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.Collections;
49 import java.util.HashSet;
50 import java.util.Iterator;
51 import java.util.LinkedHashSet;
52 import java.util.List;
56 import org.testng.annotations.Test;
58 public class AlignmentUtilsTests
61 private static final String TEST_DATA =
63 "#=GS D.melanogaster.1 AC AY119185.1/838-902\n" +
64 "#=GS D.melanogaster.2 AC AC092237.1/57223-57161\n" +
65 "#=GS D.melanogaster.3 AC AY060611.1/560-627\n" +
66 "D.melanogaster.1 G.AGCC.CU...AUGAUCGA\n" +
67 "#=GR D.melanogaster.1 SS ................((((\n" +
68 "D.melanogaster.2 C.AUUCAACU.UAUGAGGAU\n" +
69 "#=GR D.melanogaster.2 SS ................((((\n" +
70 "D.melanogaster.3 G.UGGCGCU..UAUGACGCA\n" +
71 "#=GR D.melanogaster.3 SS (.(((...(....(((((((\n" +
74 private static final String AA_SEQS_1 =
80 private static final String CDNA_SEQS_1 =
82 "AC-GG--CUC-CAA-CT\n" +
84 "-CG-TTA--ACG---AAGT\n";
86 private static final String CDNA_SEQS_2 =
93 // public static Sequence ts=new
94 // Sequence("short","ASDASDASDASDASDASDASDASDASDASDASDASDASD");
95 public static Sequence ts = new Sequence("short",
96 "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
98 @Test(groups = { "Functional" })
99 public void testExpandContext()
101 AlignmentI al = new Alignment(new Sequence[] {});
102 for (int i = 4; i < 14; i += 2)
104 SequenceI s1 = ts.deriveSequence().getSubSequence(i, i + 7);
107 System.out.println(new AppletFormatAdapter().formatSequences("Clustal",
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[] {});
157 SequenceI ds = new Sequence("Seq1", "ABCDEFGHI");
159 SequenceI seq1 = ds.deriveSequence().getSubSequence(3, 6);
160 al.addSequence(seq1);
163 * Annotate DEF with 4/5/6 respectively
165 Annotation[] anns = new Annotation[] { new Annotation(4),
166 new Annotation(5), new Annotation(6) };
167 AlignmentAnnotation ann = new AlignmentAnnotation("SS",
168 "secondary structure", anns);
169 seq1.addAlignmentAnnotation(ann);
172 * The annotations array should match aligned positions
174 assertEquals(3, ann.annotations.length);
175 assertEquals(4, ann.annotations[0].value, 0.001);
176 assertEquals(5, ann.annotations[1].value, 0.001);
177 assertEquals(6, ann.annotations[2].value, 0.001);
180 * Check annotation to sequence position mappings before expanding the
181 * sequence; these are set up in Sequence.addAlignmentAnnotation ->
182 * Annotation.setSequenceRef -> createSequenceMappings
184 assertNull(ann.getAnnotationForPosition(1));
185 assertNull(ann.getAnnotationForPosition(2));
186 assertNull(ann.getAnnotationForPosition(3));
187 assertEquals(4, ann.getAnnotationForPosition(4).value, 0.001);
188 assertEquals(5, ann.getAnnotationForPosition(5).value, 0.001);
189 assertEquals(6, ann.getAnnotationForPosition(6).value, 0.001);
190 assertNull(ann.getAnnotationForPosition(7));
191 assertNull(ann.getAnnotationForPosition(8));
192 assertNull(ann.getAnnotationForPosition(9));
195 * Expand the subsequence to the full sequence abcDEFghi
197 AlignmentI expanded = AlignmentUtils.expandContext(al, -1);
198 assertEquals("abcDEFghi", expanded.getSequenceAt(0)
199 .getSequenceAsString());
202 * Confirm the alignment and sequence have the same SS annotation,
203 * referencing the expanded sequence
205 ann = expanded.getSequenceAt(0).getAnnotation()[0];
206 assertSame(ann, expanded.getAlignmentAnnotation()[0]);
207 assertSame(expanded.getSequenceAt(0), ann.sequenceRef);
210 * The annotations array should have null values except for annotated
213 assertNull(ann.annotations[0]);
214 assertNull(ann.annotations[1]);
215 assertNull(ann.annotations[2]);
216 assertEquals(4, ann.annotations[3].value, 0.001);
217 assertEquals(5, ann.annotations[4].value, 0.001);
218 assertEquals(6, ann.annotations[5].value, 0.001);
219 assertNull(ann.annotations[6]);
220 assertNull(ann.annotations[7]);
221 assertNull(ann.annotations[8]);
224 * sequence position mappings should be unchanged
226 assertNull(ann.getAnnotationForPosition(1));
227 assertNull(ann.getAnnotationForPosition(2));
228 assertNull(ann.getAnnotationForPosition(3));
229 assertEquals(4, ann.getAnnotationForPosition(4).value, 0.001);
230 assertEquals(5, ann.getAnnotationForPosition(5).value, 0.001);
231 assertEquals(6, ann.getAnnotationForPosition(6).value, 0.001);
232 assertNull(ann.getAnnotationForPosition(7));
233 assertNull(ann.getAnnotationForPosition(8));
234 assertNull(ann.getAnnotationForPosition(9));
238 * Test method that returns a map of lists of sequences by sequence name.
