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;
42 import org.testng.annotations.BeforeClass;
43 import org.testng.annotations.Test;
47 @BeforeClass(alwaysRun = true)
48 public void setUpJvOptionPane()
50 JvOptionPane.setInteractiveMode(false);
51 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
55 // AA encoding codons as ordered on the Jalview help page Amino Acid Table
56 private static String fasta = ">B\n" + "GCT" + "GCC" + "GCA" + "GCG"
57 + "TGT" + "TGC" + "GAT" + "GAC" + "GAA" + "GAG" + "TTT" + "TTC"
58 + "GGT" + "GGC" + "GGA" + "GGG" + "CAT" + "CAC" + "ATT" + "ATC"
59 + "ATA" + "AAA" + "AAG" + "TTG" + "TTA" + "CTT" + "CTC" + "CTA"
60 + "CTG" + "ATG" + "AAT" + "AAC" + "CCT" + "CCC" + "CCA" + "CCG"
61 + "CAA" + "CAG" + "CGT" + "CGC" + "CGA" + "CGG" + "AGA" + "AGG"
62 + "TCT" + "TCC" + "TCA" + "TCG" + "AGT" + "AGC" + "ACT" + "ACC"
63 + "ACA" + "ACG" + "GTT" + "GTC" + "GTA" + "GTG" + "TGG" + "TAT"
64 + "TAC" + "TAA" + "TAG" + "TGA";
66 private static String JAL_1312_example_align_fasta = ">B.FR.83.HXB2_LAI_IIIB_BRU_K03455/45-306\n"
67 + "ATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
68 + "GGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACA\n"
69 + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTG\n"
70 + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAC\n"
71 + ">gi|27804621|gb|AY178912.1|/1-259\n"
72 + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
73 + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGGACA\n"
74 + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
75 + "TGTTCATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAT\n"
76 + ">gi|27804623|gb|AY178913.1|/1-259\n"
77 + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
78 + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGAACA\n"
79 + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
80 + "TGTTCATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
81 + ">gi|27804627|gb|AY178915.1|/1-260\n"
82 + "-TGGGAAAA-ATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
83 + "GGAGCTAGAACGATTCGCAGTTAACCCTGGCCTGTTAGAAACATCAGAAGGTTGTAGACAAATATTGGGACA\n"
84 + "GCTACAACCATCCCTTGAGACAGGATCAGAAGAACTTAAATCATTATWTAATACCATAGCAGTCCTCTATTG\n"
85 + "TGTACATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAG\n"
86 + ">gi|27804631|gb|AY178917.1|/1-261\n"
87 + "-TGGGAAAAAATTCGGTTGAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
88 + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACACCAGAAGGCTGTAGACAAATACTGGGACA\n"
89 + "GCTACAACCGTCCCTTCAGACAGGATCGGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
90 + "TGTGCATCAAAGGATAGATGTAAAAGACACCAAGGAGGCTTTAGAC\n"
91 + ">gi|27804635|gb|AY178919.1|/1-261\n"
92 + "-TGGGAGAGAATTCGGTTACGGCCAGGAGGAAAGAAAAAATATAAATTGAAACATATAGTATGGGCAGGCAG\n"
93 + "AGAGCTAGATCGATTCGCAGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAGATATTGGGACA\n"
94 + "GCTACAACCGTCCCTTAAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
95 + "TGTACATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
96 + ">gi|27804641|gb|AY178922.1|/1-261\n"
97 + "-TGGGAGAAAATTCGGTTACGGCCAGGGGGAAAGAAAAGATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
98 + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAAATACTGGGACA\n"
99 + "GTTACACCCATCCCTTCATACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
100 + "TGTGCATCAAAGGATAGAAGTAAAAGACACCAAGGAAGCTTTAGAC\n"
101 + ">gi|27804647|gb|AY178925.1|/1-261\n"
102 + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATCAATTAAAACATGTAGTATGGGCAAGCAG\n"
103 + "GGAACTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
104 + "GCTACAACCATCCCTTCAGACAGGATCAGAGGAACTTAAATCATTATTTAATACAGTAGCAGTCCTCTATTG\n"
105 + "TGTACATCAAAGAATAGATGTAAAAGACACCAAGGAAGCTCTAGAA\n"
106 + ">gi|27804649|gb|AY178926.1|/1-261\n"
107 + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
108 + "GGAGCTAGAACGATTCGCGGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAACTACTGGGACA\n"
109 + "GTTACAACCATCCCTTCAGACAGGATCAGAAGAACTCAAATCATTATATAATACAATAGCAACCCTCTATTG\n"
