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.GeneLociI;
38 import jalview.datamodel.Mapping;
39 import jalview.datamodel.SearchResultMatchI;
40 import jalview.datamodel.SearchResultsI;
41 import jalview.datamodel.Sequence;
42 import jalview.datamodel.SequenceFeature;
43 import jalview.datamodel.SequenceI;
44 import jalview.datamodel.features.SequenceFeatures;
45 import jalview.gui.JvOptionPane;
46 import jalview.io.AppletFormatAdapter;
47 import jalview.io.DataSourceType;
48 import jalview.io.FileFormat;
49 import jalview.io.FileFormatI;
50 import jalview.io.FormatAdapter;
51 import jalview.io.gff.SequenceOntologyI;
52 import jalview.util.MapList;
53 import jalview.util.MappingUtils;
54 import jalview.ws.params.InvalidArgumentException;
56 import java.io.IOException;
57 import java.util.ArrayList;
58 import java.util.Arrays;
59 import java.util.LinkedHashMap;
60 import java.util.List;
62 import java.util.TreeMap;
64 import org.testng.annotations.BeforeClass;
65 import org.testng.annotations.Test;
67 public class AlignmentUtilsTests
69 private static Sequence ts = new Sequence("short",
70 "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
72 @BeforeClass(alwaysRun = true)
73 public void setUpJvOptionPane()
75 JvOptionPane.setInteractiveMode(false);
76 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
79 @Test(groups = { "Functional" })
80 public void testExpandContext()
82 AlignmentI al = new Alignment(new Sequence[] {});
83 for (int i = 4; i < 14; i += 2)
85 SequenceI s1 = ts.deriveSequence().getSubSequence(i, i + 7);
88 System.out.println(new AppletFormatAdapter().formatSequences(
91 for (int flnk = -1; flnk < 25; flnk++)
93 AlignmentI exp = AlignmentUtils.expandContext(al, flnk);
94 System.out.println("\nFlank size: " + flnk);
95 System.out.println(new AppletFormatAdapter().formatSequences(
96 FileFormat.Clustal, exp, true));
100 * Full expansion to complete sequences
102 for (SequenceI sq : exp.getSequences())
104 String ung = sq.getSequenceAsString().replaceAll("-+", "");
105 final String errorMsg = "Flanking sequence not the same as original dataset sequence.\n"
108 + sq.getDatasetSequence().getSequenceAsString();
109 assertTrue(errorMsg, ung.equalsIgnoreCase(sq.getDatasetSequence()
110 .getSequenceAsString()));
116 * Last sequence is fully expanded, others have leading gaps to match
118 assertTrue(exp.getSequenceAt(4).getSequenceAsString()
120 assertTrue(exp.getSequenceAt(3).getSequenceAsString()
121 .startsWith("--abc"));
122 assertTrue(exp.getSequenceAt(2).getSequenceAsString()
123 .startsWith("----abc"));
124 assertTrue(exp.getSequenceAt(1).getSequenceAsString()
125 .startsWith("------abc"));
126 assertTrue(exp.getSequenceAt(0).getSequenceAsString()
127 .startsWith("--------abc"));
133 * Test that annotations are correctly adjusted by expandContext
135 @Test(groups = { "Functional" })
136 public void testExpandContext_annotation()
138 AlignmentI al = new Alignment(new Sequence[] {});
139 SequenceI ds = new Sequence("Seq1", "ABCDEFGHI");
141 SequenceI seq1 = ds.deriveSequence().getSubSequence(3, 6);
142 al.addSequence(seq1);
145 * Annotate DEF with 4/5/6 respectively
147 Annotation[] anns = new Annotation[] { new Annotation(4),
148 new Annotation(5), new Annotation(6) };
149 AlignmentAnnotation ann = new AlignmentAnnotation("SS",
150 "secondary structure", anns);
151 seq1.addAlignmentAnnotation(ann);
154 * The annotations array should match aligned positions
156 assertEquals(3, ann.annotations.length);
157 assertEquals(4, ann.annotations[0].value, 0.001);
158 assertEquals(5, ann.annotations[1].value, 0.001);
159 assertEquals(6, ann.annotations[2].value, 0.001);
162 * Check annotation to sequence position mappings before expanding the
163 * sequence; these are set up in Sequence.addAlignmentAnnotation ->
164 * Annotation.setSequenceRef -> createSequenceMappings
166 assertNull(ann.getAnnotationForPosition(1));
167 assertNull(ann.getAnnotationForPosition(2));
168 assertNull(ann.getAnnotationForPosition(3));
169 assertEquals(4, ann.getAnnotationForPosition(4).value, 0.001);
170 assertEquals(5, ann.getAnnotationForPosition(5).value, 0.001);
171 assertEquals(6, ann.getAnnotationForPosition(6).value, 0.001);
172 assertNull(ann.getAnnotationForPosition(7));
173 assertNull(ann.getAnnotationForPosition(8));
174 assertNull(ann.getAnnotationForPosition(9));
177 * Expand the subsequence to the full sequence abcDEFghi
179 AlignmentI expanded = AlignmentUtils.expandContext(al, -1);
180 assertEquals("abcDEFghi", expanded.getSequenceAt(0)
181 .getSequenceAsString());
184 * Confirm the alignment and sequence have the same SS annotation,
185 * referencing the expanded sequence
187 ann = expanded.getSequenceAt(0).getAnnotation()[0];
188 assertSame(ann, expanded.getAlignmentAnnotation()[0]);
189 assertSame(expanded.getSequenceAt(0), ann.sequenceRef);
192 * The annotations array should have null values except for annotated
195 assertNull(ann.annotations[0]);
196 assertNull(ann.annotations[1]);
197 assertNull(ann.annotations[2]);
198 assertEquals(4, ann.annotations[3].value, 0.001);
199 assertEquals(5, ann.annotations[4].value, 0.001);
200 assertEquals(6, ann.annotations[5].value, 0.001);
201 assertNull(ann.annotations[6]);
202 assertNull(ann.annotations[7]);
203 assertNull(ann.annotations[8]);
206 * sequence position mappings should be unchanged
208 assertNull(ann.getAnnotationForPosition(1));
209 assertNull(ann.getAnnotationForPosition(2));
210 assertNull(ann.getAnnotationForPosition(3));
211 assertEquals(4, ann.getAnnotationForPosition(4).value, 0.001);
212 assertEquals(5, ann.getAnnotationForPosition(5).value, 0.001);
213 assertEquals(6, ann.getAnnotationForPosition(6).value, 0.001);
214 assertNull(ann.getAnnotationForPosition(7));
215 assertNull(ann.getAnnotationForPosition(8));
216 assertNull(ann.getAnnotationForPosition(9));
220 * Test method that returns a map of lists of sequences by sequence name.
222 * @throws IOException
224 @Test(groups = { "Functional" })
225 public void testGetSequencesByName() throws IOException
227 final String data = ">Seq1Name\nKQYL\n" + ">Seq2Name\nRFPW\n"
228 + ">Seq1Name\nABCD\n";
229 AlignmentI al = loadAlignment(data, FileFormat.Fasta);
230 Map<String, List<SequenceI>> map = AlignmentUtils
231 .getSequencesByName(al);
232 assertEquals(2, map.keySet().size());
233 assertEquals(2, map.get("Seq1Name").size());
234 assertEquals("KQYL", map.get("Seq1Name").get(0).getSequenceAsString());
235 assertEquals("ABCD", map.get("Seq1Name").get(1).getSequenceAsString());
236 assertEquals(1, map.get("Seq2Name").size());
237 assertEquals("RFPW", map.get("Seq2Name").get(0).getSequenceAsString());
241 * Helper method to load an alignment and ensure dataset sequences are set up.
247 * @throws IOException
249 protected AlignmentI loadAlignment(final String data, FileFormatI format)
252 AlignmentI a = new FormatAdapter().readFile(data,
253 DataSourceType.PASTE, format);
259 * Test mapping of protein to cDNA, for the case where we have no sequence
260 * cross-references, so mappings are made first-served 1-1 where sequences
263 * @throws IOException
265 @Test(groups = { "Functional" })
266 public void testMapProteinAlignmentToCdna_noXrefs() throws IOException
268 List<SequenceI> protseqs = new ArrayList<>();
269 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
270 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
271 protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
272 AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
273 protein.setDataset(null);
275 List<SequenceI> dnaseqs = new ArrayList<>();
276 dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR
277 dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAA")); // = EIQ
278 dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ
279 dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG")); // = EIQ
280 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
281 cdna.setDataset(null);
283 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
285 // 3 mappings made, each from 1 to 1 sequence
286 assertEquals(3, protein.getCodonFrames().size());
287 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
288 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
289 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
291 // V12345 mapped to A22222
292 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
294 assertEquals(1, acf.getdnaSeqs().length);
295 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
296 acf.getdnaSeqs()[0]);
297 Mapping[] protMappings = acf.getProtMappings();
298 assertEquals(1, protMappings.length);
299 MapList mapList = protMappings[0].getMap();
300 assertEquals(3, mapList.getFromRatio());
301 assertEquals(1, mapList.getToRatio());
302 assertTrue(Arrays.equals(new int[] { 1, 9 }, mapList.getFromRanges()
304 assertEquals(1, mapList.getFromRanges().size());
305 assertTrue(Arrays.equals(new int[] { 1, 3 },
306 mapList.getToRanges().get(0)));
307 assertEquals(1, mapList.getToRanges().size());
309 // V12346 mapped to A33333
310 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
311 assertEquals(1, acf.getdnaSeqs().length);
312 assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
313 acf.getdnaSeqs()[0]);
315 // V12347 mapped to A11111
316 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
317 assertEquals(1, acf.getdnaSeqs().length);
318 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
319 acf.getdnaSeqs()[0]);
321 // no mapping involving the 'extra' A44444
322 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(3)).isEmpty());
326 * Test for the alignSequenceAs method that takes two sequences and a mapping.
328 @Test(groups = { "Functional" })
329 public void testAlignSequenceAs_withMapping_noIntrons()
331 MapList map = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 }, 3, 1);
334 * No existing gaps in dna:
336 checkAlignSequenceAs("GGGAAA", "-A-L-", false, false, map,
340 * Now introduce gaps in dna but ignore them when realigning.
342 checkAlignSequenceAs("-G-G-G-A-A-A-", "-A-L-", false, false, map,
346 * Now include gaps in dna when realigning. First retaining 'mapped' gaps
347 * only, i.e. those within the exon region.
349 checkAlignSequenceAs("-G-G--G-A--A-A-", "-A-L-", true, false, map,
350 "---G-G--G---A--A-A");
353 * Include all gaps in dna when realigning (within and without the exon
354 * region). The leading gap, and the gaps between codons, are subsumed by
355 * the protein alignment gap.
357 checkAlignSequenceAs("-G-GG--AA-A---", "-A-L-", true, true, map,
358 "---G-GG---AA-A---");
361 * Include only unmapped gaps in dna when realigning (outside the exon
362 * region). The leading gap, and the gaps between codons, are subsumed by
363 * the protein alignment gap.
365 checkAlignSequenceAs("-G-GG--AA-A-", "-A-L-", false, true, map,
370 * Test for the alignSequenceAs method that takes two sequences and a mapping.
372 @Test(groups = { "Functional" })
373 public void testAlignSequenceAs_withMapping_withIntrons()
376 * Exons at codon 2 (AAA) and 4 (TTT)
378 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
379 new int[] { 1, 2 }, 3, 1);
382 * Simple case: no gaps in dna
384 checkAlignSequenceAs("GGGAAACCCTTTGGG", "--A-L-", false, false, map,
385 "GGG---AAACCCTTTGGG");
388 * Add gaps to dna - but ignore when realigning.
390 checkAlignSequenceAs("-G-G-G--A--A---AC-CC-T-TT-GG-G-", "--A-L-",
391 false, false, map, "GGG---AAACCCTTTGGG");
394 * Add gaps to dna - include within exons only when realigning.
396 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
397 true, false, map, "GGG---A--A---ACCCT-TTGGG");
400 * Include gaps outside exons only when realigning.
402 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
403 false, true, map, "-G-G-GAAAC-CCTTT-GG-G-");
406 * Include gaps following first intron if we are 'preserving mapped gaps'
408 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
409 true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
412 * Include all gaps in dna when realigning.
