setDataset(null);
760   
761    // Xref A22222 to V12345 (should get mapped)
762  1 dnaseqs.get(1).addDBRef(new DBRefEntry("UNIPROT", "1", "V12345"));
763    // Xref V12345 to A44444 (should get mapped)
764  1 protseqs.get(0).addDBRef(new DBRefEntry("EMBL", "1", "A44444"));
765    // Xref A33333 to V12347 (sequence mismatch - should not get mapped)
766  1 dnaseqs.get(2).addDBRef(new DBRefEntry("UNIPROT", "1", "V12347"));
767    // as V12345 is mapped to A22222 and A44444, this leaves V12346 unmapped.
768    // it should get paired up with the unmapped A33333
769    // A11111 should be mapped to V12347
770    // A55555 is spare and has no xref so is not mapped
771   
772  1 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
773   
774    // 4 protein mappings made for 3 proteins, 2 to V12345, 1 each to V12346/7
775  1 assertEquals(3, protein.getCodonFrames().size());
776  1 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
777  1 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
778  1 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
779   
780    // one mapping for each of the first 4 cDNA sequences
781  1 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(0)).size());
782  1 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(1)).size());
783  1 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(2)).size());
784  1 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(3)).size());
785   
786    // V12345 mapped to A22222 and A44444
787  1 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
788    .get(0);
789  1 assertEquals(2, acf.getdnaSeqs().length);
790  1 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
791    acf.getdnaSeqs()[0]);
792  1 assertEquals(cdna.getSequenceAt(3).getDatasetSequence(),
793    acf.getdnaSeqs()[1]);
794   
795    // V12346 mapped to A33333
796  1 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
797  1 assertEquals(1, acf.getdnaSeqs().length);
798  1 assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
799    acf.getdnaSeqs()[0]);
800   
801    // V12347 mapped to A11111
802  1 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
803  1 assertEquals(1, acf.getdnaSeqs().length);
804  1 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
805    acf.getdnaSeqs()[0]);
806   
807    // no mapping involving the 'extra' A55555
808  1 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(4)).isEmpty());
809    }
810   
811    /**
812    * Test mapping of protein to cDNA, for the case where we have some sequence
813    * cross-references. Verify that once we have made an xref mapping we don't
814    * also map un-xrefd sequeces.
815    *
816    * @throws IOException
817    */
 
818  1 toggle @Test(groups = { "Functional" })
819    public void testMapProteinAlignmentToCdna_prioritiseXrefs()
820    throws IOException
821    {
822  1 List<SequenceI> protseqs = new ArrayList<>();
823  1 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
824  1 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
825  1 AlignmentI protein = new Alignment(
826    protseqs.toArray(new SequenceI[protseqs.size()]));
827  1 protein.setDataset(null);
828   
829  1 List<SequenceI> dnaseqs = new ArrayList<>();
830  1 dnaseqs.add(new Sequence("EMBL|A11111", "GAAATCCAG")); // = EIQ
831  1 dnaseqs.add(new Sequence("EMBL|A22222", "GAAATTCAG")); // = EIQ
832  1 AlignmentI cdna = new Alignment(
833    dnaseqs.toArray(new SequenceI[dnaseqs.size()]));
834  1 cdna.setDataset(null);
835   
836    // Xref A22222 to V12345 (should get mapped)
837    // A11111 should then be mapped to the unmapped V12346
838  1 dnaseqs.get(1).addDBRef(new DBRefEntry("UNIPROT", "1", "V12345"));
839   
840  1 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
841   
842    // 2 protein mappings made
843  1 assertEquals(2, protein.getCodonFrames().size());
844  1 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
845  1 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
846   
847    // one mapping for each of the cDNA sequences
848  1 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(0)).size());
849  1 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(1)).size());
850   
851    // V12345 mapped to A22222
852  1 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
853    .get(0);
854  1 assertEquals(1, acf.getdnaSeqs().length);
855  1 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
856    acf.getdnaSeqs()[0]);
857   
858    // V12346 mapped to A11111
859  1 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
860  1 assertEquals(1, acf.getdnaSeqs().length);
861  1 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
862    acf.getdnaSeqs()[0]);
863    }
864   
865    /**
866    * Test the method that shows or hides sequence annotations by type(s) and
867    * selection group.
868    */
 
869  1 toggle @Test(groups = { "Functional" })
870    public void testShowOrHideSequenceAnnotations()
871    {
872  1 SequenceI seq1 = new Sequence("Seq1", "AAA");
873  1 SequenceI seq2 = new Sequence("Seq2", "BBB");
874  1 SequenceI seq3 = new Sequence("Seq3", "CCC");
875  1 Annotation[] anns = new Annotation[] { new Annotation(2f) };
876  1 AlignmentAnnotation ann1 = new AlignmentAnnotation("Structure", "ann1",
877    anns);
878  1 ann1.setSequenceRef(seq1);
879  1 AlignmentAnnotation ann2 = new AlignmentAnnotation("Structure", "ann2",
880    anns);
881  1 ann2.setSequenceRef(seq2);
882  1 AlignmentAnnotation ann3 = new AlignmentAnnotation("Structure", "ann3",
883    anns);
884  1 AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "ann4",
885    anns);
886  1 ann4.setSequenceRef(seq1);
887  1 AlignmentAnnotation ann5 = new AlignmentAnnotation("Temp", "ann5",
888    anns);
889  1 ann5.setSequenceRef(seq2);
890  1 AlignmentAnnotation ann6 = new AlignmentAnnotation("Temp", "ann6",
891    anns);
892  1 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
893  1 al.addAnnotation(ann1); // Structure for Seq1
894  1 al.addAnnotation(ann2); // Structure for Seq2
895  1 al.addAnnotation(ann3); // Structure for no sequence
896  1 al.addAnnotation(ann4); // Temp for seq1
897  1 al.addAnnotation(ann5); // Temp for seq2
898  1 al.addAnnotation(ann6); // Temp for no sequence
899  1 List<String> types = new ArrayList<>();
900  1 List<SequenceI> scope = new ArrayList<>();
901   
902    /*
903    * Set all sequence related Structure to hidden (ann1, ann2)
904    */
905  1 types.add("Structure");
906  1 AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, false,
907    false);
908  1 assertFalse(ann1.visible);
909  1 assertFalse(ann2.visible);
910  1 assertTrue(ann3.visible); // not sequence-related, not affected
911  1 assertTrue(ann4.visible); // not Structure, not affected
912  1 assertTrue(ann5.visible); // "
913  1 assertTrue(ann6.visible); // not sequence-related, not affected
914   
915    /*
916    * Set Temp in {seq1, seq3} to hidden
917    */
918  1 types.clear();
919  1 types.add("Temp");
920  1 scope.add(seq1);
921  1 scope.add(seq3);
922  1 AlignmentUtils.showOrHideSequenceAnnotations(al, types, scope, false,
923    false);
924  1 assertFalse(ann1.visible); // unchanged
925  1 assertFalse(ann2.visible); // unchanged
926  1 assertTrue(ann3.visible); // not sequence-related, not affected
927  1 assertFalse(ann4.visible); // Temp for seq1 hidden
928  1 assertTrue(ann5.visible); // not in scope, not affected
929  1 assertTrue(ann6.visible); // not sequence-related, not affected
930   
931    /*
932    * Set Temp in all sequences to hidden
933    */
934  1 types.clear();
935  1 types.add("Temp");
936  1 scope.add(seq1);
937  1 scope.add(seq3);
938  1 AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, false,
939    false);
940  1 assertFalse(ann1.visible); // unchanged
941  1 assertFalse(ann2.visible); // unchanged
942  1 assertTrue(ann3.visible); // not sequence-related, not affected
943  1 assertFalse(ann4.visible); // Temp for seq1 hidden
944  1 assertFalse(ann5.visible); // Temp for seq2 hidden
945  1 assertTrue(ann6.visible); // not sequence-related, not affected
946   
947    /*
948    * Set all types in {seq1, seq3} to visible
949    */
950  1 types.clear();
951  1 scope.clear();
952  1 scope.add(seq1);
953  1 scope.add(seq3);
954  1 AlignmentUtils.showOrHideSequenceAnnotations(al, types, scope, true,
955    true);
956  1 assertTrue(ann1.visible); // Structure for seq1 set visible
957  1 assertFalse(ann2.visible); // not in scope, unchanged
958  1 assertTrue(ann3.visible); // not sequence-related, not affected
959  1 assertTrue(ann4.visible); // Temp for seq1 set visible
960  1 assertFalse(ann5.visible); // not in scope, unchanged
961  1 assertTrue(ann6.visible); // not sequence-related, not affected
962   
963    /*
964    * Set all types in all scope to hidden
965    */
966  1 AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, true,
967    false);
968  1 assertFalse(ann1.visible);
969  1 assertFalse(ann2.visible);
970  1 assertTrue(ann3.visible); // not sequence-related, not affected
971  1 assertFalse(ann4.visible);
972  1 assertFalse(ann5.visible);
973  1 assertTrue(ann6.visible); // not sequence-related, not affected
974    }
975   
976    /**
977    * Tests for the method that checks if one sequence cross-references another
978    */
 
979  1 toggle @Test(groups = { "Functional" })
980    public void testHasCrossRef()
981    {
982  1 assertFalse(AlignmentUtils.hasCrossRef(null, null));
983  1 SequenceI seq1 = new Sequence("EMBL|A12345", "ABCDEF");
984  1 assertFalse(AlignmentUtils.hasCrossRef(seq1, null));
985  1 assertFalse(AlignmentUtils.hasCrossRef(null, seq1));
986  1 SequenceI seq2 = new Sequence("UNIPROT|V20192", "ABCDEF");
987  1 assertFalse(AlignmentUtils.hasCrossRef(seq1, seq2));
988   
989    // different ref
990  1 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "v20193"));
991  1 assertFalse(AlignmentUtils.hasCrossRef(seq1, seq2));
992   
993    // case-insensitive; version number is ignored
994  1 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "v20192"));
995  1 assertTrue(AlignmentUtils.hasCrossRef(seq1, seq2));
996   
997    // right case!
998  1 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
999  1 assertTrue(AlignmentUtils.hasCrossRef(seq1, seq2));
1000    // test is one-way only
1001  1 assertFalse(AlignmentUtils.hasCrossRef(seq2, seq1));
1002    }
1003   
1004    /**
1005    * Tests for the method that checks if either sequence cross-references the
1006    * other
1007    */
 
1008  1 toggle @Test(groups = { "Functional" })
1009    public void testHaveCrossRef()
1010    {
1011  1 assertFalse(AlignmentUtils.hasCrossRef(null, null));
1012  1 SequenceI seq1 = new Sequence("EMBL|A12345", "ABCDEF");
1013  1 assertFalse(AlignmentUtils.haveCrossRef(seq1, null));
1014  1 assertFalse(AlignmentUtils.haveCrossRef(null, seq1));
1015  1 SequenceI seq2 = new Sequence("UNIPROT|V20192", "ABCDEF");
1016  1 assertFalse(AlignmentUtils.haveCrossRef(seq1, seq2));
1017   
1018  1 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
1019  1 assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
1020    // next is true for haveCrossRef, false for hasCrossRef
1021  1 assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
1022   
1023    // now the other way round
1024  1 seq1.setDBRefs(null);
1025  1 seq2.addDBRef(new DBRefEntry("EMBL", "1", "A12345"));
1026  1 assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
1027  1 assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
1028   
1029    // now both ways
1030  1 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
1031  1 assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
1032  1 assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
1033    }
1034   
1035    /**
1036    * Test the method that extracts the cds-only part of a dna alignment.
1037    */
 
