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.datamodel.AlignedCodonFrame;
31 import jalview.datamodel.Alignment;
32 import jalview.datamodel.AlignmentAnnotation;
33 import jalview.datamodel.AlignmentI;
34 import jalview.datamodel.Annotation;
35 import jalview.datamodel.DBRefEntry;
36 import jalview.datamodel.GeneLociI;
37 import jalview.datamodel.Mapping;
38 import jalview.datamodel.SearchResultMatchI;
39 import jalview.datamodel.SearchResultsI;
40 import jalview.datamodel.Sequence;
41 import jalview.datamodel.SequenceFeature;
42 import jalview.datamodel.SequenceI;
43 import jalview.gui.JvOptionPane;
44 import jalview.io.AppletFormatAdapter;
45 import jalview.io.DataSourceType;
46 import jalview.io.FileFormat;
47 import jalview.io.FileFormatI;
48 import jalview.io.FormatAdapter;
49 import jalview.io.gff.SequenceOntologyI;
50 import jalview.util.MapList;
51 import jalview.util.MappingUtils;
53 import java.io.IOException;
54 import java.util.ArrayList;
55 import java.util.Arrays;
56 import java.util.List;
58 import java.util.TreeMap;
60 import org.testng.annotations.BeforeClass;
61 import org.testng.annotations.Test;
63 public class AlignmentUtilsTests
65 private static Sequence ts = new Sequence("short",
66 "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
68 @BeforeClass(alwaysRun = true)
69 public void setUpJvOptionPane()
71 JvOptionPane.setInteractiveMode(false);
72 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
75 @Test(groups = { "Functional" })
76 public void testExpandContext()
78 AlignmentI al = new Alignment(new Sequence[] {});
79 for (int i = 4; i < 14; i += 2)
81 SequenceI s1 = ts.deriveSequence().getSubSequence(i, i + 7);
84 System.out.println(new AppletFormatAdapter().formatSequences(
87 for (int flnk = -1; flnk < 25; flnk++)
89 AlignmentI exp = AlignmentUtils.expandContext(al, flnk);
90 System.out.println("\nFlank size: " + flnk);
91 System.out.println(new AppletFormatAdapter().formatSequences(
92 FileFormat.Clustal, exp, true));
96 * Full expansion to complete sequences
98 for (SequenceI sq : exp.getSequences())
100 String ung = sq.getSequenceAsString().replaceAll("-+", "");
101 final String errorMsg = "Flanking sequence not the same as original dataset sequence.\n"
104 + sq.getDatasetSequence().getSequenceAsString();
105 assertTrue(errorMsg, ung.equalsIgnoreCase(sq.getDatasetSequence()
106 .getSequenceAsString()));
112 * Last sequence is fully expanded, others have leading gaps to match
114 assertTrue(exp.getSequenceAt(4).getSequenceAsString()
116 assertTrue(exp.getSequenceAt(3).getSequenceAsString()
117 .startsWith("--abc"));
118 assertTrue(exp.getSequenceAt(2).getSequenceAsString()
119 .startsWith("----abc"));
120 assertTrue(exp.getSequenceAt(1).getSequenceAsString()
121 .startsWith("------abc"));
122 assertTrue(exp.getSequenceAt(0).getSequenceAsString()
123 .startsWith("--------abc"));
129 * Test that annotations are correctly adjusted by expandContext
131 @Test(groups = { "Functional" })
132 public void testExpandContext_annotation()
134 AlignmentI al = new Alignment(new Sequence[] {});
135 SequenceI ds = new Sequence("Seq1", "ABCDEFGHI");
137 SequenceI seq1 = ds.deriveSequence().getSubSequence(3, 6);
138 al.addSequence(seq1);
141 * Annotate DEF with 4/5/6 respectively
143 Annotation[] anns = new Annotation[] { new Annotation(4),
144 new Annotation(5), new Annotation(6) };
145 AlignmentAnnotation ann = new AlignmentAnnotation("SS",
146 "secondary structure", anns);
147 seq1.addAlignmentAnnotation(ann);
150 * The annotations array should match aligned positions
152 assertEquals(3, ann.annotations.length);
153 assertEquals(4, ann.annotations[0].value, 0.001);
154 assertEquals(5, ann.annotations[1].value, 0.001);
155 assertEquals(6, ann.annotations[2].value, 0.001);
158 * Check annotation to sequence position mappings before expanding the
159 * sequence; these are set up in Sequence.addAlignmentAnnotation ->
160 * Annotation.setSequenceRef -> createSequenceMappings
162 assertNull(ann.getAnnotationForPosition(1));
163 assertNull(ann.getAnnotationForPosition(2));
164 assertNull(ann.getAnnotationForPosition(3));
165 assertEquals(4, ann.getAnnotationForPosition(4).value, 0.001);
166 assertEquals(5, ann.getAnnotationForPosition(5).value, 0.001);
167 assertEquals(6, ann.getAnnotationForPosition(6).value, 0.001);
168 assertNull(ann.getAnnotationForPosition(7));
169 assertNull(ann.getAnnotationForPosition(8));
170 assertNull(ann.getAnnotationForPosition(9));
173 * Expand the subsequence to the full sequence abcDEFghi
175 AlignmentI expanded = AlignmentUtils.expandContext(al, -1);
176 assertEquals("abcDEFghi", expanded.getSequenceAt(0)
177 .getSequenceAsString());
180 * Confirm the alignment and sequence have the same SS annotation,
181 * referencing the expanded sequence
183 ann = expanded.getSequenceAt(0).getAnnotation()[0];
184 assertSame(ann, expanded.getAlignmentAnnotation()[0]);
185 assertSame(expanded.getSequenceAt(0), ann.sequenceRef);
188 * The annotations array should have null values except for annotated
191 assertNull(ann.annotations[0]);
192 assertNull(ann.annotations[1]);
193 assertNull(ann.annotations[2]);
194 assertEquals(4, ann.annotations[3].value, 0.001);
195 assertEquals(5, ann.annotations[4].value, 0.001);
196 assertEquals(6, ann.annotations[5].value, 0.001);
197 assertNull(ann.annotations[6]);
198 assertNull(ann.annotations[7]);
199 assertNull(ann.annotations[8]);
202 * sequence position mappings should be unchanged
204 assertNull(ann.getAnnotationForPosition(1));
205 assertNull(ann.getAnnotationForPosition(2));
206 assertNull(ann.getAnnotationForPosition(3));
207 assertEquals(4, ann.getAnnotationForPosition(4).value, 0.001);
208 assertEquals(5, ann.getAnnotationForPosition(5).value, 0.001);
209 assertEquals(6, ann.getAnnotationForPosition(6).value, 0.001);
210 assertNull(ann.getAnnotationForPosition(7));
211 assertNull(ann.getAnnotationForPosition(8));
212 assertNull(ann.getAnnotationForPosition(9));
216 * Test method that returns a map of lists of sequences by sequence name.
218 * @throws IOException
220 @Test(groups = { "Functional" })
221 public void testGetSequencesByName() throws IOException
223 final String data = ">Seq1Name\nKQYL\n" + ">Seq2Name\nRFPW\n"
224 + ">Seq1Name\nABCD\n";
225 AlignmentI al = loadAlignment(data, FileFormat.Fasta);
226 Map<String, List<SequenceI>> map = AlignmentUtils
227 .getSequencesByName(al);
228 assertEquals(2, map.keySet().size());
229 assertEquals(2, map.get("Seq1Name").size());
230 assertEquals("KQYL", map.get("Seq1Name").get(0).getSequenceAsString());
231 assertEquals("ABCD", map.get("Seq1Name").get(1).getSequenceAsString());
232 assertEquals(1, map.get("Seq2Name").size());
233 assertEquals("RFPW", map.get("Seq2Name").get(0).getSequenceAsString());
237 * Helper method to load an alignment and ensure dataset sequences are set up.
243 * @throws IOException
245 protected AlignmentI loadAlignment(final String data, FileFormatI format)
248 AlignmentI a = new FormatAdapter().readFile(data,
249 DataSourceType.PASTE, format);
255 * Test mapping of protein to cDNA, for the case where we have no sequence
256 * cross-references, so mappings are made first-served 1-1 where sequences
259 * @throws IOException
261 @Test(groups = { "Functional" })
262 public void testMapProteinAlignmentToCdna_noXrefs() throws IOException
264 List<SequenceI> protseqs = new ArrayList<>();
265 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
266 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
267 protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
268 AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
269 protein.setDataset(null);
271 List<SequenceI> dnaseqs = new ArrayList<>();
272 dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR
273 dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAA")); // = EIQ
274 dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ
275 dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG")); // = EIQ
276 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
277 cdna.setDataset(null);
279 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
281 // 3 mappings made, each from 1 to 1 sequence
282 assertEquals(3, protein.getCodonFrames().size());
283 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
284 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
285 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
287 // V12345 mapped to A22222
288 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
290 assertEquals(1, acf.getdnaSeqs().length);
291 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
292 acf.getdnaSeqs()[0]);
293 Mapping[] protMappings = acf.getProtMappings();
294 assertEquals(1, protMappings.length);
295 MapList mapList = protMappings[0].getMap();
296 assertEquals(3, mapList.getFromRatio());
297 assertEquals(1, mapList.getToRatio());
298 assertTrue(Arrays.equals(new int[] { 1, 9 }, mapList.getFromRanges()
300 assertEquals(1, mapList.getFromRanges().size());
301 assertTrue(Arrays.equals(new int[] { 1, 3 },
302 mapList.getToRanges().get(0)));
303 assertEquals(1, mapList.getToRanges().size());
305 // V12346 mapped to A33333
306 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
307 assertEquals(1, acf.getdnaSeqs().length);
308 assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
309 acf.getdnaSeqs()[0]);
311 // V12347 mapped to A11111
312 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
313 assertEquals(1, acf.getdnaSeqs().length);
314 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
315 acf.getdnaSeqs()[0]);
317 // no mapping involving the 'extra' A44444
318 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(3)).isEmpty());
322 * Test for the alignSequenceAs method that takes two sequences and a mapping.
324 @Test(groups = { "Functional" })
325 public void testAlignSequenceAs_withMapping_noIntrons()
327 MapList map = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 }, 3, 1);
330 * No existing gaps in dna:
332 checkAlignSequenceAs("GGGAAA", "-A-L-", false, false, map,
336 * Now introduce gaps in dna but ignore them when realigning.
338 checkAlignSequenceAs("-G-G-G-A-A-A-", "-A-L-", false, false, map,
342 * Now include gaps in dna when realigning. First retaining 'mapped' gaps
343 * only, i.e. those within the exon region.
345 checkAlignSequenceAs("-G-G--G-A--A-A-", "-A-L-", true, false, map,
346 "---G-G--G---A--A-A");
349 * Include all gaps in dna when realigning (within and without the exon
350 * region). The leading gap, and the gaps between codons, are subsumed by
351 * the protein alignment gap.
353 checkAlignSequenceAs("-G-GG--AA-A---", "-A-L-", true, true, map,
354 "---G-GG---AA-A---");
357 * Include only unmapped gaps in dna when realigning (outside the exon
358 * region). The leading gap, and the gaps between codons, are subsumed by
359 * the protein alignment gap.
361 checkAlignSequenceAs("-G-GG--AA-A-", "-A-L-", false, true, map,
366 * Test for the alignSequenceAs method that takes two sequences and a mapping.
368 @Test(groups = { "Functional" })
369 public void testAlignSequenceAs_withMapping_withIntrons()
372 * Exons at codon 2 (AAA) and 4 (TTT)
374 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
375 new int[] { 1, 2 }, 3, 1);
378 * Simple case: no gaps in dna
380 checkAlignSequenceAs("GGGAAACCCTTTGGG", "--A-L-", false, false, map,
381 "GGG---AAACCCTTTGGG");
384 * Add gaps to dna - but ignore when realigning.
386 checkAlignSequenceAs("-G-G-G--A--A---AC-CC-T-TT-GG-G-", "--A-L-",
387 false, false, map, "GGG---AAACCCTTTGGG");
390 * Add gaps to dna - include within exons only when realigning.
392 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
393 true, false, map, "GGG---A--A---ACCCT-TTGGG");
396 * Include gaps outside exons only when realigning.
