2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.analysis;
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertFalse;
25 import static org.testng.AssertJUnit.assertNotNull;
26 import static org.testng.AssertJUnit.assertNull;
27 import static org.testng.AssertJUnit.assertSame;
28 import static org.testng.AssertJUnit.assertTrue;
30 import jalview.analysis.AlignmentUtils.DnaVariant;
31 import jalview.datamodel.AlignedCodonFrame;
32 import jalview.datamodel.Alignment;
33 import jalview.datamodel.AlignmentAnnotation;
34 import jalview.datamodel.AlignmentI;
35 import jalview.datamodel.Annotation;
36 import jalview.datamodel.DBRefEntry;
37 import jalview.datamodel.Mapping;
38 import jalview.datamodel.SearchResultMatchI;
39 import jalview.datamodel.SearchResultsI;
40 import jalview.datamodel.Sequence;
41 import jalview.datamodel.SequenceFeature;
42 import jalview.datamodel.SequenceI;
43 import jalview.io.AppletFormatAdapter;
44 import jalview.io.DataSourceType;
45 import jalview.io.FileFormat;
46 import jalview.io.FileFormatI;
47 import jalview.io.FormatAdapter;
48 import jalview.util.MapList;
49 import jalview.util.MappingUtils;
51 import java.io.IOException;
52 import java.util.ArrayList;
53 import java.util.Arrays;
54 import java.util.LinkedHashMap;
55 import java.util.List;
57 import java.util.TreeMap;
59 import org.testng.annotations.Test;
61 public class AlignmentUtilsTests
63 public static Sequence ts = new Sequence("short",
64 "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
66 @Test(groups = { "Functional" })
67 public void testExpandContext()
69 AlignmentI al = new Alignment(new Sequence[] {});
70 for (int i = 4; i < 14; i += 2)
72 SequenceI s1 = ts.deriveSequence().getSubSequence(i, i + 7);
75 System.out.println(new AppletFormatAdapter().formatSequences(
78 for (int flnk = -1; flnk < 25; flnk++)
80 AlignmentI exp = AlignmentUtils.expandContext(al, flnk);
81 System.out.println("\nFlank size: " + flnk);
82 System.out.println(new AppletFormatAdapter().formatSequences(
83 FileFormat.Clustal, exp, true));
87 * Full expansion to complete sequences
89 for (SequenceI sq : exp.getSequences())
91 String ung = sq.getSequenceAsString().replaceAll("-+", "");
92 final String errorMsg = "Flanking sequence not the same as original dataset sequence.\n"
95 + sq.getDatasetSequence().getSequenceAsString();
96 assertTrue(errorMsg, ung.equalsIgnoreCase(sq.getDatasetSequence()
97 .getSequenceAsString()));
103 * Last sequence is fully expanded, others have leading gaps to match
105 assertTrue(exp.getSequenceAt(4).getSequenceAsString()
107 assertTrue(exp.getSequenceAt(3).getSequenceAsString()
108 .startsWith("--abc"));
109 assertTrue(exp.getSequenceAt(2).getSequenceAsString()
110 .startsWith("----abc"));
111 assertTrue(exp.getSequenceAt(1).getSequenceAsString()
112 .startsWith("------abc"));
113 assertTrue(exp.getSequenceAt(0).getSequenceAsString()
114 .startsWith("--------abc"));
120 * Test that annotations are correctly adjusted by expandContext
122 @Test(groups = { "Functional" })
123 public void testExpandContext_annotation()
125 AlignmentI al = new Alignment(new Sequence[] {});
126 SequenceI ds = new Sequence("Seq1", "ABCDEFGHI");
128 SequenceI seq1 = ds.deriveSequence().getSubSequence(3, 6);
129 al.addSequence(seq1);
132 * Annotate DEF with 4/5/6 respectively
134 Annotation[] anns = new Annotation[] { new Annotation(4),
135 new Annotation(5), new Annotation(6) };
136 AlignmentAnnotation ann = new AlignmentAnnotation("SS",
137 "secondary structure", anns);
138 seq1.addAlignmentAnnotation(ann);
141 * The annotations array should match aligned positions
143 assertEquals(3, ann.annotations.length);
144 assertEquals(4, ann.annotations[0].value, 0.001);
145 assertEquals(5, ann.annotations[1].value, 0.001);
146 assertEquals(6, ann.annotations[2].value, 0.001);
149 * Check annotation to sequence position mappings before expanding the
150 * sequence; these are set up in Sequence.addAlignmentAnnotation ->
151 * Annotation.setSequenceRef -> createSequenceMappings
153 assertNull(ann.getAnnotationForPosition(1));
154 assertNull(ann.getAnnotationForPosition(2));
155 assertNull(ann.getAnnotationForPosition(3));
156 assertEquals(4, ann.getAnnotationForPosition(4).value, 0.001);
157 assertEquals(5, ann.getAnnotationForPosition(5).value, 0.001);
158 assertEquals(6, ann.getAnnotationForPosition(6).value, 0.001);
159 assertNull(ann.getAnnotationForPosition(7));
160 assertNull(ann.getAnnotationForPosition(8));
161 assertNull(ann.getAnnotationForPosition(9));
164 * Expand the subsequence to the full sequence abcDEFghi
166 AlignmentI expanded = AlignmentUtils.expandContext(al, -1);
167 assertEquals("abcDEFghi", expanded.getSequenceAt(0)
168 .getSequenceAsString());
171 * Confirm the alignment and sequence have the same SS annotation,
172 * referencing the expanded sequence
174 ann = expanded.getSequenceAt(0).getAnnotation()[0];
175 assertSame(ann, expanded.getAlignmentAnnotation()[0]);
176 assertSame(expanded.getSequenceAt(0), ann.sequenceRef);
179 * The annotations array should have null values except for annotated
182 assertNull(ann.annotations[0]);
183 assertNull(ann.annotations[1]);
184 assertNull(ann.annotations[2]);
185 assertEquals(4, ann.annotations[3].value, 0.001);
186 assertEquals(5, ann.annotations[4].value, 0.001);
187 assertEquals(6, ann.annotations[5].value, 0.001);
188 assertNull(ann.annotations[6]);
189 assertNull(ann.annotations[7]);
190 assertNull(ann.annotations[8]);
193 * sequence position mappings should be unchanged
195 assertNull(ann.getAnnotationForPosition(1));
196 assertNull(ann.getAnnotationForPosition(2));
197 assertNull(ann.getAnnotationForPosition(3));
198 assertEquals(4, ann.getAnnotationForPosition(4).value, 0.001);
199 assertEquals(5, ann.getAnnotationForPosition(5).value, 0.001);
200 assertEquals(6, ann.getAnnotationForPosition(6).value, 0.001);
201 assertNull(ann.getAnnotationForPosition(7));
202 assertNull(ann.getAnnotationForPosition(8));
203 assertNull(ann.getAnnotationForPosition(9));
207 * Test method that returns a map of lists of sequences by sequence name.
209 * @throws IOException
211 @Test(groups = { "Functional" })
212 public void testGetSequencesByName() throws IOException
214 final String data = ">Seq1Name\nKQYL\n" + ">Seq2Name\nRFPW\n"
215 + ">Seq1Name\nABCD\n";
216 AlignmentI al = loadAlignment(data, FileFormat.Fasta);
217 Map<String, List<SequenceI>> map = AlignmentUtils
218 .getSequencesByName(al);
219 assertEquals(2, map.keySet().size());
220 assertEquals(2, map.get("Seq1Name").size());
221 assertEquals("KQYL", map.get("Seq1Name").get(0).getSequenceAsString());
222 assertEquals("ABCD", map.get("Seq1Name").get(1).getSequenceAsString());
223 assertEquals(1, map.get("Seq2Name").size());
224 assertEquals("RFPW", map.get("Seq2Name").get(0).getSequenceAsString());
228 * Helper method to load an alignment and ensure dataset sequences are set up.
234 * @throws IOException
236 protected AlignmentI loadAlignment(final String data, FileFormatI format)
239 AlignmentI a = new FormatAdapter().readFile(data,
240 DataSourceType.PASTE, format);
246 * Test mapping of protein to cDNA, for the case where we have no sequence
247 * cross-references, so mappings are made first-served 1-1 where sequences
250 * @throws IOException
252 @Test(groups = { "Functional" })
253 public void testMapProteinAlignmentToCdna_noXrefs() throws IOException
255 List<SequenceI> protseqs = new ArrayList<SequenceI>();
256 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
257 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
258 protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
259 AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
260 protein.setDataset(null);
262 List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
263 dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR
264 dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAA")); // = EIQ
265 dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ
266 dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG")); // = EIQ
267 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
268 cdna.setDataset(null);
270 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
272 // 3 mappings made, each from 1 to 1 sequence
273 assertEquals(3, protein.getCodonFrames().size());
274 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
275 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
276 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
278 // V12345 mapped to A22222
279 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
281 assertEquals(1, acf.getdnaSeqs().length);
282 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
283 acf.getdnaSeqs()[0]);
284 Mapping[] protMappings = acf.getProtMappings();
285 assertEquals(1, protMappings.length);
286 MapList mapList = protMappings[0].getMap();
287 assertEquals(3, mapList.getFromRatio());
288 assertEquals(1, mapList.getToRatio());
289 assertTrue(Arrays.equals(new int[] { 1, 9 }, mapList.getFromRanges()
291 assertEquals(1, mapList.getFromRanges().size());
292 assertTrue(Arrays.equals(new int[] { 1, 3 },
293 mapList.getToRanges().get(0)));
294 assertEquals(1, mapList.getToRanges().size());
296 // V12346 mapped to A33333
297 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
298 assertEquals(1, acf.getdnaSeqs().length);
299 assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
300 acf.getdnaSeqs()[0]);
302 // V12347 mapped to A11111
303 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
304 assertEquals(1, acf.getdnaSeqs().length);
305 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
306 acf.getdnaSeqs()[0]);
308 // no mapping involving the 'extra' A44444
309 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(3)).isEmpty());
313 * Test for the alignSequenceAs method that takes two sequences and a mapping.
315 @Test(groups = { "Functional" })
316 public void testAlignSequenceAs_withMapping_noIntrons()
318 MapList map = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 }, 3, 1);
321 * No existing gaps in dna:
323 checkAlignSequenceAs("GGGAAA", "-A-L-", false, false, map,
327 * Now introduce gaps in dna but ignore them when realigning.
329 checkAlignSequenceAs("-G-G-G-A-A-A-", "-A-L-", false, false, map,
333 * Now include gaps in dna when realigning. First retaining 'mapped' gaps
334 * only, i.e. those within the exon region.
336 checkAlignSequenceAs("-G-G--G-A--A-A-", "-A-L-", true, false, map,
337 "---G-G--G---A--A-A");
340 * Include all gaps in dna when realigning (within and without the exon
341 * region). The leading gap, and the gaps between codons, are subsumed by
342 * the protein alignment gap.
344 checkAlignSequenceAs("-G-GG--AA-A---", "-A-L-", true, true, map,
345 "---G-GG---AA-A---");
348 * Include only unmapped gaps in dna when realigning (outside the exon
349 * region). The leading gap, and the gaps between codons, are subsumed by
350 * the protein alignment gap.
352 checkAlignSequenceAs("-G-GG--AA-A-", "-A-L-", false, true, map,
357 * Test for the alignSequenceAs method that takes two sequences and a mapping.
359 @Test(groups = { "Functional" })
360 public void testAlignSequenceAs_withMapping_withIntrons()
363 * Exons at codon 2 (AAA) and 4 (TTT)
365 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
366 new int[] { 1, 2 }, 3, 1);
369 * Simple case: no gaps in dna
371 checkAlignSequenceAs("GGGAAACCCTTTGGG", "--A-L-", false, false, map,
372 "GGG---AAACCCTTTGGG");
375 * Add gaps to dna - but ignore when realigning.
377 checkAlignSequenceAs("-G-G-G--A--A---AC-CC-T-TT-GG-G-", "--A-L-",
378 false, false, map, "GGG---AAACCCTTTGGG");
381 * Add gaps to dna - include within exons only when realigning.
383 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
384 true, false, map, "GGG---A--A---ACCCT-TTGGG");
387 * Include gaps outside exons only when realigning.