1038  1 toggle @Test(groups = { "Functional" })
1039    public void testMakeCdsAlignment()
1040    {
1041    /*
1042    * scenario:
1043    * dna1 --> [4, 6] [10,12] --> pep1
1044    * dna2 --> [1, 3] [7, 9] [13,15] --> pep2
1045    */
1046  1 SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
1047  1 SequenceI dna2 = new Sequence("dna2", "GGGcccTTTaaaCCC");
1048  1 SequenceI pep1 = new Sequence("pep1", "GF");
1049  1 SequenceI pep2 = new Sequence("pep2", "GFP");
1050  1 pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "pep1"));
1051  1 pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "pep2"));
1052  1 dna1.createDatasetSequence();
1053  1 dna2.createDatasetSequence();
1054  1 pep1.createDatasetSequence();
1055  1 pep2.createDatasetSequence();
1056  1 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
1057  1 dna.setDataset(null);
1058   
1059    /*
1060    * put a variant feature on dna2 base 8
1061    * - should transfer to cds2 base 5
1062    */
1063  1 dna2.addSequenceFeature(
1064    new SequenceFeature("variant", "hgmd", 8, 8, 0f, null));
1065   
1066    /*
1067    * need a sourceDbRef if we are to construct dbrefs to the CDS
1068    * sequence from the dna contig sequences
1069    */
1070  1 DBRefEntry dbref = new DBRefEntry("ENSEMBL", "0", "dna1");
1071  1 dna1.getDatasetSequence().addDBRef(dbref);
1072  1 org.testng.Assert.assertEquals(dbref, dna1.getPrimaryDBRefs().get(0));
1073  1 dbref = new DBRefEntry("ENSEMBL", "0", "dna2");
1074  1 dna2.getDatasetSequence().addDBRef(dbref);
1075  1 org.testng.Assert.assertEquals(dbref, dna2.getPrimaryDBRefs().get(0));
1076   
1077    /*
1078    * CDS sequences are 'discovered' from dna-to-protein mappings on the alignment
1079    * dataset (e.g. added from dbrefs by CrossRef.findXrefSequences)
1080    */
1081  1 MapList mapfordna1 = new MapList(new int[] { 4, 6, 10, 12 },
1082    new int[]
1083    { 1, 2 }, 3, 1);
1084  1 AlignedCodonFrame acf = new AlignedCodonFrame();
1085  1 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
1086    mapfordna1);
1087  1 dna.addCodonFrame(acf);
1088  1 MapList mapfordna2 = new MapList(new int[] { 1, 3, 7, 9, 13, 15 },
1089    new int[]
1090    { 1, 3 }, 3, 1);
1091  1 acf = new AlignedCodonFrame();
1092  1 acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(),
1093    mapfordna2);
1094  1 dna.addCodonFrame(acf);
1095   
1096    /*
1097    * In this case, mappings originally came from matching Uniprot accessions
1098    * - so need an xref on dna involving those regions.
1099    * These are normally constructed from CDS annotation
1100    */
1101  1 DBRefEntry dna1xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep1",
1102    new Mapping(mapfordna1));
1103  1 dna1.addDBRef(dna1xref);
1104  1 assertEquals(2, dna1.getDBRefs().size()); // to self and to pep1
1105  1 DBRefEntry dna2xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep2",
1106    new Mapping(mapfordna2));
1107  1 dna2.addDBRef(dna2xref);
1108  1 assertEquals(2, dna2.getDBRefs().size()); // to self and to pep2
1109   
1110    /*
1111    * execute method under test:
1112    */
1113  1 AlignmentI cds = AlignmentUtils
1114    .makeCdsAlignment(new SequenceI[]
1115    { dna1, dna2 }, dna.getDataset(), null);
1116   
1117    /*
1118    * verify cds sequences
1119    */
1120  1 assertEquals(2, cds.getSequences().size());
1121  1 assertEquals("GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
1122  1 assertEquals("GGGTTTCCC", cds.getSequenceAt(1).getSequenceAsString());
1123   
1124    /*
1125    * verify shared, extended alignment dataset
1126    */
1127  1 assertSame(dna.getDataset(), cds.getDataset());
1128  1 SequenceI cds1Dss = cds.getSequenceAt(0).getDatasetSequence();
1129  1 SequenceI cds2Dss = cds.getSequenceAt(1).getDatasetSequence();
1130  1 assertTrue(dna.getDataset().getSequences().contains(cds1Dss));
1131  1 assertTrue(dna.getDataset().getSequences().contains(cds2Dss));
1132   
1133    /*
1134    * verify CDS has a dbref with mapping to peptide
1135    */
1136  1 assertNotNull(cds1Dss.getDBRefs());
1137  1 assertEquals(2, cds1Dss.getDBRefs().size());
1138  1 dbref = cds1Dss.getDBRefs().get(0);
1139  1 assertEquals(dna1xref.getSource(), dbref.getSource());
1140    // version is via ensembl's primary ref
1141  1 assertEquals(dna1xref.getVersion(), dbref.getVersion());
1142  1 assertEquals(dna1xref.getAccessionId(), dbref.getAccessionId());
1143  1 assertNotNull(dbref.getMap());
1144  1 assertSame(pep1.getDatasetSequence(), dbref.getMap().getTo());
1145  1 MapList cdsMapping = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 },
1146    3, 1);
1147  1 assertEquals(cdsMapping, dbref.getMap().getMap());
1148   
1149    /*
1150    * verify peptide has added a dbref with reverse mapping to CDS
1151    */
1152  1 assertNotNull(pep1.getDBRefs());
1153    // FIXME pep1.getDBRefs() is 1 - is that the correct behaviour ?
1154  1 assertEquals(2, pep1.getDBRefs().size());
1155  1 dbref = pep1.getDBRefs().get(1);
1156  1 assertEquals("ENSEMBL", dbref.getSource());
1157  1 assertEquals("0", dbref.getVersion());
1158  1 assertEquals("CDS|dna1", dbref.getAccessionId());
1159  1 assertNotNull(dbref.getMap());
1160  1 assertSame(cds1Dss, dbref.getMap().getTo());
1161  1 assertEquals(cdsMapping.getInverse(), dbref.getMap().getMap());
1162   
1163    /*
1164    * verify cDNA has added a dbref with mapping to CDS
1165    */
1166  1 assertEquals(3, dna1.getDBRefs().size());
1167  1 DBRefEntry dbRefEntry = dna1.getDBRefs().get(2);
1168  1 assertSame(cds1Dss, dbRefEntry.getMap().getTo());
1169  1 MapList dnaToCdsMapping = new MapList(new int[] { 4, 6, 10, 12 },
1170    new int[]
1171    { 1, 6 }, 1, 1);
1172  1 assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap());
1173  1 assertEquals(3, dna2.getDBRefs().size());
1174  1 dbRefEntry = dna2.getDBRefs().get(2);
1175  1 assertSame(cds2Dss, dbRefEntry.getMap().getTo());
1176  1 dnaToCdsMapping = new MapList(new int[] { 1, 3, 7, 9, 13, 15 },
1177    new int[]
1178    { 1, 9 }, 1, 1);
1179  1 assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap());
1180   
1181    /*
1182    * verify CDS has added a dbref with mapping to cDNA
1183    */
1184  1 assertEquals(2, cds1Dss.getDBRefs().size());
1185  1 dbRefEntry = cds1Dss.getDBRefs().get(1);
1186  1 assertSame(dna1.getDatasetSequence(), dbRefEntry.getMap().getTo());
1187  1 MapList cdsToDnaMapping = new MapList(new int[] { 1, 6 },
1188    new int[]
1189    { 4, 6, 10, 12 }, 1, 1);
1190  1 assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap());
1191  1 assertEquals(2, cds2Dss.getDBRefs().size());
1192  1 dbRefEntry = cds2Dss.getDBRefs().get(1);
1193  1 assertSame(dna2.getDatasetSequence(), dbRefEntry.getMap().getTo());
1194  1 cdsToDnaMapping = new MapList(new int[] { 1, 9 },
1195    new int[]
1196    { 1, 3, 7, 9, 13, 15 }, 1, 1);
1197  1 assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap());
1198   
1199    /*
1200    * Verify mappings from CDS to peptide, cDNA to CDS, and cDNA to peptide
1201    * the mappings are on the shared alignment dataset
1202    * 6 mappings, 2*(DNA->CDS), 2*(DNA->Pep), 2*(CDS->Pep)
1203    */
1204  1 List<AlignedCodonFrame> cdsMappings = cds.getDataset().getCodonFrames();
1205  1 assertEquals(6, cdsMappings.size());
1206   
1207    /*
1208    * verify that mapping sets for dna and cds alignments are different
1209    * [not current behaviour - all mappings are on the alignment dataset]
1210    */
1211    // select -> subselect type to test.
1212    // Assert.assertNotSame(dna.getCodonFrames(), cds.getCodonFrames());
1213    // assertEquals(4, dna.getCodonFrames().size());
1214    // assertEquals(4, cds.getCodonFrames().size());
1215   
1216    /*
1217    * Two mappings involve pep1 (dna to pep1, cds to pep1)
1218    * Mapping from pep1 to GGGTTT in first new exon sequence
1219    */
1220  1 List<AlignedCodonFrame> pep1Mappings = MappingUtils
1221    .findMappingsForSequence(pep1, cdsMappings);
1222  1 assertEquals(2, pep1Mappings.size());
1223  1 List<AlignedCodonFrame> mappings = MappingUtils
1224    .findMappingsForSequence(cds.getSequenceAt(0), pep1Mappings);
1225  1 assertEquals(1, mappings.size());
1226   
1227    // map G to GGG
1228  1 SearchResultsI sr = MappingUtils.buildSearchResults(pep1, 1, mappings);
1229  1 assertEquals(1, sr.getResults().size());
1230  1 SearchResultMatchI m = sr.getResults().get(0);
1231  1 assertSame(cds1Dss, m.getSequence());
1232  1 assertEquals(1, m.getStart());
1233  1 assertEquals(3, m.getEnd());
1234    // map F to TTT
1235  1 sr = MappingUtils.buildSearchResults(pep1, 2, mappings);
1236  1 m = sr.getResults().get(0);
1237  1 assertSame(cds1Dss, m.getSequence());
1238  1 assertEquals(4, m.getStart());
1239  1 assertEquals(6, m.getEnd());
1240   
1241    /*
1242    * Two mappings involve pep2 (dna to pep2, cds to pep2)
1243    * Verify mapping from pep2 to GGGTTTCCC in second new exon sequence
1244    */
1245  1 List<AlignedCodonFrame> pep2Mappings = MappingUtils
1246    .findMappingsForSequence(pep2, cdsMappings);
1247  1 assertEquals(2, pep2Mappings.size());
1248  1 mappings = MappingUtils.findMappingsForSequence(cds.getSequenceAt(1),
1249    pep2Mappings);
1250  1 assertEquals(1, mappings.size());
1251    // map G to GGG
1252  1 sr = MappingUtils.buildSearchResults(pep2, 1, mappings);
1253  1 assertEquals(1, sr.getResults().size());
1254  1 m = sr.getResults().get(0);
1255  1 assertSame(cds2Dss, m.getSequence());
1256  1 assertEquals(1, m.getStart());
1257  1 assertEquals(3, m.getEnd());
1258    // map F to TTT
1259  1 sr = MappingUtils.buildSearchResults(pep2, 2, mappings);
1260  1 m = sr.getResults().get(0);
1261  1 assertSame(cds2Dss, m.getSequence());
1262  1 assertEquals(4, m.getStart());
1263  1 assertEquals(6, m.getEnd());
1264    // map P to CCC
1265  1 sr = MappingUtils.buildSearchResults(pep2, 3, mappings);
1266  1 m = sr.getResults().get(0);
1267  1 assertSame(cds2Dss, m.getSequence());
1268  1 assertEquals(7, m.getStart());
1269  1 assertEquals(9, m.getEnd());
1270   
1271    /*
1272    * check cds2 acquired a variant feature in position 5
1273    */
1274  1 List<SequenceFeature> sfs = cds2Dss.getSequenceFeatures();
1275  1 assertNotNull(sfs);
1276  1 assertEquals(1, sfs.size());
1277  1 assertEquals("variant", sfs.get(0).type);
1278  1 assertEquals(5, sfs.get(0).begin);
1279  1 assertEquals(5, sfs.get(0).end);
1280    }
1281   
1282    /**
1283    * Test the method that makes a cds-only alignment from a DNA sequence and its
1284    * product mappings, for the case where there are multiple exon mappings to
1285    * different protein products.
1286    */
 
