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.HiddenColumns;
32 import jalview.datamodel.Sequence;
33 import jalview.datamodel.SequenceI;
34 import jalview.gui.AlignViewport;
35 import jalview.gui.JvOptionPane;
36 import jalview.io.DataSourceType;
37 import jalview.io.FileFormat;
38 import jalview.io.FormatAdapter;
40 import java.io.IOException;
41 import java.util.Iterator;
43 import org.testng.annotations.BeforeClass;
44 import org.testng.annotations.Test;
48 @BeforeClass(alwaysRun = true)
49 public void setUpJvOptionPane()
51 JvOptionPane.setInteractiveMode(false);
52 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
56 // AA encoding codons as ordered on the Jalview help page Amino Acid Table
57 private static String fasta = ">B\n" + "GCT" + "GCC" + "GCA" + "GCG"
58 + "TGT" + "TGC" + "GAT" + "GAC" + "GAA" + "GAG" + "TTT" + "TTC"
59 + "GGT" + "GGC" + "GGA" + "GGG" + "CAT" + "CAC" + "ATT" + "ATC"
60 + "ATA" + "AAA" + "AAG" + "TTG" + "TTA" + "CTT" + "CTC" + "CTA"
61 + "CTG" + "ATG" + "AAT" + "AAC" + "CCT" + "CCC" + "CCA" + "CCG"
62 + "CAA" + "CAG" + "CGT" + "CGC" + "CGA" + "CGG" + "AGA" + "AGG"
63 + "TCT" + "TCC" + "TCA" + "TCG" + "AGT" + "AGC" + "ACT" + "ACC"
64 + "ACA" + "ACG" + "GTT" + "GTC" + "GTA" + "GTG" + "TGG" + "TAT"
65 + "TAC" + "TAA" + "TAG" + "TGA";
67 private static String JAL_1312_example_align_fasta = ">B.FR.83.HXB2_LAI_IIIB_BRU_K03455/45-306\n"
68 + "ATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
69 + "GGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACA\n"
70 + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTG\n"
71 + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAC\n"
72 + ">gi|27804621|gb|AY178912.1|/1-259\n"
73 + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
74 + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGGACA\n"
75 + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
76 + "TGTTCATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAT\n"
77 + ">gi|27804623|gb|AY178913.1|/1-259\n"
78 + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
79 + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGAACA\n"
80 + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
81 + "TGTTCATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
82 + ">gi|27804627|gb|AY178915.1|/1-260\n"
83 + "-TGGGAAAA-ATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
84 + "GGAGCTAGAACGATTCGCAGTTAACCCTGGCCTGTTAGAAACATCAGAAGGTTGTAGACAAATATTGGGACA\n"
85 + "GCTACAACCATCCCTTGAGACAGGATCAGAAGAACTTAAATCATTATWTAATACCATAGCAGTCCTCTATTG\n"
86 + "TGTACATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAG\n"
87 + ">gi|27804631|gb|AY178917.1|/1-261\n"
88 + "-TGGGAAAAAATTCGGTTGAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
89 + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACACCAGAAGGCTGTAGACAAATACTGGGACA\n"
90 + "GCTACAACCGTCCCTTCAGACAGGATCGGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
91 + "TGTGCATCAAAGGATAGATGTAAAAGACACCAAGGAGGCTTTAGAC\n"
92 + ">gi|27804635|gb|AY178919.1|/1-261\n"
93 + "-TGGGAGAGAATTCGGTTACGGCCAGGAGGAAAGAAAAAATATAAATTGAAACATATAGTATGGGCAGGCAG\n"
94 + "AGAGCTAGATCGATTCGCAGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAGATATTGGGACA\n"
95 + "GCTACAACCGTCCCTTAAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
96 + "TGTACATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
97 + ">gi|27804641|gb|AY178922.1|/1-261\n"
98 + "-TGGGAGAAAATTCGGTTACGGCCAGGGGGAAAGAAAAGATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
