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.assertNotNull;
25 import static org.testng.AssertJUnit.assertTrue;
27 import jalview.api.AlignViewportI;
28 import jalview.datamodel.AlignedCodon;
29 import jalview.datamodel.Alignment;
30 import jalview.datamodel.AlignmentI;
31 import jalview.datamodel.ColumnSelection;
32 import jalview.datamodel.Sequence;
33 import jalview.datamodel.SequenceI;
34 import jalview.gui.AlignViewport;
35 import jalview.io.DataSourceType;
36 import jalview.io.FileFormat;
37 import jalview.io.FormatAdapter;
39 import java.io.IOException;
41 import org.testng.annotations.Test;
46 // AA encoding codons as ordered on the Jalview help page Amino Acid Table
47 private static String fasta = ">B\n" + "GCT" + "GCC" + "GCA" + "GCG"
48 + "TGT" + "TGC" + "GAT" + "GAC" + "GAA" + "GAG" + "TTT" + "TTC"
49 + "GGT" + "GGC" + "GGA" + "GGG" + "CAT" + "CAC" + "ATT" + "ATC"
50 + "ATA" + "AAA" + "AAG" + "TTG" + "TTA" + "CTT" + "CTC" + "CTA"
51 + "CTG" + "ATG" + "AAT" + "AAC" + "CCT" + "CCC" + "CCA" + "CCG"
52 + "CAA" + "CAG" + "CGT" + "CGC" + "CGA" + "CGG" + "AGA" + "AGG"
53 + "TCT" + "TCC" + "TCA" + "TCG" + "AGT" + "AGC" + "ACT" + "ACC"
54 + "ACA" + "ACG" + "GTT" + "GTC" + "GTA" + "GTG" + "TGG" + "TAT"
55 + "TAC" + "TAA" + "TAG" + "TGA";
57 private static String JAL_1312_example_align_fasta = ">B.FR.83.HXB2_LAI_IIIB_BRU_K03455/45-306\n"
58 + "ATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
59 + "GGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACA\n"
60 + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTG\n"
61 + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAC\n"
62 + ">gi|27804621|gb|AY178912.1|/1-259\n"
63 + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
64 + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGGACA\n"
65 + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
66 + "TGTTCATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAT\n"
67 + ">gi|27804623|gb|AY178913.1|/1-259\n"
68 + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
69 + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGAACA\n"
70 + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
71 + "TGTTCATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
72 + ">gi|27804627|gb|AY178915.1|/1-260\n"
73 + "-TGGGAAAA-ATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
74 + "GGAGCTAGAACGATTCGCAGTTAACCCTGGCCTGTTAGAAACATCAGAAGGTTGTAGACAAATATTGGGACA\n"
75 + "GCTACAACCATCCCTTGAGACAGGATCAGAAGAACTTAAATCATTATWTAATACCATAGCAGTCCTCTATTG\n"
76 + "TGTACATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAG\n"
77 + ">gi|27804631|gb|AY178917.1|/1-261\n"
78 + "-TGGGAAAAAATTCGGTTGAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
79 + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACACCAGAAGGCTGTAGACAAATACTGGGACA\n"
80 + "GCTACAACCGTCCCTTCAGACAGGATCGGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
81 + "TGTGCATCAAAGGATAGATGTAAAAGACACCAAGGAGGCTTTAGAC\n"
82 + ">gi|27804635|gb|AY178919.1|/1-261\n"
83 + "-TGGGAGAGAATTCGGTTACGGCCAGGAGGAAAGAAAAAATATAAATTGAAACATATAGTATGGGCAGGCAG\n"
84 + "AGAGCTAGATCGATTCGCAGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAGATATTGGGACA\n"
85 + "GCTACAACCGTCCCTTAAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
86 + "TGTACATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
87 + ">gi|27804641|gb|AY178922.1|/1-261\n"
88 + "-TGGGAGAAAATTCGGTTACGGCCAGGGGGAAAGAAAAGATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
89 + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAAATACTGGGACA\n"
90 + "GTTACACCCATCCCTTCATACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
91 + "TGTGCATCAAAGGATAGAAGTAAAAGACACCAAGGAAGCTTTAGAC\n"
92 + ">gi|27804647|gb|AY178925.1|/1-261\n"
93 + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATCAATTAAAACATGTAGTATGGGCAAGCAG\n"
94 + "GGAACTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
95 + "GCTACAACCATCCCTTCAGACAGGATCAGAGGAACTTAAATCATTATTTAATACAGTAGCAGTCCTCTATTG\n"
96 + "TGTACATCAAAGAATAGATGTAAAAGACACCAAGGAAGCTCTAGAA\n"
97 + ">gi|27804649|gb|AY178926.1|/1-261\n"
98 + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
