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;
24 import static org.testng.AssertJUnit.assertEquals;
25 import static org.testng.AssertJUnit.assertFalse;
26 import static org.testng.AssertJUnit.assertNull;
27 import static org.testng.AssertJUnit.assertSame;
28 import static org.testng.AssertJUnit.assertTrue;
30 import jalview.datamodel.AlignedCodonFrame;
31 import jalview.datamodel.Alignment;
32 import jalview.datamodel.AlignmentAnnotation;
33 import jalview.datamodel.AlignmentI;
34 import jalview.datamodel.Annotation;
35 import jalview.datamodel.DBRefEntry;
36 import jalview.datamodel.Mapping;
37 import jalview.datamodel.SearchResults;
38 import jalview.datamodel.SearchResults.Match;
39 import jalview.datamodel.Sequence;
40 import jalview.datamodel.SequenceI;
41 import jalview.io.AppletFormatAdapter;
42 import jalview.io.FormatAdapter;
43 import jalview.util.MapList;
44 import jalview.util.MappingUtils;
46 import java.io.IOException;
47 import java.util.ArrayList;
48 import java.util.Arrays;
49 import java.util.Collections;
50 import java.util.HashSet;
51 import java.util.Iterator;
52 import java.util.LinkedHashSet;
53 import java.util.List;
57 import org.testng.annotations.Test;
59 public class AlignmentUtilsTests
62 private static final String TEST_DATA =
64 "#=GS D.melanogaster.1 AC AY119185.1/838-902\n" +
65 "#=GS D.melanogaster.2 AC AC092237.1/57223-57161\n" +
66 "#=GS D.melanogaster.3 AC AY060611.1/560-627\n" +
67 "D.melanogaster.1 G.AGCC.CU...AUGAUCGA\n" +
68 "#=GR D.melanogaster.1 SS ................((((\n" +
69 "D.melanogaster.2 C.AUUCAACU.UAUGAGGAU\n" +
70 "#=GR D.melanogaster.2 SS ................((((\n" +
71 "D.melanogaster.3 G.UGGCGCU..UAUGACGCA\n" +
72 "#=GR D.melanogaster.3 SS (.(((...(....(((((((\n" +
75 private static final String AA_SEQS_1 =
81 private static final String CDNA_SEQS_1 =
83 "AC-GG--CUC-CAA-CT\n" +
85 "-CG-TTA--ACG---AAGT\n";
87 private static final String CDNA_SEQS_2 =
94 // public static Sequence ts=new
95 // Sequence("short","ASDASDASDASDASDASDASDASDASDASDASDASDASD");
96 public static Sequence ts = new Sequence("short",
97 "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
99 @Test(groups ={ "Functional" })
100 public void testExpandContext()
102 AlignmentI al = new Alignment(new Sequence[] {});
103 for (int i = 4; i < 14; i += 2)
105 SequenceI s1=ts.deriveSequence().getSubSequence(i, i+7);
108 System.out.println(new AppletFormatAdapter().formatSequences("Clustal", al, true));
109 for (int flnk=-1;flnk<25; flnk++)
111 AlignmentI exp = AlignmentUtils.expandContext(al, flnk);
112 System.out.println("\nFlank size: " + flnk);
113 System.out.println(new AppletFormatAdapter().formatSequences(
114 "Clustal", exp, true));
118 * Full expansion to complete sequences
120 for (SequenceI sq : exp.getSequences())
122 String ung = sq.getSequenceAsString().replaceAll("-+", "");
123 final String errorMsg = "Flanking sequence not the same as original dataset sequence.\n"
126 + sq.getDatasetSequence().getSequenceAsString();
127 assertTrue(errorMsg, ung.equalsIgnoreCase(sq.getDatasetSequence()
128 .getSequenceAsString()));
134 * Last sequence is fully expanded, others have leading gaps to match
136 assertTrue(exp.getSequenceAt(4).getSequenceAsString()
138 assertTrue(exp.getSequenceAt(3).getSequenceAsString()
139 .startsWith("--abc"));
140 assertTrue(exp.getSequenceAt(2).getSequenceAsString()
141 .startsWith("----abc"));
142 assertTrue(exp.getSequenceAt(1).getSequenceAsString()
143 .startsWith("------abc"));
144 assertTrue(exp.getSequenceAt(0).getSequenceAsString()
145 .startsWith("--------abc"));
151 * Test that annotations are correctly adjusted by expandContext
153 @Test(groups ={ "Functional" })
154 public void testExpandContext_annotation()
156 AlignmentI al = new Alignment(new Sequence[]
158 SequenceI ds = new Sequence("Seq1", "ABCDEFGHI");
160 SequenceI seq1 = ds.deriveSequence().getSubSequence(3, 6);
161 al.addSequence(seq1);
164 * Annotate DEF with 4/5/6 respectively
166 Annotation[] anns = new Annotation[]
167 { new Annotation(4), new Annotation(5), new Annotation(6) };
168 AlignmentAnnotation ann = new AlignmentAnnotation("SS",
169 "secondary structure", anns);
170 seq1.addAlignmentAnnotation(ann);
173 * The annotations array should match aligned positions
175 assertEquals(3, ann.annotations.length);
176 assertEquals(4, ann.annotations[0].value, 0.001);
177 assertEquals(5, ann.annotations[1].value, 0.001);
178 assertEquals(6, ann.annotations[2].value, 0.001);
181 * Check annotation to sequence position mappings before expanding the
182 * sequence; these are set up in Sequence.addAlignmentAnnotation ->
183 * Annotation.setSequenceRef -> createSequenceMappings
185 assertNull(ann.getAnnotationForPosition(1));
186 assertNull(ann.getAnnotationForPosition(2));
187 assertNull(ann.getAnnotationForPosition(3));
188 assertEquals(4, ann.getAnnotationForPosition(4).value, 0.001);