398 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
399 false, true, map, "-G-G-GAAAC-CCTTT-GG-G-");
402 * Include gaps following first intron if we are 'preserving mapped gaps'
404 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
405 true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
408 * Include all gaps in dna when realigning.
410 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
411 true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
415 * Test for the case where not all of the protein sequence is mapped to cDNA.
417 @Test(groups = { "Functional" })
418 public void testAlignSequenceAs_withMapping_withUnmappedProtein()
421 * Exons at codon 2 (AAA) and 4 (TTT) mapped to A and P
423 final MapList map = new MapList(new int[] { 4, 6, 10, 12 }, new int[] {
427 * -L- 'aligns' ccc------
429 checkAlignSequenceAs("gggAAAcccTTTggg", "-A-L-P-", false, false, map,
430 "gggAAAccc------TTTggg");
434 * Helper method that performs and verifies the method under test.
437 * the sequence to be realigned
439 * the sequence whose alignment is to be copied
440 * @param preserveMappedGaps
441 * @param preserveUnmappedGaps
445 protected void checkAlignSequenceAs(final String alignee,
446 final String alignModel, final boolean preserveMappedGaps,
447 final boolean preserveUnmappedGaps, MapList map,
448 final String expected)
450 SequenceI alignMe = new Sequence("Seq1", alignee);
451 alignMe.createDatasetSequence();
452 SequenceI alignFrom = new Sequence("Seq2", alignModel);
453 alignFrom.createDatasetSequence();
454 AlignedCodonFrame acf = new AlignedCodonFrame();
455 acf.addMap(alignMe.getDatasetSequence(),
456 alignFrom.getDatasetSequence(), map);
458 AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "---", '-',
459 preserveMappedGaps, preserveUnmappedGaps);
460 assertEquals(expected, alignMe.getSequenceAsString());
464 * Test for the alignSequenceAs method where we preserve gaps in introns only.
466 @Test(groups = { "Functional" })
467 public void testAlignSequenceAs_keepIntronGapsOnly()
471 * Intron GGGAAA followed by exon CCCTTT
473 MapList map = new MapList(new int[] { 7, 12 }, new int[] { 1, 2 }, 3, 1);
475 checkAlignSequenceAs("GG-G-AA-A-C-CC-T-TT", "AL", false, true, map,
480 * Test the method that realigns protein to match mapped codon alignment.
482 @Test(groups = { "Functional" })
483 public void testAlignProteinAsDna()
485 // seq1 codons are [1,2,3] [4,5,6] [7,8,9] [10,11,12]
486 SequenceI dna1 = new Sequence("Seq1", "TGCCATTACCAG-");
487 // seq2 codons are [1,3,4] [5,6,7] [8,9,10] [11,12,13]
488 SequenceI dna2 = new Sequence("Seq2", "T-GCCATTACCAG");
489 // seq3 codons are [1,2,3] [4,5,7] [8,9,10] [11,12,13]
490 SequenceI dna3 = new Sequence("Seq3", "TGCCA-TTACCAG");
491 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
492 dna.setDataset(null);
494 // protein alignment will be realigned like dna
495 SequenceI prot1 = new Sequence("Seq1", "CHYQ");
496 SequenceI prot2 = new Sequence("Seq2", "CHYQ");
497 SequenceI prot3 = new Sequence("Seq3", "CHYQ");
498 SequenceI prot4 = new Sequence("Seq4", "R-QSV"); // unmapped, unchanged
499 AlignmentI protein = new Alignment(new SequenceI[] { prot1, prot2,
501 protein.setDataset(null);
503 MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1);
504 AlignedCodonFrame acf = new AlignedCodonFrame();
505 acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
506 acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map);
507 acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map);
508 ArrayList<AlignedCodonFrame> acfs = new ArrayList<>();
510 protein.setCodonFrames(acfs);
513 * Translated codon order is [1,2,3] [1,3,4] [4,5,6] [4,5,7] [5,6,7] [7,8,9]
514 * [8,9,10] [10,11,12] [11,12,13]
516 AlignmentUtils.alignProteinAsDna(protein, dna);
517 assertEquals("C-H--Y-Q-", prot1.getSequenceAsString());
518 assertEquals("-C--H-Y-Q", prot2.getSequenceAsString());
519 assertEquals("C--H--Y-Q", prot3.getSequenceAsString());
520 assertEquals("R-QSV", prot4.getSequenceAsString());
524 * Test the method that tests whether a CDNA sequence translates to a protein
527 @Test(groups = { "Functional" })
528 public void testTranslatesAs()
530 // null arguments check
531 assertFalse(AlignmentUtils.translatesAs(null, 0, null));
532 assertFalse(AlignmentUtils.translatesAs(new char[] { 't' }, 0, null));
533 assertFalse(AlignmentUtils.translatesAs(null, 0, new char[] { 'a' }));
535 // straight translation
536 assertTrue(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
537 "FPKG".toCharArray()));
538 // with extra start codon (not in protein)
539 assertTrue(AlignmentUtils.translatesAs("atgtttcccaaaggg".toCharArray(),
540 3, "FPKG".toCharArray()));
541 // with stop codon1 (not in protein)
542 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtaa".toCharArray(),
543 0, "FPKG".toCharArray()));
544 // with stop codon1 (in protein as *)
545 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtaa".toCharArray(),
546 0, "FPKG*".toCharArray()));
547 // with stop codon2 (not in protein)
548 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtag".toCharArray(),
549 0, "FPKG".toCharArray()));
550 // with stop codon3 (not in protein)
551 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtga".toCharArray(),
552 0, "FPKG".toCharArray()));
553 // with start and stop codon1
554 assertTrue(AlignmentUtils.translatesAs(
555 "atgtttcccaaagggtaa".toCharArray(), 3, "FPKG".toCharArray()));
556 // with start and stop codon1 (in protein as *)
557 assertTrue(AlignmentUtils.translatesAs(
558 "atgtttcccaaagggtaa".toCharArray(), 3, "FPKG*".toCharArray()));
559 // with start and stop codon2
560 assertTrue(AlignmentUtils.translatesAs(
561 "atgtttcccaaagggtag".toCharArray(), 3, "FPKG".toCharArray()));
562 // with start and stop codon3
563 assertTrue(AlignmentUtils.translatesAs(
564 "atgtttcccaaagggtga".toCharArray(), 3, "FPKG".toCharArray()));
566 // with embedded stop codons
567 assertTrue(AlignmentUtils.translatesAs(
568 "atgtttTAGcccaaaTAAgggtga".toCharArray(), 3,
569 "F*PK*G".toCharArray()));
572 assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
573 0, "FPMG".toCharArray()));
576 assertFalse(AlignmentUtils.translatesAs("tttcccaaagg".toCharArray(), 0,
577 "FPKG".toCharArray()));
580 assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
581 0, "FPK".toCharArray()));
583 // overlong dna (doesn't end in stop codon)
584 assertFalse(AlignmentUtils.translatesAs(
585 "tttcccaaagggttt".toCharArray(), 0, "FPKG".toCharArray()));
587 // dna + stop codon + more
588 assertFalse(AlignmentUtils.translatesAs(
589 "tttcccaaagggttaga".toCharArray(), 0, "FPKG".toCharArray()));
592 assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
593 0, "FPKGQ".toCharArray()));
597 * Test mapping of protein to cDNA, for cases where the cDNA has start and/or
598 * stop codons in addition to the protein coding sequence.
600 * @throws IOException
602 @Test(groups = { "Functional" })
603 public void testMapProteinAlignmentToCdna_withStartAndStopCodons()
606 List<SequenceI> protseqs = new ArrayList<>();
607 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
608 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
609 protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
610 AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
611 protein.setDataset(null);
613 List<SequenceI> dnaseqs = new ArrayList<>();
615 dnaseqs.add(new Sequence("EMBL|A11111", "ATGTCAGCACGC"));
617 dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAATAA"));
618 // = start +EIQ + stop
619 dnaseqs.add(new Sequence("EMBL|A33333", "ATGGAAATCCAGTAG"));
620 dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG"));
621 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
622 cdna.setDataset(null);
624 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
626 // 3 mappings made, each from 1 to 1 sequence
627 assertEquals(3, protein.getCodonFrames().size());
628 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
629 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
630 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
632 // V12345 mapped from A22222
633 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
635 assertEquals(1, acf.getdnaSeqs().length);
636 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
637 acf.getdnaSeqs()[0]);
638 Mapping[] protMappings = acf.getProtMappings();
639 assertEquals(1, protMappings.length);
640 MapList mapList = protMappings[0].getMap();
641 assertEquals(3, mapList.getFromRatio());
642 assertEquals(1, mapList.getToRatio());
643 assertTrue(Arrays.equals(new int[] { 1, 9 }, mapList.getFromRanges()
645 assertEquals(1, mapList.getFromRanges().size());
646 assertTrue(Arrays.equals(new int[] { 1, 3 },
647 mapList.getToRanges().get(0)));
648 assertEquals(1, mapList.getToRanges().size());
650 // V12346 mapped from A33333 starting position 4
651 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
652 assertEquals(1, acf.getdnaSeqs().length);
653 assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
654 acf.getdnaSeqs()[0]);
655 protMappings = acf.getProtMappings();
656 assertEquals(1, protMappings.length);
657 mapList = protMappings[0].getMap();
658 assertEquals(3, mapList.getFromRatio());
659 assertEquals(1, mapList.getToRatio());
660 assertTrue(Arrays.equals(new int[] { 4, 12 }, mapList.getFromRanges()
662 assertEquals(1, mapList.getFromRanges().size());
663 assertTrue(Arrays.equals(new int[] { 1, 3 },
664 mapList.getToRanges().get(0)));
665 assertEquals(1, mapList.getToRanges().size());
667 // V12347 mapped to A11111 starting position 4
668 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
669 assertEquals(1, acf.getdnaSeqs().length);
670 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
671 acf.getdnaSeqs()[0]);
672 protMappings = acf.getProtMappings();
673 assertEquals(1, protMappings.length);
674 mapList = protMappings[0].getMap();
675 assertEquals(3, mapList.getFromRatio());
676 assertEquals(1, mapList.getToRatio());
677 assertTrue(Arrays.equals(new int[] { 4, 12 }, mapList.getFromRanges()
679 assertEquals(1, mapList.getFromRanges().size());
680 assertTrue(Arrays.equals(new int[] { 1, 3 },
681 mapList.getToRanges().get(0)));
682 assertEquals(1, mapList.getToRanges().size());
684 // no mapping involving the 'extra' A44444
685 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(3)).isEmpty());
689 * Test mapping of protein to cDNA, for the case where we have some sequence
690 * cross-references. Verify that 1-to-many mappings are made where
691 * cross-references exist and sequences are mappable.
693 * @throws IOException
695 @Test(groups = { "Functional" })
696 public void testMapProteinAlignmentToCdna_withXrefs() throws IOException
698 List<SequenceI> protseqs = new ArrayList<>();
699 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
700 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
701 protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
702 AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
703 protein.setDataset(null);
705 List<SequenceI> dnaseqs = new ArrayList<>();
706 dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR
707 dnaseqs.add(new Sequence("EMBL|A22222", "ATGGAGATACAA")); // = start + EIQ
708 dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ
709 dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG")); // = EIQ
710 dnaseqs.add(new Sequence("EMBL|A55555", "GAGATTCAG")); // = EIQ
711 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[5]));
712 cdna.setDataset(null);
714 // Xref A22222 to V12345 (should get mapped)
715 dnaseqs.get(1).addDBRef(new DBRefEntry("UNIPROT", "1", "V12345"));
716 // Xref V12345 to A44444 (should get mapped)
717 protseqs.get(0).addDBRef(new DBRefEntry("EMBL", "1", "A44444"));
718 // Xref A33333 to V12347 (sequence mismatch - should not get mapped)
719 dnaseqs.get(2).addDBRef(new DBRefEntry("UNIPROT", "1", "V12347"));
720 // as V12345 is mapped to A22222 and A44444, this leaves V12346 unmapped.
