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.junit.Assert.assertNotEquals;
24 import static org.testng.AssertJUnit.assertEquals;
25 import static org.testng.AssertJUnit.assertFalse;
26 import static org.testng.AssertJUnit.assertNotNull;
27 import static org.testng.AssertJUnit.assertNull;
28 import static org.testng.AssertJUnit.assertSame;
29 import static org.testng.AssertJUnit.assertTrue;
31 import jalview.analysis.AlignmentUtils.DnaVariant;
32 import jalview.datamodel.AlignedCodonFrame;
33 import jalview.datamodel.Alignment;
34 import jalview.datamodel.AlignmentAnnotation;
35 import jalview.datamodel.AlignmentI;
36 import jalview.datamodel.Annotation;
37 import jalview.datamodel.DBRefEntry;
38 import jalview.datamodel.GeneLociI;
39 import jalview.datamodel.Mapping;
40 import jalview.datamodel.SearchResultMatchI;
41 import jalview.datamodel.SearchResultsI;
42 import jalview.datamodel.Sequence;
43 import jalview.datamodel.SequenceFeature;
44 import jalview.datamodel.SequenceI;
45 import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
46 import jalview.datamodel.features.SequenceFeatures;
47 import jalview.gui.JvOptionPane;
48 import jalview.io.AppletFormatAdapter;
49 import jalview.io.DataSourceType;
50 import jalview.io.FileFormat;
51 import jalview.io.FileFormatI;
52 import jalview.io.FormatAdapter;
53 import jalview.io.gff.SequenceOntologyI;
54 import jalview.util.MapList;
55 import jalview.util.MappingUtils;
57 import java.io.IOException;
58 import java.util.ArrayList;
59 import java.util.Arrays;
60 import java.util.Iterator;
61 import java.util.LinkedHashMap;
62 import java.util.List;
64 import java.util.TreeMap;
66 import org.testng.annotations.BeforeClass;
67 import org.testng.annotations.Test;
69 public class AlignmentUtilsTests
71 private static Sequence ts = new Sequence("short",
72 "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
74 @BeforeClass(alwaysRun = true)
75 public void setUpJvOptionPane()
77 JvOptionPane.setInteractiveMode(false);
78 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
81 @Test(groups = { "Functional" })
82 public void testExpandContext()
84 AlignmentI al = new Alignment(new Sequence[] {});
85 for (int i = 4; i < 14; i += 2)
87 SequenceI s1 = ts.deriveSequence().getSubSequence(i, i + 7);
90 System.out.println(new AppletFormatAdapter().formatSequences(
93 for (int flnk = -1; flnk < 25; flnk++)
95 AlignmentI exp = AlignmentUtils.expandContext(al, flnk);
96 System.out.println("\nFlank size: " + flnk);
97 System.out.println(new AppletFormatAdapter().formatSequences(
98 FileFormat.Clustal, exp, true));
102 * Full expansion to complete sequences
104 for (SequenceI sq : exp.getSequences())
106 String ung = sq.getSequenceAsString().replaceAll("-+", "");
107 final String errorMsg = "Flanking sequence not the same as original dataset sequence.\n"
110 + sq.getDatasetSequence().getSequenceAsString();
111 assertTrue(errorMsg, ung.equalsIgnoreCase(sq.getDatasetSequence()
112 .getSequenceAsString()));
118 * Last sequence is fully expanded, others have leading gaps to match
120 assertTrue(exp.getSequenceAt(4).getSequenceAsString()
122 assertTrue(exp.getSequenceAt(3).getSequenceAsString()
123 .startsWith("--abc"));
124 assertTrue(exp.getSequenceAt(2).getSequenceAsString()
125 .startsWith("----abc"));
126 assertTrue(exp.getSequenceAt(1).getSequenceAsString()
127 .startsWith("------abc"));
128 assertTrue(exp.getSequenceAt(0).getSequenceAsString()
129 .startsWith("--------abc"));
135 * Test that annotations are correctly adjusted by expandContext
137 @Test(groups = { "Functional" })
138 public void testExpandContext_annotation()
140 AlignmentI al = new Alignment(new Sequence[] {});
141 SequenceI ds = new Sequence("Seq1", "ABCDEFGHI");
143 SequenceI seq1 = ds.deriveSequence().getSubSequence(3, 6);
144 al.addSequence(seq1);
147 * Annotate DEF with 4/5/6 respectively
149 Annotation[] anns = new Annotation[] { new Annotation(4),
150 new Annotation(5), new Annotation(6) };
151 AlignmentAnnotation ann = new AlignmentAnnotation("SS",
152 "secondary structure", anns);
153 seq1.addAlignmentAnnotation(ann);
156 * The annotations array should match aligned positions
158 assertEquals(3, ann.annotations.length);
159 assertEquals(4, ann.annotations[0].value, 0.001);
160 assertEquals(5, ann.annotations[1].value, 0.001);
161 assertEquals(6, ann.annotations[2].value, 0.001);
164 * Check annotation to sequence position mappings before expanding the
165 * sequence; these are set up in Sequence.addAlignmentAnnotation ->
166 * Annotation.setSequenceRef -> createSequenceMappings
168 assertNull(ann.getAnnotationForPosition(1));
169 assertNull(ann.getAnnotationForPosition(2));
170 assertNull(ann.getAnnotationForPosition(3));
171 assertEquals(4, ann.getAnnotationForPosition(4).value, 0.001);
172 assertEquals(5, ann.getAnnotationForPosition(5).value, 0.001);
173 assertEquals(6, ann.getAnnotationForPosition(6).value, 0.001);
174 assertNull(ann.getAnnotationForPosition(7));
175 assertNull(ann.getAnnotationForPosition(8));
176 assertNull(ann.getAnnotationForPosition(9));
179 * Expand the subsequence to the full sequence abcDEFghi
181 AlignmentI expanded = AlignmentUtils.expandContext(al, -1);
182 assertEquals("abcDEFghi", expanded.getSequenceAt(0)
183 .getSequenceAsString());
186 * Confirm the alignment and sequence have the same SS annotation,
187 * referencing the expanded sequence
189 ann = expanded.getSequenceAt(0).getAnnotation()[0];
190 assertSame(ann, expanded.getAlignmentAnnotation()[0]);
191 assertSame(expanded.getSequenceAt(0), ann.sequenceRef);
194 * The annotations array should have null values except for annotated
197 assertNull(ann.annotations[0]);
198 assertNull(ann.annotations[1]);
199 assertNull(ann.annotations[2]);
200 assertEquals(4, ann.annotations[3].value, 0.001);
201 assertEquals(5, ann.annotations[4].value, 0.001);
202 assertEquals(6, ann.annotations[5].value, 0.001);
203 assertNull(ann.annotations[6]);
204 assertNull(ann.annotations[7]);
205 assertNull(ann.annotations[8]);
208 * sequence position mappings should be unchanged
210 assertNull(ann.getAnnotationForPosition(1));
211 assertNull(ann.getAnnotationForPosition(2));
212 assertNull(ann.getAnnotationForPosition(3));
213 assertEquals(4, ann.getAnnotationForPosition(4).value, 0.001);
214 assertEquals(5, ann.getAnnotationForPosition(5).value, 0.001);
215 assertEquals(6, ann.getAnnotationForPosition(6).value, 0.001);
216 assertNull(ann.getAnnotationForPosition(7));
217 assertNull(ann.getAnnotationForPosition(8));
218 assertNull(ann.getAnnotationForPosition(9));
222 * Test method that returns a map of lists of sequences by sequence name.
224 * @throws IOException
226 @Test(groups = { "Functional" })
227 public void testGetSequencesByName() throws IOException
229 final String data = ">Seq1Name\nKQYL\n" + ">Seq2Name\nRFPW\n"
230 + ">Seq1Name\nABCD\n";
231 AlignmentI al = loadAlignment(data, FileFormat.Fasta);
232 Map<String, List<SequenceI>> map = AlignmentUtils
233 .getSequencesByName(al);
234 assertEquals(2, map.keySet().size());
235 assertEquals(2, map.get("Seq1Name").size());
236 assertEquals("KQYL", map.get("Seq1Name").get(0).getSequenceAsString());
237 assertEquals("ABCD", map.get("Seq1Name").get(1).getSequenceAsString());
238 assertEquals(1, map.get("Seq2Name").size());
239 assertEquals("RFPW", map.get("Seq2Name").get(0).getSequenceAsString());
243 * Helper method to load an alignment and ensure dataset sequences are set up.
249 * @throws IOException
251 protected AlignmentI loadAlignment(final String data, FileFormatI format)
254 AlignmentI a = new FormatAdapter().readFile(data,
255 DataSourceType.PASTE, format);
261 * Test mapping of protein to cDNA, for the case where we have no sequence
262 * cross-references, so mappings are made first-served 1-1 where sequences
265 * @throws IOException
267 @Test(groups = { "Functional" })
268 public void testMapProteinAlignmentToCdna_noXrefs() throws IOException
270 List<SequenceI> protseqs = new ArrayList<>();
271 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
272 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
273 protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
274 AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
275 protein.setDataset(null);
277 List<SequenceI> dnaseqs = new ArrayList<>();
278 dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR
279 dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAA")); // = EIQ
280 dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ
281 dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG")); // = EIQ
282 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
283 cdna.setDataset(null);
285 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
287 // 3 mappings made, each from 1 to 1 sequence
288 assertEquals(3, protein.getCodonFrames().size());
289 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
290 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
291 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
293 // V12345 mapped to A22222
294 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
296 assertEquals(1, acf.getdnaSeqs().length);
297 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
298 acf.getdnaSeqs()[0]);
299 Mapping[] protMappings = acf.getProtMappings();
300 assertEquals(1, protMappings.length);
301 MapList mapList = protMappings[0].getMap();
302 assertEquals(3, mapList.getFromRatio());
303 assertEquals(1, mapList.getToRatio());
304 assertTrue(Arrays.equals(new int[] { 1, 9 }, mapList.getFromRanges()
306 assertEquals(1, mapList.getFromRanges().size());
307 assertTrue(Arrays.equals(new int[] { 1, 3 },
308 mapList.getToRanges().get(0)));
309 assertEquals(1, mapList.getToRanges().size());
311 // V12346 mapped to A33333
312 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
313 assertEquals(1, acf.getdnaSeqs().length);
314 assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
315 acf.getdnaSeqs()[0]);
317 // V12347 mapped to A11111
318 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
319 assertEquals(1, acf.getdnaSeqs().length);
320 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
321 acf.getdnaSeqs()[0]);
323 // no mapping involving the 'extra' A44444
324 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(3)).isEmpty());
328 * Test for the alignSequenceAs method that takes two sequences and a mapping.
330 @Test(groups = { "Functional" })
331 public void testAlignSequenceAs_withMapping_noIntrons()
333 MapList map = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 }, 3, 1);
336 * No existing gaps in dna:
338 checkAlignSequenceAs("GGGAAA", "-A-L-", false, false, map,
342 * Now introduce gaps in dna but ignore them when realigning.
344 checkAlignSequenceAs("-G-G-G-A-A-A-", "-A-L-", false, false, map,
348 * Now include gaps in dna when realigning. First retaining 'mapped' gaps
349 * only, i.e. those within the exon region.
351 checkAlignSequenceAs("-G-G--G-A--A-A-", "-A-L-", true, false, map,
352 "---G-G--G---A--A-A");
355 * Include all gaps in dna when realigning (within and without the exon
356 * region). The leading gap, and the gaps between codons, are subsumed by
357 * the protein alignment gap.
359 checkAlignSequenceAs("-G-GG--AA-A---", "-A-L-", true, true, map,
360 "---G-GG---AA-A---");
363 * Include only unmapped gaps in dna when realigning (outside the exon
364 * region). The leading gap, and the gaps between codons, are subsumed by
365 * the protein alignment gap.
367 checkAlignSequenceAs("-G-GG--AA-A-", "-A-L-", false, true, map,
372 * Test for the alignSequenceAs method that takes two sequences and a mapping.
374 @Test(groups = { "Functional" })
375 public void testAlignSequenceAs_withMapping_withIntrons()
378 * Exons at codon 2 (AAA) and 4 (TTT)
380 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
381 new int[] { 1, 2 }, 3, 1);
384 * Simple case: no gaps in dna
386 checkAlignSequenceAs("GGGAAACCCTTTGGG", "--A-L-", false, false, map,
387 "GGG---AAACCCTTTGGG");
390 * Add gaps to dna - but ignore when realigning.