99 + "GGAGCTAGAACGATTCGCGGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAACTACTGGGACA\n"
100 + "GTTACAACCATCCCTTCAGACAGGATCAGAAGAACTCAAATCATTATATAATACAATAGCAACCCTCTATTG\n"
101 + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCCTTAGAT\n"
102 + ">gi|27804653|gb|AY178928.1|/1-261\n"
103 + "-TGGGAAAGAATTCGGTTAAGGCCAGGGGGAAAGAAACAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
104 + "GGAGCTAGACCGATTCGCACTTAACCCCGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
105 + "GCTACAATCGTCCCTTCAGACAGGATCAGAAGAACTTAGATCACTATATAATACAGTAGCAGTCCTCTATTG\n"
106 + "TGTGCATCAAAAGATAGATGTAAAAGACACCAAGGAAGCCTTAGAC\n"
107 + ">gi|27804659|gb|AY178931.1|/1-261\n"
108 + "-TGGGAAAAAATTCGGTTACGGCCAGGAGGAAAGAAAAGATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
109 + "GGAGCTAGAACGATTYGCAGTTAATCCTGGCCTTTTAGAAACAGCAGAAGGCTGTAGACAAATACTGGGACA\n"
110 + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
111 + "TGTACATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAA\n";
115 * Corner case for this test is the presence of codons after codons that were
118 * @throws IOException
120 @Test(groups = { "Functional" })
121 public void testTranslateCdna_withUntranslatableCodons()
124 AlignmentI alf = new FormatAdapter().readFile(
125 JAL_1312_example_align_fasta, DataSourceType.PASTE,
127 ColumnSelection cs = new ColumnSelection();
128 AlignViewportI av = new AlignViewport(alf, cs);
129 Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
130 AlignmentI translated = dna.translateCdna();
131 assertNotNull("Couldn't do a full width translation of test data.",
136 * Test variant in which 15 column blocks at a time are translated (the rest
139 * @throws IOException
141 @Test(groups = { "Functional" })
142 public void testTranslateCdna_withUntranslatableCodonsAndHiddenColumns()
145 AlignmentI alf = new FormatAdapter().readFile(
146 JAL_1312_example_align_fasta, DataSourceType.PASTE,
149 for (int ipos = 0; ipos + vwidth < alf.getWidth(); ipos += vwidth)
151 ColumnSelection cs = new ColumnSelection();
154 cs.hideColumns(0, ipos - 1);
156 cs.hideColumns(ipos + vwidth, alf.getWidth());
157 int[] vcontigs = cs.getVisibleContigs(0, alf.getWidth());
158 AlignViewportI av = new AlignViewport(alf, cs);
159 Dna dna = new Dna(av, vcontigs);
160 AlignmentI transAlf = dna.translateCdna();
162 assertTrue("Translation failed (ipos=" + ipos
163 + ") No alignment data.", transAlf != null);
164 assertTrue("Translation failed (ipos=" + ipos + ") Empty alignment.",
165 transAlf.getHeight() > 0);
166 assertTrue("Translation failed (ipos=" + ipos + ") Translated "
167 + transAlf.getHeight() + " sequences from " + alf.getHeight()
168 + " sequences", alf.getHeight() == transAlf.getHeight());
173 * Test simple translation to Amino Acids (with STOP codons translated to *).
175 * @throws IOException
177 @Test(groups = { "Functional" })
178 public void testTranslateCdna_simple() throws IOException
180 AlignmentI alf = new FormatAdapter().readFile(fasta,
181 DataSourceType.PASTE, FileFormat.Fasta);
182 ColumnSelection cs = new ColumnSelection();
183 AlignViewportI av = new AlignViewport(alf, cs);
184 Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
185 AlignmentI translated = dna.translateCdna();
186 String aa = translated.getSequenceAt(0).getSequenceAsString();
188 "AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYY***",
193 * Test translation excluding hidden columns.
195 * @throws IOException
197 @Test(groups = { "Functional" })
198 public void testTranslateCdna_hiddenColumns() throws IOException
200 AlignmentI alf = new FormatAdapter().readFile(fasta,
201 DataSourceType.PASTE, FileFormat.Fasta);
202 ColumnSelection cs = new ColumnSelection();
203 cs.hideColumns(6, 14); // hide codons 3/4/5
204 cs.hideColumns(24, 35); // hide codons 9-12
205 cs.hideColumns(177, 191); // hide codons 60-64
206 AlignViewportI av = new AlignViewport(alf, cs);
207 Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
208 AlignmentI translated = dna.translateCdna();
209 String aa = translated.getSequenceAt(0).getSequenceAsString();
210 assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa);
214 * Use this test to help debug into any cases of interest.
