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.ArrayList;
47 import java.util.Arrays;
48 import java.util.List;
50 import org.testng.annotations.Test;
52 public class MappingUtilsTest
54 private AlignViewportI dnaView;
56 private AlignViewportI proteinView;
59 * Simple test of mapping with no intron involved.
61 @Test(groups = { "Functional" })
62 public void testBuildSearchResults()
64 final Sequence seq1 = new Sequence("Seq1/5-10", "C-G-TA-GC");
65 seq1.createDatasetSequence();
67 final Sequence aseq1 = new Sequence("Seq1/12-13", "-P-R");
68 aseq1.createDatasetSequence();
71 * Map dna bases 5-10 to protein residues 12-13
73 AlignedCodonFrame acf = new AlignedCodonFrame();
74 MapList map = new MapList(new int[] { 5, 10 }, new int[] { 12, 13 }, 3,
76 acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
77 List<AlignedCodonFrame> acfList = Arrays.asList(new AlignedCodonFrame[]
81 * Check protein residue 12 maps to codon 5-7, 13 to codon 8-10
83 SearchResults sr = MappingUtils.buildSearchResults(aseq1, 12, acfList);
84 assertEquals(1, sr.getResults().size());
85 Match m = sr.getResults().get(0);
86 assertEquals(seq1.getDatasetSequence(), m.getSequence());
87 assertEquals(5, m.getStart());
88 assertEquals(7, m.getEnd());
89 sr = MappingUtils.buildSearchResults(aseq1, 13, acfList);
90 assertEquals(1, sr.getResults().size());
91 m = sr.getResults().get(0);
92 assertEquals(seq1.getDatasetSequence(), m.getSequence());
93 assertEquals(8, m.getStart());
94 assertEquals(10, m.getEnd());
97 * Check inverse mappings, from codons 5-7, 8-10 to protein 12, 13
99 for (int i = 5; i < 11; i++)
101 sr = MappingUtils.buildSearchResults(seq1, i, acfList);
102 assertEquals(1, sr.getResults().size());
103 m = sr.getResults().get(0);
104 assertEquals(aseq1.getDatasetSequence(), m.getSequence());
105 int residue = i > 7 ? 13 : 12;
106 assertEquals(residue, m.getStart());
107 assertEquals(residue, m.getEnd());
112 * Simple test of mapping with introns involved.
114 @Test(groups = { "Functional" })
115 public void testBuildSearchResults_withIntron()
117 final Sequence seq1 = new Sequence("Seq1/5-17", "c-G-tAGa-GcAgCtt");
118 seq1.createDatasetSequence();
120 final Sequence aseq1 = new Sequence("Seq1/8-9", "-E-D");
121 aseq1.createDatasetSequence();
124 * Map dna bases [6, 8, 9], [11, 13, 115] to protein residues 8 and 9
126 AlignedCodonFrame acf = new AlignedCodonFrame();
127 MapList map = new MapList(new int[] { 6, 6, 8, 9, 11, 11, 13, 13, 15,
128 15 }, new int[] { 8, 9 }, 3, 1);
129 acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
130 List<AlignedCodonFrame> acfList = Arrays.asList(new AlignedCodonFrame[]
134 * Check protein residue 8 maps to [6, 8, 9]
136 SearchResults sr = MappingUtils.buildSearchResults(aseq1, 8, acfList);
137 assertEquals(2, sr.getResults().size());
138 Match m = sr.getResults().get(0);
139 assertEquals(seq1.getDatasetSequence(), m.getSequence());
140 assertEquals(6, m.getStart());
141 assertEquals(6, m.getEnd());
142 m = sr.getResults().get(1);
143 assertEquals(seq1.getDatasetSequence(), m.getSequence());
144 assertEquals(8, m.getStart());
145 assertEquals(9, m.getEnd());
148 * Check protein residue 9 maps to [11, 13, 15]
150 sr = MappingUtils.buildSearchResults(aseq1, 9, acfList);
151 assertEquals(3, sr.getResults().size());
152 m = sr.getResults().get(0);
153 assertEquals(seq1.getDatasetSequence(), m.getSequence());
154 assertEquals(11, m.getStart());
155 assertEquals(11, m.getEnd());
156 m = sr.getResults().get(1);
157 assertEquals(seq1.getDatasetSequence(), m.getSequence());
158 assertEquals(13, m.getStart());
159 assertEquals(13, m.getEnd());
160 m = sr.getResults().get(2);
161 assertEquals(seq1.getDatasetSequence(), m.getSequence());
162 assertEquals(15, m.getStart());
163 assertEquals(15, m.getEnd());
166 * Check inverse mappings, from codons to protein
168 for (int i = 5; i < 18; i++)
170 sr = MappingUtils.buildSearchResults(seq1, i, acfList);
171 int residue = (i == 6 || i == 8 || i == 9) ? 8 : (i == 11 || i == 13
175 assertEquals(0, sr.getResults().size());
178 assertEquals(1, sr.getResults().size());
179 m = sr.getResults().get(0);
180 assertEquals(aseq1.getDatasetSequence(), m.getSequence());
181 assertEquals(residue, m.getStart());
182 assertEquals(residue, m.getEnd());
187 * Test mapping a sequence group made of entire sequences.