110 + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCCTTAGAT\n"
111 + ">gi|27804653|gb|AY178928.1|/1-261\n"
112 + "-TGGGAAAGAATTCGGTTAAGGCCAGGGGGAAAGAAACAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
113 + "GGAGCTAGACCGATTCGCACTTAACCCCGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
114 + "GCTACAATCGTCCCTTCAGACAGGATCAGAAGAACTTAGATCACTATATAATACAGTAGCAGTCCTCTATTG\n"
115 + "TGTGCATCAAAAGATAGATGTAAAAGACACCAAGGAAGCCTTAGAC\n"
116 + ">gi|27804659|gb|AY178931.1|/1-261\n"
117 + "-TGGGAAAAAATTCGGTTACGGCCAGGAGGAAAGAAAAGATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
118 + "GGAGCTAGAACGATTYGCAGTTAATCCTGGCCTTTTAGAAACAGCAGAAGGCTGTAGACAAATACTGGGACA\n"
119 + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
120 + "TGTACATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAA\n";
124 * Corner case for this test is the presence of codons after codons that were
127 * @throws IOException
129 @Test(groups = { "Functional" })
130 public void testTranslateCdna_withUntranslatableCodons()
133 AlignmentI alf = new FormatAdapter().readFile(
134 JAL_1312_example_align_fasta, DataSourceType.PASTE,
136 HiddenColumns cs = new HiddenColumns();
137 AlignViewportI av = new AlignViewport(alf, cs);
138 Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
139 AlignmentI translated = dna.translateCdna();
140 assertNotNull("Couldn't do a full width translation of test data.",
145 * Test variant in which 15 column blocks at a time are translated (the rest
148 * @throws IOException
150 @Test(groups = { "Functional" })
151 public void testTranslateCdna_withUntranslatableCodonsAndHiddenColumns()
154 AlignmentI alf = new FormatAdapter().readFile(
155 JAL_1312_example_align_fasta, DataSourceType.PASTE,
158 for (int ipos = 0; ipos + vwidth < alf.getWidth(); ipos += vwidth)
160 HiddenColumns cs = new HiddenColumns();
163 cs.hideColumns(0, ipos - 1);
165 cs.hideColumns(ipos + vwidth, alf.getWidth());
166 int[] vcontigs = cs.getVisibleContigs(0, alf.getWidth());
167 AlignViewportI av = new AlignViewport(alf, cs);
168 Dna dna = new Dna(av, vcontigs);
169 AlignmentI transAlf = dna.translateCdna();
171 assertTrue("Translation failed (ipos=" + ipos
172 + ") No alignment data.", transAlf != null);
173 assertTrue("Translation failed (ipos=" + ipos + ") Empty alignment.",
174 transAlf.getHeight() > 0);
175 assertTrue("Translation failed (ipos=" + ipos + ") Translated "
176 + transAlf.getHeight() + " sequences from " + alf.getHeight()
177 + " sequences", alf.getHeight() == transAlf.getHeight());
182 * Test simple translation to Amino Acids (with STOP codons translated to *).
184 * @throws IOException
186 @Test(groups = { "Functional" })
187 public void testTranslateCdna_simple() throws IOException
189 AlignmentI alf = new FormatAdapter().readFile(fasta,
190 DataSourceType.PASTE, FileFormat.Fasta);
191 HiddenColumns cs = new HiddenColumns();
192 AlignViewportI av = new AlignViewport(alf, cs);
193 Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
194 AlignmentI translated = dna.translateCdna();
195 String aa = translated.getSequenceAt(0).getSequenceAsString();
197 "AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYY***",
202 * Test translation excluding hidden columns.
204 * @throws IOException
206 @Test(groups = { "Functional" })
207 public void testTranslateCdna_hiddenColumns() throws IOException
209 AlignmentI alf = new FormatAdapter().readFile(fasta,
210 DataSourceType.PASTE, FileFormat.Fasta);
211 HiddenColumns cs = new HiddenColumns();
212 cs.hideColumns(6, 14); // hide codons 3/4/5
213 cs.hideColumns(24, 35); // hide codons 9-12
214 cs.hideColumns(177, 191); // hide codons 60-64
215 AlignViewportI av = new AlignViewport(alf, cs);
216 Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
217 AlignmentI translated = dna.translateCdna();
218 String aa = translated.getSequenceAt(0).getSequenceAsString();
219 assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa);
223 * Use this test to help debug into any cases of interest.