240 * @throws IOException
242 @Test(groups = { "Functional" })
243 public void testGetSequencesByName() throws IOException
245 final String data = ">Seq1Name\nKQYL\n" + ">Seq2Name\nRFPW\n"
246 + ">Seq1Name\nABCD\n";
247 AlignmentI al = loadAlignment(data, "FASTA");
248 Map<String, List<SequenceI>> map = AlignmentUtils
249 .getSequencesByName(al);
250 assertEquals(2, map.keySet().size());
251 assertEquals(2, map.get("Seq1Name").size());
252 assertEquals("KQYL", map.get("Seq1Name").get(0).getSequenceAsString());
253 assertEquals("ABCD", map.get("Seq1Name").get(1).getSequenceAsString());
254 assertEquals(1, map.get("Seq2Name").size());
255 assertEquals("RFPW", map.get("Seq2Name").get(0).getSequenceAsString());
259 * Helper method to load an alignment and ensure dataset sequences are set up.
265 * @throws IOException
267 protected AlignmentI loadAlignment(final String data, String format)
270 AlignmentI a = new FormatAdapter().readFile(data,
271 AppletFormatAdapter.PASTE, format);
277 * Test mapping of protein to cDNA, for the case where we have no sequence
278 * cross-references, so mappings are made first-served 1-1 where sequences
281 * @throws IOException
283 @Test(groups = { "Functional" })
284 public void testMapProteinAlignmentToCdna_noXrefs() throws IOException
286 List<SequenceI> protseqs = new ArrayList<SequenceI>();
287 protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
288 protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
289 protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
290 AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
291 protein.setDataset(null);
293 List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
294 dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR
295 dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAA")); // = EIQ
296 dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ
297 dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG")); // = EIQ
298 AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
299 cdna.setDataset(null);
301 assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna));
303 // 3 mappings made, each from 1 to 1 sequence
304 assertEquals(3, protein.getCodonFrames().size());
305 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
306 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
307 assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
309 // V12345 mapped to A22222
310 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
312 assertEquals(1, acf.getdnaSeqs().length);
313 assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
314 acf.getdnaSeqs()[0]);
315 Mapping[] protMappings = acf.getProtMappings();
316 assertEquals(1, protMappings.length);
317 MapList mapList = protMappings[0].getMap();
318 assertEquals(3, mapList.getFromRatio());
319 assertEquals(1, mapList.getToRatio());
320 assertTrue(Arrays.equals(new int[] { 1, 9 }, mapList.getFromRanges()
322 assertEquals(1, mapList.getFromRanges().size());
323 assertTrue(Arrays.equals(new int[] { 1, 3 },
324 mapList.getToRanges().get(0)));
325 assertEquals(1, mapList.getToRanges().size());
327 // V12346 mapped to A33333
328 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
329 assertEquals(1, acf.getdnaSeqs().length);
330 assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
331 acf.getdnaSeqs()[0]);
333 // V12347 mapped to A11111
334 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
335 assertEquals(1, acf.getdnaSeqs().length);
336 assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
337 acf.getdnaSeqs()[0]);
339 // no mapping involving the 'extra' A44444
340 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(3)).isEmpty());
344 * Test for the alignSequenceAs method that takes two sequences and a mapping.
346 @Test(groups = { "Functional" })
347 public void testAlignSequenceAs_withMapping_noIntrons()
349 MapList map = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 }, 3, 1);
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[] { 4, 6, 10, 12 },
397 new int[] { 1, 2 }, 3, 1);
400 * Simple case: no gaps in dna
402 checkAlignSequenceAs("GGGAAACCCTTTGGG", "--A-L-", false, false, map,
403 "GGG---AAACCCTTTGGG");
406 * Add gaps to dna - but ignore when realigning.
408 checkAlignSequenceAs("-G-G-G--A--A---AC-CC-T-TT-GG-G-", "--A-L-",
409 false, false, map, "GGG---AAACCCTTTGGG");
412 * Add gaps to dna - include within exons only when realigning.
414 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
415 true, false, map, "GGG---A--A---ACCCT-TTGGG");
418 * Include gaps outside exons only when realigning.