99 + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAAATACTGGGACA\n"
100 + "GTTACACCCATCCCTTCATACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
101 + "TGTGCATCAAAGGATAGAAGTAAAAGACACCAAGGAAGCTTTAGAC\n"
102 + ">gi|27804647|gb|AY178925.1|/1-261\n"
103 + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATCAATTAAAACATGTAGTATGGGCAAGCAG\n"
104 + "GGAACTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
105 + "GCTACAACCATCCCTTCAGACAGGATCAGAGGAACTTAAATCATTATTTAATACAGTAGCAGTCCTCTATTG\n"
106 + "TGTACATCAAAGAATAGATGTAAAAGACACCAAGGAAGCTCTAGAA\n"
107 + ">gi|27804649|gb|AY178926.1|/1-261\n"
108 + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
109 + "GGAGCTAGAACGATTCGCGGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAACTACTGGGACA\n"
110 + "GTTACAACCATCCCTTCAGACAGGATCAGAAGAACTCAAATCATTATATAATACAATAGCAACCCTCTATTG\n"
111 + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCCTTAGAT\n"
112 + ">gi|27804653|gb|AY178928.1|/1-261\n"
113 + "-TGGGAAAGAATTCGGTTAAGGCCAGGGGGAAAGAAACAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
114 + "GGAGCTAGACCGATTCGCACTTAACCCCGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
115 + "GCTACAATCGTCCCTTCAGACAGGATCAGAAGAACTTAGATCACTATATAATACAGTAGCAGTCCTCTATTG\n"
116 + "TGTGCATCAAAAGATAGATGTAAAAGACACCAAGGAAGCCTTAGAC\n"
117 + ">gi|27804659|gb|AY178931.1|/1-261\n"
118 + "-TGGGAAAAAATTCGGTTACGGCCAGGAGGAAAGAAAAGATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
119 + "GGAGCTAGAACGATTYGCAGTTAATCCTGGCCTTTTAGAAACAGCAGAAGGCTGTAGACAAATACTGGGACA\n"
120 + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
121 + "TGTACATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAA\n";
125 * Corner case for this test is the presence of codons after codons that were
128 * @throws IOException
130 @Test(groups = { "Functional" })
131 public void testTranslateCdna_withUntranslatableCodons()
134 AlignmentI alf = new FormatAdapter().readFile(
135 JAL_1312_example_align_fasta, DataSourceType.PASTE,
137 HiddenColumns cs = new HiddenColumns();
138 AlignViewportI av = new AlignViewport(alf, cs);
139 Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth());
140 Dna dna = new Dna(av, contigs);
141 AlignmentI translated = dna.translateCdna();
142 assertNotNull("Couldn't do a full width translation of test data.",
147 * Test variant in which 15 column blocks at a time are translated (the rest
150 * @throws IOException
152 @Test(groups = { "Functional" })
153 public void testTranslateCdna_withUntranslatableCodonsAndHiddenColumns()
156 AlignmentI alf = new FormatAdapter().readFile(
157 JAL_1312_example_align_fasta, DataSourceType.PASTE,
160 for (int ipos = 0; ipos + vwidth < alf.getWidth(); ipos += vwidth)
162 HiddenColumns cs = new HiddenColumns();
165 cs.hideColumns(0, ipos - 1);
167 cs.hideColumns(ipos + vwidth, alf.getWidth());
168 Iterator<int[]> vcontigs = cs.getVisContigsIterator(0,
170 AlignViewportI av = new AlignViewport(alf, cs);
171 Dna dna = new Dna(av, vcontigs);
172 AlignmentI transAlf = dna.translateCdna();
174 assertTrue("Translation failed (ipos=" + ipos
175 + ") No alignment data.", transAlf != null);
176 assertTrue("Translation failed (ipos=" + ipos + ") Empty alignment.",
177 transAlf.getHeight() > 0);
178 assertTrue("Translation failed (ipos=" + ipos + ") Translated "
179 + transAlf.getHeight() + " sequences from " + alf.getHeight()
180 + " sequences", alf.getHeight() == transAlf.getHeight());
185 * Test simple translation to Amino Acids (with STOP codons translated to *).