389 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
390 false, true, map, "-G-G-GAAAC-CCTTT-GG-G-");
393 * Include gaps following first intron if we are 'preserving mapped gaps'
395 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
396 true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
399 * Include all gaps in dna when realigning.
401 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
402 true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
406 * Test for the case where not all of the protein sequence is mapped to cDNA.
408 @Test(groups = { "Functional" })
409 public void testAlignSequenceAs_withMapping_withUnmappedProtein()
412 * Exons at codon 2 (AAA) and 4 (TTT) mapped to A and P
414 final MapList map = new MapList(new int[] { 4, 6, 10, 12 }, new int[] {
418 * -L- 'aligns' ccc------
420 checkAlignSequenceAs("gggAAAcccTTTggg", "-A-L-P-", false, false, map,
421 "gggAAAccc------TTTggg");
425 * Helper method that performs and verifies the method under test.
428 * the sequence to be realigned
430 * the sequence whose alignment is to be copied
431 * @param preserveMappedGaps
432 * @param preserveUnmappedGaps
436 protected void checkAlignSequenceAs(final String alignee,
437 final String alignModel, final boolean preserveMappedGaps,
438 final boolean preserveUnmappedGaps, MapList map,
439 final String expected)
441 SequenceI alignMe = new Sequence("Seq1", alignee);
442 alignMe.createDatasetSequence();
443 SequenceI alignFrom = new Sequence("Seq2", alignModel);
444 alignFrom.createDatasetSequence();
445 AlignedCodonFrame acf = new AlignedCodonFrame();
446 acf.addMap(alignMe.getDatasetSequence(),
447 alignFrom.getDatasetSequence(), map);
449 AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "---", '-',
450 preserveMappedGaps, preserveUnmappedGaps);
451 assertEquals(expected, alignMe.getSequenceAsString());
455 * Test for the alignSequenceAs method where we preserve gaps in introns only.
457 @Test(groups = { "Functional" })
458 public void testAlignSequenceAs_keepIntronGapsOnly()
462 * Intron GGGAAA followed by exon CCCTTT
464 MapList map = new MapList(new int[] { 7, 12 }, new int[] { 1, 2 }, 3, 1);
466 checkAlignSequenceAs("GG-G-AA-A-C-CC-T-TT", "AL", false, true, map,
471 * Test the method that realigns protein to match mapped codon alignment.
473 @Test(groups = { "Functional" })
474 public void testAlignProteinAsDna()
476 // seq1 codons are [1,2,3] [4,5,6] [7,8,9] [10,11,12]
477 SequenceI dna1 = new Sequence("Seq1", "TGCCATTACCAG-");
478 // seq2 codons are [1,3,4] [5,6,7] [8,9,10] [11,12,13]
479 SequenceI dna2 = new Sequence("Seq2", "T-GCCATTACCAG");
480 // seq3 codons are [1,2,3] [4,5,7] [8,9,10] [11,12,13]
481 SequenceI dna3 = new Sequence("Seq3", "TGCCA-TTACCAG");
482 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
483 dna.setDataset(null);
485 // protein alignment will be realigned like dna
486 SequenceI prot1 = new Sequence("Seq1", "CHYQ");
487 SequenceI prot2 = new Sequence("Seq2", "CHYQ");
488 SequenceI prot3 = new Sequence("Seq3", "CHYQ");
489 SequenceI prot4 = new Sequence("Seq4", "R-QSV"); // unmapped, unchanged
490 AlignmentI protein = new Alignment(new SequenceI[] { prot1, prot2,
492 protein.setDataset(null);
494 MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1);
495 AlignedCodonFrame acf = new AlignedCodonFrame();
496 acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
497 acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map);
498 acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map);
499 ArrayList<AlignedCodonFrame> acfs = new ArrayList<AlignedCodonFrame>();
501 protein.setCodonFrames(acfs);
504 * Translated codon order is [1,2,3] [1,3,4] [4,5,6] [4,5,7] [5,6,7] [7,8,9]
505 * [8,9,10] [10,11,12] [11,12,13]
507 AlignmentUtils.alignProteinAsDna(protein, dna);
508 assertEquals("C-H--Y-Q-", prot1.getSequenceAsString());
509 assertEquals("-C--H-Y-Q", prot2.getSequenceAsString());
510 assertEquals("C--H--Y-Q", prot3.getSequenceAsString());
511 assertEquals("R-QSV", prot4.getSequenceAsString());
515 * Test the method that tests whether a CDNA sequence translates to a protein
518 @Test(groups = { "Functional" })
519 public void testTranslatesAs()
521 // null arguments check
522 assertFalse(AlignmentUtils.translatesAs(null, 0, null));
523 assertFalse(AlignmentUtils.translatesAs(new char[] { 't' }, 0, null));
524 assertFalse(AlignmentUtils.translatesAs(null, 0, new char[] { 'a' }));
526 // straight translation
527 assertTrue(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
528 "FPKG".toCharArray()));
529 // with extra start codon (not in protein)
530 assertTrue(AlignmentUtils.translatesAs("atgtttcccaaaggg".toCharArray(),
531 3, "FPKG".toCharArray()));
532 // with stop codon1 (not in protein)
533 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtaa".toCharArray(),
534 0, "FPKG".toCharArray()));
535 // with stop codon1 (in protein as *)
536 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtaa".toCharArray(),
537 0, "FPKG*".toCharArray()));
538 // with stop codon2 (not in protein)
539 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtag".toCharArray(),
540 0, "FPKG".toCharArray()));
541 // with stop codon3 (not in protein)
542 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtga".toCharArray(),
543 0, "FPKG".toCharArray()));
544 // with start and stop codon1
545 assertTrue(AlignmentUtils.translatesAs(
546 "atgtttcccaaagggtaa".toCharArray(), 3, "FPKG".toCharArray()));
547 // with start and stop codon1 (in protein as *)
548 assertTrue(AlignmentUtils.translatesAs(
549 "atgtttcccaaagggtaa".toCharArray(), 3, "FPKG*".toCharArray()));
550 // with start and stop codon2
551 assertTrue(AlignmentUtils.translatesAs(
552 "atgtttcccaaagggtag".toCharArray(), 3, "FPKG".toCharArray()));
553 // with start and stop codon3
554 assertTrue(AlignmentUtils.translatesAs(
555 "atgtttcccaaagggtga".toCharArray(), 3, "FPKG".toCharArray()));
557 // with embedded stop codons
558 assertTrue(AlignmentUtils.translatesAs(
559 "atgtttTAGcccaaaTAAgggtga".toCharArray(), 3,
560 "F*PK*G".toCharArray()));
563 assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
564 0, "FPMG".toCharArray()));
567 assertFalse(AlignmentUtils.translatesAs("tttcccaaagg".toCharArray(), 0,
568 "FPKG".toCharArray()));
571 assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
572 0, "FPK".toCharArray()));
574 // overlong dna (doesn't end in stop codon)
575 assertFalse(AlignmentUtils.translatesAs(
576 "tttcccaaagggttt".toCharArray(), 0, "FPKG".toCharArray()));
578 // dna + stop codon + more
579 assertFalse(AlignmentUtils.translatesAs(
580 "tttcccaaagggttaga".toCharArray(), 0, "FPKG".toCharArray()));
583 assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
584 0, "FPKGQ".toCharArray()));
588 * Test mapping of protein to cDNA, for cases where the cDNA has start and/or
589 * stop codons in addition to the protein coding sequence.
591 * @throws IOException
593 @Test(groups = { "Functional" })
594 public void testMapProteinAlignmentToCdna_withStartAndStopCodons()
597 List<SequenceI> protseqs = new ArrayList<SequenceI>();
598 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
599 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
600 protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
601 AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
602 protein.setDataset(null);
604 List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
606 dnaseqs.add(new Sequence("EMBL|A11111", "ATGTCAGCACGC"));
608 dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAATAA"));
609 // = start +EIQ + stop
610 dnaseqs.add(new Sequence("EMBL|A33333", "ATGGAAATCCAGTAG"));
611 dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG"));
612 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
613 cdna.setDataset(null);
615 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
617 // 3 mappings made, each from 1 to 1 sequence
618 assertEquals(3, protein.getCodonFrames().size());
619 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
620 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
621 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
623 // V12345 mapped from A22222
624 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
626 assertEquals(1, acf.getdnaSeqs().length);
627 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
628 acf.getdnaSeqs()[0]);
629 Mapping[] protMappings = acf.getProtMappings();
630 assertEquals(1, protMappings.length);
631 MapList mapList = protMappings[0].getMap();
632 assertEquals(3, mapList.getFromRatio());
633 assertEquals(1, mapList.getToRatio());
634 assertTrue(Arrays.equals(new int[] { 1, 9 }, mapList.getFromRanges()
636 assertEquals(1, mapList.getFromRanges().size());
637 assertTrue(Arrays.equals(new int[] { 1, 3 },
638 mapList.getToRanges().get(0)));
639 assertEquals(1, mapList.getToRanges().size());
641 // V12346 mapped from A33333 starting position 4
642 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
643 assertEquals(1, acf.getdnaSeqs().length);
644 assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
645 acf.getdnaSeqs()[0]);
646 protMappings = acf.getProtMappings();
647 assertEquals(1, protMappings.length);
648 mapList = protMappings[0].getMap();
649 assertEquals(3, mapList.getFromRatio());
650 assertEquals(1, mapList.getToRatio());
651 assertTrue(Arrays.equals(new int[] { 4, 12 }, mapList.getFromRanges()
653 assertEquals(1, mapList.getFromRanges().size());
654 assertTrue(Arrays.equals(new int[] { 1, 3 },
655 mapList.getToRanges().get(0)));
656 assertEquals(1, mapList.getToRanges().size());
658 // V12347 mapped to A11111 starting position 4
659 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
660 assertEquals(1, acf.getdnaSeqs().length);
661 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
662 acf.getdnaSeqs()[0]);
663 protMappings = acf.getProtMappings();
664 assertEquals(1, protMappings.length);
665 mapList = protMappings[0].getMap();
666 assertEquals(3, mapList.getFromRatio());
667 assertEquals(1, mapList.getToRatio());
668 assertTrue(Arrays.equals(new int[] { 4, 12 }, mapList.getFromRanges()
670 assertEquals(1, mapList.getFromRanges().size());
671 assertTrue(Arrays.equals(new int[] { 1, 3 },
672 mapList.getToRanges().get(0)));
673 assertEquals(1, mapList.getToRanges().size());
675 // no mapping involving the 'extra' A44444
676 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(3)).isEmpty());
680 * Test mapping of protein to cDNA, for the case where we have some sequence
681 * cross-references. Verify that 1-to-many mappings are made where
682 * cross-references exist and sequences are mappable.
684 * @throws IOException
686 @Test(groups = { "Functional" })
687 public void testMapProteinAlignmentToCdna_withXrefs() throws IOException
689 List<SequenceI> protseqs = new ArrayList<SequenceI>();
690 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
691 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
692 protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
693 AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
694 protein.setDataset(null);
696 List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
697 dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR
698 dnaseqs.add(new Sequence("EMBL|A22222", "ATGGAGATACAA")); // = start + EIQ
699 dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ
700 dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG")); // = EIQ
701 dnaseqs.add(new Sequence("EMBL|A55555", "GAGATTCAG")); // = EIQ
702 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[5]));
703 cdna.setDataset(null);
705 // Xref A22222 to V12345 (should get mapped)
706 dnaseqs.get(1).addDBRef(new DBRefEntry("UNIPROT", "1", "V12345"));
707 // Xref V12345 to A44444 (should get mapped)
708 protseqs.get(0).addDBRef(new DBRefEntry("EMBL", "1", "A44444"));
709 // Xref A33333 to V12347 (sequence mismatch - should not get mapped)
710 dnaseqs.get(2).addDBRef(new DBRefEntry("UNIPROT", "1", "V12347"));
711 // as V12345 is mapped to A22222 and A44444, this leaves V12346 unmapped.