420 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
421 false, true, map, "-G-G-GAAAC-CCTTT-GG-G-");
424 * Include gaps following first intron if we are 'preserving mapped gaps'
426 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
427 true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
430 * Include all gaps in dna when realigning.
432 checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
433 true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
437 * Test for the case where not all of the protein sequence is mapped to cDNA.
439 @Test(groups = { "Functional" })
440 public void testAlignSequenceAs_withMapping_withUnmappedProtein()
444 * Exons at codon 2 (AAA) and 4 (TTT) mapped to A and P
446 final MapList map = new MapList(new int[] { 4, 6, 10, 12 }, new int[] {
450 * Expect alignment does nothing (aborts realignment). Change this test
451 * first if different behaviour wanted.
453 checkAlignSequenceAs("GGGAAACCCTTTGGG", "-A-L-P-", false, false, map,
458 * Helper method that performs and verifies the method under test.
462 * @param preserveMappedGaps
463 * @param preserveUnmappedGaps
467 protected void checkAlignSequenceAs(final String dnaSeq,
468 final String proteinSeq, final boolean preserveMappedGaps,
469 final boolean preserveUnmappedGaps, MapList map,
470 final String expected)
472 SequenceI dna = new Sequence("Seq1", dnaSeq);
473 dna.createDatasetSequence();
474 SequenceI protein = new Sequence("Seq1", proteinSeq);
475 protein.createDatasetSequence();
476 AlignedCodonFrame acf = new AlignedCodonFrame();
477 acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map);
479 AlignmentUtils.alignSequenceAs(dna, protein, acf, "---", '-',
480 preserveMappedGaps, preserveUnmappedGaps);
481 assertEquals(expected, dna.getSequenceAsString());
485 * Test for the alignSequenceAs method where we preserve gaps in introns only.
487 @Test(groups = { "Functional" })
488 public void testAlignSequenceAs_keepIntronGapsOnly()
492 * Intron GGGAAA followed by exon CCCTTT
494 MapList map = new MapList(new int[] { 7, 12 }, new int[] { 1, 2 }, 3, 1);
496 checkAlignSequenceAs("GG-G-AA-A-C-CC-T-TT", "AL", false, true, map,
501 * Test for the method that generates an aligned translated sequence from one
504 @Test(groups = { "Functional" })
505 public void testGetAlignedTranslation_dnaLikeProtein()
507 // dna alignment will be replaced
508 SequenceI dna = new Sequence("Seq1", "T-G-CC-A--T-TAC-CAG-");
509 dna.createDatasetSequence();
510 // protein alignment will be 'applied' to dna
511 SequenceI protein = new Sequence("Seq1", "-CH-Y--Q-");
512 protein.createDatasetSequence();
513 MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1);
514 AlignedCodonFrame acf = new AlignedCodonFrame();
515 acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map);
517 final SequenceI aligned = AlignmentUtils.getAlignedTranslation(protein,
519 assertEquals("---TGCCAT---TAC------CAG---",
520 aligned.getSequenceAsString());
521 assertSame(aligned.getDatasetSequence(), dna.getDatasetSequence());
525 * Test the method that realigns protein to match mapped codon alignment.
527 @Test(groups = { "Functional" })
528 public void testAlignProteinAsDna()
530 // seq1 codons are [1,2,3] [4,5,6] [7,8,9] [10,11,12]
531 SequenceI dna1 = new Sequence("Seq1", "TGCCATTACCAG-");
532 // seq2 codons are [1,3,4] [5,6,7] [8,9,10] [11,12,13]
533 SequenceI dna2 = new Sequence("Seq2", "T-GCCATTACCAG");
534 // seq3 codons are [1,2,3] [4,5,7] [8,9,10] [11,12,13]
535 SequenceI dna3 = new Sequence("Seq3", "TGCCA-TTACCAG");
536 AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
537 dna.setDataset(null);
539 // protein alignment will be realigned like dna
540 SequenceI prot1 = new Sequence("Seq1", "CHYQ");
541 SequenceI prot2 = new Sequence("Seq2", "CHYQ");
542 SequenceI prot3 = new Sequence("Seq3", "CHYQ");
543 SequenceI prot4 = new Sequence("Seq4", "R-QSV"); // unmapped, unchanged
544 AlignmentI protein = new Alignment(new SequenceI[] { prot1, prot2,
546 protein.setDataset(null);
548 MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1);
549 AlignedCodonFrame acf = new AlignedCodonFrame();
550 acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
551 acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map);
552 acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map);
553 protein.setCodonFrames(Collections.singleton(acf));
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 Set<AlignedCodonFrame> mappings = new HashSet<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 Set<AlignedCodonFrame> mappings = new LinkedHashSet<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());