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.SearchResults;
39 import jalview.datamodel.SearchResults.Match;
40 import jalview.datamodel.Sequence;
41 import jalview.datamodel.SequenceFeature;
42 import jalview.datamodel.SequenceI;
43 import jalview.io.AppletFormatAdapter;
44 import jalview.io.FormatAdapter;
45 import jalview.util.MapList;
46 import jalview.util.MappingUtils;
48 import java.io.IOException;
49 import java.util.ArrayList;
50 import java.util.Arrays;
51 import java.util.LinkedHashMap;
52 import java.util.List;
54 import java.util.TreeMap;
56 import org.testng.annotations.Test;
58 public class AlignmentUtilsTests
60 public static Sequence ts = new Sequence("short",
61 "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
63 @Test(groups = { "Functional" })
64 public void testExpandContext()
66 AlignmentI al = new Alignment(new Sequence[] {});
67 for (int i = 4; i < 14; i += 2)
69 SequenceI s1 = ts.deriveSequence().getSubSequence(i, i + 7);
72 System.out.println(new AppletFormatAdapter().formatSequences("Clustal",
74 for (int flnk = -1; flnk < 25; flnk++)
76 AlignmentI exp = AlignmentUtils.expandContext(al, flnk);
77 System.out.println("\nFlank size: " + flnk);
78 System.out.println(new AppletFormatAdapter().formatSequences(
79 "Clustal", exp, true));
83 * Full expansion to complete sequences
85 for (SequenceI sq : exp.getSequences())
87 String ung = sq.getSequenceAsString().replaceAll("-+", "");
88 final String errorMsg = "Flanking sequence not the same as original dataset sequence.\n"
91 + sq.getDatasetSequence().getSequenceAsString();
92 assertTrue(errorMsg, ung.equalsIgnoreCase(sq.getDatasetSequence()
93 .getSequenceAsString()));
99 * Last sequence is fully expanded, others have leading gaps to match
101 assertTrue(exp.getSequenceAt(4).getSequenceAsString()
103 assertTrue(exp.getSequenceAt(3).getSequenceAsString()
104 .startsWith("--abc"));
105 assertTrue(exp.getSequenceAt(2).getSequenceAsString()
106 .startsWith("----abc"));
107 assertTrue(exp.getSequenceAt(1).getSequenceAsString()
108 .startsWith("------abc"));
109 assertTrue(exp.getSequenceAt(0).getSequenceAsString()
110 .startsWith("--------abc"));
116 * Test that annotations are correctly adjusted by expandContext
118 @Test(groups = { "Functional" })
119 public void testExpandContext_annotation()
121 AlignmentI al = new Alignment(new Sequence[] {});
122 SequenceI ds = new Sequence("Seq1", "ABCDEFGHI");
124 SequenceI seq1 = ds.deriveSequence().getSubSequence(3, 6);
125 al.addSequence(seq1);
128 * Annotate DEF with 4/5/6 respectively
130 Annotation[] anns = new Annotation[] { new Annotation(4),
131 new Annotation(5), new Annotation(6) };
132 AlignmentAnnotation ann = new AlignmentAnnotation("SS",
133 "secondary structure", anns);
134 seq1.addAlignmentAnnotation(ann);
137 * The annotations array should match aligned positions
139 assertEquals(3, ann.annotations.length);
140 assertEquals(4, ann.annotations[0].value, 0.001);
141 assertEquals(5, ann.annotations[1].value, 0.001);
142 assertEquals(6, ann.annotations[2].value, 0.001);
145 * Check annotation to sequence position mappings before expanding the
146 * sequence; these are set up in Sequence.addAlignmentAnnotation ->
147 * Annotation.setSequenceRef -> createSequenceMappings
149 assertNull(ann.getAnnotationForPosition(1));
150 assertNull(ann.getAnnotationForPosition(2));
151 assertNull(ann.getAnnotationForPosition(3));
152 assertEquals(4, ann.getAnnotationForPosition(4).value, 0.001);
153 assertEquals(5, ann.getAnnotationForPosition(5).value, 0.001);
154 assertEquals(6, ann.getAnnotationForPosition(6).value, 0.001);
155 assertNull(ann.getAnnotationForPosition(7));
156 assertNull(ann.getAnnotationForPosition(8));
157 assertNull(ann.getAnnotationForPosition(9));
160 * Expand the subsequence to the full sequence abcDEFghi
162 AlignmentI expanded = AlignmentUtils.expandContext(al, -1);
163 assertEquals("abcDEFghi", expanded.getSequenceAt(0)
164 .getSequenceAsString());
167 * Confirm the alignment and sequence have the same SS annotation,
168 * referencing the expanded sequence
170 ann = expanded.getSequenceAt(0).getAnnotation()[0];
171 assertSame(ann, expanded.getAlignmentAnnotation()[0]);
172 assertSame(expanded.getSequenceAt(0), ann.sequenceRef);
175 * The annotations array should have null values except for annotated
178 assertNull(ann.annotations[0]);
179 assertNull(ann.annotations[1]);
180 assertNull(ann.annotations[2]);
181 assertEquals(4, ann.annotations[3].value, 0.001);
182 assertEquals(5, ann.annotations[4].value, 0.001);
183 assertEquals(6, ann.annotations[5].value, 0.001);
184 assertNull(ann.annotations[6]);
185 assertNull(ann.annotations[7]);
186 assertNull(ann.annotations[8]);
189 * sequence position mappings should be unchanged
191 assertNull(ann.getAnnotationForPosition(1));
192 assertNull(ann.getAnnotationForPosition(2));
193 assertNull(ann.getAnnotationForPosition(3));
194 assertEquals(4, ann.getAnnotationForPosition(4).value, 0.001);
195 assertEquals(5, ann.getAnnotationForPosition(5).value, 0.001);
196 assertEquals(6, ann.getAnnotationForPosition(6).value, 0.001);
197 assertNull(ann.getAnnotationForPosition(7));
198 assertNull(ann.getAnnotationForPosition(8));
199 assertNull(ann.getAnnotationForPosition(9));
203 * Test method that returns a map of lists of sequences by sequence name.
205 * @throws IOException
207 @Test(groups = { "Functional" })
208 public void testGetSequencesByName() throws IOException
210 final String data = ">Seq1Name\nKQYL\n" + ">Seq2Name\nRFPW\n"
211 + ">Seq1Name\nABCD\n";
212 AlignmentI al = loadAlignment(data, "FASTA");
213 Map<String, List<SequenceI>> map = AlignmentUtils
214 .getSequencesByName(al);
215 assertEquals(2, map.keySet().size());
216 assertEquals(2, map.get("Seq1Name").size());
217 assertEquals("KQYL", map.get("Seq1Name").get(0).getSequenceAsString());
218 assertEquals("ABCD", map.get("Seq1Name").get(1).getSequenceAsString());
219 assertEquals(1, map.get("Seq2Name").size());
220 assertEquals("RFPW", map.get("Seq2Name").get(0).getSequenceAsString());
224 * Helper method to load an alignment and ensure dataset sequences are set up.
230 * @throws IOException
232 protected AlignmentI loadAlignment(final String data, String format)
235 AlignmentI a = new FormatAdapter().readFile(data,
236 AppletFormatAdapter.PASTE, format);
242 * Test mapping of protein to cDNA, for the case where we have no sequence
243 * cross-references, so mappings are made first-served 1-1 where sequences
246 * @throws IOException
248 @Test(groups = { "Functional" })
249 public void testMapProteinAlignmentToCdna_noXrefs() throws IOException
251 List<SequenceI> protseqs = new ArrayList<SequenceI>();
252 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
253 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
254 protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
255 AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
256 protein.setDataset(null);
258 List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
259 dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR
260 dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAA")); // = EIQ
261 dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ
262 dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG")); // = EIQ
263 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
264 cdna.setDataset(null);
266 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
268 // 3 mappings made, each from 1 to 1 sequence
269 assertEquals(3, protein.getCodonFrames().size());
270 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
271 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
272 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
274 // V12345 mapped to A22222
275 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
277 assertEquals(1, acf.getdnaSeqs().length);
278 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
279 acf.getdnaSeqs()[0]);
280 Mapping[] protMappings = acf.getProtMappings();
281 assertEquals(1, protMappings.length);
282 MapList mapList = protMappings[0].getMap();
283 assertEquals(3, mapList.getFromRatio());
284 assertEquals(1, mapList.getToRatio());
285 assertTrue(Arrays.equals(new int[] { 1, 9 }, mapList.getFromRanges()
287 assertEquals(1, mapList.getFromRanges().size());
288 assertTrue(Arrays.equals(new int[] { 1, 3 },
289 mapList.getToRanges().get(0)));
290 assertEquals(1, mapList.getToRanges().size());
292 // V12346 mapped to A33333
293 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
294 assertEquals(1, acf.getdnaSeqs().length);
295 assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
296 acf.getdnaSeqs()[0]);
298 // V12347 mapped to A11111
299 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
300 assertEquals(1, acf.getdnaSeqs().length);
301 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
302 acf.getdnaSeqs()[0]);
304 // no mapping involving the 'extra' A44444
305 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(3)).isEmpty());
309 * Test for the alignSequenceAs method that takes two sequences and a mapping.
311 @Test(groups = { "Functional" })
312 public void testAlignSequenceAs_withMapping_noIntrons()
314 MapList map = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 }, 3, 1);
317 * No existing gaps in dna:
319 checkAlignSequenceAs("GGGAAA", "-A-L-", false, false, map,
323 * Now introduce gaps in dna but ignore them when realigning.
325 checkAlignSequenceAs("-G-G-G-A-A-A-", "-A-L-", false, false, map,
329 * Now include gaps in dna when realigning. First retaining 'mapped' gaps
330 * only, i.e. those within the exon region.
332 checkAlignSequenceAs("-G-G--G-A--A-A-", "-A-L-", true, false, map,
333 "---G-G--G---A--A-A");
336 * Include all gaps in dna when realigning (within and without the exon
337 * region). The leading gap, and the gaps between codons, are subsumed by
338 * the protein alignment gap.
340 checkAlignSequenceAs("-G-GG--AA-A---", "-A-L-", true, true, map,
341 "---G-GG---AA-A---");
344 * Include only unmapped gaps in dna when realigning (outside the exon
345 * region). The leading gap, and the gaps between codons, are subsumed by
346 * the protein alignment gap.
348 checkAlignSequenceAs("-G-GG--AA-A-", "-A-L-", false, true, map,
353 * Test for the alignSequenceAs method that takes two sequences and a mapping.
355 @Test(groups = { "Functional" })
356 public void testAlignSequenceAs_withMapping_withIntrons()
359 * Exons at codon 2 (AAA) and 4 (TTT)
361 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
362 new int[] { 1, 2 }, 3, 1);
365 * Simple case: no gaps in dna
367 checkAlignSequenceAs("GGGAAACCCTTTGGG", "--A-L-", false, false, map,
368 "GGG---AAACCCTTTGGG");
371 * Add gaps to dna - but ignore when realigning.
373 checkAlignSequenceAs("-G-G-G--A--A---AC-CC-T-TT-GG-G-", "--A-L-",
374 false, false, map, "GGG---AAACCCTTTGGG");
377 * Add gaps to dna - include within exons only when realigning.
379 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
380 true, false, map, "GGG---A--A---ACCCT-TTGGG");
383 * Include gaps outside exons only when realigning.
385 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
386 false, true, map, "-G-G-GAAAC-CCTTT-GG-G-");
389 * Include gaps following first intron if we are 'preserving mapped gaps'
391 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
392 true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
395 * Include all gaps in dna when realigning.
397 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
398 true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
402 * Test for the case where not all of the protein sequence is mapped to cDNA.