189 assertEquals(5, ann.getAnnotationForPosition(5).value, 0.001);
190 assertEquals(6, ann.getAnnotationForPosition(6).value, 0.001);
191 assertNull(ann.getAnnotationForPosition(7));
192 assertNull(ann.getAnnotationForPosition(8));
193 assertNull(ann.getAnnotationForPosition(9));
196 * Expand the subsequence to the full sequence abcDEFghi
198 AlignmentI expanded = AlignmentUtils.expandContext(al, -1);
199 assertEquals("abcDEFghi", expanded.getSequenceAt(0)
200 .getSequenceAsString());
203 * Confirm the alignment and sequence have the same SS annotation,
204 * referencing the expanded sequence
206 ann = expanded.getSequenceAt(0).getAnnotation()[0];
207 assertSame(ann, expanded.getAlignmentAnnotation()[0]);
208 assertSame(expanded.getSequenceAt(0), ann.sequenceRef);
211 * The annotations array should have null values except for annotated
214 assertNull(ann.annotations[0]);
215 assertNull(ann.annotations[1]);
216 assertNull(ann.annotations[2]);
217 assertEquals(4, ann.annotations[3].value, 0.001);
218 assertEquals(5, ann.annotations[4].value, 0.001);
219 assertEquals(6, ann.annotations[5].value, 0.001);
220 assertNull(ann.annotations[6]);
221 assertNull(ann.annotations[7]);
222 assertNull(ann.annotations[8]);
225 * sequence position mappings should be unchanged
227 assertNull(ann.getAnnotationForPosition(1));
228 assertNull(ann.getAnnotationForPosition(2));
229 assertNull(ann.getAnnotationForPosition(3));
230 assertEquals(4, ann.getAnnotationForPosition(4).value, 0.001);
231 assertEquals(5, ann.getAnnotationForPosition(5).value, 0.001);
232 assertEquals(6, ann.getAnnotationForPosition(6).value, 0.001);
233 assertNull(ann.getAnnotationForPosition(7));
234 assertNull(ann.getAnnotationForPosition(8));
235 assertNull(ann.getAnnotationForPosition(9));
239 * Test method that returns a map of lists of sequences by sequence name.
241 * @throws IOException
243 @Test(groups ={ "Functional" })
244 public void testGetSequencesByName() throws IOException
246 final String data = ">Seq1Name\nKQYL\n" + ">Seq2Name\nRFPW\n"
247 + ">Seq1Name\nABCD\n";
248 AlignmentI al = loadAlignment(data, "FASTA");
249 Map<String, List<SequenceI>> map = AlignmentUtils
250 .getSequencesByName(al);
251 assertEquals(2, map.keySet().size());
252 assertEquals(2, map.get("Seq1Name").size());
253 assertEquals("KQYL", map.get("Seq1Name").get(0).getSequenceAsString());
254 assertEquals("ABCD", map.get("Seq1Name").get(1).getSequenceAsString());
255 assertEquals(1, map.get("Seq2Name").size());
256 assertEquals("RFPW", map.get("Seq2Name").get(0).getSequenceAsString());
259 * Helper method to load an alignment and ensure dataset sequences are set up.
264 * @throws IOException
266 protected AlignmentI loadAlignment(final String data, String format) throws IOException
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 testMapProteinToCdna_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.mapProteinToCdna(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(
309 protein.getSequenceAt(0)).get(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[]
319 { 1, 9 }, mapList.getFromRanges().get(0)));
320 assertEquals(1, mapList.getFromRanges().size());
321 assertTrue(Arrays.equals(new int[]
322 { 1, 3 }, 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[]
352 * No existing gaps in dna:
354 checkAlignSequenceAs("GGGAAA", "-A-L-", false, false, map,
358 * Now introduce gaps in dna but ignore them when realigning.
360 checkAlignSequenceAs("-G-G-G-A-A-A-", "-A-L-", false, false, map,
364 * Now include gaps in dna when realigning. First retaining 'mapped' gaps
365 * only, i.e. those within the exon region.
367 checkAlignSequenceAs("-G-G--G-A--A-A-", "-A-L-", true, false, map,
368 "---G-G--G---A--A-A");
371 * Include all gaps in dna when realigning (within and without the exon
372 * region). The leading gap, and the gaps between codons, are subsumed by
373 * the protein alignment gap.
375 checkAlignSequenceAs("-G-GG--AA-A-", "-A-L-", true, true, map,
379 * Include only unmapped gaps in dna when realigning (outside the exon
380 * region). The leading gap, and the gaps between codons, are subsumed by
381 * the protein alignment gap.
383 checkAlignSequenceAs("-G-GG--AA-A-", "-A-L-", false, true, map,
388 * Test for the alignSequenceAs method that takes two sequences and a mapping.
390 @Test(groups ={ "Functional" })
391 public void testAlignSequenceAs_withMapping_withIntrons()
394 * Exons at codon 2 (AAA) and 4 (TTT)
396 MapList map = new MapList(new int[]
397 { 4, 6, 10, 12 }, new int[]
401 * Simple case: no gaps in dna
403 checkAlignSequenceAs("GGGAAACCCTTTGGG", "--A-L-", false, false, map,
404 "GGG---AAACCCTTTGGG");
407 * Add gaps to dna - but ignore when realigning.
409 checkAlignSequenceAs("-G-G-G--A--A---AC-CC-T-TT-GG-G-", "--A-L-",
410 false, false, map, "GGG---AAACCCTTTGGG");
413 * Add gaps to dna - include within exons only when realigning.