1287  1 toggle @Test(groups = { "Functional" })
1288    public void testMakeCdsAlignment_multipleProteins()
1289    {
1290  1 SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
1291  1 SequenceI pep1 = new Sequence("pep1", "GF"); // GGGTTT
1292  1 SequenceI pep2 = new Sequence("pep2", "KP"); // aaaccc
1293  1 SequenceI pep3 = new Sequence("pep3", "KF"); // aaaTTT
1294  1 dna1.createDatasetSequence();
1295  1 pep1.createDatasetSequence();
1296  1 pep2.createDatasetSequence();
1297  1 pep3.createDatasetSequence();
1298  1 pep1.getDatasetSequence()
1299    .addDBRef(new DBRefEntry("EMBLCDS", "2", "A12345"));
1300  1 pep2.getDatasetSequence()
1301    .addDBRef(new DBRefEntry("EMBLCDS", "3", "A12346"));
1302  1 pep3.getDatasetSequence()
1303    .addDBRef(new DBRefEntry("EMBLCDS", "4", "A12347"));
1304   
1305    /*
1306    * Create the CDS alignment
1307    */
1308  1 AlignmentI dna = new Alignment(new SequenceI[] { dna1 });
1309  1 dna.setDataset(null);
1310   
1311    /*
1312    * Make the mappings from dna to protein
1313    */
1314    // map ...GGG...TTT to GF
1315  1 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1316    new int[]
1317    { 1, 2 }, 3, 1);
1318  1 AlignedCodonFrame acf = new AlignedCodonFrame();
1319  1 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
1320  1 dna.addCodonFrame(acf);
1321   
1322    // map aaa...ccc to KP
1323  1 map = new MapList(new int[] { 1, 3, 7, 9 }, new int[] { 1, 2 }, 3, 1);
1324  1 acf = new AlignedCodonFrame();
1325  1 acf.addMap(dna1.getDatasetSequence(), pep2.getDatasetSequence(), map);
1326  1 dna.addCodonFrame(acf);
1327   
1328    // map aaa......TTT to KF
1329  1 map = new MapList(new int[] { 1, 3, 10, 12 }, new int[] { 1, 2 }, 3, 1);
1330  1 acf = new AlignedCodonFrame();
1331  1 acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map);
1332  1 dna.addCodonFrame(acf);
1333   
1334    /*
1335    * execute method under test
1336    */
1337  1 AlignmentI cdsal = AlignmentUtils
1338    .makeCdsAlignment(new SequenceI[]
1339    { dna1 }, dna.getDataset(), null);
1340   
1341    /*
1342    * Verify we have 3 cds sequences, mapped to pep1/2/3 respectively
1343    */
1344  1 List<SequenceI> cds = cdsal.getSequences();
1345  1 assertEquals(3, cds.size());
1346   
1347    /*
1348    * verify shared, extended alignment dataset
1349    */
1350  1 assertSame(cdsal.getDataset(), dna.getDataset());
1351  1 assertTrue(dna.getDataset().getSequences()
1352    .contains(cds.get(0).getDatasetSequence()));
1353  1 assertTrue(dna.getDataset().getSequences()
1354    .contains(cds.get(1).getDatasetSequence()));
1355  1 assertTrue(dna.getDataset().getSequences()
1356    .contains(cds.get(2).getDatasetSequence()));
1357   
1358    /*
1359    * verify aligned cds sequences and their xrefs
1360    */
1361  1 SequenceI cdsSeq = cds.get(0);
1362  1 assertEquals("GGGTTT", cdsSeq.getSequenceAsString());
1363    // assertEquals("dna1|A12345", cdsSeq.getName());
1364  1 assertEquals("CDS|dna1", cdsSeq.getName());
1365    // assertEquals(1, cdsSeq.getDBRefs().length);
1366    // DBRefEntry cdsRef = cdsSeq.getDBRefs()[0];
1367    // assertEquals("EMBLCDS", cdsRef.getSource());
1368    // assertEquals("2", cdsRef.getVersion());
1369    // assertEquals("A12345", cdsRef.getAccessionId());
1370   
1371  1 cdsSeq = cds.get(1);
1372  1 assertEquals("aaaccc", cdsSeq.getSequenceAsString());
1373    // assertEquals("dna1|A12346", cdsSeq.getName());
1374  1 assertEquals("CDS|dna1", cdsSeq.getName());
1375    // assertEquals(1, cdsSeq.getDBRefs().length);
1376    // cdsRef = cdsSeq.getDBRefs()[0];
1377    // assertEquals("EMBLCDS", cdsRef.getSource());
1378    // assertEquals("3", cdsRef.getVersion());
1379    // assertEquals("A12346", cdsRef.getAccessionId());
1380   
1381  1 cdsSeq = cds.get(2);
1382  1 assertEquals("aaaTTT", cdsSeq.getSequenceAsString());
1383    // assertEquals("dna1|A12347", cdsSeq.getName());
1384  1 assertEquals("CDS|dna1", cdsSeq.getName());
1385    // assertEquals(1, cdsSeq.getDBRefs().length);
1386    // cdsRef = cdsSeq.getDBRefs()[0];
1387    // assertEquals("EMBLCDS", cdsRef.getSource());
1388    // assertEquals("4", cdsRef.getVersion());
1389    // assertEquals("A12347", cdsRef.getAccessionId());
1390   
1391    /*
1392    * Verify there are mappings from each cds sequence to its protein product
1393    * and also to its dna source
1394    */
1395  1 List<AlignedCodonFrame> newMappings = cdsal.getCodonFrames();
1396   
1397    /*
1398    * 6 mappings involve dna1 (to pep1/2/3, cds1/2/3)
1399    */
1400  1 List<AlignedCodonFrame> dnaMappings = MappingUtils
1401    .findMappingsForSequence(dna1, newMappings);
1402  1 assertEquals(6, dnaMappings.size());
1403   
1404    /*
1405    * dna1 to pep1
1406    */
1407  1 List<AlignedCodonFrame> mappings = MappingUtils
1408    .findMappingsForSequence(pep1, dnaMappings);
1409  1 assertEquals(1, mappings.size());
1410  1 assertEquals(1, mappings.get(0).getMappings().size());
1411  1 assertSame(pep1.getDatasetSequence(),
1412    mappings.get(0).getMappings().get(0).getMapping().getTo());
1413   
1414    /*
1415    * dna1 to cds1
1416    */
1417  1 List<AlignedCodonFrame> dnaToCds1Mappings = MappingUtils
1418    .findMappingsForSequence(cds.get(0), dnaMappings);
1419  1 Mapping mapping = dnaToCds1Mappings.get(0).getMappings().get(0)
1420    .getMapping();
1421  1 assertSame(cds.get(0).getDatasetSequence(), mapping.getTo());
1422  1 assertEquals("G(1) in CDS should map to G(4) in DNA", 4,
1423    mapping.getMap().getToPosition(1));
1424   
1425    /*
1426    * dna1 to pep2
1427    */
1428  1 mappings = MappingUtils.findMappingsForSequence(pep2, dnaMappings);
1429  1 assertEquals(1, mappings.size());
1430  1 assertEquals(1, mappings.get(0).getMappings().size());
1431  1 assertSame(pep2.getDatasetSequence(),
1432    mappings.get(0).getMappings().get(0).getMapping().getTo());
1433   
1434    /*
1435    * dna1 to cds2
1436    */
1437  1 List<AlignedCodonFrame> dnaToCds2Mappings = MappingUtils
1438    .findMappingsForSequence(cds.get(1), dnaMappings);
1439  1 mapping = dnaToCds2Mappings.get(0).getMappings().get(0).getMapping();
1440  1 assertSame(cds.get(1).getDatasetSequence(), mapping.getTo());
1441  1 assertEquals("c(4) in CDS should map to c(7) in DNA", 7,
1442    mapping.getMap().getToPosition(4));
1443   
1444    /*
1445    * dna1 to pep3
1446    */
1447  1 mappings = MappingUtils.findMappingsForSequence(pep3, dnaMappings);
1448  1 assertEquals(1, mappings.size());
1449  1 assertEquals(1, mappings.get(0).getMappings().size());
1450  1 assertSame(pep3.getDatasetSequence(),
1451    mappings.get(0).getMappings().get(0).getMapping().getTo());
1452   
1453    /*
1454    * dna1 to cds3
1455    */
1456  1 List<AlignedCodonFrame> dnaToCds3Mappings = MappingUtils
1457    .findMappingsForSequence(cds.get(2), dnaMappings);
1458  1 mapping = dnaToCds3Mappings.get(0).getMappings().get(0).getMapping();
1459  1 assertSame(cds.get(2).getDatasetSequence(), mapping.getTo());
1460  1 assertEquals("T(4) in CDS should map to T(10) in DNA", 10,
1461    mapping.getMap().getToPosition(4));
1462    }
1463   
 
1464  1 toggle @Test(groups = { "Functional" })
1465    public void testIsMappable()
1466    {
1467  1 SequenceI dna1 = new Sequence("dna1", "cgCAGtgGT");
1468  1 SequenceI aa1 = new Sequence("aa1", "RSG");
1469  1 SequenceI td1 = new Sequence("aa1", "QRV");
1470  1 SequenceI td2 = new Sequence("aa2", "QRV");
1471  1 AlignmentI al1 = new Alignment(new SequenceI[] { dna1 });
1472  1 AlignmentI al2 = new Alignment(new SequenceI[] { aa1 });
1473  1 AlignmentI al3 = new Alignment(new SequenceI[] { td1 });
1474  1 AlignmentI al4 = new Alignment(new SequenceI[] { td2 });
1475   
1476  1 assertFalse(AlignmentUtils.isMappable(null, null));
1477  1 assertFalse(AlignmentUtils.isMappable(al1, null));
1478  1 assertFalse(AlignmentUtils.isMappable(null, al1));
1479  1 assertFalse(AlignmentUtils.isMappable(al1, al1));
1480  1 assertFalse(AlignmentUtils.isMappable(al2, al2));
1481   
1482   
1483  1 assertTrue(AlignmentUtils.isMappable(al1, al2));
1484  1 assertTrue(AlignmentUtils.isMappable(al2, al1));
1485   
1486   
1487    // test 3di/peptide mappability
1488  1 assertFalse(AlignmentUtils.isMappable(al1, al3));
1489  1 assertFalse(AlignmentUtils.isMappable(al2, al4));
1490  1 assertFalse(AlignmentUtils.isMappable(al3, al4));
1491   
1492   
1493  1 assertTrue(AlignmentUtils.isMappable(al2, al3));
1494  1 assertTrue(AlignmentUtils.isMappable(al3, al2));
1495    }
1496   
1497    /**
1498    * Test creating a mapping when the sequences involved do not start at residue
1499    * 1
1500    *
1501    * @throws IOException
1502    */
 
1503  1 toggle @Test(groups = { "Functional" })
1504    public void testMapCdnaToProtein_forSubsequence() throws IOException
1505    {
1506  1 SequenceI prot = new Sequence("UNIPROT|V12345", "E-I--Q", 10, 12);
1507  1 prot.createDatasetSequence();
1508   
1509  1 SequenceI dna = new Sequence("EMBL|A33333", "GAA--AT-C-CAG", 40, 48);
1510  1 dna.createDatasetSequence();
1511   
1512  1 MapList map = AlignmentUtils.mapCdnaToProtein(prot, dna);
1513  1 assertEquals(10, map.getToLowest());
1514  1 assertEquals(12, map.getToHighest());
1515  1 assertEquals(40, map.getFromLowest());
1516  1 assertEquals(48, map.getFromHighest());
1517    }
1518   
1519    /**
1520    * Test for the alignSequenceAs method where we have protein mapped to protein
1521    */
 
1522  1 toggle @Test(groups = { "Functional" })
1523    public void testAlignSequenceAs_mappedProteinProtein()
1524    {
1525   
1526  1 SequenceI alignMe = new Sequence("Match", "MGAASEV");
1527  1 alignMe.createDatasetSequence();
1528  1 SequenceI alignFrom = new Sequence("Query", "LQTGYMGAASEVMFSPTRR");
1529  1 alignFrom.createDatasetSequence();
1530   
1531  1 AlignedCodonFrame acf = new AlignedCodonFrame();
1532    // this is like a domain or motif match of part of a peptide sequence
1533  1 MapList map = new MapList(new int[] { 6, 12 }, new int[] { 1, 7 }, 1,
1534    1);
1535  1 acf.addMap(alignFrom.getDatasetSequence(), alignMe.getDatasetSequence(),
1536    map);
1537   
1538  1 AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "-", '-', true,
1539    true);
1540  1 assertEquals("-----MGAASEV-------", alignMe.getSequenceAsString());
1541    }
1542   
1543    /**
1544    * Test for the alignSequenceAs method where there are trailing unmapped
1545    * residues in the model sequence
1546    */
 
1547  1 toggle @Test(groups = { "Functional" })
1548    public void testAlignSequenceAs_withTrailingPeptide()
1549    {
1550    // map first 3 codons to KPF; G is a trailing unmapped residue
1551  1 MapList map = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3, 1);
1552   
1553  1 checkAlignSequenceAs("AAACCCTTT", "K-PFG", true, true, map,
1554    "AAA---CCCTTT---");
1555    }
1556   
1557    /**
1558    * Tests for transferring features between mapped sequences
1559    */
 
1560  1 toggle @Test(groups = { "Functional" })
1561    public void testTransferFeatures()
1562    {
1563  1 SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt");
1564  1 SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
1565   
1566    // no overlap
1567  1 dna.addSequenceFeature(
1568    new SequenceFeature("type1", "desc1", 1, 2, 1f, null));
1569    // partial overlap - to [1, 1]
1570  1 dna.addSequenceFeature(
1571    new SequenceFeature("type2", "desc2", 3, 4, 2f, null));
1572    // exact overlap - to [1, 3]
1573  1 dna.addSequenceFeature(
1574    new SequenceFeature("type3", "desc3", 4, 6, 3f, null));
1575    // spanning overlap - to [2, 5]
1576  1 dna.addSequenceFeature(
1577    new SequenceFeature("type4", "desc4", 5, 11, 4f, null));
1578    // exactly overlaps whole mapped range [1, 6]
1579  1 dna.addSequenceFeature(
1580    new SequenceFeature("type5", "desc5", 4, 12, 5f, null));
1581    // no overlap (internal)
1582  1 dna.addSequenceFeature(
1583    new SequenceFeature("type6", "desc6", 7, 9, 6f, null));
1584    // no overlap (3' end)
1585  1 dna.addSequenceFeature(
1586    new SequenceFeature("type7", "desc7", 13, 15, 7f, null));
1587    // overlap (3' end) - to [6, 6]
1588  1 dna.addSequenceFeature(
1589    new SequenceFeature("type8", "desc8", 12, 12, 8f, null));
1590    // extended overlap - to [6, +]
1591  1 dna.addSequenceFeature(
1592    new SequenceFeature("type9", "desc9", 12, 13, 9f, null));
1593   
1594  1 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1595    new int[]
1596    { 1, 6 }, 1, 1);
1597   
1598    /*
1599    * transferFeatures() will build 'partial overlap' for regions
1600    * that partially overlap 5' or 3' (start or end) of target sequence
1601    */
1602  1 AlignmentUtils.transferFeatures(dna, cds, map, null);
1603  1 List<SequenceFeature> sfs = cds.getSequenceFeatures();
1604  1 assertEquals(6, sfs.size());
1605   
1606  1 SequenceFeature sf = sfs.get(0);
1607  1 assertEquals("type2", sf.getType());
1608  1 assertEquals("desc2", sf.getDescription());
1609  1 assertEquals(2f, sf.getScore());
1610  1 assertEquals(1, sf.getBegin());
1611  1 assertEquals(1, sf.getEnd());
1612   
1613  1 sf = sfs.get(1);
1614  1 assertEquals("type3", sf.getType());
1615  1 assertEquals("desc3", sf.getDescription());
1616  1 assertEquals(3f, sf.getScore());
1617  1 assertEquals(1, sf.getBegin());
1618  1 assertEquals(3, sf.getEnd());
1619   
1620  1 sf = sfs.get(2);
1621  1 assertEquals("type4", sf.getType());
1622  1 assertEquals(2, sf.getBegin());
1623  1 assertEquals(5, sf.getEnd());
1624   
1625  1 sf = sfs.get(3);
1626  1 assertEquals("type5", sf.getType());
1627  1 assertEquals(1, sf.getBegin());
1628  1 assertEquals(6, sf.getEnd());
1629   
1630  1 sf = sfs.get(4);
1631  1 assertEquals("type8", sf.getType());
1632  1 assertEquals(6, sf.getBegin());
1633  1 assertEquals(6, sf.getEnd());
1634   
1635  1 sf = sfs.get(5);
1636  1 assertEquals("type9", sf.getType());
1637  1 assertEquals(6, sf.getBegin());
1638  1 assertEquals(6, sf.getEnd());
1639    }
1640   
1641    /**
1642    * Tests for transferring features between mapped sequences
1643    */
 