404 @Test(groups = { "Functional" })
405 public void testAlignSequenceAs_withMapping_withUnmappedProtein()
408 * Exons at codon 2 (AAA) and 4 (TTT) mapped to A and P
410 final MapList map = new MapList(new int[] { 4, 6, 10, 12 }, new int[] {
414 * -L- 'aligns' ccc------
416 checkAlignSequenceAs("gggAAAcccTTTggg", "-A-L-P-", false, false, map,
417 "gggAAAccc------TTTggg");
421 * Helper method that performs and verifies the method under test.
424 * the sequence to be realigned
426 * the sequence whose alignment is to be copied
427 * @param preserveMappedGaps
428 * @param preserveUnmappedGaps
432 protected void checkAlignSequenceAs(final String alignee,
433 final String alignModel, final boolean preserveMappedGaps,
434 final boolean preserveUnmappedGaps, MapList map,
435 final String expected)
437 SequenceI alignMe = new Sequence("Seq1", alignee);
438 alignMe.createDatasetSequence();
439 SequenceI alignFrom = new Sequence("Seq2", alignModel);
440 alignFrom.createDatasetSequence();
441 AlignedCodonFrame acf = new AlignedCodonFrame();
442 acf.addMap(alignMe.getDatasetSequence(), alignFrom.getDatasetSequence(), map);
444 AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "---", '-',
445 preserveMappedGaps, preserveUnmappedGaps);
446 assertEquals(expected, alignMe.getSequenceAsString());
450 * Test for the alignSequenceAs method where we preserve gaps in introns only.
452 @Test(groups = { "Functional" })
453 public void testAlignSequenceAs_keepIntronGapsOnly()
457 * Intron GGGAAA followed by exon CCCTTT
459 MapList map = new MapList(new int[] { 7, 12 }, new int[] { 1, 2 }, 3, 1);
461 checkAlignSequenceAs("GG-G-AA-A-C-CC-T-TT", "AL", false, true, map,
466 * Test the method that realigns protein to match mapped codon alignment.
468 @Test(groups = { "Functional" })
469 public void testAlignProteinAsDna()
471 // seq1 codons are [1,2,3] [4,5,6] [7,8,9] [10,11,12]
472 SequenceI dna1 = new Sequence("Seq1", "TGCCATTACCAG-");
473 // seq2 codons are [1,3,4] [5,6,7] [8,9,10] [11,12,13]
474 SequenceI dna2 = new Sequence("Seq2", "T-GCCATTACCAG");
475 // seq3 codons are [1,2,3] [4,5,7] [8,9,10] [11,12,13]
476 SequenceI dna3 = new Sequence("Seq3", "TGCCA-TTACCAG");
477 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
478 dna.setDataset(null);
480 // protein alignment will be realigned like dna
481 SequenceI prot1 = new Sequence("Seq1", "CHYQ");
482 SequenceI prot2 = new Sequence("Seq2", "CHYQ");
483 SequenceI prot3 = new Sequence("Seq3", "CHYQ");
484 SequenceI prot4 = new Sequence("Seq4", "R-QSV"); // unmapped, unchanged
485 AlignmentI protein = new Alignment(new SequenceI[] { prot1, prot2,
487 protein.setDataset(null);
489 MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1);
490 AlignedCodonFrame acf = new AlignedCodonFrame();
491 acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
492 acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map);
493 acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map);
494 ArrayList<AlignedCodonFrame> acfs = new ArrayList<AlignedCodonFrame>();
496 protein.setCodonFrames(acfs);
499 * Translated codon order is [1,2,3] [1,3,4] [4,5,6] [4,5,7] [5,6,7] [7,8,9]
500 * [8,9,10] [10,11,12] [11,12,13]
502 AlignmentUtils.alignProteinAsDna(protein, dna);
503 assertEquals("C-H--Y-Q-", prot1.getSequenceAsString());
504 assertEquals("-C--H-Y-Q", prot2.getSequenceAsString());
505 assertEquals("C--H--Y-Q", prot3.getSequenceAsString());
506 assertEquals("R-QSV", prot4.getSequenceAsString());
510 * Test the method that tests whether a CDNA sequence translates to a protein
513 @Test(groups = { "Functional" })
514 public void testTranslatesAs()
516 // null arguments check
517 assertFalse(AlignmentUtils.translatesAs(null, 0, null));
518 assertFalse(AlignmentUtils.translatesAs(new char[] { 't' }, 0, null));
519 assertFalse(AlignmentUtils.translatesAs(null, 0, new char[] { 'a' }));
521 // straight translation
522 assertTrue(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
523 "FPKG".toCharArray()));
524 // with extra start codon (not in protein)
525 assertTrue(AlignmentUtils.translatesAs("atgtttcccaaaggg".toCharArray(),
526 3, "FPKG".toCharArray()));
527 // with stop codon1 (not in protein)
528 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtaa".toCharArray(),
529 0, "FPKG".toCharArray()));
530 // with stop codon1 (in protein as *)
531 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtaa".toCharArray(),
532 0, "FPKG*".toCharArray()));
533 // with stop codon2 (not in protein)
534 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtag".toCharArray(),
535 0, "FPKG".toCharArray()));
536 // with stop codon3 (not in protein)
537 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtga".toCharArray(),
538 0, "FPKG".toCharArray()));
539 // with start and stop codon1
540 assertTrue(AlignmentUtils.translatesAs(
541 "atgtttcccaaagggtaa".toCharArray(), 3, "FPKG".toCharArray()));
542 // with start and stop codon1 (in protein as *)
543 assertTrue(AlignmentUtils.translatesAs(
544 "atgtttcccaaagggtaa".toCharArray(), 3, "FPKG*".toCharArray()));
545 // with start and stop codon2
546 assertTrue(AlignmentUtils.translatesAs(
547 "atgtttcccaaagggtag".toCharArray(), 3, "FPKG".toCharArray()));
548 // with start and stop codon3
549 assertTrue(AlignmentUtils.translatesAs(
550 "atgtttcccaaagggtga".toCharArray(), 3, "FPKG".toCharArray()));
552 // with embedded stop codons
553 assertTrue(AlignmentUtils.translatesAs(
554 "atgtttTAGcccaaaTAAgggtga".toCharArray(), 3,
555 "F*PK*G".toCharArray()));
558 assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
559 0, "FPMG".toCharArray()));
562 assertFalse(AlignmentUtils.translatesAs("tttcccaaagg".toCharArray(), 0,
563 "FPKG".toCharArray()));
566 assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
567 0, "FPK".toCharArray()));
569 // overlong dna (doesn't end in stop codon)
570 assertFalse(AlignmentUtils.translatesAs(
571 "tttcccaaagggttt".toCharArray(), 0, "FPKG".toCharArray()));
573 // dna + stop codon + more
574 assertFalse(AlignmentUtils.translatesAs(
575 "tttcccaaagggttaga".toCharArray(), 0, "FPKG".toCharArray()));
578 assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
579 0, "FPKGQ".toCharArray()));
583 * Test mapping of protein to cDNA, for cases where the cDNA has start and/or
584 * stop codons in addition to the protein coding sequence.
586 * @throws IOException
588 @Test(groups = { "Functional" })
589 public void testMapProteinAlignmentToCdna_withStartAndStopCodons()
592 List<SequenceI> protseqs = new ArrayList<SequenceI>();
593 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
594 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
595 protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
596 AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
597 protein.setDataset(null);
599 List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
601 dnaseqs.add(new Sequence("EMBL|A11111", "ATGTCAGCACGC"));
603 dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAATAA"));
604 // = start +EIQ + stop
605 dnaseqs.add(new Sequence("EMBL|A33333", "ATGGAAATCCAGTAG"));
606 dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG"));
607 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
608 cdna.setDataset(null);
610 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
612 // 3 mappings made, each from 1 to 1 sequence
613 assertEquals(3, protein.getCodonFrames().size());
614 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
615 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
616 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
618 // V12345 mapped from A22222
619 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
621 assertEquals(1, acf.getdnaSeqs().length);
622 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
623 acf.getdnaSeqs()[0]);
624 Mapping[] protMappings = acf.getProtMappings();
625 assertEquals(1, protMappings.length);
626 MapList mapList = protMappings[0].getMap();
627 assertEquals(3, mapList.getFromRatio());
628 assertEquals(1, mapList.getToRatio());
629 assertTrue(Arrays.equals(new int[] { 1, 9 }, mapList.getFromRanges()
631 assertEquals(1, mapList.getFromRanges().size());
632 assertTrue(Arrays.equals(new int[] { 1, 3 },
633 mapList.getToRanges().get(0)));
634 assertEquals(1, mapList.getToRanges().size());
636 // V12346 mapped from A33333 starting position 4
637 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
638 assertEquals(1, acf.getdnaSeqs().length);
639 assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
640 acf.getdnaSeqs()[0]);
641 protMappings = acf.getProtMappings();
642 assertEquals(1, protMappings.length);
643 mapList = protMappings[0].getMap();
644 assertEquals(3, mapList.getFromRatio());
645 assertEquals(1, mapList.getToRatio());
646 assertTrue(Arrays.equals(new int[] { 4, 12 }, mapList.getFromRanges()
648 assertEquals(1, mapList.getFromRanges().size());
649 assertTrue(Arrays.equals(new int[] { 1, 3 },
650 mapList.getToRanges().get(0)));
651 assertEquals(1, mapList.getToRanges().size());
653 // V12347 mapped to A11111 starting position 4
654 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
655 assertEquals(1, acf.getdnaSeqs().length);
656 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
657 acf.getdnaSeqs()[0]);
658 protMappings = acf.getProtMappings();
659 assertEquals(1, protMappings.length);
660 mapList = protMappings[0].getMap();
661 assertEquals(3, mapList.getFromRatio());
662 assertEquals(1, mapList.getToRatio());
663 assertTrue(Arrays.equals(new int[] { 4, 12 }, mapList.getFromRanges()
665 assertEquals(1, mapList.getFromRanges().size());
666 assertTrue(Arrays.equals(new int[] { 1, 3 },
667 mapList.getToRanges().get(0)));
668 assertEquals(1, mapList.getToRanges().size());
670 // no mapping involving the 'extra' A44444
671 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(3)).isEmpty());
675 * Test mapping of protein to cDNA, for the case where we have some sequence
676 * cross-references. Verify that 1-to-many mappings are made where
677 * cross-references exist and sequences are mappable.
679 * @throws IOException
681 @Test(groups = { "Functional" })
682 public void testMapProteinAlignmentToCdna_withXrefs() throws IOException
684 List<SequenceI> protseqs = new ArrayList<SequenceI>();
685 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
686 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
687 protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
688 AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
689 protein.setDataset(null);
691 List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
692 dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR
693 dnaseqs.add(new Sequence("EMBL|A22222", "ATGGAGATACAA")); // = start + EIQ
694 dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ
695 dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG")); // = EIQ
696 dnaseqs.add(new Sequence("EMBL|A55555", "GAGATTCAG")); // = EIQ
697 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[5]));
698 cdna.setDataset(null);
700 // Xref A22222 to V12345 (should get mapped)
701 dnaseqs.get(1).addDBRef(new DBRefEntry("UNIPROT", "1", "V12345"));
702 // Xref V12345 to A44444 (should get mapped)
703 protseqs.get(0).addDBRef(new DBRefEntry("EMBL", "1", "A44444"));
704 // Xref A33333 to V12347 (sequence mismatch - should not get mapped)
705 dnaseqs.get(2).addDBRef(new DBRefEntry("UNIPROT", "1", "V12347"));
706 // as V12345 is mapped to A22222 and A44444, this leaves V12346 unmapped.