721 // it should get paired up with the unmapped A33333
722 // A11111 should be mapped to V12347
723 // A55555 is spare and has no xref so is not mapped
725 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
727 // 4 protein mappings made for 3 proteins, 2 to V12345, 1 each to V12346/7
728 assertEquals(3, protein.getCodonFrames().size());
729 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
730 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
731 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
733 // one mapping for each of the first 4 cDNA sequences
734 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(0)).size());
735 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(1)).size());
736 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(2)).size());
737 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(3)).size());
739 // V12345 mapped to A22222 and A44444
740 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
742 assertEquals(2, acf.getdnaSeqs().length);
743 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
744 acf.getdnaSeqs()[0]);
745 assertEquals(cdna.getSequenceAt(3).getDatasetSequence(),
746 acf.getdnaSeqs()[1]);
748 // V12346 mapped to A33333
749 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
750 assertEquals(1, acf.getdnaSeqs().length);
751 assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
752 acf.getdnaSeqs()[0]);
754 // V12347 mapped to A11111
755 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
756 assertEquals(1, acf.getdnaSeqs().length);
757 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
758 acf.getdnaSeqs()[0]);
760 // no mapping involving the 'extra' A55555
761 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(4)).isEmpty());
765 * Test mapping of protein to cDNA, for the case where we have some sequence
766 * cross-references. Verify that once we have made an xref mapping we don't
767 * also map un-xrefd sequeces.
769 * @throws IOException
771 @Test(groups = { "Functional" })
772 public void testMapProteinAlignmentToCdna_prioritiseXrefs()
775 List<SequenceI> protseqs = new ArrayList<>();
776 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
777 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
778 AlignmentI protein = new Alignment(
779 protseqs.toArray(new SequenceI[protseqs.size()]));
780 protein.setDataset(null);
782 List<SequenceI> dnaseqs = new ArrayList<>();
783 dnaseqs.add(new Sequence("EMBL|A11111", "GAAATCCAG")); // = EIQ
784 dnaseqs.add(new Sequence("EMBL|A22222", "GAAATTCAG")); // = EIQ
785 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[dnaseqs
787 cdna.setDataset(null);
789 // Xref A22222 to V12345 (should get mapped)
790 // A11111 should then be mapped to the unmapped V12346
791 dnaseqs.get(1).addDBRef(new DBRefEntry("UNIPROT", "1", "V12345"));
793 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
795 // 2 protein mappings made
796 assertEquals(2, protein.getCodonFrames().size());
797 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
798 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
800 // one mapping for each of the cDNA sequences
801 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(0)).size());
802 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(1)).size());
804 // V12345 mapped to A22222
805 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
807 assertEquals(1, acf.getdnaSeqs().length);
808 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
809 acf.getdnaSeqs()[0]);
811 // V12346 mapped to A11111
812 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
813 assertEquals(1, acf.getdnaSeqs().length);
814 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
815 acf.getdnaSeqs()[0]);
819 * Test the method that shows or hides sequence annotations by type(s) and
822 @Test(groups = { "Functional" })
823 public void testShowOrHideSequenceAnnotations()
825 SequenceI seq1 = new Sequence("Seq1", "AAA");
826 SequenceI seq2 = new Sequence("Seq2", "BBB");
827 SequenceI seq3 = new Sequence("Seq3", "CCC");
828 Annotation[] anns = new Annotation[] { new Annotation(2f) };
829 AlignmentAnnotation ann1 = new AlignmentAnnotation("Structure", "ann1",
831 ann1.setSequenceRef(seq1);
832 AlignmentAnnotation ann2 = new AlignmentAnnotation("Structure", "ann2",
834 ann2.setSequenceRef(seq2);
835 AlignmentAnnotation ann3 = new AlignmentAnnotation("Structure", "ann3",
837 AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "ann4", anns);
838 ann4.setSequenceRef(seq1);
839 AlignmentAnnotation ann5 = new AlignmentAnnotation("Temp", "ann5", anns);
840 ann5.setSequenceRef(seq2);
841 AlignmentAnnotation ann6 = new AlignmentAnnotation("Temp", "ann6", anns);
842 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
843 al.addAnnotation(ann1); // Structure for Seq1
844 al.addAnnotation(ann2); // Structure for Seq2
845 al.addAnnotation(ann3); // Structure for no sequence
846 al.addAnnotation(ann4); // Temp for seq1
847 al.addAnnotation(ann5); // Temp for seq2
848 al.addAnnotation(ann6); // Temp for no sequence
849 List<String> types = new ArrayList<>();
850 List<SequenceI> scope = new ArrayList<>();
853 * Set all sequence related Structure to hidden (ann1, ann2)
855 types.add("Structure");
856 AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, false,
858 assertFalse(ann1.visible);
859 assertFalse(ann2.visible);
860 assertTrue(ann3.visible); // not sequence-related, not affected
861 assertTrue(ann4.visible); // not Structure, not affected
862 assertTrue(ann5.visible); // "
863 assertTrue(ann6.visible); // not sequence-related, not affected
866 * Set Temp in {seq1, seq3} to hidden
872 AlignmentUtils.showOrHideSequenceAnnotations(al, types, scope, false,
874 assertFalse(ann1.visible); // unchanged
875 assertFalse(ann2.visible); // unchanged
876 assertTrue(ann3.visible); // not sequence-related, not affected
877 assertFalse(ann4.visible); // Temp for seq1 hidden
878 assertTrue(ann5.visible); // not in scope, not affected
879 assertTrue(ann6.visible); // not sequence-related, not affected
882 * Set Temp in all sequences to hidden
888 AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, false,
890 assertFalse(ann1.visible); // unchanged
891 assertFalse(ann2.visible); // unchanged
892 assertTrue(ann3.visible); // not sequence-related, not affected
893 assertFalse(ann4.visible); // Temp for seq1 hidden
894 assertFalse(ann5.visible); // Temp for seq2 hidden
895 assertTrue(ann6.visible); // not sequence-related, not affected
898 * Set all types in {seq1, seq3} to visible
904 AlignmentUtils.showOrHideSequenceAnnotations(al, types, scope, true,
906 assertTrue(ann1.visible); // Structure for seq1 set visible
907 assertFalse(ann2.visible); // not in scope, unchanged
908 assertTrue(ann3.visible); // not sequence-related, not affected
909 assertTrue(ann4.visible); // Temp for seq1 set visible
910 assertFalse(ann5.visible); // not in scope, unchanged
911 assertTrue(ann6.visible); // not sequence-related, not affected
914 * Set all types in all scope to hidden
916 AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, true,
918 assertFalse(ann1.visible);
919 assertFalse(ann2.visible);
920 assertTrue(ann3.visible); // not sequence-related, not affected
921 assertFalse(ann4.visible);
922 assertFalse(ann5.visible);
923 assertTrue(ann6.visible); // not sequence-related, not affected
927 * Tests for the method that checks if one sequence cross-references another
929 @Test(groups = { "Functional" })
930 public void testHasCrossRef()
932 assertFalse(AlignmentUtils.hasCrossRef(null, null));
933 SequenceI seq1 = new Sequence("EMBL|A12345", "ABCDEF");
934 assertFalse(AlignmentUtils.hasCrossRef(seq1, null));
935 assertFalse(AlignmentUtils.hasCrossRef(null, seq1));
936 SequenceI seq2 = new Sequence("UNIPROT|V20192", "ABCDEF");
937 assertFalse(AlignmentUtils.hasCrossRef(seq1, seq2));
940 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "v20193"));
941 assertFalse(AlignmentUtils.hasCrossRef(seq1, seq2));
943 // case-insensitive; version number is ignored
944 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "v20192"));
945 assertTrue(AlignmentUtils.hasCrossRef(seq1, seq2));
948 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
949 assertTrue(AlignmentUtils.hasCrossRef(seq1, seq2));
950 // test is one-way only
951 assertFalse(AlignmentUtils.hasCrossRef(seq2, seq1));
955 * Tests for the method that checks if either sequence cross-references the
958 @Test(groups = { "Functional" })
959 public void testHaveCrossRef()
961 assertFalse(AlignmentUtils.hasCrossRef(null, null));
962 SequenceI seq1 = new Sequence("EMBL|A12345", "ABCDEF");
963 assertFalse(AlignmentUtils.haveCrossRef(seq1, null));
964 assertFalse(AlignmentUtils.haveCrossRef(null, seq1));
965 SequenceI seq2 = new Sequence("UNIPROT|V20192", "ABCDEF");
966 assertFalse(AlignmentUtils.haveCrossRef(seq1, seq2));
968 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
969 assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
970 // next is true for haveCrossRef, false for hasCrossRef
971 assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
973 // now the other way round
974 seq1.setDBRefs(null);
975 seq2.addDBRef(new DBRefEntry("EMBL", "1", "A12345"));
976 assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
977 assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
980 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
981 assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
982 assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
986 * Test the method that extracts the cds-only part of a dna alignment.
988 @Test(groups = { "Functional" })
989 public void testMakeCdsAlignment()
993 * dna1 --> [4, 6] [10,12] --> pep1
994 * dna2 --> [1, 3] [7, 9] [13,15] --> pep2
996 SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
997 SequenceI dna2 = new Sequence("dna2", "GGGcccTTTaaaCCC");
998 SequenceI pep1 = new Sequence("pep1", "GF");
999 SequenceI pep2 = new Sequence("pep2", "GFP");
1000 pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "pep1"));
1001 pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "pep2"));
1002 dna1.createDatasetSequence();
1003 dna2.createDatasetSequence();
1004 pep1.createDatasetSequence();
1005 pep2.createDatasetSequence();
1006 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
1007 dna.setDataset(null);
1010 * put a variant feature on dna2 base 8
1011 * - should transfer to cds2 base 5
1013 dna2.addSequenceFeature(new SequenceFeature("variant", "hgmd", 8, 8,
1017 * need a sourceDbRef if we are to construct dbrefs to the CDS
1018 * sequence from the dna contig sequences
1020 DBRefEntry dbref = new DBRefEntry("ENSEMBL", "0", "dna1");
1021 dna1.getDatasetSequence().addDBRef(dbref);
1022 org.testng.Assert.assertEquals(dbref, dna1.getPrimaryDBRefs().get(0));
1023 dbref = new DBRefEntry("ENSEMBL", "0", "dna2");
1024 dna2.getDatasetSequence().addDBRef(dbref);
1025 org.testng.Assert.assertEquals(dbref, dna2.getPrimaryDBRefs().get(0));
1028 * CDS sequences are 'discovered' from dna-to-protein mappings on the alignment
1029 * dataset (e.g. added from dbrefs by CrossRef.findXrefSequences)
1031 MapList mapfordna1 = new MapList(new int[] { 4, 6, 10, 12 }, new int[] {
1033 AlignedCodonFrame acf = new AlignedCodonFrame();
1034 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
1036 dna.addCodonFrame(acf);
1037 MapList mapfordna2 = new MapList(new int[] { 1, 3, 7, 9, 13, 15 },
1038 new int[] { 1, 3 }, 3, 1);
1039 acf = new AlignedCodonFrame();
1040 acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(),
1042 dna.addCodonFrame(acf);
1045 * In this case, mappings originally came from matching Uniprot accessions
1046 * - so need an xref on dna involving those regions.
1047 * These are normally constructed from CDS annotation
1049 DBRefEntry dna1xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep1",
1050 new Mapping(mapfordna1));
1051 dna1.addDBRef(dna1xref);
1052 assertEquals(2, dna1.getDBRefs().size()); // to self and to pep1
1053 DBRefEntry dna2xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep2",
1054 new Mapping(mapfordna2));
1055 dna2.addDBRef(dna2xref);
1056 assertEquals(2, dna2.getDBRefs().size()); // to self and to pep2
1059 * execute method under test:
1061 AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
1062 dna1, dna2 }, dna.getDataset(), null);
1065 * verify cds sequences
1067 assertEquals(2, cds.getSequences().size());
1068 assertEquals("GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
1069 assertEquals("GGGTTTCCC", cds.getSequenceAt(1).getSequenceAsString());
1072 * verify shared, extended alignment dataset
1074 assertSame(dna.getDataset(), cds.getDataset());
1075 SequenceI cds1Dss = cds.getSequenceAt(0).getDatasetSequence();
1076 SequenceI cds2Dss = cds.getSequenceAt(1).getDatasetSequence();
1077 assertTrue(dna.getDataset().getSequences().contains(cds1Dss));
1078 assertTrue(dna.getDataset().getSequences().contains(cds2Dss));
1081 * verify CDS has a dbref with mapping to peptide
1083 assertNotNull(cds1Dss.getDBRefs());
1084 assertEquals(2, cds1Dss.getDBRefs().size());
1085 dbref = cds1Dss.getDBRefs().get(0);
1086 assertEquals(dna1xref.getSource(), dbref.getSource());
1087 // version is via ensembl's primary ref
1088 assertEquals(dna1xref.getVersion(), dbref.getVersion());
1089 assertEquals(dna1xref.getAccessionId(), dbref.getAccessionId());
1090 assertNotNull(dbref.getMap());
1091 assertSame(pep1.getDatasetSequence(), dbref.getMap().getTo());
1092 MapList cdsMapping = new MapList(new int[] { 1, 6 },
1093 new int[] { 1, 2 }, 3, 1);
1094 assertEquals(cdsMapping, dbref.getMap().getMap());
1097 * verify peptide has added a dbref with reverse mapping to CDS
1099 assertNotNull(pep1.getDBRefs());
1100 // FIXME pep1.getDBRefs() is 1 - is that the correct behaviour ?