415 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
416 true, false, map, "GGG---A--A---ACCCT-TTGGG");
419 * Include gaps outside exons only when realigning.
421 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
422 false, true, map, "-G-G-GAAAC-CCTTT-GG-G-");
425 * Include gaps following first intron if we are 'preserving mapped gaps'
427 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
428 true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
431 * Include all gaps in dna when realigning.
433 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
434 true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
438 * Test for the case where not all of the protein sequence is mapped to cDNA.
440 @Test(groups ={ "Functional" })
441 public void testAlignSequenceAs_withMapping_withUnmappedProtein()
445 * Exons at codon 2 (AAA) and 4 (TTT) mapped to A and P
447 final MapList map = new MapList(new int[]
448 { 4, 6, 10, 12 }, new int[]
449 { 1, 1, 3, 3 }, 3, 1);
453 * Expect alignment does nothing (aborts realignment). Change this test
454 * first if different behaviour wanted.
456 checkAlignSequenceAs("GGGAAACCCTTTGGG", "-A-L-P-", false,
457 false, map, "GGGAAACCCTTTGGG");
461 * Helper method that performs and verifies the method under test.
465 * @param preserveMappedGaps
466 * @param preserveUnmappedGaps
470 protected void checkAlignSequenceAs(final String dnaSeq,
471 final String proteinSeq, final boolean preserveMappedGaps,
472 final boolean preserveUnmappedGaps, MapList map,
473 final String expected)
475 SequenceI dna = new Sequence("Seq1", dnaSeq);
476 dna.createDatasetSequence();
477 SequenceI protein = new Sequence("Seq1", proteinSeq);
478 protein.createDatasetSequence();
479 AlignedCodonFrame acf = new AlignedCodonFrame();
480 acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map);
482 AlignmentUtils.alignSequenceAs(dna, protein, acf, "---", '-',
483 preserveMappedGaps, preserveUnmappedGaps);
484 assertEquals(expected, dna.getSequenceAsString());
488 * Test for the alignSequenceAs method where we preserve gaps in introns only.
490 @Test(groups ={ "Functional" })
491 public void testAlignSequenceAs_keepIntronGapsOnly()
495 * Intron GGGAAA followed by exon CCCTTT
497 MapList map = new MapList(new int[]
501 checkAlignSequenceAs("GG-G-AA-A-C-CC-T-TT", "AL",
502 false, true, map, "GG-G-AA-ACCCTTT");
506 * Test for the method that generates an aligned translated sequence from one
509 @Test(groups ={ "Functional" })
510 public void testGetAlignedTranslation_dnaLikeProtein()
512 // dna alignment will be replaced
513 SequenceI dna = new Sequence("Seq1", "T-G-CC-A--T-TAC-CAG-");
514 dna.createDatasetSequence();
515 // protein alignment will be 'applied' to dna
516 SequenceI protein = new Sequence("Seq1", "-CH-Y--Q-");
517 protein.createDatasetSequence();
518 MapList map = new MapList(new int[]
521 AlignedCodonFrame acf = new AlignedCodonFrame();
522 acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map);
524 final SequenceI aligned = AlignmentUtils
525 .getAlignedTranslation(protein, '-', acf);
526 assertEquals("---TGCCAT---TAC------CAG---", aligned.getSequenceAsString());
527 assertSame(aligned.getDatasetSequence(), dna.getDatasetSequence());
531 * Test the method that realigns protein to match mapped codon alignment.
533 @Test(groups ={ "Functional" })
534 public void testAlignProteinAsDna()
536 // seq1 codons are [1,2,3] [4,5,6] [7,8,9] [10,11,12]
537 SequenceI dna1 = new Sequence("Seq1", "TGCCATTACCAG-");
538 // seq2 codons are [1,3,4] [5,6,7] [8,9,10] [11,12,13]
539 SequenceI dna2 = new Sequence("Seq2", "T-GCCATTACCAG");
540 // seq3 codons are [1,2,3] [4,5,7] [8,9,10] [11,12,13]
541 SequenceI dna3 = new Sequence("Seq3", "TGCCA-TTACCAG");
542 AlignmentI dna = new Alignment(new SequenceI[]
543 { dna1, dna2, dna3 });
544 dna.setDataset(null);
546 // protein alignment will be realigned like dna
547 SequenceI prot1 = new Sequence("Seq1", "CHYQ");
548 SequenceI prot2 = new Sequence("Seq2", "CHYQ");
549 SequenceI prot3 = new Sequence("Seq3", "CHYQ");
550 AlignmentI protein = new Alignment(new SequenceI[]
551 { prot1, prot2, prot3 });
552 protein.setDataset(null);
554 MapList map = new MapList(new int[]
557 AlignedCodonFrame acf = new AlignedCodonFrame();
558 acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
559 acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map);
560 acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map);
561 protein.setCodonFrames(Collections.singleton(acf));
564 * Translated codon order is [1,2,3] [1,3,4] [4,5,6] [4,5,7] [5,6,7] [7,8,9]
565 * [8,9,10] [10,11,12] [11,12,13]
567 AlignmentUtils.alignProteinAsDna(protein, dna);
568 assertEquals("C-H--Y-Q-", prot1.getSequenceAsString());
569 assertEquals("-C--H-Y-Q", prot2.getSequenceAsString());
570 assertEquals("C--H--Y-Q", prot3.getSequenceAsString());
574 * Test the method that tests whether a CDNA sequence translates to a protein
577 @Test(groups ={ "Functional" })
578 public void testTranslatesAs()
580 assertTrue(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
581 "FPKG".toCharArray()));
582 // with start codon (not in protein)
583 assertTrue(AlignmentUtils.translatesAs("atgtttcccaaaggg".toCharArray(),
584 3, "FPKG".toCharArray()));
585 // with stop codon1 (not in protein)
586 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtaa".toCharArray(),
587 0, "FPKG".toCharArray()));
588 // with stop codon1 (in protein as *)
589 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtaa".toCharArray(),
590 0, "FPKG*".toCharArray()));
591 // with stop codon2 (not in protein)
592 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtag".toCharArray(),
593 0, "FPKG".toCharArray()));
594 // with stop codon3 (not in protein)
595 assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtga".toCharArray(),
596 0, "FPKG".toCharArray()));
597 // with start and stop codon1
598 assertTrue(AlignmentUtils.translatesAs(
599 "atgtttcccaaagggtaa".toCharArray(), 3, "FPKG".toCharArray()));
600 // with start and stop codon1 (in protein as *)
601 assertTrue(AlignmentUtils.translatesAs(
602 "atgtttcccaaagggtaa".toCharArray(), 3, "FPKG*".toCharArray()));
603 // with start and stop codon2
604 assertTrue(AlignmentUtils.translatesAs(
605 "atgtttcccaaagggtag".toCharArray(), 3, "FPKG".toCharArray()));
606 // with start and stop codon3
607 assertTrue(AlignmentUtils.translatesAs(
608 "atgtttcccaaagggtga".toCharArray(), 3, "FPKG".toCharArray()));
610 // with embedded stop codon
611 assertTrue(AlignmentUtils.translatesAs(
612 "atgtttTAGcccaaaTAAgggtga".toCharArray(), 3,
613 "F*PK*G".toCharArray()));
616 assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
618 "FPMG".toCharArray()));
622 * Test mapping of protein to cDNA, for cases where the cDNA has start and/or
623 * stop codons in addition to the protein coding sequence.
