1 package jalview.analysis;
3 import static org.junit.Assert.*;
4 import jalview.datamodel.ColumnSelection;
6 import java.io.IOException;
8 import org.junit.AfterClass;
9 import org.junit.BeforeClass;
10 import org.junit.Test;
11 import org.junit.runner.RunWith;
13 public class DnaTranslation
16 private static String JAL_1312_example_align_fasta = ">B.FR.83.HXB2_LAI_IIIB_BRU_K03455/45-306\n"
17 + "ATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
18 + "GGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACA\n"
19 + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTG\n"
20 + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAC\n"
21 + ">gi|27804621|gb|AY178912.1|/1-259\n"
22 + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
23 + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGGACA\n"
24 + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
25 + "TGTTCATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAT\n"
26 + ">gi|27804623|gb|AY178913.1|/1-259\n"
27 + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
28 + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGAACA\n"
29 + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
30 + "TGTTCATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
31 + ">gi|27804627|gb|AY178915.1|/1-260\n"
32 + "-TGGGAAAA-ATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
33 + "GGAGCTAGAACGATTCGCAGTTAACCCTGGCCTGTTAGAAACATCAGAAGGTTGTAGACAAATATTGGGACA\n"
34 + "GCTACAACCATCCCTTGAGACAGGATCAGAAGAACTTAAATCATTATWTAATACCATAGCAGTCCTCTATTG\n"
35 + "TGTACATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAG\n"
36 + ">gi|27804631|gb|AY178917.1|/1-261\n"
37 + "-TGGGAAAAAATTCGGTTGAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
38 + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACACCAGAAGGCTGTAGACAAATACTGGGACA\n"
39 + "GCTACAACCGTCCCTTCAGACAGGATCGGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
40 + "TGTGCATCAAAGGATAGATGTAAAAGACACCAAGGAGGCTTTAGAC\n"
41 + ">gi|27804635|gb|AY178919.1|/1-261\n"
42 + "-TGGGAGAGAATTCGGTTACGGCCAGGAGGAAAGAAAAAATATAAATTGAAACATATAGTATGGGCAGGCAG\n"
43 + "AGAGCTAGATCGATTCGCAGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAGATATTGGGACA\n"
44 + "GCTACAACCGTCCCTTAAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
45 + "TGTACATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
46 + ">gi|27804641|gb|AY178922.1|/1-261\n"
47 + "-TGGGAGAAAATTCGGTTACGGCCAGGGGGAAAGAAAAGATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
48 + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAAATACTGGGACA\n"
49 + "GTTACACCCATCCCTTCATACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
50 + "TGTGCATCAAAGGATAGAAGTAAAAGACACCAAGGAAGCTTTAGAC\n"
51 + ">gi|27804647|gb|AY178925.1|/1-261\n"
52 + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATCAATTAAAACATGTAGTATGGGCAAGCAG\n"
53 + "GGAACTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
54 + "GCTACAACCATCCCTTCAGACAGGATCAGAGGAACTTAAATCATTATTTAATACAGTAGCAGTCCTCTATTG\n"
55 + "TGTACATCAAAGAATAGATGTAAAAGACACCAAGGAAGCTCTAGAA\n"
56 + ">gi|27804649|gb|AY178926.1|/1-261\n"
57 + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
58 + "GGAGCTAGAACGATTCGCGGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAACTACTGGGACA\n"
59 + "GTTACAACCATCCCTTCAGACAGGATCAGAAGAACTCAAATCATTATATAATACAATAGCAACCCTCTATTG\n"
60 + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCCTTAGAT\n"
61 + ">gi|27804653|gb|AY178928.1|/1-261\n"
62 + "-TGGGAAAGAATTCGGTTAAGGCCAGGGGGAAAGAAACAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
63 + "GGAGCTAGACCGATTCGCACTTAACCCCGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
64 + "GCTACAATCGTCCCTTCAGACAGGATCAGAAGAACTTAGATCACTATATAATACAGTAGCAGTCCTCTATTG\n"
65 + "TGTGCATCAAAAGATAGATGTAAAAGACACCAAGGAAGCCTTAGAC\n"
66 + ">gi|27804659|gb|AY178931.1|/1-261\n"
67 + "-TGGGAAAAAATTCGGTTACGGCCAGGAGGAAAGAAAAGATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
68 + "GGAGCTAGAACGATTYGCAGTTAATCCTGGCCTTTTAGAAACAGCAGAAGGCTGTAGACAAATACTGGGACA\n"
69 + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
70 + "TGTACATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAA\n";
74 public void translationWithUntranslatableCodonsTest()
76 // Corner case for this test is the presence of codons after codons that
77 // were not translated.
78 jalview.datamodel.AlignmentI alf = null;
81 alf = new jalview.io.FormatAdapter().readFile(JAL_1312_example_align_fasta,
82 jalview.io.FormatAdapter.PASTE, "FASTA");
83 } catch (IOException x)
86 fail("Unexpected IOException (" + x.getMessage()
87 + ") - check test environment");
91 ColumnSelection cs = new jalview.datamodel.ColumnSelection();
92 assertNotNull("Couldn't do a full width translation of test data.",
93 jalview.analysis.Dna.CdnaTranslate(
94 alf.getSequencesArray(),
95 cs.getVisibleSequenceStrings(0, alf.getWidth(),
96 alf.getSequencesArray()), new int[]
97 { 0, alf.getWidth() - 1 }, alf.getGapCharacter(),
98 null, alf.getWidth(), null));
100 int vwidth = 15; // translate in 15 base stretches
101 for (int ipos = 0; ipos + vwidth < alf.getWidth(); ipos += vwidth)
103 ColumnSelection cs = new jalview.datamodel.ColumnSelection();
106 cs.hideColumns(0, ipos - 1);
108 cs.hideColumns(ipos + vwidth, alf.getWidth());
109 int[] vcontigs = cs.getVisibleContigs(0, alf.getWidth());
110 String[] sel = cs.getVisibleSequenceStrings(0, alf.getWidth(),
111 alf.getSequencesArray());
112 jalview.datamodel.AlignmentI transAlf = jalview.analysis.Dna
113 .CdnaTranslate(alf.getSequencesArray(), sel, vcontigs,
114 alf.getGapCharacter(), null, alf.getWidth(), null);
116 assertTrue("Translation failed (ipos=" + ipos
117 + ") No alignment data.", transAlf != null);
118 assertTrue("Translation failed (ipos=" + ipos + ") Empty algnment.",
119 transAlf.getHeight() > 0);
120 assertTrue("Translation failed (ipos=" + ipos + ") Translated "
121 + transAlf.getHeight() + " sequences from " + alf.getHeight()
122 + " sequences", alf.getHeight() == transAlf.getHeight());