414 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
415 true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
419 * Test for the case where not all of the protein sequence is mapped to cDNA.
421 @Test(groups = { "Functional" })
422 public void testAlignSequenceAs_withMapping_withUnmappedProtein()
425 * Exons at codon 2 (AAA) and 4 (TTT) mapped to A and P
427 final MapList map = new MapList(new int[] { 4, 6, 10, 12 }, new int[] {
431 * -L- 'aligns' ccc------
433 checkAlignSequenceAs("gggAAAcccTTTggg", "-A-L-P-", false, false, map,
434 "gggAAAccc------TTTggg");
438 * Helper method that performs and verifies the method under test.
441 * the sequence to be realigned
443 * the sequence whose alignment is to be copied
444 * @param preserveMappedGaps
445 * @param preserveUnmappedGaps
449 protected void checkAlignSequenceAs(final String alignee,
450 final String alignModel, final boolean preserveMappedGaps,
451 final boolean preserveUnmappedGaps, MapList map,
452 final String expected)
454 SequenceI alignMe = new Sequence("Seq1", alignee);
455 alignMe.createDatasetSequence();
456 SequenceI alignFrom = new Sequence("Seq2", alignModel);
457 alignFrom.createDatasetSequence();
458 AlignedCodonFrame acf = new AlignedCodonFrame();
459 acf.addMap(alignMe.getDatasetSequence(),
460 alignFrom.getDatasetSequence(), map);
462 AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "---", '-',
463 preserveMappedGaps, preserveUnmappedGaps);
464 assertEquals(expected, alignMe.getSequenceAsString());
468 * Test for the alignSequenceAs method where we preserve gaps in introns only.
470 @Test(groups = { "Functional" })
471 public void testAlignSequenceAs_keepIntronGapsOnly()
475 * Intron GGGAAA followed by exon CCCTTT
477 MapList map = new MapList(new int[] { 7, 12 }, new int[] { 1, 2 }, 3, 1);
479 checkAlignSequenceAs("GG-G-AA-A-C-CC-T-TT", "AL", false, true, map,
484 * Test the method that realigns protein to match mapped codon alignment.
486 @Test(groups = { "Functional" })
487 public void testAlignProteinAsDna()
489 // seq1 codons are [1,2,3] [4,5,6] [7,8,9] [10,11,12]
490 SequenceI dna1 = new Sequence("Seq1", "TGCCATTACCAG-");
491 // seq2 codons are [1,3,4] [5,6,7] [8,9,10] [11,12,13]
492 SequenceI dna2 = new Sequence("Seq2", "T-GCCATTACCAG");
493 // seq3 codons are [1,2,3] [4,5,7] [8,9,10] [11,12,13]
494 SequenceI dna3 = new Sequence("Seq3", "TGCCA-TTACCAG");
495 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
496 dna.setDataset(null);
498 // protein alignment will be realigned like dna
499 SequenceI prot1 = new Sequence("Seq1", "CHYQ");
500 SequenceI prot2 = new Sequence("Seq2", "CHYQ");
501 SequenceI prot3 = new Sequence("Seq3", "CHYQ");
502 SequenceI prot4 = new Sequence("Seq4", "R-QSV"); // unmapped, unchanged
503 AlignmentI protein = new Alignment(new SequenceI[] { prot1, prot2,
505 protein.setDataset(null);
507 MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1);
508 AlignedCodonFrame acf = new AlignedCodonFrame();
509 acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
510 acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map);
511 acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map);
512 ArrayList<AlignedCodonFrame> acfs = new ArrayList<>();
514 protein.setCodonFrames(acfs);
517 * Translated codon order is [1,2,3] [1,3,4] [4,5,6] [4,5,7] [5,6,7] [7,8,9]
518 * [8,9,10] [10,11,12] [11,12,13]
520 AlignmentUtils.alignProteinAsDna(protein, dna);
521 assertEquals("C-H--Y-Q-", prot1.getSequenceAsString());
522 assertEquals("-C--H-Y-Q", prot2.getSequenceAsString());
523 assertEquals("C--H--Y-Q", prot3.getSequenceAsString());
524 assertEquals("R-QSV", prot4.getSequenceAsString());
528 * Test the method that tests whether a CDNA sequence translates to a protein
531 @Test(groups = { "Functional" })
532 public void testTranslatesAs()
534 // null arguments check
535 assertFalse(AlignmentUtils.translatesAs(null, 0, null));
536 assertFalse(AlignmentUtils.translatesAs(new char[] { 't' }, 0, null));
537 assertFalse(AlignmentUtils.translatesAs(null, 0, new char[] { 'a' }));
539 // straight translation
540 assertTrue(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
541 "FPKG".toCharArray()));
542 // with extra start codon (not in protein)
543 assertTrue(AlignmentUtils.translatesAs("atgtttcccaaaggg".toCharArray(),
544 3, "FPKG".toCharArray()));
545 // with stop codon1 (not in protein)
546 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtaa".toCharArray(),
547 0, "FPKG".toCharArray()));
548 // with stop codon1 (in protein as *)
549 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtaa".toCharArray(),
550 0, "FPKG*".toCharArray()));
551 // with stop codon2 (not in protein)
552 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtag".toCharArray(),
553 0, "FPKG".toCharArray()));
554 // with stop codon3 (not in protein)
555 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtga".toCharArray(),
556 0, "FPKG".toCharArray()));
557 // with start and stop codon1
558 assertTrue(AlignmentUtils.translatesAs(
559 "atgtttcccaaagggtaa".toCharArray(), 3, "FPKG".toCharArray()));
560 // with start and stop codon1 (in protein as *)
561 assertTrue(AlignmentUtils.translatesAs(
562 "atgtttcccaaagggtaa".toCharArray(), 3, "FPKG*".toCharArray()));
563 // with start and stop codon2
564 assertTrue(AlignmentUtils.translatesAs(
565 "atgtttcccaaagggtag".toCharArray(), 3, "FPKG".toCharArray()));
566 // with start and stop codon3
567 assertTrue(AlignmentUtils.translatesAs(
568 "atgtttcccaaagggtga".toCharArray(), 3, "FPKG".toCharArray()));
570 // with embedded stop codons
571 assertTrue(AlignmentUtils.translatesAs(
572 "atgtttTAGcccaaaTAAgggtga".toCharArray(), 3,
573 "F*PK*G".toCharArray()));
576 assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
577 0, "FPMG".toCharArray()));
580 assertFalse(AlignmentUtils.translatesAs("tttcccaaagg".toCharArray(), 0,
581 "FPKG".toCharArray()));
584 assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
585 0, "FPK".toCharArray()));
587 // overlong dna (doesn't end in stop codon)
588 assertFalse(AlignmentUtils.translatesAs(
589 "tttcccaaagggttt".toCharArray(), 0, "FPKG".toCharArray()));
591 // dna + stop codon + more
592 assertFalse(AlignmentUtils.translatesAs(
593 "tttcccaaagggttaga".toCharArray(), 0, "FPKG".toCharArray()));
596 assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
597 0, "FPKGQ".toCharArray()));
601 * Test mapping of protein to cDNA, for cases where the cDNA has start and/or
602 * stop codons in addition to the protein coding sequence.
604 * @throws IOException
606 @Test(groups = { "Functional" })
607 public void testMapProteinAlignmentToCdna_withStartAndStopCodons()
610 List<SequenceI> protseqs = new ArrayList<>();
611 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
612 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
613 protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
614 AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
615 protein.setDataset(null);
617 List<SequenceI> dnaseqs = new ArrayList<>();
619 dnaseqs.add(new Sequence("EMBL|A11111", "ATGTCAGCACGC"));
621 dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAATAA"));
622 // = start +EIQ + stop
623 dnaseqs.add(new Sequence("EMBL|A33333", "ATGGAAATCCAGTAG"));
624 dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG"));
625 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
626 cdna.setDataset(null);
628 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
630 // 3 mappings made, each from 1 to 1 sequence
631 assertEquals(3, protein.getCodonFrames().size());
632 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
633 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
634 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
636 // V12345 mapped from A22222
637 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
639 assertEquals(1, acf.getdnaSeqs().length);
640 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
641 acf.getdnaSeqs()[0]);
642 Mapping[] protMappings = acf.getProtMappings();
643 assertEquals(1, protMappings.length);
644 MapList mapList = protMappings[0].getMap();
645 assertEquals(3, mapList.getFromRatio());
646 assertEquals(1, mapList.getToRatio());
647 assertTrue(Arrays.equals(new int[] { 1, 9 }, mapList.getFromRanges()
649 assertEquals(1, mapList.getFromRanges().size());
650 assertTrue(Arrays.equals(new int[] { 1, 3 },
651 mapList.getToRanges().get(0)));
652 assertEquals(1, mapList.getToRanges().size());
654 // V12346 mapped from A33333 starting position 4
655 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
656 assertEquals(1, acf.getdnaSeqs().length);
657 assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
658 acf.getdnaSeqs()[0]);
659 protMappings = acf.getProtMappings();
660 assertEquals(1, protMappings.length);
661 mapList = protMappings[0].getMap();
662 assertEquals(3, mapList.getFromRatio());
663 assertEquals(1, mapList.getToRatio());
664 assertTrue(Arrays.equals(new int[] { 4, 12 }, mapList.getFromRanges()
666 assertEquals(1, mapList.getFromRanges().size());
667 assertTrue(Arrays.equals(new int[] { 1, 3 },
668 mapList.getToRanges().get(0)));
669 assertEquals(1, mapList.getToRanges().size());
671 // V12347 mapped to A11111 starting position 4
672 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
673 assertEquals(1, acf.getdnaSeqs().length);
674 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
675 acf.getdnaSeqs()[0]);
676 protMappings = acf.getProtMappings();
677 assertEquals(1, protMappings.length);
678 mapList = protMappings[0].getMap();
679 assertEquals(3, mapList.getFromRatio());
680 assertEquals(1, mapList.getToRatio());
681 assertTrue(Arrays.equals(new int[] { 4, 12 }, mapList.getFromRanges()
683 assertEquals(1, mapList.getFromRanges().size());
684 assertTrue(Arrays.equals(new int[] { 1, 3 },
685 mapList.getToRanges().get(0)));
686 assertEquals(1, mapList.getToRanges().size());
688 // no mapping involving the 'extra' A44444
689 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(3)).isEmpty());
693 * Test mapping of protein to cDNA, for the case where we have some sequence
694 * cross-references. Verify that 1-to-many mappings are made where
695 * cross-references exist and sequences are mappable.
697 * @throws IOException
699 @Test(groups = { "Functional" })
700 public void testMapProteinAlignmentToCdna_withXrefs() throws IOException
702 List<SequenceI> protseqs = new ArrayList<>();
703 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
704 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
705 protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
706 AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
707 protein.setDataset(null);
709 List<SequenceI> dnaseqs = new ArrayList<>();
710 dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR
711 dnaseqs.add(new Sequence("EMBL|A22222", "ATGGAGATACAA")); // = start + EIQ
712 dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ
713 dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG")); // = EIQ
714 dnaseqs.add(new Sequence("EMBL|A55555", "GAGATTCAG")); // = EIQ
715 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[5]));
716 cdna.setDataset(null);
718 // Xref A22222 to V12345 (should get mapped)
719 dnaseqs.get(1).addDBRef(new DBRefEntry("UNIPROT", "1", "V12345"));
720 // Xref V12345 to A44444 (should get mapped)
721 protseqs.get(0).addDBRef(new DBRefEntry("EMBL", "1", "A44444"));
722 // Xref A33333 to V12347 (sequence mismatch - should not get mapped)
723 dnaseqs.get(2).addDBRef(new DBRefEntry("UNIPROT", "1", "V12347"));
724 // as V12345 is mapped to A22222 and A44444, this leaves V12346 unmapped.
