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.
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertSame;
25 import static org.testng.AssertJUnit.assertTrue;
27 import jalview.api.AlignViewportI;
28 import jalview.commands.EditCommand;
29 import jalview.commands.EditCommand.Action;
30 import jalview.commands.EditCommand.Edit;
31 import jalview.datamodel.AlignedCodonFrame;
32 import jalview.datamodel.Alignment;
33 import jalview.datamodel.AlignmentI;
34 import jalview.datamodel.ColumnSelection;
35 import jalview.datamodel.SearchResults;
36 import jalview.datamodel.SearchResults.Match;
37 import jalview.datamodel.Sequence;
38 import jalview.datamodel.SequenceGroup;
39 import jalview.datamodel.SequenceI;
40 import jalview.gui.AlignViewport;
41 import jalview.io.AppletFormatAdapter;
42 import jalview.io.FormatAdapter;
44 import java.awt.Color;
45 import java.io.IOException;
46 import java.util.Arrays;
47 import java.util.Collections;
48 import java.util.HashSet;
49 import java.util.LinkedHashSet;
50 import java.util.List;
53 import org.testng.annotations.Test;
55 public class MappingUtilsTest
57 private AlignViewportI dnaView;
59 private AlignViewportI proteinView;
62 * Simple test of mapping with no intron involved.
64 @Test(groups = { "Functional" })
65 public void testBuildSearchResults()
67 final Sequence seq1 = new Sequence("Seq1/5-10", "C-G-TA-GC");
68 seq1.createDatasetSequence();
70 final Sequence aseq1 = new Sequence("Seq1/12-13", "-P-R");
71 aseq1.createDatasetSequence();
74 * Map dna bases 5-10 to protein residues 12-13
76 AlignedCodonFrame acf = new AlignedCodonFrame();
77 MapList map = new MapList(new int[] { 5, 10 }, new int[] { 12, 13 }, 3,
79 acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
80 Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
83 * Check protein residue 12 maps to codon 5-7, 13 to codon 8-10
85 SearchResults sr = MappingUtils.buildSearchResults(aseq1, 12, acfList);
86 assertEquals(1, sr.getResults().size());
87 Match m = sr.getResults().get(0);
88 assertEquals(seq1.getDatasetSequence(), m.getSequence());
89 assertEquals(5, m.getStart());
90 assertEquals(7, m.getEnd());
91 sr = MappingUtils.buildSearchResults(aseq1, 13, acfList);
92 assertEquals(1, sr.getResults().size());
93 m = sr.getResults().get(0);
94 assertEquals(seq1.getDatasetSequence(), m.getSequence());
95 assertEquals(8, m.getStart());
96 assertEquals(10, m.getEnd());
99 * Check inverse mappings, from codons 5-7, 8-10 to protein 12, 13
101 for (int i = 5; i < 11; i++)
103 sr = MappingUtils.buildSearchResults(seq1, i, acfList);
104 assertEquals(1, sr.getResults().size());
105 m = sr.getResults().get(0);
106 assertEquals(aseq1.getDatasetSequence(), m.getSequence());
107 int residue = i > 7 ? 13 : 12;
108 assertEquals(residue, m.getStart());
109 assertEquals(residue, m.getEnd());
114 * Simple test of mapping with introns involved.
