2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.analysis;
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertFalse;
25 import static org.testng.AssertJUnit.assertNull;
26 import static org.testng.AssertJUnit.assertSame;
27 import static org.testng.AssertJUnit.assertTrue;
29 import jalview.datamodel.AlignedCodonFrame;
30 import jalview.datamodel.Alignment;
31 import jalview.datamodel.AlignmentAnnotation;
32 import jalview.datamodel.AlignmentI;
33 import jalview.datamodel.Annotation;
34 import jalview.datamodel.DBRefEntry;
35 import jalview.datamodel.Mapping;
36 import jalview.datamodel.SearchResults;
37 import jalview.datamodel.SearchResults.Match;
38 import jalview.datamodel.Sequence;
39 import jalview.datamodel.SequenceI;
40 import jalview.io.AppletFormatAdapter;
41 import jalview.io.FormatAdapter;
42 import jalview.util.MapList;
43 import jalview.util.MappingUtils;
45 import java.io.IOException;
46 import java.util.ArrayList;
47 import java.util.Arrays;
48 import java.util.HashSet;
49 import java.util.Iterator;
50 import java.util.List;
54 import org.testng.annotations.Test;
56 public class AlignmentUtilsTests
59 private static final String TEST_DATA =
61 "#=GS D.melanogaster.1 AC AY119185.1/838-902\n" +
62 "#=GS D.melanogaster.2 AC AC092237.1/57223-57161\n" +
63 "#=GS D.melanogaster.3 AC AY060611.1/560-627\n" +
64 "D.melanogaster.1 G.AGCC.CU...AUGAUCGA\n" +
65 "#=GR D.melanogaster.1 SS ................((((\n" +
66 "D.melanogaster.2 C.AUUCAACU.UAUGAGGAU\n" +
67 "#=GR D.melanogaster.2 SS ................((((\n" +
68 "D.melanogaster.3 G.UGGCGCU..UAUGACGCA\n" +
69 "#=GR D.melanogaster.3 SS (.(((...(....(((((((\n" +
72 private static final String AA_SEQS_1 =
78 private static final String CDNA_SEQS_1 =
80 "AC-GG--CUC-CAA-CT\n" +
82 "-CG-TTA--ACG---AAGT\n";
84 private static final String CDNA_SEQS_2 =
91 // public static Sequence ts=new
92 // Sequence("short","ASDASDASDASDASDASDASDASDASDASDASDASDASD");
93 public static Sequence ts = new Sequence("short",
94 "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
96 @Test(groups = { "Functional" })
97 public void testExpandContext()
99 AlignmentI al = new Alignment(new Sequence[] {});
100 for (int i = 4; i < 14; i += 2)
102 SequenceI s1 = ts.deriveSequence().getSubSequence(i, i + 7);
105 System.out.println(new AppletFormatAdapter().formatSequences("Clustal",
107 for (int flnk = -1; flnk < 25; flnk++)
109 AlignmentI exp = AlignmentUtils.expandContext(al, flnk);
110 System.out.println("\nFlank size: " + flnk);
111 System.out.println(new AppletFormatAdapter().formatSequences(
112 "Clustal", exp, true));
116 * Full expansion to complete sequences
118 for (SequenceI sq : exp.getSequences())
120 String ung = sq.getSequenceAsString().replaceAll("-+", "");
121 final String errorMsg = "Flanking sequence not the same as original dataset sequence.\n"
124 + sq.getDatasetSequence().getSequenceAsString();
125 assertTrue(errorMsg, ung.equalsIgnoreCase(sq.getDatasetSequence()
126 .getSequenceAsString()));
132 * Last sequence is fully expanded, others have leading gaps to match
134 assertTrue(exp.getSequenceAt(4).getSequenceAsString()
136 assertTrue(exp.getSequenceAt(3).getSequenceAsString()
137 .startsWith("--abc"));
138 assertTrue(exp.getSequenceAt(2).getSequenceAsString()
139 .startsWith("----abc"));
140 assertTrue(exp.getSequenceAt(1).getSequenceAsString()
141 .startsWith("------abc"));
142 assertTrue(exp.getSequenceAt(0).getSequenceAsString()
143 .startsWith("--------abc"));
149 * Test that annotations are correctly adjusted by expandContext
151 @Test(groups = { "Functional" })
152 public void testExpandContext_annotation()
154 AlignmentI al = new Alignment(new Sequence[] {});
155 SequenceI ds = new Sequence("Seq1", "ABCDEFGHI");
157 SequenceI seq1 = ds.deriveSequence().getSubSequence(3, 6);
158 al.addSequence(seq1);
161 * Annotate DEF with 4/5/6 respectively
163 Annotation[] anns = new Annotation[] { new Annotation(4),
164 new Annotation(5), new Annotation(6) };
165 AlignmentAnnotation ann = new AlignmentAnnotation("SS",
166 "secondary structure", anns);
167 seq1.addAlignmentAnnotation(ann);
170 * The annotations array should match aligned positions
172 assertEquals(3, ann.annotations.length);
173 assertEquals(4, ann.annotations[0].value, 0.001);
174 assertEquals(5, ann.annotations[1].value, 0.001);
175 assertEquals(6, ann.annotations[2].value, 0.001);
178 * Check annotation to sequence position mappings before expanding the
179 * sequence; these are set up in Sequence.addAlignmentAnnotation ->
180 * Annotation.setSequenceRef -> createSequenceMappings
182 assertNull(ann.getAnnotationForPosition(1));
183 assertNull(ann.getAnnotationForPosition(2));
184 assertNull(ann.getAnnotationForPosition(3));
185 assertEquals(4, ann.getAnnotationForPosition(4).value, 0.001);
186 assertEquals(5, ann.getAnnotationForPosition(5).value, 0.001);
187 assertEquals(6, ann.getAnnotationForPosition(6).value, 0.001);
188 assertNull(ann.getAnnotationForPosition(7));
189 assertNull(ann.getAnnotationForPosition(8));
190 assertNull(ann.getAnnotationForPosition(9));
193 * Expand the subsequence to the full sequence abcDEFghi
195 AlignmentI expanded = AlignmentUtils.expandContext(al, -1);
196 assertEquals("abcDEFghi", expanded.getSequenceAt(0)
197 .getSequenceAsString());
200 * Confirm the alignment and sequence have the same SS annotation,
201 * referencing the expanded sequence
203 ann = expanded.getSequenceAt(0).getAnnotation()[0];
204 assertSame(ann, expanded.getAlignmentAnnotation()[0]);
205 assertSame(expanded.getSequenceAt(0), ann.sequenceRef);
208 * The annotations array should have null values except for annotated
211 assertNull(ann.annotations[0]);
212 assertNull(ann.annotations[1]);
213 assertNull(ann.annotations[2]);
214 assertEquals(4, ann.annotations[3].value, 0.001);
215 assertEquals(5, ann.annotations[4].value, 0.001);
216 assertEquals(6, ann.annotations[5].value, 0.001);
217 assertNull(ann.annotations[6]);
218 assertNull(ann.annotations[7]);
219 assertNull(ann.annotations[8]);
222 * sequence position mappings should be unchanged
224 assertNull(ann.getAnnotationForPosition(1));
225 assertNull(ann.getAnnotationForPosition(2));
226 assertNull(ann.getAnnotationForPosition(3));
227 assertEquals(4, ann.getAnnotationForPosition(4).value, 0.001);
228 assertEquals(5, ann.getAnnotationForPosition(5).value, 0.001);
229 assertEquals(6, ann.getAnnotationForPosition(6).value, 0.001);
230 assertNull(ann.getAnnotationForPosition(7));
231 assertNull(ann.getAnnotationForPosition(8));
232 assertNull(ann.getAnnotationForPosition(9));
236 * Test method that returns a map of lists of sequences by sequence name.