725 // it should get paired up with the unmapped A33333
726 // A11111 should be mapped to V12347
727 // A55555 is spare and has no xref so is not mapped
729 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
731 // 4 protein mappings made for 3 proteins, 2 to V12345, 1 each to V12346/7
732 assertEquals(3, protein.getCodonFrames().size());
733 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
734 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
735 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
737 // one mapping for each of the first 4 cDNA sequences
738 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(0)).size());
739 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(1)).size());
740 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(2)).size());
741 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(3)).size());
743 // V12345 mapped to A22222 and A44444
744 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
746 assertEquals(2, acf.getdnaSeqs().length);
747 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
748 acf.getdnaSeqs()[0]);
749 assertEquals(cdna.getSequenceAt(3).getDatasetSequence(),
750 acf.getdnaSeqs()[1]);
752 // V12346 mapped to A33333
753 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
754 assertEquals(1, acf.getdnaSeqs().length);
755 assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
756 acf.getdnaSeqs()[0]);
758 // V12347 mapped to A11111
759 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
760 assertEquals(1, acf.getdnaSeqs().length);
761 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
762 acf.getdnaSeqs()[0]);
764 // no mapping involving the 'extra' A55555
765 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(4)).isEmpty());
769 * Test mapping of protein to cDNA, for the case where we have some sequence
770 * cross-references. Verify that once we have made an xref mapping we don't
771 * also map un-xrefd sequeces.
773 * @throws IOException
775 @Test(groups = { "Functional" })
776 public void testMapProteinAlignmentToCdna_prioritiseXrefs()
779 List<SequenceI> protseqs = new ArrayList<>();
780 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
781 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
782 AlignmentI protein = new Alignment(
783 protseqs.toArray(new SequenceI[protseqs.size()]));
784 protein.setDataset(null);
786 List<SequenceI> dnaseqs = new ArrayList<>();
787 dnaseqs.add(new Sequence("EMBL|A11111", "GAAATCCAG")); // = EIQ
788 dnaseqs.add(new Sequence("EMBL|A22222", "GAAATTCAG")); // = EIQ
789 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[dnaseqs
791 cdna.setDataset(null);
793 // Xref A22222 to V12345 (should get mapped)
794 // A11111 should then be mapped to the unmapped V12346
795 dnaseqs.get(1).addDBRef(new DBRefEntry("UNIPROT", "1", "V12345"));
797 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
799 // 2 protein mappings made
800 assertEquals(2, protein.getCodonFrames().size());
801 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
802 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
804 // one mapping for each of the cDNA sequences
805 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(0)).size());
806 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(1)).size());
808 // V12345 mapped to A22222
809 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
811 assertEquals(1, acf.getdnaSeqs().length);
812 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
813 acf.getdnaSeqs()[0]);
815 // V12346 mapped to A11111
816 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
817 assertEquals(1, acf.getdnaSeqs().length);
818 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
819 acf.getdnaSeqs()[0]);
823 * Test the method that shows or hides sequence annotations by type(s) and
826 @Test(groups = { "Functional" })
827 public void testShowOrHideSequenceAnnotations()
829 SequenceI seq1 = new Sequence("Seq1", "AAA");
830 SequenceI seq2 = new Sequence("Seq2", "BBB");
831 SequenceI seq3 = new Sequence("Seq3", "CCC");
832 Annotation[] anns = new Annotation[] { new Annotation(2f) };
833 AlignmentAnnotation ann1 = new AlignmentAnnotation("Structure", "ann1",
835 ann1.setSequenceRef(seq1);
836 AlignmentAnnotation ann2 = new AlignmentAnnotation("Structure", "ann2",
838 ann2.setSequenceRef(seq2);
839 AlignmentAnnotation ann3 = new AlignmentAnnotation("Structure", "ann3",
841 AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "ann4", anns);
842 ann4.setSequenceRef(seq1);
843 AlignmentAnnotation ann5 = new AlignmentAnnotation("Temp", "ann5", anns);
844 ann5.setSequenceRef(seq2);
845 AlignmentAnnotation ann6 = new AlignmentAnnotation("Temp", "ann6", anns);
846 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
847 al.addAnnotation(ann1); // Structure for Seq1
848 al.addAnnotation(ann2); // Structure for Seq2
849 al.addAnnotation(ann3); // Structure for no sequence
850 al.addAnnotation(ann4); // Temp for seq1
851 al.addAnnotation(ann5); // Temp for seq2
852 al.addAnnotation(ann6); // Temp for no sequence
853 List<String> types = new ArrayList<>();
854 List<SequenceI> scope = new ArrayList<>();
857 * Set all sequence related Structure to hidden (ann1, ann2)
859 types.add("Structure");
860 AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, false,
862 assertFalse(ann1.visible);
863 assertFalse(ann2.visible);
864 assertTrue(ann3.visible); // not sequence-related, not affected
865 assertTrue(ann4.visible); // not Structure, not affected
866 assertTrue(ann5.visible); // "
867 assertTrue(ann6.visible); // not sequence-related, not affected
870 * Set Temp in {seq1, seq3} to hidden
876 AlignmentUtils.showOrHideSequenceAnnotations(al, types, scope, false,
878 assertFalse(ann1.visible); // unchanged
879 assertFalse(ann2.visible); // unchanged
880 assertTrue(ann3.visible); // not sequence-related, not affected
881 assertFalse(ann4.visible); // Temp for seq1 hidden
882 assertTrue(ann5.visible); // not in scope, not affected
883 assertTrue(ann6.visible); // not sequence-related, not affected
886 * Set Temp in all sequences to hidden
892 AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, false,
894 assertFalse(ann1.visible); // unchanged
895 assertFalse(ann2.visible); // unchanged
896 assertTrue(ann3.visible); // not sequence-related, not affected
897 assertFalse(ann4.visible); // Temp for seq1 hidden
898 assertFalse(ann5.visible); // Temp for seq2 hidden
899 assertTrue(ann6.visible); // not sequence-related, not affected
902 * Set all types in {seq1, seq3} to visible
908 AlignmentUtils.showOrHideSequenceAnnotations(al, types, scope, true,
910 assertTrue(ann1.visible); // Structure for seq1 set visible
911 assertFalse(ann2.visible); // not in scope, unchanged
912 assertTrue(ann3.visible); // not sequence-related, not affected
913 assertTrue(ann4.visible); // Temp for seq1 set visible
914 assertFalse(ann5.visible); // not in scope, unchanged
915 assertTrue(ann6.visible); // not sequence-related, not affected
918 * Set all types in all scope to hidden
920 AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, true,
922 assertFalse(ann1.visible);
923 assertFalse(ann2.visible);
924 assertTrue(ann3.visible); // not sequence-related, not affected
925 assertFalse(ann4.visible);
926 assertFalse(ann5.visible);
927 assertTrue(ann6.visible); // not sequence-related, not affected
931 * Tests for the method that checks if one sequence cross-references another
933 @Test(groups = { "Functional" })
934 public void testHasCrossRef()
936 assertFalse(AlignmentUtils.hasCrossRef(null, null));
937 SequenceI seq1 = new Sequence("EMBL|A12345", "ABCDEF");
938 assertFalse(AlignmentUtils.hasCrossRef(seq1, null));
939 assertFalse(AlignmentUtils.hasCrossRef(null, seq1));
940 SequenceI seq2 = new Sequence("UNIPROT|V20192", "ABCDEF");
941 assertFalse(AlignmentUtils.hasCrossRef(seq1, seq2));
944 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "v20193"));
945 assertFalse(AlignmentUtils.hasCrossRef(seq1, seq2));
947 // case-insensitive; version number is ignored
948 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "v20192"));
949 assertTrue(AlignmentUtils.hasCrossRef(seq1, seq2));
952 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
953 assertTrue(AlignmentUtils.hasCrossRef(seq1, seq2));
954 // test is one-way only
955 assertFalse(AlignmentUtils.hasCrossRef(seq2, seq1));
959 * Tests for the method that checks if either sequence cross-references the
962 @Test(groups = { "Functional" })
963 public void testHaveCrossRef()
965 assertFalse(AlignmentUtils.hasCrossRef(null, null));
966 SequenceI seq1 = new Sequence("EMBL|A12345", "ABCDEF");
967 assertFalse(AlignmentUtils.haveCrossRef(seq1, null));
968 assertFalse(AlignmentUtils.haveCrossRef(null, seq1));
969 SequenceI seq2 = new Sequence("UNIPROT|V20192", "ABCDEF");
970 assertFalse(AlignmentUtils.haveCrossRef(seq1, seq2));
972 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
973 assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
974 // next is true for haveCrossRef, false for hasCrossRef
975 assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
977 // now the other way round
978 seq1.setDBRefs(null);
979 seq2.addDBRef(new DBRefEntry("EMBL", "1", "A12345"));
980 assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
981 assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
984 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
985 assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
986 assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
990 * Test the method that extracts the cds-only part of a dna alignment.
992 @Test(groups = { "Functional" })
993 public void testMakeCdsAlignment()
997 * dna1 --> [4, 6] [10,12] --> pep1
998 * dna2 --> [1, 3] [7, 9] [13,15] --> pep2
1000 SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
1001 SequenceI dna2 = new Sequence("dna2", "GGGcccTTTaaaCCC");
1002 SequenceI pep1 = new Sequence("pep1", "GF");
1003 SequenceI pep2 = new Sequence("pep2", "GFP");
1004 pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "pep1"));
1005 pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "pep2"));
1006 dna1.createDatasetSequence();
1007 dna2.createDatasetSequence();
1008 pep1.createDatasetSequence();
1009 pep2.createDatasetSequence();
1010 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
1011 dna.setDataset(null);
1014 * put a variant feature on dna2 base 8
1015 * - should transfer to cds2 base 5
1017 dna2.addSequenceFeature(new SequenceFeature("variant", "hgmd", 8, 8,
1021 * need a sourceDbRef if we are to construct dbrefs to the CDS
1022 * sequence from the dna contig sequences
1024 DBRefEntry dbref = new DBRefEntry("ENSEMBL", "0", "dna1");
1025 dna1.getDatasetSequence().addDBRef(dbref);
1026 org.testng.Assert.assertEquals(dbref, dna1.getPrimaryDBRefs().get(0));
1027 dbref = new DBRefEntry("ENSEMBL", "0", "dna2");
1028 dna2.getDatasetSequence().addDBRef(dbref);
1029 org.testng.Assert.assertEquals(dbref, dna2.getPrimaryDBRefs().get(0));
1032 * CDS sequences are 'discovered' from dna-to-protein mappings on the alignment
1033 * dataset (e.g. added from dbrefs by CrossRef.findXrefSequences)
1035 MapList mapfordna1 = new MapList(new int[] { 4, 6, 10, 12 }, new int[] {
1037 AlignedCodonFrame acf = new AlignedCodonFrame();
1038 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
1040 dna.addCodonFrame(acf);
1041 MapList mapfordna2 = new MapList(new int[] { 1, 3, 7, 9, 13, 15 },
1042 new int[] { 1, 3 }, 3, 1);
1043 acf = new AlignedCodonFrame();
1044 acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(),
1046 dna.addCodonFrame(acf);
1049 * In this case, mappings originally came from matching Uniprot accessions
1050 * - so need an xref on dna involving those regions.
1051 * These are normally constructed from CDS annotation
1053 DBRefEntry dna1xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep1",
1054 new Mapping(mapfordna1));
1055 dna1.addDBRef(dna1xref);
1056 assertEquals(2, dna1.getDBRefs().size()); // to self and to pep1
1057 DBRefEntry dna2xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep2",
1058 new Mapping(mapfordna2));
1059 dna2.addDBRef(dna2xref);
1060 assertEquals(2, dna2.getDBRefs().size()); // to self and to pep2
1063 * execute method under test:
1065 AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
1066 dna1, dna2 }, dna.getDataset(), null);
1069 * verify cds sequences
1071 assertEquals(2, cds.getSequences().size());
1072 assertEquals("GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
1073 assertEquals("GGGTTTCCC", cds.getSequenceAt(1).getSequenceAsString());
1076 * verify shared, extended alignment dataset
1078 assertSame(dna.getDataset(), cds.getDataset());
1079 SequenceI cds1Dss = cds.getSequenceAt(0).getDatasetSequence();
1080 SequenceI cds2Dss = cds.getSequenceAt(1).getDatasetSequence();
1081 assertTrue(dna.getDataset().getSequences().contains(cds1Dss));
1082 assertTrue(dna.getDataset().getSequences().contains(cds2Dss));
1085 * verify CDS has a dbref with mapping to peptide
1087 assertNotNull(cds1Dss.getDBRefs());
1088 assertEquals(2, cds1Dss.getDBRefs().size());
1089 dbref = cds1Dss.getDBRefs().get(0);
1090 assertEquals(dna1xref.getSource(), dbref.getSource());
1091 // version is via ensembl's primary ref
1092 assertEquals(dna1xref.getVersion(), dbref.getVersion());
1093 assertEquals(dna1xref.getAccessionId(), dbref.getAccessionId());
1094 assertNotNull(dbref.getMap());
1095 assertSame(pep1.getDatasetSequence(), dbref.getMap().getTo());
1096 MapList cdsMapping = new MapList(new int[] { 1, 6 },
1097 new int[] { 1, 2 }, 3, 1);
1098 assertEquals(cdsMapping, dbref.getMap().getMap());
1101 * verify peptide has added a dbref with reverse mapping to CDS
1103 assertNotNull(pep1.getDBRefs());
1104 // FIXME pep1.getDBRefs() is 1 - is that the correct behaviour ?