116 @Test(groups = { "Functional" })
117 public void testBuildSearchResults_withIntron()
119 final Sequence seq1 = new Sequence("Seq1/5-17", "c-G-tAGa-GcAgCtt");
120 seq1.createDatasetSequence();
122 final Sequence aseq1 = new Sequence("Seq1/8-9", "-E-D");
123 aseq1.createDatasetSequence();
126 * Map dna bases [6, 8, 9], [11, 13, 115] to protein residues 8 and 9
128 AlignedCodonFrame acf = new AlignedCodonFrame();
129 MapList map = new MapList(new int[] { 6, 6, 8, 9, 11, 11, 13, 13, 15,
130 15 }, new int[] { 8, 9 }, 3, 1);
131 acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
132 Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
135 * Check protein residue 8 maps to [6, 8, 9]
137 SearchResults sr = MappingUtils.buildSearchResults(aseq1, 8, acfList);
138 assertEquals(2, sr.getResults().size());
139 Match m = sr.getResults().get(0);
140 assertEquals(seq1.getDatasetSequence(), m.getSequence());
141 assertEquals(6, m.getStart());
142 assertEquals(6, m.getEnd());
143 m = sr.getResults().get(1);
144 assertEquals(seq1.getDatasetSequence(), m.getSequence());
145 assertEquals(8, m.getStart());
146 assertEquals(9, m.getEnd());
149 * Check protein residue 9 maps to [11, 13, 15]
151 sr = MappingUtils.buildSearchResults(aseq1, 9, acfList);
152 assertEquals(3, sr.getResults().size());
153 m = sr.getResults().get(0);
154 assertEquals(seq1.getDatasetSequence(), m.getSequence());
155 assertEquals(11, m.getStart());
156 assertEquals(11, m.getEnd());
157 m = sr.getResults().get(1);
158 assertEquals(seq1.getDatasetSequence(), m.getSequence());
159 assertEquals(13, m.getStart());
160 assertEquals(13, m.getEnd());
161 m = sr.getResults().get(2);
162 assertEquals(seq1.getDatasetSequence(), m.getSequence());
163 assertEquals(15, m.getStart());
164 assertEquals(15, m.getEnd());
167 * Check inverse mappings, from codons to protein
169 for (int i = 5; i < 18; i++)
171 sr = MappingUtils.buildSearchResults(seq1, i, acfList);
172 int residue = (i == 6 || i == 8 || i == 9) ? 8 : (i == 11 || i == 13
176 assertEquals(0, sr.getResults().size());
179 assertEquals(1, sr.getResults().size());
180 m = sr.getResults().get(0);
181 assertEquals(aseq1.getDatasetSequence(), m.getSequence());
182 assertEquals(residue, m.getStart());
183 assertEquals(residue, m.getEnd());
188 * Test mapping a sequence group made of entire sequences.
190 * @throws IOException
192 @Test(groups = { "Functional" })
193 public void testMapSequenceGroup_sequences() throws IOException
196 * Set up dna and protein Seq1/2/3 with mappings (held on the protein
199 AlignmentI cdna = loadAlignment(">Seq1\nACG\n>Seq2\nTGA\n>Seq3\nTAC\n",
201 cdna.setDataset(null);
202 AlignmentI protein = loadAlignment(">Seq1\nK\n>Seq2\nL\n>Seq3\nQ\n",
204 protein.setDataset(null);
205 AlignedCodonFrame acf = new AlignedCodonFrame();
206 MapList map = new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 3, 1);
207 for (int seq = 0; seq < 3; seq++)
209 acf.addMap(cdna.getSequenceAt(seq).getDatasetSequence(), protein
210 .getSequenceAt(seq).getDatasetSequence(), map);
212 Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
214 AlignViewportI dnaView = new AlignViewport(cdna);
215 AlignViewportI proteinView = new AlignViewport(protein);
216 protein.setCodonFrames(acfList);
219 * Select Seq1 and Seq3 in the protein (startRes=endRes=0)
221 SequenceGroup sg = new SequenceGroup();
222 sg.setColourText(true);
223 sg.setIdColour(Color.GREEN);
224 sg.setOutlineColour(Color.LIGHT_GRAY);
225 sg.addSequence(protein.getSequenceAt(0), false);
226 sg.addSequence(protein.getSequenceAt(2), false);
229 * Verify the mapped sequence group in dna
231 SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg,
232 proteinView, dnaView);
233 assertTrue(mappedGroup.getColourText());
234 assertSame(sg.getIdColour(), mappedGroup.getIdColour());
235 assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
236 assertEquals(2, mappedGroup.getSequences().size());
237 assertSame(cdna.getSequenceAt(0), mappedGroup.getSequences().get(0));
238 assertSame(cdna.getSequenceAt(2), mappedGroup.getSequences().get(1));
239 assertEquals(0, mappedGroup.getStartRes());
240 assertEquals(2, mappedGroup.getEndRes());
243 * Verify mapping sequence group from dna to protein
246 sg.addSequence(cdna.getSequenceAt(1), false);
247 sg.addSequence(cdna.getSequenceAt(0), false);
250 mappedGroup = MappingUtils.mapSequenceGroup(sg, dnaView, proteinView);
251 assertTrue(mappedGroup.getColourText());
252 assertSame(sg.getIdColour(), mappedGroup.getIdColour());
253 assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
254 assertEquals(2, mappedGroup.getSequences().size());
255 assertSame(protein.getSequenceAt(1), mappedGroup.getSequences().get(0));
256 assertSame(protein.getSequenceAt(0), mappedGroup.getSequences().get(1));
257 assertEquals(0, mappedGroup.getStartRes());
258 assertEquals(0, mappedGroup.getEndRes());
262 * Helper method to load an alignment and ensure dataset sequences are set up.