1644  1 toggle @Test(groups = { "Functional" })
1645    public void testTransferFeatures_withOmit()
1646    {
1647  1 SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt");
1648  1 SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
1649   
1650  1 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1651    new int[]
1652    { 1, 6 }, 1, 1);
1653   
1654    // [5, 11] maps to [2, 5]
1655  1 dna.addSequenceFeature(
1656    new SequenceFeature("type4", "desc4", 5, 11, 4f, null));
1657    // [4, 12] maps to [1, 6]
1658  1 dna.addSequenceFeature(
1659    new SequenceFeature("type5", "desc5", 4, 12, 5f, null));
1660    // [12, 12] maps to [6, 6]
1661  1 dna.addSequenceFeature(
1662    new SequenceFeature("type8", "desc8", 12, 12, 8f, null));
1663   
1664    // desc4 and desc8 are the 'omit these' varargs
1665  1 AlignmentUtils.transferFeatures(dna, cds, map, null, "type4", "type8");
1666  1 List<SequenceFeature> sfs = cds.getSequenceFeatures();
1667  1 assertEquals(1, sfs.size());
1668   
1669  1 SequenceFeature sf = sfs.get(0);
1670  1 assertEquals("type5", sf.getType());
1671  1 assertEquals(1, sf.getBegin());
1672  1 assertEquals(6, sf.getEnd());
1673    }
1674   
1675    /**
1676    * Tests for transferring features between mapped sequences
1677    */
 
1678  1 toggle @Test(groups = { "Functional" })
1679    public void testTransferFeatures_withSelect()
1680    {
1681  1 SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt");
1682  1 SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
1683   
1684  1 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1685    new int[]
1686    { 1, 6 }, 1, 1);
1687   
1688    // [5, 11] maps to [2, 5]
1689  1 dna.addSequenceFeature(
1690    new SequenceFeature("type4", "desc4", 5, 11, 4f, null));
1691    // [4, 12] maps to [1, 6]
1692  1 dna.addSequenceFeature(
1693    new SequenceFeature("type5", "desc5", 4, 12, 5f, null));
1694    // [12, 12] maps to [6, 6]
1695  1 dna.addSequenceFeature(
1696    new SequenceFeature("type8", "desc8", 12, 12, 8f, null));
1697   
1698    // "type5" is the 'select this type' argument
1699  1 AlignmentUtils.transferFeatures(dna, cds, map, "type5");
1700  1 List<SequenceFeature> sfs = cds.getSequenceFeatures();
1701  1 assertEquals(1, sfs.size());
1702   
1703  1 SequenceFeature sf = sfs.get(0);
1704  1 assertEquals("type5", sf.getType());
1705  1 assertEquals(1, sf.getBegin());
1706  1 assertEquals(6, sf.getEnd());
1707    }
1708   
1709    /**
1710    * Test the method that extracts the cds-only part of a dna alignment, for the
1711    * case where the cds should be aligned to match its nucleotide sequence.
1712    */
 
1713  1 toggle @Test(groups = { "Functional" })
1714    public void testMakeCdsAlignment_alternativeTranscripts()
1715    {
1716  1 SequenceI dna1 = new Sequence("dna1", "aaaGGGCC-----CTTTaaaGGG");
1717    // alternative transcript of same dna skips CCC codon
1718  1 SequenceI dna2 = new Sequence("dna2", "aaaGGGCC-----cttTaaaGGG");
1719    // dna3 has no mapping (protein product) so should be ignored here
1720  1 SequenceI dna3 = new Sequence("dna3", "aaaGGGCCCCCGGGcttTaaaGGG");
1721  1 SequenceI pep1 = new Sequence("pep1", "GPFG");
1722  1 SequenceI pep2 = new Sequence("pep2", "GPG");
1723  1 dna1.createDatasetSequence();
1724  1 dna2.createDatasetSequence();
1725  1 dna3.createDatasetSequence();
1726  1 pep1.createDatasetSequence();
1727  1 pep2.createDatasetSequence();
1728   
1729  1 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
1730  1 dna.setDataset(null);
1731   
1732  1 MapList map = new MapList(new int[] { 4, 12, 16, 18 },
1733    new int[]
1734    { 1, 4 }, 3, 1);
1735  1 AlignedCodonFrame acf = new AlignedCodonFrame();
1736  1 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
1737  1 dna.addCodonFrame(acf);
1738  1 map = new MapList(new int[] { 4, 8, 12, 12, 16, 18 },
1739    new int[]
1740    { 1, 3 }, 3, 1);
1741  1 acf = new AlignedCodonFrame();
1742  1 acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
1743  1 dna.addCodonFrame(acf);
1744   
1745  1 AlignmentI cds = AlignmentUtils
1746    .makeCdsAlignment(new SequenceI[]
1747    { dna1, dna2, dna3 }, dna.getDataset(), null);
1748  1 List<SequenceI> cdsSeqs = cds.getSequences();
1749  1 assertEquals(2, cdsSeqs.size());
1750  1 assertEquals("GGGCCCTTTGGG", cdsSeqs.get(0).getSequenceAsString());
1751  1 assertEquals("GGGCCTGGG", cdsSeqs.get(1).getSequenceAsString());
1752   
1753    /*
1754    * verify shared, extended alignment dataset
1755    */
1756  1 assertSame(dna.getDataset(), cds.getDataset());
1757  1 assertTrue(dna.getDataset().getSequences()
1758    .contains(cdsSeqs.get(0).getDatasetSequence()));
1759  1 assertTrue(dna.getDataset().getSequences()
1760    .contains(cdsSeqs.get(1).getDatasetSequence()));
1761   
1762    /*
1763    * Verify 6 mappings: dna1 to cds1, cds1 to pep1, dna1 to pep1
1764    * and the same for dna2/cds2/pep2
1765    */
1766  1 List<AlignedCodonFrame> mappings = cds.getCodonFrames();
1767  1 assertEquals(6, mappings.size());
1768   
1769    /*
1770    * 2 mappings involve pep1
1771    */
1772  1 List<AlignedCodonFrame> pep1Mappings = MappingUtils
1773    .findMappingsForSequence(pep1, mappings);
1774  1 assertEquals(2, pep1Mappings.size());
1775   
1776    /*
1777    * Get mapping of pep1 to cds1 and verify it
1778    * maps GPFG to 1-3,4-6,7-9,10-12
1779    */
1780  1 List<AlignedCodonFrame> pep1CdsMappings = MappingUtils
1781    .findMappingsForSequence(cds.getSequenceAt(0), pep1Mappings);
1782  1 assertEquals(1, pep1CdsMappings.size());
1783  1 SearchResultsI sr = MappingUtils.buildSearchResults(pep1, 1,
1784    pep1CdsMappings);
1785  1 assertEquals(1, sr.getResults().size());
1786  1 SearchResultMatchI m = sr.getResults().get(0);
1787  1 assertEquals(cds.getSequenceAt(0).getDatasetSequence(),
1788    m.getSequence());
1789  1 assertEquals(1, m.getStart());
1790  1 assertEquals(3, m.getEnd());
1791  1 sr = MappingUtils.buildSearchResults(pep1, 2, pep1CdsMappings);
1792  1 m = sr.getResults().get(0);
1793  1 assertEquals(4, m.getStart());
1794  1 assertEquals(6, m.getEnd());
1795  1 sr = MappingUtils.buildSearchResults(pep1, 3, pep1CdsMappings);
1796  1 m = sr.getResults().get(0);
1797  1 assertEquals(7, m.getStart());
1798  1 assertEquals(9, m.getEnd());
1799  1 sr = MappingUtils.buildSearchResults(pep1, 4, pep1CdsMappings);
1800  1 m = sr.getResults().get(0);
1801  1 assertEquals(10, m.getStart());
1802  1 assertEquals(12, m.getEnd());
1803   
1804    /*
1805    * Get mapping of pep2 to cds2 and verify it
1806    * maps GPG in pep2 to 1-3,4-6,7-9 in second CDS sequence
1807    */
1808  1 List<AlignedCodonFrame> pep2Mappings = MappingUtils
1809    .findMappingsForSequence(pep2, mappings);
1810  1 assertEquals(2, pep2Mappings.size());
1811  1 List<AlignedCodonFrame> pep2CdsMappings = MappingUtils
1812    .findMappingsForSequence(cds.getSequenceAt(1), pep2Mappings);
1813  1 assertEquals(1, pep2CdsMappings.size());
1814  1 sr = MappingUtils.buildSearchResults(pep2, 1, pep2CdsMappings);
1815  1 assertEquals(1, sr.getResults().size());
1816  1 m = sr.getResults().get(0);
1817  1 assertEquals(cds.getSequenceAt(1).getDatasetSequence(),
1818    m.getSequence());
1819  1 assertEquals(1, m.getStart());
1820  1 assertEquals(3, m.getEnd());
1821  1 sr = MappingUtils.buildSearchResults(pep2, 2, pep2CdsMappings);
1822  1 m = sr.getResults().get(0);
1823  1 assertEquals(4, m.getStart());
1824  1 assertEquals(6, m.getEnd());
1825  1 sr = MappingUtils.buildSearchResults(pep2, 3, pep2CdsMappings);
1826  1 m = sr.getResults().get(0);
1827  1 assertEquals(7, m.getStart());
1828  1 assertEquals(9, m.getEnd());
1829    }
1830   
1831    /**
1832    * Test the method that realigns protein to match mapped codon alignment.
1833    */
 
1834  1 toggle @Test(groups = { "Functional" })
1835    public void testAlignProteinAsDna_incompleteStartCodon()
1836    {
1837    // seq1: incomplete start codon (not mapped), then [3, 11]
1838  1 SequenceI dna1 = new Sequence("Seq1", "ccAAA-TTT-GGG-");
1839    // seq2 codons are [4, 5], [8, 11]
1840  1 SequenceI dna2 = new Sequence("Seq2", "ccaAA-ttT-GGG-");
1841    // seq3 incomplete start codon at 'tt'
1842  1 SequenceI dna3 = new Sequence("Seq3", "ccaaa-ttt-GGG-");
1843  1 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
1844  1 dna.setDataset(null);
1845   
1846    // prot1 has 'X' for incomplete start codon (not mapped)
1847  1 SequenceI prot1 = new Sequence("Seq1", "XKFG"); // X for incomplete start
1848  1 SequenceI prot2 = new Sequence("Seq2", "NG");
1849  1 SequenceI prot3 = new Sequence("Seq3", "XG"); // X for incomplete start
1850  1 AlignmentI protein = new Alignment(
1851    new SequenceI[]
1852    { prot1, prot2, prot3 });
1853  1 protein.setDataset(null);
1854   
1855    // map dna1 [3, 11] to prot1 [2, 4] KFG
1856  1 MapList map = new MapList(new int[] { 3, 11 }, new int[] { 2, 4 }, 3,
1857    1);
1858  1 AlignedCodonFrame acf = new AlignedCodonFrame();
1859  1 acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
1860   
1861    // map dna2 [4, 5] [8, 11] to prot2 [1, 2] NG
1862  1 map = new MapList(new int[] { 4, 5, 8, 11 }, new int[] { 1, 2 }, 3, 1);
1863  1 acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map);
1864   
1865    // map dna3 [9, 11] to prot3 [2, 2] G
1866  1 map = new MapList(new int[] { 9, 11 }, new int[] { 2, 2 }, 3, 1);
1867  1 acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map);
1868   
1869  1 ArrayList<AlignedCodonFrame> acfs = new ArrayList<>();
1870  1 acfs.add(acf);
1871  1 protein.setCodonFrames(acfs);
1872   
1873    /*
1874    * verify X is included in the aligned proteins, and placed just
1875    * before the first mapped residue
1876    * CCT is between CCC and TTT
1877    */
1878  1 AlignmentUtils.alignProteinAsDna(protein, dna);
1879  1 assertEquals("XK-FG", prot1.getSequenceAsString());
1880  1 assertEquals("--N-G", prot2.getSequenceAsString());
1881  1 assertEquals("---XG", prot3.getSequenceAsString());
1882    }
1883   
1884    /**
1885    * Tests for the method that maps the subset of a dna sequence that has CDS
1886    * (or subtype) feature - case where the start codon is incomplete.
1887    */
 