1105 assertEquals(2, pep1.getDBRefs().size());
1106 dbref = pep1.getDBRefs().get(1);
1107 assertEquals("ENSEMBL", dbref.getSource());
1108 assertEquals("0", dbref.getVersion());
1109 assertEquals("CDS|dna1", dbref.getAccessionId());
1110 assertNotNull(dbref.getMap());
1111 assertSame(cds1Dss, dbref.getMap().getTo());
1112 assertEquals(cdsMapping.getInverse(), dbref.getMap().getMap());
1115 * verify cDNA has added a dbref with mapping to CDS
1117 assertEquals(3, dna1.getDBRefs().size());
1118 DBRefEntry dbRefEntry = dna1.getDBRefs().get(2);
1119 assertSame(cds1Dss, dbRefEntry.getMap().getTo());
1120 MapList dnaToCdsMapping = new MapList(new int[] { 4, 6, 10, 12 },
1121 new int[] { 1, 6 }, 1, 1);
1122 assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap());
1123 assertEquals(3, dna2.getDBRefs().size());
1124 dbRefEntry = dna2.getDBRefs().get(2);
1125 assertSame(cds2Dss, dbRefEntry.getMap().getTo());
1126 dnaToCdsMapping = new MapList(new int[] { 1, 3, 7, 9, 13, 15 },
1127 new int[] { 1, 9 }, 1, 1);
1128 assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap());
1131 * verify CDS has added a dbref with mapping to cDNA
1133 assertEquals(2, cds1Dss.getDBRefs().size());
1134 dbRefEntry = cds1Dss.getDBRefs().get(1);
1135 assertSame(dna1.getDatasetSequence(), dbRefEntry.getMap().getTo());
1136 MapList cdsToDnaMapping = new MapList(new int[] { 1, 6 }, new int[] {
1137 4, 6, 10, 12 }, 1, 1);
1138 assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap());
1139 assertEquals(2, cds2Dss.getDBRefs().size());
1140 dbRefEntry = cds2Dss.getDBRefs().get(1);
1141 assertSame(dna2.getDatasetSequence(), dbRefEntry.getMap().getTo());
1142 cdsToDnaMapping = new MapList(new int[] { 1, 9 }, new int[] { 1, 3, 7,
1144 assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap());
1147 * Verify mappings from CDS to peptide, cDNA to CDS, and cDNA to peptide
1148 * the mappings are on the shared alignment dataset
1149 * 6 mappings, 2*(DNA->CDS), 2*(DNA->Pep), 2*(CDS->Pep)
1151 List<AlignedCodonFrame> cdsMappings = cds.getDataset().getCodonFrames();
1152 assertEquals(6, cdsMappings.size());
1155 * verify that mapping sets for dna and cds alignments are different
1156 * [not current behaviour - all mappings are on the alignment dataset]
1158 // select -> subselect type to test.
1159 // Assert.assertNotSame(dna.getCodonFrames(), cds.getCodonFrames());
1160 // assertEquals(4, dna.getCodonFrames().size());
1161 // assertEquals(4, cds.getCodonFrames().size());
1164 * Two mappings involve pep1 (dna to pep1, cds to pep1)
1165 * Mapping from pep1 to GGGTTT in first new exon sequence
1167 List<AlignedCodonFrame> pep1Mappings = MappingUtils
1168 .findMappingsForSequence(pep1, cdsMappings);
1169 assertEquals(2, pep1Mappings.size());
1170 List<AlignedCodonFrame> mappings = MappingUtils
1171 .findMappingsForSequence(cds.getSequenceAt(0), pep1Mappings);
1172 assertEquals(1, mappings.size());
1175 SearchResultsI sr = MappingUtils.buildSearchResults(pep1, 1, mappings);
1176 assertEquals(1, sr.getResults().size());
1177 SearchResultMatchI m = sr.getResults().get(0);
1178 assertSame(cds1Dss, m.getSequence());
1179 assertEquals(1, m.getStart());
1180 assertEquals(3, m.getEnd());
1182 sr = MappingUtils.buildSearchResults(pep1, 2, mappings);
1183 m = sr.getResults().get(0);
1184 assertSame(cds1Dss, m.getSequence());
1185 assertEquals(4, m.getStart());
1186 assertEquals(6, m.getEnd());
1189 * Two mappings involve pep2 (dna to pep2, cds to pep2)
1190 * Verify mapping from pep2 to GGGTTTCCC in second new exon sequence
1192 List<AlignedCodonFrame> pep2Mappings = MappingUtils
1193 .findMappingsForSequence(pep2, cdsMappings);
1194 assertEquals(2, pep2Mappings.size());
1195 mappings = MappingUtils.findMappingsForSequence(cds.getSequenceAt(1),
1197 assertEquals(1, mappings.size());
1199 sr = MappingUtils.buildSearchResults(pep2, 1, mappings);
1200 assertEquals(1, sr.getResults().size());
1201 m = sr.getResults().get(0);
1202 assertSame(cds2Dss, m.getSequence());
1203 assertEquals(1, m.getStart());
1204 assertEquals(3, m.getEnd());
1206 sr = MappingUtils.buildSearchResults(pep2, 2, mappings);
1207 m = sr.getResults().get(0);
1208 assertSame(cds2Dss, m.getSequence());
1209 assertEquals(4, m.getStart());
1210 assertEquals(6, m.getEnd());
1212 sr = MappingUtils.buildSearchResults(pep2, 3, mappings);
1213 m = sr.getResults().get(0);
1214 assertSame(cds2Dss, m.getSequence());
1215 assertEquals(7, m.getStart());
1216 assertEquals(9, m.getEnd());
1219 * check cds2 acquired a variant feature in position 5
1221 List<SequenceFeature> sfs = cds2Dss.getSequenceFeatures();
1223 assertEquals(1, sfs.size());
1224 assertEquals("variant", sfs.get(0).type);
1225 assertEquals(5, sfs.get(0).begin);
1226 assertEquals(5, sfs.get(0).end);
1230 * Test the method that makes a cds-only alignment from a DNA sequence and its
1231 * product mappings, for the case where there are multiple exon mappings to
1232 * different protein products.
1234 @Test(groups = { "Functional" })
1235 public void testMakeCdsAlignment_multipleProteins()
1237 SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
1238 SequenceI pep1 = new Sequence("pep1", "GF"); // GGGTTT
1239 SequenceI pep2 = new Sequence("pep2", "KP"); // aaaccc
1240 SequenceI pep3 = new Sequence("pep3", "KF"); // aaaTTT
1241 dna1.createDatasetSequence();
1242 pep1.createDatasetSequence();
1243 pep2.createDatasetSequence();
1244 pep3.createDatasetSequence();
1245 pep1.getDatasetSequence().addDBRef(
1246 new DBRefEntry("EMBLCDS", "2", "A12345"));
1247 pep2.getDatasetSequence().addDBRef(
1248 new DBRefEntry("EMBLCDS", "3", "A12346"));
1249 pep3.getDatasetSequence().addDBRef(
1250 new DBRefEntry("EMBLCDS", "4", "A12347"));
1253 * Create the CDS alignment
1255 AlignmentI dna = new Alignment(new SequenceI[] { dna1 });
1256 dna.setDataset(null);
1259 * Make the mappings from dna to protein
1261 // map ...GGG...TTT to GF
1262 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1263 new int[] { 1, 2 }, 3, 1);
1264 AlignedCodonFrame acf = new AlignedCodonFrame();
1265 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
1266 dna.addCodonFrame(acf);
1268 // map aaa...ccc to KP
1269 map = new MapList(new int[] { 1, 3, 7, 9 }, new int[] { 1, 2 }, 3, 1);
1270 acf = new AlignedCodonFrame();
1271 acf.addMap(dna1.getDatasetSequence(), pep2.getDatasetSequence(), map);
1272 dna.addCodonFrame(acf);
1274 // map aaa......TTT to KF
1275 map = new MapList(new int[] { 1, 3, 10, 12 }, new int[] { 1, 2 }, 3, 1);
1276 acf = new AlignedCodonFrame();
1277 acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map);
1278 dna.addCodonFrame(acf);
1281 * execute method under test
1283 AlignmentI cdsal = AlignmentUtils.makeCdsAlignment(
1284 new SequenceI[] { dna1 }, dna.getDataset(), null);
1287 * Verify we have 3 cds sequences, mapped to pep1/2/3 respectively
1289 List<SequenceI> cds = cdsal.getSequences();
1290 assertEquals(3, cds.size());
1293 * verify shared, extended alignment dataset
1295 assertSame(cdsal.getDataset(), dna.getDataset());
1296 assertTrue(dna.getDataset().getSequences()
1297 .contains(cds.get(0).getDatasetSequence()));
1298 assertTrue(dna.getDataset().getSequences()
1299 .contains(cds.get(1).getDatasetSequence()));
1300 assertTrue(dna.getDataset().getSequences()
1301 .contains(cds.get(2).getDatasetSequence()));
1304 * verify aligned cds sequences and their xrefs
1306 SequenceI cdsSeq = cds.get(0);
1307 assertEquals("GGGTTT", cdsSeq.getSequenceAsString());
1308 // assertEquals("dna1|A12345", cdsSeq.getName());
1309 assertEquals("CDS|dna1", cdsSeq.getName());
1310 // assertEquals(1, cdsSeq.getDBRefs().length);
1311 // DBRefEntry cdsRef = cdsSeq.getDBRefs()[0];
1312 // assertEquals("EMBLCDS", cdsRef.getSource());
1313 // assertEquals("2", cdsRef.getVersion());
1314 // assertEquals("A12345", cdsRef.getAccessionId());
1316 cdsSeq = cds.get(1);
1317 assertEquals("aaaccc", cdsSeq.getSequenceAsString());
1318 // assertEquals("dna1|A12346", cdsSeq.getName());
1319 assertEquals("CDS|dna1", cdsSeq.getName());
1320 // assertEquals(1, cdsSeq.getDBRefs().length);
1321 // cdsRef = cdsSeq.getDBRefs()[0];
1322 // assertEquals("EMBLCDS", cdsRef.getSource());
1323 // assertEquals("3", cdsRef.getVersion());
1324 // assertEquals("A12346", cdsRef.getAccessionId());
1326 cdsSeq = cds.get(2);
1327 assertEquals("aaaTTT", cdsSeq.getSequenceAsString());
1328 // assertEquals("dna1|A12347", cdsSeq.getName());
1329 assertEquals("CDS|dna1", cdsSeq.getName());
1330 // assertEquals(1, cdsSeq.getDBRefs().length);
1331 // cdsRef = cdsSeq.getDBRefs()[0];
1332 // assertEquals("EMBLCDS", cdsRef.getSource());
1333 // assertEquals("4", cdsRef.getVersion());
1334 // assertEquals("A12347", cdsRef.getAccessionId());
1337 * Verify there are mappings from each cds sequence to its protein product
1338 * and also to its dna source
1340 List<AlignedCodonFrame> newMappings = cdsal.getCodonFrames();
1343 * 6 mappings involve dna1 (to pep1/2/3, cds1/2/3)
1345 List<AlignedCodonFrame> dnaMappings = MappingUtils
1346 .findMappingsForSequence(dna1, newMappings);
1347 assertEquals(6, dnaMappings.size());
1352 List<AlignedCodonFrame> mappings = MappingUtils
1353 .findMappingsForSequence(pep1, dnaMappings);