712 // it should get paired up with the unmapped A33333
713 // A11111 should be mapped to V12347
714 // A55555 is spare and has no xref so is not mapped
716 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
718 // 4 protein mappings made for 3 proteins, 2 to V12345, 1 each to V12346/7
719 assertEquals(3, protein.getCodonFrames().size());
720 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
721 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
722 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
724 // one mapping for each of the first 4 cDNA sequences
725 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(0)).size());
726 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(1)).size());
727 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(2)).size());
728 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(3)).size());
730 // V12345 mapped to A22222 and A44444
731 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
733 assertEquals(2, acf.getdnaSeqs().length);
734 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
735 acf.getdnaSeqs()[0]);
736 assertEquals(cdna.getSequenceAt(3).getDatasetSequence(),
737 acf.getdnaSeqs()[1]);
739 // V12346 mapped to A33333
740 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
741 assertEquals(1, acf.getdnaSeqs().length);
742 assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
743 acf.getdnaSeqs()[0]);
745 // V12347 mapped to A11111
746 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
747 assertEquals(1, acf.getdnaSeqs().length);
748 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
749 acf.getdnaSeqs()[0]);
751 // no mapping involving the 'extra' A55555
752 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(4)).isEmpty());
756 * Test mapping of protein to cDNA, for the case where we have some sequence
757 * cross-references. Verify that once we have made an xref mapping we don't
758 * also map un-xrefd sequeces.
760 * @throws IOException
762 @Test(groups = { "Functional" })
763 public void testMapProteinAlignmentToCdna_prioritiseXrefs()
766 List<SequenceI> protseqs = new ArrayList<SequenceI>();
767 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
768 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
769 AlignmentI protein = new Alignment(
770 protseqs.toArray(new SequenceI[protseqs.size()]));
771 protein.setDataset(null);
773 List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
774 dnaseqs.add(new Sequence("EMBL|A11111", "GAAATCCAG")); // = EIQ
775 dnaseqs.add(new Sequence("EMBL|A22222", "GAAATTCAG")); // = EIQ
776 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[dnaseqs
778 cdna.setDataset(null);
780 // Xref A22222 to V12345 (should get mapped)
781 // A11111 should then be mapped to the unmapped V12346
782 dnaseqs.get(1).addDBRef(new DBRefEntry("UNIPROT", "1", "V12345"));
784 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
786 // 2 protein mappings made
787 assertEquals(2, protein.getCodonFrames().size());
788 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
789 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
791 // one mapping for each of the cDNA sequences
792 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(0)).size());
793 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(1)).size());
795 // V12345 mapped to A22222
796 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
798 assertEquals(1, acf.getdnaSeqs().length);
799 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
800 acf.getdnaSeqs()[0]);
802 // V12346 mapped to A11111
803 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
804 assertEquals(1, acf.getdnaSeqs().length);
805 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
806 acf.getdnaSeqs()[0]);
810 * Test the method that shows or hides sequence annotations by type(s) and
813 @Test(groups = { "Functional" })
814 public void testShowOrHideSequenceAnnotations()
816 SequenceI seq1 = new Sequence("Seq1", "AAA");
817 SequenceI seq2 = new Sequence("Seq2", "BBB");
818 SequenceI seq3 = new Sequence("Seq3", "CCC");
819 Annotation[] anns = new Annotation[] { new Annotation(2f) };
820 AlignmentAnnotation ann1 = new AlignmentAnnotation("Structure", "ann1",
822 ann1.setSequenceRef(seq1);
823 AlignmentAnnotation ann2 = new AlignmentAnnotation("Structure", "ann2",
825 ann2.setSequenceRef(seq2);
826 AlignmentAnnotation ann3 = new AlignmentAnnotation("Structure", "ann3",
828 AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "ann4", anns);
829 ann4.setSequenceRef(seq1);
830 AlignmentAnnotation ann5 = new AlignmentAnnotation("Temp", "ann5", anns);
831 ann5.setSequenceRef(seq2);
832 AlignmentAnnotation ann6 = new AlignmentAnnotation("Temp", "ann6", anns);
833 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
834 al.addAnnotation(ann1); // Structure for Seq1
835 al.addAnnotation(ann2); // Structure for Seq2
836 al.addAnnotation(ann3); // Structure for no sequence
837 al.addAnnotation(ann4); // Temp for seq1
838 al.addAnnotation(ann5); // Temp for seq2
839 al.addAnnotation(ann6); // Temp for no sequence
840 List<String> types = new ArrayList<String>();
841 List<SequenceI> scope = new ArrayList<SequenceI>();
844 * Set all sequence related Structure to hidden (ann1, ann2)
846 types.add("Structure");
847 AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, false,
849 assertFalse(ann1.visible);
850 assertFalse(ann2.visible);
851 assertTrue(ann3.visible); // not sequence-related, not affected
852 assertTrue(ann4.visible); // not Structure, not affected
853 assertTrue(ann5.visible); // "
854 assertTrue(ann6.visible); // not sequence-related, not affected
857 * Set Temp in {seq1, seq3} to hidden
863 AlignmentUtils.showOrHideSequenceAnnotations(al, types, scope, false,
865 assertFalse(ann1.visible); // unchanged
866 assertFalse(ann2.visible); // unchanged
867 assertTrue(ann3.visible); // not sequence-related, not affected
868 assertFalse(ann4.visible); // Temp for seq1 hidden
869 assertTrue(ann5.visible); // not in scope, not affected
870 assertTrue(ann6.visible); // not sequence-related, not affected
873 * Set Temp in all sequences to hidden
879 AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, false,
881 assertFalse(ann1.visible); // unchanged
882 assertFalse(ann2.visible); // unchanged
883 assertTrue(ann3.visible); // not sequence-related, not affected
884 assertFalse(ann4.visible); // Temp for seq1 hidden
885 assertFalse(ann5.visible); // Temp for seq2 hidden
886 assertTrue(ann6.visible); // not sequence-related, not affected
889 * Set all types in {seq1, seq3} to visible
895 AlignmentUtils.showOrHideSequenceAnnotations(al, types, scope, true,
897 assertTrue(ann1.visible); // Structure for seq1 set visible
898 assertFalse(ann2.visible); // not in scope, unchanged
899 assertTrue(ann3.visible); // not sequence-related, not affected
900 assertTrue(ann4.visible); // Temp for seq1 set visible
901 assertFalse(ann5.visible); // not in scope, unchanged
902 assertTrue(ann6.visible); // not sequence-related, not affected
905 * Set all types in all scope to hidden
907 AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, true,
909 assertFalse(ann1.visible);
910 assertFalse(ann2.visible);
911 assertTrue(ann3.visible); // not sequence-related, not affected
912 assertFalse(ann4.visible);
913 assertFalse(ann5.visible);
914 assertTrue(ann6.visible); // not sequence-related, not affected
918 * Tests for the method that checks if one sequence cross-references another
920 @Test(groups = { "Functional" })
921 public void testHasCrossRef()
923 assertFalse(AlignmentUtils.hasCrossRef(null, null));
924 SequenceI seq1 = new Sequence("EMBL|A12345", "ABCDEF");
925 assertFalse(AlignmentUtils.hasCrossRef(seq1, null));
926 assertFalse(AlignmentUtils.hasCrossRef(null, seq1));
927 SequenceI seq2 = new Sequence("UNIPROT|V20192", "ABCDEF");
928 assertFalse(AlignmentUtils.hasCrossRef(seq1, seq2));
931 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "v20193"));
932 assertFalse(AlignmentUtils.hasCrossRef(seq1, seq2));
934 // case-insensitive; version number is ignored
935 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "v20192"));
936 assertTrue(AlignmentUtils.hasCrossRef(seq1, seq2));
939 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
940 assertTrue(AlignmentUtils.hasCrossRef(seq1, seq2));
941 // test is one-way only
942 assertFalse(AlignmentUtils.hasCrossRef(seq2, seq1));
946 * Tests for the method that checks if either sequence cross-references the
949 @Test(groups = { "Functional" })
950 public void testHaveCrossRef()
952 assertFalse(AlignmentUtils.hasCrossRef(null, null));
953 SequenceI seq1 = new Sequence("EMBL|A12345", "ABCDEF");
954 assertFalse(AlignmentUtils.haveCrossRef(seq1, null));
955 assertFalse(AlignmentUtils.haveCrossRef(null, seq1));
956 SequenceI seq2 = new Sequence("UNIPROT|V20192", "ABCDEF");
957 assertFalse(AlignmentUtils.haveCrossRef(seq1, seq2));
959 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
960 assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
961 // next is true for haveCrossRef, false for hasCrossRef
962 assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
964 // now the other way round
965 seq1.setDBRefs(null);
966 seq2.addDBRef(new DBRefEntry("EMBL", "1", "A12345"));
967 assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
968 assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
971 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
972 assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
973 assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
977 * Test the method that extracts the cds-only part of a dna alignment.
979 @Test(groups = { "Functional" })
980 public void testMakeCdsAlignment()
984 * dna1 --> [4, 6] [10,12] --> pep1
985 * dna2 --> [1, 3] [7, 9] [13,15] --> pep2
987 SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
988 SequenceI dna2 = new Sequence("dna2", "GGGcccTTTaaaCCC");
989 SequenceI pep1 = new Sequence("pep1", "GF");
990 SequenceI pep2 = new Sequence("pep2", "GFP");
991 pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "pep1"));
992 pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "pep2"));
993 dna1.createDatasetSequence();
994 dna2.createDatasetSequence();
995 pep1.createDatasetSequence();
996 pep2.createDatasetSequence();
997 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
998 dna.setDataset(null);
1001 * put a variant feature on dna2 base 8
1002 * - should transfer to cds2 base 5
1004 dna2.addSequenceFeature(new SequenceFeature("variant", "hgmd", 8, 8,
1008 * need a sourceDbRef if we are to construct dbrefs to the CDS
1009 * sequence from the dna contig sequences
1011 DBRefEntry dbref = new DBRefEntry("ENSEMBL", "0", "dna1");
1012 dna1.getDatasetSequence().addDBRef(dbref);
1013 org.testng.Assert.assertEquals(dbref, dna1.getPrimaryDBRefs().get(0));
1014 dbref = new DBRefEntry("ENSEMBL", "0", "dna2");
1015 dna2.getDatasetSequence().addDBRef(dbref);
1016 org.testng.Assert.assertEquals(dbref, dna2.getPrimaryDBRefs().get(0));
1019 * CDS sequences are 'discovered' from dna-to-protein mappings on the alignment
1020 * dataset (e.g. added from dbrefs by CrossRef.findXrefSequences)
1022 MapList mapfordna1 = new MapList(new int[] { 4, 6, 10, 12 }, new int[] {
1024 AlignedCodonFrame acf = new AlignedCodonFrame();
1025 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
1027 dna.addCodonFrame(acf);
1028 MapList mapfordna2 = new MapList(new int[] { 1, 3, 7, 9, 13, 15 },
1029 new int[] { 1, 3 }, 3, 1);
1030 acf = new AlignedCodonFrame();
1031 acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(),
1033 dna.addCodonFrame(acf);
1036 * In this case, mappings originally came from matching Uniprot accessions - so need an xref on dna involving those regions. These are normally constructed from CDS annotation
1038 DBRefEntry dna1xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep1",
1039 new Mapping(mapfordna1));
1040 dna1.getDatasetSequence().addDBRef(dna1xref);
1041 DBRefEntry dna2xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep2",
1042 new Mapping(mapfordna2));
1043 dna2.getDatasetSequence().addDBRef(dna2xref);
1046 * execute method under test:
1048 AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
1049 dna1, dna2 }, dna.getDataset(), null);
1052 * verify cds sequences
1054 assertEquals(2, cds.getSequences().size());
1055 assertEquals("GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
1056 assertEquals("GGGTTTCCC", cds.getSequenceAt(1).getSequenceAsString());
1059 * verify shared, extended alignment dataset
1061 assertSame(dna.getDataset(), cds.getDataset());
1062 SequenceI cds1Dss = cds.getSequenceAt(0).getDatasetSequence();
1063 SequenceI cds2Dss = cds.getSequenceAt(1).getDatasetSequence();
1064 assertTrue(dna.getDataset().getSequences().contains(cds1Dss));
1065 assertTrue(dna.getDataset().getSequences().contains(cds2Dss));
1068 * verify CDS has a dbref with mapping to peptide
1070 assertNotNull(cds1Dss.getDBRefs());
1071 assertEquals(2, cds1Dss.getDBRefs().length);
1072 dbref = cds1Dss.getDBRefs()[0];
1073 assertEquals(dna1xref.getSource(), dbref.getSource());
1074 // version is via ensembl's primary ref
1075 assertEquals(dna1xref.getVersion(), dbref.getVersion());
1076 assertEquals(dna1xref.getAccessionId(), dbref.getAccessionId());
1077 assertNotNull(dbref.getMap());
1078 assertSame(pep1.getDatasetSequence(), dbref.getMap().getTo());
1079 MapList cdsMapping = new MapList(new int[] { 1, 6 },
1080 new int[] { 1, 2 }, 3, 1);
1081 assertEquals(cdsMapping, dbref.getMap().getMap());
1084 * verify peptide has added a dbref with reverse mapping to CDS
1086 assertNotNull(pep1.getDBRefs());
1087 // FIXME pep1.getDBRefs() is 1 - is that the correct behaviour ?