1888  1 toggle @Test(groups = "Functional")
1889    public void testFindCdsPositions_fivePrimeIncomplete()
1890    {
1891  1 SequenceI dnaSeq = new Sequence("dna", "aaagGGCCCaaaTTTttt");
1892  1 dnaSeq.createDatasetSequence();
1893  1 SequenceI ds = dnaSeq.getDatasetSequence();
1894   
1895    // CDS for dna 5-6 (incomplete codon), 7-9
1896  1 SequenceFeature sf = new SequenceFeature("CDS", "", 5, 9, 0f, null);
1897  1 sf.setPhase("2"); // skip 2 bases to start of next codon
1898  1 ds.addSequenceFeature(sf);
1899    // CDS for dna 13-15
1900  1 sf = new SequenceFeature("CDS_predicted", "", 13, 15, 0f, null);
1901  1 ds.addSequenceFeature(sf);
1902   
1903  1 List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
1904   
1905    /*
1906    * check the mapping starts with the first complete codon
1907    */
1908  1 assertEquals(6, MappingUtils.getLength(ranges));
1909  1 assertEquals(2, ranges.size());
1910  1 assertEquals(7, ranges.get(0)[0]);
1911  1 assertEquals(9, ranges.get(0)[1]);
1912  1 assertEquals(13, ranges.get(1)[0]);
1913  1 assertEquals(15, ranges.get(1)[1]);
1914    }
1915   
1916    /**
1917    * Tests for the method that maps the subset of a dna sequence that has CDS
1918    * (or subtype) feature.
1919    */
 
1920  1 toggle @Test(groups = "Functional")
1921    public void testFindCdsPositions()
1922    {
1923  1 SequenceI dnaSeq = new Sequence("dna", "aaaGGGcccAAATTTttt");
1924  1 dnaSeq.createDatasetSequence();
1925  1 SequenceI ds = dnaSeq.getDatasetSequence();
1926   
1927    // CDS for dna 10-12
1928  1 SequenceFeature sf = new SequenceFeature("CDS_predicted", "", 10, 12,
1929    0f, null);
1930  1 sf.setStrand("+");
1931  1 ds.addSequenceFeature(sf);
1932    // CDS for dna 4-6
1933  1 sf = new SequenceFeature("CDS", "", 4, 6, 0f, null);
1934  1 sf.setStrand("+");
1935  1 ds.addSequenceFeature(sf);
1936    // exon feature should be ignored here
1937  1 sf = new SequenceFeature("exon", "", 7, 9, 0f, null);
1938  1 ds.addSequenceFeature(sf);
1939   
1940  1 List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
1941    /*
1942    * verify ranges { [4-6], [12-10] }
1943    * note CDS ranges are ordered ascending even if the CDS
1944    * features are not
1945    */
1946  1 assertEquals(6, MappingUtils.getLength(ranges));
1947  1 assertEquals(2, ranges.size());
1948  1 assertEquals(4, ranges.get(0)[0]);
1949  1 assertEquals(6, ranges.get(0)[1]);
1950  1 assertEquals(10, ranges.get(1)[0]);
1951  1 assertEquals(12, ranges.get(1)[1]);
1952    }
1953   
1954    /**
1955    * Tests for the method that maps the subset of a dna sequence that has CDS
1956    * (or subtype) feature, with CDS strand = '-' (reverse)
1957    */
1958    // test turned off as currently findCdsPositions is not strand-dependent
1959    // left in case it comes around again...
 
1960  0 toggle @Test(groups = "Functional", enabled = false)
1961    public void testFindCdsPositions_reverseStrand()
1962    {
1963  0 SequenceI dnaSeq = new Sequence("dna", "aaaGGGcccAAATTTttt");
1964  0 dnaSeq.createDatasetSequence();
1965  0 SequenceI ds = dnaSeq.getDatasetSequence();
1966   
1967    // CDS for dna 4-6
1968  0 SequenceFeature sf = new SequenceFeature("CDS", "", 4, 6, 0f, null);
1969  0 sf.setStrand("-");
1970  0 ds.addSequenceFeature(sf);
1971    // exon feature should be ignored here
1972  0 sf = new SequenceFeature("exon", "", 7, 9, 0f, null);
1973  0 ds.addSequenceFeature(sf);
1974    // CDS for dna 10-12
1975  0 sf = new SequenceFeature("CDS_predicted", "", 10, 12, 0f, null);
1976  0 sf.setStrand("-");
1977  0 ds.addSequenceFeature(sf);
1978   
1979  0 List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
1980    /*
1981    * verify ranges { [12-10], [6-4] }
1982    */
1983  0 assertEquals(6, MappingUtils.getLength(ranges));
1984  0 assertEquals(2, ranges.size());
1985  0 assertEquals(12, ranges.get(0)[0]);
1986  0 assertEquals(10, ranges.get(0)[1]);
1987  0 assertEquals(6, ranges.get(1)[0]);
1988  0 assertEquals(4, ranges.get(1)[1]);
1989    }
1990   
1991    /**
1992    * Tests for the method that maps the subset of a dna sequence that has CDS
1993    * (or subtype) feature - reverse strand case where the start codon is
1994    * incomplete.
1995    */
 
1996  0 toggle @Test(groups = "Functional", enabled = false)
1997    // test turned off as currently findCdsPositions is not strand-dependent
1998    // left in case it comes around again...
1999    public void testFindCdsPositions_reverseStrandThreePrimeIncomplete()
2000    {
2001  0 SequenceI dnaSeq = new Sequence("dna", "aaagGGCCCaaaTTTttt");
2002  0 dnaSeq.createDatasetSequence();
2003  0 SequenceI ds = dnaSeq.getDatasetSequence();
2004   
2005    // CDS for dna 5-9
2006  0 SequenceFeature sf = new SequenceFeature("CDS", "", 5, 9, 0f, null);
2007  0 sf.setStrand("-");
2008  0 ds.addSequenceFeature(sf);
2009    // CDS for dna 13-15
2010  0 sf = new SequenceFeature("CDS_predicted", "", 13, 15, 0f, null);
2011  0 sf.setStrand("-");
2012  0 sf.setPhase("2"); // skip 2 bases to start of next codon
2013  0 ds.addSequenceFeature(sf);
2014   
2015  0 List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
2016   
2017    /*
2018    * check the mapping starts with the first complete codon
2019    * expect ranges [13, 13], [9, 5]
2020    */
2021  0 assertEquals(6, MappingUtils.getLength(ranges));
2022  0 assertEquals(2, ranges.size());
2023  0 assertEquals(13, ranges.get(0)[0]);
2024  0 assertEquals(13, ranges.get(0)[1]);
2025  0 assertEquals(9, ranges.get(1)[0]);
2026  0 assertEquals(5, ranges.get(1)[1]);
2027    }
2028   
 
2029  1 toggle @Test(groups = "Functional")
2030    public void testAlignAs_alternateTranscriptsUngapped()
2031    {
2032  1 SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
2033  1 SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
2034  1 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
2035  1 ((Alignment) dna).createDatasetAlignment();
2036  1 SequenceI cds1 = new Sequence("cds1", "GGGTTT");
2037  1 SequenceI cds2 = new Sequence("cds2", "CCCAAA");
2038  1 AlignmentI cds = new Alignment(new SequenceI[] { cds1, cds2 });
2039  1 ((Alignment) cds).createDatasetAlignment();
2040   
2041  1 AlignedCodonFrame acf = new AlignedCodonFrame();
2042  1 MapList map = new MapList(new int[] { 4, 9 }, new int[] { 1, 6 }, 1, 1);
2043  1 acf.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(), map);
2044  1 map = new MapList(new int[] { 1, 3, 10, 12 }, new int[] { 1, 6 }, 1, 1);
2045  1 acf.addMap(dna2.getDatasetSequence(), cds2.getDatasetSequence(), map);
2046   
2047    /*
2048    * verify CDS alignment is as:
2049    * cccGGGTTTaaa (cdna)
2050    * CCCgggtttAAA (cdna)
2051    *
2052    * ---GGGTTT--- (cds)
2053    * CCC------AAA (cds)
2054    */
2055  1 dna.addCodonFrame(acf);
2056  1 AlignmentUtils.alignAs(cds, dna);
2057  1 assertEquals("---GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
2058  1 assertEquals("CCC------AAA",
2059    cds.getSequenceAt(1).getSequenceAsString());
2060    }
2061   
 
2062  1 toggle @Test(groups = { "Functional" })
2063    public void testAddMappedPositions()
2064    {
2065  1 SequenceI from = new Sequence("dna", "ggAA-ATcc-TT-g");
2066  1 SequenceI seq1 = new Sequence("cds", "AAATTT");
2067  1 from.createDatasetSequence();
2068  1 seq1.createDatasetSequence();
2069  1 Mapping mapping = new Mapping(seq1,
2070    new MapList(new int[]
2071    { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1));
2072  1 Map<Integer, Map<SequenceI, Character>> map = new TreeMap<>();
2073  1 AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
2074   
2075    /*
2076    * verify map has seq1 residues in columns 3,4,6,7,11,12
2077    */
2078  1 assertEquals(6, map.size());
2079  1 assertEquals('A', map.get(3).get(seq1).charValue());
2080  1 assertEquals('A', map.get(4).get(seq1).charValue());
2081  1 assertEquals('A', map.get(6).get(seq1).charValue());
2082  1 assertEquals('T', map.get(7).get(seq1).charValue());
2083  1 assertEquals('T', map.get(11).get(seq1).charValue());
2084  1 assertEquals('T', map.get(12).get(seq1).charValue());
2085   
2086    /*
2087    *
2088    */
2089    }
2090   
2091    /**
2092    * Test case where the mapping 'from' range includes a stop codon which is
2093    * absent in the 'to' range
2094    */
 
2095  1 toggle @Test(groups = { "Functional" })
2096    public void testAddMappedPositions_withStopCodon()
2097    {
2098  1 SequenceI from = new Sequence("dna", "ggAA-ATcc-TT-g");
2099  1 SequenceI seq1 = new Sequence("cds", "AAATTT");
2100  1 from.createDatasetSequence();
2101  1 seq1.createDatasetSequence();
2102  1 Mapping mapping = new Mapping(seq1,
2103    new MapList(new int[]
2104    { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1));
2105  1 Map<Integer, Map<SequenceI, Character>> map = new TreeMap<>();
2106  1 AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
2107   
2108    /*
2109    * verify map has seq1 residues in columns 3,4,6,7,11,12
2110    */
2111  1 assertEquals(6, map.size());
2112  1 assertEquals('A', map.get(3).get(seq1).charValue());
2113  1 assertEquals('A', map.get(4).get(seq1).charValue());
2114  1 assertEquals('A', map.get(6).get(seq1).charValue());
2115  1 assertEquals('T', map.get(7).get(seq1).charValue());
2116  1 assertEquals('T', map.get(11).get(seq1).charValue());
2117  1 assertEquals('T', map.get(12).get(seq1).charValue());
2118    }
2119   
2120    /**
2121    * Test for the case where the products for which we want CDS are specified.
2122    * This is to represent the case where EMBL has CDS mappings to both Uniprot
2123    * and EMBLCDSPROTEIN. makeCdsAlignment() should only return the mappings for
2124    * the protein sequences specified.
2125    */
 