1354 assertEquals(1, mappings.size());
1355 assertEquals(1, mappings.get(0).getMappings().size());
1356 assertSame(pep1.getDatasetSequence(), mappings.get(0).getMappings()
1357 .get(0).getMapping().getTo());
1362 List<AlignedCodonFrame> dnaToCds1Mappings = MappingUtils
1363 .findMappingsForSequence(cds.get(0), dnaMappings);
1364 Mapping mapping = dnaToCds1Mappings.get(0).getMappings().get(0)
1366 assertSame(cds.get(0).getDatasetSequence(), mapping.getTo());
1367 assertEquals("G(1) in CDS should map to G(4) in DNA", 4, mapping
1368 .getMap().getToPosition(1));
1373 mappings = MappingUtils.findMappingsForSequence(pep2, dnaMappings);
1374 assertEquals(1, mappings.size());
1375 assertEquals(1, mappings.get(0).getMappings().size());
1376 assertSame(pep2.getDatasetSequence(), mappings.get(0).getMappings()
1377 .get(0).getMapping().getTo());
1382 List<AlignedCodonFrame> dnaToCds2Mappings = MappingUtils
1383 .findMappingsForSequence(cds.get(1), dnaMappings);
1384 mapping = dnaToCds2Mappings.get(0).getMappings().get(0).getMapping();
1385 assertSame(cds.get(1).getDatasetSequence(), mapping.getTo());
1386 assertEquals("c(4) in CDS should map to c(7) in DNA", 7, mapping
1387 .getMap().getToPosition(4));
1392 mappings = MappingUtils.findMappingsForSequence(pep3, dnaMappings);
1393 assertEquals(1, mappings.size());
1394 assertEquals(1, mappings.get(0).getMappings().size());
1395 assertSame(pep3.getDatasetSequence(), mappings.get(0).getMappings()
1396 .get(0).getMapping().getTo());
1401 List<AlignedCodonFrame> dnaToCds3Mappings = MappingUtils
1402 .findMappingsForSequence(cds.get(2), dnaMappings);
1403 mapping = dnaToCds3Mappings.get(0).getMappings().get(0).getMapping();
1404 assertSame(cds.get(2).getDatasetSequence(), mapping.getTo());
1405 assertEquals("T(4) in CDS should map to T(10) in DNA", 10, mapping
1406 .getMap().getToPosition(4));
1409 @Test(groups = { "Functional" })
1410 public void testIsMappable()
1412 SequenceI dna1 = new Sequence("dna1", "cgCAGtgGT");
1413 SequenceI aa1 = new Sequence("aa1", "RSG");
1414 AlignmentI al1 = new Alignment(new SequenceI[] { dna1 });
1415 AlignmentI al2 = new Alignment(new SequenceI[] { aa1 });
1417 assertFalse(AlignmentUtils.isMappable(null, null));
1418 assertFalse(AlignmentUtils.isMappable(al1, null));
1419 assertFalse(AlignmentUtils.isMappable(null, al1));
1420 assertFalse(AlignmentUtils.isMappable(al1, al1));
1421 assertFalse(AlignmentUtils.isMappable(al2, al2));
1423 assertTrue(AlignmentUtils.isMappable(al1, al2));
1424 assertTrue(AlignmentUtils.isMappable(al2, al1));
1428 * Test creating a mapping when the sequences involved do not start at residue
1431 * @throws IOException
1433 @Test(groups = { "Functional" })
1434 public void testMapCdnaToProtein_forSubsequence() throws IOException
1436 SequenceI prot = new Sequence("UNIPROT|V12345", "E-I--Q", 10, 12);
1437 prot.createDatasetSequence();
1439 SequenceI dna = new Sequence("EMBL|A33333", "GAA--AT-C-CAG", 40, 48);
1440 dna.createDatasetSequence();
1442 MapList map = AlignmentUtils.mapCdnaToProtein(prot, dna);
1443 assertEquals(10, map.getToLowest());
1444 assertEquals(12, map.getToHighest());
1445 assertEquals(40, map.getFromLowest());
1446 assertEquals(48, map.getFromHighest());
1450 * Test for the alignSequenceAs method where we have protein mapped to protein
1452 @Test(groups = { "Functional" })
1453 public void testAlignSequenceAs_mappedProteinProtein()
1456 SequenceI alignMe = new Sequence("Match", "MGAASEV");
1457 alignMe.createDatasetSequence();
1458 SequenceI alignFrom = new Sequence("Query", "LQTGYMGAASEVMFSPTRR");
1459 alignFrom.createDatasetSequence();
1461 AlignedCodonFrame acf = new AlignedCodonFrame();
1462 // this is like a domain or motif match of part of a peptide sequence
1463 MapList map = new MapList(new int[] { 6, 12 }, new int[] { 1, 7 }, 1, 1);
1464 acf.addMap(alignFrom.getDatasetSequence(),
1465 alignMe.getDatasetSequence(), map);
1467 AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "-", '-', true,
1469 assertEquals("-----MGAASEV-------", alignMe.getSequenceAsString());
1473 * Test for the alignSequenceAs method where there are trailing unmapped
1474 * residues in the model sequence
1476 @Test(groups = { "Functional" })
1477 public void testAlignSequenceAs_withTrailingPeptide()
1479 // map first 3 codons to KPF; G is a trailing unmapped residue
1480 MapList map = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3, 1);
1482 checkAlignSequenceAs("AAACCCTTT", "K-PFG", true, true, map,
1487 * Tests for transferring features between mapped sequences
1489 @Test(groups = { "Functional" })
1490 public void testTransferFeatures()
1492 SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt");
1493 SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
1496 dna.addSequenceFeature(new SequenceFeature("type1", "desc1", 1, 2, 1f,
1498 // partial overlap - to [1, 1]
1499 dna.addSequenceFeature(new SequenceFeature("type2", "desc2", 3, 4, 2f,
1501 // exact overlap - to [1, 3]
1502 dna.addSequenceFeature(new SequenceFeature("type3", "desc3", 4, 6, 3f,
1504 // spanning overlap - to [2, 5]
1505 dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f,
1507 // exactly overlaps whole mapped range [1, 6]
1508 dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f,
1510 // no overlap (internal)
1511 dna.addSequenceFeature(new SequenceFeature("type6", "desc6", 7, 9, 6f,
1513 // no overlap (3' end)
1514 dna.addSequenceFeature(new SequenceFeature("type7", "desc7", 13, 15,
1516 // overlap (3' end) - to [6, 6]
1517 dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12,
1519 // extended overlap - to [6, +]
1520 dna.addSequenceFeature(new SequenceFeature("type9", "desc9", 12, 13,
1523 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1524 new int[] { 1, 6 }, 1, 1);
1527 * transferFeatures() will build 'partial overlap' for regions
1528 * that partially overlap 5' or 3' (start or end) of target sequence
1530 AlignmentUtils.transferFeatures(dna, cds, map, null);
1531 List<SequenceFeature> sfs = cds.getSequenceFeatures();
1532 assertEquals(6, sfs.size());
1534 SequenceFeature sf = sfs.get(0);
1535 assertEquals("type2", sf.getType());
1536 assertEquals("desc2", sf.getDescription());
1537 assertEquals(2f, sf.getScore());
1538 assertEquals(1, sf.getBegin());
1539 assertEquals(1, sf.getEnd());
1542 assertEquals("type3", sf.getType());
1543 assertEquals("desc3", sf.getDescription());
1544 assertEquals(3f, sf.getScore());
1545 assertEquals(1, sf.getBegin());
1546 assertEquals(3, sf.getEnd());
1549 assertEquals("type4", sf.getType());
1550 assertEquals(2, sf.getBegin());
1551 assertEquals(5, sf.getEnd());
1554 assertEquals("type5", sf.getType());
1555 assertEquals(1, sf.getBegin());
1556 assertEquals(6, sf.getEnd());
1559 assertEquals("type8", sf.getType());
1560 assertEquals(6, sf.getBegin());
1561 assertEquals(6, sf.getEnd());
1564 assertEquals("type9", sf.getType());
1565 assertEquals(6, sf.getBegin());
1566 assertEquals(6, sf.getEnd());
1570 * Tests for transferring features between mapped sequences
1572 @Test(groups = { "Functional" })
1573 public void testTransferFeatures_withOmit()
1575 SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt");
1576 SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
1578 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1579 new int[] { 1, 6 }, 1, 1);
1581 // [5, 11] maps to [2, 5]
1582 dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f,
1584 // [4, 12] maps to [1, 6]
1585 dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f,
1587 // [12, 12] maps to [6, 6]
1588 dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12,
1591 // desc4 and desc8 are the 'omit these' varargs
1592 AlignmentUtils.transferFeatures(dna, cds, map, null, "type4", "type8");
1593 List<SequenceFeature> sfs = cds.getSequenceFeatures();
1594 assertEquals(1, sfs.size());
1596 SequenceFeature sf = sfs.get(0);
1597 assertEquals("type5", sf.getType());
1598 assertEquals(1, sf.getBegin());
1599 assertEquals(6, sf.getEnd());
1603 * Tests for transferring features between mapped sequences
1605 @Test(groups = { "Functional" })
1606 public void testTransferFeatures_withSelect()
1608 SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt");
1609 SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
1611 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1612 new int[] { 1, 6 }, 1, 1);
1614 // [5, 11] maps to [2, 5]
1615 dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f,
1617 // [4, 12] maps to [1, 6]
1618 dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f,
1620 // [12, 12] maps to [6, 6]
1621 dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12,
1624 // "type5" is the 'select this type' argument
1625 AlignmentUtils.transferFeatures(dna, cds, map, "type5");
1626 List<SequenceFeature> sfs = cds.getSequenceFeatures();
1627 assertEquals(1, sfs.size());
1629 SequenceFeature sf = sfs.get(0);
1630 assertEquals("type5", sf.getType());
1631 assertEquals(1, sf.getBegin());
1632 assertEquals(6, sf.getEnd());
1636 * Test the method that extracts the cds-only part of a dna alignment, for the
1637 * case where the cds should be aligned to match its nucleotide sequence.