187 * @throws IOException
189 @Test(groups = { "Functional" })
190 public void testTranslateCdna_simple() throws IOException
192 AlignmentI alf = new FormatAdapter().readFile(fasta,
193 DataSourceType.PASTE, FileFormat.Fasta);
194 HiddenColumns cs = new HiddenColumns();
195 AlignViewportI av = new AlignViewport(alf, cs);
196 Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth());
197 Dna dna = new Dna(av, contigs);
198 AlignmentI translated = dna.translateCdna();
199 String aa = translated.getSequenceAt(0).getSequenceAsString();
201 "AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYY***",
206 * Test translation excluding hidden columns.
208 * @throws IOException
210 @Test(groups = { "Functional" })
211 public void testTranslateCdna_hiddenColumns() throws IOException
213 AlignmentI alf = new FormatAdapter().readFile(fasta,
214 DataSourceType.PASTE, FileFormat.Fasta);
215 HiddenColumns cs = new HiddenColumns();
216 cs.hideColumns(6, 14); // hide codons 3/4/5
217 cs.hideColumns(24, 35); // hide codons 9-12
218 cs.hideColumns(177, 191); // hide codons 60-64
219 AlignViewportI av = new AlignViewport(alf, cs);
220 Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth());
221 Dna dna = new Dna(av, contigs);
222 AlignmentI translated = dna.translateCdna();
223 String aa = translated.getSequenceAt(0).getSequenceAsString();
224 assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa);
228 * Use this test to help debug into any cases of interest.
230 @Test(groups = { "Functional" })
231 public void testCompareCodonPos_oneOnly()
233 assertFollows("-AA--A", "G--GG"); // 2 shifted seq2, 3 shifted seq1
237 * Tests for method that compares 'alignment' of two codon position triplets.
239 @Test(groups = { "Functional" })
240 public void testCompareCodonPos()
243 * Returns 0 for any null argument
245 assertEquals(0, Dna.compareCodonPos(new AlignedCodon(1, 2, 3), null));
246 assertEquals(0, Dna.compareCodonPos(null, new AlignedCodon(1, 2, 3)));
249 * Work through 27 combinations. First 9 cases where first position matches.
251 assertMatches("AAA", "GGG"); // 2 and 3 match
252 assertFollows("AA-A", "GGG"); // 2 matches, 3 shifted seq1
253 assertPrecedes("AAA", "GG-G"); // 2 matches, 3 shifted seq2
254 assertFollows("A-AA", "GG-G"); // 2 shifted seq1, 3 matches
255 assertFollows("A-A-A", "GG-G"); // 2 shifted seq1, 3 shifted seq1
256 assertPrecedes("A-AA", "GG--G"); // 2 shifted seq1, 3 shifted seq2
257 assertPrecedes("AA-A", "G-GG"); // 2 shifted seq2, 3 matches
258 assertFollows("AA--A", "G-GG"); // 2 shifted seq2, 3 shifted seq1
259 assertPrecedes("AAA", "G-GG"); // 2 shifted seq2, 3 shifted seq2
262 * 9 cases where first position is shifted in first sequence.