225 @Test(groups = { "Functional" })
226 public void testCompareCodonPos_oneOnly()
228 assertFollows("-AA--A", "G--GG"); // 2 shifted seq2, 3 shifted seq1
232 * Tests for method that compares 'alignment' of two codon position triplets.
234 @Test(groups = { "Functional" })
235 public void testCompareCodonPos()
238 * Returns 0 for any null argument
240 assertEquals(0, Dna.compareCodonPos(new AlignedCodon(1, 2, 3), null));
241 assertEquals(0, Dna.compareCodonPos(null, new AlignedCodon(1, 2, 3)));
244 * Work through 27 combinations. First 9 cases where first position matches.
246 assertMatches("AAA", "GGG"); // 2 and 3 match
247 assertFollows("AA-A", "GGG"); // 2 matches, 3 shifted seq1
248 assertPrecedes("AAA", "GG-G"); // 2 matches, 3 shifted seq2
249 assertFollows("A-AA", "GG-G"); // 2 shifted seq1, 3 matches
250 assertFollows("A-A-A", "GG-G"); // 2 shifted seq1, 3 shifted seq1
251 assertPrecedes("A-AA", "GG--G"); // 2 shifted seq1, 3 shifted seq2
252 assertPrecedes("AA-A", "G-GG"); // 2 shifted seq2, 3 matches
253 assertFollows("AA--A", "G-GG"); // 2 shifted seq2, 3 shifted seq1
254 assertPrecedes("AAA", "G-GG"); // 2 shifted seq2, 3 shifted seq2
257 * 9 cases where first position is shifted in first sequence.
259 assertFollows("-AAA", "G-GG"); // 2 and 3 match
260 assertFollows("-AA-A", "G-GG"); // 2 matches, 3 shifted seq1
261 // 'enclosing' case: pick first to start precedes
262 assertFollows("-AAA", "G-G-G"); // 2 matches, 3 shifted seq2
263 assertFollows("-A-AA", "G-G-G"); // 2 shifted seq1, 3 matches
264 assertFollows("-A-A-A", "G-G-G"); // 2 shifted seq1, 3 shifted seq1
265 // 'enclosing' case: pick first to start precedes
266 assertFollows("-A-AA", "G-G--G"); // 2 shifted seq1, 3 shifted seq2
267 assertFollows("-AA-A", "G--GG"); // 2 shifted seq2, 3 matches
268 assertFollows("-AA--A", "G--GG"); // 2 shifted seq2, 3 shifted seq1
269 assertPrecedes("-AAA", "G--GG"); // 2 shifted seq2, 3 shifted seq2
272 * 9 cases where first position is shifted in second sequence.
274 assertPrecedes("A-AA", "-GGG"); // 2 and 3 match
275 assertPrecedes("A-A-A", "-GGG"); // 2 matches, 3 shifted seq1
276 assertPrecedes("A-AA", "-GG-G"); // 2 matches, 3 shifted seq2
277 assertPrecedes("A--AA", "-GG-G"); // 2 shifted seq1, 3 matches
278 // 'enclosing' case with middle base deciding:
279 assertFollows("A--AA", "-GGG"); // 2 shifted seq1, 3 shifted seq1
280 assertPrecedes("A--AA", "-GG--G"); // 2 shifted seq1, 3 shifted seq2
281 assertPrecedes("AA-A", "-GGG"); // 2 shifted seq2, 3 matches
282 assertPrecedes("AA--A", "-GGG"); // 2 shifted seq2, 3 shifted seq1
283 assertPrecedes("AAA", "-GGG"); // 2 shifted seq2, 3 shifted seq2
287 * This test generates a random cDNA alignment and its translation, then
288 * reorders the cDNA and retranslates, and verifies that the translations are
289 * the same (apart from ordering).
291 @Test(groups = { "Functional" })
292 public void testTranslateCdna_sequenceOrderIndependent()
295 * Generate cDNA - 8 sequences of 12 bases each.
297 AlignmentI cdna = new AlignmentGenerator(true)
298 .generate(12, 8, 97, 5, 5);
299 HiddenColumns cs = new HiddenColumns();
300 AlignViewportI av = new AlignViewport(cdna, cs);
301 Dna dna = new Dna(av, new int[] { 0, cdna.getWidth() - 1 });
302 AlignmentI translated = dna.translateCdna();
305 * Jumble the cDNA sequences and translate.