189 * @throws IOException
191 @Test(groups = { "Functional" })
192 public void testMapSequenceGroup_sequences() throws IOException
195 * Set up dna and protein Seq1/2/3 with mappings (held on the protein
198 AlignmentI cdna = loadAlignment(">Seq1\nACG\n>Seq2\nTGA\n>Seq3\nTAC\n",
200 cdna.setDataset(null);
201 AlignmentI protein = loadAlignment(">Seq1\nK\n>Seq2\nL\n>Seq3\nQ\n",
203 protein.setDataset(null);
204 AlignedCodonFrame acf = new AlignedCodonFrame();
205 MapList map = new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 3, 1);
206 for (int seq = 0; seq < 3; seq++)
208 acf.addMap(cdna.getSequenceAt(seq).getDatasetSequence(), protein
209 .getSequenceAt(seq).getDatasetSequence(), map);
211 List<AlignedCodonFrame> acfList = Arrays.asList(new AlignedCodonFrame[]
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 * Map (upper-case = coding):
347 * Seq1/10-18 AC-GctGtC-T to Seq1/40 -K-P
348 * Seq2/20-27 Tc-GA-G-T-T to Seq2/20-27 L--Q
349 * Seq3/30-38 TtTT-AaCGg- to Seq3/60-61\nG--S
351 AlignmentI cdna = loadAlignment(">Seq1/10-18\nAC-GctGtC-T\n"
352 + ">Seq2/20-27\nTc-GA-G-T-Tc\n" + ">Seq3/30-38\nTtTT-AaCGg-\n",
354 cdna.setDataset(null);
355 AlignmentI protein = loadAlignment(
356 ">Seq1/40-41\n-K-P\n>Seq2/50-51\nL--Q\n>Seq3/60-61\nG--S\n",
358 protein.setDataset(null);
360 // map first dna to first protein seq
361 AlignedCodonFrame acf = new AlignedCodonFrame();
362 MapList map = new MapList(new int[] { 10, 12, 15, 15, 17, 18 },
363 new int[] { 40, 41 }, 3, 1);
364 acf.addMap(cdna.getSequenceAt(0).getDatasetSequence(), protein
365 .getSequenceAt(0).getDatasetSequence(), map);
367 // map second dna to second protein seq
368 map = new MapList(new int[] { 20, 20, 22, 23, 24, 26 }, new int[] { 50,
370 acf.addMap(cdna.getSequenceAt(1).getDatasetSequence(), protein
371 .getSequenceAt(1).getDatasetSequence(), map);
373 // map third dna to third protein seq
374 map = new MapList(new int[] { 30, 30, 32, 34, 36, 37 }, new int[] { 60,
376 acf.addMap(cdna.getSequenceAt(2).getDatasetSequence(), protein
377 .getSequenceAt(2).getDatasetSequence(), map);
378 List<AlignedCodonFrame> acfList = Arrays.asList(new AlignedCodonFrame[]
381 dnaView = new AlignViewport(cdna);
382 proteinView = new AlignViewport(protein);
383 protein.setCodonFrames(acfList);
387 * Test mapping a column selection in dna to its protein equivalent
389 * @throws IOException
391 @Test(groups = { "Functional" })
392 public void testMapColumnSelection_dnaToProtein() throws IOException
394 setupMappedAlignments();
396 ColumnSelection colsel = new ColumnSelection();
399 * Column 0 in dna picks up first bases which map to residue 1, columns 0-1
402 colsel.addElement(0);
403 ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, dnaView,
405 assertEquals("[0, 1]", cs.getSelected().toString());
408 * Columns 3-5 in dna map to the first residues in protein Seq1, Seq2, and
409 * the first two in Seq3. Overall to columns 0, 1, 3 (col2 is all gaps).