707 // it should get paired up with the unmapped A33333
708 // A11111 should be mapped to V12347
709 // A55555 is spare and has no xref so is not mapped
711 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
713 // 4 protein mappings made for 3 proteins, 2 to V12345, 1 each to V12346/7
714 assertEquals(3, protein.getCodonFrames().size());
715 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
716 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
717 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
719 // one mapping for each of the first 4 cDNA sequences
720 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(0)).size());
721 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(1)).size());
722 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(2)).size());
723 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(3)).size());
725 // V12345 mapped to A22222 and A44444
726 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
728 assertEquals(2, acf.getdnaSeqs().length);
729 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
730 acf.getdnaSeqs()[0]);
731 assertEquals(cdna.getSequenceAt(3).getDatasetSequence(),
732 acf.getdnaSeqs()[1]);
734 // V12346 mapped to A33333
735 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
736 assertEquals(1, acf.getdnaSeqs().length);
737 assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
738 acf.getdnaSeqs()[0]);
740 // V12347 mapped to A11111
741 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
742 assertEquals(1, acf.getdnaSeqs().length);
743 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
744 acf.getdnaSeqs()[0]);
746 // no mapping involving the 'extra' A55555
747 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(4)).isEmpty());
751 * Test mapping of protein to cDNA, for the case where we have some sequence
752 * cross-references. Verify that once we have made an xref mapping we don't
753 * also map un-xrefd sequeces.
755 * @throws IOException
757 @Test(groups = { "Functional" })
758 public void testMapProteinAlignmentToCdna_prioritiseXrefs()
761 List<SequenceI> protseqs = new ArrayList<SequenceI>();
762 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
763 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
764 AlignmentI protein = new Alignment(
765 protseqs.toArray(new SequenceI[protseqs.size()]));
766 protein.setDataset(null);
768 List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
769 dnaseqs.add(new Sequence("EMBL|A11111", "GAAATCCAG")); // = EIQ
770 dnaseqs.add(new Sequence("EMBL|A22222", "GAAATTCAG")); // = EIQ
771 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[dnaseqs
773 cdna.setDataset(null);
775 // Xref A22222 to V12345 (should get mapped)
776 // A11111 should then be mapped to the unmapped V12346
777 dnaseqs.get(1).addDBRef(new DBRefEntry("UNIPROT", "1", "V12345"));
779 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
781 // 2 protein mappings made
782 assertEquals(2, protein.getCodonFrames().size());
783 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
784 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
786 // one mapping for each of the cDNA sequences
787 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(0)).size());
788 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(1)).size());
790 // V12345 mapped to A22222
791 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
793 assertEquals(1, acf.getdnaSeqs().length);
794 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
795 acf.getdnaSeqs()[0]);
797 // V12346 mapped to A11111
798 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
799 assertEquals(1, acf.getdnaSeqs().length);
800 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
801 acf.getdnaSeqs()[0]);
805 * Test the method that shows or hides sequence annotations by type(s) and
808 @Test(groups = { "Functional" })
809 public void testShowOrHideSequenceAnnotations()
811 SequenceI seq1 = new Sequence("Seq1", "AAA");
812 SequenceI seq2 = new Sequence("Seq2", "BBB");
813 SequenceI seq3 = new Sequence("Seq3", "CCC");
814 Annotation[] anns = new Annotation[] { new Annotation(2f) };
815 AlignmentAnnotation ann1 = new AlignmentAnnotation("Structure", "ann1",
817 ann1.setSequenceRef(seq1);
818 AlignmentAnnotation ann2 = new AlignmentAnnotation("Structure", "ann2",
820 ann2.setSequenceRef(seq2);
821 AlignmentAnnotation ann3 = new AlignmentAnnotation("Structure", "ann3",
823 AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "ann4", anns);
824 ann4.setSequenceRef(seq1);
825 AlignmentAnnotation ann5 = new AlignmentAnnotation("Temp", "ann5", anns);
826 ann5.setSequenceRef(seq2);
827 AlignmentAnnotation ann6 = new AlignmentAnnotation("Temp", "ann6", anns);
828 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
829 al.addAnnotation(ann1); // Structure for Seq1
830 al.addAnnotation(ann2); // Structure for Seq2
831 al.addAnnotation(ann3); // Structure for no sequence
832 al.addAnnotation(ann4); // Temp for seq1
833 al.addAnnotation(ann5); // Temp for seq2
834 al.addAnnotation(ann6); // Temp for no sequence
835 List<String> types = new ArrayList<String>();
836 List<SequenceI> scope = new ArrayList<SequenceI>();
839 * Set all sequence related Structure to hidden (ann1, ann2)
841 types.add("Structure");
842 AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, false,
844 assertFalse(ann1.visible);
845 assertFalse(ann2.visible);
846 assertTrue(ann3.visible); // not sequence-related, not affected
847 assertTrue(ann4.visible); // not Structure, not affected
848 assertTrue(ann5.visible); // "
849 assertTrue(ann6.visible); // not sequence-related, not affected
852 * Set Temp in {seq1, seq3} to hidden
858 AlignmentUtils.showOrHideSequenceAnnotations(al, types, scope, false,
860 assertFalse(ann1.visible); // unchanged
861 assertFalse(ann2.visible); // unchanged
862 assertTrue(ann3.visible); // not sequence-related, not affected
863 assertFalse(ann4.visible); // Temp for seq1 hidden
864 assertTrue(ann5.visible); // not in scope, not affected
865 assertTrue(ann6.visible); // not sequence-related, not affected
868 * Set Temp in all sequences to hidden
874 AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, false,
876 assertFalse(ann1.visible); // unchanged
877 assertFalse(ann2.visible); // unchanged
878 assertTrue(ann3.visible); // not sequence-related, not affected
879 assertFalse(ann4.visible); // Temp for seq1 hidden
880 assertFalse(ann5.visible); // Temp for seq2 hidden
881 assertTrue(ann6.visible); // not sequence-related, not affected
884 * Set all types in {seq1, seq3} to visible
890 AlignmentUtils.showOrHideSequenceAnnotations(al, types, scope, true,
892 assertTrue(ann1.visible); // Structure for seq1 set visible
893 assertFalse(ann2.visible); // not in scope, unchanged
894 assertTrue(ann3.visible); // not sequence-related, not affected
895 assertTrue(ann4.visible); // Temp for seq1 set visible
896 assertFalse(ann5.visible); // not in scope, unchanged
897 assertTrue(ann6.visible); // not sequence-related, not affected
900 * Set all types in all scope to hidden
902 AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, true,
904 assertFalse(ann1.visible);
905 assertFalse(ann2.visible);
906 assertTrue(ann3.visible); // not sequence-related, not affected
907 assertFalse(ann4.visible);
908 assertFalse(ann5.visible);
909 assertTrue(ann6.visible); // not sequence-related, not affected
913 * Tests for the method that checks if one sequence cross-references another
915 @Test(groups = { "Functional" })
916 public void testHasCrossRef()
918 assertFalse(AlignmentUtils.hasCrossRef(null, null));
919 SequenceI seq1 = new Sequence("EMBL|A12345", "ABCDEF");
920 assertFalse(AlignmentUtils.hasCrossRef(seq1, null));
921 assertFalse(AlignmentUtils.hasCrossRef(null, seq1));
922 SequenceI seq2 = new Sequence("UNIPROT|V20192", "ABCDEF");
923 assertFalse(AlignmentUtils.hasCrossRef(seq1, seq2));
926 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "v20193"));
927 assertFalse(AlignmentUtils.hasCrossRef(seq1, seq2));
929 // case-insensitive; version number is ignored
930 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "v20192"));
931 assertTrue(AlignmentUtils.hasCrossRef(seq1, seq2));
934 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
935 assertTrue(AlignmentUtils.hasCrossRef(seq1, seq2));
936 // test is one-way only
937 assertFalse(AlignmentUtils.hasCrossRef(seq2, seq1));
941 * Tests for the method that checks if either sequence cross-references the
944 @Test(groups = { "Functional" })
945 public void testHaveCrossRef()
947 assertFalse(AlignmentUtils.hasCrossRef(null, null));
948 SequenceI seq1 = new Sequence("EMBL|A12345", "ABCDEF");
949 assertFalse(AlignmentUtils.haveCrossRef(seq1, null));
950 assertFalse(AlignmentUtils.haveCrossRef(null, seq1));
951 SequenceI seq2 = new Sequence("UNIPROT|V20192", "ABCDEF");
952 assertFalse(AlignmentUtils.haveCrossRef(seq1, seq2));
954 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
955 assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
956 // next is true for haveCrossRef, false for hasCrossRef
957 assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
959 // now the other way round
960 seq1.setDBRefs(null);
961 seq2.addDBRef(new DBRefEntry("EMBL", "1", "A12345"));
962 assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
963 assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
966 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
967 assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
968 assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
972 * Test the method that extracts the cds-only part of a dna alignment.
974 @Test(groups = { "Functional" })
975 public void testMakeCdsAlignment()
979 * dna1 --> [4, 6] [10,12] --> pep1
980 * dna2 --> [1, 3] [7, 9] [13,15] --> pep1
982 SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
983 SequenceI dna2 = new Sequence("dna2", "GGGcccTTTaaaCCC");
984 SequenceI pep1 = new Sequence("pep1", "GF");
985 SequenceI pep2 = new Sequence("pep2", "GFP");
986 pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "pep1"));
987 pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "pep2"));
988 dna1.createDatasetSequence();
989 dna2.createDatasetSequence();
990 pep1.createDatasetSequence();
991 pep2.createDatasetSequence();
992 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
993 dna.setDataset(null);
996 * need a sourceDbRef if we are to construct dbrefs to the CDS
999 DBRefEntry dbref = new DBRefEntry("ENSEMBL", "0", "dna1");
1000 dna1.getDatasetSequence().addDBRef(dbref);
1001 org.testng.Assert.assertEquals(dbref, dna1.getPrimaryDBRefs().get(0));
1002 dbref = new DBRefEntry("ENSEMBL", "0", "dna2");
1003 dna2.getDatasetSequence().addDBRef(dbref);
1004 org.testng.Assert.assertEquals(dbref, dna2.getPrimaryDBRefs().get(0));
1007 * CDS sequences are 'discovered' from dna-to-protein mappings on the alignment
1008 * dataset (e.g. added from dbrefs by CrossRef.findXrefSequences)
1010 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1011 new int[] { 1, 2 }, 3, 1);
1012 AlignedCodonFrame acf = new AlignedCodonFrame();
1013 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
1014 dna.addCodonFrame(acf);
1015 map = new MapList(new int[] { 1, 3, 7, 9, 13, 15 }, new int[] { 1, 3 },
1017 acf = new AlignedCodonFrame();
1018 acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
1019 dna.addCodonFrame(acf);
1022 * execute method under test:
1024 AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
1025 dna1, dna2 }, dna.getDataset(), null);
1028 * verify cds sequences
1030 assertEquals(2, cds.getSequences().size());
1031 assertEquals("GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
1032 assertEquals("GGGTTTCCC", cds.getSequenceAt(1).getSequenceAsString());
1035 * verify shared, extended alignment dataset
1037 assertSame(dna.getDataset(), cds.getDataset());
1038 SequenceI cds1Dss = cds.getSequenceAt(0).getDatasetSequence();
1039 SequenceI cds2Dss = cds.getSequenceAt(1).getDatasetSequence();
1040 assertTrue(dna.getDataset().getSequences().contains(cds1Dss));
1041 assertTrue(dna.getDataset().getSequences().contains(cds2Dss));
1044 * verify CDS has a dbref with mapping to peptide
1046 assertNotNull(cds1Dss.getDBRefs());
1047 assertEquals(1, cds1Dss.getDBRefs().length);
1048 dbref = cds1Dss.getDBRefs()[0];
1049 assertEquals("UNIPROT", dbref.getSource());
1050 assertEquals("0", dbref.getVersion());
1051 assertEquals("pep1", dbref.getAccessionId());
1052 assertNotNull(dbref.getMap());
1053 assertSame(pep1.getDatasetSequence(), dbref.getMap().getTo());
1054 MapList cdsMapping = new MapList(new int[] { 1, 6 },
1055 new int[] { 1, 2 }, 3, 1);
1056 assertEquals(cdsMapping, dbref.getMap().getMap());
1059 * verify peptide has added a dbref with reverse mapping to CDS
1061 assertNotNull(pep1.getDBRefs());
1062 assertEquals(2, pep1.getDBRefs().length);
1063 dbref = pep1.getDBRefs()[1];
1064 assertEquals("ENSEMBL", dbref.getSource());
1065 assertEquals("0", dbref.getVersion());
1066 assertEquals("CDS|dna1", dbref.getAccessionId());
1067 assertNotNull(dbref.getMap());
1068 assertSame(cds1Dss, dbref.getMap().getTo());
1069 assertEquals(cdsMapping.getInverse(), dbref.getMap().getMap());
1072 * Verify mappings from CDS to peptide, cDNA to CDS, and cDNA to peptide
1073 * the mappings are on the shared alignment dataset
1074 * 6 mappings, 2*(DNA->CDS), 2*(DNA->Pep), 2*(CDS->Pep)
1076 List<AlignedCodonFrame> cdsMappings = cds.getDataset().getCodonFrames();
1077 assertEquals(6, cdsMappings.size());
1080 * verify that mapping sets for dna and cds alignments are different
1081 * [not current behaviour - all mappings are on the alignment dataset]
1083 // select -> subselect type to test.
