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.gui.JvOptionPane;
36 import jalview.io.FormatAdapter;
38 import java.io.IOException;
40 import org.testng.annotations.BeforeClass;
41 import org.testng.annotations.Test;
45 @BeforeClass(alwaysRun = true)
46 public void setUpJvOptionPane()
48 JvOptionPane.setInteractiveMode(false);
49 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
53 // AA encoding codons as ordered on the Jalview help page Amino Acid Table
54 private static String fasta = ">B\n" + "GCT" + "GCC" + "GCA" + "GCG"
55 + "TGT" + "TGC" + "GAT" + "GAC" + "GAA" + "GAG" + "TTT" + "TTC"
56 + "GGT" + "GGC" + "GGA" + "GGG" + "CAT" + "CAC" + "ATT" + "ATC"
57 + "ATA" + "AAA" + "AAG" + "TTG" + "TTA" + "CTT" + "CTC" + "CTA"
58 + "CTG" + "ATG" + "AAT" + "AAC" + "CCT" + "CCC" + "CCA" + "CCG"
59 + "CAA" + "CAG" + "CGT" + "CGC" + "CGA" + "CGG" + "AGA" + "AGG"
60 + "TCT" + "TCC" + "TCA" + "TCG" + "AGT" + "AGC" + "ACT" + "ACC"
61 + "ACA" + "ACG" + "GTT" + "GTC" + "GTA" + "GTG" + "TGG" + "TAT"
62 + "TAC" + "TAA" + "TAG" + "TGA";
64 private static String JAL_1312_example_align_fasta = ">B.FR.83.HXB2_LAI_IIIB_BRU_K03455/45-306\n"
65 + "ATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
66 + "GGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACA\n"
67 + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTG\n"
68 + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAC\n"
69 + ">gi|27804621|gb|AY178912.1|/1-259\n"
70 + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
71 + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGGACA\n"
72 + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
73 + "TGTTCATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAT\n"
74 + ">gi|27804623|gb|AY178913.1|/1-259\n"
75 + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
76 + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGAACA\n"
77 + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
78 + "TGTTCATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
79 + ">gi|27804627|gb|AY178915.1|/1-260\n"
80 + "-TGGGAAAA-ATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
81 + "GGAGCTAGAACGATTCGCAGTTAACCCTGGCCTGTTAGAAACATCAGAAGGTTGTAGACAAATATTGGGACA\n"
82 + "GCTACAACCATCCCTTGAGACAGGATCAGAAGAACTTAAATCATTATWTAATACCATAGCAGTCCTCTATTG\n"
83 + "TGTACATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAG\n"
84 + ">gi|27804631|gb|AY178917.1|/1-261\n"
85 + "-TGGGAAAAAATTCGGTTGAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
86 + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACACCAGAAGGCTGTAGACAAATACTGGGACA\n"
87 + "GCTACAACCGTCCCTTCAGACAGGATCGGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
88 + "TGTGCATCAAAGGATAGATGTAAAAGACACCAAGGAGGCTTTAGAC\n"
89 + ">gi|27804635|gb|AY178919.1|/1-261\n"
90 + "-TGGGAGAGAATTCGGTTACGGCCAGGAGGAAAGAAAAAATATAAATTGAAACATATAGTATGGGCAGGCAG\n"
91 + "AGAGCTAGATCGATTCGCAGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAGATATTGGGACA\n"
92 + "GCTACAACCGTCCCTTAAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
93 + "TGTACATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
94 + ">gi|27804641|gb|AY178922.1|/1-261\n"
95 + "-TGGGAGAAAATTCGGTTACGGCCAGGGGGAAAGAAAAGATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
96 + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAAATACTGGGACA\n"
97 + "GTTACACCCATCCCTTCATACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
98 + "TGTGCATCAAAGGATAGAAGTAAAAGACACCAAGGAAGCTTTAGAC\n"
99 + ">gi|27804647|gb|AY178925.1|/1-261\n"
100 + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATCAATTAAAACATGTAGTATGGGCAAGCAG\n"
101 + "GGAACTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
102 + "GCTACAACCATCCCTTCAGACAGGATCAGAGGAACTTAAATCATTATTTAATACAGTAGCAGTCCTCTATTG\n"
103 + "TGTACATCAAAGAATAGATGTAAAAGACACCAAGGAAGCTCTAGAA\n"
104 + ">gi|27804649|gb|AY178926.1|/1-261\n"
105 + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
106 + "GGAGCTAGAACGATTCGCGGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAACTACTGGGACA\n"
107 + "GTTACAACCATCCCTTCAGACAGGATCAGAAGAACTCAAATCATTATATAATACAATAGCAACCCTCTATTG\n"