625 * @throws IOException
627 @Test(groups ={ "Functional" })
628 public void testMapProteinToCdna_withStartAndStopCodons()
631 List<SequenceI> protseqs = new ArrayList<SequenceI>();
632 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
633 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
634 protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
635 AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
636 protein.setDataset(null);
638 List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
640 dnaseqs.add(new Sequence("EMBL|A11111", "ATGTCAGCACGC"));
642 dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAATAA"));
643 // = start +EIQ + stop
644 dnaseqs.add(new Sequence("EMBL|A33333", "ATGGAAATCCAGTAG"));
645 dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG"));
646 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
647 cdna.setDataset(null);
649 assertTrue(AlignmentUtils.mapProteinToCdna(protein, cdna));
651 // 3 mappings made, each from 1 to 1 sequence
652 assertEquals(3, protein.getCodonFrames().size());
653 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
654 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
655 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
657 // V12345 mapped from A22222
658 AlignedCodonFrame acf = protein.getCodonFrame(
659 protein.getSequenceAt(0)).get(0);
660 assertEquals(1, acf.getdnaSeqs().length);
661 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
662 acf.getdnaSeqs()[0]);
663 Mapping[] protMappings = acf.getProtMappings();
664 assertEquals(1, protMappings.length);
665 MapList mapList = protMappings[0].getMap();
666 assertEquals(3, mapList.getFromRatio());
667 assertEquals(1, mapList.getToRatio());
668 assertTrue(Arrays.equals(new int[]
669 { 1, 9 }, mapList.getFromRanges().get(0)));
670 assertEquals(1, mapList.getFromRanges().size());
671 assertTrue(Arrays.equals(new int[]
672 { 1, 3 }, mapList.getToRanges().get(0)));
673 assertEquals(1, mapList.getToRanges().size());
675 // V12346 mapped from A33333 starting position 4
676 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
677 assertEquals(1, acf.getdnaSeqs().length);
678 assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
679 acf.getdnaSeqs()[0]);
680 protMappings = acf.getProtMappings();
681 assertEquals(1, protMappings.length);
682 mapList = protMappings[0].getMap();
683 assertEquals(3, mapList.getFromRatio());
684 assertEquals(1, mapList.getToRatio());
685 assertTrue(Arrays.equals(new int[]
686 { 4, 12 }, mapList.getFromRanges().get(0)));
687 assertEquals(1, mapList.getFromRanges().size());
688 assertTrue(Arrays.equals(new int[]
689 { 1, 3 }, mapList.getToRanges().get(0)));
690 assertEquals(1, mapList.getToRanges().size());
692 // V12347 mapped to A11111 starting position 4
693 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
694 assertEquals(1, acf.getdnaSeqs().length);
695 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
696 acf.getdnaSeqs()[0]);
697 protMappings = acf.getProtMappings();
698 assertEquals(1, protMappings.length);
699 mapList = protMappings[0].getMap();
700 assertEquals(3, mapList.getFromRatio());
701 assertEquals(1, mapList.getToRatio());
702 assertTrue(Arrays.equals(new int[]
703 { 4, 12 }, mapList.getFromRanges().get(0)));
704 assertEquals(1, mapList.getFromRanges().size());
705 assertTrue(Arrays.equals(new int[]
706 { 1, 3 }, mapList.getToRanges().get(0)));
707 assertEquals(1, mapList.getToRanges().size());
709 // no mapping involving the 'extra' A44444
710 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(3)).isEmpty());
714 * Test mapping of protein to cDNA, for the case where we have some sequence
715 * cross-references. Verify that 1-to-many mappings are made where
716 * cross-references exist and sequences are mappable.