392 checkAlignSequenceAs("-G-G-G--A--A---AC-CC-T-TT-GG-G-", "--A-L-",
393 false, false, map, "GGG---AAACCCTTTGGG");
396 * Add gaps to dna - include within exons only when realigning.
398 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
399 true, false, map, "GGG---A--A---ACCCT-TTGGG");
402 * Include gaps outside exons only when realigning.
404 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
405 false, true, map, "-G-G-GAAAC-CCTTT-GG-G-");
408 * Include gaps following first intron if we are 'preserving mapped gaps'
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-");
414 * Include all gaps in dna when realigning.
416 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
417 true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
421 * Test for the case where not all of the protein sequence is mapped to cDNA.
423 @Test(groups = { "Functional" })
424 public void testAlignSequenceAs_withMapping_withUnmappedProtein()
427 * Exons at codon 2 (AAA) and 4 (TTT) mapped to A and P
429 final MapList map = new MapList(new int[] { 4, 6, 10, 12 }, new int[] {
433 * -L- 'aligns' ccc------
435 checkAlignSequenceAs("gggAAAcccTTTggg", "-A-L-P-", false, false, map,
436 "gggAAAccc------TTTggg");
440 * Helper method that performs and verifies the method under test.
443 * the sequence to be realigned
445 * the sequence whose alignment is to be copied
446 * @param preserveMappedGaps
447 * @param preserveUnmappedGaps
451 protected void checkAlignSequenceAs(final String alignee,
452 final String alignModel, final boolean preserveMappedGaps,
453 final boolean preserveUnmappedGaps, MapList map,
454 final String expected)
456 SequenceI alignMe = new Sequence("Seq1", alignee);
457 alignMe.createDatasetSequence();
458 SequenceI alignFrom = new Sequence("Seq2", alignModel);
459 alignFrom.createDatasetSequence();
460 AlignedCodonFrame acf = new AlignedCodonFrame();
461 acf.addMap(alignMe.getDatasetSequence(),
462 alignFrom.getDatasetSequence(), map);
464 AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "---", '-',
465 preserveMappedGaps, preserveUnmappedGaps);
466 assertEquals(expected, alignMe.getSequenceAsString());
470 * Test for the alignSequenceAs method where we preserve gaps in introns only.
472 @Test(groups = { "Functional" })
473 public void testAlignSequenceAs_keepIntronGapsOnly()
477 * Intron GGGAAA followed by exon CCCTTT
479 MapList map = new MapList(new int[] { 7, 12 }, new int[] { 1, 2 }, 3, 1);
481 checkAlignSequenceAs("GG-G-AA-A-C-CC-T-TT", "AL", false, true, map,
486 * Test the method that realigns protein to match mapped codon alignment.
488 @Test(groups = { "Functional" })
489 public void testAlignProteinAsDna()
491 // seq1 codons are [1,2,3] [4,5,6] [7,8,9] [10,11,12]
492 SequenceI dna1 = new Sequence("Seq1", "TGCCATTACCAG-");
493 // seq2 codons are [1,3,4] [5,6,7] [8,9,10] [11,12,13]
494 SequenceI dna2 = new Sequence("Seq2", "T-GCCATTACCAG");
495 // seq3 codons are [1,2,3] [4,5,7] [8,9,10] [11,12,13]
496 SequenceI dna3 = new Sequence("Seq3", "TGCCA-TTACCAG");
497 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
498 dna.setDataset(null);
500 // protein alignment will be realigned like dna
501 SequenceI prot1 = new Sequence("Seq1", "CHYQ");
502 SequenceI prot2 = new Sequence("Seq2", "CHYQ");
503 SequenceI prot3 = new Sequence("Seq3", "CHYQ");
504 SequenceI prot4 = new Sequence("Seq4", "R-QSV"); // unmapped, unchanged
505 AlignmentI protein = new Alignment(new SequenceI[] { prot1, prot2,
507 protein.setDataset(null);
509 MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1);
510 AlignedCodonFrame acf = new AlignedCodonFrame();
511 acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
512 acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map);
513 acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map);
514 ArrayList<AlignedCodonFrame> acfs = new ArrayList<>();
516 protein.setCodonFrames(acfs);
519 * Translated codon order is [1,2,3] [1,3,4] [4,5,6] [4,5,7] [5,6,7] [7,8,9]
520 * [8,9,10] [10,11,12] [11,12,13]
522 AlignmentUtils.alignProteinAsDna(protein, dna);
523 assertEquals("C-H--Y-Q-", prot1.getSequenceAsString());
524 assertEquals("-C--H-Y-Q", prot2.getSequenceAsString());
525 assertEquals("C--H--Y-Q", prot3.getSequenceAsString());
526 assertEquals("R-QSV", prot4.getSequenceAsString());
530 * Test the method that tests whether a CDNA sequence translates to a protein
533 @Test(groups = { "Functional" })
534 public void testTranslatesAs()
536 // null arguments check
537 assertFalse(AlignmentUtils.translatesAs(null, 0, null));
538 assertFalse(AlignmentUtils.translatesAs(new char[] { 't' }, 0, null));
539 assertFalse(AlignmentUtils.translatesAs(null, 0, new char[] { 'a' }));
541 // straight translation
542 assertTrue(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
543 "FPKG".toCharArray()));
544 // with extra start codon (not in protein)
545 assertTrue(AlignmentUtils.translatesAs("atgtttcccaaaggg".toCharArray(),
546 3, "FPKG".toCharArray()));
547 // with stop codon1 (not in protein)
548 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtaa".toCharArray(),
549 0, "FPKG".toCharArray()));
550 // with stop codon1 (in protein as *)
551 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtaa".toCharArray(),
552 0, "FPKG*".toCharArray()));
553 // with stop codon2 (not in protein)
554 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtag".toCharArray(),
555 0, "FPKG".toCharArray()));
556 // with stop codon3 (not in protein)
557 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtga".toCharArray(),
558 0, "FPKG".toCharArray()));
559 // with start and stop codon1
560 assertTrue(AlignmentUtils.translatesAs(
561 "atgtttcccaaagggtaa".toCharArray(), 3, "FPKG".toCharArray()));
562 // with start and stop codon1 (in protein as *)
563 assertTrue(AlignmentUtils.translatesAs(
564 "atgtttcccaaagggtaa".toCharArray(), 3, "FPKG*".toCharArray()));
565 // with start and stop codon2
566 assertTrue(AlignmentUtils.translatesAs(
567 "atgtttcccaaagggtag".toCharArray(), 3, "FPKG".toCharArray()));
568 // with start and stop codon3
569 assertTrue(AlignmentUtils.translatesAs(
570 "atgtttcccaaagggtga".toCharArray(), 3, "FPKG".toCharArray()));
572 // with embedded stop codons
573 assertTrue(AlignmentUtils.translatesAs(
574 "atgtttTAGcccaaaTAAgggtga".toCharArray(), 3,
575 "F*PK*G".toCharArray()));
578 assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
579 0, "FPMG".toCharArray()));
582 assertFalse(AlignmentUtils.translatesAs("tttcccaaagg".toCharArray(), 0,
583 "FPKG".toCharArray()));
586 assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
587 0, "FPK".toCharArray()));
589 // overlong dna (doesn't end in stop codon)
590 assertFalse(AlignmentUtils.translatesAs(
591 "tttcccaaagggttt".toCharArray(), 0, "FPKG".toCharArray()));
593 // dna + stop codon + more
594 assertFalse(AlignmentUtils.translatesAs(
595 "tttcccaaagggttaga".toCharArray(), 0, "FPKG".toCharArray()));
598 assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
599 0, "FPKGQ".toCharArray()));
603 * Test mapping of protein to cDNA, for cases where the cDNA has start and/or
604 * stop codons in addition to the protein coding sequence.
606 * @throws IOException
608 @Test(groups = { "Functional" })
609 public void testMapProteinAlignmentToCdna_withStartAndStopCodons()
612 List<SequenceI> protseqs = new ArrayList<>();
613 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
614 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
615 protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
616 AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
617 protein.setDataset(null);
619 List<SequenceI> dnaseqs = new ArrayList<>();
621 dnaseqs.add(new Sequence("EMBL|A11111", "ATGTCAGCACGC"));
623 dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAATAA"));
624 // = start +EIQ + stop
625 dnaseqs.add(new Sequence("EMBL|A33333", "ATGGAAATCCAGTAG"));
626 dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG"));
627 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
628 cdna.setDataset(null);
630 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
632 // 3 mappings made, each from 1 to 1 sequence
633 assertEquals(3, protein.getCodonFrames().size());
634 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
635 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
636 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
638 // V12345 mapped from A22222
639 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
641 assertEquals(1, acf.getdnaSeqs().length);
642 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
643 acf.getdnaSeqs()[0]);
644 Mapping[] protMappings = acf.getProtMappings();
645 assertEquals(1, protMappings.length);
646 MapList mapList = protMappings[0].getMap();
647 assertEquals(3, mapList.getFromRatio());
648 assertEquals(1, mapList.getToRatio());
649 assertTrue(Arrays.equals(new int[] { 1, 9 }, mapList.getFromRanges()
651 assertEquals(1, mapList.getFromRanges().size());
652 assertTrue(Arrays.equals(new int[] { 1, 3 },
653 mapList.getToRanges().get(0)));
654 assertEquals(1, mapList.getToRanges().size());
656 // V12346 mapped from A33333 starting position 4
657 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
658 assertEquals(1, acf.getdnaSeqs().length);
659 assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
660 acf.getdnaSeqs()[0]);
661 protMappings = acf.getProtMappings();
662 assertEquals(1, protMappings.length);
663 mapList = protMappings[0].getMap();
664 assertEquals(3, mapList.getFromRatio());
665 assertEquals(1, mapList.getToRatio());
666 assertTrue(Arrays.equals(new int[] { 4, 12 }, mapList.getFromRanges()
668 assertEquals(1, mapList.getFromRanges().size());
669 assertTrue(Arrays.equals(new int[] { 1, 3 },
670 mapList.getToRanges().get(0)));
671 assertEquals(1, mapList.getToRanges().size());
673 // V12347 mapped to A11111 starting position 4
674 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
675 assertEquals(1, acf.getdnaSeqs().length);
676 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
677 acf.getdnaSeqs()[0]);
678 protMappings = acf.getProtMappings();
679 assertEquals(1, protMappings.length);
680 mapList = protMappings[0].getMap();
681 assertEquals(3, mapList.getFromRatio());
682 assertEquals(1, mapList.getToRatio());
683 assertTrue(Arrays.equals(new int[] { 4, 12 }, mapList.getFromRanges()
685 assertEquals(1, mapList.getFromRanges().size());
686 assertTrue(Arrays.equals(new int[] { 1, 3 },
687 mapList.getToRanges().get(0)));
688 assertEquals(1, mapList.getToRanges().size());
690 // no mapping involving the 'extra' A44444
691 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(3)).isEmpty());
695 * Test mapping of protein to cDNA, for the case where we have some sequence
696 * cross-references. Verify that 1-to-many mappings are made where
697 * cross-references exist and sequences are mappable.
699 * @throws IOException
701 @Test(groups = { "Functional" })
702 public void testMapProteinAlignmentToCdna_withXrefs() throws IOException
704 List<SequenceI> protseqs = new ArrayList<>();
705 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
706 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
707 protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
708 AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
709 protein.setDataset(null);
711 List<SequenceI> dnaseqs = new ArrayList<>();
712 dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR
713 dnaseqs.add(new Sequence("EMBL|A22222", "ATGGAGATACAA")); // = start + EIQ
714 dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ
715 dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG")); // = EIQ
716 dnaseqs.add(new Sequence("EMBL|A55555", "GAGATTCAG")); // = EIQ
717 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[5]));
718 cdna.setDataset(null);
720 // Xref A22222 to V12345 (should get mapped)
721 dnaseqs.get(1).addDBRef(new DBRefEntry("UNIPROT", "1", "V12345"));
722 // Xref V12345 to A44444 (should get mapped)
723 protseqs.get(0).addDBRef(new DBRefEntry("EMBL", "1", "A44444"));
724 // Xref A33333 to V12347 (sequence mismatch - should not get mapped)
725 dnaseqs.get(2).addDBRef(new DBRefEntry("UNIPROT", "1", "V12347"));
726 // as V12345 is mapped to A22222 and A44444, this leaves V12346 unmapped.