108 + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCCTTAGAT\n"
109 + ">gi|27804653|gb|AY178928.1|/1-261\n"
110 + "-TGGGAAAGAATTCGGTTAAGGCCAGGGGGAAAGAAACAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
111 + "GGAGCTAGACCGATTCGCACTTAACCCCGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
112 + "GCTACAATCGTCCCTTCAGACAGGATCAGAAGAACTTAGATCACTATATAATACAGTAGCAGTCCTCTATTG\n"
113 + "TGTGCATCAAAAGATAGATGTAAAAGACACCAAGGAAGCCTTAGAC\n"
114 + ">gi|27804659|gb|AY178931.1|/1-261\n"
115 + "-TGGGAAAAAATTCGGTTACGGCCAGGAGGAAAGAAAAGATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
116 + "GGAGCTAGAACGATTYGCAGTTAATCCTGGCCTTTTAGAAACAGCAGAAGGCTGTAGACAAATACTGGGACA\n"
117 + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
118 + "TGTACATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAA\n";
122 * Corner case for this test is the presence of codons after codons that were
125 * @throws IOException
127 @Test(groups = { "Functional" })
128 public void testTranslateCdna_withUntranslatableCodons()
131 AlignmentI alf = new FormatAdapter().readFile(
132 JAL_1312_example_align_fasta, jalview.io.FormatAdapter.PASTE,
134 ColumnSelection cs = new ColumnSelection();
135 AlignViewportI av = new AlignViewport(alf, cs);
136 Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
137 AlignmentI translated = dna.translateCdna();
138 assertNotNull("Couldn't do a full width translation of test data.",
143 * Test variant in which 15 column blocks at a time are translated (the rest
146 * @throws IOException
148 @Test(groups = { "Functional" })
149 public void testTranslateCdna_withUntranslatableCodonsAndHiddenColumns()
152 AlignmentI alf = new FormatAdapter().readFile(
153 JAL_1312_example_align_fasta, jalview.io.FormatAdapter.PASTE,
156 for (int ipos = 0; ipos + vwidth < alf.getWidth(); ipos += vwidth)
158 ColumnSelection cs = new ColumnSelection();
161 cs.hideColumns(0, ipos - 1);
163 cs.hideColumns(ipos + vwidth, alf.getWidth());
164 int[] vcontigs = cs.getVisibleContigs(0, alf.getWidth());
165 AlignViewportI av = new AlignViewport(alf, cs);
166 Dna dna = new Dna(av, vcontigs);
167 AlignmentI transAlf = dna.translateCdna();
169 assertTrue("Translation failed (ipos=" + ipos
170 + ") No alignment data.", transAlf != null);
171 assertTrue("Translation failed (ipos=" + ipos + ") Empty alignment.",
172 transAlf.getHeight() > 0);
173 assertTrue("Translation failed (ipos=" + ipos + ") Translated "
174 + transAlf.getHeight() + " sequences from " + alf.getHeight()
175 + " sequences", alf.getHeight() == transAlf.getHeight());
180 * Test simple translation to Amino Acids (with STOP codons translated to *).
182 * @throws IOException
184 @Test(groups = { "Functional" })
185 public void testTranslateCdna_simple() throws IOException
187 AlignmentI alf = new FormatAdapter().readFile(fasta,
188 FormatAdapter.PASTE, "FASTA");
189 ColumnSelection cs = new ColumnSelection();
190 AlignViewportI av = new AlignViewport(alf, cs);
191 Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
192 AlignmentI translated = dna.translateCdna();
193 String aa = translated.getSequenceAt(0).getSequenceAsString();
195 "AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYY***",
200 * Test translation excluding hidden columns.
202 * @throws IOException
204 @Test(groups = { "Functional" })
205 public void testTranslateCdna_hiddenColumns() throws IOException
207 AlignmentI alf = new FormatAdapter().readFile(fasta,
208 FormatAdapter.PASTE, "FASTA");
209 ColumnSelection cs = new jalview.datamodel.ColumnSelection();
210 cs.hideColumns(6, 14); // hide codons 3/4/5
211 cs.hideColumns(24, 35); // hide codons 9-12
212 cs.hideColumns(177, 191); // hide codons 60-64
213 AlignViewportI av = new AlignViewport(alf, cs);
214 Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
215 AlignmentI translated = dna.translateCdna();
216 String aa = translated.getSequenceAt(0).getSequenceAsString();
217 assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa);
221 * Use this test to help debug into any cases of interest.