307 SequenceI[] sorted = new SequenceI[cdna.getHeight()];
308 final int[] jumbler = new int[] { 6, 7, 3, 4, 2, 0, 1, 5 };
310 for (int i : jumbler)
312 sorted[seqNo++] = cdna.getSequenceAt(i);
314 AlignmentI cdnaReordered = new Alignment(sorted);
315 av = new AlignViewport(cdnaReordered, cs);
316 dna = new Dna(av, new int[] { 0, cdna.getWidth() - 1 });
317 AlignmentI translated2 = dna.translateCdna();
320 * Check translated sequences are the same in both alignments.
322 System.out.println("Original");
323 System.out.println(translated.toString());
324 System.out.println("Sorted");
325 System.out.println(translated2.toString());
327 int sortedSequenceIndex = 0;
328 for (int originalSequenceIndex : jumbler)
330 final String translation1 = translated.getSequenceAt(
331 originalSequenceIndex).getSequenceAsString();
332 final String translation2 = translated2.getSequenceAt(
333 sortedSequenceIndex).getSequenceAsString();
334 assertEquals(translation2, translation1);
335 sortedSequenceIndex++;
340 * Test that all the cases in testCompareCodonPos have a 'symmetric'
341 * comparison (without checking the actual comparison result).
343 @Test(groups = { "Functional" })
344 public void testCompareCodonPos_isSymmetric()
346 assertSymmetric("AAA", "GGG");
347 assertSymmetric("AA-A", "GGG");
348 assertSymmetric("AAA", "GG-G");
349 assertSymmetric("A-AA", "GG-G");
350 assertSymmetric("A-A-A", "GG-G");
351 assertSymmetric("A-AA", "GG--G");
352 assertSymmetric("AA-A", "G-GG");
353 assertSymmetric("AA--A", "G-GG");
354 assertSymmetric("AAA", "G-GG");
355 assertSymmetric("-AAA", "G-GG");
356 assertSymmetric("-AA-A", "G-GG");
357 assertSymmetric("-AAA", "G-G-G");
358 assertSymmetric("-A-AA", "G-G-G");
359 assertSymmetric("-A-A-A", "G-G-G");
360 assertSymmetric("-A-AA", "G-G--G");
361 assertSymmetric("-AA-A", "G--GG");
362 assertSymmetric("-AA--A", "G--GG");
363 assertSymmetric("-AAA", "G--GG");
364 assertSymmetric("A-AA", "-GGG");
365 assertSymmetric("A-A-A", "-GGG");
366 assertSymmetric("A-AA", "-GG-G");
367 assertSymmetric("A--AA", "-GG-G");
368 assertSymmetric("A--AA", "-GGG");
369 assertSymmetric("A--AA", "-GG--G");
370 assertSymmetric("AA-A", "-GGG");
371 assertSymmetric("AA--A", "-GGG");
372 assertSymmetric("AAA", "-GGG");
375 private void assertSymmetric(String codon1, String codon2)
377 assertEquals("Comparison of '" + codon1 + "' and '" + codon2
378 + " not symmetric", Integer.signum(compare(codon1, codon2)),
379 -Integer.signum(compare(codon2, codon1)));
383 * Assert that the first sequence should map to the same position as the
384 * second in a translated alignment. Also checks that this is true if the
385 * order of the codons is reversed.
390 private void assertMatches(String codon1, String codon2)
392 assertEquals("Expected '" + codon1 + "' matches '" + codon2 + "'", 0,
393 compare(codon1, codon2));
394 assertEquals("Expected '" + codon2 + "' matches '" + codon1 + "'", 0,
395 compare(codon2, codon1));
399 * Assert that the first sequence should precede the second in a translated
405 private void assertPrecedes(String codon1, String codon2)
407 assertEquals("Expected '" + codon1 + "' precedes '" + codon2 + "'",
408 -1, compare(codon1, codon2));
412 * Assert that the first sequence should follow the second in a translated
418 private void assertFollows(String codon1, String codon2)
420 assertEquals("Expected '" + codon1 + "' follows '" + codon2 + "'", 1,
421 compare(codon1, codon2));
425 * Convert two nucleotide strings to base positions and pass to
426 * Dna.compareCodonPos, return the result.
432 private int compare(String s1, String s2)
434 final AlignedCodon cd1 = convertCodon(s1);
435 final AlignedCodon cd2 = convertCodon(s2);
436 System.out.println("K: " + s1 + " " + cd1.toString());
437 System.out.println("G: " + s2 + " " + cd2.toString());
438 System.out.println();
439 return Dna.compareCodonPos(cd1, cd2);
443 * Convert a string e.g. "-GC-T" to base positions e.g. [1, 2, 4]. The string
444 * should have exactly 3 non-gap characters, and use '-' for gaps.