216 @Test(groups = { "Functional" })
217 public void testCompareCodonPos_oneOnly()
219 assertFollows("-AA--A", "G--GG"); // 2 shifted seq2, 3 shifted seq1
223 * Tests for method that compares 'alignment' of two codon position triplets.
225 @Test(groups = { "Functional" })
226 public void testCompareCodonPos()
229 * Returns 0 for any null argument
231 assertEquals(0, Dna.compareCodonPos(new AlignedCodon(1, 2, 3), null));
232 assertEquals(0, Dna.compareCodonPos(null, new AlignedCodon(1, 2, 3)));
235 * Work through 27 combinations. First 9 cases where first position matches.
237 assertMatches("AAA", "GGG"); // 2 and 3 match
238 assertFollows("AA-A", "GGG"); // 2 matches, 3 shifted seq1
239 assertPrecedes("AAA", "GG-G"); // 2 matches, 3 shifted seq2
240 assertFollows("A-AA", "GG-G"); // 2 shifted seq1, 3 matches
241 assertFollows("A-A-A", "GG-G"); // 2 shifted seq1, 3 shifted seq1
242 assertPrecedes("A-AA", "GG--G"); // 2 shifted seq1, 3 shifted seq2
243 assertPrecedes("AA-A", "G-GG"); // 2 shifted seq2, 3 matches
244 assertFollows("AA--A", "G-GG"); // 2 shifted seq2, 3 shifted seq1
245 assertPrecedes("AAA", "G-GG"); // 2 shifted seq2, 3 shifted seq2
248 * 9 cases where first position is shifted in first sequence.
250 assertFollows("-AAA", "G-GG"); // 2 and 3 match
251 assertFollows("-AA-A", "G-GG"); // 2 matches, 3 shifted seq1
252 // 'enclosing' case: pick first to start precedes
253 assertFollows("-AAA", "G-G-G"); // 2 matches, 3 shifted seq2
254 assertFollows("-A-AA", "G-G-G"); // 2 shifted seq1, 3 matches
255 assertFollows("-A-A-A", "G-G-G"); // 2 shifted seq1, 3 shifted seq1
256 // 'enclosing' case: pick first to start precedes
257 assertFollows("-A-AA", "G-G--G"); // 2 shifted seq1, 3 shifted seq2
258 assertFollows("-AA-A", "G--GG"); // 2 shifted seq2, 3 matches
259 assertFollows("-AA--A", "G--GG"); // 2 shifted seq2, 3 shifted seq1
260 assertPrecedes("-AAA", "G--GG"); // 2 shifted seq2, 3 shifted seq2
263 * 9 cases where first position is shifted in second sequence.
265 assertPrecedes("A-AA", "-GGG"); // 2 and 3 match
266 assertPrecedes("A-A-A", "-GGG"); // 2 matches, 3 shifted seq1
267 assertPrecedes("A-AA", "-GG-G"); // 2 matches, 3 shifted seq2
268 assertPrecedes("A--AA", "-GG-G"); // 2 shifted seq1, 3 matches
269 // 'enclosing' case with middle base deciding:
270 assertFollows("A--AA", "-GGG"); // 2 shifted seq1, 3 shifted seq1
271 assertPrecedes("A--AA", "-GG--G"); // 2 shifted seq1, 3 shifted seq2
272 assertPrecedes("AA-A", "-GGG"); // 2 shifted seq2, 3 matches
273 assertPrecedes("AA--A", "-GGG"); // 2 shifted seq2, 3 shifted seq1
274 assertPrecedes("AAA", "-GGG"); // 2 shifted seq2, 3 shifted seq2
278 * This test generates a random cDNA alignment and its translation, then
279 * reorders the cDNA and retranslates, and verifies that the translations are
280 * the same (apart from ordering).
282 @Test(groups = { "Functional" })
283 public void testTranslateCdna_sequenceOrderIndependent()
286 * Generate cDNA - 8 sequences of 12 bases each.
288 AlignmentI cdna = new DnaAlignmentGenerator().generate(12, 8, 97, 5, 5);
289 ColumnSelection cs = new ColumnSelection();
290 AlignViewportI av = new AlignViewport(cdna, cs);
291 Dna dna = new Dna(av, new int[] { 0, cdna.getWidth() - 1 });
292 AlignmentI translated = dna.translateCdna();
295 * Jumble the cDNA sequences and translate.