264 assertFollows("-AAA", "G-GG"); // 2 and 3 match
265 assertFollows("-AA-A", "G-GG"); // 2 matches, 3 shifted seq1
266 // 'enclosing' case: pick first to start precedes
267 assertFollows("-AAA", "G-G-G"); // 2 matches, 3 shifted seq2
268 assertFollows("-A-AA", "G-G-G"); // 2 shifted seq1, 3 matches
269 assertFollows("-A-A-A", "G-G-G"); // 2 shifted seq1, 3 shifted seq1
270 // 'enclosing' case: pick first to start precedes
271 assertFollows("-A-AA", "G-G--G"); // 2 shifted seq1, 3 shifted seq2
272 assertFollows("-AA-A", "G--GG"); // 2 shifted seq2, 3 matches
273 assertFollows("-AA--A", "G--GG"); // 2 shifted seq2, 3 shifted seq1
274 assertPrecedes("-AAA", "G--GG"); // 2 shifted seq2, 3 shifted seq2
277 * 9 cases where first position is shifted in second sequence.
279 assertPrecedes("A-AA", "-GGG"); // 2 and 3 match
280 assertPrecedes("A-A-A", "-GGG"); // 2 matches, 3 shifted seq1
281 assertPrecedes("A-AA", "-GG-G"); // 2 matches, 3 shifted seq2
282 assertPrecedes("A--AA", "-GG-G"); // 2 shifted seq1, 3 matches
283 // 'enclosing' case with middle base deciding:
284 assertFollows("A--AA", "-GGG"); // 2 shifted seq1, 3 shifted seq1
285 assertPrecedes("A--AA", "-GG--G"); // 2 shifted seq1, 3 shifted seq2
286 assertPrecedes("AA-A", "-GGG"); // 2 shifted seq2, 3 matches
287 assertPrecedes("AA--A", "-GGG"); // 2 shifted seq2, 3 shifted seq1
288 assertPrecedes("AAA", "-GGG"); // 2 shifted seq2, 3 shifted seq2
292 * This test generates a random cDNA alignment and its translation, then
293 * reorders the cDNA and retranslates, and verifies that the translations are
294 * the same (apart from ordering).
296 @Test(groups = { "Functional" })
297 public void testTranslateCdna_sequenceOrderIndependent()
300 * Generate cDNA - 8 sequences of 12 bases each.
302 AlignmentI cdna = new AlignmentGenerator(true)
303 .generate(12, 8, 97, 5, 5);
304 HiddenColumns cs = new HiddenColumns();
305 AlignViewportI av = new AlignViewport(cdna, cs);
306 Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth());
307 Dna dna = new Dna(av, contigs);
308 AlignmentI translated = dna.translateCdna();
311 * Jumble the cDNA sequences and translate.
313 SequenceI[] sorted = new SequenceI[cdna.getHeight()];
314 final int[] jumbler = new int[] { 6, 7, 3, 4, 2, 0, 1, 5 };
316 for (int i : jumbler)
318 sorted[seqNo++] = cdna.getSequenceAt(i);
320 AlignmentI cdnaReordered = new Alignment(sorted);
321 av = new AlignViewport(cdnaReordered, cs);
322 contigs = cs.getVisContigsIterator(0, cdna.getWidth());
323 dna = new Dna(av, contigs);
324 AlignmentI translated2 = dna.translateCdna();
327 * Check translated sequences are the same in both alignments.
329 System.out.println("Original");
330 System.out.println(translated.toString());
331 System.out.println("Sorted");
332 System.out.println(translated2.toString());
334 int sortedSequenceIndex = 0;
335 for (int originalSequenceIndex : jumbler)
337 final String translation1 = translated.getSequenceAt(
338 originalSequenceIndex).getSequenceAsString();
339 final String translation2 = translated2.getSequenceAt(
340 sortedSequenceIndex).getSequenceAsString();
341 assertEquals(translation2, translation1);
342 sortedSequenceIndex++;
347 * Test that all the cases in testCompareCodonPos have a 'symmetric'
348 * comparison (without checking the actual comparison result).