411 colsel.addElement(3);
412 colsel.addElement(4);
413 colsel.addElement(5);
414 cs = MappingUtils.mapColumnSelection(colsel, dnaView, proteinView);
415 assertEquals("[0, 1, 3]", cs.getSelected().toString());
418 @Test(groups = { "Functional" })
419 public void testMapColumnSelection_null() throws IOException
421 setupMappedAlignments();
422 ColumnSelection cs = MappingUtils.mapColumnSelection(null, dnaView,
424 assertTrue("mapped selection not empty", cs.getSelected().isEmpty());
428 * Tests for the method that converts a series of [start, end] ranges to
431 @Test(groups = { "Functional" })
432 public void testFlattenRanges()
434 assertEquals("[1, 2, 3, 4]",
435 Arrays.toString(MappingUtils.flattenRanges(new int[] { 1, 4 })));
438 Arrays.toString(MappingUtils.flattenRanges(new int[] { 1, 2, 3,
442 Arrays.toString(MappingUtils.flattenRanges(new int[] { 1, 1, 2,
445 "[1, 2, 3, 4, 7, 8, 9, 12]",
446 Arrays.toString(MappingUtils.flattenRanges(new int[] { 1, 4, 7,
448 // trailing unpaired start position is ignored:
450 "[1, 2, 3, 4, 7, 8, 9, 12]",
451 Arrays.toString(MappingUtils.flattenRanges(new int[] { 1, 4, 7,
456 * Test mapping a sequence group made of entire columns.
458 * @throws IOException
460 @Test(groups = { "Functional" })
461 public void testMapSequenceGroup_columns() throws IOException
464 * Set up dna and protein Seq1/2/3 with mappings (held on the protein
467 AlignmentI cdna = loadAlignment(
468 ">Seq1\nACGGCA\n>Seq2\nTGACAG\n>Seq3\nTACGTA\n", "FASTA");
469 cdna.setDataset(null);
470 AlignmentI protein = loadAlignment(">Seq1\nKA\n>Seq2\nLQ\n>Seq3\nQV\n",
472 protein.setDataset(null);
473 AlignedCodonFrame acf = new AlignedCodonFrame();
474 MapList map = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 }, 3, 1);
475 for (int seq = 0; seq < 3; seq++)
477 acf.addMap(cdna.getSequenceAt(seq).getDatasetSequence(), protein
478 .getSequenceAt(seq).getDatasetSequence(), map);
480 List<AlignedCodonFrame> acfList = Arrays.asList(new AlignedCodonFrame[]
483 AlignViewportI dnaView = new AlignViewport(cdna);
484 AlignViewportI proteinView = new AlignViewport(protein);
485 protein.setCodonFrames(acfList);
488 * Select all sequences, column 2 in the protein
490 SequenceGroup sg = new SequenceGroup();
491 sg.setColourText(true);
492 sg.setIdColour(Color.GREEN);
493 sg.setOutlineColour(Color.LIGHT_GRAY);
494 sg.addSequence(protein.getSequenceAt(0), false);
495 sg.addSequence(protein.getSequenceAt(1), false);
496 sg.addSequence(protein.getSequenceAt(2), false);
501 * Verify the mapped sequence group in dna
503 SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg,
504 proteinView, dnaView);
505 assertTrue(mappedGroup.getColourText());
506 assertSame(sg.getIdColour(), mappedGroup.getIdColour());
507 assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
508 assertEquals(3, mappedGroup.getSequences().size());
509 assertSame(cdna.getSequenceAt(0), mappedGroup.getSequences().get(0));
510 assertSame(cdna.getSequenceAt(1), mappedGroup.getSequences().get(1));
511 assertSame(cdna.getSequenceAt(2), mappedGroup.getSequences().get(2));
512 assertEquals(3, mappedGroup.getStartRes());
513 assertEquals(5, mappedGroup.getEndRes());
516 * Verify mapping sequence group from dna to protein
519 sg.addSequence(cdna.getSequenceAt(0), false);
520 sg.addSequence(cdna.getSequenceAt(1), false);
521 sg.addSequence(cdna.getSequenceAt(2), false);
522 // select columns 2 and 3 in DNA which span protein columns 0 and 1
525 mappedGroup = MappingUtils.mapSequenceGroup(sg, dnaView, proteinView);
526 assertTrue(mappedGroup.getColourText());
527 assertSame(sg.getIdColour(), mappedGroup.getIdColour());
528 assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
529 assertEquals(3, mappedGroup.getSequences().size());
530 assertSame(protein.getSequenceAt(0), mappedGroup.getSequences().get(0));
531 assertSame(protein.getSequenceAt(1), mappedGroup.getSequences().get(1));
532 assertSame(protein.getSequenceAt(2), mappedGroup.getSequences().get(2));
533 assertEquals(0, mappedGroup.getStartRes());
534 assertEquals(1, mappedGroup.getEndRes());
538 * Test mapping a sequence group made of a sequences/columns region.