727 // it should get paired up with the unmapped A33333
728 // A11111 should be mapped to V12347
729 // A55555 is spare and has no xref so is not mapped
731 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
733 // 4 protein mappings made for 3 proteins, 2 to V12345, 1 each to V12346/7
734 assertEquals(3, protein.getCodonFrames().size());
735 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
736 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
737 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
739 // one mapping for each of the first 4 cDNA sequences
740 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(0)).size());
741 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(1)).size());
742 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(2)).size());
743 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(3)).size());
745 // V12345 mapped to A22222 and A44444
746 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
748 assertEquals(2, acf.getdnaSeqs().length);
749 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
750 acf.getdnaSeqs()[0]);
751 assertEquals(cdna.getSequenceAt(3).getDatasetSequence(),
752 acf.getdnaSeqs()[1]);
754 // V12346 mapped to A33333
755 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
756 assertEquals(1, acf.getdnaSeqs().length);
757 assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
758 acf.getdnaSeqs()[0]);
760 // V12347 mapped to A11111
761 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
762 assertEquals(1, acf.getdnaSeqs().length);
763 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
764 acf.getdnaSeqs()[0]);
766 // no mapping involving the 'extra' A55555
767 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(4)).isEmpty());
771 * Test mapping of protein to cDNA, for the case where we have some sequence
772 * cross-references. Verify that once we have made an xref mapping we don't
773 * also map un-xrefd sequeces.
775 * @throws IOException
777 @Test(groups = { "Functional" })
778 public void testMapProteinAlignmentToCdna_prioritiseXrefs()
781 List<SequenceI> protseqs = new ArrayList<>();
782 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
783 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
784 AlignmentI protein = new Alignment(
785 protseqs.toArray(new SequenceI[protseqs.size()]));
786 protein.setDataset(null);
788 List<SequenceI> dnaseqs = new ArrayList<>();
789 dnaseqs.add(new Sequence("EMBL|A11111", "GAAATCCAG")); // = EIQ
790 dnaseqs.add(new Sequence("EMBL|A22222", "GAAATTCAG")); // = EIQ
791 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[dnaseqs
793 cdna.setDataset(null);
795 // Xref A22222 to V12345 (should get mapped)
796 // A11111 should then be mapped to the unmapped V12346
797 dnaseqs.get(1).addDBRef(new DBRefEntry("UNIPROT", "1", "V12345"));
799 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
801 // 2 protein mappings made
802 assertEquals(2, protein.getCodonFrames().size());
803 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
804 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
806 // one mapping for each of the cDNA sequences
807 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(0)).size());
808 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(1)).size());
810 // V12345 mapped to A22222
811 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
813 assertEquals(1, acf.getdnaSeqs().length);
814 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
815 acf.getdnaSeqs()[0]);
817 // V12346 mapped to A11111
818 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
819 assertEquals(1, acf.getdnaSeqs().length);
820 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
821 acf.getdnaSeqs()[0]);
825 * Test the method that shows or hides sequence annotations by type(s) and
828 @Test(groups = { "Functional" })
829 public void testShowOrHideSequenceAnnotations()
831 SequenceI seq1 = new Sequence("Seq1", "AAA");
832 SequenceI seq2 = new Sequence("Seq2", "BBB");
833 SequenceI seq3 = new Sequence("Seq3", "CCC");
834 Annotation[] anns = new Annotation[] { new Annotation(2f) };
835 AlignmentAnnotation ann1 = new AlignmentAnnotation("Structure", "ann1",
837 ann1.setSequenceRef(seq1);
838 AlignmentAnnotation ann2 = new AlignmentAnnotation("Structure", "ann2",
840 ann2.setSequenceRef(seq2);
841 AlignmentAnnotation ann3 = new AlignmentAnnotation("Structure", "ann3",
843 AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "ann4", anns);
844 ann4.setSequenceRef(seq1);
845 AlignmentAnnotation ann5 = new AlignmentAnnotation("Temp", "ann5", anns);
846 ann5.setSequenceRef(seq2);
847 AlignmentAnnotation ann6 = new AlignmentAnnotation("Temp", "ann6", anns);
848 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
849 al.addAnnotation(ann1); // Structure for Seq1
850 al.addAnnotation(ann2); // Structure for Seq2
851 al.addAnnotation(ann3); // Structure for no sequence
852 al.addAnnotation(ann4); // Temp for seq1
853 al.addAnnotation(ann5); // Temp for seq2
854 al.addAnnotation(ann6); // Temp for no sequence
855 List<String> types = new ArrayList<>();
856 List<SequenceI> scope = new ArrayList<>();
859 * Set all sequence related Structure to hidden (ann1, ann2)
861 types.add("Structure");
862 AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, false,
864 assertFalse(ann1.visible);
865 assertFalse(ann2.visible);
866 assertTrue(ann3.visible); // not sequence-related, not affected
867 assertTrue(ann4.visible); // not Structure, not affected
868 assertTrue(ann5.visible); // "
869 assertTrue(ann6.visible); // not sequence-related, not affected
872 * Set Temp in {seq1, seq3} to hidden
878 AlignmentUtils.showOrHideSequenceAnnotations(al, types, scope, false,
880 assertFalse(ann1.visible); // unchanged
881 assertFalse(ann2.visible); // unchanged
882 assertTrue(ann3.visible); // not sequence-related, not affected
883 assertFalse(ann4.visible); // Temp for seq1 hidden
884 assertTrue(ann5.visible); // not in scope, not affected
885 assertTrue(ann6.visible); // not sequence-related, not affected
888 * Set Temp in all sequences to hidden
894 AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, false,
896 assertFalse(ann1.visible); // unchanged
897 assertFalse(ann2.visible); // unchanged
898 assertTrue(ann3.visible); // not sequence-related, not affected
899 assertFalse(ann4.visible); // Temp for seq1 hidden
900 assertFalse(ann5.visible); // Temp for seq2 hidden
901 assertTrue(ann6.visible); // not sequence-related, not affected
904 * Set all types in {seq1, seq3} to visible
910 AlignmentUtils.showOrHideSequenceAnnotations(al, types, scope, true,
912 assertTrue(ann1.visible); // Structure for seq1 set visible
913 assertFalse(ann2.visible); // not in scope, unchanged
914 assertTrue(ann3.visible); // not sequence-related, not affected
915 assertTrue(ann4.visible); // Temp for seq1 set visible
916 assertFalse(ann5.visible); // not in scope, unchanged
917 assertTrue(ann6.visible); // not sequence-related, not affected
920 * Set all types in all scope to hidden
922 AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, true,
924 assertFalse(ann1.visible);
925 assertFalse(ann2.visible);
926 assertTrue(ann3.visible); // not sequence-related, not affected
927 assertFalse(ann4.visible);
928 assertFalse(ann5.visible);
929 assertTrue(ann6.visible); // not sequence-related, not affected
933 * Tests for the method that checks if one sequence cross-references another
935 @Test(groups = { "Functional" })
936 public void testHasCrossRef()
938 assertFalse(AlignmentUtils.hasCrossRef(null, null));
939 SequenceI seq1 = new Sequence("EMBL|A12345", "ABCDEF");
940 assertFalse(AlignmentUtils.hasCrossRef(seq1, null));
941 assertFalse(AlignmentUtils.hasCrossRef(null, seq1));
942 SequenceI seq2 = new Sequence("UNIPROT|V20192", "ABCDEF");
943 assertFalse(AlignmentUtils.hasCrossRef(seq1, seq2));
946 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "v20193"));
947 assertFalse(AlignmentUtils.hasCrossRef(seq1, seq2));
949 // case-insensitive; version number is ignored
950 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "v20192"));
951 assertTrue(AlignmentUtils.hasCrossRef(seq1, seq2));
954 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
955 assertTrue(AlignmentUtils.hasCrossRef(seq1, seq2));
956 // test is one-way only
957 assertFalse(AlignmentUtils.hasCrossRef(seq2, seq1));
961 * Tests for the method that checks if either sequence cross-references the
964 @Test(groups = { "Functional" })
965 public void testHaveCrossRef()
967 assertFalse(AlignmentUtils.hasCrossRef(null, null));
968 SequenceI seq1 = new Sequence("EMBL|A12345", "ABCDEF");
969 assertFalse(AlignmentUtils.haveCrossRef(seq1, null));
970 assertFalse(AlignmentUtils.haveCrossRef(null, seq1));
971 SequenceI seq2 = new Sequence("UNIPROT|V20192", "ABCDEF");
972 assertFalse(AlignmentUtils.haveCrossRef(seq1, seq2));
974 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
975 assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
976 // next is true for haveCrossRef, false for hasCrossRef
977 assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
979 // now the other way round
980 seq1.setDBRefs(null);
981 seq2.addDBRef(new DBRefEntry("EMBL", "1", "A12345"));
982 assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
983 assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
986 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
987 assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
988 assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
992 * Test the method that extracts the cds-only part of a dna alignment.
994 @Test(groups = { "Functional" })
995 public void testMakeCdsAlignment()
999 * dna1 --> [4, 6] [10,12] --> pep1
1000 * dna2 --> [1, 3] [7, 9] [13,15] --> pep2
1002 SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
1003 SequenceI dna2 = new Sequence("dna2", "GGGcccTTTaaaCCC");
1004 SequenceI pep1 = new Sequence("pep1", "GF");
1005 SequenceI pep2 = new Sequence("pep2", "GFP");
1006 pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "pep1"));
1007 pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "pep2"));
1008 dna1.createDatasetSequence();
1009 dna2.createDatasetSequence();
1010 pep1.createDatasetSequence();
1011 pep2.createDatasetSequence();
1012 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
1013 dna.setDataset(null);
1016 * put a variant feature on dna2 base 8
1017 * - should transfer to cds2 base 5
1019 dna2.addSequenceFeature(new SequenceFeature("variant", "hgmd", 8, 8,
1023 * need a sourceDbRef if we are to construct dbrefs to the CDS
1024 * sequence from the dna contig sequences
1026 DBRefEntry dbref = new DBRefEntry("ENSEMBL", "0", "dna1");
1027 dna1.getDatasetSequence().addDBRef(dbref);
1028 org.testng.Assert.assertEquals(dbref, dna1.getPrimaryDBRefs().get(0));
1029 dbref = new DBRefEntry("ENSEMBL", "0", "dna2");
1030 dna2.getDatasetSequence().addDBRef(dbref);
1031 org.testng.Assert.assertEquals(dbref, dna2.getPrimaryDBRefs().get(0));
1034 * CDS sequences are 'discovered' from dna-to-protein mappings on the alignment
1035 * dataset (e.g. added from dbrefs by CrossRef.findXrefSequences)
1037 MapList mapfordna1 = new MapList(new int[] { 4, 6, 10, 12 }, new int[] {
1039 AlignedCodonFrame acf = new AlignedCodonFrame();
1040 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
1042 dna.addCodonFrame(acf);
1043 MapList mapfordna2 = new MapList(new int[] { 1, 3, 7, 9, 13, 15 },
1044 new int[] { 1, 3 }, 3, 1);
1045 acf = new AlignedCodonFrame();
1046 acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(),
1048 dna.addCodonFrame(acf);
1051 * In this case, mappings originally came from matching Uniprot accessions
1052 * - so need an xref on dna involving those regions.
1053 * These are normally constructed from CDS annotation
1055 DBRefEntry dna1xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep1",
1056 new Mapping(mapfordna1));
1057 dna1.addDBRef(dna1xref);
1058 assertEquals(2, dna1.getDBRefs().length); // to self and to pep1
1059 DBRefEntry dna2xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep2",
1060 new Mapping(mapfordna2));
1061 dna2.addDBRef(dna2xref);
1062 assertEquals(2, dna2.getDBRefs().length); // to self and to pep2
1065 * execute method under test:
1067 AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
1068 dna1, dna2 }, dna.getDataset(), null);
1071 * verify cds sequences
1073 assertEquals(2, cds.getSequences().size());
1074 assertEquals("GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
1075 assertEquals("GGGTTTCCC", cds.getSequenceAt(1).getSequenceAsString());
1078 * verify shared, extended alignment dataset
1080 assertSame(dna.getDataset(), cds.getDataset());
1081 SequenceI cds1Dss = cds.getSequenceAt(0).getDatasetSequence();
1082 SequenceI cds2Dss = cds.getSequenceAt(1).getDatasetSequence();
1083 assertTrue(dna.getDataset().getSequences().contains(cds1Dss));
1084 assertTrue(dna.getDataset().getSequences().contains(cds2Dss));
1087 * verify CDS has a dbref with mapping to peptide
1089 assertNotNull(cds1Dss.getDBRefs());
1090 assertEquals(2, cds1Dss.getDBRefs().length);
1091 dbref = cds1Dss.getDBRefs()[0];
1092 assertEquals(dna1xref.getSource(), dbref.getSource());
1093 // version is via ensembl's primary ref
1094 assertEquals(dna1xref.getVersion(), dbref.getVersion());
1095 assertEquals(dna1xref.getAccessionId(), dbref.getAccessionId());
1096 assertNotNull(dbref.getMap());
1097 assertSame(pep1.getDatasetSequence(), dbref.getMap().getTo());
1098 MapList cdsMapping = new MapList(new int[] { 1, 6 },
1099 new int[] { 1, 2 }, 3, 1);
1100 assertEquals(cdsMapping, dbref.getMap().getMap());
1103 * verify peptide has added a dbref with reverse mapping to CDS
1105 assertNotNull(pep1.getDBRefs());
1106 // FIXME pep1.getDBRefs() is 1 - is that the correct behaviour ?