718 * @throws IOException
720 @Test(groups ={ "Functional" })
721 public void testMapProteinToCdna_withXrefs() throws IOException
723 List<SequenceI> protseqs = new ArrayList<SequenceI>();
724 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
725 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
726 protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
727 AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
728 protein.setDataset(null);
730 List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
731 dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR
732 dnaseqs.add(new Sequence("EMBL|A22222", "ATGGAGATACAA")); // = start + EIQ
733 dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ
734 dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG")); // = EIQ
735 dnaseqs.add(new Sequence("EMBL|A55555", "GAGATTCAG")); // = EIQ
736 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[5]));
737 cdna.setDataset(null);
739 // Xref A22222 to V12345 (should get mapped)
740 dnaseqs.get(1).addDBRef(new DBRefEntry("UNIPROT", "1", "V12345"));
741 // Xref V12345 to A44444 (should get mapped)
742 protseqs.get(0).addDBRef(new DBRefEntry("EMBL", "1", "A44444"));
743 // Xref A33333 to V12347 (sequence mismatch - should not get mapped)
744 dnaseqs.get(2).addDBRef(new DBRefEntry("UNIPROT", "1", "V12347"));
745 // as V12345 is mapped to A22222 and A44444, this leaves V12346 unmapped.
746 // it should get paired up with the unmapped A33333
747 // A11111 should be mapped to V12347
748 // A55555 is spare and has no xref so is not mapped
750 assertTrue(AlignmentUtils.mapProteinToCdna(protein, cdna));
752 // 4 protein mappings made for 3 proteins, 2 to V12345, 1 each to V12346/7
753 assertEquals(3, protein.getCodonFrames().size());
754 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
755 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
756 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
758 // one mapping for each of the first 4 cDNA sequences
759 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(0)).size());
760 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(1)).size());
761 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(2)).size());
762 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(3)).size());
764 // V12345 mapped to A22222 and A44444
765 AlignedCodonFrame acf = protein.getCodonFrame(
766 protein.getSequenceAt(0)).get(0);
767 assertEquals(2, acf.getdnaSeqs().length);
768 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
769 acf.getdnaSeqs()[0]);
770 assertEquals(cdna.getSequenceAt(3).getDatasetSequence(),
771 acf.getdnaSeqs()[1]);
773 // V12346 mapped to A33333
774 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
775 assertEquals(1, acf.getdnaSeqs().length);
776 assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
777 acf.getdnaSeqs()[0]);
779 // V12347 mapped to A11111
780 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
781 assertEquals(1, acf.getdnaSeqs().length);
782 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
783 acf.getdnaSeqs()[0]);
785 // no mapping involving the 'extra' A55555
786 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(4)).isEmpty());
790 * Test mapping of protein to cDNA, for the case where we have some sequence
791 * cross-references. Verify that once we have made an xref mapping we don't
792 * also map un-xrefd sequeces.
794 * @throws IOException
796 @Test(groups ={ "Functional" })
797 public void testMapProteinToCdna_prioritiseXrefs() throws IOException
799 List<SequenceI> protseqs = new ArrayList<SequenceI>();
800 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
801 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
802 AlignmentI protein = new Alignment(
803 protseqs.toArray(new SequenceI[protseqs.size()]));
804 protein.setDataset(null);
806 List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
807 dnaseqs.add(new Sequence("EMBL|A11111", "GAAATCCAG")); // = EIQ
808 dnaseqs.add(new Sequence("EMBL|A22222", "GAAATTCAG")); // = EIQ
809 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[dnaseqs
811 cdna.setDataset(null);
813 // Xref A22222 to V12345 (should get mapped)
814 // A11111 should then be mapped to the unmapped V12346
815 dnaseqs.get(1).addDBRef(new DBRefEntry("UNIPROT", "1", "V12345"));
817 assertTrue(AlignmentUtils.mapProteinToCdna(protein, cdna));
819 // 2 protein mappings made
820 assertEquals(2, protein.getCodonFrames().size());
821 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
822 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
824 // one mapping for each of the cDNA sequences
825 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(0)).size());
826 assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(1)).size());
828 // V12345 mapped to A22222
829 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
831 assertEquals(1, acf.getdnaSeqs().length);
832 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
833 acf.getdnaSeqs()[0]);
835 // V12346 mapped to A11111
836 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
837 assertEquals(1, acf.getdnaSeqs().length);
838 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
839 acf.getdnaSeqs()[0]);
843 * Test the method that shows or hides sequence annotations by type(s) and
846 @Test(groups ={ "Functional" })
847 public void testShowOrHideSequenceAnnotations()
849 SequenceI seq1 = new Sequence("Seq1", "AAA");
850 SequenceI seq2 = new Sequence("Seq2", "BBB");
851 SequenceI seq3 = new Sequence("Seq3", "CCC");
852 Annotation[] anns = new Annotation[]