268 * @throws IOException
270 protected AlignmentI loadAlignment(final String data, String format)
273 AlignmentI a = new FormatAdapter().readFile(data,
274 AppletFormatAdapter.PASTE, format);
280 * Test mapping a column selection in protein to its dna equivalent
282 * @throws IOException
284 @Test(groups = { "Functional" })
285 public void testMapColumnSelection_proteinToDna() throws IOException
287 setupMappedAlignments();
289 ColumnSelection colsel = new ColumnSelection();
292 * Column 0 in protein picks up Seq2/L, Seq3/G which map to cols 0-4 and 0-3
293 * in dna respectively, overall 0-4
295 colsel.addElement(0);
296 ColumnSelection cs = MappingUtils.mapColumnSelection(colsel,
297 proteinView, dnaView);
298 assertEquals("[0, 1, 2, 3, 4]", cs.getSelected().toString());
301 * Column 1 in protein picks up Seq1/K which maps to cols 0-3 in dna
304 colsel.addElement(1);
305 cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView);
306 assertEquals("[0, 1, 2, 3]", cs.getSelected().toString());
309 * Column 2 in protein picks up gaps only - no mapping
312 colsel.addElement(2);
313 cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView);
314 assertEquals("[]", cs.getSelected().toString());
317 * Column 3 in protein picks up Seq1/P, Seq2/Q, Seq3/S which map to columns
318 * 6-9, 6-10, 5-8 respectively, overall to 5-10
321 colsel.addElement(3);
322 cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView);
323 assertEquals("[5, 6, 7, 8, 9, 10]", cs.getSelected().toString());
326 * Combine selection of columns 1 and 3 to get a discontiguous mapped
330 colsel.addElement(1);
331 colsel.addElement(3);
332 cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView);
333 assertEquals("[0, 1, 2, 3, 5, 6, 7, 8, 9, 10]", cs.getSelected()
338 * Set up mappings for tests from 3 dna to 3 protein sequences. Sequences have
339 * offset start positions for a more general test case.
341 * @throws IOException
343 protected void setupMappedAlignments() throws IOException
346 * Set up dna and protein Seq1/2/3 with mappings (held on the protein
347 * viewport). Lower case for introns.
349 AlignmentI cdna = loadAlignment(">Seq1/10-18\nAC-GctGtC-T\n"
350 + ">Seq2/20-27\nTc-GA-G-T-Tc\n" + ">Seq3/30-38\nTtTT-AaCGg-\n",
352 cdna.setDataset(null);
353 AlignmentI protein = loadAlignment(
354 ">Seq1/40-41\n-K-P\n>Seq2/50-51\nL--Q\n>Seq3/60-61\nG--S\n",
356 protein.setDataset(null);
358 // map first dna to first protein seq
359 AlignedCodonFrame acf = new AlignedCodonFrame();
360 MapList map = new MapList(new int[] { 10, 12, 15, 15, 17, 18 },
361 new int[] { 40, 41 }, 3, 1);
362 acf.addMap(cdna.getSequenceAt(0).getDatasetSequence(), protein
363 .getSequenceAt(0).getDatasetSequence(), map);
365 // map second dna to second protein seq
366 map = new MapList(new int[] { 20, 20, 22, 23, 24, 26 }, new int[] { 50,
369 acf.addMap(cdna.getSequenceAt(1).getDatasetSequence(), protein
370 .getSequenceAt(1).getDatasetSequence(), map);
372 // map third dna to third protein seq
373 map = new MapList(new int[] { 30, 30, 32, 34, 36, 37 }, new int[] { 60,
375 acf.addMap(cdna.getSequenceAt(2).getDatasetSequence(), protein
376 .getSequenceAt(2).getDatasetSequence(), map);
377 Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
379 dnaView = new AlignViewport(cdna);
380 proteinView = new AlignViewport(protein);
381 protein.setCodonFrames(acfList);
385 * Test mapping a column selection in dna to its protein equivalent
387 * @throws IOException
389 @Test(groups = { "Functional" })
390 public void testMapColumnSelection_dnaToProtein() throws IOException
392 setupMappedAlignments();
394 ColumnSelection colsel = new ColumnSelection();
397 * Column 0 in dna picks up first bases which map to residue 1, columns 0-1
400 colsel.addElement(0);
401 ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, dnaView,
403 assertEquals("[0, 1]", cs.getSelected().toString());
406 * Columns 3-5 in dna map to the first residues in protein Seq1, Seq2, and
407 * the first two in Seq3. Overall to columns 0, 1, 3 (col2 is all gaps).