1107 assertEquals(2, pep1.getDBRefs().length);
1108 dbref = pep1.getDBRefs()[1];
1109 assertEquals("ENSEMBL", dbref.getSource());
1110 assertEquals("0", dbref.getVersion());
1111 assertEquals("CDS|dna1", dbref.getAccessionId());
1112 assertNotNull(dbref.getMap());
1113 assertSame(cds1Dss, dbref.getMap().getTo());
1114 assertEquals(cdsMapping.getInverse(), dbref.getMap().getMap());
1117 * verify cDNA has added a dbref with mapping to CDS
1119 assertEquals(3, dna1.getDBRefs().length);
1120 DBRefEntry dbRefEntry = dna1.getDBRefs()[2];
1121 assertSame(cds1Dss, dbRefEntry.getMap().getTo());
1122 MapList dnaToCdsMapping = new MapList(new int[] { 4, 6, 10, 12 },
1123 new int[] { 1, 6 }, 1, 1);
1124 assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap());
1125 assertEquals(3, dna2.getDBRefs().length);
1126 dbRefEntry = dna2.getDBRefs()[2];
1127 assertSame(cds2Dss, dbRefEntry.getMap().getTo());
1128 dnaToCdsMapping = new MapList(new int[] { 1, 3, 7, 9, 13, 15 },
1129 new int[] { 1, 9 }, 1, 1);
1130 assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap());
1133 * verify CDS has added a dbref with mapping to cDNA
1135 assertEquals(2, cds1Dss.getDBRefs().length);
1136 dbRefEntry = cds1Dss.getDBRefs()[1];
1137 assertSame(dna1.getDatasetSequence(), dbRefEntry.getMap().getTo());
1138 MapList cdsToDnaMapping = new MapList(new int[] { 1, 6 }, new int[] {
1139 4, 6, 10, 12 }, 1, 1);
1140 assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap());
1141 assertEquals(2, cds2Dss.getDBRefs().length);
1142 dbRefEntry = cds2Dss.getDBRefs()[1];
1143 assertSame(dna2.getDatasetSequence(), dbRefEntry.getMap().getTo());
1144 cdsToDnaMapping = new MapList(new int[] { 1, 9 }, new int[] { 1, 3, 7,
1146 assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap());
1149 * Verify mappings from CDS to peptide, cDNA to CDS, and cDNA to peptide
1150 * the mappings are on the shared alignment dataset
1151 * 6 mappings, 2*(DNA->CDS), 2*(DNA->Pep), 2*(CDS->Pep)
1153 List<AlignedCodonFrame> cdsMappings = cds.getDataset().getCodonFrames();
1154 assertEquals(6, cdsMappings.size());
1157 * verify that mapping sets for dna and cds alignments are different
1158 * [not current behaviour - all mappings are on the alignment dataset]
1160 // select -> subselect type to test.
1161 // Assert.assertNotSame(dna.getCodonFrames(), cds.getCodonFrames());
1162 // assertEquals(4, dna.getCodonFrames().size());
1163 // assertEquals(4, cds.getCodonFrames().size());
1166 * Two mappings involve pep1 (dna to pep1, cds to pep1)
1167 * Mapping from pep1 to GGGTTT in first new exon sequence
1169 List<AlignedCodonFrame> pep1Mappings = MappingUtils
1170 .findMappingsForSequence(pep1, cdsMappings);
1171 assertEquals(2, pep1Mappings.size());
1172 List<AlignedCodonFrame> mappings = MappingUtils
1173 .findMappingsForSequence(cds.getSequenceAt(0), pep1Mappings);
1174 assertEquals(1, mappings.size());
1177 SearchResultsI sr = MappingUtils.buildSearchResults(pep1, 1, mappings);
1178 assertEquals(1, sr.getResults().size());
1179 SearchResultMatchI m = sr.getResults().get(0);
1180 assertSame(cds1Dss, m.getSequence());
1181 assertEquals(1, m.getStart());
1182 assertEquals(3, m.getEnd());
1184 sr = MappingUtils.buildSearchResults(pep1, 2, mappings);
1185 m = sr.getResults().get(0);
1186 assertSame(cds1Dss, m.getSequence());
1187 assertEquals(4, m.getStart());
1188 assertEquals(6, m.getEnd());
1191 * Two mappings involve pep2 (dna to pep2, cds to pep2)
1192 * Verify mapping from pep2 to GGGTTTCCC in second new exon sequence
1194 List<AlignedCodonFrame> pep2Mappings = MappingUtils
1195 .findMappingsForSequence(pep2, cdsMappings);
1196 assertEquals(2, pep2Mappings.size());
1197 mappings = MappingUtils.findMappingsForSequence(cds.getSequenceAt(1),
1199 assertEquals(1, mappings.size());
1201 sr = MappingUtils.buildSearchResults(pep2, 1, mappings);
1202 assertEquals(1, sr.getResults().size());
1203 m = sr.getResults().get(0);
1204 assertSame(cds2Dss, m.getSequence());
1205 assertEquals(1, m.getStart());
1206 assertEquals(3, m.getEnd());
1208 sr = MappingUtils.buildSearchResults(pep2, 2, mappings);
1209 m = sr.getResults().get(0);
1210 assertSame(cds2Dss, m.getSequence());
1211 assertEquals(4, m.getStart());
1212 assertEquals(6, m.getEnd());
1214 sr = MappingUtils.buildSearchResults(pep2, 3, mappings);
1215 m = sr.getResults().get(0);
1216 assertSame(cds2Dss, m.getSequence());
1217 assertEquals(7, m.getStart());
1218 assertEquals(9, m.getEnd());
1221 * check cds2 acquired a variant feature in position 5
1223 List<SequenceFeature> sfs = cds2Dss.getSequenceFeatures();
1225 assertEquals(1, sfs.size());
1226 assertEquals("variant", sfs.get(0).type);
1227 assertEquals(5, sfs.get(0).begin);
1228 assertEquals(5, sfs.get(0).end);
1232 * Test the method that makes a cds-only alignment from a DNA sequence and its
1233 * product mappings, for the case where there are multiple exon mappings to
1234 * different protein products.
1236 @Test(groups = { "Functional" })
1237 public void testMakeCdsAlignment_multipleProteins()
1239 SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
1240 SequenceI pep1 = new Sequence("pep1", "GF"); // GGGTTT
1241 SequenceI pep2 = new Sequence("pep2", "KP"); // aaaccc
1242 SequenceI pep3 = new Sequence("pep3", "KF"); // aaaTTT
1243 dna1.createDatasetSequence();
1244 pep1.createDatasetSequence();
1245 pep2.createDatasetSequence();
1246 pep3.createDatasetSequence();
1247 pep1.getDatasetSequence().addDBRef(
1248 new DBRefEntry("EMBLCDS", "2", "A12345"));
1249 pep2.getDatasetSequence().addDBRef(
1250 new DBRefEntry("EMBLCDS", "3", "A12346"));
1251 pep3.getDatasetSequence().addDBRef(
1252 new DBRefEntry("EMBLCDS", "4", "A12347"));
1255 * Create the CDS alignment
1257 AlignmentI dna = new Alignment(new SequenceI[] { dna1 });
1258 dna.setDataset(null);
1261 * Make the mappings from dna to protein
1263 // map ...GGG...TTT to GF
1264 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1265 new int[] { 1, 2 }, 3, 1);
1266 AlignedCodonFrame acf = new AlignedCodonFrame();
1267 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
1268 dna.addCodonFrame(acf);
1270 // map aaa...ccc to KP
1271 map = new MapList(new int[] { 1, 3, 7, 9 }, new int[] { 1, 2 }, 3, 1);
1272 acf = new AlignedCodonFrame();
1273 acf.addMap(dna1.getDatasetSequence(), pep2.getDatasetSequence(), map);
1274 dna.addCodonFrame(acf);
1276 // map aaa......TTT to KF
1277 map = new MapList(new int[] { 1, 3, 10, 12 }, new int[] { 1, 2 }, 3, 1);
1278 acf = new AlignedCodonFrame();
1279 acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map);
1280 dna.addCodonFrame(acf);
1283 * execute method under test
1285 AlignmentI cdsal = AlignmentUtils.makeCdsAlignment(
1286 new SequenceI[] { dna1 }, dna.getDataset(), null);
1289 * Verify we have 3 cds sequences, mapped to pep1/2/3 respectively
1291 List<SequenceI> cds = cdsal.getSequences();
1292 assertEquals(3, cds.size());
1295 * verify shared, extended alignment dataset
1297 assertSame(cdsal.getDataset(), dna.getDataset());
1298 assertTrue(dna.getDataset().getSequences()
1299 .contains(cds.get(0).getDatasetSequence()));
1300 assertTrue(dna.getDataset().getSequences()
1301 .contains(cds.get(1).getDatasetSequence()));
1302 assertTrue(dna.getDataset().getSequences()
1303 .contains(cds.get(2).getDatasetSequence()));
1306 * verify aligned cds sequences and their xrefs
1308 SequenceI cdsSeq = cds.get(0);
1309 assertEquals("GGGTTT", cdsSeq.getSequenceAsString());
1310 // assertEquals("dna1|A12345", cdsSeq.getName());
1311 assertEquals("CDS|dna1", cdsSeq.getName());
1312 // assertEquals(1, cdsSeq.getDBRefs().length);
1313 // DBRefEntry cdsRef = cdsSeq.getDBRefs()[0];
1314 // assertEquals("EMBLCDS", cdsRef.getSource());
1315 // assertEquals("2", cdsRef.getVersion());
1316 // assertEquals("A12345", cdsRef.getAccessionId());
1318 cdsSeq = cds.get(1);
1319 assertEquals("aaaccc", cdsSeq.getSequenceAsString());
1320 // assertEquals("dna1|A12346", cdsSeq.getName());
1321 assertEquals("CDS|dna1", cdsSeq.getName());
1322 // assertEquals(1, cdsSeq.getDBRefs().length);
1323 // cdsRef = cdsSeq.getDBRefs()[0];
1324 // assertEquals("EMBLCDS", cdsRef.getSource());
1325 // assertEquals("3", cdsRef.getVersion());
1326 // assertEquals("A12346", cdsRef.getAccessionId());
1328 cdsSeq = cds.get(2);
1329 assertEquals("aaaTTT", cdsSeq.getSequenceAsString());
1330 // assertEquals("dna1|A12347", cdsSeq.getName());
1331 assertEquals("CDS|dna1", cdsSeq.getName());
1332 // assertEquals(1, cdsSeq.getDBRefs().length);
1333 // cdsRef = cdsSeq.getDBRefs()[0];
1334 // assertEquals("EMBLCDS", cdsRef.getSource());
1335 // assertEquals("4", cdsRef.getVersion());
1336 // assertEquals("A12347", cdsRef.getAccessionId());
1339 * Verify there are mappings from each cds sequence to its protein product
1340 * and also to its dna source
1342 List<AlignedCodonFrame> newMappings = cdsal.getCodonFrames();
1345 * 6 mappings involve dna1 (to pep1/2/3, cds1/2/3)
1347 List<AlignedCodonFrame> dnaMappings = MappingUtils
1348 .findMappingsForSequence(dna1, newMappings);
1349 assertEquals(6, dnaMappings.size());
1354 List<AlignedCodonFrame> mappings = MappingUtils
1355 .findMappingsForSequence(pep1, dnaMappings);
1356 assertEquals(1, mappings.size());
1357 assertEquals(1, mappings.get(0).getMappings().size());
1358 assertSame(pep1.getDatasetSequence(), mappings.get(0).getMappings()
1359 .get(0).getMapping().getTo());
1364 List<AlignedCodonFrame> dnaToCds1Mappings = MappingUtils
1365 .findMappingsForSequence(cds.get(0), dnaMappings);
1366 Mapping mapping = dnaToCds1Mappings.get(0).getMappings().get(0)
1368 assertSame(cds.get(0).getDatasetSequence(), mapping.getTo());
1369 assertEquals("G(1) in CDS should map to G(4) in DNA", 4, mapping
1370 .getMap().getToPosition(1));
1375 mappings = MappingUtils.findMappingsForSequence(pep2, dnaMappings);
1376 assertEquals(1, mappings.size());
1377 assertEquals(1, mappings.get(0).getMappings().size());
1378 assertSame(pep2.getDatasetSequence(), mappings.get(0).getMappings()
1379 .get(0).getMapping().getTo());
1384 List<AlignedCodonFrame> dnaToCds2Mappings = MappingUtils
1385 .findMappingsForSequence(cds.get(1), dnaMappings);
1386 mapping = dnaToCds2Mappings.get(0).getMappings().get(0).getMapping();
1387 assertSame(cds.get(1).getDatasetSequence(), mapping.getTo());
1388 assertEquals("c(4) in CDS should map to c(7) in DNA", 7, mapping
1389 .getMap().getToPosition(4));
1394 mappings = MappingUtils.findMappingsForSequence(pep3, dnaMappings);
1395 assertEquals(1, mappings.size());
1396 assertEquals(1, mappings.get(0).getMappings().size());
1397 assertSame(pep3.getDatasetSequence(), mappings.get(0).getMappings()
1398 .get(0).getMapping().getTo());
1403 List<AlignedCodonFrame> dnaToCds3Mappings = MappingUtils
1404 .findMappingsForSequence(cds.get(2), dnaMappings);
1405 mapping = dnaToCds3Mappings.get(0).getMappings().get(0).getMapping();
1406 assertSame(cds.get(2).getDatasetSequence(), mapping.getTo());
1407 assertEquals("T(4) in CDS should map to T(10) in DNA", 10, mapping
1408 .getMap().getToPosition(4));
1411 @Test(groups = { "Functional" })
1412 public void testIsMappable()
1414 SequenceI dna1 = new Sequence("dna1", "cgCAGtgGT");
1415 SequenceI aa1 = new Sequence("aa1", "RSG");
1416 AlignmentI al1 = new Alignment(new SequenceI[] { dna1 });
1417 AlignmentI al2 = new Alignment(new SequenceI[] { aa1 });
1419 assertFalse(AlignmentUtils.isMappable(null, null));
1420 assertFalse(AlignmentUtils.isMappable(al1, null));