297 SequenceI[] sorted = new SequenceI[cdna.getHeight()];
298 final int[] jumbler = new int[] { 6, 7, 3, 4, 2, 0, 1, 5 };
300 for (int i : jumbler)
302 sorted[seqNo++] = cdna.getSequenceAt(i);
304 AlignmentI cdnaReordered = new Alignment(sorted);
305 av = new AlignViewport(cdnaReordered, cs);
306 dna = new Dna(av, new int[] { 0, cdna.getWidth() - 1 });
307 AlignmentI translated2 = dna.translateCdna();
310 * Check translated sequences are the same in both alignments.
312 System.out.println("Original");
313 System.out.println(translated.toString());
314 System.out.println("Sorted");
315 System.out.println(translated2.toString());
317 int sortedSequenceIndex = 0;
318 for (int originalSequenceIndex : jumbler)
320 final String translation1 = translated.getSequenceAt(
321 originalSequenceIndex).getSequenceAsString();
322 final String translation2 = translated2.getSequenceAt(
323 sortedSequenceIndex).getSequenceAsString();
324 assertEquals(translation2, translation1);
325 sortedSequenceIndex++;
330 * Test that all the cases in testCompareCodonPos have a 'symmetric'
331 * comparison (without checking the actual comparison result).
333 @Test(groups = { "Functional" })
334 public void testCompareCodonPos_isSymmetric()
336 assertSymmetric("AAA", "GGG");
337 assertSymmetric("AA-A", "GGG");
338 assertSymmetric("AAA", "GG-G");
339 assertSymmetric("A-AA", "GG-G");
340 assertSymmetric("A-A-A", "GG-G");
341 assertSymmetric("A-AA", "GG--G");
342 assertSymmetric("AA-A", "G-GG");
343 assertSymmetric("AA--A", "G-GG");
344 assertSymmetric("AAA", "G-GG");
345 assertSymmetric("-AAA", "G-GG");
346 assertSymmetric("-AA-A", "G-GG");
347 assertSymmetric("-AAA", "G-G-G");
348 assertSymmetric("-A-AA", "G-G-G");
349 assertSymmetric("-A-A-A", "G-G-G");
350 assertSymmetric("-A-AA", "G-G--G");
351 assertSymmetric("-AA-A", "G--GG");
352 assertSymmetric("-AA--A", "G--GG");
353 assertSymmetric("-AAA", "G--GG");
354 assertSymmetric("A-AA", "-GGG");
355 assertSymmetric("A-A-A", "-GGG");
356 assertSymmetric("A-AA", "-GG-G");
357 assertSymmetric("A--AA", "-GG-G");
358 assertSymmetric("A--AA", "-GGG");
359 assertSymmetric("A--AA", "-GG--G");
360 assertSymmetric("AA-A", "-GGG");
361 assertSymmetric("AA--A", "-GGG");
362 assertSymmetric("AAA", "-GGG");
365 private void assertSymmetric(String codon1, String codon2)
367 assertEquals("Comparison of '" + codon1 + "' and '" + codon2
368 + " not symmetric", Integer.signum(compare(codon1, codon2)),
369 -Integer.signum(compare(codon2, codon1)));
373 * Assert that the first sequence should map to the same position as the
374 * second in a translated alignment. Also checks that this is true if the
375 * order of the codons is reversed.
380 private void assertMatches(String codon1, String codon2)
382 assertEquals("Expected '" + codon1 + "' matches '" + codon2 + "'", 0,
383 compare(codon1, codon2));
384 assertEquals("Expected '" + codon2 + "' matches '" + codon1 + "'", 0,
385 compare(codon2, codon1));
389 * Assert that the first sequence should precede the second in a translated
395 private void assertPrecedes(String codon1, String codon2)
397 assertEquals("Expected '" + codon1 + "' precedes '" + codon2 + "'",
398 -1, compare(codon1, codon2));
402 * Assert that the first sequence should follow the second in a translated
408 private void assertFollows(String codon1, String codon2)
410 assertEquals("Expected '" + codon1 + "' follows '" + codon2 + "'", 1,
411 compare(codon1, codon2));
415 * Convert two nucleotide strings to base positions and pass to
416 * Dna.compareCodonPos, return the result.
422 private int compare(String s1, String s2)
424 final AlignedCodon cd1 = convertCodon(s1);
425 final AlignedCodon cd2 = convertCodon(s2);
426 System.out.println("K: " + s1 + " " + cd1.toString());
427 System.out.println("G: " + s2 + " " + cd2.toString());
428 System.out.println();
429 return Dna.compareCodonPos(cd1, cd2);
433 * Convert a string e.g. "-GC-T" to base positions e.g. [1, 2, 4]. The string
434 * should have exactly 3 non-gap characters, and use '-' for gaps.