2126  1 toggle @Test(groups = { "Functional" })
2127    public void testMakeCdsAlignment_filterProducts()
2128    {
2129  1 SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
2130  1 SequenceI dna2 = new Sequence("dna2", "GGGcccTTTaaaCCC");
2131  1 SequenceI pep1 = new Sequence("Uniprot|pep1", "GF");
2132  1 SequenceI pep2 = new Sequence("Uniprot|pep2", "GFP");
2133  1 SequenceI pep3 = new Sequence("EMBL|pep3", "GF");
2134  1 SequenceI pep4 = new Sequence("EMBL|pep4", "GFP");
2135  1 dna1.createDatasetSequence();
2136  1 dna2.createDatasetSequence();
2137  1 pep1.createDatasetSequence();
2138  1 pep2.createDatasetSequence();
2139  1 pep3.createDatasetSequence();
2140  1 pep4.createDatasetSequence();
2141  1 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
2142  1 dna.setDataset(null);
2143  1 AlignmentI emblPeptides = new Alignment(new SequenceI[] { pep3, pep4 });
2144  1 emblPeptides.setDataset(null);
2145   
2146  1 AlignedCodonFrame acf = new AlignedCodonFrame();
2147  1 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
2148    new int[]
2149    { 1, 2 }, 3, 1);
2150  1 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
2151  1 acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map);
2152  1 dna.addCodonFrame(acf);
2153   
2154  1 acf = new AlignedCodonFrame();
2155  1 map = new MapList(new int[] { 1, 3, 7, 9, 13, 15 }, new int[] { 1, 3 },
2156    3, 1);
2157  1 acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
2158  1 acf.addMap(dna2.getDatasetSequence(), pep4.getDatasetSequence(), map);
2159  1 dna.addCodonFrame(acf);
2160   
2161    /*
2162    * execute method under test to find CDS for EMBL peptides only
2163    */
2164  1 AlignmentI cds = AlignmentUtils
2165    .makeCdsAlignment(new SequenceI[]
2166    { dna1, dna2 }, dna.getDataset(),
2167    emblPeptides.getSequencesArray());
2168   
2169  1 assertEquals(2, cds.getSequences().size());
2170  1 assertEquals("GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
2171  1 assertEquals("GGGTTTCCC", cds.getSequenceAt(1).getSequenceAsString());
2172   
2173    /*
2174    * verify shared, extended alignment dataset
2175    */
2176  1 assertSame(dna.getDataset(), cds.getDataset());
2177  1 assertTrue(dna.getDataset().getSequences()
2178    .contains(cds.getSequenceAt(0).getDatasetSequence()));
2179  1 assertTrue(dna.getDataset().getSequences()
2180    .contains(cds.getSequenceAt(1).getDatasetSequence()));
2181   
2182    /*
2183    * Verify mappings from CDS to peptide, cDNA to CDS, and cDNA to peptide
2184    * the mappings are on the shared alignment dataset
2185    */
2186  1 List<AlignedCodonFrame> cdsMappings = cds.getDataset().getCodonFrames();
2187    /*
2188    * 6 mappings, 2*(DNA->CDS), 2*(DNA->Pep), 2*(CDS->Pep)
2189    */
2190  1 assertEquals(6, cdsMappings.size());
2191   
2192    /*
2193    * verify that mapping sets for dna and cds alignments are different
2194    * [not current behaviour - all mappings are on the alignment dataset]
2195    */
2196    // select -> subselect type to test.
2197    // Assert.assertNotSame(dna.getCodonFrames(), cds.getCodonFrames());
2198    // assertEquals(4, dna.getCodonFrames().size());
2199    // assertEquals(4, cds.getCodonFrames().size());
2200   
2201    /*
2202    * Two mappings involve pep3 (dna to pep3, cds to pep3)
2203    * Mapping from pep3 to GGGTTT in first new exon sequence
2204    */
2205  1 List<AlignedCodonFrame> pep3Mappings = MappingUtils
2206    .findMappingsForSequence(pep3, cdsMappings);
2207  1 assertEquals(2, pep3Mappings.size());
2208  1 List<AlignedCodonFrame> mappings = MappingUtils
2209    .findMappingsForSequence(cds.getSequenceAt(0), pep3Mappings);
2210  1 assertEquals(1, mappings.size());
2211   
2212    // map G to GGG
2213  1 SearchResultsI sr = MappingUtils.buildSearchResults(pep3, 1, mappings);
2214  1 assertEquals(1, sr.getResults().size());
2215  1 SearchResultMatchI m = sr.getResults().get(0);
2216  1 assertSame(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
2217  1 assertEquals(1, m.getStart());
2218  1 assertEquals(3, m.getEnd());
2219    // map F to TTT
2220  1 sr = MappingUtils.buildSearchResults(pep3, 2, mappings);
2221  1 m = sr.getResults().get(0);
2222  1 assertSame(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
2223  1 assertEquals(4, m.getStart());
2224  1 assertEquals(6, m.getEnd());
2225   
2226    /*
2227    * Two mappings involve pep4 (dna to pep4, cds to pep4)
2228    * Verify mapping from pep4 to GGGTTTCCC in second new exon sequence
2229    */
2230  1 List<AlignedCodonFrame> pep4Mappings = MappingUtils
2231    .findMappingsForSequence(pep4, cdsMappings);
2232  1 assertEquals(2, pep4Mappings.size());
2233  1 mappings = MappingUtils.findMappingsForSequence(cds.getSequenceAt(1),
2234    pep4Mappings);
2235  1 assertEquals(1, mappings.size());
2236    // map G to GGG
2237  1 sr = MappingUtils.buildSearchResults(pep4, 1, mappings);
2238  1 assertEquals(1, sr.getResults().size());
2239  1 m = sr.getResults().get(0);
2240  1 assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
2241  1 assertEquals(1, m.getStart());
2242  1 assertEquals(3, m.getEnd());
2243    // map F to TTT
2244  1 sr = MappingUtils.buildSearchResults(pep4, 2, mappings);
2245  1 m = sr.getResults().get(0);
2246  1 assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
2247  1 assertEquals(4, m.getStart());
2248  1 assertEquals(6, m.getEnd());
2249    // map P to CCC
2250  1 sr = MappingUtils.buildSearchResults(pep4, 3, mappings);
2251  1 m = sr.getResults().get(0);
2252  1 assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
2253  1 assertEquals(7, m.getStart());
2254  1 assertEquals(9, m.getEnd());
2255    }
2256   
2257    /**
2258    * Test the method that just copies aligned sequences, provided all sequences
2259    * to be aligned share the aligned sequence's dataset
2260    */
 
2261  1 toggle @Test(groups = "Functional")
2262    public void testAlignAsSameSequences()
2263    {
2264  1 SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
2265  1 SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
2266  1 AlignmentI al1 = new Alignment(new SequenceI[] { dna1, dna2 });
2267  1 ((Alignment) al1).createDatasetAlignment();
2268   
2269  1 SequenceI dna3 = new Sequence(dna1);
2270  1 SequenceI dna4 = new Sequence(dna2);
2271  1 assertSame(dna3.getDatasetSequence(), dna1.getDatasetSequence());
2272  1 assertSame(dna4.getDatasetSequence(), dna2.getDatasetSequence());
2273  1 String seq1 = "-cc-GG-GT-TT--aaa";
2274  1 dna3.setSequence(seq1);
2275  1 String seq2 = "C--C-Cgg--gtt-tAA-A-";
2276  1 dna4.setSequence(seq2);
2277  1 AlignmentI al2 = new Alignment(new SequenceI[] { dna3, dna4 });
2278  1 ((Alignment) al2).createDatasetAlignment();
2279   
2280    /*
2281    * alignment removes gapped columns (two internal, two trailing)
2282    */
2283  1 assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
2284  1 String aligned1 = "-cc-GG-GTTT-aaa";
2285  1 assertEquals(aligned1, al1.getSequenceAt(0).getSequenceAsString());
2286  1 String aligned2 = "C--C-Cgg-gtttAAA";
2287  1 assertEquals(aligned2, al1.getSequenceAt(1).getSequenceAsString());
2288   
2289    /*
2290    * add another sequence to 'aligned' - should still succeed, since
2291    * unaligned sequences still share a dataset with aligned sequences
2292    */
2293  1 SequenceI dna5 = new Sequence("dna5", "CCCgggtttAAA");
2294  1 dna5.createDatasetSequence();
2295  1 al2.addSequence(dna5);
2296  1 assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
2297  1 assertEquals(aligned1, al1.getSequenceAt(0).getSequenceAsString());
2298  1 assertEquals(aligned2, al1.getSequenceAt(1).getSequenceAsString());
2299   
2300    /*
2301    * add another sequence to 'unaligned' - should fail, since now not
2302    * all unaligned sequences share a dataset with aligned sequences
2303    */
2304  1 SequenceI dna6 = new Sequence("dna6", "CCCgggtttAAA");
2305  1 dna6.createDatasetSequence();
2306  1 al1.addSequence(dna6);
2307    // JAL-2110 JBP Comment: what's the use case for this behaviour ?
2308  1 assertFalse(AlignmentUtils.alignAsSameSequences(al1, al2));
2309    }
2310   
 
2311  1 toggle @Test(groups = "Functional")
2312    public void testAlignAsSameSequencesMultipleSubSeq()
2313    {
2314  1 SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
2315  1 SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
2316  1 SequenceI as1 = dna1.deriveSequence(); // cccGGGTTTaaa/1-12
2317  1 SequenceI as2 = dna1.deriveSequence().getSubSequence(3, 7); // GGGT/4-7
2318  1 SequenceI as3 = dna2.deriveSequence(); // CCCgggtttAAA/1-12
2319  1 as1.insertCharAt(6, 5, '-');
2320  1 assertEquals("cccGGG-----TTTaaa", as1.getSequenceAsString());
2321  1 as2.insertCharAt(6, 5, '-');
2322  1 assertEquals("GGGT-----", as2.getSequenceAsString());
2323  1 as3.insertCharAt(3, 5, '-');
2324  1 assertEquals("CCC-----gggtttAAA", as3.getSequenceAsString());
2325  1 AlignmentI aligned = new Alignment(new SequenceI[] { as1, as2, as3 });
2326   
2327    // why do we need to cast this still ?
2328  1 ((Alignment) aligned).createDatasetAlignment();
2329  1 SequenceI uas1 = dna1.deriveSequence();
2330  1 SequenceI uas2 = dna1.deriveSequence().getSubSequence(3, 7);
2331  1 SequenceI uas3 = dna2.deriveSequence();
2332  1 AlignmentI tobealigned = new Alignment(
2333    new SequenceI[]
2334    { uas1, uas2, uas3 });
2335  1 ((Alignment) tobealigned).createDatasetAlignment();
2336   
2337    /*
2338    * alignAs lines up dataset sequences and removes empty columns (two)
2339    */
2340  1 assertTrue(AlignmentUtils.alignAsSameSequences(tobealigned, aligned));
2341  1 assertEquals("cccGGG---TTTaaa", uas1.getSequenceAsString());
2342  1 assertEquals("GGGT", uas2.getSequenceAsString());
2343  1 assertEquals("CCC---gggtttAAA", uas3.getSequenceAsString());
2344    }
2345   
 
2346  1 toggle @Test(groups = { "Functional" })
2347    public void testTransferGeneLoci()
2348    {
2349  1 SequenceI from = new Sequence("transcript",
2350    "aaacccgggTTTAAACCCGGGtttaaacccgggttt");
2351  1 SequenceI to = new Sequence("CDS", "TTTAAACCCGGG");
2352  1 MapList map = new MapList(new int[] { 1, 12 }, new int[] { 10, 21 }, 1,
2353    1);
2354   
2355    /*
2356    * first with nothing to transfer
2357    */
2358  1 AlignmentUtils.transferGeneLoci(from, map, to);
2359  1 assertNull(to.getGeneLoci());
2360   
2361    /*
2362    * next with gene loci set on 'from' sequence
2363    */
2364  1 int[] exons = new int[] { 100, 105, 155, 164, 210, 229 };
2365  1 MapList geneMap = new MapList(new int[] { 1, 36 }, exons, 1, 1);
2366  1 from.setGeneLoci("human", "GRCh38", "7", geneMap);
2367  1 AlignmentUtils.transferGeneLoci(from, map, to);
2368   
2369  1 GeneLociI toLoci = to.getGeneLoci();
2370  1 assertNotNull(toLoci);
2371    // DBRefEntry constructor upper-cases 'source'
2372  1 assertEquals("HUMAN", toLoci.getSpeciesId());
2373  1 assertEquals("GRCh38", toLoci.getAssemblyId());
2374  1 assertEquals("7", toLoci.getChromosomeId());
2375   
2376    /*
2377    * transcript 'exons' are 1-6, 7-16, 17-36
2378    * CDS 1:12 is transcript 10-21
2379    * transcript 'CDS' is 10-16, 17-21
2380    * which is 'gene' 158-164, 210-214
2381    */
2382  1 MapList toMap = toLoci.getMapping();
2383  1 assertEquals(1, toMap.getFromRanges().size());
2384  1 assertEquals(2, toMap.getFromRanges().get(0).length);
2385  1 assertEquals(1, toMap.getFromRanges().get(0)[0]);
2386  1 assertEquals(12, toMap.getFromRanges().get(0)[1]);
2387  1 assertEquals(2, toMap.getToRanges().size());
2388  1 assertEquals(2, toMap.getToRanges().get(0).length);
2389  1 assertEquals(158, toMap.getToRanges().get(0)[0]);
2390  1 assertEquals(164, toMap.getToRanges().get(0)[1]);
2391  1 assertEquals(210, toMap.getToRanges().get(1)[0]);
2392  1 assertEquals(214, toMap.getToRanges().get(1)[1]);
2393    // or summarised as (but toString might change in future):
2394  1 assertEquals("[ [1, 12] ] 1:1 to [ [158, 164] [210, 214] ]",
2395    toMap.toString());
2396   
2397    /*
2398    * an existing value is not overridden
2399    */
2400  1 geneMap = new MapList(new int[] { 1, 36 }, new int[] { 36, 1 }, 1, 1);
2401  1 from.setGeneLoci("inhuman", "GRCh37", "6", geneMap);
2402  1 AlignmentUtils.transferGeneLoci(from, map, to);
2403  1 assertEquals("GRCh38", toLoci.getAssemblyId());
2404  1 assertEquals("7", toLoci.getChromosomeId());
2405  1 toMap = toLoci.getMapping();
2406  1 assertEquals("[ [1, 12] ] 1:1 to [ [158, 164] [210, 214] ]",
2407    toMap.toString());
2408    }
2409   
2410    /**
2411    * Tests for the method that maps nucleotide to protein based on CDS features
2412    */
 