1421 assertFalse(AlignmentUtils.isMappable(null, al1));
1422 assertFalse(AlignmentUtils.isMappable(al1, al1));
1423 assertFalse(AlignmentUtils.isMappable(al2, al2));
1425 assertTrue(AlignmentUtils.isMappable(al1, al2));
1426 assertTrue(AlignmentUtils.isMappable(al2, al1));
1430 * Test creating a mapping when the sequences involved do not start at residue
1433 * @throws IOException
1435 @Test(groups = { "Functional" })
1436 public void testMapCdnaToProtein_forSubsequence() throws IOException
1438 SequenceI prot = new Sequence("UNIPROT|V12345", "E-I--Q", 10, 12);
1439 prot.createDatasetSequence();
1441 SequenceI dna = new Sequence("EMBL|A33333", "GAA--AT-C-CAG", 40, 48);
1442 dna.createDatasetSequence();
1444 MapList map = AlignmentUtils.mapCdnaToProtein(prot, dna);
1445 assertEquals(10, map.getToLowest());
1446 assertEquals(12, map.getToHighest());
1447 assertEquals(40, map.getFromLowest());
1448 assertEquals(48, map.getFromHighest());
1452 * Test for the alignSequenceAs method where we have protein mapped to protein
1454 @Test(groups = { "Functional" })
1455 public void testAlignSequenceAs_mappedProteinProtein()
1458 SequenceI alignMe = new Sequence("Match", "MGAASEV");
1459 alignMe.createDatasetSequence();
1460 SequenceI alignFrom = new Sequence("Query", "LQTGYMGAASEVMFSPTRR");
1461 alignFrom.createDatasetSequence();
1463 AlignedCodonFrame acf = new AlignedCodonFrame();
1464 // this is like a domain or motif match of part of a peptide sequence
1465 MapList map = new MapList(new int[] { 6, 12 }, new int[] { 1, 7 }, 1, 1);
1466 acf.addMap(alignFrom.getDatasetSequence(),
1467 alignMe.getDatasetSequence(), map);
1469 AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "-", '-', true,
1471 assertEquals("-----MGAASEV-------", alignMe.getSequenceAsString());
1475 * Test for the alignSequenceAs method where there are trailing unmapped
1476 * residues in the model sequence
1478 @Test(groups = { "Functional" })
1479 public void testAlignSequenceAs_withTrailingPeptide()
1481 // map first 3 codons to KPF; G is a trailing unmapped residue
1482 MapList map = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3, 1);
1484 checkAlignSequenceAs("AAACCCTTT", "K-PFG", true, true, map,
1489 * Tests for transferring features between mapped sequences
1491 @Test(groups = { "Functional" })
1492 public void testTransferFeatures()
1494 SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt");
1495 SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
1498 dna.addSequenceFeature(new SequenceFeature("type1", "desc1", 1, 2, 1f,
1500 // partial overlap - to [1, 1]
1501 dna.addSequenceFeature(new SequenceFeature("type2", "desc2", 3, 4, 2f,
1503 // exact overlap - to [1, 3]
1504 dna.addSequenceFeature(new SequenceFeature("type3", "desc3", 4, 6, 3f,
1506 // spanning overlap - to [2, 5]
1507 dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f,
1509 // exactly overlaps whole mapped range [1, 6]
1510 dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f,
1512 // no overlap (internal)
1513 dna.addSequenceFeature(new SequenceFeature("type6", "desc6", 7, 9, 6f,
1515 // no overlap (3' end)
1516 dna.addSequenceFeature(new SequenceFeature("type7", "desc7", 13, 15,
1518 // overlap (3' end) - to [6, 6]
1519 dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12,
1521 // extended overlap - to [6, +]
1522 dna.addSequenceFeature(new SequenceFeature("type9", "desc9", 12, 13,
1525 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1526 new int[] { 1, 6 }, 1, 1);
1529 * transferFeatures() will build 'partial overlap' for regions
1530 * that partially overlap 5' or 3' (start or end) of target sequence
1532 AlignmentUtils.transferFeatures(dna, cds, map, null);
1533 List<SequenceFeature> sfs = cds.getSequenceFeatures();
1534 assertEquals(6, sfs.size());
1536 SequenceFeature sf = sfs.get(0);
1537 assertEquals("type2", sf.getType());
1538 assertEquals("desc2", sf.getDescription());
1539 assertEquals(2f, sf.getScore());
1540 assertEquals(1, sf.getBegin());
1541 assertEquals(1, sf.getEnd());
1544 assertEquals("type3", sf.getType());
1545 assertEquals("desc3", sf.getDescription());
1546 assertEquals(3f, sf.getScore());
1547 assertEquals(1, sf.getBegin());
1548 assertEquals(3, sf.getEnd());
1551 assertEquals("type4", sf.getType());
1552 assertEquals(2, sf.getBegin());
1553 assertEquals(5, sf.getEnd());
1556 assertEquals("type5", sf.getType());
1557 assertEquals(1, sf.getBegin());
1558 assertEquals(6, sf.getEnd());
1561 assertEquals("type8", sf.getType());
1562 assertEquals(6, sf.getBegin());
1563 assertEquals(6, sf.getEnd());
1566 assertEquals("type9", sf.getType());
1567 assertEquals(6, sf.getBegin());
1568 assertEquals(6, sf.getEnd());
1572 * Tests for transferring features between mapped sequences
1574 @Test(groups = { "Functional" })
1575 public void testTransferFeatures_withOmit()
1577 SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt");
1578 SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
1580 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1581 new int[] { 1, 6 }, 1, 1);
1583 // [5, 11] maps to [2, 5]
1584 dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f,
1586 // [4, 12] maps to [1, 6]
1587 dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f,
1589 // [12, 12] maps to [6, 6]
1590 dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12,
1593 // desc4 and desc8 are the 'omit these' varargs
1594 AlignmentUtils.transferFeatures(dna, cds, map, null, "type4", "type8");
1595 List<SequenceFeature> sfs = cds.getSequenceFeatures();
1596 assertEquals(1, sfs.size());
1598 SequenceFeature sf = sfs.get(0);
1599 assertEquals("type5", sf.getType());
1600 assertEquals(1, sf.getBegin());
1601 assertEquals(6, sf.getEnd());
1605 * Tests for transferring features between mapped sequences
1607 @Test(groups = { "Functional" })
1608 public void testTransferFeatures_withSelect()
1610 SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt");
1611 SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
1613 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1614 new int[] { 1, 6 }, 1, 1);
1616 // [5, 11] maps to [2, 5]
1617 dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f,
1619 // [4, 12] maps to [1, 6]
1620 dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f,
1622 // [12, 12] maps to [6, 6]
1623 dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12,
1626 // "type5" is the 'select this type' argument
1627 AlignmentUtils.transferFeatures(dna, cds, map, "type5");
1628 List<SequenceFeature> sfs = cds.getSequenceFeatures();
1629 assertEquals(1, sfs.size());
1631 SequenceFeature sf = sfs.get(0);
1632 assertEquals("type5", sf.getType());
1633 assertEquals(1, sf.getBegin());
1634 assertEquals(6, sf.getEnd());
1638 * Test the method that extracts the cds-only part of a dna alignment, for the
1639 * case where the cds should be aligned to match its nucleotide sequence.
1641 @Test(groups = { "Functional" })
1642 public void testMakeCdsAlignment_alternativeTranscripts()
1644 SequenceI dna1 = new Sequence("dna1", "aaaGGGCC-----CTTTaaaGGG");
1645 // alternative transcript of same dna skips CCC codon
1646 SequenceI dna2 = new Sequence("dna2", "aaaGGGCC-----cttTaaaGGG");
1647 // dna3 has no mapping (protein product) so should be ignored here
1648 SequenceI dna3 = new Sequence("dna3", "aaaGGGCCCCCGGGcttTaaaGGG");
1649 SequenceI pep1 = new Sequence("pep1", "GPFG");
1650 SequenceI pep2 = new Sequence("pep2", "GPG");
1651 dna1.createDatasetSequence();
1652 dna2.createDatasetSequence();
1653 dna3.createDatasetSequence();
1654 pep1.createDatasetSequence();
1655 pep2.createDatasetSequence();
1657 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
1658 dna.setDataset(null);
1660 MapList map = new MapList(new int[] { 4, 12, 16, 18 },
1661 new int[] { 1, 4 }, 3, 1);
1662 AlignedCodonFrame acf = new AlignedCodonFrame();
1663 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
1664 dna.addCodonFrame(acf);
1665 map = new MapList(new int[] { 4, 8, 12, 12, 16, 18 },
1666 new int[] { 1, 3 }, 3, 1);
1667 acf = new AlignedCodonFrame();
1668 acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
1669 dna.addCodonFrame(acf);
1671 AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
1672 dna1, dna2, dna3 }, dna.getDataset(), null);
1673 List<SequenceI> cdsSeqs = cds.getSequences();
1674 assertEquals(2, cdsSeqs.size());
1675 assertEquals("GGGCCCTTTGGG", cdsSeqs.get(0).getSequenceAsString());
1676 assertEquals("GGGCCTGGG", cdsSeqs.get(1).getSequenceAsString());
1679 * verify shared, extended alignment dataset
1681 assertSame(dna.getDataset(), cds.getDataset());
1682 assertTrue(dna.getDataset().getSequences()
1683 .contains(cdsSeqs.get(0).getDatasetSequence()));
1684 assertTrue(dna.getDataset().getSequences()
1685 .contains(cdsSeqs.get(1).getDatasetSequence()));
1688 * Verify 6 mappings: dna1 to cds1, cds1 to pep1, dna1 to pep1
1689 * and the same for dna2/cds2/pep2
1691 List<AlignedCodonFrame> mappings = cds.getCodonFrames();
1692 assertEquals(6, mappings.size());
1695 * 2 mappings involve pep1
1697 List<AlignedCodonFrame> pep1Mappings = MappingUtils
1698 .findMappingsForSequence(pep1, mappings);
1699 assertEquals(2, pep1Mappings.size());
1702 * Get mapping of pep1 to cds1 and verify it
1703 * maps GPFG to 1-3,4-6,7-9,10-12
1705 List<AlignedCodonFrame> pep1CdsMappings = MappingUtils
1706 .findMappingsForSequence(cds.getSequenceAt(0), pep1Mappings);
1707 assertEquals(1, pep1CdsMappings.size());
1708 SearchResultsI sr = MappingUtils.buildSearchResults(pep1, 1,
1710 assertEquals(1, sr.getResults().size());
1711 SearchResultMatchI m = sr.getResults().get(0);
1712 assertEquals(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
1713 assertEquals(1, m.getStart());
1714 assertEquals(3, m.getEnd());
1715 sr = MappingUtils.buildSearchResults(pep1, 2, pep1CdsMappings);
1716 m = sr.getResults().get(0);
1717 assertEquals(4, m.getStart());
1718 assertEquals(6, m.getEnd());
1719 sr = MappingUtils.buildSearchResults(pep1, 3, pep1CdsMappings);
1720 m = sr.getResults().get(0);
1721 assertEquals(7, m.getStart());
1722 assertEquals(9, m.getEnd());
1723 sr = MappingUtils.buildSearchResults(pep1, 4, pep1CdsMappings);
1724 m = sr.getResults().get(0);
1725 assertEquals(10, m.getStart());
1726 assertEquals(12, m.getEnd());
1729 * Get mapping of pep2 to cds2 and verify it
1730 * maps GPG in pep2 to 1-3,4-6,7-9 in second CDS sequence
1732 List<AlignedCodonFrame> pep2Mappings = MappingUtils
1733 .findMappingsForSequence(pep2, mappings);
1734 assertEquals(2, pep2Mappings.size());
1735 List<AlignedCodonFrame> pep2CdsMappings = MappingUtils
1736 .findMappingsForSequence(cds.getSequenceAt(1), pep2Mappings);
1737 assertEquals(1, pep2CdsMappings.size());
1738 sr = MappingUtils.buildSearchResults(pep2, 1, pep2CdsMappings);
1739 assertEquals(1, sr.getResults().size());
1740 m = sr.getResults().get(0);
1741 assertEquals(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
1742 assertEquals(1, m.getStart());
1743 assertEquals(3, m.getEnd());
1744 sr = MappingUtils.buildSearchResults(pep2, 2, pep2CdsMappings);
1745 m = sr.getResults().get(0);
1746 assertEquals(4, m.getStart());
1747 assertEquals(6, m.getEnd());
1748 sr = MappingUtils.buildSearchResults(pep2, 3, pep2CdsMappings);
1749 m = sr.getResults().get(0);
1750 assertEquals(7, m.getStart());
1751 assertEquals(9, m.getEnd());
1755 * Test the method that realigns protein to match mapped codon alignment.