223 @Test(groups = { "Functional" })
224 public void testCompareCodonPos_oneOnly()
226 assertFollows("-AA--A", "G--GG"); // 2 shifted seq2, 3 shifted seq1
230 * Tests for method that compares 'alignment' of two codon position triplets.
232 @Test(groups = { "Functional" })
233 public void testCompareCodonPos()
236 * Returns 0 for any null argument
238 assertEquals(0, Dna.compareCodonPos(new AlignedCodon(1, 2, 3), null));
239 assertEquals(0, Dna.compareCodonPos(null, new AlignedCodon(1, 2, 3)));
242 * Work through 27 combinations. First 9 cases where first position matches.
244 assertMatches("AAA", "GGG"); // 2 and 3 match
245 assertFollows("AA-A", "GGG"); // 2 matches, 3 shifted seq1
246 assertPrecedes("AAA", "GG-G"); // 2 matches, 3 shifted seq2
247 assertFollows("A-AA", "GG-G"); // 2 shifted seq1, 3 matches
248 assertFollows("A-A-A", "GG-G"); // 2 shifted seq1, 3 shifted seq1
249 assertPrecedes("A-AA", "GG--G"); // 2 shifted seq1, 3 shifted seq2
250 assertPrecedes("AA-A", "G-GG"); // 2 shifted seq2, 3 matches
251 assertFollows("AA--A", "G-GG"); // 2 shifted seq2, 3 shifted seq1
252 assertPrecedes("AAA", "G-GG"); // 2 shifted seq2, 3 shifted seq2
255 * 9 cases where first position is shifted in first sequence.
257 assertFollows("-AAA", "G-GG"); // 2 and 3 match
258 assertFollows("-AA-A", "G-GG"); // 2 matches, 3 shifted seq1
259 // 'enclosing' case: pick first to start precedes
260 assertFollows("-AAA", "G-G-G"); // 2 matches, 3 shifted seq2
261 assertFollows("-A-AA", "G-G-G"); // 2 shifted seq1, 3 matches
262 assertFollows("-A-A-A", "G-G-G"); // 2 shifted seq1, 3 shifted seq1
263 // 'enclosing' case: pick first to start precedes
264 assertFollows("-A-AA", "G-G--G"); // 2 shifted seq1, 3 shifted seq2
265 assertFollows("-AA-A", "G--GG"); // 2 shifted seq2, 3 matches
266 assertFollows("-AA--A", "G--GG"); // 2 shifted seq2, 3 shifted seq1
267 assertPrecedes("-AAA", "G--GG"); // 2 shifted seq2, 3 shifted seq2
270 * 9 cases where first position is shifted in second sequence.
272 assertPrecedes("A-AA", "-GGG"); // 2 and 3 match
273 assertPrecedes("A-A-A", "-GGG"); // 2 matches, 3 shifted seq1
274 assertPrecedes("A-AA", "-GG-G"); // 2 matches, 3 shifted seq2
275 assertPrecedes("A--AA", "-GG-G"); // 2 shifted seq1, 3 matches
276 // 'enclosing' case with middle base deciding:
277 assertFollows("A--AA", "-GGG"); // 2 shifted seq1, 3 shifted seq1
278 assertPrecedes("A--AA", "-GG--G"); // 2 shifted seq1, 3 shifted seq2
279 assertPrecedes("AA-A", "-GGG"); // 2 shifted seq2, 3 matches
280 assertPrecedes("AA--A", "-GGG"); // 2 shifted seq2, 3 shifted seq1
281 assertPrecedes("AAA", "-GGG"); // 2 shifted seq2, 3 shifted seq2
285 * This test generates a random cDNA alignment and its translation, then
286 * reorders the cDNA and retranslates, and verifies that the translations are
287 * the same (apart from ordering).
289 @Test(groups = { "Functional" })
290 public void testTranslateCdna_sequenceOrderIndependent()
293 * Generate cDNA - 8 sequences of 12 bases each.
295 AlignmentI cdna = new DnaAlignmentGenerator().generate(12, 8, 97, 5, 5);
296 ColumnSelection cs = new ColumnSelection();
297 AlignViewportI av = new AlignViewport(cdna, cs);
298 Dna dna = new Dna(av, new int[] { 0, cdna.getWidth() - 1 });
299 AlignmentI translated = dna.translateCdna();
302 * Jumble the cDNA sequences and translate.