2413  1 toggle @Test(groups = "Functional")
2414    public void testMapCdsToProtein()
2415    {
2416  1 SequenceI peptide = new Sequence("pep", "KLQ");
2417   
2418    /*
2419    * Case 1: CDS 3 times length of peptide
2420    * NB method only checks lengths match, not translation
2421    */
2422  1 SequenceI dna = new Sequence("dna", "AACGacgtCTCCT");
2423  1 dna.createDatasetSequence();
2424  1 dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
2425  1 dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 13, null));
2426  1 MapList ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2427  1 assertEquals(3, ml.getFromRatio());
2428  1 assertEquals(1, ml.getToRatio());
2429  1 assertEquals("[[1, 3]]",
2430    Arrays.deepToString(ml.getToRanges().toArray()));
2431  1 assertEquals("[[1, 4], [9, 13]]",
2432    Arrays.deepToString(ml.getFromRanges().toArray()));
2433   
2434    /*
2435    * Case 2: CDS 3 times length of peptide + stop codon
2436    * (note code does not currently check trailing codon is a stop codon)
2437    */
2438  1 dna = new Sequence("dna", "AACGacgtCTCCTCCC");
2439  1 dna.createDatasetSequence();
2440  1 dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
2441  1 dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 16, null));
2442  1 ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2443  1 assertEquals(3, ml.getFromRatio());
2444  1 assertEquals(1, ml.getToRatio());
2445  1 assertEquals("[[1, 3]]",
2446    Arrays.deepToString(ml.getToRanges().toArray()));
2447  1 assertEquals("[[1, 4], [9, 13]]",
2448    Arrays.deepToString(ml.getFromRanges().toArray()));
2449   
2450    /*
2451    * Case 3: CDS longer than 3 * peptide + stop codon - no mapping is made
2452    */
2453  1 dna = new Sequence("dna", "AACGacgtCTCCTTGATCA");
2454  1 dna.createDatasetSequence();
2455  1 dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
2456  1 dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 19, null));
2457  1 ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2458  1 assertNull(ml);
2459   
2460    /*
2461    * Case 4: CDS shorter than 3 * peptide - no mapping is made
2462    */
2463  1 dna = new Sequence("dna", "AACGacgtCTCC");
2464  1 dna.createDatasetSequence();
2465  1 dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
2466  1 dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 12, null));
2467  1 ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2468  1 assertNull(ml);
2469   
2470    /*
2471    * Case 5: CDS 3 times length of peptide + part codon - mapping is truncated
2472    */
2473  1 dna = new Sequence("dna", "AACGacgtCTCCTTG");
2474  1 dna.createDatasetSequence();
2475  1 dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
2476  1 dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 15, null));
2477  1 ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2478  1 assertEquals(3, ml.getFromRatio());
2479  1 assertEquals(1, ml.getToRatio());
2480  1 assertEquals("[[1, 3]]",
2481    Arrays.deepToString(ml.getToRanges().toArray()));
2482  1 assertEquals("[[1, 4], [9, 13]]",
2483    Arrays.deepToString(ml.getFromRanges().toArray()));
2484   
2485    /*
2486    * Case 6: incomplete start codon corresponding to X in peptide
2487    */
2488  1 dna = new Sequence("dna", "ACGacgtCTCCTTGG");
2489  1 dna.createDatasetSequence();
2490  1 SequenceFeature sf = new SequenceFeature("CDS", "", 1, 3, null);
2491  1 sf.setPhase("2"); // skip 2 positions (AC) to start of next codon (GCT)
2492  1 dna.addSequenceFeature(sf);
2493  1 dna.addSequenceFeature(new SequenceFeature("CDS", "", 8, 15, null));
2494  1 peptide = new Sequence("pep", "XLQ");
2495  1 ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2496  1 assertEquals("[[2, 3]]",
2497    Arrays.deepToString(ml.getToRanges().toArray()));
2498  1 assertEquals("[[3, 3], [8, 12]]",
2499    Arrays.deepToString(ml.getFromRanges().toArray()));
2500    }
2501   
2502    /**
2503    * Tests for the method that locates the CDS sequence that has a mapping to
2504    * the given protein. That is, given a transcript-to-peptide mapping, find the
2505    * cds-to-peptide mapping that relates to both, and return the CDS sequence.
2506    */
 
2507  1 toggle @Test(groups = "Functional")
2508    public void testFindCdsForProtein()
2509    {
2510  1 List<AlignedCodonFrame> mappings = new ArrayList<>();
2511  1 AlignedCodonFrame acf1 = new AlignedCodonFrame();
2512  1 mappings.add(acf1);
2513   
2514  1 SequenceI dna1 = new Sequence("dna1", "cgatATcgGCTATCTATGacg");
2515  1 dna1.createDatasetSequence();
2516   
2517    // NB we currently exclude STOP codon from CDS sequences
2518    // the test would need to change if this changes in future
2519  1 SequenceI cds1 = new Sequence("cds1", "ATGCTATCT");
2520  1 cds1.createDatasetSequence();
2521   
2522  1 SequenceI pep1 = new Sequence("pep1", "MLS");
2523  1 pep1.createDatasetSequence();
2524  1 List<AlignedCodonFrame> seqMappings = new ArrayList<>();
2525  1 MapList mapList = new MapList(new int[] { 5, 6, 9, 15 },
2526    new int[]
2527    { 1, 3 }, 3, 1);
2528  1 Mapping dnaToPeptide = new Mapping(pep1.getDatasetSequence(), mapList);
2529   
2530    // add dna to peptide mapping
2531  1 seqMappings.add(acf1);
2532  1 acf1.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
2533    mapList);
2534   
2535    /*
2536    * first case - no dna-to-CDS mapping exists - search fails
2537    */
2538  1 SequenceI seq = AlignmentUtils.findCdsForProtein(mappings, dna1,
2539    seqMappings, dnaToPeptide);
2540  1 assertNull(seq);
2541   
2542    /*
2543    * second case - CDS-to-peptide mapping exists but no dna-to-CDS
2544    * - search fails
2545    */
2546    // todo this test fails if the mapping is added to acf1, not acf2
2547    // need to tidy up use of lists of mappings in AlignedCodonFrame
2548  1 AlignedCodonFrame acf2 = new AlignedCodonFrame();
2549  1 mappings.add(acf2);
2550  1 MapList cdsToPeptideMapping = new MapList(new int[] { 1, 9 },
2551    new int[]
2552    { 1, 3 }, 3, 1);
2553  1 acf2.addMap(cds1.getDatasetSequence(), pep1.getDatasetSequence(),
2554    cdsToPeptideMapping);
2555  1 assertNull(AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
2556    dnaToPeptide));
2557   
2558    /*
2559    * third case - add dna-to-CDS mapping - CDS is now found!
2560    */
2561  1 MapList dnaToCdsMapping = new MapList(new int[] { 5, 6, 9, 15 },
2562    new int[]
2563    { 1, 9 }, 1, 1);
2564  1 acf1.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(),
2565    dnaToCdsMapping);
2566  1 seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
2567    dnaToPeptide);
2568  1 assertSame(seq, cds1.getDatasetSequence());
2569    }
2570   
2571    /**
2572    * Tests for the method that locates the CDS sequence that has a mapping to
2573    * the given protein. That is, given a transcript-to-peptide mapping, find the
2574    * cds-to-peptide mapping that relates to both, and return the CDS sequence.
2575    * This test is for the case where transcript and CDS are the same length.
2576    */
 
2577  1 toggle @Test(groups = "Functional")
2578    public void testFindCdsForProtein_noUTR()
2579    {
2580  1 List<AlignedCodonFrame> mappings = new ArrayList<>();
2581  1 AlignedCodonFrame acf1 = new AlignedCodonFrame();
2582  1 mappings.add(acf1);
2583   
2584  1 SequenceI dna1 = new Sequence("dna1", "ATGCTATCTTAA");
2585  1 dna1.createDatasetSequence();
2586   
2587    // NB we currently exclude STOP codon from CDS sequences
2588    // the test would need to change if this changes in future
2589  1 SequenceI cds1 = new Sequence("cds1", "ATGCTATCT");
2590  1 cds1.createDatasetSequence();
2591   
2592  1 SequenceI pep1 = new Sequence("pep1", "MLS");
2593  1 pep1.createDatasetSequence();
2594  1 List<AlignedCodonFrame> seqMappings = new ArrayList<>();
2595  1 MapList mapList = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3,
2596    1);
2597  1 Mapping dnaToPeptide = new Mapping(pep1.getDatasetSequence(), mapList);
2598   
2599    // add dna to peptide mapping
2600  1 seqMappings.add(acf1);
2601  1 acf1.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
2602    mapList);
2603   
2604    /*
2605    * first case - transcript lacks CDS features - it appears to be
2606    * the CDS sequence and is returned
2607    */
2608  1 SequenceI seq = AlignmentUtils.findCdsForProtein(mappings, dna1,
2609    seqMappings, dnaToPeptide);
2610  1 assertSame(seq, dna1.getDatasetSequence());
2611   
2612    /*
2613    * second case - transcript has CDS feature - this means it is
2614    * not returned as a match for CDS (CDS sequences don't have CDS features)
2615    */
2616  1 dna1.addSequenceFeature(
2617    new SequenceFeature(SequenceOntologyI.CDS, "cds", 1, 12, null));
2618  1 seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
2619    dnaToPeptide);
2620  1 assertNull(seq);
2621   
2622    /*
2623    * third case - CDS-to-peptide mapping exists but no dna-to-CDS
2624    * - search fails
2625    */
2626    // todo this test fails if the mapping is added to acf1, not acf2
2627    // need to tidy up use of lists of mappings in AlignedCodonFrame
2628  1 AlignedCodonFrame acf2 = new AlignedCodonFrame();
2629  1 mappings.add(acf2);
2630  1 MapList cdsToPeptideMapping = new MapList(new int[] { 1, 9 },
2631    new int[]
2632    { 1, 3 }, 3, 1);
2633  1 acf2.addMap(cds1.getDatasetSequence(), pep1.getDatasetSequence(),
2634    cdsToPeptideMapping);
2635  1 assertNull(AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
2636    dnaToPeptide));
2637   
2638    /*
2639    * fourth case - add dna-to-CDS mapping - CDS is now found!
2640    */
2641  1 MapList dnaToCdsMapping = new MapList(new int[] { 1, 9 },
2642    new int[]
2643    { 1, 9 }, 1, 1);
2644  1 acf1.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(),
2645    dnaToCdsMapping);
2646  1 seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
2647    dnaToPeptide);
2648  1 assertSame(seq, cds1.getDatasetSequence());
2649    }
2650   
 
2651  1 toggle @Test(groups = "Functional")
2652    public void testAddReferenceAnnotations()
2653    {
2654  1 SequenceI longseq = new Sequence("longA", "ASDASDASDASDAASDASDASDASDA");
2655  1 Annotation[] aa = new Annotation[longseq.getLength()];
2656   
2657  27 for (int p = 0; p < aa.length; p++)
2658    {
2659  26 aa[p] = new Annotation("P", "pos " + (p + 1), (char) 0,
2660    (float) p + 1);
2661    }
2662  1 AlignmentAnnotation refAnnot = new AlignmentAnnotation("LongSeqAnnot",
2663    "Annotations", aa);
2664  1 refAnnot.setCalcId("Test");
2665  1 longseq.addAlignmentAnnotation(refAnnot);
2666  1 verifyExpectedSequenceAnnotation(refAnnot);
2667   
2668  1 Alignment ourAl = new Alignment(
2669    new SequenceI[]
2670    { longseq.getSubSequence(5, 10),
2671    longseq.getSubSequence(7, 12) });
2672  1 ourAl.createDatasetAlignment();
2673   
2674    // transfer annotation
2675  1 SortedMap<String, String> tipEntries = new TreeMap<>();
2676  1 Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
2677   
2678  1 AlignmentUtils.findAddableReferenceAnnotations(ourAl.getSequences(),
2679    tipEntries, candidates, ourAl);
2680  1 AlignmentUtils.addReferenceAnnotations(candidates, ourAl, null);
2681   
2682  1 assertNotNull(ourAl.getAlignmentAnnotation());
2683  1 assertEquals(ourAl.getAlignmentAnnotation().length, 2);
2684   
2685  1 for (AlignmentAnnotation alan : ourAl.getAlignmentAnnotation())
2686    {
2687  2 verifyExpectedSequenceAnnotation(alan);
2688    }
2689    // Everything above works for 2.11.3 and 2.11.2.x.
2690    // now simulate copy/paste to new alignment
2691  1 SequenceI[] newSeqAl = new SequenceI[2];
2692    // copy sequences but no annotation
2693  1 newSeqAl[0] = new Sequence(ourAl.getSequenceAt(0),
2694    ourAl.getSequenceAt(0).getAnnotation());
2695  1 newSeqAl[1] = new Sequence(ourAl.getSequenceAt(1),
2696    ourAl.getSequenceAt(1).getAnnotation());
2697   
2698  1 Alignment newAl = new Alignment(newSeqAl);
2699    // delete annotation
2700  1 for (SequenceI sq : newAl.getSequences())
2701    {
2702  2 sq.setAlignmentAnnotation(new AlignmentAnnotation[0]);
2703    }
2704    // JAL-4182 scenario test
2705  1 SequenceGroup sg = new SequenceGroup(Arrays.asList(newSeqAl));
2706  1 sg.setStartRes(0);
2707  1 sg.setEndRes(newAl.getWidth());
2708  1 AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[0],
2709    newSeqAl[0].getDatasetSequence().getAnnotation()[0], sg);
2710  1 AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[1],
2711    newSeqAl[1].getDatasetSequence().getAnnotation()[0], sg);
2712  1 for (AlignmentAnnotation alan : newAl.getAlignmentAnnotation())
2713    {
2714  2 verifyExpectedSequenceAnnotation(alan);
2715    }
2716    }
2717   
2718    /**
2719    * helper - tests annotation is mapped to position it was originally created
2720    * for
2721    *
2722    * @param alan
2723    */
 