1757 @Test(groups = { "Functional" })
1758 public void testAlignProteinAsDna_incompleteStartCodon()
1760 // seq1: incomplete start codon (not mapped), then [3, 11]
1761 SequenceI dna1 = new Sequence("Seq1", "ccAAA-TTT-GGG-");
1762 // seq2 codons are [4, 5], [8, 11]
1763 SequenceI dna2 = new Sequence("Seq2", "ccaAA-ttT-GGG-");
1764 // seq3 incomplete start codon at 'tt'
1765 SequenceI dna3 = new Sequence("Seq3", "ccaaa-ttt-GGG-");
1766 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
1767 dna.setDataset(null);
1769 // prot1 has 'X' for incomplete start codon (not mapped)
1770 SequenceI prot1 = new Sequence("Seq1", "XKFG"); // X for incomplete start
1771 SequenceI prot2 = new Sequence("Seq2", "NG");
1772 SequenceI prot3 = new Sequence("Seq3", "XG"); // X for incomplete start
1773 AlignmentI protein = new Alignment(new SequenceI[] { prot1, prot2,
1775 protein.setDataset(null);
1777 // map dna1 [3, 11] to prot1 [2, 4] KFG
1778 MapList map = new MapList(new int[] { 3, 11 }, new int[] { 2, 4 }, 3, 1);
1779 AlignedCodonFrame acf = new AlignedCodonFrame();
1780 acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
1782 // map dna2 [4, 5] [8, 11] to prot2 [1, 2] NG
1783 map = new MapList(new int[] { 4, 5, 8, 11 }, new int[] { 1, 2 }, 3, 1);
1784 acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map);
1786 // map dna3 [9, 11] to prot3 [2, 2] G
1787 map = new MapList(new int[] { 9, 11 }, new int[] { 2, 2 }, 3, 1);
1788 acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map);
1790 ArrayList<AlignedCodonFrame> acfs = new ArrayList<>();
1792 protein.setCodonFrames(acfs);
1793 Iterator<SequenceI> protseq = protein.getSequences().iterator();
1794 for (SequenceI dnaseq:dna.getSequences()) {
1795 assertCanResolveProteinCDS(dnaseq,protseq.next(),protein);
1798 * verify X is included in the aligned proteins, and placed just
1799 * before the first mapped residue
1800 * CCT is between CCC and TTT
1802 AlignmentUtils.alignProteinAsDna(protein, dna);
1803 assertEquals("XK-FG", prot1.getSequenceAsString());
1804 assertEquals("--N-G", prot2.getSequenceAsString());
1805 assertEquals("---XG", prot3.getSequenceAsString());
1809 * assert that we can resolve the protein product in the given alignment given a DNA sequence with CDS mapping
1813 private void assertCanResolveProteinCDS(SequenceI dnaseq, SequenceI expProtein, AlignmentI protein)
1815 // try a few different methods to check all work
1816 SequenceI aprot=null;
1817 for (AlignedCodonFrame cf:protein.getCodonFrame(dnaseq))
1819 aprot=cf.getAaForDnaSeq(dnaseq);
1822 assertTrue("getAaForDnaSeq didn't return expected protein sequence",aprot!=expProtein);
1826 assertNotNull("Didn't locate any proteins via AlignmentI.getCodonFrame .. AlignCodonFrame.getAaForDnaSeq", aprot);
1827 // try mapping utils -
1828 List<AlignedCodonFrame> mu_mappings=MappingUtils.findMappingsForSequence(dnaseq, protein.getCodonFrames());
1829 assertNotNull("No mappings found for dnaseq in protein alignment via MappingUtils.findMappingsForSequence",mu_mappings);
1830 assertNotEquals("No mappings found for dnaseq in protein alignment via MappingUtils.findMappingsForSequence",0,mu_mappings.size());
1831 SequenceI mu_alignedprot=null;
1832 List<SequenceToSequenceMapping> foundMap=null;
1833 for (AlignedCodonFrame cf:mu_mappings)
1835 foundMap=new ArrayList<>();
1836 mu_alignedprot = cf.findAlignedSequence(dnaseq, protein,foundMap);
1837 if (mu_alignedprot!=null) {
1841 assertNotNull("Didn't locate proteins via MappingUtils.findMappingsForSequence",mu_alignedprot);
1842 assertTrue("findAlignedSequence didn't return expected protein sequence",mu_alignedprot==expProtein);
1846 * Tests for the method that maps the subset of a dna sequence that has CDS
1847 * (or subtype) feature - case where the start codon is incomplete.
1849 @Test(groups = "Functional")
1850 public void testFindCdsPositions_fivePrimeIncomplete()
1852 SequenceI dnaSeq = new Sequence("dna", "aaagGGCCCaaaTTTttt");
1853 dnaSeq.createDatasetSequence();
1854 SequenceI ds = dnaSeq.getDatasetSequence();
1856 // CDS for dna 5-6 (incomplete codon), 7-9
1857 SequenceFeature sf = new SequenceFeature("CDS", "", 5, 9, 0f, null);
1858 sf.setPhase("2"); // skip 2 bases to start of next codon
1859 ds.addSequenceFeature(sf);
1860 // CDS for dna 13-15
1861 sf = new SequenceFeature("CDS_predicted", "", 13, 15, 0f, null);
1862 ds.addSequenceFeature(sf);
1864 List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
1867 * check the mapping starts with the first complete codon
1869 assertEquals(6, MappingUtils.getLength(ranges));
1870 assertEquals(2, ranges.size());
1871 assertEquals(7, ranges.get(0)[0]);
1872 assertEquals(9, ranges.get(0)[1]);
1873 assertEquals(13, ranges.get(1)[0]);
1874 assertEquals(15, ranges.get(1)[1]);
1878 * Tests for the method that maps the subset of a dna sequence that has CDS
1879 * (or subtype) feature.
1881 @Test(groups = "Functional")
1882 public void testFindCdsPositions()
1884 SequenceI dnaSeq = new Sequence("dna", "aaaGGGcccAAATTTttt");
1885 dnaSeq.createDatasetSequence();
1886 SequenceI ds = dnaSeq.getDatasetSequence();
1888 // CDS for dna 10-12
1889 SequenceFeature sf = new SequenceFeature("CDS_predicted", "", 10, 12,
1892 ds.addSequenceFeature(sf);
1894 sf = new SequenceFeature("CDS", "", 4, 6, 0f, null);
1896 ds.addSequenceFeature(sf);
1897 // exon feature should be ignored here
1898 sf = new SequenceFeature("exon", "", 7, 9, 0f, null);
1899 ds.addSequenceFeature(sf);
1901 List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
1903 * verify ranges { [4-6], [12-10] }
1904 * note CDS ranges are ordered ascending even if the CDS
1907 assertEquals(6, MappingUtils.getLength(ranges));
1908 assertEquals(2, ranges.size());
1909 assertEquals(4, ranges.get(0)[0]);
1910 assertEquals(6, ranges.get(0)[1]);
1911 assertEquals(10, ranges.get(1)[0]);
1912 assertEquals(12, ranges.get(1)[1]);
1916 * Tests for the method that maps the subset of a dna sequence that has CDS
1917 * (or subtype) feature, with CDS strand = '-' (reverse)
1919 // test turned off as currently findCdsPositions is not strand-dependent
1920 // left in case it comes around again...
1921 @Test(groups = "Functional", enabled = false)
1922 public void testFindCdsPositions_reverseStrand()
1924 SequenceI dnaSeq = new Sequence("dna", "aaaGGGcccAAATTTttt");
1925 dnaSeq.createDatasetSequence();
1926 SequenceI ds = dnaSeq.getDatasetSequence();
1929 SequenceFeature sf = new SequenceFeature("CDS", "", 4, 6, 0f, null);
1931 ds.addSequenceFeature(sf);
1932 // exon feature should be ignored here
1933 sf = new SequenceFeature("exon", "", 7, 9, 0f, null);
1934 ds.addSequenceFeature(sf);
1935 // CDS for dna 10-12
1936 sf = new SequenceFeature("CDS_predicted", "", 10, 12, 0f, null);
1938 ds.addSequenceFeature(sf);
1940 List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
1942 * verify ranges { [12-10], [6-4] }
1944 assertEquals(6, MappingUtils.getLength(ranges));
1945 assertEquals(2, ranges.size());
1946 assertEquals(12, ranges.get(0)[0]);
1947 assertEquals(10, ranges.get(0)[1]);
1948 assertEquals(6, ranges.get(1)[0]);
1949 assertEquals(4, ranges.get(1)[1]);
1953 * Tests for the method that maps the subset of a dna sequence that has CDS
1954 * (or subtype) feature - reverse strand case where the start codon is
1957 @Test(groups = "Functional", enabled = false)
1958 // test turned off as currently findCdsPositions is not strand-dependent
1959 // left in case it comes around again...