853 { new Annotation(2f) };
854 AlignmentAnnotation ann1 = new AlignmentAnnotation("Structure", "ann1",
856 ann1.setSequenceRef(seq1);
857 AlignmentAnnotation ann2 = new AlignmentAnnotation("Structure", "ann2",
859 ann2.setSequenceRef(seq2);
860 AlignmentAnnotation ann3 = new AlignmentAnnotation("Structure", "ann3",
862 AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "ann4", anns);
863 ann4.setSequenceRef(seq1);
864 AlignmentAnnotation ann5 = new AlignmentAnnotation("Temp", "ann5", anns);
865 ann5.setSequenceRef(seq2);
866 AlignmentAnnotation ann6 = new AlignmentAnnotation("Temp", "ann6", anns);
867 AlignmentI al = new Alignment(new SequenceI[] {seq1, seq2, seq3});
868 al.addAnnotation(ann1); // Structure for Seq1
869 al.addAnnotation(ann2); // Structure for Seq2
870 al.addAnnotation(ann3); // Structure for no sequence
871 al.addAnnotation(ann4); // Temp for seq1
872 al.addAnnotation(ann5); // Temp for seq2
873 al.addAnnotation(ann6); // Temp for no sequence
874 List<String> types = new ArrayList<String>();
875 List<SequenceI> scope = new ArrayList<SequenceI>();
878 * Set all sequence related Structure to hidden (ann1, ann2)
880 types.add("Structure");
881 AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, false,
883 assertFalse(ann1.visible);
884 assertFalse(ann2.visible);
885 assertTrue(ann3.visible); // not sequence-related, not affected
886 assertTrue(ann4.visible); // not Structure, not affected
887 assertTrue(ann5.visible); // "
888 assertTrue(ann6.visible); // not sequence-related, not affected
891 * Set Temp in {seq1, seq3} to hidden
897 AlignmentUtils.showOrHideSequenceAnnotations(al, types, scope, false,
899 assertFalse(ann1.visible); // unchanged
900 assertFalse(ann2.visible); // unchanged
901 assertTrue(ann3.visible); // not sequence-related, not affected
902 assertFalse(ann4.visible); // Temp for seq1 hidden
903 assertTrue(ann5.visible); // not in scope, not affected
904 assertTrue(ann6.visible); // not sequence-related, not affected
907 * Set Temp in all sequences to hidden
913 AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, false,
915 assertFalse(ann1.visible); // unchanged
916 assertFalse(ann2.visible); // unchanged
917 assertTrue(ann3.visible); // not sequence-related, not affected
918 assertFalse(ann4.visible); // Temp for seq1 hidden
919 assertFalse(ann5.visible); // Temp for seq2 hidden
920 assertTrue(ann6.visible); // not sequence-related, not affected
923 * Set all types in {seq1, seq3} to visible
929 AlignmentUtils.showOrHideSequenceAnnotations(al, types, scope, true,
931 assertTrue(ann1.visible); // Structure for seq1 set visible
932 assertFalse(ann2.visible); // not in scope, unchanged
933 assertTrue(ann3.visible); // not sequence-related, not affected
934 assertTrue(ann4.visible); // Temp for seq1 set visible
935 assertFalse(ann5.visible); // not in scope, unchanged
936 assertTrue(ann6.visible); // not sequence-related, not affected
939 * Set all types in all scope to hidden
941 AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, true,
943 assertFalse(ann1.visible);
944 assertFalse(ann2.visible);
945 assertTrue(ann3.visible); // not sequence-related, not affected
946 assertFalse(ann4.visible);
947 assertFalse(ann5.visible);
948 assertTrue(ann6.visible); // not sequence-related, not affected
952 * Tests for the method that checks if one sequence cross-references another
954 @Test(groups ={ "Functional" })
955 public void testHasCrossRef()
957 assertFalse(AlignmentUtils.hasCrossRef(null, null));
958 SequenceI seq1 = new Sequence("EMBL|A12345", "ABCDEF");
959 assertFalse(AlignmentUtils.hasCrossRef(seq1, null));
960 assertFalse(AlignmentUtils.hasCrossRef(null, seq1));
961 SequenceI seq2 = new Sequence("UNIPROT|V20192", "ABCDEF");
962 assertFalse(AlignmentUtils.hasCrossRef(seq1, seq2));
965 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "v20193"));
966 assertFalse(AlignmentUtils.hasCrossRef(seq1, seq2));
968 // case-insensitive; version number is ignored
969 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "v20192"));
970 assertTrue(AlignmentUtils.hasCrossRef(seq1, seq2));
973 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
974 assertTrue(AlignmentUtils.hasCrossRef(seq1, seq2));
975 // test is one-way only
976 assertFalse(AlignmentUtils.hasCrossRef(seq2, seq1));
980 * Tests for the method that checks if either sequence cross-references the
983 @Test(groups ={ "Functional" })
984 public void testHaveCrossRef()
986 assertFalse(AlignmentUtils.hasCrossRef(null, null));
987 SequenceI seq1 = new Sequence("EMBL|A12345", "ABCDEF");
988 assertFalse(AlignmentUtils.haveCrossRef(seq1, null));
989 assertFalse(AlignmentUtils.haveCrossRef(null, seq1));
990 SequenceI seq2 = new Sequence("UNIPROT|V20192", "ABCDEF");
991 assertFalse(AlignmentUtils.haveCrossRef(seq1, seq2));
993 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
994 assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
995 // next is true for haveCrossRef, false for hasCrossRef
996 assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
998 // now the other way round
1000 seq2.addDBRef(new DBRefEntry("EMBL", "1", "A12345"));
1001 assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
1002 assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
1005 seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
1006 assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
1007 assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
1011 * Test the method that extracts the exon-only part of a dna alignment.