238 * @throws IOException
240 @Test(groups = { "Functional" })
241 public void testGetSequencesByName() throws IOException
243 final String data = ">Seq1Name\nKQYL\n" + ">Seq2Name\nRFPW\n"
244 + ">Seq1Name\nABCD\n";
245 AlignmentI al = loadAlignment(data, "FASTA");
246 Map<String, List<SequenceI>> map = AlignmentUtils
247 .getSequencesByName(al);
248 assertEquals(2, map.keySet().size());
249 assertEquals(2, map.get("Seq1Name").size());
250 assertEquals("KQYL", map.get("Seq1Name").get(0).getSequenceAsString());
251 assertEquals("ABCD", map.get("Seq1Name").get(1).getSequenceAsString());
252 assertEquals(1, map.get("Seq2Name").size());
253 assertEquals("RFPW", map.get("Seq2Name").get(0).getSequenceAsString());
257 * Helper method to load an alignment and ensure dataset sequences are set up.
263 * @throws IOException
265 protected AlignmentI loadAlignment(final String data, String format)
268 AlignmentI a = new FormatAdapter().readFile(data,
269 AppletFormatAdapter.PASTE, format);
275 * Test mapping of protein to cDNA, for the case where we have no sequence
276 * cross-references, so mappings are made first-served 1-1 where sequences
279 * @throws IOException
281 @Test(groups = { "Functional" })
282 public void testMapProteinAlignmentToCdna_noXrefs() throws IOException
284 List<SequenceI> protseqs = new ArrayList<SequenceI>();
285 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
286 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
287 protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
288 AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
289 protein.setDataset(null);
291 List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
292 dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR
293 dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAA")); // = EIQ
294 dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ
295 dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG")); // = EIQ
296 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
297 cdna.setDataset(null);
299 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
301 // 3 mappings made, each from 1 to 1 sequence
302 assertEquals(3, protein.getCodonFrames().size());
303 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
304 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
305 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
307 // V12345 mapped to A22222
308 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
310 assertEquals(1, acf.getdnaSeqs().length);
311 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
312 acf.getdnaSeqs()[0]);
313 Mapping[] protMappings = acf.getProtMappings();
314 assertEquals(1, protMappings.length);
315 MapList mapList = protMappings[0].getMap();
316 assertEquals(3, mapList.getFromRatio());
317 assertEquals(1, mapList.getToRatio());
318 assertTrue(Arrays.equals(new int[] { 1, 9 }, mapList.getFromRanges()
320 assertEquals(1, mapList.getFromRanges().size());
321 assertTrue(Arrays.equals(new int[] { 1, 3 },
322 mapList.getToRanges().get(0)));
323 assertEquals(1, mapList.getToRanges().size());
325 // V12346 mapped to A33333
326 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
327 assertEquals(1, acf.getdnaSeqs().length);
328 assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
329 acf.getdnaSeqs()[0]);
331 // V12347 mapped to A11111
332 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
333 assertEquals(1, acf.getdnaSeqs().length);
334 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
335 acf.getdnaSeqs()[0]);
337 // no mapping involving the 'extra' A44444
338 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(3)).isEmpty());
342 * Test for the alignSequenceAs method that takes two sequences and a mapping.
344 @Test(groups = { "Functional" })
345 public void testAlignSequenceAs_withMapping_noIntrons()
347 MapList map = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 }, 3, 1);
350 * No existing gaps in dna:
352 checkAlignSequenceAs("GGGAAA", "-A-L-", false, false, map,
356 * Now introduce gaps in dna but ignore them when realigning.
358 checkAlignSequenceAs("-G-G-G-A-A-A-", "-A-L-", false, false, map,
362 * Now include gaps in dna when realigning. First retaining 'mapped' gaps
363 * only, i.e. those within the exon region.
365 checkAlignSequenceAs("-G-G--G-A--A-A-", "-A-L-", true, false, map,
366 "---G-G--G---A--A-A");
369 * Include all gaps in dna when realigning (within and without the exon
370 * region). The leading gap, and the gaps between codons, are subsumed by
371 * the protein alignment gap.
373 checkAlignSequenceAs("-G-GG--AA-A---", "-A-L-", true, true, map,
374 "---G-GG---AA-A---");
377 * Include only unmapped gaps in dna when realigning (outside the exon
378 * region). The leading gap, and the gaps between codons, are subsumed by
379 * the protein alignment gap.