1084 // Assert.assertNotSame(dna.getCodonFrames(), cds.getCodonFrames());
1085 // assertEquals(4, dna.getCodonFrames().size());
1086 // assertEquals(4, cds.getCodonFrames().size());
1089 * Two mappings involve pep1 (dna to pep1, cds to pep1)
1090 * Mapping from pep1 to GGGTTT in first new exon sequence
1092 List<AlignedCodonFrame> pep1Mappings = MappingUtils
1093 .findMappingsForSequence(pep1, cdsMappings);
1094 assertEquals(2, pep1Mappings.size());
1095 List<AlignedCodonFrame> mappings = MappingUtils
1096 .findMappingsForSequence(cds.getSequenceAt(0), pep1Mappings);
1097 assertEquals(1, mappings.size());
1100 SearchResults sr = MappingUtils.buildSearchResults(pep1, 1, mappings);
1101 assertEquals(1, sr.getResults().size());
1102 Match m = sr.getResults().get(0);
1103 assertSame(cds1Dss, m.getSequence());
1104 assertEquals(1, m.getStart());
1105 assertEquals(3, m.getEnd());
1107 sr = MappingUtils.buildSearchResults(pep1, 2, mappings);
1108 m = sr.getResults().get(0);
1109 assertSame(cds1Dss, m.getSequence());
1110 assertEquals(4, m.getStart());
1111 assertEquals(6, m.getEnd());
1114 * Two mappings involve pep2 (dna to pep2, cds to pep2)
1115 * Verify mapping from pep2 to GGGTTTCCC in second new exon sequence
1117 List<AlignedCodonFrame> pep2Mappings = MappingUtils
1118 .findMappingsForSequence(pep2, cdsMappings);
1119 assertEquals(2, pep2Mappings.size());
1120 mappings = MappingUtils.findMappingsForSequence(cds.getSequenceAt(1),
1122 assertEquals(1, mappings.size());
1124 sr = MappingUtils.buildSearchResults(pep2, 1, mappings);
1125 assertEquals(1, sr.getResults().size());
1126 m = sr.getResults().get(0);
1127 assertSame(cds2Dss, m.getSequence());
1128 assertEquals(1, m.getStart());
1129 assertEquals(3, m.getEnd());
1131 sr = MappingUtils.buildSearchResults(pep2, 2, mappings);
1132 m = sr.getResults().get(0);
1133 assertSame(cds2Dss, m.getSequence());
1134 assertEquals(4, m.getStart());
1135 assertEquals(6, m.getEnd());
1137 sr = MappingUtils.buildSearchResults(pep2, 3, mappings);
1138 m = sr.getResults().get(0);
1139 assertSame(cds2Dss, m.getSequence());
1140 assertEquals(7, m.getStart());
1141 assertEquals(9, m.getEnd());
1145 * Test the method that makes a cds-only alignment from a DNA sequence and its
1146 * product mappings, for the case where there are multiple exon mappings to
1147 * different protein products.
1149 @Test(groups = { "Functional" })
1150 public void testMakeCdsAlignment_multipleProteins()
1152 SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
1153 SequenceI pep1 = new Sequence("pep1", "GF"); // GGGTTT
1154 SequenceI pep2 = new Sequence("pep2", "KP"); // aaaccc
1155 SequenceI pep3 = new Sequence("pep3", "KF"); // aaaTTT
1156 dna1.createDatasetSequence();
1157 pep1.createDatasetSequence();
1158 pep2.createDatasetSequence();
1159 pep3.createDatasetSequence();
1160 pep1.getDatasetSequence().addDBRef(
1161 new DBRefEntry("EMBLCDS", "2", "A12345"));
1162 pep2.getDatasetSequence().addDBRef(
1163 new DBRefEntry("EMBLCDS", "3", "A12346"));
1164 pep3.getDatasetSequence().addDBRef(
1165 new DBRefEntry("EMBLCDS", "4", "A12347"));
1168 * Create the CDS alignment
1170 AlignmentI dna = new Alignment(new SequenceI[] { dna1 });
1171 dna.setDataset(null);
1174 * Make the mappings from dna to protein
1176 // map ...GGG...TTT to GF
1177 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1178 new int[] { 1, 2 }, 3, 1);
1179 AlignedCodonFrame acf = new AlignedCodonFrame();
1180 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
1181 dna.addCodonFrame(acf);
1183 // map aaa...ccc to KP
1184 map = new MapList(new int[] { 1, 3, 7, 9 }, new int[] { 1, 2 }, 3, 1);
1185 acf = new AlignedCodonFrame();
1186 acf.addMap(dna1.getDatasetSequence(), pep2.getDatasetSequence(), map);
1187 dna.addCodonFrame(acf);
1189 // map aaa......TTT to KF
1190 map = new MapList(new int[] { 1, 3, 10, 12 }, new int[] { 1, 2 }, 3, 1);
1191 acf = new AlignedCodonFrame();
1192 acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map);
1193 dna.addCodonFrame(acf);
1196 * execute method under test
1198 AlignmentI cdsal = AlignmentUtils.makeCdsAlignment(
1199 new SequenceI[] { dna1 }, dna.getDataset(), null);
1202 * Verify we have 3 cds sequences, mapped to pep1/2/3 respectively
1204 List<SequenceI> cds = cdsal.getSequences();
1205 assertEquals(3, cds.size());
1208 * verify shared, extended alignment dataset
1210 assertSame(cdsal.getDataset(), dna.getDataset());
1211 assertTrue(dna.getDataset().getSequences()
1212 .contains(cds.get(0).getDatasetSequence()));
1213 assertTrue(dna.getDataset().getSequences()
1214 .contains(cds.get(1).getDatasetSequence()));
1215 assertTrue(dna.getDataset().getSequences()
1216 .contains(cds.get(2).getDatasetSequence()));
1219 * verify aligned cds sequences and their xrefs
1221 SequenceI cdsSeq = cds.get(0);
1222 assertEquals("GGGTTT", cdsSeq.getSequenceAsString());
1223 // assertEquals("dna1|A12345", cdsSeq.getName());
1224 assertEquals("CDS|dna1", cdsSeq.getName());
1225 // assertEquals(1, cdsSeq.getDBRefs().length);
1226 // DBRefEntry cdsRef = cdsSeq.getDBRefs()[0];
1227 // assertEquals("EMBLCDS", cdsRef.getSource());
1228 // assertEquals("2", cdsRef.getVersion());
1229 // assertEquals("A12345", cdsRef.getAccessionId());
1231 cdsSeq = cds.get(1);
1232 assertEquals("aaaccc", cdsSeq.getSequenceAsString());
1233 // assertEquals("dna1|A12346", cdsSeq.getName());
1234 assertEquals("CDS|dna1", cdsSeq.getName());
1235 // assertEquals(1, cdsSeq.getDBRefs().length);
1236 // cdsRef = cdsSeq.getDBRefs()[0];
1237 // assertEquals("EMBLCDS", cdsRef.getSource());
1238 // assertEquals("3", cdsRef.getVersion());
1239 // assertEquals("A12346", cdsRef.getAccessionId());
1241 cdsSeq = cds.get(2);
1242 assertEquals("aaaTTT", cdsSeq.getSequenceAsString());
1243 // assertEquals("dna1|A12347", cdsSeq.getName());
1244 assertEquals("CDS|dna1", cdsSeq.getName());
1245 // assertEquals(1, cdsSeq.getDBRefs().length);
1246 // cdsRef = cdsSeq.getDBRefs()[0];
1247 // assertEquals("EMBLCDS", cdsRef.getSource());
1248 // assertEquals("4", cdsRef.getVersion());
1249 // assertEquals("A12347", cdsRef.getAccessionId());
1252 * Verify there are mappings from each cds sequence to its protein product
1253 * and also to its dna source
1255 List<AlignedCodonFrame> newMappings = cdsal.getCodonFrames();
1258 * 6 mappings involve dna1 (to pep1/2/3, cds1/2/3)
1260 List<AlignedCodonFrame> dnaMappings = MappingUtils
1261 .findMappingsForSequence(dna1, newMappings);
1262 assertEquals(6, dnaMappings.size());
1267 List<AlignedCodonFrame> mappings = MappingUtils
1268 .findMappingsForSequence(pep1, dnaMappings);
1269 assertEquals(1, mappings.size());
1270 assertEquals(1, mappings.get(0).getMappings().size());
1271 assertSame(pep1.getDatasetSequence(), mappings.get(0).getMappings()
1272 .get(0).getMapping().getTo());
1277 List<AlignedCodonFrame> dnaToCds1Mappings = MappingUtils
1278 .findMappingsForSequence(cds.get(0), dnaMappings);
1279 Mapping mapping = dnaToCds1Mappings.get(0).getMappings().get(0)
1281 assertSame(cds.get(0).getDatasetSequence(), mapping
1283 assertEquals("G(1) in CDS should map to G(4) in DNA", 4, mapping
1284 .getMap().getToPosition(1));
1289 mappings = MappingUtils.findMappingsForSequence(pep2, dnaMappings);
1290 assertEquals(1, mappings.size());
1291 assertEquals(1, mappings.get(0).getMappings().size());
1292 assertSame(pep2.getDatasetSequence(), mappings.get(0).getMappings()
1293 .get(0).getMapping().getTo());
1298 List<AlignedCodonFrame> dnaToCds2Mappings = MappingUtils
1299 .findMappingsForSequence(cds.get(1), dnaMappings);
1300 mapping = dnaToCds2Mappings.get(0).getMappings().get(0).getMapping();
1301 assertSame(cds.get(1).getDatasetSequence(), mapping.getTo());
1302 assertEquals("c(4) in CDS should map to c(7) in DNA", 7, mapping
1303 .getMap().getToPosition(4));
1308 mappings = MappingUtils.findMappingsForSequence(pep3, dnaMappings);
1309 assertEquals(1, mappings.size());
1310 assertEquals(1, mappings.get(0).getMappings().size());
1311 assertSame(pep3.getDatasetSequence(), mappings.get(0).getMappings()
1312 .get(0).getMapping().getTo());
1317 List<AlignedCodonFrame> dnaToCds3Mappings = MappingUtils
1318 .findMappingsForSequence(cds.get(2), dnaMappings);
1319 mapping = dnaToCds3Mappings.get(0).getMappings().get(0).getMapping();
1320 assertSame(cds.get(2).getDatasetSequence(), mapping.getTo());
1321 assertEquals("T(4) in CDS should map to T(10) in DNA", 10, mapping
1322 .getMap().getToPosition(4));
1325 @Test(groups = { "Functional" })
1326 public void testIsMappable()
1328 SequenceI dna1 = new Sequence("dna1", "cgCAGtgGT");
1329 SequenceI aa1 = new Sequence("aa1", "RSG");
1330 AlignmentI al1 = new Alignment(new SequenceI[] { dna1 });
1331 AlignmentI al2 = new Alignment(new SequenceI[] { aa1 });
1333 assertFalse(AlignmentUtils.isMappable(null, null));
1334 assertFalse(AlignmentUtils.isMappable(al1, null));
1335 assertFalse(AlignmentUtils.isMappable(null, al1));
1336 assertFalse(AlignmentUtils.isMappable(al1, al1));
1337 assertFalse(AlignmentUtils.isMappable(al2, al2));
1339 assertTrue(AlignmentUtils.isMappable(al1, al2));
1340 assertTrue(AlignmentUtils.isMappable(al2, al1));
1344 * Test creating a mapping when the sequences involved do not start at residue
1347 * @throws IOException
1349 @Test(groups = { "Functional" })
1350 public void testMapCdnaToProtein_forSubsequence()
1353 SequenceI prot = new Sequence("UNIPROT|V12345", "E-I--Q", 10, 12);
1354 prot.createDatasetSequence();
1356 SequenceI dna = new Sequence("EMBL|A33333", "GAA--AT-C-CAG", 40, 48);
1357 dna.createDatasetSequence();
1359 MapList map = AlignmentUtils.mapCdnaToProtein(prot, dna);
1360 assertEquals(10, map.getToLowest());
1361 assertEquals(12, map.getToHighest());
1362 assertEquals(40, map.getFromLowest());
1363 assertEquals(48, map.getFromHighest());
1367 * Test for the alignSequenceAs method where we have protein mapped to protein
1369 @Test(groups = { "Functional" })
1370 public void testAlignSequenceAs_mappedProteinProtein()
1373 SequenceI alignMe = new Sequence("Match", "MGAASEV");
1374 alignMe.createDatasetSequence();