1088 assertEquals(2, pep1.getDBRefs().length);
1089 dbref = pep1.getDBRefs()[1];
1090 assertEquals("ENSEMBL", dbref.getSource());
1091 assertEquals("0", dbref.getVersion());
1092 assertEquals("CDS|dna1", dbref.getAccessionId());
1093 assertNotNull(dbref.getMap());
1094 assertSame(cds1Dss, dbref.getMap().getTo());
1095 assertEquals(cdsMapping.getInverse(), dbref.getMap().getMap());
1098 * Verify mappings from CDS to peptide, cDNA to CDS, and cDNA to peptide
1099 * the mappings are on the shared alignment dataset
1100 * 6 mappings, 2*(DNA->CDS), 2*(DNA->Pep), 2*(CDS->Pep)
1102 List<AlignedCodonFrame> cdsMappings = cds.getDataset().getCodonFrames();
1103 assertEquals(6, cdsMappings.size());
1106 * verify that mapping sets for dna and cds alignments are different
1107 * [not current behaviour - all mappings are on the alignment dataset]
1109 // select -> subselect type to test.
1110 // Assert.assertNotSame(dna.getCodonFrames(), cds.getCodonFrames());
1111 // assertEquals(4, dna.getCodonFrames().size());
1112 // assertEquals(4, cds.getCodonFrames().size());
1115 * Two mappings involve pep1 (dna to pep1, cds to pep1)
1116 * Mapping from pep1 to GGGTTT in first new exon sequence
1118 List<AlignedCodonFrame> pep1Mappings = MappingUtils
1119 .findMappingsForSequence(pep1, cdsMappings);
1120 assertEquals(2, pep1Mappings.size());
1121 List<AlignedCodonFrame> mappings = MappingUtils
1122 .findMappingsForSequence(cds.getSequenceAt(0), pep1Mappings);
1123 assertEquals(1, mappings.size());
1126 SearchResultsI sr = MappingUtils.buildSearchResults(pep1, 1, mappings);
1127 assertEquals(1, sr.getResults().size());
1128 SearchResultMatchI m = sr.getResults().get(0);
1129 assertSame(cds1Dss, m.getSequence());
1130 assertEquals(1, m.getStart());
1131 assertEquals(3, m.getEnd());
1133 sr = MappingUtils.buildSearchResults(pep1, 2, mappings);
1134 m = sr.getResults().get(0);
1135 assertSame(cds1Dss, m.getSequence());
1136 assertEquals(4, m.getStart());
1137 assertEquals(6, m.getEnd());
1140 * Two mappings involve pep2 (dna to pep2, cds to pep2)
1141 * Verify mapping from pep2 to GGGTTTCCC in second new exon sequence
1143 List<AlignedCodonFrame> pep2Mappings = MappingUtils
1144 .findMappingsForSequence(pep2, cdsMappings);
1145 assertEquals(2, pep2Mappings.size());
1146 mappings = MappingUtils.findMappingsForSequence(cds.getSequenceAt(1),
1148 assertEquals(1, mappings.size());
1150 sr = MappingUtils.buildSearchResults(pep2, 1, mappings);
1151 assertEquals(1, sr.getResults().size());
1152 m = sr.getResults().get(0);
1153 assertSame(cds2Dss, m.getSequence());
1154 assertEquals(1, m.getStart());
1155 assertEquals(3, m.getEnd());
1157 sr = MappingUtils.buildSearchResults(pep2, 2, mappings);
1158 m = sr.getResults().get(0);
1159 assertSame(cds2Dss, m.getSequence());
1160 assertEquals(4, m.getStart());
1161 assertEquals(6, m.getEnd());
1163 sr = MappingUtils.buildSearchResults(pep2, 3, mappings);
1164 m = sr.getResults().get(0);
1165 assertSame(cds2Dss, m.getSequence());
1166 assertEquals(7, m.getStart());
1167 assertEquals(9, m.getEnd());
1170 * check cds2 acquired a variant feature in position 5
1172 SequenceFeature[] sfs = cds2Dss.getSequenceFeatures();
1174 assertEquals(1, sfs.length);
1175 assertEquals("variant", sfs[0].type);
1176 assertEquals(5, sfs[0].begin);
1177 assertEquals(5, sfs[0].end);
1181 * Test the method that makes a cds-only alignment from a DNA sequence and its
1182 * product mappings, for the case where there are multiple exon mappings to
1183 * different protein products.
1185 @Test(groups = { "Functional" })
1186 public void testMakeCdsAlignment_multipleProteins()
1188 SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
1189 SequenceI pep1 = new Sequence("pep1", "GF"); // GGGTTT
1190 SequenceI pep2 = new Sequence("pep2", "KP"); // aaaccc
1191 SequenceI pep3 = new Sequence("pep3", "KF"); // aaaTTT
1192 dna1.createDatasetSequence();
1193 pep1.createDatasetSequence();
1194 pep2.createDatasetSequence();
1195 pep3.createDatasetSequence();
1196 pep1.getDatasetSequence().addDBRef(
1197 new DBRefEntry("EMBLCDS", "2", "A12345"));
1198 pep2.getDatasetSequence().addDBRef(
1199 new DBRefEntry("EMBLCDS", "3", "A12346"));
1200 pep3.getDatasetSequence().addDBRef(
1201 new DBRefEntry("EMBLCDS", "4", "A12347"));
1204 * Create the CDS alignment
1206 AlignmentI dna = new Alignment(new SequenceI[] { dna1 });
1207 dna.setDataset(null);
1210 * Make the mappings from dna to protein
1212 // map ...GGG...TTT to GF
1213 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1214 new int[] { 1, 2 }, 3, 1);
1215 AlignedCodonFrame acf = new AlignedCodonFrame();
1216 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
1217 dna.addCodonFrame(acf);
1219 // map aaa...ccc to KP
1220 map = new MapList(new int[] { 1, 3, 7, 9 }, new int[] { 1, 2 }, 3, 1);
1221 acf = new AlignedCodonFrame();
1222 acf.addMap(dna1.getDatasetSequence(), pep2.getDatasetSequence(), map);
1223 dna.addCodonFrame(acf);
1225 // map aaa......TTT to KF
1226 map = new MapList(new int[] { 1, 3, 10, 12 }, new int[] { 1, 2 }, 3, 1);
1227 acf = new AlignedCodonFrame();
1228 acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map);
1229 dna.addCodonFrame(acf);
1232 * execute method under test
1234 AlignmentI cdsal = AlignmentUtils.makeCdsAlignment(
1235 new SequenceI[] { dna1 }, dna.getDataset(), null);
1238 * Verify we have 3 cds sequences, mapped to pep1/2/3 respectively
1240 List<SequenceI> cds = cdsal.getSequences();
1241 assertEquals(3, cds.size());
1244 * verify shared, extended alignment dataset
1246 assertSame(cdsal.getDataset(), dna.getDataset());
1247 assertTrue(dna.getDataset().getSequences()
1248 .contains(cds.get(0).getDatasetSequence()));
1249 assertTrue(dna.getDataset().getSequences()
1250 .contains(cds.get(1).getDatasetSequence()));
1251 assertTrue(dna.getDataset().getSequences()
1252 .contains(cds.get(2).getDatasetSequence()));
1255 * verify aligned cds sequences and their xrefs
1257 SequenceI cdsSeq = cds.get(0);
1258 assertEquals("GGGTTT", cdsSeq.getSequenceAsString());
1259 // assertEquals("dna1|A12345", cdsSeq.getName());
1260 assertEquals("CDS|dna1", cdsSeq.getName());
1261 // assertEquals(1, cdsSeq.getDBRefs().length);
1262 // DBRefEntry cdsRef = cdsSeq.getDBRefs()[0];
1263 // assertEquals("EMBLCDS", cdsRef.getSource());
1264 // assertEquals("2", cdsRef.getVersion());
1265 // assertEquals("A12345", cdsRef.getAccessionId());
1267 cdsSeq = cds.get(1);
1268 assertEquals("aaaccc", cdsSeq.getSequenceAsString());
1269 // assertEquals("dna1|A12346", cdsSeq.getName());
1270 assertEquals("CDS|dna1", cdsSeq.getName());
1271 // assertEquals(1, cdsSeq.getDBRefs().length);
1272 // cdsRef = cdsSeq.getDBRefs()[0];
1273 // assertEquals("EMBLCDS", cdsRef.getSource());
1274 // assertEquals("3", cdsRef.getVersion());
1275 // assertEquals("A12346", cdsRef.getAccessionId());
1277 cdsSeq = cds.get(2);
1278 assertEquals("aaaTTT", cdsSeq.getSequenceAsString());
1279 // assertEquals("dna1|A12347", cdsSeq.getName());
1280 assertEquals("CDS|dna1", cdsSeq.getName());
1281 // assertEquals(1, cdsSeq.getDBRefs().length);
1282 // cdsRef = cdsSeq.getDBRefs()[0];
1283 // assertEquals("EMBLCDS", cdsRef.getSource());
1284 // assertEquals("4", cdsRef.getVersion());
1285 // assertEquals("A12347", cdsRef.getAccessionId());
1288 * Verify there are mappings from each cds sequence to its protein product
1289 * and also to its dna source
1291 List<AlignedCodonFrame> newMappings = cdsal.getCodonFrames();
1294 * 6 mappings involve dna1 (to pep1/2/3, cds1/2/3)
1296 List<AlignedCodonFrame> dnaMappings = MappingUtils
1297 .findMappingsForSequence(dna1, newMappings);
1298 assertEquals(6, dnaMappings.size());
1303 List<AlignedCodonFrame> mappings = MappingUtils
1304 .findMappingsForSequence(pep1, dnaMappings);
1305 assertEquals(1, mappings.size());
1306 assertEquals(1, mappings.get(0).getMappings().size());
1307 assertSame(pep1.getDatasetSequence(), mappings.get(0).getMappings()
1308 .get(0).getMapping().getTo());
1313 List<AlignedCodonFrame> dnaToCds1Mappings = MappingUtils
1314 .findMappingsForSequence(cds.get(0), dnaMappings);
1315 Mapping mapping = dnaToCds1Mappings.get(0).getMappings().get(0)
1317 assertSame(cds.get(0).getDatasetSequence(), mapping.getTo());
1318 assertEquals("G(1) in CDS should map to G(4) in DNA", 4, mapping
1319 .getMap().getToPosition(1));
1324 mappings = MappingUtils.findMappingsForSequence(pep2, dnaMappings);
1325 assertEquals(1, mappings.size());
1326 assertEquals(1, mappings.get(0).getMappings().size());
1327 assertSame(pep2.getDatasetSequence(), mappings.get(0).getMappings()
1328 .get(0).getMapping().getTo());
1333 List<AlignedCodonFrame> dnaToCds2Mappings = MappingUtils
1334 .findMappingsForSequence(cds.get(1), dnaMappings);
1335 mapping = dnaToCds2Mappings.get(0).getMappings().get(0).getMapping();
1336 assertSame(cds.get(1).getDatasetSequence(), mapping.getTo());
1337 assertEquals("c(4) in CDS should map to c(7) in DNA", 7, mapping
1338 .getMap().getToPosition(4));
1343 mappings = MappingUtils.findMappingsForSequence(pep3, dnaMappings);
1344 assertEquals(1, mappings.size());
1345 assertEquals(1, mappings.get(0).getMappings().size());
1346 assertSame(pep3.getDatasetSequence(), mappings.get(0).getMappings()
1347 .get(0).getMapping().getTo());
1352 List<AlignedCodonFrame> dnaToCds3Mappings = MappingUtils
1353 .findMappingsForSequence(cds.get(2), dnaMappings);
1354 mapping = dnaToCds3Mappings.get(0).getMappings().get(0).getMapping();
1355 assertSame(cds.get(2).getDatasetSequence(), mapping.getTo());
1356 assertEquals("T(4) in CDS should map to T(10) in DNA", 10, mapping
1357 .getMap().getToPosition(4));
1360 @Test(groups = { "Functional" })
1361 public void testIsMappable()
1363 SequenceI dna1 = new Sequence("dna1", "cgCAGtgGT");
1364 SequenceI aa1 = new Sequence("aa1", "RSG");
1365 AlignmentI al1 = new Alignment(new SequenceI[] { dna1 });
1366 AlignmentI al2 = new Alignment(new SequenceI[] { aa1 });
1368 assertFalse(AlignmentUtils.isMappable(null, null));
1369 assertFalse(AlignmentUtils.isMappable(al1, null));
1370 assertFalse(AlignmentUtils.isMappable(null, al1));
1371 assertFalse(AlignmentUtils.isMappable(al1, al1));
1372 assertFalse(AlignmentUtils.isMappable(al2, al2));
1374 assertTrue(AlignmentUtils.isMappable(al1, al2));
1375 assertTrue(AlignmentUtils.isMappable(al2, al1));
1379 * Test creating a mapping when the sequences involved do not start at residue
1382 * @throws IOException
1384 @Test(groups = { "Functional" })
1385 public void testMapCdnaToProtein_forSubsequence() throws IOException
1387 SequenceI prot = new Sequence("UNIPROT|V12345", "E-I--Q", 10, 12);
1388 prot.createDatasetSequence();
1390 SequenceI dna = new Sequence("EMBL|A33333", "GAA--AT-C-CAG", 40, 48);