304 SequenceI[] sorted = new SequenceI[cdna.getHeight()];
305 final int[] jumbler = new int[] { 6, 7, 3, 4, 2, 0, 1, 5 };
307 for (int i : jumbler)
309 sorted[seqNo++] = cdna.getSequenceAt(i);
311 AlignmentI cdnaReordered = new Alignment(sorted);
312 av = new AlignViewport(cdnaReordered, cs);
313 dna = new Dna(av, new int[] { 0, cdna.getWidth() - 1 });
314 AlignmentI translated2 = dna.translateCdna();
317 * Check translated sequences are the same in both alignments.
319 System.out.println("Original");
320 System.out.println(translated.toString());
321 System.out.println("Sorted");
322 System.out.println(translated2.toString());
324 int sortedSequenceIndex = 0;
325 for (int originalSequenceIndex : jumbler)
327 final String translation1 = translated.getSequenceAt(
328 originalSequenceIndex).getSequenceAsString();
329 final String translation2 = translated2.getSequenceAt(
330 sortedSequenceIndex).getSequenceAsString();
331 assertEquals(translation2, translation1);
332 sortedSequenceIndex++;
337 * Test that all the cases in testCompareCodonPos have a 'symmetric'
338 * comparison (without checking the actual comparison result).
340 @Test(groups = { "Functional" })
341 public void testCompareCodonPos_isSymmetric()
343 assertSymmetric("AAA", "GGG");
344 assertSymmetric("AA-A", "GGG");
345 assertSymmetric("AAA", "GG-G");
346 assertSymmetric("A-AA", "GG-G");
347 assertSymmetric("A-A-A", "GG-G");
348 assertSymmetric("A-AA", "GG--G");
349 assertSymmetric("AA-A", "G-GG");
350 assertSymmetric("AA--A", "G-GG");
351 assertSymmetric("AAA", "G-GG");
352 assertSymmetric("-AAA", "G-GG");
353 assertSymmetric("-AA-A", "G-GG");
354 assertSymmetric("-AAA", "G-G-G");
355 assertSymmetric("-A-AA", "G-G-G");
356 assertSymmetric("-A-A-A", "G-G-G");
357 assertSymmetric("-A-AA", "G-G--G");
358 assertSymmetric("-AA-A", "G--GG");
359 assertSymmetric("-AA--A", "G--GG");
360 assertSymmetric("-AAA", "G--GG");
361 assertSymmetric("A-AA", "-GGG");
362 assertSymmetric("A-A-A", "-GGG");
363 assertSymmetric("A-AA", "-GG-G");
364 assertSymmetric("A--AA", "-GG-G");
365 assertSymmetric("A--AA", "-GGG");
366 assertSymmetric("A--AA", "-GG--G");
367 assertSymmetric("AA-A", "-GGG");
368 assertSymmetric("AA--A", "-GGG");
369 assertSymmetric("AAA", "-GGG");
372 private void assertSymmetric(String codon1, String codon2)
374 assertEquals("Comparison of '" + codon1 + "' and '" + codon2
375 + " not symmetric", Integer.signum(compare(codon1, codon2)),
376 -Integer.signum(compare(codon2, codon1)));
380 * Assert that the first sequence should map to the same position as the
381 * second in a translated alignment. Also checks that this is true if the
382 * order of the codons is reversed.
387 private void assertMatches(String codon1, String codon2)
389 assertEquals("Expected '" + codon1 + "' matches '" + codon2 + "'", 0,
390 compare(codon1, codon2));
391 assertEquals("Expected '" + codon2 + "' matches '" + codon1 + "'", 0,
392 compare(codon2, codon1));
396 * Assert that the first sequence should precede the second in a translated
402 private void assertPrecedes(String codon1, String codon2)
404 assertEquals("Expected '" + codon1 + "' precedes '" + codon2 + "'",
405 -1, compare(codon1, codon2));
409 * Assert that the first sequence should follow the second in a translated
415 private void assertFollows(String codon1, String codon2)
417 assertEquals("Expected '" + codon1 + "' follows '" + codon2 + "'", 1,
418 compare(codon1, codon2));
422 * Convert two nucleotide strings to base positions and pass to
423 * Dna.compareCodonPos, return the result.
429 private int compare(String s1, String s2)
431 final AlignedCodon cd1 = convertCodon(s1);
432 final AlignedCodon cd2 = convertCodon(s2);
433 System.out.println("K: " + s1 + " " + cd1.toString());
434 System.out.println("G: " + s2 + " " + cd2.toString());
435 System.out.println();
436 return Dna.compareCodonPos(cd1, cd2);
440 * Convert a string e.g. "-GC-T" to base positions e.g. [1, 2, 4]. The string
441 * should have exactly 3 non-gap characters, and use '-' for gaps.