1639 @Test(groups = { "Functional" })
1640 public void testMakeCdsAlignment_alternativeTranscripts()
1642 SequenceI dna1 = new Sequence("dna1", "aaaGGGCC-----CTTTaaaGGG");
1643 // alternative transcript of same dna skips CCC codon
1644 SequenceI dna2 = new Sequence("dna2", "aaaGGGCC-----cttTaaaGGG");
1645 // dna3 has no mapping (protein product) so should be ignored here
1646 SequenceI dna3 = new Sequence("dna3", "aaaGGGCCCCCGGGcttTaaaGGG");
1647 SequenceI pep1 = new Sequence("pep1", "GPFG");
1648 SequenceI pep2 = new Sequence("pep2", "GPG");
1649 dna1.createDatasetSequence();
1650 dna2.createDatasetSequence();
1651 dna3.createDatasetSequence();
1652 pep1.createDatasetSequence();
1653 pep2.createDatasetSequence();
1655 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
1656 dna.setDataset(null);
1658 MapList map = new MapList(new int[] { 4, 12, 16, 18 },
1659 new int[] { 1, 4 }, 3, 1);
1660 AlignedCodonFrame acf = new AlignedCodonFrame();
1661 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
1662 dna.addCodonFrame(acf);
1663 map = new MapList(new int[] { 4, 8, 12, 12, 16, 18 },
1664 new int[] { 1, 3 }, 3, 1);
1665 acf = new AlignedCodonFrame();
1666 acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
1667 dna.addCodonFrame(acf);
1669 AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
1670 dna1, dna2, dna3 }, dna.getDataset(), null);
1671 List<SequenceI> cdsSeqs = cds.getSequences();
1672 assertEquals(2, cdsSeqs.size());
1673 assertEquals("GGGCCCTTTGGG", cdsSeqs.get(0).getSequenceAsString());
1674 assertEquals("GGGCCTGGG", cdsSeqs.get(1).getSequenceAsString());
1677 * verify shared, extended alignment dataset
1679 assertSame(dna.getDataset(), cds.getDataset());
1680 assertTrue(dna.getDataset().getSequences()
1681 .contains(cdsSeqs.get(0).getDatasetSequence()));
1682 assertTrue(dna.getDataset().getSequences()
1683 .contains(cdsSeqs.get(1).getDatasetSequence()));
1686 * Verify 6 mappings: dna1 to cds1, cds1 to pep1, dna1 to pep1
1687 * and the same for dna2/cds2/pep2
1689 List<AlignedCodonFrame> mappings = cds.getCodonFrames();
1690 assertEquals(6, mappings.size());
1693 * 2 mappings involve pep1
1695 List<AlignedCodonFrame> pep1Mappings = MappingUtils
1696 .findMappingsForSequence(pep1, mappings);
1697 assertEquals(2, pep1Mappings.size());
1700 * Get mapping of pep1 to cds1 and verify it
1701 * maps GPFG to 1-3,4-6,7-9,10-12
1703 List<AlignedCodonFrame> pep1CdsMappings = MappingUtils
1704 .findMappingsForSequence(cds.getSequenceAt(0), pep1Mappings);
1705 assertEquals(1, pep1CdsMappings.size());
1706 SearchResultsI sr = MappingUtils.buildSearchResults(pep1, 1,
1708 assertEquals(1, sr.getResults().size());
1709 SearchResultMatchI m = sr.getResults().get(0);
1710 assertEquals(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
1711 assertEquals(1, m.getStart());
1712 assertEquals(3, m.getEnd());
1713 sr = MappingUtils.buildSearchResults(pep1, 2, pep1CdsMappings);
1714 m = sr.getResults().get(0);
1715 assertEquals(4, m.getStart());
1716 assertEquals(6, m.getEnd());
1717 sr = MappingUtils.buildSearchResults(pep1, 3, pep1CdsMappings);
1718 m = sr.getResults().get(0);
1719 assertEquals(7, m.getStart());
1720 assertEquals(9, m.getEnd());
1721 sr = MappingUtils.buildSearchResults(pep1, 4, pep1CdsMappings);
1722 m = sr.getResults().get(0);
1723 assertEquals(10, m.getStart());
1724 assertEquals(12, m.getEnd());
1727 * Get mapping of pep2 to cds2 and verify it
1728 * maps GPG in pep2 to 1-3,4-6,7-9 in second CDS sequence
1730 List<AlignedCodonFrame> pep2Mappings = MappingUtils
1731 .findMappingsForSequence(pep2, mappings);
1732 assertEquals(2, pep2Mappings.size());
1733 List<AlignedCodonFrame> pep2CdsMappings = MappingUtils
1734 .findMappingsForSequence(cds.getSequenceAt(1), pep2Mappings);
1735 assertEquals(1, pep2CdsMappings.size());
1736 sr = MappingUtils.buildSearchResults(pep2, 1, pep2CdsMappings);
1737 assertEquals(1, sr.getResults().size());
1738 m = sr.getResults().get(0);
1739 assertEquals(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
1740 assertEquals(1, m.getStart());
1741 assertEquals(3, m.getEnd());
1742 sr = MappingUtils.buildSearchResults(pep2, 2, pep2CdsMappings);
1743 m = sr.getResults().get(0);
1744 assertEquals(4, m.getStart());
1745 assertEquals(6, m.getEnd());
1746 sr = MappingUtils.buildSearchResults(pep2, 3, pep2CdsMappings);
1747 m = sr.getResults().get(0);
1748 assertEquals(7, m.getStart());
1749 assertEquals(9, m.getEnd());
1753 * Test the method that realigns protein to match mapped codon alignment.
1755 @Test(groups = { "Functional" })
1756 public void testAlignProteinAsDna_incompleteStartCodon()
1758 // seq1: incomplete start codon (not mapped), then [3, 11]
1759 SequenceI dna1 = new Sequence("Seq1", "ccAAA-TTT-GGG-");
1760 // seq2 codons are [4, 5], [8, 11]
1761 SequenceI dna2 = new Sequence("Seq2", "ccaAA-ttT-GGG-");
1762 // seq3 incomplete start codon at 'tt'
1763 SequenceI dna3 = new Sequence("Seq3", "ccaaa-ttt-GGG-");
1764 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
1765 dna.setDataset(null);
1767 // prot1 has 'X' for incomplete start codon (not mapped)
1768 SequenceI prot1 = new Sequence("Seq1", "XKFG"); // X for incomplete start
1769 SequenceI prot2 = new Sequence("Seq2", "NG");
1770 SequenceI prot3 = new Sequence("Seq3", "XG"); // X for incomplete start
1771 AlignmentI protein = new Alignment(new SequenceI[] { prot1, prot2,
1773 protein.setDataset(null);
1775 // map dna1 [3, 11] to prot1 [2, 4] KFG
1776 MapList map = new MapList(new int[] { 3, 11 }, new int[] { 2, 4 }, 3, 1);
1777 AlignedCodonFrame acf = new AlignedCodonFrame();
1778 acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
1780 // map dna2 [4, 5] [8, 11] to prot2 [1, 2] NG
1781 map = new MapList(new int[] { 4, 5, 8, 11 }, new int[] { 1, 2 }, 3, 1);
1782 acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map);
1784 // map dna3 [9, 11] to prot3 [2, 2] G
1785 map = new MapList(new int[] { 9, 11 }, new int[] { 2, 2 }, 3, 1);
1786 acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map);
1788 ArrayList<AlignedCodonFrame> acfs = new ArrayList<>();
1790 protein.setCodonFrames(acfs);
1793 * verify X is included in the aligned proteins, and placed just
1794 * before the first mapped residue
1795 * CCT is between CCC and TTT
1797 AlignmentUtils.alignProteinAsDna(protein, dna);
1798 assertEquals("XK-FG", prot1.getSequenceAsString());
1799 assertEquals("--N-G", prot2.getSequenceAsString());
1800 assertEquals("---XG", prot3.getSequenceAsString());
1804 * Tests for the method that maps the subset of a dna sequence that has CDS
1805 * (or subtype) feature - case where the start codon is incomplete.
1807 @Test(groups = "Functional")
1808 public void testFindCdsPositions_fivePrimeIncomplete()
1810 SequenceI dnaSeq = new Sequence("dna", "aaagGGCCCaaaTTTttt");
1811 dnaSeq.createDatasetSequence();
1812 SequenceI ds = dnaSeq.getDatasetSequence();
1814 // CDS for dna 5-6 (incomplete codon), 7-9
1815 SequenceFeature sf = new SequenceFeature("CDS", "", 5, 9, 0f, null);
1816 sf.setPhase("2"); // skip 2 bases to start of next codon
1817 ds.addSequenceFeature(sf);
1818 // CDS for dna 13-15
1819 sf = new SequenceFeature("CDS_predicted", "", 13, 15, 0f, null);
1820 ds.addSequenceFeature(sf);
1822 List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
1825 * check the mapping starts with the first complete codon
1827 assertEquals(6, MappingUtils.getLength(ranges));
1828 assertEquals(2, ranges.size());
1829 assertEquals(7, ranges.get(0)[0]);
1830 assertEquals(9, ranges.get(0)[1]);
1831 assertEquals(13, ranges.get(1)[0]);
1832 assertEquals(15, ranges.get(1)[1]);
1836 * Tests for the method that maps the subset of a dna sequence that has CDS
1837 * (or subtype) feature.
1839 @Test(groups = "Functional")
1840 public void testFindCdsPositions()
1842 SequenceI dnaSeq = new Sequence("dna", "aaaGGGcccAAATTTttt");
1843 dnaSeq.createDatasetSequence();
1844 SequenceI ds = dnaSeq.getDatasetSequence();
1846 // CDS for dna 10-12
1847 SequenceFeature sf = new SequenceFeature("CDS_predicted", "", 10, 12,
1850 ds.addSequenceFeature(sf);
1852 sf = new SequenceFeature("CDS", "", 4, 6, 0f, null);
1854 ds.addSequenceFeature(sf);
1855 // exon feature should be ignored here
1856 sf = new SequenceFeature("exon", "", 7, 9, 0f, null);
1857 ds.addSequenceFeature(sf);
1859 List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
1861 * verify ranges { [4-6], [12-10] }
1862 * note CDS ranges are ordered ascending even if the CDS
1865 assertEquals(6, MappingUtils.getLength(ranges));
1866 assertEquals(2, ranges.size());
1867 assertEquals(4, ranges.get(0)[0]);
1868 assertEquals(6, ranges.get(0)[1]);
1869 assertEquals(10, ranges.get(1)[0]);
1870 assertEquals(12, ranges.get(1)[1]);
1874 * Tests for the method that maps the subset of a dna sequence that has CDS
1875 * (or subtype) feature, with CDS strand = '-' (reverse)
1877 // test turned off as currently findCdsPositions is not strand-dependent
1878 // left in case it comes around again...
1879 @Test(groups = "Functional", enabled = false)
1880 public void testFindCdsPositions_reverseStrand()
1882 SequenceI dnaSeq = new Sequence("dna", "aaaGGGcccAAATTTttt");
1883 dnaSeq.createDatasetSequence();
1884 SequenceI ds = dnaSeq.getDatasetSequence();
1887 SequenceFeature sf = new SequenceFeature("CDS", "", 4, 6, 0f, null);
1889 ds.addSequenceFeature(sf);
1890 // exon feature should be ignored here
1891 sf = new SequenceFeature("exon", "", 7, 9, 0f, null);
1892 ds.addSequenceFeature(sf);
1893 // CDS for dna 10-12
1894 sf = new SequenceFeature("CDS_predicted", "", 10, 12, 0f, null);
1896 ds.addSequenceFeature(sf);
1898 List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
1900 * verify ranges { [12-10], [6-4] }
1902 assertEquals(6, MappingUtils.getLength(ranges));
1903 assertEquals(2, ranges.size());
1904 assertEquals(12, ranges.get(0)[0]);
1905 assertEquals(10, ranges.get(0)[1]);
1906 assertEquals(6, ranges.get(1)[0]);
1907 assertEquals(4, ranges.get(1)[1]);
1911 * Tests for the method that maps the subset of a dna sequence that has CDS
1912 * (or subtype) feature - reverse strand case where the start codon is
1915 @Test(groups = "Functional", enabled = false)
1916 // test turned off as currently findCdsPositions is not strand-dependent
1917 // left in case it comes around again...