381 checkAlignSequenceAs("-G-GG--AA-A-", "-A-L-", false, true, map,
386 * Test for the alignSequenceAs method that takes two sequences and a mapping.
388 @Test(groups = { "Functional" })
389 public void testAlignSequenceAs_withMapping_withIntrons()
392 * Exons at codon 2 (AAA) and 4 (TTT)
394 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
395 new int[] { 1, 2 }, 3, 1);
398 * Simple case: no gaps in dna
400 checkAlignSequenceAs("GGGAAACCCTTTGGG", "--A-L-", false, false, map,
401 "GGG---AAACCCTTTGGG");
404 * Add gaps to dna - but ignore when realigning.
406 checkAlignSequenceAs("-G-G-G--A--A---AC-CC-T-TT-GG-G-", "--A-L-",
407 false, false, map, "GGG---AAACCCTTTGGG");
410 * Add gaps to dna - include within exons only when realigning.
412 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
413 true, false, map, "GGG---A--A---ACCCT-TTGGG");
416 * Include gaps outside exons only when realigning.
418 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
419 false, true, map, "-G-G-GAAAC-CCTTT-GG-G-");
422 * Include gaps following first intron if we are 'preserving mapped gaps'
424 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
425 true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
428 * Include all gaps in dna when realigning.
430 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
431 true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
435 * Test for the case where not all of the protein sequence is mapped to cDNA.
437 @Test(groups = { "Functional" })
438 public void testAlignSequenceAs_withMapping_withUnmappedProtein()
441 * Exons at codon 2 (AAA) and 4 (TTT) mapped to A and P
443 final MapList map = new MapList(new int[] { 4, 6, 10, 12 }, new int[] {
447 * -L- 'aligns' ccc------
449 checkAlignSequenceAs("gggAAAcccTTTggg", "-A-L-P-", false, false, map,
450 "gggAAAccc------TTTggg");
454 * Helper method that performs and verifies the method under test.
457 * the sequence to be realigned
459 * the sequence whose alignment is to be copied
460 * @param preserveMappedGaps
461 * @param preserveUnmappedGaps
465 protected void checkAlignSequenceAs(final String alignee,
466 final String alignModel, final boolean preserveMappedGaps,
467 final boolean preserveUnmappedGaps, MapList map,
468 final String expected)
470 SequenceI alignMe = new Sequence("Seq1", alignee);
471 alignMe.createDatasetSequence();
472 SequenceI alignFrom = new Sequence("Seq2", alignModel);
473 alignFrom.createDatasetSequence();
474 AlignedCodonFrame acf = new AlignedCodonFrame();
475 acf.addMap(alignMe.getDatasetSequence(), alignFrom.getDatasetSequence(), map);
477 AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "---", '-',
478 preserveMappedGaps, preserveUnmappedGaps);
479 assertEquals(expected, alignMe.getSequenceAsString());
483 * Test for the alignSequenceAs method where we preserve gaps in introns only.
485 @Test(groups = { "Functional" })
486 public void testAlignSequenceAs_keepIntronGapsOnly()
490 * Intron GGGAAA followed by exon CCCTTT
492 MapList map = new MapList(new int[] { 7, 12 }, new int[] { 1, 2 }, 3, 1);
494 checkAlignSequenceAs("GG-G-AA-A-C-CC-T-TT", "AL", false, true, map,
499 * Test for the method that generates an aligned translated sequence from one
502 @Test(groups = { "Functional" })
503 public void testGetAlignedTranslation_dnaLikeProtein()
505 // dna alignment will be replaced
506 SequenceI dna = new Sequence("Seq1", "T-G-CC-A--T-TAC-CAG-");
507 dna.createDatasetSequence();
508 // protein alignment will be 'applied' to dna
509 SequenceI protein = new Sequence("Seq1", "-CH-Y--Q-");
510 protein.createDatasetSequence();
511 MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1);
512 AlignedCodonFrame acf = new AlignedCodonFrame();
513 acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map);
515 final SequenceI aligned = AlignmentUtils.getAlignedTranslation(protein,
517 assertEquals("---TGCCAT---TAC------CAG---",
518 aligned.getSequenceAsString());
519 assertSame(aligned.getDatasetSequence(), dna.getDatasetSequence());
523 * Test the method that realigns protein to match mapped codon alignment.
525 @Test(groups = { "Functional" })
526 public void testAlignProteinAsDna()
528 // seq1 codons are [1,2,3] [4,5,6] [7,8,9] [10,11,12]
529 SequenceI dna1 = new Sequence("Seq1", "TGCCATTACCAG-");
530 // seq2 codons are [1,3,4] [5,6,7] [8,9,10] [11,12,13]
531 SequenceI dna2 = new Sequence("Seq2", "T-GCCATTACCAG");
532 // seq3 codons are [1,2,3] [4,5,7] [8,9,10] [11,12,13]
533 SequenceI dna3 = new Sequence("Seq3", "TGCCA-TTACCAG");
534 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
535 dna.setDataset(null);
537 // protein alignment will be realigned like dna
538 SequenceI prot1 = new Sequence("Seq1", "CHYQ");
539 SequenceI prot2 = new Sequence("Seq2", "CHYQ");
540 SequenceI prot3 = new Sequence("Seq3", "CHYQ");
541 SequenceI prot4 = new Sequence("Seq4", "R-QSV"); // unmapped, unchanged
542 AlignmentI protein = new Alignment(new SequenceI[] { prot1, prot2,
544 protein.setDataset(null);
546 MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1);
547 AlignedCodonFrame acf = new AlignedCodonFrame();
548 acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
549 acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map);
550 acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map);
551 ArrayList<AlignedCodonFrame> acfs = new ArrayList<AlignedCodonFrame>();
553 protein.setCodonFrames(acfs);
556 * Translated codon order is [1,2,3] [1,3,4] [4,5,6] [4,5,7] [5,6,7] [7,8,9]
557 * [8,9,10] [10,11,12] [11,12,13]
559 AlignmentUtils.alignProteinAsDna(protein, dna);
560 assertEquals("C-H--Y-Q-", prot1.getSequenceAsString());
561 assertEquals("-C--H-Y-Q", prot2.getSequenceAsString());
562 assertEquals("C--H--Y-Q", prot3.getSequenceAsString());