409 colsel.addElement(3);
410 colsel.addElement(4);
411 colsel.addElement(5);
412 cs = MappingUtils.mapColumnSelection(colsel, dnaView, proteinView);
413 assertEquals("[0, 1, 3]", cs.getSelected().toString());
416 @Test(groups = { "Functional" })
417 public void testMapColumnSelection_null() throws IOException
419 setupMappedAlignments();
420 ColumnSelection cs = MappingUtils.mapColumnSelection(null, dnaView,
422 assertTrue("mapped selection not empty", cs.getSelected().isEmpty());
426 * Tests for the method that converts a series of [start, end] ranges to
429 @Test(groups = { "Functional" })
430 public void testFlattenRanges()
432 assertEquals("[1, 2, 3, 4]",
433 Arrays.toString(MappingUtils.flattenRanges(new int[] { 1, 4 })));
436 Arrays.toString(MappingUtils.flattenRanges(new int[] { 1, 2, 3,
440 Arrays.toString(MappingUtils.flattenRanges(new int[] { 1, 1, 2,
443 "[1, 2, 3, 4, 7, 8, 9, 12]",
444 Arrays.toString(MappingUtils.flattenRanges(new int[] { 1, 4, 7,
446 // unpaired start position is ignored:
448 "[1, 2, 3, 4, 7, 8, 9, 12]",
449 Arrays.toString(MappingUtils.flattenRanges(new int[] { 1, 4, 7,
454 * Test mapping a sequence group made of entire columns.
456 * @throws IOException
458 @Test(groups = { "Functional" })
459 public void testMapSequenceGroup_columns() throws IOException
462 * Set up dna and protein Seq1/2/3 with mappings (held on the protein
465 AlignmentI cdna = loadAlignment(
466 ">Seq1\nACGGCA\n>Seq2\nTGACAG\n>Seq3\nTACGTA\n", "FASTA");
467 cdna.setDataset(null);
468 AlignmentI protein = loadAlignment(">Seq1\nKA\n>Seq2\nLQ\n>Seq3\nQV\n",
470 protein.setDataset(null);
471 AlignedCodonFrame acf = new AlignedCodonFrame();
472 MapList map = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 }, 3, 1);
473 for (int seq = 0; seq < 3; seq++)
475 acf.addMap(cdna.getSequenceAt(seq).getDatasetSequence(), protein
476 .getSequenceAt(seq).getDatasetSequence(), map);
478 Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
480 AlignViewportI dnaView = new AlignViewport(cdna);
481 AlignViewportI proteinView = new AlignViewport(protein);
482 protein.setCodonFrames(acfList);
485 * Select all sequences, column 2 in the protein
487 SequenceGroup sg = new SequenceGroup();
488 sg.setColourText(true);
489 sg.setIdColour(Color.GREEN);
490 sg.setOutlineColour(Color.LIGHT_GRAY);
491 sg.addSequence(protein.getSequenceAt(0), false);
492 sg.addSequence(protein.getSequenceAt(1), false);
493 sg.addSequence(protein.getSequenceAt(2), false);
498 * Verify the mapped sequence group in dna
500 SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg,
501 proteinView, dnaView);
502 assertTrue(mappedGroup.getColourText());
503 assertSame(sg.getIdColour(), mappedGroup.getIdColour());
504 assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
505 assertEquals(3, mappedGroup.getSequences().size());
506 assertSame(cdna.getSequenceAt(0), mappedGroup.getSequences().get(0));
507 assertSame(cdna.getSequenceAt(1), mappedGroup.getSequences().get(1));
508 assertSame(cdna.getSequenceAt(2), mappedGroup.getSequences().get(2));
509 assertEquals(3, mappedGroup.getStartRes());
510 assertEquals(5, mappedGroup.getEndRes());
513 * Verify mapping sequence group from dna to protein
516 sg.addSequence(cdna.getSequenceAt(0), false);
517 sg.addSequence(cdna.getSequenceAt(1), false);
518 sg.addSequence(cdna.getSequenceAt(2), false);
519 // select columns 2 and 3 in DNA which span protein columns 0 and 1
522 mappedGroup = MappingUtils.mapSequenceGroup(sg, dnaView, proteinView);
523 assertTrue(mappedGroup.getColourText());
524 assertSame(sg.getIdColour(), mappedGroup.getIdColour());
525 assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
526 assertEquals(3, mappedGroup.getSequences().size());
527 assertSame(protein.getSequenceAt(0), mappedGroup.getSequences().get(0));
528 assertSame(protein.getSequenceAt(1), mappedGroup.getSequences().get(1));
529 assertSame(protein.getSequenceAt(2), mappedGroup.getSequences().get(2));
530 assertEquals(0, mappedGroup.getStartRes());
531 assertEquals(1, mappedGroup.getEndRes());
535 * Test mapping a sequence group made of a sequences/columns region.