1960 public void testFindCdsPositions_reverseStrandThreePrimeIncomplete()
1962 SequenceI dnaSeq = new Sequence("dna", "aaagGGCCCaaaTTTttt");
1963 dnaSeq.createDatasetSequence();
1964 SequenceI ds = dnaSeq.getDatasetSequence();
1967 SequenceFeature sf = new SequenceFeature("CDS", "", 5, 9, 0f, null);
1969 ds.addSequenceFeature(sf);
1970 // CDS for dna 13-15
1971 sf = new SequenceFeature("CDS_predicted", "", 13, 15, 0f, null);
1973 sf.setPhase("2"); // skip 2 bases to start of next codon
1974 ds.addSequenceFeature(sf);
1976 List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
1979 * check the mapping starts with the first complete codon
1980 * expect ranges [13, 13], [9, 5]
1982 assertEquals(6, MappingUtils.getLength(ranges));
1983 assertEquals(2, ranges.size());
1984 assertEquals(13, ranges.get(0)[0]);
1985 assertEquals(13, ranges.get(0)[1]);
1986 assertEquals(9, ranges.get(1)[0]);
1987 assertEquals(5, ranges.get(1)[1]);
1990 @Test(groups = "Functional")
1991 public void testAlignAs_alternateTranscriptsUngapped()
1993 SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
1994 SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
1995 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
1996 ((Alignment) dna).createDatasetAlignment();
1997 SequenceI cds1 = new Sequence("cds1", "GGGTTT");
1998 SequenceI cds2 = new Sequence("cds2", "CCCAAA");
1999 AlignmentI cds = new Alignment(new SequenceI[] { cds1, cds2 });
2000 ((Alignment) cds).createDatasetAlignment();
2002 AlignedCodonFrame acf = new AlignedCodonFrame();
2003 MapList map = new MapList(new int[] { 4, 9 }, new int[] { 1, 6 }, 1, 1);
2004 acf.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(), map);
2005 map = new MapList(new int[] { 1, 3, 10, 12 }, new int[] { 1, 6 }, 1, 1);
2006 acf.addMap(dna2.getDatasetSequence(), cds2.getDatasetSequence(), map);
2009 * verify CDS alignment is as:
2010 * cccGGGTTTaaa (cdna)
2011 * CCCgggtttAAA (cdna)
2013 * ---GGGTTT--- (cds)
2014 * CCC------AAA (cds)
2016 dna.addCodonFrame(acf);
2017 AlignmentUtils.alignAs(cds, dna);
2018 assertEquals("---GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
2019 assertEquals("CCC------AAA", cds.getSequenceAt(1).getSequenceAsString());
2022 @Test(groups = { "Functional" })
2023 public void testAddMappedPositions()
2025 SequenceI from = new Sequence("dna", "ggAA-ATcc-TT-g");
2026 SequenceI seq1 = new Sequence("cds", "AAATTT");
2027 from.createDatasetSequence();
2028 seq1.createDatasetSequence();
2029 Mapping mapping = new Mapping(seq1, new MapList(
2030 new int[] { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1));
2031 Map<Integer, Map<SequenceI, Character>> map = new TreeMap<>();
2032 AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
2035 * verify map has seq1 residues in columns 3,4,6,7,11,12
2037 assertEquals(6, map.size());
2038 assertEquals('A', map.get(3).get(seq1).charValue());
2039 assertEquals('A', map.get(4).get(seq1).charValue());
2040 assertEquals('A', map.get(6).get(seq1).charValue());
2041 assertEquals('T', map.get(7).get(seq1).charValue());
2042 assertEquals('T', map.get(11).get(seq1).charValue());
2043 assertEquals('T', map.get(12).get(seq1).charValue());
2051 * Test case where the mapping 'from' range includes a stop codon which is
2052 * absent in the 'to' range
2054 @Test(groups = { "Functional" })
2055 public void testAddMappedPositions_withStopCodon()
2057 SequenceI from = new Sequence("dna", "ggAA-ATcc-TT-g");
2058 SequenceI seq1 = new Sequence("cds", "AAATTT");
2059 from.createDatasetSequence();
2060 seq1.createDatasetSequence();
2061 Mapping mapping = new Mapping(seq1, new MapList(
2062 new int[] { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1));
2063 Map<Integer, Map<SequenceI, Character>> map = new TreeMap<>();
2064 AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
2067 * verify map has seq1 residues in columns 3,4,6,7,11,12
2069 assertEquals(6, map.size());
2070 assertEquals('A', map.get(3).get(seq1).charValue());
2071 assertEquals('A', map.get(4).get(seq1).charValue());
2072 assertEquals('A', map.get(6).get(seq1).charValue());
2073 assertEquals('T', map.get(7).get(seq1).charValue());
2074 assertEquals('T', map.get(11).get(seq1).charValue());
2075 assertEquals('T', map.get(12).get(seq1).charValue());
2079 * Test for the case where the products for which we want CDS are specified.
2080 * This is to represent the case where EMBL has CDS mappings to both Uniprot
2081 * and EMBLCDSPROTEIN. makeCdsAlignment() should only return the mappings for
2082 * the protein sequences specified.
2084 @Test(groups = { "Functional" })
2085 public void testMakeCdsAlignment_filterProducts()
2087 SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
2088 SequenceI dna2 = new Sequence("dna2", "GGGcccTTTaaaCCC");
2089 SequenceI pep1 = new Sequence("Uniprot|pep1", "GF");
2090 SequenceI pep2 = new Sequence("Uniprot|pep2", "GFP");
2091 SequenceI pep3 = new Sequence("EMBL|pep3", "GF");
2092 SequenceI pep4 = new Sequence("EMBL|pep4", "GFP");
2093 dna1.createDatasetSequence();
2094 dna2.createDatasetSequence();
2095 pep1.createDatasetSequence();
2096 pep2.createDatasetSequence();
2097 pep3.createDatasetSequence();
2098 pep4.createDatasetSequence();
2099 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
2100 dna.setDataset(null);
2101 AlignmentI emblPeptides = new Alignment(new SequenceI[] { pep3, pep4 });
2102 emblPeptides.setDataset(null);
2104 AlignedCodonFrame acf = new AlignedCodonFrame();
2105 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
2106 new int[] { 1, 2 }, 3, 1);
2107 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
2108 acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map);
2109 dna.addCodonFrame(acf);
2111 acf = new AlignedCodonFrame();
2112 map = new MapList(new int[] { 1, 3, 7, 9, 13, 15 }, new int[] { 1, 3 },
2114 acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
2115 acf.addMap(dna2.getDatasetSequence(), pep4.getDatasetSequence(), map);
2116 dna.addCodonFrame(acf);
2119 * execute method under test to find CDS for EMBL peptides only
2121 AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
2122 dna1, dna2 }, dna.getDataset(), emblPeptides.getSequencesArray());
2124 assertEquals(2, cds.getSequences().size());
2125 assertEquals("GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
2126 assertEquals("GGGTTTCCC", cds.getSequenceAt(1).getSequenceAsString());
2129 * verify shared, extended alignment dataset
2131 assertSame(dna.getDataset(), cds.getDataset());
2132 assertTrue(dna.getDataset().getSequences()
2133 .contains(cds.getSequenceAt(0).getDatasetSequence()));
2134 assertTrue(dna.getDataset().getSequences()
2135 .contains(cds.getSequenceAt(1).getDatasetSequence()));
2138 * Verify mappings from CDS to peptide, cDNA to CDS, and cDNA to peptide
2139 * the mappings are on the shared alignment dataset
2141 List<AlignedCodonFrame> cdsMappings = cds.getDataset().getCodonFrames();
2143 * 6 mappings, 2*(DNA->CDS), 2*(DNA->Pep), 2*(CDS->Pep)
2145 assertEquals(6, cdsMappings.size());
2148 * verify that mapping sets for dna and cds alignments are different
2149 * [not current behaviour - all mappings are on the alignment dataset]
2151 // select -> subselect type to test.
2152 // Assert.assertNotSame(dna.getCodonFrames(), cds.getCodonFrames());
2153 // assertEquals(4, dna.getCodonFrames().size());
2154 // assertEquals(4, cds.getCodonFrames().size());
2157 * Two mappings involve pep3 (dna to pep3, cds to pep3)
2158 * Mapping from pep3 to GGGTTT in first new exon sequence
2160 List<AlignedCodonFrame> pep3Mappings = MappingUtils
2161 .findMappingsForSequence(pep3, cdsMappings);
2162 assertEquals(2, pep3Mappings.size());
2163 List<AlignedCodonFrame> mappings = MappingUtils
2164 .findMappingsForSequence(cds.getSequenceAt(0), pep3Mappings);
2165 assertEquals(1, mappings.size());
2168 SearchResultsI sr = MappingUtils.buildSearchResults(pep3, 1, mappings);
2169 assertEquals(1, sr.getResults().size());
2170 SearchResultMatchI m = sr.getResults().get(0);
2171 assertSame(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
2172 assertEquals(1, m.getStart());
2173 assertEquals(3, m.getEnd());
2175 sr = MappingUtils.buildSearchResults(pep3, 2, mappings);
2176 m = sr.getResults().get(0);
2177 assertSame(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
2178 assertEquals(4, m.getStart());
2179 assertEquals(6, m.getEnd());
2182 * Two mappings involve pep4 (dna to pep4, cds to pep4)
2183 * Verify mapping from pep4 to GGGTTTCCC in second new exon sequence
2185 List<AlignedCodonFrame> pep4Mappings = MappingUtils
2186 .findMappingsForSequence(pep4, cdsMappings);
2187 assertEquals(2, pep4Mappings.size());
2188 mappings = MappingUtils.findMappingsForSequence(cds.getSequenceAt(1),
2190 assertEquals(1, mappings.size());
2192 sr = MappingUtils.buildSearchResults(pep4, 1, mappings);
2193 assertEquals(1, sr.getResults().size());
2194 m = sr.getResults().get(0);
2195 assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
2196 assertEquals(1, m.getStart());
2197 assertEquals(3, m.getEnd());
2199 sr = MappingUtils.buildSearchResults(pep4, 2, mappings);
2200 m = sr.getResults().get(0);
2201 assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
2202 assertEquals(4, m.getStart());
2203 assertEquals(6, m.getEnd());
2205 sr = MappingUtils.buildSearchResults(pep4, 3, mappings);
2206 m = sr.getResults().get(0);
2207 assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
2208 assertEquals(7, m.getStart());
2209 assertEquals(9, m.getEnd());
2213 * Test the method that just copies aligned sequences, provided all sequences
2214 * to be aligned share the aligned sequence's dataset
2216 @Test(groups = "Functional")
2217 public void testAlignAsSameSequences()
2219 SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
2220 SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
2221 AlignmentI al1 = new Alignment(new SequenceI[] { dna1, dna2 });
2222 ((Alignment) al1).createDatasetAlignment();
2224 SequenceI dna3 = new Sequence(dna1);
2225 SequenceI dna4 = new Sequence(dna2);
2226 assertSame(dna3.getDatasetSequence(), dna1.getDatasetSequence());
2227 assertSame(dna4.getDatasetSequence(), dna2.getDatasetSequence());
2228 String seq1 = "-cc-GG-GT-TT--aaa";
2229 dna3.setSequence(seq1);
2230 String seq2 = "C--C-Cgg--gtt-tAA-A-";
2231 dna4.setSequence(seq2);
2232 AlignmentI al2 = new Alignment(new SequenceI[] { dna3, dna4 });
2233 ((Alignment) al2).createDatasetAlignment();
2236 * alignment removes gapped columns (two internal, two trailing)
2238 assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
2239 String aligned1 = "-cc-GG-GTTT-aaa";
2240 assertEquals(aligned1,
2241 al1.getSequenceAt(0).getSequenceAsString());
2242 String aligned2 = "C--C-Cgg-gtttAAA";
2243 assertEquals(aligned2,
2244 al1.getSequenceAt(1).getSequenceAsString());
2247 * add another sequence to 'aligned' - should still succeed, since
2248 * unaligned sequences still share a dataset with aligned sequences
2250 SequenceI dna5 = new Sequence("dna5", "CCCgggtttAAA");
2251 dna5.createDatasetSequence();
2252 al2.addSequence(dna5);
2253 assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
2254 assertEquals(aligned1, al1.getSequenceAt(0).getSequenceAsString());
2255 assertEquals(aligned2, al1.getSequenceAt(1).getSequenceAsString());
2258 * add another sequence to 'unaligned' - should fail, since now not
2259 * all unaligned sequences share a dataset with aligned sequences
2261 SequenceI dna6 = new Sequence("dna6", "CCCgggtttAAA");
2262 dna6.createDatasetSequence();
2263 al1.addSequence(dna6);
2264 // JAL-2110 JBP Comment: what's the use case for this behaviour ?
2265 assertFalse(AlignmentUtils.alignAsSameSequences(al1, al2));
2268 @Test(groups = "Functional")
2269 public void testAlignAsSameSequencesMultipleSubSeq()
2271 SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
2272 SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
2273 SequenceI as1 = dna1.deriveSequence(); // cccGGGTTTaaa/1-12
2274 SequenceI as2 = dna1.deriveSequence().getSubSequence(3, 7); // GGGT/4-7
2275 SequenceI as3 = dna2.deriveSequence(); // CCCgggtttAAA/1-12
2276 as1.insertCharAt(6, 5, '-');
2277 assertEquals("cccGGG-----TTTaaa", as1.getSequenceAsString());
2278 as2.insertCharAt(6, 5, '-');
2279 assertEquals("GGGT-----", as2.getSequenceAsString());
2280 as3.insertCharAt(3, 5, '-');
2281 assertEquals("CCC-----gggtttAAA", as3.getSequenceAsString());
2282 AlignmentI aligned = new Alignment(new SequenceI[] { as1, as2, as3 });
2284 // why do we need to cast this still ?