540 * @throws IOException
542 @Test(groups = { "Functional" })
543 public void testMapSequenceGroup_region() throws IOException
546 * Set up gapped dna and protein Seq1/2/3 with mappings (held on the protein
549 AlignmentI cdna = loadAlignment(
550 ">Seq1\nA-CG-GC--AT-CA\n>Seq2\n-TG-AC-AG-T-AT\n>Seq3\n-T--ACG-TAAT-G\n",
552 cdna.setDataset(null);
553 AlignmentI protein = loadAlignment(
554 ">Seq1\n-KA-S\n>Seq2\n--L-QY\n>Seq3\nQ-V-M\n", "FASTA");
555 protein.setDataset(null);
556 AlignedCodonFrame acf = new AlignedCodonFrame();
557 MapList map = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3, 1);
558 for (int seq = 0; seq < 3; seq++)
560 acf.addMap(cdna.getSequenceAt(seq).getDatasetSequence(), protein
561 .getSequenceAt(seq).getDatasetSequence(), map);
563 List<AlignedCodonFrame> acfList = Arrays.asList(new AlignedCodonFrame[]
566 AlignViewportI dnaView = new AlignViewport(cdna);
567 AlignViewportI proteinView = new AlignViewport(protein);
568 protein.setCodonFrames(acfList);
571 * Select Seq1 and Seq2 in the protein, column 1 (K/-). Expect mapped
572 * sequence group to cover Seq1, columns 0-3 (ACG). Because the selection
573 * only includes a gap in Seq2 there is no mappable selection region in the
576 SequenceGroup sg = new SequenceGroup();
577 sg.setColourText(true);
578 sg.setIdColour(Color.GREEN);
579 sg.setOutlineColour(Color.LIGHT_GRAY);
580 sg.addSequence(protein.getSequenceAt(0), false);
581 sg.addSequence(protein.getSequenceAt(1), false);
586 * Verify the mapped sequence group in dna
588 SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg,
589 proteinView, dnaView);
590 assertTrue(mappedGroup.getColourText());
591 assertSame(sg.getIdColour(), mappedGroup.getIdColour());
592 assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
593 assertEquals(1, mappedGroup.getSequences().size());
594 assertSame(cdna.getSequenceAt(0), mappedGroup.getSequences().get(0));
595 // Seq2 in protein has a gap in column 1 - ignored
596 // Seq1 has K which should map to columns 0-3 in Seq1
597 assertEquals(0, mappedGroup.getStartRes());
598 assertEquals(3, mappedGroup.getEndRes());
601 * Now select cols 2-4 in protein. These cover Seq1:AS Seq2:LQ Seq3:VM which
602 * extend over DNA columns 3-12, 1-7, 6-13 respectively, or 1-13 overall.