350 @Test(groups = { "Functional" })
351 public void testCompareCodonPos_isSymmetric()
353 assertSymmetric("AAA", "GGG");
354 assertSymmetric("AA-A", "GGG");
355 assertSymmetric("AAA", "GG-G");
356 assertSymmetric("A-AA", "GG-G");
357 assertSymmetric("A-A-A", "GG-G");
358 assertSymmetric("A-AA", "GG--G");
359 assertSymmetric("AA-A", "G-GG");
360 assertSymmetric("AA--A", "G-GG");
361 assertSymmetric("AAA", "G-GG");
362 assertSymmetric("-AAA", "G-GG");
363 assertSymmetric("-AA-A", "G-GG");
364 assertSymmetric("-AAA", "G-G-G");
365 assertSymmetric("-A-AA", "G-G-G");
366 assertSymmetric("-A-A-A", "G-G-G");
367 assertSymmetric("-A-AA", "G-G--G");
368 assertSymmetric("-AA-A", "G--GG");
369 assertSymmetric("-AA--A", "G--GG");
370 assertSymmetric("-AAA", "G--GG");
371 assertSymmetric("A-AA", "-GGG");
372 assertSymmetric("A-A-A", "-GGG");
373 assertSymmetric("A-AA", "-GG-G");
374 assertSymmetric("A--AA", "-GG-G");
375 assertSymmetric("A--AA", "-GGG");
376 assertSymmetric("A--AA", "-GG--G");
377 assertSymmetric("AA-A", "-GGG");
378 assertSymmetric("AA--A", "-GGG");
379 assertSymmetric("AAA", "-GGG");
382 private void assertSymmetric(String codon1, String codon2)
384 assertEquals("Comparison of '" + codon1 + "' and '" + codon2
385 + " not symmetric", Integer.signum(compare(codon1, codon2)),
386 -Integer.signum(compare(codon2, codon1)));
390 * Assert that the first sequence should map to the same position as the
391 * second in a translated alignment. Also checks that this is true if the
392 * order of the codons is reversed.
397 private void assertMatches(String codon1, String codon2)
399 assertEquals("Expected '" + codon1 + "' matches '" + codon2 + "'", 0,
400 compare(codon1, codon2));
401 assertEquals("Expected '" + codon2 + "' matches '" + codon1 + "'", 0,
402 compare(codon2, codon1));
406 * Assert that the first sequence should precede the second in a translated
412 private void assertPrecedes(String codon1, String codon2)
414 assertEquals("Expected '" + codon1 + "' precedes '" + codon2 + "'",
415 -1, compare(codon1, codon2));
419 * Assert that the first sequence should follow the second in a translated
425 private void assertFollows(String codon1, String codon2)
427 assertEquals("Expected '" + codon1 + "' follows '" + codon2 + "'", 1,
428 compare(codon1, codon2));
432 * Convert two nucleotide strings to base positions and pass to
433 * Dna.compareCodonPos, return the result.
439 private int compare(String s1, String s2)
441 final AlignedCodon cd1 = convertCodon(s1);
442 final AlignedCodon cd2 = convertCodon(s2);
443 System.out.println("K: " + s1 + " " + cd1.toString());
444 System.out.println("G: " + s2 + " " + cd2.toString());
445 System.out.println();
446 return Dna.compareCodonPos(cd1, cd2);
450 * Convert a string e.g. "-GC-T" to base positions e.g. [1, 2, 4]. The string
451 * should have exactly 3 non-gap characters, and use '-' for gaps.
456 private AlignedCodon convertCodon(String s)
458 int[] codon = new int[3];
460 for (int j = 0; j < s.length(); j++)
462 if (s.charAt(j) != '-')
467 return new AlignedCodon(codon[0], codon[1], codon[2]);
471 * Weirdly, maybe worth a test to prove the helper method of this test class.