563 assertEquals("R-QSV", prot4.getSequenceAsString());
567 * Test the method that tests whether a CDNA sequence translates to a protein
570 @Test(groups = { "Functional" })
571 public void testTranslatesAs()
573 assertTrue(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
574 "FPKG".toCharArray()));
575 // with start codon (not in protein)
576 assertTrue(AlignmentUtils.translatesAs("atgtttcccaaaggg".toCharArray(),
577 3, "FPKG".toCharArray()));
578 // with stop codon1 (not in protein)
579 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtaa".toCharArray(),
580 0, "FPKG".toCharArray()));
581 // with stop codon1 (in protein as *)
582 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtaa".toCharArray(),
583 0, "FPKG*".toCharArray()));
584 // with stop codon2 (not in protein)
585 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtag".toCharArray(),
586 0, "FPKG".toCharArray()));
587 // with stop codon3 (not in protein)
588 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtga".toCharArray(),
589 0, "FPKG".toCharArray()));
590 // with start and stop codon1
591 assertTrue(AlignmentUtils.translatesAs(
592 "atgtttcccaaagggtaa".toCharArray(), 3, "FPKG".toCharArray()));
593 // with start and stop codon1 (in protein as *)
594 assertTrue(AlignmentUtils.translatesAs(
595 "atgtttcccaaagggtaa".toCharArray(), 3, "FPKG*".toCharArray()));
596 // with start and stop codon2
597 assertTrue(AlignmentUtils.translatesAs(
598 "atgtttcccaaagggtag".toCharArray(), 3, "FPKG".toCharArray()));
599 // with start and stop codon3
600 assertTrue(AlignmentUtils.translatesAs(
601 "atgtttcccaaagggtga".toCharArray(), 3, "FPKG".toCharArray()));
603 // with embedded stop codon
604 assertTrue(AlignmentUtils.translatesAs(
605 "atgtttTAGcccaaaTAAgggtga".toCharArray(), 3,
606 "F*PK*G".toCharArray()));
609 assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
610 0, "FPMG".toCharArray()));
614 * Test mapping of protein to cDNA, for cases where the cDNA has start and/or
615 * stop codons in addition to the protein coding sequence.
617 * @throws IOException
619 @Test(groups = { "Functional" })
620 public void testMapProteinAlignmentToCdna_withStartAndStopCodons()
623 List<SequenceI> protseqs = new ArrayList<SequenceI>();
624 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
625 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
626 protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
627 AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
628 protein.setDataset(null);
630 List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
632 dnaseqs.add(new Sequence("EMBL|A11111", "ATGTCAGCACGC"));
634 dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAATAA"));
635 // = start +EIQ + stop
636 dnaseqs.add(new Sequence("EMBL|A33333", "ATGGAAATCCAGTAG"));
637 dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG"));
638 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
639 cdna.setDataset(null);
641 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
643 // 3 mappings made, each from 1 to 1 sequence
644 assertEquals(3, protein.getCodonFrames().size());
645 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
646 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
647 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
649 // V12345 mapped from A22222
650 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
652 assertEquals(1, acf.getdnaSeqs().length);
653 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
654 acf.getdnaSeqs()[0]);
655 Mapping[] protMappings = acf.getProtMappings();
656 assertEquals(1, protMappings.length);
657 MapList mapList = protMappings[0].getMap();
658 assertEquals(3, mapList.getFromRatio());
659 assertEquals(1, mapList.getToRatio());
660 assertTrue(Arrays.equals(new int[] { 1, 9 }, mapList.getFromRanges()
662 assertEquals(1, mapList.getFromRanges().size());
663 assertTrue(Arrays.equals(new int[] { 1, 3 },
664 mapList.getToRanges().get(0)));
665 assertEquals(1, mapList.getToRanges().size());
667 // V12346 mapped from A33333 starting position 4
668 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
669 assertEquals(1, acf.getdnaSeqs().length);
670 assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
671 acf.getdnaSeqs()[0]);
672 protMappings = acf.getProtMappings();
673 assertEquals(1, protMappings.length);
674 mapList = protMappings[0].getMap();
675 assertEquals(3, mapList.getFromRatio());
676 assertEquals(1, mapList.getToRatio());
677 assertTrue(Arrays.equals(new int[] { 4, 12 }, mapList.getFromRanges()
679 assertEquals(1, mapList.getFromRanges().size());
680 assertTrue(Arrays.equals(new int[] { 1, 3 },
681 mapList.getToRanges().get(0)));
682 assertEquals(1, mapList.getToRanges().size());
684 // V12347 mapped to A11111 starting position 4
685 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
686 assertEquals(1, acf.getdnaSeqs().length);
687 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
688 acf.getdnaSeqs()[0]);
689 protMappings = acf.getProtMappings();
690 assertEquals(1, protMappings.length);
691 mapList = protMappings[0].getMap();
692 assertEquals(3, mapList.getFromRatio());
693 assertEquals(1, mapList.getToRatio());
694 assertTrue(Arrays.equals(new int[] { 4, 12 }, mapList.getFromRanges()
696 assertEquals(1, mapList.getFromRanges().size());
697 assertTrue(Arrays.equals(new int[] { 1, 3 },
698 mapList.getToRanges().get(0)));
699 assertEquals(1, mapList.getToRanges().size());
701 // no mapping involving the 'extra' A44444
702 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(3)).isEmpty());
706 * Test mapping of protein to cDNA, for the case where we have some sequence
707 * cross-references. Verify that 1-to-many mappings are made where
708 * cross-references exist and sequences are mappable.