606 mappedGroup = MappingUtils.mapSequenceGroup(sg, proteinView, dnaView);
607 assertEquals(1, mappedGroup.getStartRes());
608 assertEquals(13, mappedGroup.getEndRes());
611 * Verify mapping sequence group from dna to protein
614 sg.addSequence(cdna.getSequenceAt(0), false);
616 // select columns 4,5 - includes Seq1:codon2 (A) only
619 mappedGroup = MappingUtils.mapSequenceGroup(sg, dnaView, proteinView);
620 assertEquals(2, mappedGroup.getStartRes());
621 assertEquals(2, mappedGroup.getEndRes());
623 // add Seq2 to dna selection cols 4-5 include codons 1 and 2 (LQ)
624 sg.addSequence(cdna.getSequenceAt(1), false);
625 mappedGroup = MappingUtils.mapSequenceGroup(sg, dnaView, proteinView);
626 assertEquals(2, mappedGroup.getStartRes());
627 assertEquals(4, mappedGroup.getEndRes());
629 // add Seq3 to dna selection cols 4-5 include codon 1 (Q)
630 sg.addSequence(cdna.getSequenceAt(2), false);
631 mappedGroup = MappingUtils.mapSequenceGroup(sg, dnaView, proteinView);
632 assertEquals(0, mappedGroup.getStartRes());
633 assertEquals(4, mappedGroup.getEndRes());
636 @Test(groups = { "Functional" })
637 public void testFindMappingsForSequence()
639 SequenceI seq1 = new Sequence("Seq1", "ABC");
640 SequenceI seq2 = new Sequence("Seq2", "ABC");
641 SequenceI seq3 = new Sequence("Seq3", "ABC");
642 SequenceI seq4 = new Sequence("Seq4", "ABC");
643 seq1.createDatasetSequence();
644 seq2.createDatasetSequence();
645 seq3.createDatasetSequence();
646 seq4.createDatasetSequence();
649 * Create mappings from seq1 to seq2, seq2 to seq1, seq3 to seq1
651 AlignedCodonFrame acf1 = new AlignedCodonFrame();
652 MapList map = new MapList(new int[] { 1, 3 }, new int[] { 1, 3 }, 1, 1);
653 acf1.addMap(seq1.getDatasetSequence(), seq2.getDatasetSequence(), map);
654 AlignedCodonFrame acf2 = new AlignedCodonFrame();
655 acf2.addMap(seq2.getDatasetSequence(), seq1.getDatasetSequence(), map);
656 AlignedCodonFrame acf3 = new AlignedCodonFrame();
657 acf3.addMap(seq3.getDatasetSequence(), seq1.getDatasetSequence(), map);
659 List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
665 * Seq1 has three mappings
667 List<AlignedCodonFrame> result = MappingUtils.findMappingsForSequence(
669 assertEquals(3, result.size());
670 assertTrue(result.contains(acf1));
671 assertTrue(result.contains(acf2));
672 assertTrue(result.contains(acf3));
675 * Seq2 has two mappings
677 result = MappingUtils.findMappingsForSequence(seq2, mappings);
678 assertEquals(2, result.size());
679 assertTrue(result.contains(acf1));
680 assertTrue(result.contains(acf2));
683 * Seq3 has one mapping
685 result = MappingUtils.findMappingsForSequence(seq3, mappings);
686 assertEquals(1, result.size());
687 assertTrue(result.contains(acf3));
690 * Seq4 has no mappings
692 result = MappingUtils.findMappingsForSequence(seq4, mappings);
693 assertEquals(0, result.size());
695 result = MappingUtils.findMappingsForSequence(null, mappings);
696 assertEquals(0, result.size());
698 result = MappingUtils.findMappingsForSequence(seq1, null);
699 assertEquals(0, result.size());
701 result = MappingUtils.findMappingsForSequence(null, null);
702 assertEquals(0, result.size());
705 @Test(groups = { "Functional" })
706 public void testMapEditCommand()
708 SequenceI dna = new Sequence("Seq1", "---ACG---GCATCA", 8, 16);
709 SequenceI protein = new Sequence("Seq2", "-T-AS", 5, 7);
710 dna.createDatasetSequence();
711 protein.createDatasetSequence();
712 AlignedCodonFrame acf = new AlignedCodonFrame();
713 MapList map = new MapList(new int[] { 8, 16 }, new int[] { 5, 7 }, 3, 1);
714 acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map);
715 List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
718 AlignmentI prot = new Alignment(new SequenceI[] { protein });
719 prot.setCodonFrames(mappings);
720 AlignmentI nuc = new Alignment(new SequenceI[] { dna });
723 * construct and perform the edit command to turn "-T-AS" in to "-T-A--S"
724 * i.e. insert two gaps at column 4
726 EditCommand ec = new EditCommand();
727 final Edit edit = ec.new Edit(Action.INSERT_GAP,
728 new SequenceI[] { protein }, 4, 2, '-');
729 ec.appendEdit(edit, prot, true, null);
732 * the mapped edit command should be to insert 6 gaps before base 4 in the
733 * nucleotide sequence, which corresponds to aligned column 12 in the dna
735 EditCommand mappedEdit = MappingUtils.mapEditCommand(ec, false, nuc,
737 assertEquals(1, mappedEdit.getEdits().size());
738 Edit e = mappedEdit.getEdits().get(0);
739 assertEquals(1, e.getSequences().length);
740 assertEquals(dna, e.getSequences()[0]);
741 assertEquals(12, e.getPosition());
742 assertEquals(6, e.getNumber());
746 * Tests for the method that converts a series of [start, end] ranges to
747 * single positions, where the mapping is to a reverse strand i.e. start is
748 * greater than end point mapped to
750 @Test(groups = { "Functional" })
751 public void testFlattenRanges_reverseStrand()
753 assertEquals("[4, 3, 2, 1]",
754 Arrays.toString(MappingUtils.flattenRanges(new int[] { 4, 1 })));
757 Arrays.toString(MappingUtils.flattenRanges(new int[] { 4, 3, 2,
761 Arrays.toString(MappingUtils.flattenRanges(new int[] { 4, 4, 3,
764 "[12, 9, 8, 7, 4, 3, 2, 1]",
765 Arrays.toString(MappingUtils.flattenRanges(new int[] { 12, 12,
767 // forwards and backwards anyone?