1013 @Test(groups ={ "Functional" })
1014 public void testMakeExonAlignment()
1016 SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
1017 SequenceI dna2 = new Sequence("dna2", "GGGcccTTTaaaCCC");
1018 SequenceI pep1 = new Sequence("pep1", "GF");
1019 SequenceI pep2 = new Sequence("pep2", "GFP");
1020 dna1.createDatasetSequence();
1021 dna2.createDatasetSequence();
1022 pep1.createDatasetSequence();
1023 pep2.createDatasetSequence();
1025 Set<AlignedCodonFrame> mappings = new HashSet<AlignedCodonFrame>();
1026 MapList map = new MapList(new int[]
1027 { 4, 6, 10, 12 }, new int[]
1029 AlignedCodonFrame acf = new AlignedCodonFrame();
1030 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
1032 map = new MapList(new int[]
1033 { 1, 3, 7, 9, 13, 15 }, new int[]
1035 acf = new AlignedCodonFrame();
1036 acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
1039 AlignmentI exons = AlignmentUtils.makeExonAlignment(new SequenceI[]
1040 { dna1, dna2 }, mappings);
1041 assertEquals(2, exons.getSequences().size());
1042 assertEquals("GGGTTT", exons.getSequenceAt(0).getSequenceAsString());
1043 assertEquals("GGGTTTCCC", exons.getSequenceAt(1).getSequenceAsString());
1046 * Verify updated mappings
1048 assertEquals(2, mappings.size());
1051 * Mapping from pep1 to GGGTTT in first new exon sequence
1053 List<AlignedCodonFrame> pep1Mapping = MappingUtils
1054 .findMappingsForSequence(pep1, mappings);
1055 assertEquals(1, pep1Mapping.size());
1057 SearchResults sr = MappingUtils.buildSearchResults(pep1, 1, mappings);
1058 assertEquals(1, sr.getResults().size());
1059 Match m = sr.getResults().get(0);
1060 assertEquals(exons.getSequenceAt(0).getDatasetSequence(),
1062 assertEquals(1, m.getStart());
1063 assertEquals(3, m.getEnd());
1065 sr = MappingUtils.buildSearchResults(pep1, 2, mappings);
1066 m = sr.getResults().get(0);
1067 assertEquals(exons.getSequenceAt(0).getDatasetSequence(),
1069 assertEquals(4, m.getStart());
1070 assertEquals(6, m.getEnd());
1073 * Mapping from pep2 to GGGTTTCCC in second new exon sequence
1075 List<AlignedCodonFrame> pep2Mapping = MappingUtils
1076 .findMappingsForSequence(pep2, mappings);
1077 assertEquals(1, pep2Mapping.size());
1079 sr = MappingUtils.buildSearchResults(pep2, 1, mappings);
1080 assertEquals(1, sr.getResults().size());
1081 m = sr.getResults().get(0);
1082 assertEquals(exons.getSequenceAt(1).getDatasetSequence(),
1084 assertEquals(1, m.getStart());
1085 assertEquals(3, m.getEnd());
1087 sr = MappingUtils.buildSearchResults(pep2, 2, mappings);
1088 m = sr.getResults().get(0);
1089 assertEquals(exons.getSequenceAt(1).getDatasetSequence(),
1091 assertEquals(4, m.getStart());
1092 assertEquals(6, m.getEnd());
1094 sr = MappingUtils.buildSearchResults(pep2, 3, mappings);
1095 m = sr.getResults().get(0);
1096 assertEquals(exons.getSequenceAt(1).getDatasetSequence(),
1098 assertEquals(7, m.getStart());
1099 assertEquals(9, m.getEnd());
1103 * Test the method that makes an exon-only sequence from a DNA sequence and
1104 * its product mapping. Test includes the expected case that the DNA sequence
1105 * already has a protein product (Uniprot translation) which in turn has an
1106 * x-ref to the EMBLCDS record.
1108 @Test(groups ={ "Functional" })
1109 public void testMakeExonSequences()
1111 SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
1112 SequenceI pep1 = new Sequence("pep1", "GF");
1113 dna1.createDatasetSequence();
1114 pep1.createDatasetSequence();
1115 pep1.getDatasetSequence().addDBRef(
1116 new DBRefEntry("EMBLCDS", "2", "A12345"));
1119 * Make the mapping from dna to protein. The protein sequence has a DBRef to
1122 Set<AlignedCodonFrame> mappings = new HashSet<AlignedCodonFrame>();
1123 MapList map = new MapList(new int[]
1124 { 4, 6, 10, 12 }, new int[]
1126 AlignedCodonFrame acf = new AlignedCodonFrame();
1127 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
1130 AlignedCodonFrame newMapping = new AlignedCodonFrame();
1131 List<SequenceI> exons = AlignmentUtils.makeExonSequences(dna1, acf,
1133 assertEquals(1, exons.size());
1134 SequenceI exon = exons.get(0);
1136 assertEquals("GGGTTT", exon.getSequenceAsString());
1137 assertEquals("dna1|A12345", exon.getName());
1138 assertEquals(1, exon.getDBRef().length);
1139 DBRefEntry cdsRef = exon.getDBRef()[0];
1140 assertEquals("EMBLCDS", cdsRef.getSource());
1141 assertEquals("2", cdsRef.getVersion());
1142 assertEquals("A12345", cdsRef.getAccessionId());
1146 * Test the method that makes an exon-only alignment from a DNA sequence and
1147 * its product mappings, for the case where there are multiple exon mappings
1148 * to different protein products.
1150 @Test(groups ={ "Functional" })
1151 public void testMakeExonAlignment_multipleProteins()
1153 SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
1154 SequenceI pep1 = new Sequence("pep1", "GF"); // GGGTTT
1155 SequenceI pep2 = new Sequence("pep2", "KP"); // aaaccc
1156 SequenceI pep3 = new Sequence("pep3", "KF"); // aaaTTT
1157 dna1.createDatasetSequence();
1158 pep1.createDatasetSequence();
1159 pep2.createDatasetSequence();
1160 pep3.createDatasetSequence();
1161 pep1.getDatasetSequence().addDBRef(
1162 new DBRefEntry("EMBLCDS", "2", "A12345"));
1163 pep2.getDatasetSequence().addDBRef(
1164 new DBRefEntry("EMBLCDS", "3", "A12346"));
1165 pep3.getDatasetSequence().addDBRef(
1166 new DBRefEntry("EMBLCDS", "4", "A12347"));
1169 * Make the mappings from dna to protein. Using LinkedHashset is a
1170 * convenience so results are in the input order. There is no assertion that
1171 * the generated exon sequences are in any particular order.