1101 assertEquals(2, pep1.getDBRefs().size());
1102 dbref = pep1.getDBRefs().get(1);
1103 assertEquals("ENSEMBL", dbref.getSource());
1104 assertEquals("0", dbref.getVersion());
1105 assertEquals("CDS|dna1", dbref.getAccessionId());
1106 assertNotNull(dbref.getMap());
1107 assertSame(cds1Dss, dbref.getMap().getTo());
1108 assertEquals(cdsMapping.getInverse(), dbref.getMap().getMap());
1111 * verify cDNA has added a dbref with mapping to CDS
1113 assertEquals(3, dna1.getDBRefs().size());
1114 DBRefEntry dbRefEntry = dna1.getDBRefs().get(2);
1115 assertSame(cds1Dss, dbRefEntry.getMap().getTo());
1116 MapList dnaToCdsMapping = new MapList(new int[] { 4, 6, 10, 12 },
1117 new int[] { 1, 6 }, 1, 1);
1118 assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap());
1119 assertEquals(3, dna2.getDBRefs().size());
1120 dbRefEntry = dna2.getDBRefs().get(2);
1121 assertSame(cds2Dss, dbRefEntry.getMap().getTo());
1122 dnaToCdsMapping = new MapList(new int[] { 1, 3, 7, 9, 13, 15 },
1123 new int[] { 1, 9 }, 1, 1);
1124 assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap());
1127 * verify CDS has added a dbref with mapping to cDNA
1129 assertEquals(2, cds1Dss.getDBRefs().size());
1130 dbRefEntry = cds1Dss.getDBRefs().get(1);
1131 assertSame(dna1.getDatasetSequence(), dbRefEntry.getMap().getTo());
1132 MapList cdsToDnaMapping = new MapList(new int[] { 1, 6 }, new int[] {
1133 4, 6, 10, 12 }, 1, 1);
1134 assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap());
1135 assertEquals(2, cds2Dss.getDBRefs().size());
1136 dbRefEntry = cds2Dss.getDBRefs().get(1);
1137 assertSame(dna2.getDatasetSequence(), dbRefEntry.getMap().getTo());
1138 cdsToDnaMapping = new MapList(new int[] { 1, 9 }, new int[] { 1, 3, 7,
1140 assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap());
1143 * Verify mappings from CDS to peptide, cDNA to CDS, and cDNA to peptide
1144 * the mappings are on the shared alignment dataset
1145 * 6 mappings, 2*(DNA->CDS), 2*(DNA->Pep), 2*(CDS->Pep)
1147 List<AlignedCodonFrame> cdsMappings = cds.getDataset().getCodonFrames();
1148 assertEquals(6, cdsMappings.size());
1151 * verify that mapping sets for dna and cds alignments are different
1152 * [not current behaviour - all mappings are on the alignment dataset]
1154 // select -> subselect type to test.
1155 // Assert.assertNotSame(dna.getCodonFrames(), cds.getCodonFrames());
1156 // assertEquals(4, dna.getCodonFrames().size());
1157 // assertEquals(4, cds.getCodonFrames().size());
1160 * Two mappings involve pep1 (dna to pep1, cds to pep1)
1161 * Mapping from pep1 to GGGTTT in first new exon sequence
1163 List<AlignedCodonFrame> pep1Mappings = MappingUtils
1164 .findMappingsForSequence(pep1, cdsMappings);
1165 assertEquals(2, pep1Mappings.size());
1166 List<AlignedCodonFrame> mappings = MappingUtils
1167 .findMappingsForSequence(cds.getSequenceAt(0), pep1Mappings);
1168 assertEquals(1, mappings.size());
1171 SearchResultsI sr = MappingUtils.buildSearchResults(pep1, 1, mappings);
1172 assertEquals(1, sr.getResults().size());
1173 SearchResultMatchI m = sr.getResults().get(0);
1174 assertSame(cds1Dss, m.getSequence());
1175 assertEquals(1, m.getStart());
1176 assertEquals(3, m.getEnd());
1178 sr = MappingUtils.buildSearchResults(pep1, 2, mappings);
1179 m = sr.getResults().get(0);
1180 assertSame(cds1Dss, m.getSequence());
1181 assertEquals(4, m.getStart());
1182 assertEquals(6, m.getEnd());
1185 * Two mappings involve pep2 (dna to pep2, cds to pep2)
1186 * Verify mapping from pep2 to GGGTTTCCC in second new exon sequence
1188 List<AlignedCodonFrame> pep2Mappings = MappingUtils
1189 .findMappingsForSequence(pep2, cdsMappings);
1190 assertEquals(2, pep2Mappings.size());
1191 mappings = MappingUtils.findMappingsForSequence(cds.getSequenceAt(1),
1193 assertEquals(1, mappings.size());
1195 sr = MappingUtils.buildSearchResults(pep2, 1, mappings);
1196 assertEquals(1, sr.getResults().size());
1197 m = sr.getResults().get(0);
1198 assertSame(cds2Dss, m.getSequence());
1199 assertEquals(1, m.getStart());
1200 assertEquals(3, m.getEnd());
1202 sr = MappingUtils.buildSearchResults(pep2, 2, mappings);
1203 m = sr.getResults().get(0);
1204 assertSame(cds2Dss, m.getSequence());
1205 assertEquals(4, m.getStart());
1206 assertEquals(6, m.getEnd());
1208 sr = MappingUtils.buildSearchResults(pep2, 3, mappings);
1209 m = sr.getResults().get(0);
1210 assertSame(cds2Dss, m.getSequence());
1211 assertEquals(7, m.getStart());
1212 assertEquals(9, m.getEnd());
1215 * check cds2 acquired a variant feature in position 5
1217 List<SequenceFeature> sfs = cds2Dss.getSequenceFeatures();
1219 assertEquals(1, sfs.size());
1220 assertEquals("variant", sfs.get(0).type);
1221 assertEquals(5, sfs.get(0).begin);
1222 assertEquals(5, sfs.get(0).end);
1226 * Test the method that makes a cds-only alignment from a DNA sequence and its
1227 * product mappings, for the case where there are multiple exon mappings to
1228 * different protein products.
1230 @Test(groups = { "Functional" })
1231 public void testMakeCdsAlignment_multipleProteins()
1233 SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
1234 SequenceI pep1 = new Sequence("pep1", "GF"); // GGGTTT
1235 SequenceI pep2 = new Sequence("pep2", "KP"); // aaaccc
1236 SequenceI pep3 = new Sequence("pep3", "KF"); // aaaTTT
1237 dna1.createDatasetSequence();
1238 pep1.createDatasetSequence();
1239 pep2.createDatasetSequence();
1240 pep3.createDatasetSequence();
1241 pep1.getDatasetSequence().addDBRef(
1242 new DBRefEntry("EMBLCDS", "2", "A12345"));
1243 pep2.getDatasetSequence().addDBRef(
1244 new DBRefEntry("EMBLCDS", "3", "A12346"));
1245 pep3.getDatasetSequence().addDBRef(
1246 new DBRefEntry("EMBLCDS", "4", "A12347"));
1249 * Create the CDS alignment
1251 AlignmentI dna = new Alignment(new SequenceI[] { dna1 });
1252 dna.setDataset(null);
1255 * Make the mappings from dna to protein
1257 // map ...GGG...TTT to GF
1258 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1259 new int[] { 1, 2 }, 3, 1);
1260 AlignedCodonFrame acf = new AlignedCodonFrame();
1261 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
1262 dna.addCodonFrame(acf);
1264 // map aaa...ccc to KP
1265 map = new MapList(new int[] { 1, 3, 7, 9 }, new int[] { 1, 2 }, 3, 1);
1266 acf = new AlignedCodonFrame();
1267 acf.addMap(dna1.getDatasetSequence(), pep2.getDatasetSequence(), map);
1268 dna.addCodonFrame(acf);
1270 // map aaa......TTT to KF
1271 map = new MapList(new int[] { 1, 3, 10, 12 }, new int[] { 1, 2 }, 3, 1);
1272 acf = new AlignedCodonFrame();
1273 acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map);
1274 dna.addCodonFrame(acf);
1277 * execute method under test
1279 AlignmentI cdsal = AlignmentUtils.makeCdsAlignment(
1280 new SequenceI[] { dna1 }, dna.getDataset(), null);
1283 * Verify we have 3 cds sequences, mapped to pep1/2/3 respectively
1285 List<SequenceI> cds = cdsal.getSequences();
1286 assertEquals(3, cds.size());
1289 * verify shared, extended alignment dataset
1291 assertSame(cdsal.getDataset(), dna.getDataset());
1292 assertTrue(dna.getDataset().getSequences()
1293 .contains(cds.get(0).getDatasetSequence()));
1294 assertTrue(dna.getDataset().getSequences()
1295 .contains(cds.get(1).getDatasetSequence()));
1296 assertTrue(dna.getDataset().getSequences()
1297 .contains(cds.get(2).getDatasetSequence()));
1300 * verify aligned cds sequences and their xrefs
1302 SequenceI cdsSeq = cds.get(0);
1303 assertEquals("GGGTTT", cdsSeq.getSequenceAsString());
1304 // assertEquals("dna1|A12345", cdsSeq.getName());
1305 assertEquals("CDS|dna1", cdsSeq.getName());
1306 // assertEquals(1, cdsSeq.getDBRefs().length);
1307 // DBRefEntry cdsRef = cdsSeq.getDBRefs()[0];
1308 // assertEquals("EMBLCDS", cdsRef.getSource());
1309 // assertEquals("2", cdsRef.getVersion());
1310 // assertEquals("A12345", cdsRef.getAccessionId());
1312 cdsSeq = cds.get(1);
1313 assertEquals("aaaccc", cdsSeq.getSequenceAsString());
1314 // assertEquals("dna1|A12346", cdsSeq.getName());
1315 assertEquals("CDS|dna1", cdsSeq.getName());
1316 // assertEquals(1, cdsSeq.getDBRefs().length);
1317 // cdsRef = cdsSeq.getDBRefs()[0];
1318 // assertEquals("EMBLCDS", cdsRef.getSource());
1319 // assertEquals("3", cdsRef.getVersion());
1320 // assertEquals("A12346", cdsRef.getAccessionId());
1322 cdsSeq = cds.get(2);
1323 assertEquals("aaaTTT", cdsSeq.getSequenceAsString());
1324 // assertEquals("dna1|A12347", cdsSeq.getName());
1325 assertEquals("CDS|dna1", cdsSeq.getName());
1326 // assertEquals(1, cdsSeq.getDBRefs().length);
1327 // cdsRef = cdsSeq.getDBRefs()[0];
1328 // assertEquals("EMBLCDS", cdsRef.getSource());
1329 // assertEquals("4", cdsRef.getVersion());
1330 // assertEquals("A12347", cdsRef.getAccessionId());
1333 * Verify there are mappings from each cds sequence to its protein product
1334 * and also to its dna source
1336 List<AlignedCodonFrame> newMappings = cdsal.getCodonFrames();
1339 * 6 mappings involve dna1 (to pep1/2/3, cds1/2/3)
1341 List<AlignedCodonFrame> dnaMappings = MappingUtils
1342 .findMappingsForSequence(dna1, newMappings);
1343 assertEquals(6, dnaMappings.size());
1348 List<AlignedCodonFrame> mappings = MappingUtils
1349 .findMappingsForSequence(pep1, dnaMappings);