710 * @throws IOException
712 @Test(groups = { "Functional" })
713 public void testMapProteinAlignmentToCdna_withXrefs() throws IOException
715 List<SequenceI> protseqs = new ArrayList<SequenceI>();
716 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
717 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
718 protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
719 AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
720 protein.setDataset(null);
722 List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
723 dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR
724 dnaseqs.add(new Sequence("EMBL|A22222", "ATGGAGATACAA")); // = start + EIQ
725 dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ
726 dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG")); // = EIQ
727 dnaseqs.add(new Sequence("EMBL|A55555", "GAGATTCAG")); // = EIQ
728 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[5]));
729 cdna.setDataset(null);
731 // Xref A22222 to V12345 (should get mapped)
732 dnaseqs.get(1).addDBRef(new DBRefEntry("UNIPROT", "1", "V12345"));
733 // Xref V12345 to A44444 (should get mapped)
734 protseqs.get(0).addDBRef(new DBRefEntry("EMBL", "1", "A44444"));
735 // Xref A33333 to V12347 (sequence mismatch - should not get mapped)
736 dnaseqs.get(2).addDBRef(new DBRefEntry("UNIPROT", "1", "V12347"));
737 // as V12345 is mapped to A22222 and A44444, this leaves V12346 unmapped.
738 // it should get paired up with the unmapped A33333
739 // A11111 should be mapped to V12347
740 // A55555 is spare and has no xref so is not mapped
742 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
744 // 4 protein mappings made for 3 proteins, 2 to V12345, 1 each to V12346/7
745 assertEquals(3, protein.getCodonFrames().size());
746 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
747 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
748 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
750 // one mapping for each of the first 4 cDNA sequences
751 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(0)).size());
752 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(1)).size());
753 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(2)).size());
754 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(3)).size());
756 // V12345 mapped to A22222 and A44444
757 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
759 assertEquals(2, acf.getdnaSeqs().length);
760 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
761 acf.getdnaSeqs()[0]);
762 assertEquals(cdna.getSequenceAt(3).getDatasetSequence(),
763 acf.getdnaSeqs()[1]);
765 // V12346 mapped to A33333
766 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
767 assertEquals(1, acf.getdnaSeqs().length);
768 assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
769 acf.getdnaSeqs()[0]);
771 // V12347 mapped to A11111
772 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
773 assertEquals(1, acf.getdnaSeqs().length);
774 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
775 acf.getdnaSeqs()[0]);
777 // no mapping involving the 'extra' A55555
778 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(4)).isEmpty());
782 * Test mapping of protein to cDNA, for the case where we have some sequence
783 * cross-references. Verify that once we have made an xref mapping we don't
784 * also map un-xrefd sequeces.
786 * @throws IOException
788 @Test(groups = { "Functional" })
789 public void testMapProteinAlignmentToCdna_prioritiseXrefs()
792 List<SequenceI> protseqs = new ArrayList<SequenceI>();
793 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
794 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
795 AlignmentI protein = new Alignment(
796 protseqs.toArray(new SequenceI[protseqs.size()]));
797 protein.setDataset(null);
799 List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
800 dnaseqs.add(new Sequence("EMBL|A11111", "GAAATCCAG")); // = EIQ
801 dnaseqs.add(new Sequence("EMBL|A22222", "GAAATTCAG")); // = EIQ
802 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[dnaseqs
804 cdna.setDataset(null);
806 // Xref A22222 to V12345 (should get mapped)
807 // A11111 should then be mapped to the unmapped V12346
808 dnaseqs.get(1).addDBRef(new DBRefEntry("UNIPROT", "1", "V12345"));
810 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
812 // 2 protein mappings made
813 assertEquals(2, protein.getCodonFrames().size());
814 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
815 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
817 // one mapping for each of the cDNA sequences
818 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(0)).size());
819 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(1)).size());
821 // V12345 mapped to A22222
822 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
824 assertEquals(1, acf.getdnaSeqs().length);
825 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
826 acf.getdnaSeqs()[0]);
828 // V12346 mapped to A11111
829 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
830 assertEquals(1, acf.getdnaSeqs().length);
831 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
832 acf.getdnaSeqs()[0]);
836 * Test the method that shows or hides sequence annotations by type(s) and
839 @Test(groups = { "Functional" })
840 public void testShowOrHideSequenceAnnotations()
842 SequenceI seq1 = new Sequence("Seq1", "AAA");
843 SequenceI seq2 = new Sequence("Seq2", "BBB");
844 SequenceI seq3 = new Sequence("Seq3", "CCC");
845 Annotation[] anns = new Annotation[] { new Annotation(2f) };
846 AlignmentAnnotation ann1 = new AlignmentAnnotation("Structure", "ann1",
848 ann1.setSequenceRef(seq1);
849 AlignmentAnnotation ann2 = new AlignmentAnnotation("Structure", "ann2",
851 ann2.setSequenceRef(seq2);
852 AlignmentAnnotation ann3 = new AlignmentAnnotation("Structure", "ann3",
854 AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "ann4", anns);
855 ann4.setSequenceRef(seq1);
856 AlignmentAnnotation ann5 = new AlignmentAnnotation("Temp", "ann5", anns);
857 ann5.setSequenceRef(seq2);
858 AlignmentAnnotation ann6 = new AlignmentAnnotation("Temp", "ann6", anns);
859 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
860 al.addAnnotation(ann1); // Structure for Seq1
861 al.addAnnotation(ann2); // Structure for Seq2
862 al.addAnnotation(ann3); // Structure for no sequence
863 al.addAnnotation(ann4); // Temp for seq1
864 al.addAnnotation(ann5); // Temp for seq2
865 al.addAnnotation(ann6); // Temp for no sequence
866 List<String> types = new ArrayList<String>();
867 List<SequenceI> scope = new ArrayList<SequenceI>();
870 * Set all sequence related Structure to hidden (ann1, ann2)
872 types.add("Structure");
873 AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, false,
875 assertFalse(ann1.visible);
876 assertFalse(ann2.visible);
877 assertTrue(ann3.visible); // not sequence-related, not affected
878 assertTrue(ann4.visible); // not Structure, not affected
879 assertTrue(ann5.visible); // "
880 assertTrue(ann6.visible); // not sequence-related, not affected
883 * Set Temp in {seq1, seq3} to hidden
889 AlignmentUtils.showOrHideSequenceAnnotations(al, types, scope, false,