1918 public void testFindCdsPositions_reverseStrandThreePrimeIncomplete()
1920 SequenceI dnaSeq = new Sequence("dna", "aaagGGCCCaaaTTTttt");
1921 dnaSeq.createDatasetSequence();
1922 SequenceI ds = dnaSeq.getDatasetSequence();
1925 SequenceFeature sf = new SequenceFeature("CDS", "", 5, 9, 0f, null);
1927 ds.addSequenceFeature(sf);
1928 // CDS for dna 13-15
1929 sf = new SequenceFeature("CDS_predicted", "", 13, 15, 0f, null);
1931 sf.setPhase("2"); // skip 2 bases to start of next codon
1932 ds.addSequenceFeature(sf);
1934 List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
1937 * check the mapping starts with the first complete codon
1938 * expect ranges [13, 13], [9, 5]
1940 assertEquals(6, MappingUtils.getLength(ranges));
1941 assertEquals(2, ranges.size());
1942 assertEquals(13, ranges.get(0)[0]);
1943 assertEquals(13, ranges.get(0)[1]);
1944 assertEquals(9, ranges.get(1)[0]);
1945 assertEquals(5, ranges.get(1)[1]);
1948 @Test(groups = "Functional")
1949 public void testAlignAs_alternateTranscriptsUngapped()
1951 SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
1952 SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
1953 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
1954 ((Alignment) dna).createDatasetAlignment();
1955 SequenceI cds1 = new Sequence("cds1", "GGGTTT");
1956 SequenceI cds2 = new Sequence("cds2", "CCCAAA");
1957 AlignmentI cds = new Alignment(new SequenceI[] { cds1, cds2 });
1958 ((Alignment) cds).createDatasetAlignment();
1960 AlignedCodonFrame acf = new AlignedCodonFrame();
1961 MapList map = new MapList(new int[] { 4, 9 }, new int[] { 1, 6 }, 1, 1);
1962 acf.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(), map);
1963 map = new MapList(new int[] { 1, 3, 10, 12 }, new int[] { 1, 6 }, 1, 1);
1964 acf.addMap(dna2.getDatasetSequence(), cds2.getDatasetSequence(), map);
1967 * verify CDS alignment is as:
1968 * cccGGGTTTaaa (cdna)
1969 * CCCgggtttAAA (cdna)
1971 * ---GGGTTT--- (cds)
1972 * CCC------AAA (cds)
1974 dna.addCodonFrame(acf);
1975 AlignmentUtils.alignAs(cds, dna);
1976 assertEquals("---GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
1977 assertEquals("CCC------AAA", cds.getSequenceAt(1).getSequenceAsString());
1980 @Test(groups = { "Functional" })
1981 public void testAddMappedPositions()
1983 SequenceI from = new Sequence("dna", "ggAA-ATcc-TT-g");
1984 SequenceI seq1 = new Sequence("cds", "AAATTT");
1985 from.createDatasetSequence();
1986 seq1.createDatasetSequence();
1987 Mapping mapping = new Mapping(seq1, new MapList(
1988 new int[] { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1));
1989 Map<Integer, Map<SequenceI, Character>> map = new TreeMap<>();
1990 AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
1993 * verify map has seq1 residues in columns 3,4,6,7,11,12
1995 assertEquals(6, map.size());
1996 assertEquals('A', map.get(3).get(seq1).charValue());
1997 assertEquals('A', map.get(4).get(seq1).charValue());
1998 assertEquals('A', map.get(6).get(seq1).charValue());
1999 assertEquals('T', map.get(7).get(seq1).charValue());
2000 assertEquals('T', map.get(11).get(seq1).charValue());
2001 assertEquals('T', map.get(12).get(seq1).charValue());
2009 * Test case where the mapping 'from' range includes a stop codon which is
2010 * absent in the 'to' range
2012 @Test(groups = { "Functional" })
2013 public void testAddMappedPositions_withStopCodon()
2015 SequenceI from = new Sequence("dna", "ggAA-ATcc-TT-g");
2016 SequenceI seq1 = new Sequence("cds", "AAATTT");
2017 from.createDatasetSequence();
2018 seq1.createDatasetSequence();
2019 Mapping mapping = new Mapping(seq1, new MapList(
2020 new int[] { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1));
2021 Map<Integer, Map<SequenceI, Character>> map = new TreeMap<>();
2022 AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
2025 * verify map has seq1 residues in columns 3,4,6,7,11,12
2027 assertEquals(6, map.size());
2028 assertEquals('A', map.get(3).get(seq1).charValue());
2029 assertEquals('A', map.get(4).get(seq1).charValue());
2030 assertEquals('A', map.get(6).get(seq1).charValue());
2031 assertEquals('T', map.get(7).get(seq1).charValue());
2032 assertEquals('T', map.get(11).get(seq1).charValue());
2033 assertEquals('T', map.get(12).get(seq1).charValue());
2037 * Test for the case where the products for which we want CDS are specified.
2038 * This is to represent the case where EMBL has CDS mappings to both Uniprot
2039 * and EMBLCDSPROTEIN. makeCdsAlignment() should only return the mappings for
2040 * the protein sequences specified.
2042 @Test(groups = { "Functional" })
2043 public void testMakeCdsAlignment_filterProducts()
2045 SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
2046 SequenceI dna2 = new Sequence("dna2", "GGGcccTTTaaaCCC");
2047 SequenceI pep1 = new Sequence("Uniprot|pep1", "GF");
2048 SequenceI pep2 = new Sequence("Uniprot|pep2", "GFP");
2049 SequenceI pep3 = new Sequence("EMBL|pep3", "GF");
2050 SequenceI pep4 = new Sequence("EMBL|pep4", "GFP");
2051 dna1.createDatasetSequence();
2052 dna2.createDatasetSequence();
2053 pep1.createDatasetSequence();
2054 pep2.createDatasetSequence();
2055 pep3.createDatasetSequence();
2056 pep4.createDatasetSequence();
2057 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
2058 dna.setDataset(null);
2059 AlignmentI emblPeptides = new Alignment(new SequenceI[] { pep3, pep4 });
2060 emblPeptides.setDataset(null);
2062 AlignedCodonFrame acf = new AlignedCodonFrame();
2063 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
2064 new int[] { 1, 2 }, 3, 1);
2065 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
2066 acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map);
2067 dna.addCodonFrame(acf);
2069 acf = new AlignedCodonFrame();
2070 map = new MapList(new int[] { 1, 3, 7, 9, 13, 15 }, new int[] { 1, 3 },
2072 acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
2073 acf.addMap(dna2.getDatasetSequence(), pep4.getDatasetSequence(), map);
2074 dna.addCodonFrame(acf);
2077 * execute method under test to find CDS for EMBL peptides only
2079 AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
2080 dna1, dna2 }, dna.getDataset(), emblPeptides.getSequencesArray());
2082 assertEquals(2, cds.getSequences().size());
2083 assertEquals("GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
2084 assertEquals("GGGTTTCCC", cds.getSequenceAt(1).getSequenceAsString());
2087 * verify shared, extended alignment dataset
2089 assertSame(dna.getDataset(), cds.getDataset());
2090 assertTrue(dna.getDataset().getSequences()
2091 .contains(cds.getSequenceAt(0).getDatasetSequence()));
2092 assertTrue(dna.getDataset().getSequences()
2093 .contains(cds.getSequenceAt(1).getDatasetSequence()));
2096 * Verify mappings from CDS to peptide, cDNA to CDS, and cDNA to peptide
2097 * the mappings are on the shared alignment dataset
2099 List<AlignedCodonFrame> cdsMappings = cds.getDataset().getCodonFrames();
2101 * 6 mappings, 2*(DNA->CDS), 2*(DNA->Pep), 2*(CDS->Pep)
2103 assertEquals(6, cdsMappings.size());
2106 * verify that mapping sets for dna and cds alignments are different
2107 * [not current behaviour - all mappings are on the alignment dataset]
2109 // select -> subselect type to test.
2110 // Assert.assertNotSame(dna.getCodonFrames(), cds.getCodonFrames());
2111 // assertEquals(4, dna.getCodonFrames().size());
2112 // assertEquals(4, cds.getCodonFrames().size());
2115 * Two mappings involve pep3 (dna to pep3, cds to pep3)
2116 * Mapping from pep3 to GGGTTT in first new exon sequence
2118 List<AlignedCodonFrame> pep3Mappings = MappingUtils
2119 .findMappingsForSequence(pep3, cdsMappings);
2120 assertEquals(2, pep3Mappings.size());
2121 List<AlignedCodonFrame> mappings = MappingUtils
2122 .findMappingsForSequence(cds.getSequenceAt(0), pep3Mappings);
2123 assertEquals(1, mappings.size());
2126 SearchResultsI sr = MappingUtils.buildSearchResults(pep3, 1, mappings);
2127 assertEquals(1, sr.getResults().size());
2128 SearchResultMatchI m = sr.getResults().get(0);
2129 assertSame(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
2130 assertEquals(1, m.getStart());
2131 assertEquals(3, m.getEnd());
2133 sr = MappingUtils.buildSearchResults(pep3, 2, mappings);
2134 m = sr.getResults().get(0);
2135 assertSame(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
2136 assertEquals(4, m.getStart());
2137 assertEquals(6, m.getEnd());
2140 * Two mappings involve pep4 (dna to pep4, cds to pep4)
2141 * Verify mapping from pep4 to GGGTTTCCC in second new exon sequence
2143 List<AlignedCodonFrame> pep4Mappings = MappingUtils
2144 .findMappingsForSequence(pep4, cdsMappings);
2145 assertEquals(2, pep4Mappings.size());
2146 mappings = MappingUtils.findMappingsForSequence(cds.getSequenceAt(1),
2148 assertEquals(1, mappings.size());
2150 sr = MappingUtils.buildSearchResults(pep4, 1, mappings);
2151 assertEquals(1, sr.getResults().size());
2152 m = sr.getResults().get(0);
2153 assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
2154 assertEquals(1, m.getStart());
2155 assertEquals(3, m.getEnd());
2157 sr = MappingUtils.buildSearchResults(pep4, 2, mappings);
2158 m = sr.getResults().get(0);
2159 assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
2160 assertEquals(4, m.getStart());
2161 assertEquals(6, m.getEnd());
2163 sr = MappingUtils.buildSearchResults(pep4, 3, mappings);
2164 m = sr.getResults().get(0);
2165 assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
2166 assertEquals(7, m.getStart());
2167 assertEquals(9, m.getEnd());
2171 * Test the method that just copies aligned sequences, provided all sequences
2172 * to be aligned share the aligned sequence's dataset
2174 @Test(groups = "Functional")
2175 public void testAlignAsSameSequences()
2177 SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
2178 SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
2179 AlignmentI al1 = new Alignment(new SequenceI[] { dna1, dna2 });
2180 ((Alignment) al1).createDatasetAlignment();
2182 SequenceI dna3 = new Sequence(dna1);
2183 SequenceI dna4 = new Sequence(dna2);
2184 assertSame(dna3.getDatasetSequence(), dna1.getDatasetSequence());
2185 assertSame(dna4.getDatasetSequence(), dna2.getDatasetSequence());
2186 String seq1 = "-cc-GG-GT-TT--aaa";
2187 dna3.setSequence(seq1);
2188 String seq2 = "C--C-Cgg--gtt-tAA-A-";
2189 dna4.setSequence(seq2);
2190 AlignmentI al2 = new Alignment(new SequenceI[] { dna3, dna4 });
2191 ((Alignment) al2).createDatasetAlignment();
2194 * alignment removes gapped columns (two internal, two trailing)
2196 assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
2197 String aligned1 = "-cc-GG-GTTT-aaa";
2198 assertEquals(aligned1,
2199 al1.getSequenceAt(0).getSequenceAsString());
2200 String aligned2 = "C--C-Cgg-gtttAAA";
2201 assertEquals(aligned2,
2202 al1.getSequenceAt(1).getSequenceAsString());
2205 * add another sequence to 'aligned' - should still succeed, since
2206 * unaligned sequences still share a dataset with aligned sequences
2208 SequenceI dna5 = new Sequence("dna5", "CCCgggtttAAA");
2209 dna5.createDatasetSequence();
2210 al2.addSequence(dna5);
2211 assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
2212 assertEquals(aligned1, al1.getSequenceAt(0).getSequenceAsString());
2213 assertEquals(aligned2, al1.getSequenceAt(1).getSequenceAsString());
2216 * add another sequence to 'unaligned' - should fail, since now not
2217 * all unaligned sequences share a dataset with aligned sequences
2219 SequenceI dna6 = new Sequence("dna6", "CCCgggtttAAA");
2220 dna6.createDatasetSequence();
2221 al1.addSequence(dna6);
2222 // JAL-2110 JBP Comment: what's the use case for this behaviour ?
2223 assertFalse(AlignmentUtils.alignAsSameSequences(al1, al2));
2226 @Test(groups = "Functional")
2227 public void testAlignAsSameSequencesMultipleSubSeq()
2229 SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
2230 SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
2231 SequenceI as1 = dna1.deriveSequence(); // cccGGGTTTaaa/1-12
2232 SequenceI as2 = dna1.deriveSequence().getSubSequence(3, 7); // GGGT/4-7
2233 SequenceI as3 = dna2.deriveSequence(); // CCCgggtttAAA/1-12
2234 as1.insertCharAt(6, 5, '-');
2235 assertEquals("cccGGG-----TTTaaa", as1.getSequenceAsString());
2236 as2.insertCharAt(6, 5, '-');
2237 assertEquals("GGGT-----", as2.getSequenceAsString());
2238 as3.insertCharAt(3, 5, '-');
2239 assertEquals("CCC-----gggtttAAA", as3.getSequenceAsString());
2240 AlignmentI aligned = new Alignment(new SequenceI[] { as1, as2, as3 });
2242 // why do we need to cast this still ?