769 "[4, 5, 6, 3, 2, 1]",
770 Arrays.toString(MappingUtils.flattenRanges(new int[] { 4, 6, 3,
772 // backwards and forwards
774 "[3, 2, 1, 4, 5, 6]",
775 Arrays.toString(MappingUtils.flattenRanges(new int[] { 3, 1, 4,
777 // trailing unpaired start position is ignored:
779 "[12, 9, 8, 7, 4, 3, 2]",
780 Arrays.toString(MappingUtils.flattenRanges(new int[] { 12, 12,
785 * Test mapping a column selection including hidden columns
787 * @throws IOException
789 @Test(groups = { "Functional" })
790 public void testMapColumnSelection_hiddenColumns() throws IOException
792 setupMappedAlignments();
794 ColumnSelection proteinSelection = new ColumnSelection();
797 * Column 0 in protein picks up Seq2/L, Seq3/G which map to cols 0-4 and 0-3
798 * in dna respectively, overall 0-4
800 proteinSelection.hideColumns(0);
801 ColumnSelection dnaSelection = MappingUtils.mapColumnSelection(proteinSelection,
802 proteinView, dnaView);
803 assertEquals("[]", dnaSelection.getSelected().toString());
804 List<int[]> hidden = dnaSelection.getHiddenColumns();
805 assertEquals(1, hidden.size());
806 assertEquals("[0, 4]", Arrays.toString(hidden.get(0)));
809 * Column 1 in protein picks up Seq1/K which maps to cols 0-3 in dna
811 proteinSelection.revealAllHiddenColumns();
812 // the unhidden columns are now marked selected!
813 assertEquals("[0]", proteinSelection.getSelected().toString());
814 // deselect these or hideColumns will be expanded to include 0
815 proteinSelection.clear();
816 proteinSelection.hideColumns(1);
817 dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView);
818 hidden = dnaSelection.getHiddenColumns();
819 assertEquals(1, hidden.size());
820 assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
823 * Column 2 in protein picks up gaps only - no mapping
825 proteinSelection.revealAllHiddenColumns();
826 proteinSelection.clear();
827 proteinSelection.hideColumns(2);
828 dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView);
829 assertTrue(dnaSelection.getHiddenColumns().isEmpty());
832 * Column 3 in protein picks up Seq1/P, Seq2/Q, Seq3/S which map to columns
833 * 6-9, 6-10, 5-8 respectively, overall to 5-10
835 proteinSelection.revealAllHiddenColumns();
836 proteinSelection.clear();
837 proteinSelection.hideColumns(3); // 5-10 hidden in dna
838 proteinSelection.addElement(1); // 0-3 selected in dna
839 dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView);
840 assertEquals("[0, 1, 2, 3]", dnaSelection.getSelected().toString());
841 hidden = dnaSelection.getHiddenColumns();
842 assertEquals(1, hidden.size());
843 assertEquals("[5, 10]", Arrays.toString(hidden.get(0)));
846 * Combine hiding columns 1 and 3 to get discontiguous hidden columns
848 proteinSelection.revealAllHiddenColumns();
849 proteinSelection.clear();
850 proteinSelection.hideColumns(1);
851 proteinSelection.hideColumns(3);
852 dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView);
853 hidden = dnaSelection.getHiddenColumns();
854 assertEquals(2, hidden.size());
855 assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
856 assertEquals("[5, 10]", Arrays.toString(hidden.get(1)));