1350 assertEquals(1, mappings.size());
1351 assertEquals(1, mappings.get(0).getMappings().size());
1352 assertSame(pep1.getDatasetSequence(), mappings.get(0).getMappings()
1353 .get(0).getMapping().getTo());
1358 List<AlignedCodonFrame> dnaToCds1Mappings = MappingUtils
1359 .findMappingsForSequence(cds.get(0), dnaMappings);
1360 Mapping mapping = dnaToCds1Mappings.get(0).getMappings().get(0)
1362 assertSame(cds.get(0).getDatasetSequence(), mapping.getTo());
1363 assertEquals("G(1) in CDS should map to G(4) in DNA", 4, mapping
1364 .getMap().getToPosition(1));
1369 mappings = MappingUtils.findMappingsForSequence(pep2, dnaMappings);
1370 assertEquals(1, mappings.size());
1371 assertEquals(1, mappings.get(0).getMappings().size());
1372 assertSame(pep2.getDatasetSequence(), mappings.get(0).getMappings()
1373 .get(0).getMapping().getTo());
1378 List<AlignedCodonFrame> dnaToCds2Mappings = MappingUtils
1379 .findMappingsForSequence(cds.get(1), dnaMappings);
1380 mapping = dnaToCds2Mappings.get(0).getMappings().get(0).getMapping();
1381 assertSame(cds.get(1).getDatasetSequence(), mapping.getTo());
1382 assertEquals("c(4) in CDS should map to c(7) in DNA", 7, mapping
1383 .getMap().getToPosition(4));
1388 mappings = MappingUtils.findMappingsForSequence(pep3, dnaMappings);
1389 assertEquals(1, mappings.size());
1390 assertEquals(1, mappings.get(0).getMappings().size());
1391 assertSame(pep3.getDatasetSequence(), mappings.get(0).getMappings()
1392 .get(0).getMapping().getTo());
1397 List<AlignedCodonFrame> dnaToCds3Mappings = MappingUtils
1398 .findMappingsForSequence(cds.get(2), dnaMappings);
1399 mapping = dnaToCds3Mappings.get(0).getMappings().get(0).getMapping();
1400 assertSame(cds.get(2).getDatasetSequence(), mapping.getTo());
1401 assertEquals("T(4) in CDS should map to T(10) in DNA", 10, mapping
1402 .getMap().getToPosition(4));
1405 @Test(groups = { "Functional" })
1406 public void testIsMappable()
1408 SequenceI dna1 = new Sequence("dna1", "cgCAGtgGT");
1409 SequenceI aa1 = new Sequence("aa1", "RSG");
1410 AlignmentI al1 = new Alignment(new SequenceI[] { dna1 });
1411 AlignmentI al2 = new Alignment(new SequenceI[] { aa1 });
1413 assertFalse(AlignmentUtils.isMappable(null, null));
1414 assertFalse(AlignmentUtils.isMappable(al1, null));
1415 assertFalse(AlignmentUtils.isMappable(null, al1));
1416 assertFalse(AlignmentUtils.isMappable(al1, al1));
1417 assertFalse(AlignmentUtils.isMappable(al2, al2));
1419 assertTrue(AlignmentUtils.isMappable(al1, al2));
1420 assertTrue(AlignmentUtils.isMappable(al2, al1));
1424 * Test creating a mapping when the sequences involved do not start at residue
1427 * @throws IOException
1429 @Test(groups = { "Functional" })
1430 public void testMapCdnaToProtein_forSubsequence() throws IOException
1432 SequenceI prot = new Sequence("UNIPROT|V12345", "E-I--Q", 10, 12);
1433 prot.createDatasetSequence();
1435 SequenceI dna = new Sequence("EMBL|A33333", "GAA--AT-C-CAG", 40, 48);
1436 dna.createDatasetSequence();
1438 MapList map = AlignmentUtils.mapCdnaToProtein(prot, dna);
1439 assertEquals(10, map.getToLowest());
1440 assertEquals(12, map.getToHighest());
1441 assertEquals(40, map.getFromLowest());
1442 assertEquals(48, map.getFromHighest());
1446 * Test for the alignSequenceAs method where we have protein mapped to protein
1448 @Test(groups = { "Functional" })
1449 public void testAlignSequenceAs_mappedProteinProtein()
1452 SequenceI alignMe = new Sequence("Match", "MGAASEV");
1453 alignMe.createDatasetSequence();
1454 SequenceI alignFrom = new Sequence("Query", "LQTGYMGAASEVMFSPTRR");
1455 alignFrom.createDatasetSequence();
1457 AlignedCodonFrame acf = new AlignedCodonFrame();
1458 // this is like a domain or motif match of part of a peptide sequence
1459 MapList map = new MapList(new int[] { 6, 12 }, new int[] { 1, 7 }, 1, 1);
1460 acf.addMap(alignFrom.getDatasetSequence(),
1461 alignMe.getDatasetSequence(), map);
1463 AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "-", '-', true,
1465 assertEquals("-----MGAASEV-------", alignMe.getSequenceAsString());
1469 * Test for the alignSequenceAs method where there are trailing unmapped
1470 * residues in the model sequence
1472 @Test(groups = { "Functional" })
1473 public void testAlignSequenceAs_withTrailingPeptide()
1475 // map first 3 codons to KPF; G is a trailing unmapped residue
1476 MapList map = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3, 1);
1478 checkAlignSequenceAs("AAACCCTTT", "K-PFG", true, true, map,
1483 * Tests for transferring features between mapped sequences
1485 @Test(groups = { "Functional" })
1486 public void testTransferFeatures()
1488 SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt");
1489 SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
1492 dna.addSequenceFeature(new SequenceFeature("type1", "desc1", 1, 2, 1f,
1494 // partial overlap - to [1, 1]
1495 dna.addSequenceFeature(new SequenceFeature("type2", "desc2", 3, 4, 2f,
1497 // exact overlap - to [1, 3]
1498 dna.addSequenceFeature(new SequenceFeature("type3", "desc3", 4, 6, 3f,
1500 // spanning overlap - to [2, 5]
1501 dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f,
1503 // exactly overlaps whole mapped range [1, 6]
1504 dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f,
1506 // no overlap (internal)
1507 dna.addSequenceFeature(new SequenceFeature("type6", "desc6", 7, 9, 6f,
1509 // no overlap (3' end)
1510 dna.addSequenceFeature(new SequenceFeature("type7", "desc7", 13, 15,
1512 // overlap (3' end) - to [6, 6]
1513 dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12,
1515 // extended overlap - to [6, +]
1516 dna.addSequenceFeature(new SequenceFeature("type9", "desc9", 12, 13,
1519 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1520 new int[] { 1, 6 }, 1, 1);
1523 * transferFeatures() will build 'partial overlap' for regions
1524 * that partially overlap 5' or 3' (start or end) of target sequence
1526 AlignmentUtils.transferFeatures(dna, cds, map, null);
1527 List<SequenceFeature> sfs = cds.getSequenceFeatures();
1528 assertEquals(6, sfs.size());
1530 SequenceFeature sf = sfs.get(0);
1531 assertEquals("type2", sf.getType());
1532 assertEquals("desc2", sf.getDescription());
1533 assertEquals(2f, sf.getScore());
1534 assertEquals(1, sf.getBegin());
1535 assertEquals(1, sf.getEnd());
1538 assertEquals("type3", sf.getType());
1539 assertEquals("desc3", sf.getDescription());
1540 assertEquals(3f, sf.getScore());
1541 assertEquals(1, sf.getBegin());
1542 assertEquals(3, sf.getEnd());
1545 assertEquals("type4", sf.getType());
1546 assertEquals(2, sf.getBegin());
1547 assertEquals(5, sf.getEnd());
1550 assertEquals("type5", sf.getType());
1551 assertEquals(1, sf.getBegin());
1552 assertEquals(6, sf.getEnd());
1555 assertEquals("type8", sf.getType());
1556 assertEquals(6, sf.getBegin());
1557 assertEquals(6, sf.getEnd());
1560 assertEquals("type9", sf.getType());
1561 assertEquals(6, sf.getBegin());
1562 assertEquals(6, sf.getEnd());
1566 * Tests for transferring features between mapped sequences
1568 @Test(groups = { "Functional" })
1569 public void testTransferFeatures_withOmit()
1571 SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt");
1572 SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
1574 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1575 new int[] { 1, 6 }, 1, 1);
1577 // [5, 11] maps to [2, 5]
1578 dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f,
1580 // [4, 12] maps to [1, 6]
1581 dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f,
1583 // [12, 12] maps to [6, 6]
1584 dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12,
1587 // desc4 and desc8 are the 'omit these' varargs
1588 AlignmentUtils.transferFeatures(dna, cds, map, null, "type4", "type8");
1589 List<SequenceFeature> sfs = cds.getSequenceFeatures();
1590 assertEquals(1, sfs.size());
1592 SequenceFeature sf = sfs.get(0);
1593 assertEquals("type5", sf.getType());
1594 assertEquals(1, sf.getBegin());
1595 assertEquals(6, sf.getEnd());
1599 * Tests for transferring features between mapped sequences
1601 @Test(groups = { "Functional" })
1602 public void testTransferFeatures_withSelect()
1604 SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt");
1605 SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
1607 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1608 new int[] { 1, 6 }, 1, 1);
1610 // [5, 11] maps to [2, 5]
1611 dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f,
1613 // [4, 12] maps to [1, 6]
1614 dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f,
1616 // [12, 12] maps to [6, 6]
1617 dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12,
1620 // "type5" is the 'select this type' argument
1621 AlignmentUtils.transferFeatures(dna, cds, map, "type5");
1622 List<SequenceFeature> sfs = cds.getSequenceFeatures();
1623 assertEquals(1, sfs.size());
1625 SequenceFeature sf = sfs.get(0);
1626 assertEquals("type5", sf.getType());
1627 assertEquals(1, sf.getBegin());
1628 assertEquals(6, sf.getEnd());
1632 * Test the method that extracts the cds-only part of a dna alignment, for the
1633 * case where the cds should be aligned to match its nucleotide sequence.