1375 SequenceI alignFrom = new Sequence("Query", "LQTGYMGAASEVMFSPTRR");
1376 alignFrom.createDatasetSequence();
1378 AlignedCodonFrame acf = new AlignedCodonFrame();
1379 // this is like a domain or motif match of part of a peptide sequence
1380 MapList map = new MapList(new int[] { 6, 12 }, new int[] { 1, 7 }, 1, 1);
1381 acf.addMap(alignFrom.getDatasetSequence(),
1382 alignMe.getDatasetSequence(), map);
1384 AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "-", '-', true,
1386 assertEquals("-----MGAASEV-------", alignMe.getSequenceAsString());
1390 * Test for the alignSequenceAs method where there are trailing unmapped
1391 * residues in the model sequence
1393 @Test(groups = { "Functional" })
1394 public void testAlignSequenceAs_withTrailingPeptide()
1396 // map first 3 codons to KPF; G is a trailing unmapped residue
1397 MapList map = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3, 1);
1399 checkAlignSequenceAs("AAACCCTTT", "K-PFG", true, true, map,
1404 * Tests for transferring features between mapped sequences
1406 @Test(groups = { "Functional" })
1407 public void testTransferFeatures()
1409 SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt");
1410 SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
1413 dna.addSequenceFeature(new SequenceFeature("type1", "desc1", 1, 2, 1f,
1415 // partial overlap - to [1, 1]
1416 dna.addSequenceFeature(new SequenceFeature("type2", "desc2", 3, 4, 2f,
1418 // exact overlap - to [1, 3]
1419 dna.addSequenceFeature(new SequenceFeature("type3", "desc3", 4, 6, 3f,
1421 // spanning overlap - to [2, 5]
1422 dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f,
1424 // exactly overlaps whole mapped range [1, 6]
1425 dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f,
1427 // no overlap (internal)
1428 dna.addSequenceFeature(new SequenceFeature("type6", "desc6", 7, 9, 6f,
1430 // no overlap (3' end)
1431 dna.addSequenceFeature(new SequenceFeature("type7", "desc7", 13, 15,
1433 // overlap (3' end) - to [6, 6]
1434 dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12,
1436 // extended overlap - to [6, +]
1437 dna.addSequenceFeature(new SequenceFeature("type9", "desc9", 12, 13,
1440 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1441 new int[] { 1, 6 }, 1, 1);
1444 * transferFeatures() will build 'partial overlap' for regions
1445 * that partially overlap 5' or 3' (start or end) of target sequence
1447 AlignmentUtils.transferFeatures(dna, cds, map, null);
1448 SequenceFeature[] sfs = cds.getSequenceFeatures();
1449 assertEquals(6, sfs.length);
1451 SequenceFeature sf = sfs[0];
1452 assertEquals("type2", sf.getType());
1453 assertEquals("desc2", sf.getDescription());
1454 assertEquals(2f, sf.getScore());
1455 assertEquals(1, sf.getBegin());
1456 assertEquals(1, sf.getEnd());
1459 assertEquals("type3", sf.getType());
1460 assertEquals("desc3", sf.getDescription());
1461 assertEquals(3f, sf.getScore());
1462 assertEquals(1, sf.getBegin());
1463 assertEquals(3, sf.getEnd());
1466 assertEquals("type4", sf.getType());
1467 assertEquals(2, sf.getBegin());
1468 assertEquals(5, sf.getEnd());
1471 assertEquals("type5", sf.getType());
1472 assertEquals(1, sf.getBegin());
1473 assertEquals(6, sf.getEnd());
1476 assertEquals("type8", sf.getType());
1477 assertEquals(6, sf.getBegin());
1478 assertEquals(6, sf.getEnd());
1481 assertEquals("type9", sf.getType());
1482 assertEquals(6, sf.getBegin());
1483 assertEquals(6, sf.getEnd());
1487 * Tests for transferring features between mapped sequences
1489 @Test(groups = { "Functional" })
1490 public void testTransferFeatures_withOmit()
1492 SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt");
1493 SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
1495 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1496 new int[] { 1, 6 }, 1, 1);
1498 // [5, 11] maps to [2, 5]
1499 dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f,
1501 // [4, 12] maps to [1, 6]
1502 dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f,
1504 // [12, 12] maps to [6, 6]
1505 dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12,
1508 // desc4 and desc8 are the 'omit these' varargs
1509 AlignmentUtils.transferFeatures(dna, cds, map, null, "type4", "type8");
1510 SequenceFeature[] sfs = cds.getSequenceFeatures();
1511 assertEquals(1, sfs.length);
1513 SequenceFeature sf = sfs[0];
1514 assertEquals("type5", sf.getType());
1515 assertEquals(1, sf.getBegin());
1516 assertEquals(6, sf.getEnd());
1520 * Tests for transferring features between mapped sequences
1522 @Test(groups = { "Functional" })
1523 public void testTransferFeatures_withSelect()
1525 SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt");
1526 SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
1528 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1529 new int[] { 1, 6 }, 1, 1);
1531 // [5, 11] maps to [2, 5]
1532 dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f,
1534 // [4, 12] maps to [1, 6]
1535 dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f,
1537 // [12, 12] maps to [6, 6]
1538 dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12,
1541 // "type5" is the 'select this type' argument
1542 AlignmentUtils.transferFeatures(dna, cds, map, "type5");
1543 SequenceFeature[] sfs = cds.getSequenceFeatures();
1544 assertEquals(1, sfs.length);
1546 SequenceFeature sf = sfs[0];
1547 assertEquals("type5", sf.getType());
1548 assertEquals(1, sf.getBegin());
1549 assertEquals(6, sf.getEnd());
1553 * Test the method that extracts the cds-only part of a dna alignment, for the
1554 * case where the cds should be aligned to match its nucleotide sequence.
1556 @Test(groups = { "Functional" })
1557 public void testMakeCdsAlignment_alternativeTranscripts()
1559 SequenceI dna1 = new Sequence("dna1", "aaaGGGCC-----CTTTaaaGGG");
1560 // alternative transcript of same dna skips CCC codon
1561 SequenceI dna2 = new Sequence("dna2", "aaaGGGCC-----cttTaaaGGG");
1562 // dna3 has no mapping (protein product) so should be ignored here
1563 SequenceI dna3 = new Sequence("dna3", "aaaGGGCCCCCGGGcttTaaaGGG");
1564 SequenceI pep1 = new Sequence("pep1", "GPFG");
1565 SequenceI pep2 = new Sequence("pep2", "GPG");
1566 dna1.createDatasetSequence();
1567 dna2.createDatasetSequence();
1568 dna3.createDatasetSequence();
1569 pep1.createDatasetSequence();
1570 pep2.createDatasetSequence();
1572 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
1573 dna.setDataset(null);
1575 MapList map = new MapList(new int[] { 4, 12, 16, 18 },
1576 new int[] { 1, 4 }, 3, 1);
1577 AlignedCodonFrame acf = new AlignedCodonFrame();
1578 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
1579 dna.addCodonFrame(acf);
1580 map = new MapList(new int[] { 4, 8, 12, 12, 16, 18 },
1583 acf = new AlignedCodonFrame();
1584 acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
1585 dna.addCodonFrame(acf);
1587 AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
1588 dna1, dna2, dna3 }, dna.getDataset(), null);
1589 List<SequenceI> cdsSeqs = cds.getSequences();
1590 assertEquals(2, cdsSeqs.size());
1591 assertEquals("GGGCCCTTTGGG", cdsSeqs.get(0).getSequenceAsString());
1592 assertEquals("GGGCCTGGG", cdsSeqs.get(1).getSequenceAsString());
1595 * verify shared, extended alignment dataset
1597 assertSame(dna.getDataset(), cds.getDataset());
1598 assertTrue(dna.getDataset().getSequences()
1599 .contains(cdsSeqs.get(0).getDatasetSequence()));
1600 assertTrue(dna.getDataset().getSequences()
1601 .contains(cdsSeqs.get(1).getDatasetSequence()));
1604 * Verify 6 mappings: dna1 to cds1, cds1 to pep1, dna1 to pep1
1605 * and the same for dna2/cds2/pep2
1607 List<AlignedCodonFrame> mappings = cds.getCodonFrames();
1608 assertEquals(6, mappings.size());
1611 * 2 mappings involve pep1
1613 List<AlignedCodonFrame> pep1Mappings = MappingUtils
1614 .findMappingsForSequence(pep1, mappings);
1615 assertEquals(2, pep1Mappings.size());
1618 * Get mapping of pep1 to cds1 and verify it
1619 * maps GPFG to 1-3,4-6,7-9,10-12
1621 List<AlignedCodonFrame> pep1CdsMappings = MappingUtils
1622 .findMappingsForSequence(cds.getSequenceAt(0), pep1Mappings);
1623 assertEquals(1, pep1CdsMappings.size());
1624 SearchResults sr = MappingUtils.buildSearchResults(pep1, 1,
1626 assertEquals(1, sr.getResults().size());
1627 Match m = sr.getResults().get(0);
1628 assertEquals(cds.getSequenceAt(0).getDatasetSequence(),
1630 assertEquals(1, m.getStart());
1631 assertEquals(3, m.getEnd());
1632 sr = MappingUtils.buildSearchResults(pep1, 2, pep1CdsMappings);
1633 m = sr.getResults().get(0);
1634 assertEquals(4, m.getStart());
1635 assertEquals(6, m.getEnd());
1636 sr = MappingUtils.buildSearchResults(pep1, 3, pep1CdsMappings);
1637 m = sr.getResults().get(0);
1638 assertEquals(7, m.getStart());
1639 assertEquals(9, m.getEnd());
1640 sr = MappingUtils.buildSearchResults(pep1, 4, pep1CdsMappings);
1641 m = sr.getResults().get(0);
1642 assertEquals(10, m.getStart());
1643 assertEquals(12, m.getEnd());
1646 * Get mapping of pep2 to cds2 and verify it
1647 * maps GPG in pep2 to 1-3,4-6,7-9 in second CDS sequence
1649 List<AlignedCodonFrame> pep2Mappings = MappingUtils
1650 .findMappingsForSequence(pep2, mappings);
1651 assertEquals(2, pep2Mappings.size());
1652 List<AlignedCodonFrame> pep2CdsMappings = MappingUtils
1653 .findMappingsForSequence(cds.getSequenceAt(1), pep2Mappings);
1654 assertEquals(1, pep2CdsMappings.size());
1655 sr = MappingUtils.buildSearchResults(pep2, 1, pep2CdsMappings);
1656 assertEquals(1, sr.getResults().size());
1657 m = sr.getResults().get(0);
1658 assertEquals(cds.getSequenceAt(1).getDatasetSequence(),
1660 assertEquals(1, m.getStart());
1661 assertEquals(3, m.getEnd());
1662 sr = MappingUtils.buildSearchResults(pep2, 2, pep2CdsMappings);
1663 m = sr.getResults().get(0);
1664 assertEquals(4, m.getStart());
1665 assertEquals(6, m.getEnd());
1666 sr = MappingUtils.buildSearchResults(pep2, 3, pep2CdsMappings);
1667 m = sr.getResults().get(0);
1668 assertEquals(7, m.getStart());
1669 assertEquals(9, m.getEnd());
1673 * Test the method that realigns protein to match mapped codon alignment.