2724  5 toggle private void verifyExpectedSequenceAnnotation(AlignmentAnnotation alan)
2725    {
2726  51 for (int c = 0; c < alan.annotations.length; c++)
2727    {
2728  46 Annotation a = alan.annotations[c];
2729  46 if (a != null)
2730    {
2731  46 assertEquals("Misaligned annotation at " + c,
2732    (float) alan.sequenceRef.findPosition(c), a.value);
2733    }
2734    else
2735    {
2736  0 assertTrue("Unexpected Null at position " + c,
2737    c >= alan.sequenceRef.getLength()
2738    || Comparison.isGap(alan.sequenceRef.getCharAt(c)));
2739    }
2740    }
2741    }
2742   
 
2743  1 toggle @Test(groups = "Functional")
2744    public void testAddReferenceContactMap()
2745    {
2746  1 SequenceI sq = new Sequence("a", "SSSQ");
2747  1 ContactMatrixI cm = new SeqDistanceContactMatrix(4);
2748  1 AlignmentAnnotation cm_aan = sq.addContactList(cm);
2749  1 cm_aan.description = cm_aan.description + " cm1";
2750  1 SequenceI dssq = sq.createDatasetSequence();
2751   
2752    // remove annotation on our non-dataset sequence
2753  1 sq.removeAlignmentAnnotation(sq.getAnnotation()[0]);
2754    // test transfer
2755  1 Alignment al = new Alignment(new SequenceI[] { sq });
2756  1 SortedMap<String, String> tipEntries = new TreeMap<>();
2757  1 Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
2758   
2759  1 AlignmentUtils.findAddableReferenceAnnotations(al.getSequences(),
2760    tipEntries, candidates, al);
2761  1 AlignmentUtils.addReferenceAnnotations(candidates, al, null);
2762  1 assertTrue("No contact map annotation transferred",
2763    al.getAlignmentAnnotation() != null
2764    && al.getAlignmentAnnotation().length == 1);
2765  1 AlignmentAnnotation alan = al.findAnnotations(sq, null, cm_aan.label)
2766    .iterator().next();
2767  1 ContactMatrixI t_cm = al.getContactMatrixFor(alan);
2768  1 assertNotNull("No contact map for the transferred annotation row.",
2769    t_cm);
2770  1 assertTrue(t_cm instanceof SeqDistanceContactMatrix);
2771  1 assertTrue(((SeqDistanceContactMatrix) t_cm).hasReferenceSeq());
2772   
2773  1 ContactListI cl = al.getContactListFor(alan, 1);
2774  1 assertNotNull(
2775    "No contact matrix recovered after reference annotation transfer",
2776    cl);
2777    // semantics of sequence associated contact list is slightly tricky - column
2778    // 3 in alignment should have data
2779  1 cl = al.getContactListFor(alan, 3);
2780  1 assertNotNull(
2781    "Contact matrix should have data for last position in sequence",
2782    cl);
2783   
2784  1 ContactMatrixI cm2 = new SeqDistanceContactMatrix(4);
2785  1 dssq.addContactList(cm2);
2786  1 tipEntries = new TreeMap<>();
2787  1 candidates = new LinkedHashMap<>();
2788   
2789  1 AlignmentUtils.findAddableReferenceAnnotations(al.getSequences(),
2790    tipEntries, candidates, al);
2791  1 AlignmentUtils.addReferenceAnnotations(candidates, al, null);
2792  1 assertTrue("Expected two contact map annotation transferred",
2793    al.getAlignmentAnnotation() != null
2794    && al.getAlignmentAnnotation().length == 2);
2795   
2796    }
2797   
 
2798  5 toggle @Test(
2799    groups = "Functional",
2800    dataProvider = "SecondaryStructureAnnotations")
2801    public void testSecondaryStructurePresentAndSources(
2802    AlignmentAnnotation[] annotations, boolean expectedSSPresent,
2803    ArrayList<String> expectedSSSources)
2804    {
2805  5 Assert.assertEquals(expectedSSPresent,
2806    AlignmentUtils.isSecondaryStructurePresent(annotations));
2807    }
2808   
 
2809  1 toggle @DataProvider(name = "SecondaryStructureAnnotations")
2810    public static Object[][] provideSecondaryStructureAnnotations()
2811    {
2812  1 AlignmentAnnotation ann1 = new AlignmentAnnotation(
2813    "Secondary Structure", "Secondary Structure",
2814    new Annotation[] {});
2815  1 AlignmentAnnotation ann2 = new AlignmentAnnotation("jnetpred",
2816    "jnetpred", new Annotation[] {});
2817  1 AlignmentAnnotation ann3 = new AlignmentAnnotation("Temp", "Temp",
2818    new Annotation[] {});
2819  1 AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "Temp",
2820    new Annotation[] {});
2821   
2822  1 List<String> ssSources1 = new ArrayList<>(
2823    Arrays.asList("3D Structures"));
2824  1 List<String> ssSources2 = new ArrayList<>(Arrays.asList("JPred"));
2825  1 List<String> ssSources3 = new ArrayList<>(
2826    Arrays.asList("3D Structures", "JPred"));
2827  1 List<String> ssSources4 = new ArrayList<>();
2828   
2829  1 return new Object[][] {
2830    { new AlignmentAnnotation[]
2831    { ann1, ann3, ann4 }, true, ssSources1 },
2832    { new AlignmentAnnotation[]
2833    { ann2, ann3, ann4 }, true, ssSources2 },
2834    { new AlignmentAnnotation[]
2835    { ann3, ann4 }, false, ssSources4 },
2836    { new AlignmentAnnotation[] {}, false, ssSources4 },
2837    { new AlignmentAnnotation[]
2838    { ann1, ann2, ann3, ann4 }, true, ssSources3 } };
2839    }
2840   
 
2841  0 toggle @Test(dataProvider = "SecondaryStructureAnnotationColours")
2842    public void testSecondaryStructureAnnotationColour(char symbol,
2843    Color expectedColor)
2844    {
2845  0 Color actualColor = AlignmentUtils
2846    .getSecondaryStructureAnnotationColour(symbol);
2847  0 Assert.assertEquals(actualColor, expectedColor);
2848    }
2849   
 
2850  0 toggle @DataProvider(name = "SecondaryStructureAnnotationColours")
2851    public static Object[][] provideSecondaryStructureAnnotationColours()
2852    {
2853  0 return new Object[][] { { 'C', Color.gray }, { 'E', Color.green },
2854    { 'H', Color.red },
2855    { '-', Color.white } };
2856    }
2857   
 
2858  0 toggle @Test(dataProvider = "SSAnnotationPresence")
2859    public void testIsSSAnnotationPresent(
2860    Map<SequenceI, List<AlignmentAnnotation>> annotations,
2861    boolean expectedPresence)
2862    {
2863  0 boolean actualPresence = AlignmentUtils
2864    .isSSAnnotationPresent(annotations);
2865  0 Assert.assertEquals(actualPresence, expectedPresence);
2866    }
2867   
 
2868  0 toggle @DataProvider(name = "SSAnnotationPresence")
2869    public static Object[][] provideSSAnnotationPresence()
2870    {
2871  0 Map<SequenceI, List<AlignmentAnnotation>> annotations1 = new HashMap<>();
2872  0 SequenceI seq1 = new Sequence("Seq1", "ASD---ASD---ASD", 37, 45);
2873  0 List<AlignmentAnnotation> annotationsList1 = new ArrayList<>();
2874  0 annotationsList1.add(new AlignmentAnnotation("Secondary Structure",
2875    "Secondary Structure", new Annotation[] {}));
2876  0 annotations1.put(seq1, annotationsList1); // Annotation present secondary
2877    // structure for seq1
2878   
2879  0 Map<SequenceI, List<AlignmentAnnotation>> annotations2 = new HashMap<>();
2880  0 SequenceI seq2 = new Sequence("Seq2", "ASD---ASD------", 37, 42);
2881  0 List<AlignmentAnnotation> annotationsList2 = new ArrayList<>();
2882  0 annotationsList2.add(new AlignmentAnnotation("Other Annotation",
2883    "Other Annotation", new Annotation[] {}));
2884  0 annotations2.put(seq2, annotationsList2); // Annotation not related to any
2885    // of secondary structure for seq2
2886   
2887  0 Map<SequenceI, List<AlignmentAnnotation>> annotations3 = new HashMap<>();
2888    // Empty annotation map
2889   
2890  0 Map<SequenceI, List<AlignmentAnnotation>> annotations4 = new HashMap<>();
2891  0 SequenceI seq4 = new Sequence("Seq4", "ASD---ASD---AS-", 37, 44);
2892  0 List<AlignmentAnnotation> annotationsList4 = new ArrayList<>();
2893  0 annotationsList4.add(new AlignmentAnnotation("jnetpred", "jnetpred",
2894    new Annotation[] {}));
2895  0 annotations4.put(seq4, annotationsList4); // Annotation present from JPred
2896    // for seq4
2897   
2898  0 return new Object[][] { { annotations1, true }, // Annotations present
2899    // secondary structure
2900    // present
2901    { annotations2, false }, // No annotations related to any of the
2902    // secondary structure present
2903    { annotations3, false }, // Empty annotation map
2904    { annotations4, true }, // Annotations present from JPred secondary
2905    // structure present
2906    };
2907    }
2908   
 
2909  0 toggle @DataProvider(name = "SSSourceFromAnnotationDescription")
2910    public static Object[][] provideSSSourceFromAnnotationDescription()
2911    {
2912  0 Map<SequenceI, List<AlignmentAnnotation>> annotations1 = new HashMap<>();
2913  0 SequenceI seq1 = new Sequence("Seq1", "ASD---ASD---ASD", 37, 45);
2914  0 List<AlignmentAnnotation> annotationsList1 = new ArrayList<>();
2915  0 annotationsList1.add(new AlignmentAnnotation("jnetpred", "JPred Output",
2916    new Annotation[] {}));
2917  0 annotations1.put(seq1, annotationsList1); // Annotation present from JPred
2918    // for seq1
2919   
2920  0 Map<SequenceI, List<AlignmentAnnotation>> annotations2 = new HashMap<>();
2921  0 SequenceI seq2 = new Sequence("Seq2", "ASD---ASD------", 37, 42);
2922  0 List<AlignmentAnnotation> annotationsList2 = new ArrayList<>();
2923  0 annotationsList2.add(new AlignmentAnnotation("Secondary Structure",
2924    "Secondary Structure for af-q43517-f1A", new Annotation[] {}));
2925  0 annotations2.put(seq2, annotationsList2); // Annotation present secondary
2926    // structure from Alphafold for
2927    // seq2
2928   
2929  0 Map<SequenceI, List<AlignmentAnnotation>> annotations3 = new HashMap<>();
2930    // Empty annotation map
2931   
2932  0 Map<SequenceI, List<AlignmentAnnotation>> annotations4 = new HashMap<>();
2933  0 SequenceI seq4 = new Sequence("Seq4", "ASD---ASD---AS-", 37, 44);
2934  0 List<AlignmentAnnotation> annotationsList4 = new ArrayList<>();
2935  0 annotationsList4.add(new AlignmentAnnotation("Secondary Structure",
2936    "Secondary Structure for 4zhpA", new Annotation[] {}));
2937  0 annotations4.put(seq4, annotationsList4); // Annotation present secondary
2938    // structure from pdb for seq4
2939   
2940  0 Map<SequenceI, List<AlignmentAnnotation>> annotations5 = new HashMap<>();
2941  0 SequenceI seq5 = new Sequence("Seq5", "ASD---ASD---AS-", 37, 44);
2942  0 List<AlignmentAnnotation> annotationsList5 = new ArrayList<>();
2943  0 annotationsList5.add(new AlignmentAnnotation("Secondary Structure",
2944    "Secondary Structure for p09911_54-147__3a7wzn.1.p3502557454997462030P",
2945    new Annotation[] {}));
2946  0 annotations5.put(seq5, annotationsList5); // Annotation present secondary
2947    // structure from Swiss model for
2948    // seq5
2949   
2950    // JPred Output - JPred
2951    // Secondary Structure for af-q43517-f1A - Alphafold
2952    // Secondary Structure for 4zhpA - Experimental
2953    // Secondary Structure for p09911_54-147__3a7wzn.1.p3502557454997462030P -
2954    // Swiss Model
2955   
2956  0 return new Object[][] { { annotations1, "JPred" },
2957    { annotations2, "Alphafold" },
2958    { annotations3, null },
2959    { annotations4, "PDB" },
2960    { annotations5, "Swiss Model" } };
2961    }
2962   
2963    }
  • Report generated by OpenClover v 4.4.1 on Mon Nov 18 2024 09:54:26 GMT using coverage data from Mon Nov 18 2024 09:54:15 GMT.
  • OpenClover is free and open-source software.