1635 @Test(groups = { "Functional" })
1636 public void testMakeCdsAlignment_alternativeTranscripts()
1638 SequenceI dna1 = new Sequence("dna1", "aaaGGGCC-----CTTTaaaGGG");
1639 // alternative transcript of same dna skips CCC codon
1640 SequenceI dna2 = new Sequence("dna2", "aaaGGGCC-----cttTaaaGGG");
1641 // dna3 has no mapping (protein product) so should be ignored here
1642 SequenceI dna3 = new Sequence("dna3", "aaaGGGCCCCCGGGcttTaaaGGG");
1643 SequenceI pep1 = new Sequence("pep1", "GPFG");
1644 SequenceI pep2 = new Sequence("pep2", "GPG");
1645 dna1.createDatasetSequence();
1646 dna2.createDatasetSequence();
1647 dna3.createDatasetSequence();
1648 pep1.createDatasetSequence();
1649 pep2.createDatasetSequence();
1651 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
1652 dna.setDataset(null);
1654 MapList map = new MapList(new int[] { 4, 12, 16, 18 },
1655 new int[] { 1, 4 }, 3, 1);
1656 AlignedCodonFrame acf = new AlignedCodonFrame();
1657 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
1658 dna.addCodonFrame(acf);
1659 map = new MapList(new int[] { 4, 8, 12, 12, 16, 18 },
1660 new int[] { 1, 3 }, 3, 1);
1661 acf = new AlignedCodonFrame();
1662 acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
1663 dna.addCodonFrame(acf);
1665 AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
1666 dna1, dna2, dna3 }, dna.getDataset(), null);
1667 List<SequenceI> cdsSeqs = cds.getSequences();
1668 assertEquals(2, cdsSeqs.size());
1669 assertEquals("GGGCCCTTTGGG", cdsSeqs.get(0).getSequenceAsString());
1670 assertEquals("GGGCCTGGG", cdsSeqs.get(1).getSequenceAsString());
1673 * verify shared, extended alignment dataset
1675 assertSame(dna.getDataset(), cds.getDataset());
1676 assertTrue(dna.getDataset().getSequences()
1677 .contains(cdsSeqs.get(0).getDatasetSequence()));
1678 assertTrue(dna.getDataset().getSequences()
1679 .contains(cdsSeqs.get(1).getDatasetSequence()));
1682 * Verify 6 mappings: dna1 to cds1, cds1 to pep1, dna1 to pep1
1683 * and the same for dna2/cds2/pep2
1685 List<AlignedCodonFrame> mappings = cds.getCodonFrames();
1686 assertEquals(6, mappings.size());
1689 * 2 mappings involve pep1
1691 List<AlignedCodonFrame> pep1Mappings = MappingUtils
1692 .findMappingsForSequence(pep1, mappings);
1693 assertEquals(2, pep1Mappings.size());
1696 * Get mapping of pep1 to cds1 and verify it
1697 * maps GPFG to 1-3,4-6,7-9,10-12
1699 List<AlignedCodonFrame> pep1CdsMappings = MappingUtils
1700 .findMappingsForSequence(cds.getSequenceAt(0), pep1Mappings);
1701 assertEquals(1, pep1CdsMappings.size());
1702 SearchResultsI sr = MappingUtils.buildSearchResults(pep1, 1,
1704 assertEquals(1, sr.getResults().size());
1705 SearchResultMatchI m = sr.getResults().get(0);
1706 assertEquals(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
1707 assertEquals(1, m.getStart());
1708 assertEquals(3, m.getEnd());
1709 sr = MappingUtils.buildSearchResults(pep1, 2, pep1CdsMappings);
1710 m = sr.getResults().get(0);
1711 assertEquals(4, m.getStart());
1712 assertEquals(6, m.getEnd());
1713 sr = MappingUtils.buildSearchResults(pep1, 3, pep1CdsMappings);
1714 m = sr.getResults().get(0);
1715 assertEquals(7, m.getStart());
1716 assertEquals(9, m.getEnd());
1717 sr = MappingUtils.buildSearchResults(pep1, 4, pep1CdsMappings);
1718 m = sr.getResults().get(0);
1719 assertEquals(10, m.getStart());
1720 assertEquals(12, m.getEnd());
1723 * Get mapping of pep2 to cds2 and verify it
1724 * maps GPG in pep2 to 1-3,4-6,7-9 in second CDS sequence
1726 List<AlignedCodonFrame> pep2Mappings = MappingUtils
1727 .findMappingsForSequence(pep2, mappings);
1728 assertEquals(2, pep2Mappings.size());
1729 List<AlignedCodonFrame> pep2CdsMappings = MappingUtils
1730 .findMappingsForSequence(cds.getSequenceAt(1), pep2Mappings);
1731 assertEquals(1, pep2CdsMappings.size());
1732 sr = MappingUtils.buildSearchResults(pep2, 1, pep2CdsMappings);
1733 assertEquals(1, sr.getResults().size());
1734 m = sr.getResults().get(0);
1735 assertEquals(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
1736 assertEquals(1, m.getStart());
1737 assertEquals(3, m.getEnd());
1738 sr = MappingUtils.buildSearchResults(pep2, 2, pep2CdsMappings);
1739 m = sr.getResults().get(0);
1740 assertEquals(4, m.getStart());
1741 assertEquals(6, m.getEnd());
1742 sr = MappingUtils.buildSearchResults(pep2, 3, pep2CdsMappings);
1743 m = sr.getResults().get(0);
1744 assertEquals(7, m.getStart());
1745 assertEquals(9, m.getEnd());
1749 * Test the method that realigns protein to match mapped codon alignment.
1751 @Test(groups = { "Functional" })
1752 public void testAlignProteinAsDna_incompleteStartCodon()
1754 // seq1: incomplete start codon (not mapped), then [3, 11]
1755 SequenceI dna1 = new Sequence("Seq1", "ccAAA-TTT-GGG-");
1756 // seq2 codons are [4, 5], [8, 11]
1757 SequenceI dna2 = new Sequence("Seq2", "ccaAA-ttT-GGG-");
1758 // seq3 incomplete start codon at 'tt'
1759 SequenceI dna3 = new Sequence("Seq3", "ccaaa-ttt-GGG-");
1760 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
1761 dna.setDataset(null);
1763 // prot1 has 'X' for incomplete start codon (not mapped)
1764 SequenceI prot1 = new Sequence("Seq1", "XKFG"); // X for incomplete start
1765 SequenceI prot2 = new Sequence("Seq2", "NG");
1766 SequenceI prot3 = new Sequence("Seq3", "XG"); // X for incomplete start
1767 AlignmentI protein = new Alignment(new SequenceI[] { prot1, prot2,
1769 protein.setDataset(null);
1771 // map dna1 [3, 11] to prot1 [2, 4] KFG
1772 MapList map = new MapList(new int[] { 3, 11 }, new int[] { 2, 4 }, 3, 1);
1773 AlignedCodonFrame acf = new AlignedCodonFrame();
1774 acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
1776 // map dna2 [4, 5] [8, 11] to prot2 [1, 2] NG
1777 map = new MapList(new int[] { 4, 5, 8, 11 }, new int[] { 1, 2 }, 3, 1);
1778 acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map);
1780 // map dna3 [9, 11] to prot3 [2, 2] G
1781 map = new MapList(new int[] { 9, 11 }, new int[] { 2, 2 }, 3, 1);
1782 acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map);
1784 ArrayList<AlignedCodonFrame> acfs = new ArrayList<>();
1786 protein.setCodonFrames(acfs);
1789 * verify X is included in the aligned proteins, and placed just
1790 * before the first mapped residue
1791 * CCT is between CCC and TTT
1793 AlignmentUtils.alignProteinAsDna(protein, dna);
1794 assertEquals("XK-FG", prot1.getSequenceAsString());
1795 assertEquals("--N-G", prot2.getSequenceAsString());
1796 assertEquals("---XG", prot3.getSequenceAsString());
1800 * Tests for the method that maps the subset of a dna sequence that has CDS
1801 * (or subtype) feature - case where the start codon is incomplete.
1803 @Test(groups = "Functional")
1804 public void testFindCdsPositions_fivePrimeIncomplete()
1806 SequenceI dnaSeq = new Sequence("dna", "aaagGGCCCaaaTTTttt");
1807 dnaSeq.createDatasetSequence();
1808 SequenceI ds = dnaSeq.getDatasetSequence();
1810 // CDS for dna 5-6 (incomplete codon), 7-9
1811 SequenceFeature sf = new SequenceFeature("CDS", "", 5, 9, 0f, null);
1812 sf.setPhase("2"); // skip 2 bases to start of next codon
1813 ds.addSequenceFeature(sf);
1814 // CDS for dna 13-15
1815 sf = new SequenceFeature("CDS_predicted", "", 13, 15, 0f, null);
1816 ds.addSequenceFeature(sf);
1818 List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
1821 * check the mapping starts with the first complete codon
1823 assertEquals(6, MappingUtils.getLength(ranges));
1824 assertEquals(2, ranges.size());
1825 assertEquals(7, ranges.get(0)[0]);
1826 assertEquals(9, ranges.get(0)[1]);
1827 assertEquals(13, ranges.get(1)[0]);
1828 assertEquals(15, ranges.get(1)[1]);
1832 * Tests for the method that maps the subset of a dna sequence that has CDS
1833 * (or subtype) feature.
1835 @Test(groups = "Functional")
1836 public void testFindCdsPositions()
1838 SequenceI dnaSeq = new Sequence("dna", "aaaGGGcccAAATTTttt");
1839 dnaSeq.createDatasetSequence();
1840 SequenceI ds = dnaSeq.getDatasetSequence();
1842 // CDS for dna 10-12
1843 SequenceFeature sf = new SequenceFeature("CDS_predicted", "", 10, 12,
1846 ds.addSequenceFeature(sf);
1848 sf = new SequenceFeature("CDS", "", 4, 6, 0f, null);
1850 ds.addSequenceFeature(sf);
1851 // exon feature should be ignored here
1852 sf = new SequenceFeature("exon", "", 7, 9, 0f, null);
1853 ds.addSequenceFeature(sf);
1855 List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
1857 * verify ranges { [4-6], [12-10] }
1858 * note CDS ranges are ordered ascending even if the CDS
1861 assertEquals(6, MappingUtils.getLength(ranges));
1862 assertEquals(2, ranges.size());
1863 assertEquals(4, ranges.get(0)[0]);
1864 assertEquals(6, ranges.get(0)[1]);
1865 assertEquals(10, ranges.get(1)[0]);
1866 assertEquals(12, ranges.get(1)[1]);
1870 * Tests for the method that maps the subset of a dna sequence that has CDS
1871 * (or subtype) feature, with CDS strand = '-' (reverse)
1873 // test turned off as currently findCdsPositions is not strand-dependent
1874 // left in case it comes around again...
1875 @Test(groups = "Functional", enabled = false)
1876 public void testFindCdsPositions_reverseStrand()
1878 SequenceI dnaSeq = new Sequence("dna", "aaaGGGcccAAATTTttt");
1879 dnaSeq.createDatasetSequence();
1880 SequenceI ds = dnaSeq.getDatasetSequence();
1883 SequenceFeature sf = new SequenceFeature("CDS", "", 4, 6, 0f, null);
1885 ds.addSequenceFeature(sf);
1886 // exon feature should be ignored here
1887 sf = new SequenceFeature("exon", "", 7, 9, 0f, null);
1888 ds.addSequenceFeature(sf);
1889 // CDS for dna 10-12
1890 sf = new SequenceFeature("CDS_predicted", "", 10, 12, 0f, null);
1892 ds.addSequenceFeature(sf);
1894 List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
1896 * verify ranges { [12-10], [6-4] }
1898 assertEquals(6, MappingUtils.getLength(ranges));
1899 assertEquals(2, ranges.size());
1900 assertEquals(12, ranges.get(0)[0]);
1901 assertEquals(10, ranges.get(0)[1]);
1902 assertEquals(6, ranges.get(1)[0]);
1903 assertEquals(4, ranges.get(1)[1]);
1907 * Tests for the method that maps the subset of a dna sequence that has CDS
1908 * (or subtype) feature - reverse strand case where the start codon is
1911 @Test(groups = "Functional", enabled = false)
1912 // test turned off as currently findCdsPositions is not strand-dependent
1913 // left in case it comes around again...