1391 dna.createDatasetSequence();
1393 MapList map = AlignmentUtils.mapCdnaToProtein(prot, dna);
1394 assertEquals(10, map.getToLowest());
1395 assertEquals(12, map.getToHighest());
1396 assertEquals(40, map.getFromLowest());
1397 assertEquals(48, map.getFromHighest());
1401 * Test for the alignSequenceAs method where we have protein mapped to protein
1403 @Test(groups = { "Functional" })
1404 public void testAlignSequenceAs_mappedProteinProtein()
1407 SequenceI alignMe = new Sequence("Match", "MGAASEV");
1408 alignMe.createDatasetSequence();
1409 SequenceI alignFrom = new Sequence("Query", "LQTGYMGAASEVMFSPTRR");
1410 alignFrom.createDatasetSequence();
1412 AlignedCodonFrame acf = new AlignedCodonFrame();
1413 // this is like a domain or motif match of part of a peptide sequence
1414 MapList map = new MapList(new int[] { 6, 12 }, new int[] { 1, 7 }, 1, 1);
1415 acf.addMap(alignFrom.getDatasetSequence(),
1416 alignMe.getDatasetSequence(), map);
1418 AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "-", '-', true,
1420 assertEquals("-----MGAASEV-------", alignMe.getSequenceAsString());
1424 * Test for the alignSequenceAs method where there are trailing unmapped
1425 * residues in the model sequence
1427 @Test(groups = { "Functional" })
1428 public void testAlignSequenceAs_withTrailingPeptide()
1430 // map first 3 codons to KPF; G is a trailing unmapped residue
1431 MapList map = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3, 1);
1433 checkAlignSequenceAs("AAACCCTTT", "K-PFG", true, true, map,
1438 * Tests for transferring features between mapped sequences
1440 @Test(groups = { "Functional" })
1441 public void testTransferFeatures()
1443 SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt");
1444 SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
1447 dna.addSequenceFeature(new SequenceFeature("type1", "desc1", 1, 2, 1f,
1449 // partial overlap - to [1, 1]
1450 dna.addSequenceFeature(new SequenceFeature("type2", "desc2", 3, 4, 2f,
1452 // exact overlap - to [1, 3]
1453 dna.addSequenceFeature(new SequenceFeature("type3", "desc3", 4, 6, 3f,
1455 // spanning overlap - to [2, 5]
1456 dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f,
1458 // exactly overlaps whole mapped range [1, 6]
1459 dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f,
1461 // no overlap (internal)
1462 dna.addSequenceFeature(new SequenceFeature("type6", "desc6", 7, 9, 6f,
1464 // no overlap (3' end)
1465 dna.addSequenceFeature(new SequenceFeature("type7", "desc7", 13, 15,
1467 // overlap (3' end) - to [6, 6]
1468 dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12,
1470 // extended overlap - to [6, +]
1471 dna.addSequenceFeature(new SequenceFeature("type9", "desc9", 12, 13,
1474 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1475 new int[] { 1, 6 }, 1, 1);
1478 * transferFeatures() will build 'partial overlap' for regions
1479 * that partially overlap 5' or 3' (start or end) of target sequence
1481 AlignmentUtils.transferFeatures(dna, cds, map, null);
1482 SequenceFeature[] sfs = cds.getSequenceFeatures();
1483 assertEquals(6, sfs.length);
1485 SequenceFeature sf = sfs[0];
1486 assertEquals("type2", sf.getType());
1487 assertEquals("desc2", sf.getDescription());
1488 assertEquals(2f, sf.getScore());
1489 assertEquals(1, sf.getBegin());
1490 assertEquals(1, sf.getEnd());
1493 assertEquals("type3", sf.getType());
1494 assertEquals("desc3", sf.getDescription());
1495 assertEquals(3f, sf.getScore());
1496 assertEquals(1, sf.getBegin());
1497 assertEquals(3, sf.getEnd());
1500 assertEquals("type4", sf.getType());
1501 assertEquals(2, sf.getBegin());
1502 assertEquals(5, sf.getEnd());
1505 assertEquals("type5", sf.getType());
1506 assertEquals(1, sf.getBegin());
1507 assertEquals(6, sf.getEnd());
1510 assertEquals("type8", sf.getType());
1511 assertEquals(6, sf.getBegin());
1512 assertEquals(6, sf.getEnd());
1515 assertEquals("type9", sf.getType());
1516 assertEquals(6, sf.getBegin());
1517 assertEquals(6, sf.getEnd());
1521 * Tests for transferring features between mapped sequences
1523 @Test(groups = { "Functional" })
1524 public void testTransferFeatures_withOmit()
1526 SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt");
1527 SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
1529 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1530 new int[] { 1, 6 }, 1, 1);
1532 // [5, 11] maps to [2, 5]
1533 dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f,
1535 // [4, 12] maps to [1, 6]
1536 dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f,
1538 // [12, 12] maps to [6, 6]
1539 dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12,
1542 // desc4 and desc8 are the 'omit these' varargs
1543 AlignmentUtils.transferFeatures(dna, cds, map, null, "type4", "type8");
1544 SequenceFeature[] sfs = cds.getSequenceFeatures();
1545 assertEquals(1, sfs.length);
1547 SequenceFeature sf = sfs[0];
1548 assertEquals("type5", sf.getType());
1549 assertEquals(1, sf.getBegin());
1550 assertEquals(6, sf.getEnd());
1554 * Tests for transferring features between mapped sequences
1556 @Test(groups = { "Functional" })
1557 public void testTransferFeatures_withSelect()
1559 SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt");
1560 SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
1562 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1563 new int[] { 1, 6 }, 1, 1);
1565 // [5, 11] maps to [2, 5]
1566 dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f,
1568 // [4, 12] maps to [1, 6]
1569 dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f,
1571 // [12, 12] maps to [6, 6]
1572 dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12,
1575 // "type5" is the 'select this type' argument
1576 AlignmentUtils.transferFeatures(dna, cds, map, "type5");
1577 SequenceFeature[] sfs = cds.getSequenceFeatures();
1578 assertEquals(1, sfs.length);
1580 SequenceFeature sf = sfs[0];
1581 assertEquals("type5", sf.getType());
1582 assertEquals(1, sf.getBegin());
1583 assertEquals(6, sf.getEnd());
1587 * Test the method that extracts the cds-only part of a dna alignment, for the
1588 * case where the cds should be aligned to match its nucleotide sequence.
1590 @Test(groups = { "Functional" })
1591 public void testMakeCdsAlignment_alternativeTranscripts()
1593 SequenceI dna1 = new Sequence("dna1", "aaaGGGCC-----CTTTaaaGGG");
1594 // alternative transcript of same dna skips CCC codon
1595 SequenceI dna2 = new Sequence("dna2", "aaaGGGCC-----cttTaaaGGG");
1596 // dna3 has no mapping (protein product) so should be ignored here
1597 SequenceI dna3 = new Sequence("dna3", "aaaGGGCCCCCGGGcttTaaaGGG");
1598 SequenceI pep1 = new Sequence("pep1", "GPFG");
1599 SequenceI pep2 = new Sequence("pep2", "GPG");
1600 dna1.createDatasetSequence();
1601 dna2.createDatasetSequence();
1602 dna3.createDatasetSequence();
1603 pep1.createDatasetSequence();
1604 pep2.createDatasetSequence();
1606 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
1607 dna.setDataset(null);
1609 MapList map = new MapList(new int[] { 4, 12, 16, 18 },
1610 new int[] { 1, 4 }, 3, 1);
1611 AlignedCodonFrame acf = new AlignedCodonFrame();
1612 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
1613 dna.addCodonFrame(acf);
1614 map = new MapList(new int[] { 4, 8, 12, 12, 16, 18 },
1615 new int[] { 1, 3 }, 3, 1);
1616 acf = new AlignedCodonFrame();
1617 acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
1618 dna.addCodonFrame(acf);
1620 AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
1621 dna1, dna2, dna3 }, dna.getDataset(), null);
1622 List<SequenceI> cdsSeqs = cds.getSequences();
1623 assertEquals(2, cdsSeqs.size());
1624 assertEquals("GGGCCCTTTGGG", cdsSeqs.get(0).getSequenceAsString());
1625 assertEquals("GGGCCTGGG", cdsSeqs.get(1).getSequenceAsString());
1628 * verify shared, extended alignment dataset
1630 assertSame(dna.getDataset(), cds.getDataset());
1631 assertTrue(dna.getDataset().getSequences()
1632 .contains(cdsSeqs.get(0).getDatasetSequence()));
1633 assertTrue(dna.getDataset().getSequences()
1634 .contains(cdsSeqs.get(1).getDatasetSequence()));
1637 * Verify 6 mappings: dna1 to cds1, cds1 to pep1, dna1 to pep1
1638 * and the same for dna2/cds2/pep2
1640 List<AlignedCodonFrame> mappings = cds.getCodonFrames();
1641 assertEquals(6, mappings.size());
1644 * 2 mappings involve pep1
1646 List<AlignedCodonFrame> pep1Mappings = MappingUtils
1647 .findMappingsForSequence(pep1, mappings);
1648 assertEquals(2, pep1Mappings.size());
1651 * Get mapping of pep1 to cds1 and verify it
1652 * maps GPFG to 1-3,4-6,7-9,10-12
1654 List<AlignedCodonFrame> pep1CdsMappings = MappingUtils
1655 .findMappingsForSequence(cds.getSequenceAt(0), pep1Mappings);
1656 assertEquals(1, pep1CdsMappings.size());
1657 SearchResultsI sr = MappingUtils.buildSearchResults(pep1, 1,
1659 assertEquals(1, sr.getResults().size());
1660 SearchResultMatchI m = sr.getResults().get(0);
1661 assertEquals(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
1662 assertEquals(1, m.getStart());
1663 assertEquals(3, m.getEnd());
1664 sr = MappingUtils.buildSearchResults(pep1, 2, pep1CdsMappings);
1665 m = sr.getResults().get(0);
1666 assertEquals(4, m.getStart());
1667 assertEquals(6, m.getEnd());
1668 sr = MappingUtils.buildSearchResults(pep1, 3, pep1CdsMappings);
1669 m = sr.getResults().get(0);
1670 assertEquals(7, m.getStart());
1671 assertEquals(9, m.getEnd());
1672 sr = MappingUtils.buildSearchResults(pep1, 4, pep1CdsMappings);
1673 m = sr.getResults().get(0);
1674 assertEquals(10, m.getStart());
1675 assertEquals(12, m.getEnd());
1678 * Get mapping of pep2 to cds2 and verify it
1679 * maps GPG in pep2 to 1-3,4-6,7-9 in second CDS sequence
1681 List<AlignedCodonFrame> pep2Mappings = MappingUtils
1682 .findMappingsForSequence(pep2, mappings);
1683 assertEquals(2, pep2Mappings.size());
1684 List<AlignedCodonFrame> pep2CdsMappings = MappingUtils
1685 .findMappingsForSequence(cds.getSequenceAt(1), pep2Mappings);
1686 assertEquals(1, pep2CdsMappings.size());
1687 sr = MappingUtils.buildSearchResults(pep2, 1, pep2CdsMappings);
1688 assertEquals(1, sr.getResults().size());
1689 m = sr.getResults().get(0);
1690 assertEquals(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
1691 assertEquals(1, m.getStart());
1692 assertEquals(3, m.getEnd());
1693 sr = MappingUtils.buildSearchResults(pep2, 2, pep2CdsMappings);
1694 m = sr.getResults().get(0);
1695 assertEquals(4, m.getStart());
1696 assertEquals(6, m.getEnd());
1697 sr = MappingUtils.buildSearchResults(pep2, 3, pep2CdsMappings);
1698 m = sr.getResults().get(0);
1699 assertEquals(7, m.getStart());
1700 assertEquals(9, m.getEnd());
1704 * Test the method that realigns protein to match mapped codon alignment.