891 assertFalse(ann1.visible); // unchanged
892 assertFalse(ann2.visible); // unchanged
893 assertTrue(ann3.visible); // not sequence-related, not affected
894 assertFalse(ann4.visible); // Temp for seq1 hidden
895 assertTrue(ann5.visible); // not in scope, not affected
896 assertTrue(ann6.visible); // not sequence-related, not affected
899 * Set Temp in all sequences to hidden
905 AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, false,
907 assertFalse(ann1.visible); // unchanged
908 assertFalse(ann2.visible); // unchanged
909 assertTrue(ann3.visible); // not sequence-related, not affected
910 assertFalse(ann4.visible); // Temp for seq1 hidden
911 assertFalse(ann5.visible); // Temp for seq2 hidden
912 assertTrue(ann6.visible); // not sequence-related, not affected
915 * Set all types in {seq1, seq3} to visible
921 AlignmentUtils.showOrHideSequenceAnnotations(al, types, scope, true,
923 assertTrue(ann1.visible); // Structure for seq1 set visible
924 assertFalse(ann2.visible); // not in scope, unchanged
925 assertTrue(ann3.visible); // not sequence-related, not affected
926 assertTrue(ann4.visible); // Temp for seq1 set visible
927 assertFalse(ann5.visible); // not in scope, unchanged
928 assertTrue(ann6.visible); // not sequence-related, not affected
931 * Set all types in all scope to hidden
933 AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, true,
935 assertFalse(ann1.visible);
936 assertFalse(ann2.visible);
937 assertTrue(ann3.visible); // not sequence-related, not affected
938 assertFalse(ann4.visible);
939 assertFalse(ann5.visible);
940 assertTrue(ann6.visible); // not sequence-related, not affected
944 * Tests for the method that checks if one sequence cross-references another
946 @Test(groups = { "Functional" })
947 public void testHasCrossRef()
949 assertFalse(AlignmentUtils.hasCrossRef(null, null));
950 SequenceI seq1 = new Sequence("EMBL|A12345", "ABCDEF");
951 assertFalse(AlignmentUtils.hasCrossRef(seq1, null));
952 assertFalse(AlignmentUtils.hasCrossRef(null, seq1));
953 SequenceI seq2 = new Sequence("UNIPROT|V20192", "ABCDEF");
954 assertFalse(AlignmentUtils.hasCrossRef(seq1, seq2));
957 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "v20193"));
958 assertFalse(AlignmentUtils.hasCrossRef(seq1, seq2));
960 // case-insensitive; version number is ignored
961 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "v20192"));
962 assertTrue(AlignmentUtils.hasCrossRef(seq1, seq2));
965 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
966 assertTrue(AlignmentUtils.hasCrossRef(seq1, seq2));
967 // test is one-way only
968 assertFalse(AlignmentUtils.hasCrossRef(seq2, seq1));
972 * Tests for the method that checks if either sequence cross-references the
975 @Test(groups = { "Functional" })
976 public void testHaveCrossRef()
978 assertFalse(AlignmentUtils.hasCrossRef(null, null));
979 SequenceI seq1 = new Sequence("EMBL|A12345", "ABCDEF");
980 assertFalse(AlignmentUtils.haveCrossRef(seq1, null));
981 assertFalse(AlignmentUtils.haveCrossRef(null, seq1));
982 SequenceI seq2 = new Sequence("UNIPROT|V20192", "ABCDEF");
983 assertFalse(AlignmentUtils.haveCrossRef(seq1, seq2));
985 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
986 assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
987 // next is true for haveCrossRef, false for hasCrossRef
988 assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
990 // now the other way round
992 seq2.addDBRef(new DBRefEntry("EMBL", "1", "A12345"));
993 assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
994 assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
997 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
998 assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
999 assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
1003 * Test the method that extracts the exon-only part of a dna alignment.
1005 @Test(groups = { "Functional" })
1006 public void testMakeExonAlignment()
1008 SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
1009 SequenceI dna2 = new Sequence("dna2", "GGGcccTTTaaaCCC");
1010 SequenceI pep1 = new Sequence("pep1", "GF");
1011 SequenceI pep2 = new Sequence("pep2", "GFP");
1012 dna1.createDatasetSequence();
1013 dna2.createDatasetSequence();
1014 pep1.createDatasetSequence();
1015 pep2.createDatasetSequence();
1017 List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
1018 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1019 new int[] { 1, 2 }, 3, 1);
1020 AlignedCodonFrame acf = new AlignedCodonFrame();
1021 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
1023 map = new MapList(new int[] { 1, 3, 7, 9, 13, 15 }, new int[] { 1, 3 },
1025 acf = new AlignedCodonFrame();
1026 acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
1029 AlignmentI exons = AlignmentUtils.makeExonAlignment(new SequenceI[] {
1030 dna1, dna2 }, mappings);
1031 assertEquals(2, exons.getSequences().size());
1032 assertEquals("GGGTTT", exons.getSequenceAt(0).getSequenceAsString());
1033 assertEquals("GGGTTTCCC", exons.getSequenceAt(1).getSequenceAsString());
1036 * Verify updated mappings
1038 assertEquals(2, mappings.size());
1041 * Mapping from pep1 to GGGTTT in first new exon sequence
1043 List<AlignedCodonFrame> pep1Mapping = MappingUtils
1044 .findMappingsForSequence(pep1, mappings);
1045 assertEquals(1, pep1Mapping.size());
1047 SearchResults sr = MappingUtils.buildSearchResults(pep1, 1, mappings);
1048 assertEquals(1, sr.getResults().size());
1049 Match m = sr.getResults().get(0);
1050 assertEquals(exons.getSequenceAt(0).getDatasetSequence(),
1052 assertEquals(1, m.getStart());
1053 assertEquals(3, m.getEnd());
1055 sr = MappingUtils.buildSearchResults(pep1, 2, mappings);
1056 m = sr.getResults().get(0);
1057 assertEquals(exons.getSequenceAt(0).getDatasetSequence(),
1059 assertEquals(4, m.getStart());
1060 assertEquals(6, m.getEnd());
1063 * Mapping from pep2 to GGGTTTCCC in second new exon sequence
1065 List<AlignedCodonFrame> pep2Mapping = MappingUtils
1066 .findMappingsForSequence(pep2, mappings);
1067 assertEquals(1, pep2Mapping.size());
1069 sr = MappingUtils.buildSearchResults(pep2, 1, mappings);
1070 assertEquals(1, sr.getResults().size());
1071 m = sr.getResults().get(0);
1072 assertEquals(exons.getSequenceAt(1).getDatasetSequence(),
1074 assertEquals(1, m.getStart());
1075 assertEquals(3, m.getEnd());
1077 sr = MappingUtils.buildSearchResults(pep2, 2, mappings);
1078 m = sr.getResults().get(0);
1079 assertEquals(exons.getSequenceAt(1).getDatasetSequence(),
1081 assertEquals(4, m.getStart());
1082 assertEquals(6, m.getEnd());
1084 sr = MappingUtils.buildSearchResults(pep2, 3, mappings);
1085 m = sr.getResults().get(0);
1086 assertEquals(exons.getSequenceAt(1).getDatasetSequence(),
1088 assertEquals(7, m.getStart());
1089 assertEquals(9, m.getEnd());
1093 * Test the method that makes an exon-only sequence from a DNA sequence and
1094 * its product mapping. Test includes the expected case that the DNA sequence
1095 * already has a protein product (Uniprot translation) which in turn has an
1096 * x-ref to the EMBLCDS record.