1173 Set<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
1174 // map ...GGG...TTT to GF
1175 MapList map = new MapList(new int[]
1176 { 4, 6, 10, 12 }, new int[]
1178 AlignedCodonFrame acf = new AlignedCodonFrame();
1179 acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
1182 // map aaa...ccc to KP
1183 map = new MapList(new int[]
1184 { 1, 3, 7, 9 }, new int[]
1186 acf = new AlignedCodonFrame();
1187 acf.addMap(dna1.getDatasetSequence(), pep2.getDatasetSequence(), map);
1190 // map aaa......TTT to KF
1191 map = new MapList(new int[]
1192 { 1, 3, 10, 12 }, new int[]
1194 acf = new AlignedCodonFrame();
1195 acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map);
1199 * Create the Exon alignment; also replaces the dna-to-protein mappings with
1200 * exon-to-protein and exon-to-dna mappings
1202 AlignmentI exal = AlignmentUtils.makeExonAlignment(new SequenceI[]
1203 { dna1 }, mappings);
1206 * Verify we have 3 exon sequences, mapped to pep1/2/3 respectively
1208 List<SequenceI> exons = exal.getSequences();
1209 assertEquals(3, exons.size());
1211 SequenceI exon = exons.get(0);
1212 assertEquals("GGGTTT", exon.getSequenceAsString());
1213 assertEquals("dna1|A12345", exon.getName());
1214 assertEquals(1, exon.getDBRef().length);
1215 DBRefEntry cdsRef = exon.getDBRef()[0];
1216 assertEquals("EMBLCDS", cdsRef.getSource());
1217 assertEquals("2", cdsRef.getVersion());
1218 assertEquals("A12345", cdsRef.getAccessionId());
1220 exon = exons.get(1);
1221 assertEquals("aaaccc", exon.getSequenceAsString());
1222 assertEquals("dna1|A12346", exon.getName());
1223 assertEquals(1, exon.getDBRef().length);
1224 cdsRef = exon.getDBRef()[0];
1225 assertEquals("EMBLCDS", cdsRef.getSource());
1226 assertEquals("3", cdsRef.getVersion());
1227 assertEquals("A12346", cdsRef.getAccessionId());
1229 exon = exons.get(2);
1230 assertEquals("aaaTTT", exon.getSequenceAsString());
1231 assertEquals("dna1|A12347", exon.getName());
1232 assertEquals(1, exon.getDBRef().length);
1233 cdsRef = exon.getDBRef()[0];
1234 assertEquals("EMBLCDS", cdsRef.getSource());
1235 assertEquals("4", cdsRef.getVersion());
1236 assertEquals("A12347", cdsRef.getAccessionId());
1239 * Verify there are mappings from each exon sequence to its protein product
1240 * and also to its dna source
1242 Iterator<AlignedCodonFrame> newMappingsIterator = mappings.iterator();
1244 // mappings for dna1 - exon1 - pep1
1245 AlignedCodonFrame exonMapping = newMappingsIterator.next();
1246 List<Mapping> dnaMappings = exonMapping.getMappingsForSequence(dna1);
1247 assertEquals(1, dnaMappings.size());
1248 assertSame(exons.get(0).getDatasetSequence(), dnaMappings.get(0)
1250 assertEquals("G(1) in CDS should map to G(4) in DNA", 4, dnaMappings
1251 .get(0).getMap().getToPosition(1));
1252 List<Mapping> peptideMappings = exonMapping
1253 .getMappingsForSequence(pep1);
1254 assertEquals(1, peptideMappings.size());
1255 assertSame(pep1.getDatasetSequence(), peptideMappings.get(0).getTo());
1257 // mappings for dna1 - exon2 - pep2
1258 exonMapping = newMappingsIterator.next();
1259 dnaMappings = exonMapping.getMappingsForSequence(dna1);
1260 assertEquals(1, dnaMappings.size());
1261 assertSame(exons.get(1).getDatasetSequence(), dnaMappings.get(0)
1263 assertEquals("c(4) in CDS should map to c(7) in DNA", 7, dnaMappings
1264 .get(0).getMap().getToPosition(4));
1265 peptideMappings = exonMapping.getMappingsForSequence(pep2);
1266 assertEquals(1, peptideMappings.size());
1267 assertSame(pep2.getDatasetSequence(), peptideMappings.get(0).getTo());
1269 // mappings for dna1 - exon3 - pep3
1270 exonMapping = newMappingsIterator.next();
1271 dnaMappings = exonMapping.getMappingsForSequence(dna1);
1272 assertEquals(1, dnaMappings.size());
1273 assertSame(exons.get(2).getDatasetSequence(), dnaMappings.get(0)
1275 assertEquals("T(4) in CDS should map to T(10) in DNA", 10, dnaMappings
1276 .get(0).getMap().getToPosition(4));
1277 peptideMappings = exonMapping.getMappingsForSequence(pep3);
1278 assertEquals(1, peptideMappings.size());
1279 assertSame(pep3.getDatasetSequence(), peptideMappings.get(0).getTo());
1282 @Test(groups = { "Functional" })
1283 public void testIsMappable()
1285 SequenceI dna1 = new Sequence("dna1", "cgCAGtgGT");
1286 SequenceI aa1 = new Sequence("aa1", "RSG");
1287 AlignmentI al1 = new Alignment(new SequenceI[] { dna1 });
1288 AlignmentI al2 = new Alignment(new SequenceI[] { aa1 });
1290 assertFalse(AlignmentUtils.isMappable(null, null));
1291 assertFalse(AlignmentUtils.isMappable(al1, null));
1292 assertFalse(AlignmentUtils.isMappable(null, al1));
1293 assertFalse(AlignmentUtils.isMappable(al1, al1));
1294 assertFalse(AlignmentUtils.isMappable(al2, al2));
1296 assertTrue(AlignmentUtils.isMappable(al1, al2));
1297 assertTrue(AlignmentUtils.isMappable(al2, al1));