1706 @Test(groups = { "Functional" })
1707 public void testAlignProteinAsDna_incompleteStartCodon()
1709 // seq1: incomplete start codon (not mapped), then [3, 11]
1710 SequenceI dna1 = new Sequence("Seq1", "ccAAA-TTT-GGG-");
1711 // seq2 codons are [4, 5], [8, 11]
1712 SequenceI dna2 = new Sequence("Seq2", "ccaAA-ttT-GGG-");
1713 // seq3 incomplete start codon at 'tt'
1714 SequenceI dna3 = new Sequence("Seq3", "ccaaa-ttt-GGG-");
1715 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
1716 dna.setDataset(null);
1718 // prot1 has 'X' for incomplete start codon (not mapped)
1719 SequenceI prot1 = new Sequence("Seq1", "XKFG"); // X for incomplete start
1720 SequenceI prot2 = new Sequence("Seq2", "NG");
1721 SequenceI prot3 = new Sequence("Seq3", "XG"); // X for incomplete start
1722 AlignmentI protein = new Alignment(new SequenceI[] { prot1, prot2,
1724 protein.setDataset(null);
1726 // map dna1 [3, 11] to prot1 [2, 4] KFG
1727 MapList map = new MapList(new int[] { 3, 11 }, new int[] { 2, 4 }, 3, 1);
1728 AlignedCodonFrame acf = new AlignedCodonFrame();
1729 acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
1731 // map dna2 [4, 5] [8, 11] to prot2 [1, 2] NG
1732 map = new MapList(new int[] { 4, 5, 8, 11 }, new int[] { 1, 2 }, 3, 1);
1733 acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map);
1735 // map dna3 [9, 11] to prot3 [2, 2] G
1736 map = new MapList(new int[] { 9, 11 }, new int[] { 2, 2 }, 3, 1);
1737 acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map);
1739 ArrayList<AlignedCodonFrame> acfs = new ArrayList<AlignedCodonFrame>();
1741 protein.setCodonFrames(acfs);
1744 * verify X is included in the aligned proteins, and placed just
1745 * before the first mapped residue
1746 * CCT is between CCC and TTT
1748 AlignmentUtils.alignProteinAsDna(protein, dna);
1749 assertEquals("XK-FG", prot1.getSequenceAsString());
1750 assertEquals("--N-G", prot2.getSequenceAsString());
1751 assertEquals("---XG", prot3.getSequenceAsString());
1755 * Tests for the method that maps the subset of a dna sequence that has CDS
1756 * (or subtype) feature - case where the start codon is incomplete.
1758 @Test(groups = "Functional")
1759 public void testFindCdsPositions_fivePrimeIncomplete()
1761 SequenceI dnaSeq = new Sequence("dna", "aaagGGCCCaaaTTTttt");
1762 dnaSeq.createDatasetSequence();
1763 SequenceI ds = dnaSeq.getDatasetSequence();
1765 // CDS for dna 5-6 (incomplete codon), 7-9
1766 SequenceFeature sf = new SequenceFeature("CDS", "", 5, 9, 0f, null);
1767 sf.setPhase("2"); // skip 2 bases to start of next codon
1768 ds.addSequenceFeature(sf);
1769 // CDS for dna 13-15
1770 sf = new SequenceFeature("CDS_predicted", "", 13, 15, 0f, null);
1771 ds.addSequenceFeature(sf);
1773 List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
1776 * check the mapping starts with the first complete codon
1778 assertEquals(6, MappingUtils.getLength(ranges));
1779 assertEquals(2, ranges.size());
1780 assertEquals(7, ranges.get(0)[0]);
1781 assertEquals(9, ranges.get(0)[1]);
1782 assertEquals(13, ranges.get(1)[0]);
1783 assertEquals(15, ranges.get(1)[1]);
1787 * Tests for the method that maps the subset of a dna sequence that has CDS
1788 * (or subtype) feature.
1790 @Test(groups = "Functional")
1791 public void testFindCdsPositions()
1793 SequenceI dnaSeq = new Sequence("dna", "aaaGGGcccAAATTTttt");
1794 dnaSeq.createDatasetSequence();
1795 SequenceI ds = dnaSeq.getDatasetSequence();
1797 // CDS for dna 10-12
1798 SequenceFeature sf = new SequenceFeature("CDS_predicted", "", 10, 12,
1801 ds.addSequenceFeature(sf);
1803 sf = new SequenceFeature("CDS", "", 4, 6, 0f, null);
1805 ds.addSequenceFeature(sf);
1806 // exon feature should be ignored here
1807 sf = new SequenceFeature("exon", "", 7, 9, 0f, null);
1808 ds.addSequenceFeature(sf);
1810 List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
1812 * verify ranges { [4-6], [12-10] }
1813 * note CDS ranges are ordered ascending even if the CDS
1816 assertEquals(6, MappingUtils.getLength(ranges));
1817 assertEquals(2, ranges.size());
1818 assertEquals(4, ranges.get(0)[0]);
1819 assertEquals(6, ranges.get(0)[1]);
1820 assertEquals(10, ranges.get(1)[0]);
1821 assertEquals(12, ranges.get(1)[1]);
1825 * Test the method that computes a map of codon variants for each protein
1826 * position from "sequence_variant" features on dna
1828 @Test(groups = "Functional")
1829 public void testBuildDnaVariantsMap()
1831 SequenceI dna = new Sequence("dna", "atgAAATTTGGGCCCtag");
1832 MapList map = new MapList(new int[] { 1, 18 }, new int[] { 1, 5 }, 3, 1);
1835 * first with no variants on dna
1837 LinkedHashMap<Integer, List<DnaVariant>[]> variantsMap = AlignmentUtils
1838 .buildDnaVariantsMap(dna, map);
1839 assertTrue(variantsMap.isEmpty());
1842 * single allele codon 1, on base 1
1844 SequenceFeature sf1 = new SequenceFeature("sequence_variant", "", 1, 1,
1846 sf1.setValue("alleles", "T");
1847 sf1.setValue("ID", "sequence_variant:rs758803211");
1848 dna.addSequenceFeature(sf1);
1851 * two alleles codon 2, on bases 2 and 3 (distinct variants)
1853 SequenceFeature sf2 = new SequenceFeature("sequence_variant", "", 5, 5,
1855 sf2.setValue("alleles", "T");
1856 sf2.setValue("ID", "sequence_variant:rs758803212");
1857 dna.addSequenceFeature(sf2);
1858 SequenceFeature sf3 = new SequenceFeature("sequence_variant", "", 6, 6,
1860 sf3.setValue("alleles", "G");
1861 sf3.setValue("ID", "sequence_variant:rs758803213");
1862 dna.addSequenceFeature(sf3);
1865 * two alleles codon 3, both on base 2 (one variant)
1867 SequenceFeature sf4 = new SequenceFeature("sequence_variant", "", 8, 8,
1869 sf4.setValue("alleles", "C, G");
1870 sf4.setValue("ID", "sequence_variant:rs758803214");
1871 dna.addSequenceFeature(sf4);
1873 // no alleles on codon 4
1876 * alleles on codon 5 on all 3 bases (distinct variants)
1878 SequenceFeature sf5 = new SequenceFeature("sequence_variant", "", 13,
1880 sf5.setValue("alleles", "C, G"); // (C duplicates given base value)
1881 sf5.setValue("ID", "sequence_variant:rs758803215");
1882 dna.addSequenceFeature(sf5);
1883 SequenceFeature sf6 = new SequenceFeature("sequence_variant", "", 14,
1885 sf6.setValue("alleles", "g, a"); // should force to upper-case
1886 sf6.setValue("ID", "sequence_variant:rs758803216");
1887 dna.addSequenceFeature(sf6);
1888 SequenceFeature sf7 = new SequenceFeature("sequence_variant", "", 15,
1890 sf7.setValue("alleles", "A, T");
1891 sf7.setValue("ID", "sequence_variant:rs758803217");
1892 dna.addSequenceFeature(sf7);
1895 * build map - expect variants on positions 1, 2, 3, 5
1897 variantsMap = AlignmentUtils.buildDnaVariantsMap(dna, map);
1898 assertEquals(4, variantsMap.size());
1901 * protein residue 1: variant on codon (ATG) base 1, not on 2 or 3
1903 List<DnaVariant>[] pep1Variants = variantsMap.get(1);
1904 assertEquals(3, pep1Variants.length);
1905 assertEquals(1, pep1Variants[0].size());
1906 assertEquals("A", pep1Variants[0].get(0).base); // codon[1] base
1907 assertSame(sf1, pep1Variants[0].get(0).variant); // codon[1] variant
1908 assertEquals(1, pep1Variants[1].size());
1909 assertEquals("T", pep1Variants[1].get(0).base); // codon[2] base
1910 assertNull(pep1Variants[1].get(0).variant); // no variant here
1911 assertEquals(1, pep1Variants[2].size());
1912 assertEquals("G", pep1Variants[2].get(0).base); // codon[3] base
1913 assertNull(pep1Variants[2].get(0).variant); // no variant here
1916 * protein residue 2: variants on codon (AAA) bases 2 and 3
1918 List<DnaVariant>[] pep2Variants = variantsMap.get(2);
1919 assertEquals(3, pep2Variants.length);
1920 assertEquals(1, pep2Variants[0].size());
1921 // codon[1] base recorded while processing variant on codon[2]
1922 assertEquals("A", pep2Variants[0].get(0).base);
1923 assertNull(pep2Variants[0].get(0).variant); // no variant here
1924 // codon[2] base and variant:
1925 assertEquals(1, pep2Variants[1].size());
1926 assertEquals("A", pep2Variants[1].get(0).base);
1927 assertSame(sf2, pep2Variants[1].get(0).variant);
1928 // codon[3] base was recorded when processing codon[2] variant
1929 // and then the variant for codon[3] added to it
1930 assertEquals(1, pep2Variants[2].size());
1931 assertEquals("A", pep2Variants[2].get(0).base);
1932 assertSame(sf3, pep2Variants[2].get(0).variant);
1935 * protein residue 3: variants on codon (TTT) base 2 only
1937 List<DnaVariant>[] pep3Variants = variantsMap.get(3);
1938 assertEquals(3, pep3Variants.length);
1939 assertEquals(1, pep3Variants[0].size());
1940 assertEquals("T", pep3Variants[0].get(0).base); // codon[1] base
1941 assertNull(pep3Variants[0].get(0).variant); // no variant here
1942 assertEquals(1, pep3Variants[1].size());
1943 assertEquals("T", pep3Variants[1].get(0).base); // codon[2] base