1098 @Test(groups = { "Functional" })
1099 public void testMakeExonSequences()
1101 SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
1102 SequenceI pep1 = new Sequence("pep1", "GF");
1103 dna1.createDatasetSequence();
1104 pep1.createDatasetSequence();
1105 pep1.getDatasetSequence().addDBRef(
1106 new DBRefEntry("EMBLCDS", "2", "A12345"));
1109 * Make the mapping from dna to protein. The protein sequence has a DBRef to
1112 Set<AlignedCodonFrame> mappings = new HashSet<AlignedCodonFrame>();
1113 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1114 new int[] { 1, 2 }, 3, 1);
1115 AlignedCodonFrame acf = new AlignedCodonFrame();
1116 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
1119 AlignedCodonFrame newMapping = new AlignedCodonFrame();
1120 List<SequenceI> exons = AlignmentUtils.makeExonSequences(dna1, acf,
1122 assertEquals(1, exons.size());
1123 SequenceI exon = exons.get(0);
1125 assertEquals("GGGTTT", exon.getSequenceAsString());
1126 assertEquals("dna1|A12345", exon.getName());
1127 assertEquals(1, exon.getDBRef().length);
1128 DBRefEntry cdsRef = exon.getDBRef()[0];
1129 assertEquals("EMBLCDS", cdsRef.getSource());
1130 assertEquals("2", cdsRef.getVersion());
1131 assertEquals("A12345", cdsRef.getAccessionId());
1135 * Test the method that makes an exon-only alignment from a DNA sequence and
1136 * its product mappings, for the case where there are multiple exon mappings
1137 * to different protein products.
1139 @Test(groups = { "Functional" })
1140 public void testMakeExonAlignment_multipleProteins()
1142 SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
1143 SequenceI pep1 = new Sequence("pep1", "GF"); // GGGTTT
1144 SequenceI pep2 = new Sequence("pep2", "KP"); // aaaccc
1145 SequenceI pep3 = new Sequence("pep3", "KF"); // aaaTTT
1146 dna1.createDatasetSequence();
1147 pep1.createDatasetSequence();
1148 pep2.createDatasetSequence();
1149 pep3.createDatasetSequence();
1150 pep1.getDatasetSequence().addDBRef(
1151 new DBRefEntry("EMBLCDS", "2", "A12345"));
1152 pep2.getDatasetSequence().addDBRef(
1153 new DBRefEntry("EMBLCDS", "3", "A12346"));
1154 pep3.getDatasetSequence().addDBRef(
1155 new DBRefEntry("EMBLCDS", "4", "A12347"));
1158 * Make the mappings from dna to protein. Using LinkedHashset is a
1159 * convenience so results are in the input order. There is no assertion that
1160 * the generated exon sequences are in any particular order.
1162 List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
1163 // map ...GGG...TTT to GF
1164 MapList map = new MapList(new int[] { 4, 6, 10, 12 },
1165 new int[] { 1, 2 }, 3, 1);
1166 AlignedCodonFrame acf = new AlignedCodonFrame();
1167 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
1170 // map aaa...ccc to KP
1171 map = new MapList(new int[] { 1, 3, 7, 9 }, new int[] { 1, 2 }, 3, 1);
1172 acf = new AlignedCodonFrame();
1173 acf.addMap(dna1.getDatasetSequence(), pep2.getDatasetSequence(), map);
1176 // map aaa......TTT to KF
1177 map = new MapList(new int[] { 1, 3, 10, 12 }, new int[] { 1, 2 }, 3, 1);
1178 acf = new AlignedCodonFrame();
1179 acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map);
1183 * Create the Exon alignment; also replaces the dna-to-protein mappings with
1184 * exon-to-protein and exon-to-dna mappings
1186 AlignmentI exal = AlignmentUtils.makeExonAlignment(
1187 new SequenceI[] { dna1 }, mappings);
1190 * Verify we have 3 exon sequences, mapped to pep1/2/3 respectively
1192 List<SequenceI> exons = exal.getSequences();
1193 assertEquals(3, exons.size());
1195 SequenceI exon = exons.get(0);
1196 assertEquals("GGGTTT", exon.getSequenceAsString());
1197 assertEquals("dna1|A12345", exon.getName());
1198 assertEquals(1, exon.getDBRef().length);
1199 DBRefEntry cdsRef = exon.getDBRef()[0];
1200 assertEquals("EMBLCDS", cdsRef.getSource());
1201 assertEquals("2", cdsRef.getVersion());
1202 assertEquals("A12345", cdsRef.getAccessionId());
1204 exon = exons.get(1);
1205 assertEquals("aaaccc", exon.getSequenceAsString());
1206 assertEquals("dna1|A12346", exon.getName());
1207 assertEquals(1, exon.getDBRef().length);
1208 cdsRef = exon.getDBRef()[0];
1209 assertEquals("EMBLCDS", cdsRef.getSource());
1210 assertEquals("3", cdsRef.getVersion());
1211 assertEquals("A12346", cdsRef.getAccessionId());
1213 exon = exons.get(2);
1214 assertEquals("aaaTTT", exon.getSequenceAsString());
1215 assertEquals("dna1|A12347", exon.getName());
1216 assertEquals(1, exon.getDBRef().length);
1217 cdsRef = exon.getDBRef()[0];
1218 assertEquals("EMBLCDS", cdsRef.getSource());
1219 assertEquals("4", cdsRef.getVersion());