1914 public void testFindCdsPositions_reverseStrandThreePrimeIncomplete()
1916 SequenceI dnaSeq = new Sequence("dna", "aaagGGCCCaaaTTTttt");
1917 dnaSeq.createDatasetSequence();
1918 SequenceI ds = dnaSeq.getDatasetSequence();
1921 SequenceFeature sf = new SequenceFeature("CDS", "", 5, 9, 0f, null);
1923 ds.addSequenceFeature(sf);
1924 // CDS for dna 13-15
1925 sf = new SequenceFeature("CDS_predicted", "", 13, 15, 0f, null);
1927 sf.setPhase("2"); // skip 2 bases to start of next codon
1928 ds.addSequenceFeature(sf);
1930 List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
1933 * check the mapping starts with the first complete codon
1934 * expect ranges [13, 13], [9, 5]
1936 assertEquals(6, MappingUtils.getLength(ranges));
1937 assertEquals(2, ranges.size());
1938 assertEquals(13, ranges.get(0)[0]);
1939 assertEquals(13, ranges.get(0)[1]);
1940 assertEquals(9, ranges.get(1)[0]);
1941 assertEquals(5, ranges.get(1)[1]);
1944 @Test(groups = "Functional")
1945 public void testAlignAs_alternateTranscriptsUngapped()
1947 SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
1948 SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
1949 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
1950 ((Alignment) dna).createDatasetAlignment();
1951 SequenceI cds1 = new Sequence("cds1", "GGGTTT");
1952 SequenceI cds2 = new Sequence("cds2", "CCCAAA");
1953 AlignmentI cds = new Alignment(new SequenceI[] { cds1, cds2 });
1954 ((Alignment) cds).createDatasetAlignment();
1956 AlignedCodonFrame acf = new AlignedCodonFrame();
1957 MapList map = new MapList(new int[] { 4, 9 }, new int[] { 1, 6 }, 1, 1);
1958 acf.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(), map);
1959 map = new MapList(new int[] { 1, 3, 10, 12 }, new int[] { 1, 6 }, 1, 1);
1960 acf.addMap(dna2.getDatasetSequence(), cds2.getDatasetSequence(), map);
1963 * verify CDS alignment is as:
1964 * cccGGGTTTaaa (cdna)
1965 * CCCgggtttAAA (cdna)
1967 * ---GGGTTT--- (cds)
1968 * CCC------AAA (cds)
1970 dna.addCodonFrame(acf);
1971 AlignmentUtils.alignAs(cds, dna);
1972 assertEquals("---GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
1973 assertEquals("CCC------AAA", cds.getSequenceAt(1).getSequenceAsString());
1976 @Test(groups = { "Functional" })
1977 public void testAddMappedPositions()
1979 SequenceI from = new Sequence("dna", "ggAA-ATcc-TT-g");
1980 SequenceI seq1 = new Sequence("cds", "AAATTT");
1981 from.createDatasetSequence();
1982 seq1.createDatasetSequence();
1983 Mapping mapping = new Mapping(seq1, new MapList(
1984 new int[] { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1));
1985 Map<Integer, Map<SequenceI, Character>> map = new TreeMap<>();
1986 AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
1989 * verify map has seq1 residues in columns 3,4,6,7,11,12
1991 assertEquals(6, map.size());
1992 assertEquals('A', map.get(3).get(seq1).charValue());
1993 assertEquals('A', map.get(4).get(seq1).charValue());
1994 assertEquals('A', map.get(6).get(seq1).charValue());
1995 assertEquals('T', map.get(7).get(seq1).charValue());
1996 assertEquals('T', map.get(11).get(seq1).charValue());
1997 assertEquals('T', map.get(12).get(seq1).charValue());
2005 * Test case where the mapping 'from' range includes a stop codon which is
2006 * absent in the 'to' range
2008 @Test(groups = { "Functional" })
2009 public void testAddMappedPositions_withStopCodon()
2011 SequenceI from = new Sequence("dna", "ggAA-ATcc-TT-g");
2012 SequenceI seq1 = new Sequence("cds", "AAATTT");
2013 from.createDatasetSequence();
2014 seq1.createDatasetSequence();
2015 Mapping mapping = new Mapping(seq1, new MapList(
2016 new int[] { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1));
2017 Map<Integer, Map<SequenceI, Character>> map = new TreeMap<>();
2018 AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
2021 * verify map has seq1 residues in columns 3,4,6,7,11,12
2023 assertEquals(6, map.size());
2024 assertEquals('A', map.get(3).get(seq1).charValue());
2025 assertEquals('A', map.get(4).get(seq1).charValue());
2026 assertEquals('A', map.get(6).get(seq1).charValue());
2027 assertEquals('T', map.get(7).get(seq1).charValue());
2028 assertEquals('T', map.get(11).get(seq1).charValue());
2029 assertEquals('T', map.get(12).get(seq1).charValue());
2033 * Test for the case where the products for which we want CDS are specified.
2034 * This is to represent the case where EMBL has CDS mappings to both Uniprot
2035 * and EMBLCDSPROTEIN. makeCdsAlignment() should only return the mappings for
2036 * the protein sequences specified.
2038 @Test(groups = { "Functional" })
2039 public void testMakeCdsAlignment_filterProducts()
2041 SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
2042 SequenceI dna2 = new Sequence("dna2", "GGGcccTTTaaaCCC");
2043 SequenceI pep1 = new Sequence("Uniprot|pep1", "GF");
2044 SequenceI pep2 = new Sequence("Uniprot|pep2", "GFP");
2045 SequenceI pep3 = new Sequence("EMBL|pep3", "GF");
2046 SequenceI pep4 = new Sequence("EMBL|pep4", "GFP");
2047 dna1.createDatasetSequence();
2048 dna2.createDatasetSequence();
2049 pep1.createDatasetSequence();
2050 pep2.createDatasetSequence();
2051 pep3.createDatasetSequence();
2052 pep4.createDatasetSequence();
2053 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
2054 dna.setDataset(null);
2055 AlignmentI emblPeptides = new Alignment(new SequenceI[] { pep3, pep4 });
2056 emblPeptides.setDataset(null);
2058 AlignedCodonFrame acf = new AlignedCodonFrame();
2059 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
2060 new int[] { 1, 2 }, 3, 1);
2061 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
2062 acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map);
2063 dna.addCodonFrame(acf);
2065 acf = new AlignedCodonFrame();
2066 map = new MapList(new int[] { 1, 3, 7, 9, 13, 15 }, new int[] { 1, 3 },
2068 acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
2069 acf.addMap(dna2.getDatasetSequence(), pep4.getDatasetSequence(), map);
2070 dna.addCodonFrame(acf);
2073 * execute method under test to find CDS for EMBL peptides only
2075 AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
2076 dna1, dna2 }, dna.getDataset(), emblPeptides.getSequencesArray());
2078 assertEquals(2, cds.getSequences().size());
2079 assertEquals("GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
2080 assertEquals("GGGTTTCCC", cds.getSequenceAt(1).getSequenceAsString());
2083 * verify shared, extended alignment dataset
2085 assertSame(dna.getDataset(), cds.getDataset());
2086 assertTrue(dna.getDataset().getSequences()
2087 .contains(cds.getSequenceAt(0).getDatasetSequence()));
2088 assertTrue(dna.getDataset().getSequences()
2089 .contains(cds.getSequenceAt(1).getDatasetSequence()));
2092 * Verify mappings from CDS to peptide, cDNA to CDS, and cDNA to peptide
2093 * the mappings are on the shared alignment dataset
2095 List<AlignedCodonFrame> cdsMappings = cds.getDataset().getCodonFrames();
2097 * 6 mappings, 2*(DNA->CDS), 2*(DNA->Pep), 2*(CDS->Pep)
2099 assertEquals(6, cdsMappings.size());
2102 * verify that mapping sets for dna and cds alignments are different
2103 * [not current behaviour - all mappings are on the alignment dataset]
2105 // select -> subselect type to test.
2106 // Assert.assertNotSame(dna.getCodonFrames(), cds.getCodonFrames());
2107 // assertEquals(4, dna.getCodonFrames().size());
2108 // assertEquals(4, cds.getCodonFrames().size());
2111 * Two mappings involve pep3 (dna to pep3, cds to pep3)
2112 * Mapping from pep3 to GGGTTT in first new exon sequence
2114 List<AlignedCodonFrame> pep3Mappings = MappingUtils
2115 .findMappingsForSequence(pep3, cdsMappings);
2116 assertEquals(2, pep3Mappings.size());
2117 List<AlignedCodonFrame> mappings = MappingUtils
2118 .findMappingsForSequence(cds.getSequenceAt(0), pep3Mappings);
2119 assertEquals(1, mappings.size());
2122 SearchResultsI sr = MappingUtils.buildSearchResults(pep3, 1, mappings);
2123 assertEquals(1, sr.getResults().size());
2124 SearchResultMatchI m = sr.getResults().get(0);
2125 assertSame(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
2126 assertEquals(1, m.getStart());
2127 assertEquals(3, m.getEnd());
2129 sr = MappingUtils.buildSearchResults(pep3, 2, mappings);
2130 m = sr.getResults().get(0);
2131 assertSame(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
2132 assertEquals(4, m.getStart());
2133 assertEquals(6, m.getEnd());
2136 * Two mappings involve pep4 (dna to pep4, cds to pep4)
2137 * Verify mapping from pep4 to GGGTTTCCC in second new exon sequence
2139 List<AlignedCodonFrame> pep4Mappings = MappingUtils
2140 .findMappingsForSequence(pep4, cdsMappings);
2141 assertEquals(2, pep4Mappings.size());
2142 mappings = MappingUtils.findMappingsForSequence(cds.getSequenceAt(1),
2144 assertEquals(1, mappings.size());
2146 sr = MappingUtils.buildSearchResults(pep4, 1, mappings);
2147 assertEquals(1, sr.getResults().size());
2148 m = sr.getResults().get(0);
2149 assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
2150 assertEquals(1, m.getStart());
2151 assertEquals(3, m.getEnd());
2153 sr = MappingUtils.buildSearchResults(pep4, 2, mappings);
2154 m = sr.getResults().get(0);
2155 assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
2156 assertEquals(4, m.getStart());
2157 assertEquals(6, m.getEnd());
2159 sr = MappingUtils.buildSearchResults(pep4, 3, mappings);
2160 m = sr.getResults().get(0);
2161 assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
2162 assertEquals(7, m.getStart());
2163 assertEquals(9, m.getEnd());
2167 * Test the method that just copies aligned sequences, provided all sequences
2168 * to be aligned share the aligned sequence's dataset
2170 @Test(groups = "Functional")
2171 public void testAlignAsSameSequences()
2173 SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
2174 SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
2175 AlignmentI al1 = new Alignment(new SequenceI[] { dna1, dna2 });
2176 ((Alignment) al1).createDatasetAlignment();
2178 SequenceI dna3 = new Sequence(dna1);
2179 SequenceI dna4 = new Sequence(dna2);
2180 assertSame(dna3.getDatasetSequence(), dna1.getDatasetSequence());
2181 assertSame(dna4.getDatasetSequence(), dna2.getDatasetSequence());
2182 String seq1 = "-cc-GG-GT-TT--aaa";
2183 dna3.setSequence(seq1);
2184 String seq2 = "C--C-Cgg--gtt-tAA-A-";
2185 dna4.setSequence(seq2);
2186 AlignmentI al2 = new Alignment(new SequenceI[] { dna3, dna4 });
2187 ((Alignment) al2).createDatasetAlignment();
2190 * alignment removes gapped columns (two internal, two trailing)
2192 assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
2193 String aligned1 = "-cc-GG-GTTT-aaa";
2194 assertEquals(aligned1,
2195 al1.getSequenceAt(0).getSequenceAsString());
2196 String aligned2 = "C--C-Cgg-gtttAAA";
2197 assertEquals(aligned2,
2198 al1.getSequenceAt(1).getSequenceAsString());
2201 * add another sequence to 'aligned' - should still succeed, since
2202 * unaligned sequences still share a dataset with aligned sequences
2204 SequenceI dna5 = new Sequence("dna5", "CCCgggtttAAA");
2205 dna5.createDatasetSequence();
2206 al2.addSequence(dna5);
2207 assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
2208 assertEquals(aligned1, al1.getSequenceAt(0).getSequenceAsString());
2209 assertEquals(aligned2, al1.getSequenceAt(1).getSequenceAsString());
2212 * add another sequence to 'unaligned' - should fail, since now not
2213 * all unaligned sequences share a dataset with aligned sequences
2215 SequenceI dna6 = new Sequence("dna6", "CCCgggtttAAA");
2216 dna6.createDatasetSequence();
2217 al1.addSequence(dna6);
2218 // JAL-2110 JBP Comment: what's the use case for this behaviour ?
2219 assertFalse(AlignmentUtils.alignAsSameSequences(al1, al2));
2222 @Test(groups = "Functional")
2223 public void testAlignAsSameSequencesMultipleSubSeq()
2225 SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
2226 SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
2227 SequenceI as1 = dna1.deriveSequence(); // cccGGGTTTaaa/1-12
2228 SequenceI as2 = dna1.deriveSequence().getSubSequence(3, 7); // GGGT/4-7
2229 SequenceI as3 = dna2.deriveSequence(); // CCCgggtttAAA/1-12
2230 as1.insertCharAt(6, 5, '-');
2231 assertEquals("cccGGG-----TTTaaa", as1.getSequenceAsString());
2232 as2.insertCharAt(6, 5, '-');
2233 assertEquals("GGGT-----", as2.getSequenceAsString());
2234 as3.insertCharAt(3, 5, '-');
2235 assertEquals("CCC-----gggtttAAA", as3.getSequenceAsString());
2236 AlignmentI aligned = new Alignment(new SequenceI[] { as1, as2, as3 });
2238 // why do we need to cast this still ?