1944 assertSame(sf4, pep3Variants[1].get(0).variant); // codon[2] variant
1945 assertEquals(1, pep3Variants[2].size());
1946 assertEquals("T", pep3Variants[2].get(0).base); // codon[3] base
1947 assertNull(pep3Variants[2].get(0).variant); // no variant here
1950 * three variants on protein position 5
1952 List<DnaVariant>[] pep5Variants = variantsMap.get(5);
1953 assertEquals(3, pep5Variants.length);
1954 assertEquals(1, pep5Variants[0].size());
1955 assertEquals("C", pep5Variants[0].get(0).base); // codon[1] base
1956 assertSame(sf5, pep5Variants[0].get(0).variant); // codon[1] variant
1957 assertEquals(1, pep5Variants[1].size());
1958 assertEquals("C", pep5Variants[1].get(0).base); // codon[2] base
1959 assertSame(sf6, pep5Variants[1].get(0).variant); // codon[2] variant
1960 assertEquals(1, pep5Variants[2].size());
1961 assertEquals("C", pep5Variants[2].get(0).base); // codon[3] base
1962 assertSame(sf7, pep5Variants[2].get(0).variant); // codon[3] variant
1966 * Tests for the method that computes all peptide variants given codon
1969 @Test(groups = "Functional")
1970 public void testComputePeptideVariants()
1973 * scenario: AAATTTCCC codes for KFP
1975 * GAA -> E source: Ensembl
1976 * CAA -> Q source: dbSNP
1977 * AAG synonymous source: COSMIC
1978 * AAT -> N source: Ensembl
1979 * ...TTC synonymous source: dbSNP
1980 * ......CAC,CGC -> H,R source: COSMIC
1981 * (one variant with two alleles)
1983 SequenceI peptide = new Sequence("pep/10-12", "KFP");
1986 * two distinct variants for codon 1 position 1
1987 * second one has clinical significance
1989 String ensembl = "Ensembl";
1990 String dbSnp = "dbSNP";
1991 String cosmic = "COSMIC";
1992 SequenceFeature sf1 = new SequenceFeature("sequence_variant", "", 1, 1,
1994 sf1.setValue("alleles", "A,G"); // GAA -> E
1995 sf1.setValue("ID", "var1.125A>G");
1996 SequenceFeature sf2 = new SequenceFeature("sequence_variant", "", 1, 1,
1998 sf2.setValue("alleles", "A,C"); // CAA -> Q
1999 sf2.setValue("ID", "var2");
2000 sf2.setValue("clinical_significance", "Dodgy");
2001 SequenceFeature sf3 = new SequenceFeature("sequence_variant", "", 3, 3,
2003 sf3.setValue("alleles", "A,G"); // synonymous
2004 sf3.setValue("ID", "var3");
2005 sf3.setValue("clinical_significance", "None");
2006 SequenceFeature sf4 = new SequenceFeature("sequence_variant", "", 3, 3,
2008 sf4.setValue("alleles", "A,T"); // AAT -> N
2009 sf4.setValue("ID", "sequence_variant:var4"); // prefix gets stripped off
2010 sf4.setValue("clinical_significance", "Benign");
2011 SequenceFeature sf5 = new SequenceFeature("sequence_variant", "", 6, 6,
2013 sf5.setValue("alleles", "T,C"); // synonymous
2014 sf5.setValue("ID", "var5");
2015 sf5.setValue("clinical_significance", "Bad");
2016 SequenceFeature sf6 = new SequenceFeature("sequence_variant", "", 8, 8,
2018 sf6.setValue("alleles", "C,A,G"); // CAC,CGC -> H,R
2019 sf6.setValue("ID", "var6");
2020 sf6.setValue("clinical_significance", "Good");
2022 List<DnaVariant> codon1Variants = new ArrayList<DnaVariant>();
2023 List<DnaVariant> codon2Variants = new ArrayList<DnaVariant>();
2024 List<DnaVariant> codon3Variants = new ArrayList<DnaVariant>();
2025 List<DnaVariant> codonVariants[] = new ArrayList[3];
2026 codonVariants[0] = codon1Variants;
2027 codonVariants[1] = codon2Variants;
2028 codonVariants[2] = codon3Variants;
2031 * compute variants for protein position 1
2033 codon1Variants.add(new DnaVariant("A", sf1));
2034 codon1Variants.add(new DnaVariant("A", sf2));
2035 codon2Variants.add(new DnaVariant("A"));
2036 codon2Variants.add(new DnaVariant("A"));
2037 codon3Variants.add(new DnaVariant("A", sf3));
2038 codon3Variants.add(new DnaVariant("A", sf4));
2039 AlignmentUtils.computePeptideVariants(peptide, 1, codonVariants);
2042 * compute variants for protein position 2
2044 codon1Variants.clear();
2045 codon2Variants.clear();
2046 codon3Variants.clear();
2047 codon1Variants.add(new DnaVariant("T"));
2048 codon2Variants.add(new DnaVariant("T"));
2049 codon3Variants.add(new DnaVariant("T", sf5));
2050 AlignmentUtils.computePeptideVariants(peptide, 2, codonVariants);
2053 * compute variants for protein position 3
2055 codon1Variants.clear();
2056 codon2Variants.clear();
2057 codon3Variants.clear();
2058 codon1Variants.add(new DnaVariant("C"));
2059 codon2Variants.add(new DnaVariant("C", sf6));
2060 codon3Variants.add(new DnaVariant("C"));
2061 AlignmentUtils.computePeptideVariants(peptide, 3, codonVariants);
2064 * verify added sequence features for
2065 * var1 K -> E Ensembl
2067 * var4 K -> N Ensembl
2068 * var6 P -> H COSMIC
2069 * var6 P -> R COSMIC
2071 SequenceFeature[] sfs = peptide.getSequenceFeatures();
2072 assertEquals(5, sfs.length);
2074 SequenceFeature sf = sfs[0];
2075 assertEquals(1, sf.getBegin());
2076 assertEquals(1, sf.getEnd());
2077 assertEquals("p.Lys1Glu", sf.getDescription());
2078 assertEquals("var1.125A>G", sf.getValue("ID"));
2079 assertNull(sf.getValue("clinical_significance"));
2080 assertEquals("ID=var1.125A>G", sf.getAttributes());
2081 assertEquals(1, sf.links.size());
2082 // link to variation is urlencoded
2084 "p.Lys1Glu var1.125A>G|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var1.125A%3EG",
2086 assertEquals(ensembl, sf.getFeatureGroup());
2089 assertEquals(1, sf.getBegin());
2090 assertEquals(1, sf.getEnd());
2091 assertEquals("p.Lys1Gln", sf.getDescription());
2092 assertEquals("var2", sf.getValue("ID"));
2093 assertEquals("Dodgy", sf.getValue("clinical_significance"));
2094 assertEquals("ID=var2;clinical_significance=Dodgy", sf.getAttributes());
2095 assertEquals(1, sf.links.size());
2097 "p.Lys1Gln var2|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var2",
2099 assertEquals(dbSnp, sf.getFeatureGroup());
2102 assertEquals(1, sf.getBegin());
2103 assertEquals(1, sf.getEnd());
2104 assertEquals("p.Lys1Asn", sf.getDescription());
2105 assertEquals("var4", sf.getValue("ID"));
2106 assertEquals("Benign", sf.getValue("clinical_significance"));
2107 assertEquals("ID=var4;clinical_significance=Benign", sf.getAttributes());
2108 assertEquals(1, sf.links.size());
2110 "p.Lys1Asn var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
2112 assertEquals(ensembl, sf.getFeatureGroup());
2114 // var5 generates two distinct protein variant features
2116 assertEquals(3, sf.getBegin());
2117 assertEquals(3, sf.getEnd());
2118 assertEquals("p.Pro3His", sf.getDescription());
2119 assertEquals("var6", sf.getValue("ID"));
2120 assertEquals("Good", sf.getValue("clinical_significance"));
2121 assertEquals("ID=var6;clinical_significance=Good", sf.getAttributes());
2122 assertEquals(1, sf.links.size());
2124 "p.Pro3His var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
2126 assertEquals(cosmic, sf.getFeatureGroup());
2129 assertEquals(3, sf.getBegin());
2130 assertEquals(3, sf.getEnd());
2131 assertEquals("p.Pro3Arg", sf.getDescription());
2132 assertEquals("var6", sf.getValue("ID"));
2133 assertEquals("Good", sf.getValue("clinical_significance"));
2134 assertEquals("ID=var6;clinical_significance=Good", sf.getAttributes());
2135 assertEquals(1, sf.links.size());
2137 "p.Pro3Arg var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
2139 assertEquals(cosmic, sf.getFeatureGroup());
2143 * Tests for the method that maps the subset of a dna sequence that has CDS
2144 * (or subtype) feature, with CDS strand = '-' (reverse)
2146 // test turned off as currently findCdsPositions is not strand-dependent
2147 // left in case it comes around again...
2148 @Test(groups = "Functional", enabled = false)
2149 public void testFindCdsPositions_reverseStrand()
2151 SequenceI dnaSeq = new Sequence("dna", "aaaGGGcccAAATTTttt");
2152 dnaSeq.createDatasetSequence();
2153 SequenceI ds = dnaSeq.getDatasetSequence();
2156 SequenceFeature sf = new SequenceFeature("CDS", "", 4, 6, 0f, null);
2158 ds.addSequenceFeature(sf);
2159 // exon feature should be ignored here
2160 sf = new SequenceFeature("exon", "", 7, 9, 0f, null);
2161 ds.addSequenceFeature(sf);
2162 // CDS for dna 10-12
2163 sf = new SequenceFeature("CDS_predicted", "", 10, 12, 0f, null);
2165 ds.addSequenceFeature(sf);
2167 List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
2169 * verify ranges { [12-10], [6-4] }
2171 assertEquals(6, MappingUtils.getLength(ranges));
2172 assertEquals(2, ranges.size());
2173 assertEquals(12, ranges.get(0)[0]);
2174 assertEquals(10, ranges.get(0)[1]);
2175 assertEquals(6, ranges.get(1)[0]);
2176 assertEquals(4, ranges.get(1)[1]);
2180 * Tests for the method that maps the subset of a dna sequence that has CDS
2181 * (or subtype) feature - reverse strand case where the start codon is
2184 @Test(groups = "Functional", enabled = false)
2185 // test turned off as currently findCdsPositions is not strand-dependent
2186 // left in case it comes around again...