446 private AlignedCodon convertCodon(String s)
448 int[] codon = new int[3];
450 for (int j = 0; j < s.length(); j++)
452 if (s.charAt(j) != '-')
457 return new AlignedCodon(codon[0], codon[1], codon[2]);
461 * Weirdly, maybe worth a test to prove the helper method of this test class.
463 @Test(groups = { "Functional" })
464 public void testConvertCodon()
466 assertEquals("[0, 1, 2]", convertCodon("AAA").toString());
467 assertEquals("[0, 2, 5]", convertCodon("A-A--A").toString());
468 assertEquals("[1, 3, 4]", convertCodon("-A-AA-").toString());
472 * Test dna complementing
474 @Test(groups = "Functional")
475 public void testGetComplement()
477 assertEquals('t', Dna.getComplement('a'));
478 assertEquals('T', Dna.getComplement('A'));
479 assertEquals('a', Dna.getComplement('t'));
480 assertEquals('A', Dna.getComplement('T'));
481 assertEquals('c', Dna.getComplement('g'));
482 assertEquals('C', Dna.getComplement('G'));
483 assertEquals('g', Dna.getComplement('c'));
484 assertEquals('G', Dna.getComplement('C'));
485 // note uU --> aA but not vice versa
486 assertEquals('a', Dna.getComplement('u'));
487 assertEquals('A', Dna.getComplement('U'));
488 // ambiguity codes, see http://www.bioinformatics.org/sms/iupac.html
489 assertEquals('r', Dna.getComplement('y'));
490 assertEquals('R', Dna.getComplement('Y'));
491 assertEquals('y', Dna.getComplement('r'));
492 assertEquals('Y', Dna.getComplement('R'));
493 assertEquals('k', Dna.getComplement('m'));
494 assertEquals('K', Dna.getComplement('M'));
495 assertEquals('m', Dna.getComplement('k'));
496 assertEquals('M', Dna.getComplement('K'));
497 assertEquals('b', Dna.getComplement('v'));
498 assertEquals('B', Dna.getComplement('V'));
499 assertEquals('v', Dna.getComplement('b'));
500 assertEquals('V', Dna.getComplement('B'));
501 assertEquals('d', Dna.getComplement('h'));
502 assertEquals('D', Dna.getComplement('H'));
503 assertEquals('h', Dna.getComplement('d'));
504 assertEquals('H', Dna.getComplement('D'));
505 assertEquals('Q', Dna.getComplement('Q'));
508 @Test(groups = "Functional")
509 public void testReverseSequence()
511 String seq = "-Ac-GtU--rYkMbVdHNX-";
512 String seqRev = new StringBuilder(seq).reverse().toString();
515 SequenceI reversed = Dna.reverseSequence("Seq1", seq, false);
516 assertEquals(1, reversed.getStart());
517 assertEquals(15, reversed.getEnd());
518 assertEquals(20, reversed.getLength());
519 assertEquals(seqRev, reversed.getSequenceAsString());
520 assertEquals("Seq1|rev", reversed.getName());
522 // reverse complement:
523 SequenceI revcomp = Dna.reverseSequence("Seq1", seq, true);
524 assertEquals("-XNDhBvKmRy--AaC-gT-", revcomp.getSequenceAsString());
525 assertEquals("Seq1|revcomp", revcomp.getName());
528 @Test(groups = "Functional")
529 public void testReverseCdna()
531 String seq = "-Ac-GtU--rYkMbVdHNX-";
532 String seqRev = new StringBuilder(seq).reverse().toString();
533 String seqDs = seq.replaceAll("-", "");
534 String seqDsRev = new StringBuilder(seqDs).reverse().toString();
536 SequenceI dna = new Sequence("Seq1", seq);
537 Alignment al = new Alignment(new SequenceI[] { dna });
538 al.createDatasetAlignment();
539 assertEquals(seqDs, al.getSequenceAt(0).getDatasetSequence()
540 .getSequenceAsString());
542 ColumnSelection cs = new ColumnSelection();
543 AlignViewportI av = new AlignViewport(al, cs);
544 Dna testee = new Dna(av, new int[] { 0, al.getWidth() - 1 });
545 AlignmentI reversed = testee.reverseCdna(false);
546 assertEquals(1, reversed.getHeight());
547 assertEquals(seqRev, reversed.getSequenceAt(0).getSequenceAsString());
548 assertEquals(seqDsRev, reversed.getSequenceAt(0).getDatasetSequence()
549 .getSequenceAsString());