537 * @throws IOException
539 @Test(groups = { "Functional" })
540 public void testMapSequenceGroup_region() throws IOException
543 * Set up gapped dna and protein Seq1/2/3 with mappings (held on the protein
546 AlignmentI cdna = loadAlignment(
547 ">Seq1\nA-CG-GC--AT-CA\n>Seq2\n-TG-AC-AG-T-AT\n>Seq3\n-T--ACG-TAAT-G\n",
549 cdna.setDataset(null);
550 AlignmentI protein = loadAlignment(
551 ">Seq1\n-KA-S\n>Seq2\n--L-QY\n>Seq3\nQ-V-M\n", "FASTA");
552 protein.setDataset(null);
553 AlignedCodonFrame acf = new AlignedCodonFrame();
554 MapList map = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3, 1);
555 for (int seq = 0; seq < 3; seq++)
557 acf.addMap(cdna.getSequenceAt(seq).getDatasetSequence(), protein
558 .getSequenceAt(seq).getDatasetSequence(), map);
560 Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
562 AlignViewportI dnaView = new AlignViewport(cdna);
563 AlignViewportI proteinView = new AlignViewport(protein);
564 protein.setCodonFrames(acfList);
567 * Select Seq1 and Seq2 in the protein, column 1 (K/-). Expect mapped
568 * sequence group to cover Seq1, columns 0-3 (ACG). Because the selection
569 * only includes a gap in Seq2 there is no mappable selection region in the
572 SequenceGroup sg = new SequenceGroup();
573 sg.setColourText(true);
574 sg.setIdColour(Color.GREEN);
575 sg.setOutlineColour(Color.LIGHT_GRAY);
576 sg.addSequence(protein.getSequenceAt(0), false);
577 sg.addSequence(protein.getSequenceAt(1), false);
582 * Verify the mapped sequence group in dna
584 SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg,
585 proteinView, dnaView);
586 assertTrue(mappedGroup.getColourText());
587 assertSame(sg.getIdColour(), mappedGroup.getIdColour());
588 assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
589 assertEquals(1, mappedGroup.getSequences().size());
590 assertSame(cdna.getSequenceAt(0), mappedGroup.getSequences().get(0));
591 // Seq2 in protein has a gap in column 1 - ignored
592 // Seq1 has K which should map to columns 0-3 in Seq1
593 assertEquals(0, mappedGroup.getStartRes());
594 assertEquals(3, mappedGroup.getEndRes());
597 * Now select cols 2-4 in protein. These cover Seq1:AS Seq2:LQ Seq3:VM which
598 * extend over DNA columns 3-12, 1-7, 6-13 respectively, or 1-13 overall.