449 private AlignedCodon convertCodon(String s)
451 int[] codon = new int[3];
453 for (int j = 0; j < s.length(); j++)
455 if (s.charAt(j) != '-')
460 return new AlignedCodon(codon[0], codon[1], codon[2]);
464 * Weirdly, maybe worth a test to prove the helper method of this test class.
466 @Test(groups = { "Functional" })
467 public void testConvertCodon()
469 assertEquals("[0, 1, 2]", convertCodon("AAA").toString());
470 assertEquals("[0, 2, 5]", convertCodon("A-A--A").toString());
471 assertEquals("[1, 3, 4]", convertCodon("-A-AA-").toString());
475 * Test dna complementing
477 @Test(groups = "Functional")
478 public void testGetComplement()
480 assertEquals('t', Dna.getComplement('a'));
481 assertEquals('T', Dna.getComplement('A'));
482 assertEquals('a', Dna.getComplement('t'));
483 assertEquals('A', Dna.getComplement('T'));
484 assertEquals('c', Dna.getComplement('g'));
485 assertEquals('C', Dna.getComplement('G'));
486 assertEquals('g', Dna.getComplement('c'));
487 assertEquals('G', Dna.getComplement('C'));
488 // note uU --> aA but not vice versa
489 assertEquals('a', Dna.getComplement('u'));
490 assertEquals('A', Dna.getComplement('U'));
491 // ambiguity codes, see http://www.bioinformatics.org/sms/iupac.html
492 assertEquals('r', Dna.getComplement('y'));
493 assertEquals('R', Dna.getComplement('Y'));
494 assertEquals('y', Dna.getComplement('r'));
495 assertEquals('Y', Dna.getComplement('R'));
496 assertEquals('k', Dna.getComplement('m'));
497 assertEquals('K', Dna.getComplement('M'));
498 assertEquals('m', Dna.getComplement('k'));
499 assertEquals('M', Dna.getComplement('K'));
500 assertEquals('b', Dna.getComplement('v'));
501 assertEquals('B', Dna.getComplement('V'));
502 assertEquals('v', Dna.getComplement('b'));
503 assertEquals('V', Dna.getComplement('B'));
504 assertEquals('d', Dna.getComplement('h'));
505 assertEquals('D', Dna.getComplement('H'));
506 assertEquals('h', Dna.getComplement('d'));
507 assertEquals('H', Dna.getComplement('D'));
508 assertEquals('Q', Dna.getComplement('Q'));
511 @Test(groups = "Functional")
512 public void testReverseSequence()
514 String seq = "-Ac-GtU--rYkMbVdHNX-";
515 String seqRev = new StringBuilder(seq).reverse().toString();
518 SequenceI reversed = Dna.reverseSequence("Seq1", seq, false);
519 assertEquals(1, reversed.getStart());
520 assertEquals(15, reversed.getEnd());
521 assertEquals(20, reversed.getLength());
522 assertEquals(seqRev, reversed.getSequenceAsString());
523 assertEquals("Seq1|rev", reversed.getName());
525 // reverse complement:
526 SequenceI revcomp = Dna.reverseSequence("Seq1", seq, true);
527 assertEquals("-XNDhBvKmRy--AaC-gT-", revcomp.getSequenceAsString());
528 assertEquals("Seq1|revcomp", revcomp.getName());
531 @Test(groups = "Functional")
532 public void testReverseCdna()
534 String seq = "-Ac-GtU--rYkMbVdHNX-";
535 String seqRev = new StringBuilder(seq).reverse().toString();
536 String seqDs = seq.replaceAll("-", "");
537 String seqDsRev = new StringBuilder(seqDs).reverse().toString();
539 SequenceI dna = new Sequence("Seq1", seq);
540 Alignment al = new Alignment(new SequenceI[] { dna });
541 al.createDatasetAlignment();
542 assertEquals(seqDs, al.getSequenceAt(0).getDatasetSequence()
543 .getSequenceAsString());
545 HiddenColumns cs = new HiddenColumns();
546 AlignViewportI av = new AlignViewport(al, cs);
547 Dna testee = new Dna(av, new int[] { 0, al.getWidth() - 1 });
548 AlignmentI reversed = testee.reverseCdna(false);
549 assertEquals(1, reversed.getHeight());
550 assertEquals(seqRev, reversed.getSequenceAt(0).getSequenceAsString());
551 assertEquals(seqDsRev, reversed.getSequenceAt(0).getDatasetSequence()
552 .getSequenceAsString());