473 @Test(groups = { "Functional" })
474 public void testConvertCodon()
476 assertEquals("[0, 1, 2]", convertCodon("AAA").toString());
477 assertEquals("[0, 2, 5]", convertCodon("A-A--A").toString());
478 assertEquals("[1, 3, 4]", convertCodon("-A-AA-").toString());
482 * Test dna complementing
484 @Test(groups = "Functional")
485 public void testGetComplement()
487 assertEquals('t', Dna.getComplement('a'));
488 assertEquals('T', Dna.getComplement('A'));
489 assertEquals('a', Dna.getComplement('t'));
490 assertEquals('A', Dna.getComplement('T'));
491 assertEquals('c', Dna.getComplement('g'));
492 assertEquals('C', Dna.getComplement('G'));
493 assertEquals('g', Dna.getComplement('c'));
494 assertEquals('G', Dna.getComplement('C'));
495 // note uU --> aA but not vice versa
496 assertEquals('a', Dna.getComplement('u'));
497 assertEquals('A', Dna.getComplement('U'));
498 // ambiguity codes, see http://www.bioinformatics.org/sms/iupac.html
499 assertEquals('r', Dna.getComplement('y'));
500 assertEquals('R', Dna.getComplement('Y'));
501 assertEquals('y', Dna.getComplement('r'));
502 assertEquals('Y', Dna.getComplement('R'));
503 assertEquals('k', Dna.getComplement('m'));
504 assertEquals('K', Dna.getComplement('M'));
505 assertEquals('m', Dna.getComplement('k'));
506 assertEquals('M', Dna.getComplement('K'));
507 assertEquals('b', Dna.getComplement('v'));
508 assertEquals('B', Dna.getComplement('V'));
509 assertEquals('v', Dna.getComplement('b'));
510 assertEquals('V', Dna.getComplement('B'));
511 assertEquals('d', Dna.getComplement('h'));
512 assertEquals('D', Dna.getComplement('H'));
513 assertEquals('h', Dna.getComplement('d'));
514 assertEquals('H', Dna.getComplement('D'));
515 assertEquals('Q', Dna.getComplement('Q'));
518 @Test(groups = "Functional")
519 public void testReverseSequence()
521 String seq = "-Ac-GtU--rYkMbVdHNX-";
522 String seqRev = new StringBuilder(seq).reverse().toString();
525 SequenceI reversed = Dna.reverseSequence("Seq1", seq, false);
526 assertEquals(1, reversed.getStart());
527 assertEquals(15, reversed.getEnd());
528 assertEquals(20, reversed.getLength());
529 assertEquals(seqRev, reversed.getSequenceAsString());
530 assertEquals("Seq1|rev", reversed.getName());
532 // reverse complement:
533 SequenceI revcomp = Dna.reverseSequence("Seq1", seq, true);
534 assertEquals("-XNDhBvKmRy--AaC-gT-", revcomp.getSequenceAsString());
535 assertEquals("Seq1|revcomp", revcomp.getName());
538 @Test(groups = "Functional")
539 public void testReverseCdna()
541 String seq = "-Ac-GtU--rYkMbVdHNX-";
542 String seqRev = new StringBuilder(seq).reverse().toString();
543 String seqDs = seq.replaceAll("-", "");
544 String seqDsRev = new StringBuilder(seqDs).reverse().toString();
546 SequenceI dna = new Sequence("Seq1", seq);
547 Alignment al = new Alignment(new SequenceI[] { dna });
548 al.createDatasetAlignment();
549 assertEquals(seqDs, al.getSequenceAt(0).getDatasetSequence()
550 .getSequenceAsString());
552 HiddenColumns cs = new HiddenColumns();
553 AlignViewportI av = new AlignViewport(al, cs);
554 Iterator<int[]> contigs = cs.getVisContigsIterator(0, al.getWidth());
555 Dna testee = new Dna(av, contigs);
556 AlignmentI reversed = testee.reverseCdna(false);
557 assertEquals(1, reversed.getHeight());
558 assertEquals(seqRev, reversed.getSequenceAt(0).getSequenceAsString());
559 assertEquals(seqDsRev, reversed.getSequenceAt(0).getDatasetSequence()
560 .getSequenceAsString());