1675 @Test(groups = { "Functional" })
1676 public void testAlignProteinAsDna_incompleteStartCodon()
1678 // seq1: incomplete start codon (not mapped), then [3, 11]
1679 SequenceI dna1 = new Sequence("Seq1", "ccAAA-TTT-GGG-");
1680 // seq2 codons are [4, 5], [8, 11]
1681 SequenceI dna2 = new Sequence("Seq2", "ccaAA-ttT-GGG-");
1682 // seq3 incomplete start codon at 'tt'
1683 SequenceI dna3 = new Sequence("Seq3", "ccaaa-ttt-GGG-");
1684 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
1685 dna.setDataset(null);
1687 // prot1 has 'X' for incomplete start codon (not mapped)
1688 SequenceI prot1 = new Sequence("Seq1", "XKFG"); // X for incomplete start
1689 SequenceI prot2 = new Sequence("Seq2", "NG");
1690 SequenceI prot3 = new Sequence("Seq3", "XG"); // X for incomplete start
1691 AlignmentI protein = new Alignment(new SequenceI[] { prot1, prot2,
1693 protein.setDataset(null);
1695 // map dna1 [3, 11] to prot1 [2, 4] KFG
1696 MapList map = new MapList(new int[] { 3, 11 }, new int[] { 2, 4 }, 3, 1);
1697 AlignedCodonFrame acf = new AlignedCodonFrame();
1698 acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
1700 // map dna2 [4, 5] [8, 11] to prot2 [1, 2] NG
1701 map = new MapList(new int[] { 4, 5, 8, 11 }, new int[] { 1, 2 }, 3, 1);
1702 acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map);
1704 // map dna3 [9, 11] to prot3 [2, 2] G
1705 map = new MapList(new int[] { 9, 11 }, new int[] { 2, 2 }, 3, 1);
1706 acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map);
1708 ArrayList<AlignedCodonFrame> acfs = new ArrayList<AlignedCodonFrame>();
1710 protein.setCodonFrames(acfs);
1713 * verify X is included in the aligned proteins, and placed just
1714 * before the first mapped residue
1715 * CCT is between CCC and TTT
1717 AlignmentUtils.alignProteinAsDna(protein, dna);
1718 assertEquals("XK-FG", prot1.getSequenceAsString());
1719 assertEquals("--N-G", prot2.getSequenceAsString());
1720 assertEquals("---XG", prot3.getSequenceAsString());
1724 * Tests for the method that maps the subset of a dna sequence that has CDS
1725 * (or subtype) feature - case where the start codon is incomplete.
1727 @Test(groups = "Functional")
1728 public void testFindCdsPositions_fivePrimeIncomplete()
1730 SequenceI dnaSeq = new Sequence("dna", "aaagGGCCCaaaTTTttt");
1731 dnaSeq.createDatasetSequence();
1732 SequenceI ds = dnaSeq.getDatasetSequence();
1734 // CDS for dna 5-6 (incomplete codon), 7-9
1735 SequenceFeature sf = new SequenceFeature("CDS", "", 5, 9, 0f, null);
1736 sf.setPhase("2"); // skip 2 bases to start of next codon
1737 ds.addSequenceFeature(sf);
1738 // CDS for dna 13-15
1739 sf = new SequenceFeature("CDS_predicted", "", 13, 15, 0f, null);
1740 ds.addSequenceFeature(sf);
1742 List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
1745 * check the mapping starts with the first complete codon
1747 assertEquals(6, MappingUtils.getLength(ranges));
1748 assertEquals(2, ranges.size());
1749 assertEquals(7, ranges.get(0)[0]);
1750 assertEquals(9, ranges.get(0)[1]);
1751 assertEquals(13, ranges.get(1)[0]);
1752 assertEquals(15, ranges.get(1)[1]);
1756 * Tests for the method that maps the subset of a dna sequence that has CDS
1757 * (or subtype) feature.
1759 @Test(groups = "Functional")
1760 public void testFindCdsPositions()
1762 SequenceI dnaSeq = new Sequence("dna", "aaaGGGcccAAATTTttt");
1763 dnaSeq.createDatasetSequence();
1764 SequenceI ds = dnaSeq.getDatasetSequence();
1766 // CDS for dna 10-12
1767 SequenceFeature sf = new SequenceFeature("CDS_predicted", "", 10, 12,
1770 ds.addSequenceFeature(sf);
1772 sf = new SequenceFeature("CDS", "", 4, 6, 0f, null);
1774 ds.addSequenceFeature(sf);
1775 // exon feature should be ignored here
1776 sf = new SequenceFeature("exon", "", 7, 9, 0f, null);
1777 ds.addSequenceFeature(sf);
1779 List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
1781 * verify ranges { [4-6], [12-10] }
1782 * note CDS ranges are ordered ascending even if the CDS
1785 assertEquals(6, MappingUtils.getLength(ranges));
1786 assertEquals(2, ranges.size());
1787 assertEquals(4, ranges.get(0)[0]);
1788 assertEquals(6, ranges.get(0)[1]);
1789 assertEquals(10, ranges.get(1)[0]);
1790 assertEquals(12, ranges.get(1)[1]);
1794 * Test the method that computes a map of codon variants for each protein
1795 * position from "sequence_variant" features on dna
1797 @Test(groups = "Functional")
1798 public void testBuildDnaVariantsMap()
1800 SequenceI dna = new Sequence("dna", "atgAAATTTGGGCCCtag");
1801 MapList map = new MapList(new int[] { 1, 18 }, new int[] { 1, 5 }, 3, 1);
1804 * first with no variants on dna
1806 LinkedHashMap<Integer, List<DnaVariant>[]> variantsMap = AlignmentUtils
1807 .buildDnaVariantsMap(dna, map);
1808 assertTrue(variantsMap.isEmpty());
1811 * single allele codon 1, on base 1
1813 SequenceFeature sf1 = new SequenceFeature("sequence_variant", "", 1, 1,
1815 sf1.setValue("alleles", "T");
1816 sf1.setValue("ID", "sequence_variant:rs758803211");
1817 dna.addSequenceFeature(sf1);
1820 * two alleles codon 2, on bases 2 and 3 (distinct variants)
1822 SequenceFeature sf2 = new SequenceFeature("sequence_variant", "", 5, 5,
1824 sf2.setValue("alleles", "T");
1825 sf2.setValue("ID", "sequence_variant:rs758803212");
1826 dna.addSequenceFeature(sf2);
1827 SequenceFeature sf3 = new SequenceFeature("sequence_variant", "", 6, 6,
1829 sf3.setValue("alleles", "G");
1830 sf3.setValue("ID", "sequence_variant:rs758803213");
1831 dna.addSequenceFeature(sf3);
1834 * two alleles codon 3, both on base 2 (one variant)
1836 SequenceFeature sf4 = new SequenceFeature("sequence_variant", "", 8, 8,
1838 sf4.setValue("alleles", "C, G");
1839 sf4.setValue("ID", "sequence_variant:rs758803214");
1840 dna.addSequenceFeature(sf4);
1842 // no alleles on codon 4
1845 * alleles on codon 5 on all 3 bases (distinct variants)
1847 SequenceFeature sf5 = new SequenceFeature("sequence_variant", "", 13,
1849 sf5.setValue("alleles", "C, G"); // (C duplicates given base value)
1850 sf5.setValue("ID", "sequence_variant:rs758803215");
1851 dna.addSequenceFeature(sf5);
1852 SequenceFeature sf6 = new SequenceFeature("sequence_variant", "", 14,
1854 sf6.setValue("alleles", "g, a"); // should force to upper-case
1855 sf6.setValue("ID", "sequence_variant:rs758803216");
1856 dna.addSequenceFeature(sf6);
1857 SequenceFeature sf7 = new SequenceFeature("sequence_variant", "", 15,
1859 sf7.setValue("alleles", "A, T");
1860 sf7.setValue("ID", "sequence_variant:rs758803217");
1861 dna.addSequenceFeature(sf7);
1864 * build map - expect variants on positions 1, 2, 3, 5
1866 variantsMap = AlignmentUtils.buildDnaVariantsMap(dna, map);
1867 assertEquals(4, variantsMap.size());
1870 * protein residue 1: variant on codon (ATG) base 1, not on 2 or 3
1872 List<DnaVariant>[] pep1Variants = variantsMap.get(1);
1873 assertEquals(3, pep1Variants.length);
1874 assertEquals(1, pep1Variants[0].size());
1875 assertEquals("A", pep1Variants[0].get(0).base); // codon[1] base
1876 assertSame(sf1, pep1Variants[0].get(0).variant); // codon[1] variant
1877 assertEquals(1, pep1Variants[1].size());
1878 assertEquals("T", pep1Variants[1].get(0).base); // codon[2] base
1879 assertNull(pep1Variants[1].get(0).variant); // no variant here
1880 assertEquals(1, pep1Variants[2].size());
1881 assertEquals("G", pep1Variants[2].get(0).base); // codon[3] base
1882 assertNull(pep1Variants[2].get(0).variant); // no variant here
1885 * protein residue 2: variants on codon (AAA) bases 2 and 3
1887 List<DnaVariant>[] pep2Variants = variantsMap.get(2);
1888 assertEquals(3, pep2Variants.length);
1889 assertEquals(1, pep2Variants[0].size());
1890 // codon[1] base recorded while processing variant on codon[2]
1891 assertEquals("A", pep2Variants[0].get(0).base);
1892 assertNull(pep2Variants[0].get(0).variant); // no variant here
1893 // codon[2] base and variant:
1894 assertEquals(1, pep2Variants[1].size());
1895 assertEquals("A", pep2Variants[1].get(0).base);
1896 assertSame(sf2, pep2Variants[1].get(0).variant);
1897 // codon[3] base was recorded when processing codon[2] variant
1898 // and then the variant for codon[3] added to it
1899 assertEquals(1, pep2Variants[2].size());
1900 assertEquals("A", pep2Variants[2].get(0).base);
1901 assertSame(sf3, pep2Variants[2].get(0).variant);
1904 * protein residue 3: variants on codon (TTT) base 2 only
1906 List<DnaVariant>[] pep3Variants = variantsMap.get(3);
1907 assertEquals(3, pep3Variants.length);
1908 assertEquals(1, pep3Variants[0].size());
1909 assertEquals("T", pep3Variants[0].get(0).base); // codon[1] base