2239 ((Alignment) aligned).createDatasetAlignment();
2240 SequenceI uas1 = dna1.deriveSequence();
2241 SequenceI uas2 = dna1.deriveSequence().getSubSequence(3, 7);
2242 SequenceI uas3 = dna2.deriveSequence();
2243 AlignmentI tobealigned = new Alignment(new SequenceI[] { uas1, uas2,
2245 ((Alignment) tobealigned).createDatasetAlignment();
2248 * alignAs lines up dataset sequences and removes empty columns (two)
2250 assertTrue(AlignmentUtils.alignAsSameSequences(tobealigned, aligned));
2251 assertEquals("cccGGG---TTTaaa", uas1.getSequenceAsString());
2252 assertEquals("GGGT", uas2.getSequenceAsString());
2253 assertEquals("CCC---gggtttAAA", uas3.getSequenceAsString());
2256 @Test(groups = { "Functional" })
2257 public void testTransferGeneLoci()
2259 SequenceI from = new Sequence("transcript",
2260 "aaacccgggTTTAAACCCGGGtttaaacccgggttt");
2261 SequenceI to = new Sequence("CDS", "TTTAAACCCGGG");
2262 MapList map = new MapList(new int[] { 1, 12 }, new int[] { 10, 21 }, 1,
2266 * first with nothing to transfer
2268 AlignmentUtils.transferGeneLoci(from, map, to);
2269 assertNull(to.getGeneLoci());
2272 * next with gene loci set on 'from' sequence
2274 int[] exons = new int[] { 100, 105, 155, 164, 210, 229 };
2275 MapList geneMap = new MapList(new int[] { 1, 36 }, exons, 1, 1);
2276 from.setGeneLoci("human", "GRCh38", "7", geneMap);
2277 AlignmentUtils.transferGeneLoci(from, map, to);
2279 GeneLociI toLoci = to.getGeneLoci();
2280 assertNotNull(toLoci);
2281 // DBRefEntry constructor upper-cases 'source'
2282 assertEquals("HUMAN", toLoci.getSpeciesId());
2283 assertEquals("GRCh38", toLoci.getAssemblyId());
2284 assertEquals("7", toLoci.getChromosomeId());
2287 * transcript 'exons' are 1-6, 7-16, 17-36
2288 * CDS 1:12 is transcript 10-21
2289 * transcript 'CDS' is 10-16, 17-21
2290 * which is 'gene' 158-164, 210-214
2292 MapList toMap = toLoci.getMapping();
2293 assertEquals(1, toMap.getFromRanges().size());
2294 assertEquals(2, toMap.getFromRanges().get(0).length);
2295 assertEquals(1, toMap.getFromRanges().get(0)[0]);
2296 assertEquals(12, toMap.getFromRanges().get(0)[1]);
2297 assertEquals(2, toMap.getToRanges().size());
2298 assertEquals(2, toMap.getToRanges().get(0).length);
2299 assertEquals(158, toMap.getToRanges().get(0)[0]);
2300 assertEquals(164, toMap.getToRanges().get(0)[1]);
2301 assertEquals(210, toMap.getToRanges().get(1)[0]);
2302 assertEquals(214, toMap.getToRanges().get(1)[1]);
2303 // or summarised as (but toString might change in future):
2304 assertEquals("[ [1, 12] ] 1:1 to [ [158, 164] [210, 214] ]",
2308 * an existing value is not overridden
2310 geneMap = new MapList(new int[] { 1, 36 }, new int[] { 36, 1 }, 1, 1);
2311 from.setGeneLoci("inhuman", "GRCh37", "6", geneMap);
2312 AlignmentUtils.transferGeneLoci(from, map, to);
2313 assertEquals("GRCh38", toLoci.getAssemblyId());
2314 assertEquals("7", toLoci.getChromosomeId());
2315 toMap = toLoci.getMapping();
2316 assertEquals("[ [1, 12] ] 1:1 to [ [158, 164] [210, 214] ]",
2321 * Tests for the method that maps nucleotide to protein based on CDS features
2323 @Test(groups = "Functional")
2324 public void testMapCdsToProtein()
2326 SequenceI peptide = new Sequence("pep", "KLQ");
2329 * Case 1: CDS 3 times length of peptide
2330 * NB method only checks lengths match, not translation
2332 SequenceI dna = new Sequence("dna", "AACGacgtCTCCT");
2333 dna.createDatasetSequence();
2334 dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
2335 dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 13, null));
2336 MapList ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2337 assertEquals(3, ml.getFromRatio());
2338 assertEquals(1, ml.getToRatio());
2339 assertEquals("[[1, 3]]",
2340 Arrays.deepToString(ml.getToRanges().toArray()));
2341 assertEquals("[[1, 4], [9, 13]]",
2342 Arrays.deepToString(ml.getFromRanges().toArray()));
2345 * Case 2: CDS 3 times length of peptide + stop codon
2346 * (note code does not currently check trailing codon is a stop codon)
2348 dna = new Sequence("dna", "AACGacgtCTCCTCCC");
2349 dna.createDatasetSequence();
2350 dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
2351 dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 16, null));
2352 ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2353 assertEquals(3, ml.getFromRatio());
2354 assertEquals(1, ml.getToRatio());
2355 assertEquals("[[1, 3]]",
2356 Arrays.deepToString(ml.getToRanges().toArray()));
2357 assertEquals("[[1, 4], [9, 13]]",
2358 Arrays.deepToString(ml.getFromRanges().toArray()));
2361 * Case 3: CDS longer than 3 * peptide + stop codon - no mapping is made
2363 dna = new Sequence("dna", "AACGacgtCTCCTTGATCA");
2364 dna.createDatasetSequence();
2365 dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
2366 dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 19, null));
2367 ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2371 * Case 4: CDS shorter than 3 * peptide - no mapping is made
2373 dna = new Sequence("dna", "AACGacgtCTCC");
2374 dna.createDatasetSequence();
2375 dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
2376 dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 12, null));
2377 ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2381 * Case 5: CDS 3 times length of peptide + part codon - mapping is truncated
2383 dna = new Sequence("dna", "AACGacgtCTCCTTG");
2384 dna.createDatasetSequence();
2385 dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
2386 dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 15, null));
2387 ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2388 assertEquals(3, ml.getFromRatio());
2389 assertEquals(1, ml.getToRatio());
2390 assertEquals("[[1, 3]]",
2391 Arrays.deepToString(ml.getToRanges().toArray()));
2392 assertEquals("[[1, 4], [9, 13]]",
2393 Arrays.deepToString(ml.getFromRanges().toArray()));
2396 * Case 6: incomplete start codon corresponding to X in peptide
2398 dna = new Sequence("dna", "ACGacgtCTCCTTGG");
2399 dna.createDatasetSequence();
2400 SequenceFeature sf = new SequenceFeature("CDS", "", 1, 3, null);
2401 sf.setPhase("2"); // skip 2 positions (AC) to start of next codon (GCT)
2402 dna.addSequenceFeature(sf);
2403 dna.addSequenceFeature(new SequenceFeature("CDS", "", 8, 15, null));
2404 peptide = new Sequence("pep", "XLQ");
2405 ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2406 assertEquals("[[2, 3]]",
2407 Arrays.deepToString(ml.getToRanges().toArray()));
2408 assertEquals("[[3, 3], [8, 12]]",
2409 Arrays.deepToString(ml.getFromRanges().toArray()));
2413 * Tests for the method that locates the CDS sequence that has a mapping to
2414 * the given protein. That is, given a transcript-to-peptide mapping, find the
2415 * cds-to-peptide mapping that relates to both, and return the CDS sequence.
2418 public void testFindCdsForProtein()
2420 List<AlignedCodonFrame> mappings = new ArrayList<>();
2421 AlignedCodonFrame acf1 = new AlignedCodonFrame();
2424 SequenceI dna1 = new Sequence("dna1", "cgatATcgGCTATCTATGacg");
2425 dna1.createDatasetSequence();
2427 // NB we currently exclude STOP codon from CDS sequences
2428 // the test would need to change if this changes in future
2429 SequenceI cds1 = new Sequence("cds1", "ATGCTATCT");
2430 cds1.createDatasetSequence();
2432 SequenceI pep1 = new Sequence("pep1", "MLS");
2433 pep1.createDatasetSequence();
2434 List<AlignedCodonFrame> seqMappings = new ArrayList<>();
2435 MapList mapList = new MapList(
2437 { 5, 6, 9, 15 }, new int[] { 1, 3 }, 3, 1);
2438 Mapping dnaToPeptide = new Mapping(pep1.getDatasetSequence(), mapList);
2440 // add dna to peptide mapping
2441 seqMappings.add(acf1);
2442 acf1.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
2446 * first case - no dna-to-CDS mapping exists - search fails
2448 SequenceI seq = AlignmentUtils.findCdsForProtein(mappings, dna1,
2449 seqMappings, dnaToPeptide);
2453 * second case - CDS-to-peptide mapping exists but no dna-to-CDS
2456 // todo this test fails if the mapping is added to acf1, not acf2
2457 // need to tidy up use of lists of mappings in AlignedCodonFrame
2458 AlignedCodonFrame acf2 = new AlignedCodonFrame();
2460 MapList cdsToPeptideMapping = new MapList(new int[]
2461 { 1, 9 }, new int[] { 1, 3 }, 3, 1);
2462 acf2.addMap(cds1.getDatasetSequence(), pep1.getDatasetSequence(),
2463 cdsToPeptideMapping);
2464 assertNull(AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
2468 * third case - add dna-to-CDS mapping - CDS is now found!
2470 MapList dnaToCdsMapping = new MapList(new int[] { 5, 6, 9, 15 },
2473 acf1.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(),
2475 seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
2477 assertSame(seq, cds1.getDatasetSequence());
2481 * Tests for the method that locates the CDS sequence that has a mapping to
2482 * the given protein. That is, given a transcript-to-peptide mapping, find the
2483 * cds-to-peptide mapping that relates to both, and return the CDS sequence.
2484 * This test is for the case where transcript and CDS are the same length.
2487 public void testFindCdsForProtein_noUTR()
2489 List<AlignedCodonFrame> mappings = new ArrayList<>();
2490 AlignedCodonFrame acf1 = new AlignedCodonFrame();
2493 SequenceI dna1 = new Sequence("dna1", "ATGCTATCTTAA");
2494 dna1.createDatasetSequence();
2496 // NB we currently exclude STOP codon from CDS sequences
2497 // the test would need to change if this changes in future
2498 SequenceI cds1 = new Sequence("cds1", "ATGCTATCT");
2499 cds1.createDatasetSequence();
2501 SequenceI pep1 = new Sequence("pep1", "MLS");
2502 pep1.createDatasetSequence();
2503 List<AlignedCodonFrame> seqMappings = new ArrayList<>();
2504 MapList mapList = new MapList(
2506 { 1, 9 }, new int[] { 1, 3 }, 3, 1);
2507 Mapping dnaToPeptide = new Mapping(pep1.getDatasetSequence(), mapList);
2509 // add dna to peptide mapping
2510 seqMappings.add(acf1);
2511 acf1.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
2515 * first case - transcript lacks CDS features - it appears to be
2516 * the CDS sequence and is returned
2518 SequenceI seq = AlignmentUtils.findCdsForProtein(mappings, dna1,
2519 seqMappings, dnaToPeptide);
2520 assertSame(seq, dna1.getDatasetSequence());
2523 * second case - transcript has CDS feature - this means it is
2524 * not returned as a match for CDS (CDS sequences don't have CDS features)
2526 dna1.addSequenceFeature(
2527 new SequenceFeature(SequenceOntologyI.CDS, "cds", 1, 12, null));
2528 seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
2533 * third case - CDS-to-peptide mapping exists but no dna-to-CDS
2536 // todo this test fails if the mapping is added to acf1, not acf2
2537 // need to tidy up use of lists of mappings in AlignedCodonFrame
2538 AlignedCodonFrame acf2 = new AlignedCodonFrame();
2540 MapList cdsToPeptideMapping = new MapList(new int[]
2541 { 1, 9 }, new int[] { 1, 3 }, 3, 1);
2542 acf2.addMap(cds1.getDatasetSequence(), pep1.getDatasetSequence(),
2543 cdsToPeptideMapping);
2544 assertNull(AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
2548 * fourth case - add dna-to-CDS mapping - CDS is now found!
2550 MapList dnaToCdsMapping = new MapList(new int[] { 1, 9 },
2553 acf1.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(),
2555 seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
2557 assertSame(seq, cds1.getDatasetSequence());