2285 ((Alignment) aligned).createDatasetAlignment();
2286 SequenceI uas1 = dna1.deriveSequence();
2287 SequenceI uas2 = dna1.deriveSequence().getSubSequence(3, 7);
2288 SequenceI uas3 = dna2.deriveSequence();
2289 AlignmentI tobealigned = new Alignment(new SequenceI[] { uas1, uas2,
2291 ((Alignment) tobealigned).createDatasetAlignment();
2294 * alignAs lines up dataset sequences and removes empty columns (two)
2296 assertTrue(AlignmentUtils.alignAsSameSequences(tobealigned, aligned));
2297 assertEquals("cccGGG---TTTaaa", uas1.getSequenceAsString());
2298 assertEquals("GGGT", uas2.getSequenceAsString());
2299 assertEquals("CCC---gggtttAAA", uas3.getSequenceAsString());
2302 @Test(groups = { "Functional" })
2303 public void testTransferGeneLoci()
2305 SequenceI from = new Sequence("transcript",
2306 "aaacccgggTTTAAACCCGGGtttaaacccgggttt");
2307 SequenceI to = new Sequence("CDS", "TTTAAACCCGGG");
2308 MapList map = new MapList(new int[] { 1, 12 }, new int[] { 10, 21 }, 1,
2312 * first with nothing to transfer
2314 AlignmentUtils.transferGeneLoci(from, map, to);
2315 assertNull(to.getGeneLoci());
2318 * next with gene loci set on 'from' sequence
2320 int[] exons = new int[] { 100, 105, 155, 164, 210, 229 };
2321 MapList geneMap = new MapList(new int[] { 1, 36 }, exons, 1, 1);
2322 from.setGeneLoci("human", "GRCh38", "7", geneMap);
2323 AlignmentUtils.transferGeneLoci(from, map, to);
2325 GeneLociI toLoci = to.getGeneLoci();
2326 assertNotNull(toLoci);
2327 // DBRefEntry constructor upper-cases 'source'
2328 assertEquals("HUMAN", toLoci.getSpeciesId());
2329 assertEquals("GRCh38", toLoci.getAssemblyId());
2330 assertEquals("7", toLoci.getChromosomeId());
2333 * transcript 'exons' are 1-6, 7-16, 17-36
2334 * CDS 1:12 is transcript 10-21
2335 * transcript 'CDS' is 10-16, 17-21
2336 * which is 'gene' 158-164, 210-214
2338 MapList toMap = toLoci.getMapping();
2339 assertEquals(1, toMap.getFromRanges().size());
2340 assertEquals(2, toMap.getFromRanges().get(0).length);
2341 assertEquals(1, toMap.getFromRanges().get(0)[0]);
2342 assertEquals(12, toMap.getFromRanges().get(0)[1]);
2343 assertEquals(2, toMap.getToRanges().size());
2344 assertEquals(2, toMap.getToRanges().get(0).length);
2345 assertEquals(158, toMap.getToRanges().get(0)[0]);
2346 assertEquals(164, toMap.getToRanges().get(0)[1]);
2347 assertEquals(210, toMap.getToRanges().get(1)[0]);
2348 assertEquals(214, toMap.getToRanges().get(1)[1]);
2349 // or summarised as (but toString might change in future):
2350 assertEquals("[ [1, 12] ] 1:1 to [ [158, 164] [210, 214] ]",
2354 * an existing value is not overridden
2356 geneMap = new MapList(new int[] { 1, 36 }, new int[] { 36, 1 }, 1, 1);
2357 from.setGeneLoci("inhuman", "GRCh37", "6", geneMap);
2358 AlignmentUtils.transferGeneLoci(from, map, to);
2359 assertEquals("GRCh38", toLoci.getAssemblyId());
2360 assertEquals("7", toLoci.getChromosomeId());
2361 toMap = toLoci.getMapping();
2362 assertEquals("[ [1, 12] ] 1:1 to [ [158, 164] [210, 214] ]",
2367 * Tests for the method that maps nucleotide to protein based on CDS features
2369 @Test(groups = "Functional")
2370 public void testMapCdsToProtein()
2372 SequenceI peptide = new Sequence("pep", "KLQ");
2375 * Case 1: CDS 3 times length of peptide
2376 * NB method only checks lengths match, not translation
2378 SequenceI dna = new Sequence("dna", "AACGacgtCTCCT");
2379 dna.createDatasetSequence();
2380 dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
2381 dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 13, null));
2382 MapList ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2383 assertEquals(3, ml.getFromRatio());
2384 assertEquals(1, ml.getToRatio());
2385 assertEquals("[[1, 3]]",
2386 Arrays.deepToString(ml.getToRanges().toArray()));
2387 assertEquals("[[1, 4], [9, 13]]",
2388 Arrays.deepToString(ml.getFromRanges().toArray()));
2391 * Case 2: CDS 3 times length of peptide + stop codon
2392 * (note code does not currently check trailing codon is a stop codon)
2394 dna = new Sequence("dna", "AACGacgtCTCCTCCC");
2395 dna.createDatasetSequence();
2396 dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
2397 dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 16, null));
2398 ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2399 assertEquals(3, ml.getFromRatio());
2400 assertEquals(1, ml.getToRatio());
2401 assertEquals("[[1, 3]]",
2402 Arrays.deepToString(ml.getToRanges().toArray()));
2403 assertEquals("[[1, 4], [9, 13]]",
2404 Arrays.deepToString(ml.getFromRanges().toArray()));
2407 * Case 3: CDS longer than 3 * peptide + stop codon - no mapping is made
2409 dna = new Sequence("dna", "AACGacgtCTCCTTGATCA");
2410 dna.createDatasetSequence();
2411 dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
2412 dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 19, null));
2413 ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2417 * Case 4: CDS shorter than 3 * peptide - no mapping is made
2419 dna = new Sequence("dna", "AACGacgtCTCC");
2420 dna.createDatasetSequence();
2421 dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
2422 dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 12, null));
2423 ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2427 * Case 5: CDS 3 times length of peptide + part codon - mapping is truncated
2429 dna = new Sequence("dna", "AACGacgtCTCCTTG");
2430 dna.createDatasetSequence();
2431 dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
2432 dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 15, null));
2433 ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2434 assertEquals(3, ml.getFromRatio());
2435 assertEquals(1, ml.getToRatio());
2436 assertEquals("[[1, 3]]",
2437 Arrays.deepToString(ml.getToRanges().toArray()));
2438 assertEquals("[[1, 4], [9, 13]]",
2439 Arrays.deepToString(ml.getFromRanges().toArray()));
2442 * Case 6: incomplete start codon corresponding to X in peptide
2444 dna = new Sequence("dna", "ACGacgtCTCCTTGG");
2445 dna.createDatasetSequence();
2446 SequenceFeature sf = new SequenceFeature("CDS", "", 1, 3, null);
2447 sf.setPhase("2"); // skip 2 positions (AC) to start of next codon (GCT)
2448 dna.addSequenceFeature(sf);
2449 dna.addSequenceFeature(new SequenceFeature("CDS", "", 8, 15, null));
2450 peptide = new Sequence("pep", "XLQ");
2451 ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
2452 assertEquals("[[2, 3]]",
2453 Arrays.deepToString(ml.getToRanges().toArray()));
2454 assertEquals("[[3, 3], [8, 12]]",
2455 Arrays.deepToString(ml.getFromRanges().toArray()));
2459 * Tests for the method that locates the CDS sequence that has a mapping to
2460 * the given protein. That is, given a transcript-to-peptide mapping, find the
2461 * cds-to-peptide mapping that relates to both, and return the CDS sequence.
2464 public void testFindCdsForProtein()
2466 List<AlignedCodonFrame> mappings = new ArrayList<>();
2467 AlignedCodonFrame acf1 = new AlignedCodonFrame();
2470 SequenceI dna1 = new Sequence("dna1", "cgatATcgGCTATCTATGacg");
2471 dna1.createDatasetSequence();
2473 // NB we currently exclude STOP codon from CDS sequences
2474 // the test would need to change if this changes in future
2475 SequenceI cds1 = new Sequence("cds1", "ATGCTATCT");
2476 cds1.createDatasetSequence();
2478 SequenceI pep1 = new Sequence("pep1", "MLS");
2479 pep1.createDatasetSequence();
2480 List<AlignedCodonFrame> seqMappings = new ArrayList<>();
2481 MapList mapList = new MapList(
2483 { 5, 6, 9, 15 }, new int[] { 1, 3 }, 3, 1);
2484 Mapping dnaToPeptide = new Mapping(pep1.getDatasetSequence(), mapList);
2486 // add dna to peptide mapping
2487 seqMappings.add(acf1);
2488 acf1.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
2492 * first case - no dna-to-CDS mapping exists - search fails
2494 SequenceI seq = AlignmentUtils.findCdsForProtein(mappings, dna1,
2495 seqMappings, dnaToPeptide);
2499 * second case - CDS-to-peptide mapping exists but no dna-to-CDS
2502 // todo this test fails if the mapping is added to acf1, not acf2
2503 // need to tidy up use of lists of mappings in AlignedCodonFrame
2504 AlignedCodonFrame acf2 = new AlignedCodonFrame();
2506 MapList cdsToPeptideMapping = new MapList(new int[]
2507 { 1, 9 }, new int[] { 1, 3 }, 3, 1);
2508 acf2.addMap(cds1.getDatasetSequence(), pep1.getDatasetSequence(),
2509 cdsToPeptideMapping);
2510 assertNull(AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
2514 * third case - add dna-to-CDS mapping - CDS is now found!
2516 MapList dnaToCdsMapping = new MapList(new int[] { 5, 6, 9, 15 },
2519 acf1.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(),
2521 seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
2523 assertSame(seq, cds1.getDatasetSequence());
2527 * Tests for the method that locates the CDS sequence that has a mapping to
2528 * the given protein. That is, given a transcript-to-peptide mapping, find the
2529 * cds-to-peptide mapping that relates to both, and return the CDS sequence.
2530 * This test is for the case where transcript and CDS are the same length.
2533 public void testFindCdsForProtein_noUTR()
2535 List<AlignedCodonFrame> mappings = new ArrayList<>();
2536 AlignedCodonFrame acf1 = new AlignedCodonFrame();
2539 SequenceI dna1 = new Sequence("dna1", "ATGCTATCTTAA");
2540 dna1.createDatasetSequence();
2542 // NB we currently exclude STOP codon from CDS sequences
2543 // the test would need to change if this changes in future
2544 SequenceI cds1 = new Sequence("cds1", "ATGCTATCT");
2545 cds1.createDatasetSequence();
2547 SequenceI pep1 = new Sequence("pep1", "MLS");
2548 pep1.createDatasetSequence();
2549 List<AlignedCodonFrame> seqMappings = new ArrayList<>();
2550 MapList mapList = new MapList(
2552 { 1, 9 }, new int[] { 1, 3 }, 3, 1);
2553 Mapping dnaToPeptide = new Mapping(pep1.getDatasetSequence(), mapList);
2555 // add dna to peptide mapping
2556 seqMappings.add(acf1);
2557 acf1.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
2561 * first case - transcript lacks CDS features - it appears to be
2562 * the CDS sequence and is returned
2564 SequenceI seq = AlignmentUtils.findCdsForProtein(mappings, dna1,
2565 seqMappings, dnaToPeptide);
2566 assertSame(seq, dna1.getDatasetSequence());
2569 * second case - transcript has CDS feature - this means it is
2570 * not returned as a match for CDS (CDS sequences don't have CDS features)
2572 dna1.addSequenceFeature(
2573 new SequenceFeature(SequenceOntologyI.CDS, "cds", 1, 12, null));
2574 seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
2579 * third case - CDS-to-peptide mapping exists but no dna-to-CDS
2582 // todo this test fails if the mapping is added to acf1, not acf2
2583 // need to tidy up use of lists of mappings in AlignedCodonFrame
2584 AlignedCodonFrame acf2 = new AlignedCodonFrame();
2586 MapList cdsToPeptideMapping = new MapList(new int[]
2587 { 1, 9 }, new int[] { 1, 3 }, 3, 1);
2588 acf2.addMap(cds1.getDatasetSequence(), pep1.getDatasetSequence(),
2589 cdsToPeptideMapping);
2590 assertNull(AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
2594 * fourth case - add dna-to-CDS mapping - CDS is now found!
2596 MapList dnaToCdsMapping = new MapList(new int[] { 1, 9 },
2599 acf1.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(),
2601 seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
2603 assertSame(seq, cds1.getDatasetSequence());