1910 assertNull(pep3Variants[0].get(0).variant); // no variant here
1911 assertEquals(1, pep3Variants[1].size());
1912 assertEquals("T", pep3Variants[1].get(0).base); // codon[2] base
1913 assertSame(sf4, pep3Variants[1].get(0).variant); // codon[2] variant
1914 assertEquals(1, pep3Variants[2].size());
1915 assertEquals("T", pep3Variants[2].get(0).base); // codon[3] base
1916 assertNull(pep3Variants[2].get(0).variant); // no variant here
1919 * three variants on protein position 5
1921 List<DnaVariant>[] pep5Variants = variantsMap.get(5);
1922 assertEquals(3, pep5Variants.length);
1923 assertEquals(1, pep5Variants[0].size());
1924 assertEquals("C", pep5Variants[0].get(0).base); // codon[1] base
1925 assertSame(sf5, pep5Variants[0].get(0).variant); // codon[1] variant
1926 assertEquals(1, pep5Variants[1].size());
1927 assertEquals("C", pep5Variants[1].get(0).base); // codon[2] base
1928 assertSame(sf6, pep5Variants[1].get(0).variant); // codon[2] variant
1929 assertEquals(1, pep5Variants[2].size());
1930 assertEquals("C", pep5Variants[2].get(0).base); // codon[3] base
1931 assertSame(sf7, pep5Variants[2].get(0).variant); // codon[3] variant
1935 * Tests for the method that computes all peptide variants given codon
1938 @Test(groups = "Functional")
1939 public void testComputePeptideVariants()
1942 * scenario: AAATTTCCC codes for KFP, with variants
1948 * CAC,CGC -> H,R (as one variant)
1950 SequenceI peptide = new Sequence("pep/10-12", "KFP");
1953 * two distinct variants for codon 1 position 1
1954 * second one has clinical significance
1956 SequenceFeature sf1 = new SequenceFeature("sequence_variant", "", 1, 1,
1958 sf1.setValue("alleles", "A,G"); // GAA -> E
1959 sf1.setValue("ID", "var1.125A>G");
1960 SequenceFeature sf2 = new SequenceFeature("sequence_variant", "", 1, 1,
1962 sf2.setValue("alleles", "A,C"); // CAA -> Q
1963 sf2.setValue("ID", "var2");
1964 sf2.setValue("clinical_significance", "Dodgy");
1965 SequenceFeature sf3 = new SequenceFeature("sequence_variant", "", 3, 3,
1967 sf3.setValue("alleles", "A,G"); // synonymous
1968 sf3.setValue("ID", "var3");
1969 sf3.setValue("clinical_significance", "None");
1970 SequenceFeature sf4 = new SequenceFeature("sequence_variant", "", 3, 3,
1972 sf4.setValue("alleles", "A,T"); // AAT -> N
1973 sf4.setValue("ID", "sequence_variant:var4"); // prefix gets stripped off
1974 sf4.setValue("clinical_significance", "Benign");
1975 SequenceFeature sf5 = new SequenceFeature("sequence_variant", "", 6, 6,
1977 sf5.setValue("alleles", "T,C"); // synonymous
1978 sf5.setValue("ID", "var5");
1979 sf5.setValue("clinical_significance", "Bad");
1980 SequenceFeature sf6 = new SequenceFeature("sequence_variant", "", 8, 8,
1982 sf6.setValue("alleles", "C,A,G"); // CAC,CGC -> H,R
1983 sf6.setValue("ID", "var6");
1984 sf6.setValue("clinical_significance", "Good");
1986 List<DnaVariant> codon1Variants = new ArrayList<DnaVariant>();
1987 List<DnaVariant> codon2Variants = new ArrayList<DnaVariant>();
1988 List<DnaVariant> codon3Variants = new ArrayList<DnaVariant>();
1989 List<DnaVariant> codonVariants[] = new ArrayList[3];
1990 codonVariants[0] = codon1Variants;
1991 codonVariants[1] = codon2Variants;
1992 codonVariants[2] = codon3Variants;
1995 * compute variants for protein position 1
1997 codon1Variants.add(new DnaVariant("A", sf1));
1998 codon1Variants.add(new DnaVariant("A", sf2));
1999 codon2Variants.add(new DnaVariant("A"));
2000 codon2Variants.add(new DnaVariant("A"));
2001 codon3Variants.add(new DnaVariant("A", sf3));
2002 codon3Variants.add(new DnaVariant("A", sf4));
2003 AlignmentUtils.computePeptideVariants(peptide, 1, codonVariants);
2006 * compute variants for protein position 2
2008 codon1Variants.clear();
2009 codon2Variants.clear();
2010 codon3Variants.clear();
2011 codon1Variants.add(new DnaVariant("T"));
2012 codon2Variants.add(new DnaVariant("T"));
2013 codon3Variants.add(new DnaVariant("T", sf5));
2014 AlignmentUtils.computePeptideVariants(peptide, 2, codonVariants);
2017 * compute variants for protein position 3
2019 codon1Variants.clear();
2020 codon2Variants.clear();
2021 codon3Variants.clear();
2022 codon1Variants.add(new DnaVariant("C"));
2023 codon2Variants.add(new DnaVariant("C", sf6));
2024 codon3Variants.add(new DnaVariant("C"));
2025 AlignmentUtils.computePeptideVariants(peptide, 3, codonVariants);
2028 * verify added sequence features for
2035 SequenceFeature[] sfs = peptide.getSequenceFeatures();
2036 assertEquals(5, sfs.length);
2037 SequenceFeature sf = sfs[0];
2038 assertEquals(1, sf.getBegin());
2039 assertEquals(1, sf.getEnd());
2040 assertEquals("p.Lys1Glu", sf.getDescription());
2041 assertEquals("var1.125A>G", sf.getValue("ID"));
2042 assertNull(sf.getValue("clinical_significance"));
2043 assertEquals("ID=var1.125A>G", sf.getAttributes());
2044 assertEquals(1, sf.links.size());
2045 // link to variation is urlencoded
2047 "p.Lys1Glu var1.125A>G|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var1.125A%3EG",
2049 assertEquals("Jalview", sf.getFeatureGroup());
2051 assertEquals(1, sf.getBegin());
2052 assertEquals(1, sf.getEnd());
2053 assertEquals("p.Lys1Gln", sf.getDescription());
2054 assertEquals("var2", sf.getValue("ID"));
2055 assertEquals("Dodgy", sf.getValue("clinical_significance"));
2056 assertEquals("ID=var2;clinical_significance=Dodgy", sf.getAttributes());
2057 assertEquals(1, sf.links.size());
2059 "p.Lys1Gln var2|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var2",
2061 assertEquals("Jalview", sf.getFeatureGroup());
2063 assertEquals(1, sf.getBegin());
2064 assertEquals(1, sf.getEnd());
2065 assertEquals("p.Lys1Asn", sf.getDescription());
2066 assertEquals("var4", sf.getValue("ID"));
2067 assertEquals("Benign", sf.getValue("clinical_significance"));
2068 assertEquals("ID=var4;clinical_significance=Benign", sf.getAttributes());
2069 assertEquals(1, sf.links.size());
2071 "p.Lys1Asn var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
2073 assertEquals("Jalview", sf.getFeatureGroup());
2075 assertEquals(3, sf.getBegin());
2076 assertEquals(3, sf.getEnd());
2077 assertEquals("p.Pro3His", sf.getDescription());
2078 assertEquals("var6", sf.getValue("ID"));
2079 assertEquals("Good", sf.getValue("clinical_significance"));
2080 assertEquals("ID=var6;clinical_significance=Good", sf.getAttributes());
2081 assertEquals(1, sf.links.size());
2083 "p.Pro3His var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
2085 // var5 generates two distinct protein variant features
2086 assertEquals("Jalview", sf.getFeatureGroup());
2088 assertEquals(3, sf.getBegin());
2089 assertEquals(3, sf.getEnd());
2090 assertEquals("p.Pro3Arg", sf.getDescription());
2091 assertEquals("var6", sf.getValue("ID"));
2092 assertEquals("Good", sf.getValue("clinical_significance"));
2093 assertEquals("ID=var6;clinical_significance=Good", sf.getAttributes());
2094 assertEquals(1, sf.links.size());
2096 "p.Pro3Arg var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
2098 assertEquals("Jalview", sf.getFeatureGroup());
2102 * Tests for the method that maps the subset of a dna sequence that has CDS
2103 * (or subtype) feature, with CDS strand = '-' (reverse)
2105 // test turned off as currently findCdsPositions is not strand-dependent
2106 // left in case it comes around again...
2107 @Test(groups = "Functional", enabled = false)
2108 public void testFindCdsPositions_reverseStrand()
2110 SequenceI dnaSeq = new Sequence("dna", "aaaGGGcccAAATTTttt");
2111 dnaSeq.createDatasetSequence();
2112 SequenceI ds = dnaSeq.getDatasetSequence();
2115 SequenceFeature sf = new SequenceFeature("CDS", "", 4, 6, 0f, null);
2117 ds.addSequenceFeature(sf);
2118 // exon feature should be ignored here
2119 sf = new SequenceFeature("exon", "", 7, 9, 0f, null);
2120 ds.addSequenceFeature(sf);
2121 // CDS for dna 10-12
2122 sf = new SequenceFeature("CDS_predicted", "", 10, 12, 0f, null);
2124 ds.addSequenceFeature(sf);
2126 List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
2128 * verify ranges { [12-10], [6-4] }
2130 assertEquals(6, MappingUtils.getLength(ranges));
2131 assertEquals(2, ranges.size());
2132 assertEquals(12, ranges.get(0)[0]);
2133 assertEquals(10, ranges.get(0)[1]);
2134 assertEquals(6, ranges.get(1)[0]);
2135 assertEquals(4, ranges.get(1)[1]);
2139 * Tests for the method that maps the subset of a dna sequence that has CDS
2140 * (or subtype) feature - reverse strand case where the start codon is
2143 @Test(groups = "Functional", enabled = false)
2144 // test turned off as currently findCdsPositions is not strand-dependent
2145 // left in case it comes around again...