602 mappedGroup = MappingUtils.mapSequenceGroup(sg, proteinView, dnaView);
603 assertEquals(1, mappedGroup.getStartRes());
604 assertEquals(13, mappedGroup.getEndRes());
607 * Verify mapping sequence group from dna to protein
610 sg.addSequence(cdna.getSequenceAt(0), false);
612 // select columns 4,5 - includes Seq1:codon2 (A) only
615 mappedGroup = MappingUtils.mapSequenceGroup(sg, dnaView, proteinView);
616 assertEquals(2, mappedGroup.getStartRes());
617 assertEquals(2, mappedGroup.getEndRes());
619 // add Seq2 to dna selection cols 4-5 include codons 1 and 2 (LQ)
620 sg.addSequence(cdna.getSequenceAt(1), false);
621 mappedGroup = MappingUtils.mapSequenceGroup(sg, dnaView, proteinView);
622 assertEquals(2, mappedGroup.getStartRes());
623 assertEquals(4, mappedGroup.getEndRes());
625 // add Seq3 to dna selection cols 4-5 include codon 1 (Q)
626 sg.addSequence(cdna.getSequenceAt(2), false);
627 mappedGroup = MappingUtils.mapSequenceGroup(sg, dnaView, proteinView);
628 assertEquals(0, mappedGroup.getStartRes());
629 assertEquals(4, mappedGroup.getEndRes());
632 @Test(groups = { "Functional" })
633 public void testFindMappingsForSequence()
635 SequenceI seq1 = new Sequence("Seq1", "ABC");
636 SequenceI seq2 = new Sequence("Seq2", "ABC");
637 SequenceI seq3 = new Sequence("Seq3", "ABC");
638 SequenceI seq4 = new Sequence("Seq4", "ABC");
639 seq1.createDatasetSequence();
640 seq2.createDatasetSequence();
641 seq3.createDatasetSequence();
642 seq4.createDatasetSequence();
645 * Create mappings from seq1 to seq2, seq2 to seq1, seq3 to seq1
647 AlignedCodonFrame acf1 = new AlignedCodonFrame();
648 MapList map = new MapList(new int[] { 1, 3 }, new int[] { 1, 3 }, 1, 1);
649 acf1.addMap(seq1.getDatasetSequence(), seq2.getDatasetSequence(), map);
650 AlignedCodonFrame acf2 = new AlignedCodonFrame();
651 acf2.addMap(seq2.getDatasetSequence(), seq1.getDatasetSequence(), map);
652 AlignedCodonFrame acf3 = new AlignedCodonFrame();
653 acf3.addMap(seq3.getDatasetSequence(), seq1.getDatasetSequence(), map);
655 Set<AlignedCodonFrame> mappings = new HashSet<AlignedCodonFrame>();
661 * Seq1 has three mappings
663 List<AlignedCodonFrame> result = MappingUtils.findMappingsForSequence(
665 assertEquals(3, result.size());
666 assertTrue(result.contains(acf1));
667 assertTrue(result.contains(acf2));
668 assertTrue(result.contains(acf3));
671 * Seq2 has two mappings
673 result = MappingUtils.findMappingsForSequence(seq2, mappings);
674 assertEquals(2, result.size());
675 assertTrue(result.contains(acf1));
676 assertTrue(result.contains(acf2));
679 * Seq3 has one mapping
681 result = MappingUtils.findMappingsForSequence(seq3, mappings);
682 assertEquals(1, result.size());
683 assertTrue(result.contains(acf3));
686 * Seq4 has no mappings
688 result = MappingUtils.findMappingsForSequence(seq4, mappings);
689 assertEquals(0, result.size());
691 result = MappingUtils.findMappingsForSequence(null, mappings);
692 assertEquals(0, result.size());
694 result = MappingUtils.findMappingsForSequence(seq1, null);
695 assertEquals(0, result.size());
697 result = MappingUtils.findMappingsForSequence(null, null);
698 assertEquals(0, result.size());
701 @Test(groups = { "Functional" })
702 public void testMapEditCommand()
704 SequenceI dna = new Sequence("Seq1", "---ACG---GCATCA", 8, 16);
705 SequenceI protein = new Sequence("Seq2", "-T-AS", 5, 7);
706 dna.createDatasetSequence();
707 protein.createDatasetSequence();
708 AlignedCodonFrame acf = new AlignedCodonFrame();
709 MapList map = new MapList(new int[] { 8, 16 }, new int[] { 5, 7 }, 3, 1);
710 acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map);
711 Set<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
714 AlignmentI prot = new Alignment(new SequenceI[] { protein });
715 prot.setCodonFrames(mappings);
716 AlignmentI nuc = new Alignment(new SequenceI[] { dna });
719 * construct and perform the edit command to turn "-T-AS" in to "-T-A--S"
720 * i.e. insert two gaps at column 4
722 EditCommand ec = new EditCommand();
723 final Edit edit = ec.new Edit(Action.INSERT_GAP,
724 new SequenceI[] { protein }, 4, 2, '-');
725 ec.appendEdit(edit, prot, true, null);
728 * the mapped edit command should be to insert 6 gaps before base 4 in the
729 * nucleotide sequence, which corresponds to aligned column 12 in the dna
731 EditCommand mappedEdit = MappingUtils.mapEditCommand(ec, false, nuc,
733 assertEquals(1, mappedEdit.getEdits().size());
734 Edit e = mappedEdit.getEdits().get(0);
735 assertEquals(1, e.getSequences().length);
736 assertEquals(dna, e.getSequences()[0]);
737 assertEquals(12, e.getPosition());
738 assertEquals(6, e.getNumber());