2243 ((Alignment) aligned).createDatasetAlignment();
2244 SequenceI uas1 = dna1.deriveSequence();
2245 SequenceI uas2 = dna1.deriveSequence().getSubSequence(3, 7);
2246 SequenceI uas3 = dna2.deriveSequence();
2247 AlignmentI tobealigned = new Alignment(new SequenceI[] { uas1, uas2,
2249 ((Alignment) tobealigned).createDatasetAlignment();
2252 * alignAs lines up dataset sequences and removes empty columns (two)
2254 assertTrue(AlignmentUtils.alignAsSameSequences(tobealigned, aligned));
2255 assertEquals("cccGGG---TTTaaa", uas1.getSequenceAsString());
2256 assertEquals("GGGT", uas2.getSequenceAsString());
2257 assertEquals("CCC---gggtttAAA", uas3.getSequenceAsString());
2260 @Test(groups = { "Functional" })
2261 public void testTransferGeneLoci()
2263 SequenceI from = new Sequence("transcript",
2264 "aaacccgggTTTAAACCCGGGtttaaacccgggttt");
2265 SequenceI to = new Sequence("CDS", "TTTAAACCCGGG");
2266 MapList map = new MapList(new int[] { 1, 12 }, new int[] { 10, 21 }, 1,
2270 * first with nothing to transfer
2272 AlignmentUtils.transferGeneLoci(from, map, to);
2273 assertNull(to.getGeneLoci());
2276 * next with gene loci set on 'from' sequence
2278 int[] exons = new int[] { 100, 105, 155, 164, 210, 229 };
2279 MapList geneMap = new MapList(new int[] { 1, 36 }, exons, 1, 1);
2280 from.setGeneLoci("human", "GRCh38", "7", geneMap);
2281 AlignmentUtils.transferGeneLoci(from, map, to);
2283 GeneLociI toLoci = to.getGeneLoci();
2284 assertNotNull(toLoci);
2285 // DBRefEntry constructor upper-cases 'source'
2286 assertEquals("HUMAN", toLoci.getSpeciesId());
2287 assertEquals("GRCh38", toLoci.getAssemblyId());
2288 assertEquals("7", toLoci.getChromosomeId());
2291 * transcript 'exons' are 1-6, 7-16, 17-36
2292 * CDS 1:12 is transcript 10-21
2293 * transcript 'CDS' is 10-16, 17-21
2294 * which is 'gene' 158-164, 210-214
2296 MapList toMap = toLoci.getMapping();
2297 assertEquals(1, toMap.getFromRanges().size());
2298 assertEquals(2, toMap.getFromRanges().get(0).length);
2299 assertEquals(1, toMap.getFromRanges().get(0)[0]);
2300 assertEquals(12, toMap.getFromRanges().get(0)[1]);
2301 assertEquals(2, toMap.getToRanges().size());
2302 assertEquals(2, toMap.getToRanges().get(0).length);
2303 assertEquals(158, toMap.getToRanges().get(0)[0]);
2304 assertEquals(164, toMap.getToRanges().get(0)[1]);
2305 assertEquals(210, toMap.getToRanges().get(1)[0]);
2306 assertEquals(214, toMap.getToRanges().get(1)[1]);
2307 // or summarised as (but toString might change in future):
2308 assertEquals("[ [1, 12] ] 1:1 to [ [158, 164] [210, 214] ]",
2312 * an existing value is not overridden
2314 geneMap = new MapList(new int[] { 1, 36 }, new int[] { 36, 1 }, 1, 1);
2315 from.setGeneLoci("inhuman", "GRCh37", "6", geneMap);
2316 AlignmentUtils.transferGeneLoci(from, map, to);
2317 assertEquals("GRCh38", toLoci.getAssemblyId());
2318 assertEquals("7", toLoci.getChromosomeId());
2319 toMap = toLoci.getMapping();
2320 assertEquals("[ [1, 12] ] 1:1 to [ [158, 164] [210, 214] ]",
2325 * Tests for the method that maps nucleotide to protein based on CDS features
2327 @Test(groups = "Functional")
2328 public void testMapCdsToProtein()
2330 SequenceI peptide = new Sequence("pep", "KLQ");
2333 * Case 1: CDS 3 times length of peptide
2334 * NB method only checks lengths match, not translation
2336 SequenceI dna = new Sequence("dna", "AACGacgtCTCCT");
2337 dna.createDatasetSequence();
2338 dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
2339 dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 13, null));
2340 MapList ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2341 assertEquals(3, ml.getFromRatio());
2342 assertEquals(1, ml.getToRatio());
2343 assertEquals("[[1, 3]]",
2344 Arrays.deepToString(ml.getToRanges().toArray()));
2345 assertEquals("[[1, 4], [9, 13]]",
2346 Arrays.deepToString(ml.getFromRanges().toArray()));
2349 * Case 2: CDS 3 times length of peptide + stop codon
2350 * (note code does not currently check trailing codon is a stop codon)
2352 dna = new Sequence("dna", "AACGacgtCTCCTCCC");
2353 dna.createDatasetSequence();
2354 dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
2355 dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 16, null));
2356 ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2357 assertEquals(3, ml.getFromRatio());
2358 assertEquals(1, ml.getToRatio());
2359 assertEquals("[[1, 3]]",
2360 Arrays.deepToString(ml.getToRanges().toArray()));
2361 assertEquals("[[1, 4], [9, 13]]",
2362 Arrays.deepToString(ml.getFromRanges().toArray()));
2365 * Case 3: CDS longer than 3 * peptide + stop codon - no mapping is made
2367 dna = new Sequence("dna", "AACGacgtCTCCTTGATCA");
2368 dna.createDatasetSequence();
2369 dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
2370 dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 19, null));
2371 ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2375 * Case 4: CDS shorter than 3 * peptide - no mapping is made
2377 dna = new Sequence("dna", "AACGacgtCTCC");
2378 dna.createDatasetSequence();
2379 dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
2380 dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 12, null));
2381 ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2385 * Case 5: CDS 3 times length of peptide + part codon - mapping is truncated
2387 dna = new Sequence("dna", "AACGacgtCTCCTTG");
2388 dna.createDatasetSequence();
2389 dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
2390 dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 15, null));
2391 ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2392 assertEquals(3, ml.getFromRatio());
2393 assertEquals(1, ml.getToRatio());
2394 assertEquals("[[1, 3]]",
2395 Arrays.deepToString(ml.getToRanges().toArray()));
2396 assertEquals("[[1, 4], [9, 13]]",
2397 Arrays.deepToString(ml.getFromRanges().toArray()));
2400 * Case 6: incomplete start codon corresponding to X in peptide
2402 dna = new Sequence("dna", "ACGacgtCTCCTTGG");
2403 dna.createDatasetSequence();
2404 SequenceFeature sf = new SequenceFeature("CDS", "", 1, 3, null);
2405 sf.setPhase("2"); // skip 2 positions (AC) to start of next codon (GCT)
2406 dna.addSequenceFeature(sf);
2407 dna.addSequenceFeature(new SequenceFeature("CDS", "", 8, 15, null));
2408 peptide = new Sequence("pep", "XLQ");
2409 ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2410 assertEquals("[[2, 3]]",
2411 Arrays.deepToString(ml.getToRanges().toArray()));
2412 assertEquals("[[3, 3], [8, 12]]",
2413 Arrays.deepToString(ml.getFromRanges().toArray()));
2417 * Tests for the method that locates the CDS sequence that has a mapping to
2418 * the given protein. That is, given a transcript-to-peptide mapping, find the
2419 * cds-to-peptide mapping that relates to both, and return the CDS sequence.
2422 public void testFindCdsForProtein()
2424 List<AlignedCodonFrame> mappings = new ArrayList<>();
2425 AlignedCodonFrame acf1 = new AlignedCodonFrame();
2428 SequenceI dna1 = new Sequence("dna1", "cgatATcgGCTATCTATGacg");
2429 dna1.createDatasetSequence();
2431 // NB we currently exclude STOP codon from CDS sequences
2432 // the test would need to change if this changes in future
2433 SequenceI cds1 = new Sequence("cds1", "ATGCTATCT");
2434 cds1.createDatasetSequence();
2436 SequenceI pep1 = new Sequence("pep1", "MLS");
2437 pep1.createDatasetSequence();
2438 List<AlignedCodonFrame> seqMappings = new ArrayList<>();
2439 MapList mapList = new MapList(
2441 { 5, 6, 9, 15 }, new int[] { 1, 3 }, 3, 1);
2442 Mapping dnaToPeptide = new Mapping(pep1.getDatasetSequence(), mapList);
2444 // add dna to peptide mapping
2445 seqMappings.add(acf1);
2446 acf1.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
2450 * first case - no dna-to-CDS mapping exists - search fails
2452 SequenceI seq = AlignmentUtils.findCdsForProtein(mappings, dna1,
2453 seqMappings, dnaToPeptide);
2457 * second case - CDS-to-peptide mapping exists but no dna-to-CDS
2460 // todo this test fails if the mapping is added to acf1, not acf2
2461 // need to tidy up use of lists of mappings in AlignedCodonFrame
2462 AlignedCodonFrame acf2 = new AlignedCodonFrame();
2464 MapList cdsToPeptideMapping = new MapList(new int[]
2465 { 1, 9 }, new int[] { 1, 3 }, 3, 1);
2466 acf2.addMap(cds1.getDatasetSequence(), pep1.getDatasetSequence(),
2467 cdsToPeptideMapping);
2468 assertNull(AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
2472 * third case - add dna-to-CDS mapping - CDS is now found!
2474 MapList dnaToCdsMapping = new MapList(new int[] { 5, 6, 9, 15 },
2477 acf1.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(),
2479 seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
2481 assertSame(seq, cds1.getDatasetSequence());
2485 * Tests for the method that locates the CDS sequence that has a mapping to
2486 * the given protein. That is, given a transcript-to-peptide mapping, find the
2487 * cds-to-peptide mapping that relates to both, and return the CDS sequence.
2488 * This test is for the case where transcript and CDS are the same length.
2491 public void testFindCdsForProtein_noUTR()
2493 List<AlignedCodonFrame> mappings = new ArrayList<>();
2494 AlignedCodonFrame acf1 = new AlignedCodonFrame();
2497 SequenceI dna1 = new Sequence("dna1", "ATGCTATCTTAA");
2498 dna1.createDatasetSequence();
2500 // NB we currently exclude STOP codon from CDS sequences
2501 // the test would need to change if this changes in future
2502 SequenceI cds1 = new Sequence("cds1", "ATGCTATCT");
2503 cds1.createDatasetSequence();
2505 SequenceI pep1 = new Sequence("pep1", "MLS");
2506 pep1.createDatasetSequence();
2507 List<AlignedCodonFrame> seqMappings = new ArrayList<>();
2508 MapList mapList = new MapList(
2510 { 1, 9 }, new int[] { 1, 3 }, 3, 1);
2511 Mapping dnaToPeptide = new Mapping(pep1.getDatasetSequence(), mapList);
2513 // add dna to peptide mapping
2514 seqMappings.add(acf1);
2515 acf1.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
2519 * first case - transcript lacks CDS features - it appears to be
2520 * the CDS sequence and is returned
2522 SequenceI seq = AlignmentUtils.findCdsForProtein(mappings, dna1,
2523 seqMappings, dnaToPeptide);
2524 assertSame(seq, dna1.getDatasetSequence());
2527 * second case - transcript has CDS feature - this means it is
2528 * not returned as a match for CDS (CDS sequences don't have CDS features)
2530 dna1.addSequenceFeature(
2531 new SequenceFeature(SequenceOntologyI.CDS, "cds", 1, 12, null));
2532 seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
2537 * third case - CDS-to-peptide mapping exists but no dna-to-CDS
2540 // todo this test fails if the mapping is added to acf1, not acf2
2541 // need to tidy up use of lists of mappings in AlignedCodonFrame
2542 AlignedCodonFrame acf2 = new AlignedCodonFrame();
2544 MapList cdsToPeptideMapping = new MapList(new int[]
2545 { 1, 9 }, new int[] { 1, 3 }, 3, 1);
2546 acf2.addMap(cds1.getDatasetSequence(), pep1.getDatasetSequence(),
2547 cdsToPeptideMapping);
2548 assertNull(AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
2552 * fourth case - add dna-to-CDS mapping - CDS is now found!
2554 MapList dnaToCdsMapping = new MapList(new int[] { 1, 9 },
2557 acf1.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(),
2559 seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
2561 assertSame(seq, cds1.getDatasetSequence());