2146 public void testFindCdsPositions_reverseStrandThreePrimeIncomplete()
2148 SequenceI dnaSeq = new Sequence("dna", "aaagGGCCCaaaTTTttt");
2149 dnaSeq.createDatasetSequence();
2150 SequenceI ds = dnaSeq.getDatasetSequence();
2153 SequenceFeature sf = new SequenceFeature("CDS", "", 5, 9, 0f, null);
2155 ds.addSequenceFeature(sf);
2156 // CDS for dna 13-15
2157 sf = new SequenceFeature("CDS_predicted", "", 13, 15, 0f, null);
2159 sf.setPhase("2"); // skip 2 bases to start of next codon
2160 ds.addSequenceFeature(sf);
2162 List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
2165 * check the mapping starts with the first complete codon
2166 * expect ranges [13, 13], [9, 5]
2168 assertEquals(6, MappingUtils.getLength(ranges));
2169 assertEquals(2, ranges.size());
2170 assertEquals(13, ranges.get(0)[0]);
2171 assertEquals(13, ranges.get(0)[1]);
2172 assertEquals(9, ranges.get(1)[0]);
2173 assertEquals(5, ranges.get(1)[1]);
2176 @Test(groups = "Functional")
2177 public void testAlignAs_alternateTranscriptsUngapped()
2179 SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
2180 SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
2181 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
2182 ((Alignment) dna).createDatasetAlignment();
2183 SequenceI cds1 = new Sequence("cds1", "GGGTTT");
2184 SequenceI cds2 = new Sequence("cds2", "CCCAAA");
2185 AlignmentI cds = new Alignment(new SequenceI[] { cds1, cds2 });
2186 ((Alignment) cds).createDatasetAlignment();
2188 AlignedCodonFrame acf = new AlignedCodonFrame();
2189 MapList map = new MapList(new int[] { 4, 9 }, new int[] { 1, 6 }, 1, 1);
2190 acf.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(), map);
2191 map = new MapList(new int[] { 1, 3, 10, 12 }, new int[] { 1, 6 }, 1, 1);
2192 acf.addMap(dna2.getDatasetSequence(), cds2.getDatasetSequence(), map);
2195 * verify CDS alignment is as:
2196 * cccGGGTTTaaa (cdna)
2197 * CCCgggtttAAA (cdna)
2199 * ---GGGTTT--- (cds)
2200 * CCC------AAA (cds)
2202 dna.addCodonFrame(acf);
2203 AlignmentUtils.alignAs(cds, dna);
2204 assertEquals("---GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
2205 assertEquals("CCC------AAA", cds.getSequenceAt(1).getSequenceAsString());
2208 @Test(groups = { "Functional" })
2209 public void testAddMappedPositions()
2211 SequenceI from = new Sequence("dna", "ggAA-ATcc-TT-g");
2212 SequenceI seq1 = new Sequence("cds", "AAATTT");
2213 from.createDatasetSequence();
2214 seq1.createDatasetSequence();
2215 Mapping mapping = new Mapping(seq1, new MapList(
2216 new int[] { 3, 6, 9, 10 },
2217 new int[] { 1, 6 }, 1, 1));
2218 Map<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
2219 AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
2222 * verify map has seq1 residues in columns 3,4,6,7,11,12
2224 assertEquals(6, map.size());
2225 assertEquals('A', map.get(3).get(seq1).charValue());
2226 assertEquals('A', map.get(4).get(seq1).charValue());
2227 assertEquals('A', map.get(6).get(seq1).charValue());
2228 assertEquals('T', map.get(7).get(seq1).charValue());
2229 assertEquals('T', map.get(11).get(seq1).charValue());
2230 assertEquals('T', map.get(12).get(seq1).charValue());
2238 * Test case where the mapping 'from' range includes a stop codon which is
2239 * absent in the 'to' range
2241 @Test(groups = { "Functional" })
2242 public void testAddMappedPositions_withStopCodon()
2244 SequenceI from = new Sequence("dna", "ggAA-ATcc-TT-g");
2245 SequenceI seq1 = new Sequence("cds", "AAATTT");
2246 from.createDatasetSequence();
2247 seq1.createDatasetSequence();
2248 Mapping mapping = new Mapping(seq1, new MapList(
2249 new int[] { 3, 6, 9, 10 },
2250 new int[] { 1, 6 }, 1, 1));
2251 Map<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
2252 AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
2255 * verify map has seq1 residues in columns 3,4,6,7,11,12
2257 assertEquals(6, map.size());
2258 assertEquals('A', map.get(3).get(seq1).charValue());
2259 assertEquals('A', map.get(4).get(seq1).charValue());
2260 assertEquals('A', map.get(6).get(seq1).charValue());
2261 assertEquals('T', map.get(7).get(seq1).charValue());
2262 assertEquals('T', map.get(11).get(seq1).charValue());
2263 assertEquals('T', map.get(12).get(seq1).charValue());
2267 * Test for the case where the products for which we want CDS are specified.
2268 * This is to represent the case where EMBL has CDS mappings to both Uniprot
2269 * and EMBLCDSPROTEIN. makeCdsAlignment() should only return the mappings for
2270 * the protein sequences specified.
2272 @Test(groups = { "Functional" })
2273 public void testMakeCdsAlignment_filterProducts()
2275 SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
2276 SequenceI dna2 = new Sequence("dna2", "GGGcccTTTaaaCCC");
2277 SequenceI pep1 = new Sequence("Uniprot|pep1", "GF");
2278 SequenceI pep2 = new Sequence("Uniprot|pep2", "GFP");
2279 SequenceI pep3 = new Sequence("EMBL|pep3", "GF");
2280 SequenceI pep4 = new Sequence("EMBL|pep4", "GFP");
2281 dna1.createDatasetSequence();
2282 dna2.createDatasetSequence();
2283 pep1.createDatasetSequence();
2284 pep2.createDatasetSequence();
2285 pep3.createDatasetSequence();
2286 pep4.createDatasetSequence();
2287 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
2288 dna.setDataset(null);
2289 AlignmentI emblPeptides = new Alignment(new SequenceI[] { pep3, pep4 });
2290 emblPeptides.setDataset(null);
2292 AlignedCodonFrame acf = new AlignedCodonFrame();
2293 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
2294 new int[] { 1, 2 }, 3, 1);
2295 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
2296 acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map);
2297 dna.addCodonFrame(acf);
2299 acf = new AlignedCodonFrame();
2300 map = new MapList(new int[] { 1, 3, 7, 9, 13, 15 }, new int[] { 1, 3 },
2302 acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
2303 acf.addMap(dna2.getDatasetSequence(), pep4.getDatasetSequence(), map);
2304 dna.addCodonFrame(acf);
2307 * execute method under test to find CDS for EMBL peptides only
2309 AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
2310 dna1, dna2 }, dna.getDataset(), emblPeptides.getSequencesArray());
2312 assertEquals(2, cds.getSequences().size());
2313 assertEquals("GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
2314 assertEquals("GGGTTTCCC", cds.getSequenceAt(1).getSequenceAsString());
2317 * verify shared, extended alignment dataset
2319 assertSame(dna.getDataset(), cds.getDataset());
2320 assertTrue(dna.getDataset().getSequences()
2321 .contains(cds.getSequenceAt(0).getDatasetSequence()));
2322 assertTrue(dna.getDataset().getSequences()
2323 .contains(cds.getSequenceAt(1).getDatasetSequence()));
2326 * Verify mappings from CDS to peptide, cDNA to CDS, and cDNA to peptide
2327 * the mappings are on the shared alignment dataset
2329 List<AlignedCodonFrame> cdsMappings = cds.getDataset().getCodonFrames();
2331 * 6 mappings, 2*(DNA->CDS), 2*(DNA->Pep), 2*(CDS->Pep)
2333 assertEquals(6, cdsMappings.size());
2336 * verify that mapping sets for dna and cds alignments are different
2337 * [not current behaviour - all mappings are on the alignment dataset]
2339 // select -> subselect type to test.
2340 // Assert.assertNotSame(dna.getCodonFrames(), cds.getCodonFrames());
2341 // assertEquals(4, dna.getCodonFrames().size());
2342 // assertEquals(4, cds.getCodonFrames().size());
2345 * Two mappings involve pep3 (dna to pep3, cds to pep3)
2346 * Mapping from pep3 to GGGTTT in first new exon sequence
2348 List<AlignedCodonFrame> pep3Mappings = MappingUtils
2349 .findMappingsForSequence(pep3, cdsMappings);
2350 assertEquals(2, pep3Mappings.size());
2351 List<AlignedCodonFrame> mappings = MappingUtils
2352 .findMappingsForSequence(cds.getSequenceAt(0), pep3Mappings);
2353 assertEquals(1, mappings.size());
2356 SearchResults sr = MappingUtils.buildSearchResults(pep3, 1, mappings);
2357 assertEquals(1, sr.getResults().size());
2358 Match m = sr.getResults().get(0);
2359 assertSame(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
2360 assertEquals(1, m.getStart());
2361 assertEquals(3, m.getEnd());
2363 sr = MappingUtils.buildSearchResults(pep3, 2, mappings);
2364 m = sr.getResults().get(0);
2365 assertSame(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
2366 assertEquals(4, m.getStart());
2367 assertEquals(6, m.getEnd());
2370 * Two mappings involve pep4 (dna to pep4, cds to pep4)
2371 * Verify mapping from pep4 to GGGTTTCCC in second new exon sequence
2373 List<AlignedCodonFrame> pep4Mappings = MappingUtils
2374 .findMappingsForSequence(pep4, cdsMappings);
2375 assertEquals(2, pep4Mappings.size());
2376 mappings = MappingUtils.findMappingsForSequence(cds.getSequenceAt(1),
2378 assertEquals(1, mappings.size());
2380 sr = MappingUtils.buildSearchResults(pep4, 1, mappings);
2381 assertEquals(1, sr.getResults().size());
2382 m = sr.getResults().get(0);
2383 assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
2384 assertEquals(1, m.getStart());
2385 assertEquals(3, m.getEnd());
2387 sr = MappingUtils.buildSearchResults(pep4, 2, mappings);
2388 m = sr.getResults().get(0);
2389 assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
2390 assertEquals(4, m.getStart());
2391 assertEquals(6, m.getEnd());
2393 sr = MappingUtils.buildSearchResults(pep4, 3, mappings);
2394 m = sr.getResults().get(0);
2395 assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
2396 assertEquals(7, m.getStart());
2397 assertEquals(9, m.getEnd());
2401 * Test the method that just copies aligned sequences, provided all sequences
2402 * to be aligned share the aligned sequence's dataset
2404 @Test(groups = "Functional")
2405 public void testAlignAsSameSequences()
2407 SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
2408 SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
2409 AlignmentI al1 = new Alignment(new SequenceI[] { dna1, dna2 });
2410 ((Alignment) al1).createDatasetAlignment();
2412 SequenceI dna3 = new Sequence(dna1);
2413 SequenceI dna4 = new Sequence(dna2);
2414 assertSame(dna3.getDatasetSequence(), dna1.getDatasetSequence());
2415 assertSame(dna4.getDatasetSequence(), dna2.getDatasetSequence());
2416 String seq1 = "-cc-GG-GT-TT--aaa";
2417 dna3.setSequence(seq1);
2418 String seq2 = "C--C-Cgg--gtt-tAA-A-";
2419 dna4.setSequence(seq2);
2420 AlignmentI al2 = new Alignment(new SequenceI[] { dna3, dna4 });
2421 ((Alignment) al2).createDatasetAlignment();
2423 assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
2424 assertEquals(seq1, al1.getSequenceAt(0).getSequenceAsString());
2425 assertEquals(seq2, al1.getSequenceAt(1).getSequenceAsString());
2428 * add another sequence to 'aligned' - should still succeed, since
2429 * unaligned sequences still share a dataset with aligned sequences
2431 SequenceI dna5 = new Sequence("dna5", "CCCgggtttAAA");
2432 dna5.createDatasetSequence();
2433 al2.addSequence(dna5);
2434 assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
2435 assertEquals(seq1, al1.getSequenceAt(0).getSequenceAsString());
2436 assertEquals(seq2, al1.getSequenceAt(1).getSequenceAsString());
2439 * add another sequence to 'unaligned' - should fail, since now not
2440 * all unaligned sequences share a dataset with aligned sequences
2442 SequenceI dna6 = new Sequence("dna6", "CCCgggtttAAA");
2443 dna6.createDatasetSequence();
2444 al1.addSequence(dna6);
2445 // JAL-2110 JBP Comment: what's the use case for this behaviour ?
2446 assertFalse(AlignmentUtils.alignAsSameSequences(al1, al2));
2449 @Test(groups = "Functional")
2450 public void testAlignAsSameSequencesMultipleSubSeq()
2452 SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
2453 SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
2454 SequenceI as1 = dna1.deriveSequence(), as2 = dna1.deriveSequence()
2455 .getSubSequence(3, 7), as3 = dna2.deriveSequence();
2456 as1.insertCharAt(6, 5, '-');
2457 String s_as1 = as1.getSequenceAsString();
2458 as2.insertCharAt(6, 5, '-');
2459 String s_as2 = as2.getSequenceAsString();
2460 as3.insertCharAt(6, 5, '-');
2461 String s_as3 = as3.getSequenceAsString();
2462 AlignmentI aligned = new Alignment(new SequenceI[] { as1, as2, as3 });
2464 // why do we need to cast this still ?
2465 ((Alignment) aligned).createDatasetAlignment();
2466 SequenceI uas1 = dna1.deriveSequence(), uas2 = dna1.deriveSequence()
2467 .getSubSequence(3, 7), uas3 = dna2.deriveSequence();
2468 AlignmentI tobealigned = new Alignment(new SequenceI[] { uas1, uas2,
2470 ((Alignment) tobealigned).createDatasetAlignment();
2472 assertTrue(AlignmentUtils.alignAsSameSequences(tobealigned, aligned));
2473 assertEquals(s_as1, uas1.getSequenceAsString());
2474 assertEquals(s_as2, uas2.getSequenceAsString());
2475 assertEquals(s_as3, uas3.getSequenceAsString());