2187 public void testFindCdsPositions_reverseStrandThreePrimeIncomplete()
2189 SequenceI dnaSeq = new Sequence("dna", "aaagGGCCCaaaTTTttt");
2190 dnaSeq.createDatasetSequence();
2191 SequenceI ds = dnaSeq.getDatasetSequence();
2194 SequenceFeature sf = new SequenceFeature("CDS", "", 5, 9, 0f, null);
2196 ds.addSequenceFeature(sf);
2197 // CDS for dna 13-15
2198 sf = new SequenceFeature("CDS_predicted", "", 13, 15, 0f, null);
2200 sf.setPhase("2"); // skip 2 bases to start of next codon
2201 ds.addSequenceFeature(sf);
2203 List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
2206 * check the mapping starts with the first complete codon
2207 * expect ranges [13, 13], [9, 5]
2209 assertEquals(6, MappingUtils.getLength(ranges));
2210 assertEquals(2, ranges.size());
2211 assertEquals(13, ranges.get(0)[0]);
2212 assertEquals(13, ranges.get(0)[1]);
2213 assertEquals(9, ranges.get(1)[0]);
2214 assertEquals(5, ranges.get(1)[1]);
2217 @Test(groups = "Functional")
2218 public void testAlignAs_alternateTranscriptsUngapped()
2220 SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
2221 SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
2222 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
2223 ((Alignment) dna).createDatasetAlignment();
2224 SequenceI cds1 = new Sequence("cds1", "GGGTTT");
2225 SequenceI cds2 = new Sequence("cds2", "CCCAAA");
2226 AlignmentI cds = new Alignment(new SequenceI[] { cds1, cds2 });
2227 ((Alignment) cds).createDatasetAlignment();
2229 AlignedCodonFrame acf = new AlignedCodonFrame();
2230 MapList map = new MapList(new int[] { 4, 9 }, new int[] { 1, 6 }, 1, 1);
2231 acf.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(), map);
2232 map = new MapList(new int[] { 1, 3, 10, 12 }, new int[] { 1, 6 }, 1, 1);
2233 acf.addMap(dna2.getDatasetSequence(), cds2.getDatasetSequence(), map);
2236 * verify CDS alignment is as:
2237 * cccGGGTTTaaa (cdna)
2238 * CCCgggtttAAA (cdna)
2240 * ---GGGTTT--- (cds)
2241 * CCC------AAA (cds)
2243 dna.addCodonFrame(acf);
2244 AlignmentUtils.alignAs(cds, dna);
2245 assertEquals("---GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
2246 assertEquals("CCC------AAA", cds.getSequenceAt(1).getSequenceAsString());
2249 @Test(groups = { "Functional" })
2250 public void testAddMappedPositions()
2252 SequenceI from = new Sequence("dna", "ggAA-ATcc-TT-g");
2253 SequenceI seq1 = new Sequence("cds", "AAATTT");
2254 from.createDatasetSequence();
2255 seq1.createDatasetSequence();
2256 Mapping mapping = new Mapping(seq1, new MapList(
2257 new int[] { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1));
2258 Map<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
2259 AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
2262 * verify map has seq1 residues in columns 3,4,6,7,11,12
2264 assertEquals(6, map.size());
2265 assertEquals('A', map.get(3).get(seq1).charValue());
2266 assertEquals('A', map.get(4).get(seq1).charValue());
2267 assertEquals('A', map.get(6).get(seq1).charValue());
2268 assertEquals('T', map.get(7).get(seq1).charValue());
2269 assertEquals('T', map.get(11).get(seq1).charValue());
2270 assertEquals('T', map.get(12).get(seq1).charValue());
2278 * Test case where the mapping 'from' range includes a stop codon which is
2279 * absent in the 'to' range
2281 @Test(groups = { "Functional" })
2282 public void testAddMappedPositions_withStopCodon()
2284 SequenceI from = new Sequence("dna", "ggAA-ATcc-TT-g");
2285 SequenceI seq1 = new Sequence("cds", "AAATTT");
2286 from.createDatasetSequence();
2287 seq1.createDatasetSequence();
2288 Mapping mapping = new Mapping(seq1, new MapList(
2289 new int[] { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1));
2290 Map<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
2291 AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
2294 * verify map has seq1 residues in columns 3,4,6,7,11,12
2296 assertEquals(6, map.size());
2297 assertEquals('A', map.get(3).get(seq1).charValue());
2298 assertEquals('A', map.get(4).get(seq1).charValue());
2299 assertEquals('A', map.get(6).get(seq1).charValue());
2300 assertEquals('T', map.get(7).get(seq1).charValue());
2301 assertEquals('T', map.get(11).get(seq1).charValue());
2302 assertEquals('T', map.get(12).get(seq1).charValue());
2306 * Test for the case where the products for which we want CDS are specified.
2307 * This is to represent the case where EMBL has CDS mappings to both Uniprot
2308 * and EMBLCDSPROTEIN. makeCdsAlignment() should only return the mappings for
2309 * the protein sequences specified.
2311 @Test(groups = { "Functional" })
2312 public void testMakeCdsAlignment_filterProducts()
2314 SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
2315 SequenceI dna2 = new Sequence("dna2", "GGGcccTTTaaaCCC");
2316 SequenceI pep1 = new Sequence("Uniprot|pep1", "GF");
2317 SequenceI pep2 = new Sequence("Uniprot|pep2", "GFP");
2318 SequenceI pep3 = new Sequence("EMBL|pep3", "GF");
2319 SequenceI pep4 = new Sequence("EMBL|pep4", "GFP");
2320 dna1.createDatasetSequence();
2321 dna2.createDatasetSequence();
2322 pep1.createDatasetSequence();
2323 pep2.createDatasetSequence();
2324 pep3.createDatasetSequence();
2325 pep4.createDatasetSequence();
2326 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
2327 dna.setDataset(null);
2328 AlignmentI emblPeptides = new Alignment(new SequenceI[] { pep3, pep4 });
2329 emblPeptides.setDataset(null);
2331 AlignedCodonFrame acf = new AlignedCodonFrame();
2332 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
2333 new int[] { 1, 2 }, 3, 1);
2334 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
2335 acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map);
2336 dna.addCodonFrame(acf);
2338 acf = new AlignedCodonFrame();
2339 map = new MapList(new int[] { 1, 3, 7, 9, 13, 15 }, new int[] { 1, 3 },
2341 acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
2342 acf.addMap(dna2.getDatasetSequence(), pep4.getDatasetSequence(), map);
2343 dna.addCodonFrame(acf);
2346 * execute method under test to find CDS for EMBL peptides only
2348 AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
2349 dna1, dna2 }, dna.getDataset(), emblPeptides.getSequencesArray());
2351 assertEquals(2, cds.getSequences().size());
2352 assertEquals("GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
2353 assertEquals("GGGTTTCCC", cds.getSequenceAt(1).getSequenceAsString());
2356 * verify shared, extended alignment dataset
2358 assertSame(dna.getDataset(), cds.getDataset());
2359 assertTrue(dna.getDataset().getSequences()
2360 .contains(cds.getSequenceAt(0).getDatasetSequence()));
2361 assertTrue(dna.getDataset().getSequences()
2362 .contains(cds.getSequenceAt(1).getDatasetSequence()));
2365 * Verify mappings from CDS to peptide, cDNA to CDS, and cDNA to peptide
2366 * the mappings are on the shared alignment dataset
2368 List<AlignedCodonFrame> cdsMappings = cds.getDataset().getCodonFrames();
2370 * 6 mappings, 2*(DNA->CDS), 2*(DNA->Pep), 2*(CDS->Pep)
2372 assertEquals(6, cdsMappings.size());
2375 * verify that mapping sets for dna and cds alignments are different
2376 * [not current behaviour - all mappings are on the alignment dataset]
2378 // select -> subselect type to test.
2379 // Assert.assertNotSame(dna.getCodonFrames(), cds.getCodonFrames());
2380 // assertEquals(4, dna.getCodonFrames().size());
2381 // assertEquals(4, cds.getCodonFrames().size());
2384 * Two mappings involve pep3 (dna to pep3, cds to pep3)
2385 * Mapping from pep3 to GGGTTT in first new exon sequence
2387 List<AlignedCodonFrame> pep3Mappings = MappingUtils
2388 .findMappingsForSequence(pep3, cdsMappings);
2389 assertEquals(2, pep3Mappings.size());
2390 List<AlignedCodonFrame> mappings = MappingUtils
2391 .findMappingsForSequence(cds.getSequenceAt(0), pep3Mappings);
2392 assertEquals(1, mappings.size());
2395 SearchResultsI sr = MappingUtils.buildSearchResults(pep3, 1, mappings);
2396 assertEquals(1, sr.getResults().size());
2397 SearchResultMatchI m = sr.getResults().get(0);
2398 assertSame(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
2399 assertEquals(1, m.getStart());
2400 assertEquals(3, m.getEnd());
2402 sr = MappingUtils.buildSearchResults(pep3, 2, mappings);
2403 m = sr.getResults().get(0);
2404 assertSame(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
2405 assertEquals(4, m.getStart());
2406 assertEquals(6, m.getEnd());
2409 * Two mappings involve pep4 (dna to pep4, cds to pep4)
2410 * Verify mapping from pep4 to GGGTTTCCC in second new exon sequence
2412 List<AlignedCodonFrame> pep4Mappings = MappingUtils
2413 .findMappingsForSequence(pep4, cdsMappings);
2414 assertEquals(2, pep4Mappings.size());
2415 mappings = MappingUtils.findMappingsForSequence(cds.getSequenceAt(1),
2417 assertEquals(1, mappings.size());
2419 sr = MappingUtils.buildSearchResults(pep4, 1, mappings);
2420 assertEquals(1, sr.getResults().size());
2421 m = sr.getResults().get(0);
2422 assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
2423 assertEquals(1, m.getStart());
2424 assertEquals(3, m.getEnd());
2426 sr = MappingUtils.buildSearchResults(pep4, 2, mappings);
2427 m = sr.getResults().get(0);
2428 assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
2429 assertEquals(4, m.getStart());
2430 assertEquals(6, m.getEnd());
2432 sr = MappingUtils.buildSearchResults(pep4, 3, mappings);
2433 m = sr.getResults().get(0);
2434 assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
2435 assertEquals(7, m.getStart());
2436 assertEquals(9, m.getEnd());
2440 * Test the method that just copies aligned sequences, provided all sequences
2441 * to be aligned share the aligned sequence's dataset
2443 @Test(groups = "Functional")
2444 public void testAlignAsSameSequences()
2446 SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
2447 SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
2448 AlignmentI al1 = new Alignment(new SequenceI[] { dna1, dna2 });
2449 ((Alignment) al1).createDatasetAlignment();
2451 SequenceI dna3 = new Sequence(dna1);
2452 SequenceI dna4 = new Sequence(dna2);
2453 assertSame(dna3.getDatasetSequence(), dna1.getDatasetSequence());
2454 assertSame(dna4.getDatasetSequence(), dna2.getDatasetSequence());
2455 String seq1 = "-cc-GG-GT-TT--aaa";
2456 dna3.setSequence(seq1);
2457 String seq2 = "C--C-Cgg--gtt-tAA-A-";
2458 dna4.setSequence(seq2);
2459 AlignmentI al2 = new Alignment(new SequenceI[] { dna3, dna4 });
2460 ((Alignment) al2).createDatasetAlignment();
2462 assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
2463 assertEquals(seq1, al1.getSequenceAt(0).getSequenceAsString());
2464 assertEquals(seq2, al1.getSequenceAt(1).getSequenceAsString());
2467 * add another sequence to 'aligned' - should still succeed, since
2468 * unaligned sequences still share a dataset with aligned sequences
2470 SequenceI dna5 = new Sequence("dna5", "CCCgggtttAAA");
2471 dna5.createDatasetSequence();
2472 al2.addSequence(dna5);
2473 assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
2474 assertEquals(seq1, al1.getSequenceAt(0).getSequenceAsString());
2475 assertEquals(seq2, al1.getSequenceAt(1).getSequenceAsString());
2478 * add another sequence to 'unaligned' - should fail, since now not
2479 * all unaligned sequences share a dataset with aligned sequences
2481 SequenceI dna6 = new Sequence("dna6", "CCCgggtttAAA");
2482 dna6.createDatasetSequence();
2483 al1.addSequence(dna6);
2484 // JAL-2110 JBP Comment: what's the use case for this behaviour ?
2485 assertFalse(AlignmentUtils.alignAsSameSequences(al1, al2));
2488 @Test(groups = "Functional")
2489 public void testAlignAsSameSequencesMultipleSubSeq()
2491 SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
2492 SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
2493 SequenceI as1 = dna1.deriveSequence();
2494 SequenceI as2 = dna1.deriveSequence().getSubSequence(3, 7);
2495 SequenceI as3 = dna2.deriveSequence();
2496 as1.insertCharAt(6, 5, '-');
2497 String s_as1 = as1.getSequenceAsString();
2498 as2.insertCharAt(6, 5, '-');
2499 String s_as2 = as2.getSequenceAsString();
2500 as3.insertCharAt(6, 5, '-');
2501 String s_as3 = as3.getSequenceAsString();
2502 AlignmentI aligned = new Alignment(new SequenceI[] { as1, as2, as3 });
2504 // why do we need to cast this still ?
2505 ((Alignment) aligned).createDatasetAlignment();
2506 SequenceI uas1 = dna1.deriveSequence();
2507 SequenceI uas2 = dna1.deriveSequence().getSubSequence(3, 7);
2508 SequenceI uas3 = dna2.deriveSequence();
2509 AlignmentI tobealigned = new Alignment(new SequenceI[] { uas1, uas2,
2511 ((Alignment) tobealigned).createDatasetAlignment();
2513 assertTrue(AlignmentUtils.alignAsSameSequences(tobealigned, aligned));
2514 assertEquals(s_as1, uas1.getSequenceAsString());
2515 assertEquals(s_as2, uas2.getSequenceAsString());
2516 assertEquals(s_as3, uas3.getSequenceAsString());