439 private AlignedCodon convertCodon(String s)
441 int[] codon = new int[3];
443 for (int j = 0; j < s.length(); j++)
445 if (s.charAt(j) != '-')
450 return new AlignedCodon(codon[0], codon[1], codon[2]);
454 * Weirdly, maybe worth a test to prove the helper method of this test class.
456 @Test(groups = { "Functional" })
457 public void testConvertCodon()
459 assertEquals("[0, 1, 2]", convertCodon("AAA").toString());
460 assertEquals("[0, 2, 5]", convertCodon("A-A--A").toString());
461 assertEquals("[1, 3, 4]", convertCodon("-A-AA-").toString());
465 * Test dna complementing
467 @Test(groups = "Functional")
468 public void testGetComplement()
470 assertEquals('t', Dna.getComplement('a'));
471 assertEquals('T', Dna.getComplement('A'));
472 assertEquals('a', Dna.getComplement('t'));
473 assertEquals('A', Dna.getComplement('T'));
474 assertEquals('c', Dna.getComplement('g'));
475 assertEquals('C', Dna.getComplement('G'));
476 assertEquals('g', Dna.getComplement('c'));
477 assertEquals('G', Dna.getComplement('C'));
478 // note uU --> aA but not vice versa
479 assertEquals('a', Dna.getComplement('u'));
480 assertEquals('A', Dna.getComplement('U'));
481 // ambiguity codes, see http://www.bioinformatics.org/sms/iupac.html
482 assertEquals('r', Dna.getComplement('y'));
483 assertEquals('R', Dna.getComplement('Y'));
484 assertEquals('y', Dna.getComplement('r'));
485 assertEquals('Y', Dna.getComplement('R'));
486 assertEquals('k', Dna.getComplement('m'));
487 assertEquals('K', Dna.getComplement('M'));
488 assertEquals('m', Dna.getComplement('k'));
489 assertEquals('M', Dna.getComplement('K'));
490 assertEquals('b', Dna.getComplement('v'));
491 assertEquals('B', Dna.getComplement('V'));
492 assertEquals('v', Dna.getComplement('b'));
493 assertEquals('V', Dna.getComplement('B'));
494 assertEquals('d', Dna.getComplement('h'));
495 assertEquals('D', Dna.getComplement('H'));
496 assertEquals('h', Dna.getComplement('d'));
497 assertEquals('H', Dna.getComplement('D'));
498 assertEquals('Q', Dna.getComplement('Q'));
501 @Test(groups = "Functional")
502 public void testReverseSequence()
504 String seq = "-Ac-GtU--rYkMbVdHNX-";
505 String seqRev = new StringBuilder(seq).reverse().toString();
508 SequenceI reversed = Dna.reverseSequence("Seq1", seq, false);
509 assertEquals(1, reversed.getStart());
510 assertEquals(15, reversed.getEnd());
511 assertEquals(20, reversed.getLength());
512 assertEquals(seqRev, reversed.getSequenceAsString());
513 assertEquals("Seq1|rev", reversed.getName());
515 // reverse complement:
516 SequenceI revcomp = Dna.reverseSequence("Seq1", seq, true);
517 assertEquals("-XNDhBvKmRy--AaC-gT-", revcomp.getSequenceAsString());
518 assertEquals("Seq1|revcomp", revcomp.getName());
521 @Test(groups = "Functional")
522 public void testReverseCdna()
524 String seq = "-Ac-GtU--rYkMbVdHNX-";
525 String seqRev = new StringBuilder(seq).reverse().toString();
526 String seqDs = seq.replaceAll("-", "");
527 String seqDsRev = new StringBuilder(seqDs).reverse().toString();
529 SequenceI dna = new Sequence("Seq1", seq);
530 Alignment al = new Alignment(new SequenceI[] { dna });
531 al.createDatasetAlignment();
532 assertEquals(seqDs, al.getSequenceAt(0).getDatasetSequence()
533 .getSequenceAsString());
535 ColumnSelection cs = new ColumnSelection();
536 AlignViewportI av = new AlignViewport(al, cs);
537 Dna testee = new Dna(av, new int[] { 0, al.getWidth() - 1 });
538 AlignmentI reversed = testee.reverseCdna(false);
539 assertEquals(1, reversed.getHeight());
540 assertEquals(seqRev, reversed.getSequenceAt(0).getSequenceAsString());
541 assertEquals(seqDsRev, reversed.getSequenceAt(0).getDatasetSequence()
542 .getSequenceAsString());