1220 assertEquals("A12347", cdsRef.getAccessionId());
1223 * Verify there are mappings from each exon sequence to its protein product
1224 * and also to its dna source
1226 Iterator<AlignedCodonFrame> newMappingsIterator = mappings.iterator();
1228 // mappings for dna1 - exon1 - pep1
1229 AlignedCodonFrame exonMapping = newMappingsIterator.next();
1230 List<Mapping> dnaMappings = exonMapping.getMappingsForSequence(dna1);
1231 assertEquals(1, dnaMappings.size());
1232 assertSame(exons.get(0).getDatasetSequence(), dnaMappings.get(0)
1234 assertEquals("G(1) in CDS should map to G(4) in DNA", 4, dnaMappings
1235 .get(0).getMap().getToPosition(1));
1236 List<Mapping> peptideMappings = exonMapping
1237 .getMappingsForSequence(pep1);
1238 assertEquals(1, peptideMappings.size());
1239 assertSame(pep1.getDatasetSequence(), peptideMappings.get(0).getTo());
1241 // mappings for dna1 - exon2 - pep2
1242 exonMapping = newMappingsIterator.next();
1243 dnaMappings = exonMapping.getMappingsForSequence(dna1);
1244 assertEquals(1, dnaMappings.size());
1245 assertSame(exons.get(1).getDatasetSequence(), dnaMappings.get(0)
1247 assertEquals("c(4) in CDS should map to c(7) in DNA", 7, dnaMappings
1248 .get(0).getMap().getToPosition(4));
1249 peptideMappings = exonMapping.getMappingsForSequence(pep2);
1250 assertEquals(1, peptideMappings.size());
1251 assertSame(pep2.getDatasetSequence(), peptideMappings.get(0).getTo());
1253 // mappings for dna1 - exon3 - pep3
1254 exonMapping = newMappingsIterator.next();
1255 dnaMappings = exonMapping.getMappingsForSequence(dna1);
1256 assertEquals(1, dnaMappings.size());
1257 assertSame(exons.get(2).getDatasetSequence(), dnaMappings.get(0)
1259 assertEquals("T(4) in CDS should map to T(10) in DNA", 10, dnaMappings
1260 .get(0).getMap().getToPosition(4));
1261 peptideMappings = exonMapping.getMappingsForSequence(pep3);
1262 assertEquals(1, peptideMappings.size());
1263 assertSame(pep3.getDatasetSequence(), peptideMappings.get(0).getTo());
1266 @Test(groups = { "Functional" })
1267 public void testIsMappable()
1269 SequenceI dna1 = new Sequence("dna1", "cgCAGtgGT");
1270 SequenceI aa1 = new Sequence("aa1", "RSG");
1271 AlignmentI al1 = new Alignment(new SequenceI[] { dna1 });
1272 AlignmentI al2 = new Alignment(new SequenceI[] { aa1 });
1274 assertFalse(AlignmentUtils.isMappable(null, null));
1275 assertFalse(AlignmentUtils.isMappable(al1, null));
1276 assertFalse(AlignmentUtils.isMappable(null, al1));
1277 assertFalse(AlignmentUtils.isMappable(al1, al1));
1278 assertFalse(AlignmentUtils.isMappable(al2, al2));
1280 assertTrue(AlignmentUtils.isMappable(al1, al2));
1281 assertTrue(AlignmentUtils.isMappable(al2, al1));
1285 * Test creating a mapping when the sequences involved do not start at residue
1288 * @throws IOException
1290 @Test(groups = { "Functional" })
1291 public void testMapProteinSequenceToCdna_forSubsequence()
1294 SequenceI prot = new Sequence("UNIPROT|V12345", "E-I--Q", 10, 12);
1295 prot.createDatasetSequence();
1297 SequenceI dna = new Sequence("EMBL|A33333", "GAA--AT-C-CAG", 40, 48);
1298 dna.createDatasetSequence();
1300 MapList map = AlignmentUtils.mapProteinSequenceToCdna(prot, dna);
1301 assertEquals(10, map.getToLowest());
1302 assertEquals(12, map.getToHighest());
1303 assertEquals(40, map.getFromLowest());
1304 assertEquals(48, map.getFromHighest());
1308 * Test for the alignSequenceAs method where we have protein mapped to protein
1310 @Test(groups = { "Functional" })
1311 public void testAlignSequenceAs_mappedProteinProtein()
1314 SequenceI alignMe = new Sequence("Match", "MGAASEV");
1315 alignMe.createDatasetSequence();
1316 SequenceI alignFrom = new Sequence("Query", "LQTGYMGAASEVMFSPTRR");
1317 alignFrom.createDatasetSequence();
1319 AlignedCodonFrame acf = new AlignedCodonFrame();
1320 // this is like a domain or motif match of part of a peptide sequence
1321 MapList map = new MapList(new int[] { 6, 12 }, new int[] { 1, 7 }, 1, 1);
1322 acf.addMap(alignFrom.getDatasetSequence(),
1323 alignMe.getDatasetSequence(), map);
1325 AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "-", '-', true,
1327 assertEquals("-----MGAASEV-------", alignMe.getSequenceAsString());
1331 * Test for the alignSequenceAs method where there are trailing unmapped
1332 * residues in the model sequence
1334 @Test(groups = { "Functional" })
1335 public void testAlignSequenceAs_withTrailingPeptide()
1337 // map first 3 codons to KPF; G is a trailing unmapped residue
1338 MapList map = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3, 1);
1340 checkAlignSequenceAs("AAACCCTTT", "K-PFG", true, true, map,