2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
3 * Copyright (C) 2014 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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.analysis;
21 import static org.junit.Assert.*;
22 import jalview.datamodel.ColumnSelection;
24 import java.io.IOException;
26 import org.junit.AfterClass;
27 import org.junit.BeforeClass;
28 import org.junit.Test;
29 import org.junit.runner.RunWith;
31 public class DnaTranslation
34 private static String JAL_1312_example_align_fasta = ">B.FR.83.HXB2_LAI_IIIB_BRU_K03455/45-306\n"
35 + "ATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
36 + "GGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACA\n"
37 + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTG\n"
38 + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAC\n"
39 + ">gi|27804621|gb|AY178912.1|/1-259\n"
40 + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
41 + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGGACA\n"
42 + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
43 + "TGTTCATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAT\n"
44 + ">gi|27804623|gb|AY178913.1|/1-259\n"
45 + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
46 + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGAACA\n"
47 + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
48 + "TGTTCATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
49 + ">gi|27804627|gb|AY178915.1|/1-260\n"
50 + "-TGGGAAAA-ATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
51 + "GGAGCTAGAACGATTCGCAGTTAACCCTGGCCTGTTAGAAACATCAGAAGGTTGTAGACAAATATTGGGACA\n"
52 + "GCTACAACCATCCCTTGAGACAGGATCAGAAGAACTTAAATCATTATWTAATACCATAGCAGTCCTCTATTG\n"
53 + "TGTACATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAG\n"
54 + ">gi|27804631|gb|AY178917.1|/1-261\n"
55 + "-TGGGAAAAAATTCGGTTGAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
56 + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACACCAGAAGGCTGTAGACAAATACTGGGACA\n"
57 + "GCTACAACCGTCCCTTCAGACAGGATCGGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
58 + "TGTGCATCAAAGGATAGATGTAAAAGACACCAAGGAGGCTTTAGAC\n"
59 + ">gi|27804635|gb|AY178919.1|/1-261\n"
60 + "-TGGGAGAGAATTCGGTTACGGCCAGGAGGAAAGAAAAAATATAAATTGAAACATATAGTATGGGCAGGCAG\n"
61 + "AGAGCTAGATCGATTCGCAGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAGATATTGGGACA\n"
62 + "GCTACAACCGTCCCTTAAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
63 + "TGTACATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
64 + ">gi|27804641|gb|AY178922.1|/1-261\n"
65 + "-TGGGAGAAAATTCGGTTACGGCCAGGGGGAAAGAAAAGATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
66 + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAAATACTGGGACA\n"
67 + "GTTACACCCATCCCTTCATACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
68 + "TGTGCATCAAAGGATAGAAGTAAAAGACACCAAGGAAGCTTTAGAC\n"
69 + ">gi|27804647|gb|AY178925.1|/1-261\n"
70 + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATCAATTAAAACATGTAGTATGGGCAAGCAG\n"
71 + "GGAACTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
72 + "GCTACAACCATCCCTTCAGACAGGATCAGAGGAACTTAAATCATTATTTAATACAGTAGCAGTCCTCTATTG\n"
73 + "TGTACATCAAAGAATAGATGTAAAAGACACCAAGGAAGCTCTAGAA\n"
74 + ">gi|27804649|gb|AY178926.1|/1-261\n"
75 + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
76 + "GGAGCTAGAACGATTCGCGGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAACTACTGGGACA\n"
77 + "GTTACAACCATCCCTTCAGACAGGATCAGAAGAACTCAAATCATTATATAATACAATAGCAACCCTCTATTG\n"
78 + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCCTTAGAT\n"
79 + ">gi|27804653|gb|AY178928.1|/1-261\n"
80 + "-TGGGAAAGAATTCGGTTAAGGCCAGGGGGAAAGAAACAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
81 + "GGAGCTAGACCGATTCGCACTTAACCCCGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
82 + "GCTACAATCGTCCCTTCAGACAGGATCAGAAGAACTTAGATCACTATATAATACAGTAGCAGTCCTCTATTG\n"
83 + "TGTGCATCAAAAGATAGATGTAAAAGACACCAAGGAAGCCTTAGAC\n"
84 + ">gi|27804659|gb|AY178931.1|/1-261\n"
85 + "-TGGGAAAAAATTCGGTTACGGCCAGGAGGAAAGAAAAGATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
86 + "GGAGCTAGAACGATTYGCAGTTAATCCTGGCCTTTTAGAAACAGCAGAAGGCTGTAGACAAATACTGGGACA\n"
87 + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
88 + "TGTACATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAA\n";
92 public void translationWithUntranslatableCodonsTest()
94 // Corner case for this test is the presence of codons after codons that
95 // were not translated.
96 jalview.datamodel.AlignmentI alf = null;
99 alf = new jalview.io.FormatAdapter().readFile(JAL_1312_example_align_fasta,
100 jalview.io.FormatAdapter.PASTE, "FASTA");
101 } catch (IOException x)
104 fail("Unexpected IOException (" + x.getMessage()
105 + ") - check test environment");
109 ColumnSelection cs = new jalview.datamodel.ColumnSelection();
110 assertNotNull("Couldn't do a full width translation of test data.",
111 jalview.analysis.Dna.CdnaTranslate(
112 alf.getSequencesArray(),
113 cs.getVisibleSequenceStrings(0, alf.getWidth(),
114 alf.getSequencesArray()), new int[]
115 { 0, alf.getWidth() - 1 }, alf.getGapCharacter(),
116 null, alf.getWidth(), null));
118 int vwidth = 15; // translate in 15 base stretches
119 for (int ipos = 0; ipos + vwidth < alf.getWidth(); ipos += vwidth)
121 ColumnSelection cs = new jalview.datamodel.ColumnSelection();
124 cs.hideColumns(0, ipos - 1);
126 cs.hideColumns(ipos + vwidth, alf.getWidth());
127 int[] vcontigs = cs.getVisibleContigs(0, alf.getWidth());
128 String[] sel = cs.getVisibleSequenceStrings(0, alf.getWidth(),
129 alf.getSequencesArray());
130 jalview.datamodel.AlignmentI transAlf = jalview.analysis.Dna
131 .CdnaTranslate(alf.getSequencesArray(), sel, vcontigs,
132 alf.getGapCharacter(), null, alf.getWidth(), null);
134 assertTrue("Translation failed (ipos=" + ipos
135 + ") No alignment data.", transAlf != null);
136 assertTrue("Translation failed (ipos=" + ipos + ") Empty algnment.",
137 transAlf.getHeight() > 0);
138 assertTrue("Translation failed (ipos=" + ipos + ") Translated "
139 + transAlf.getHeight() + " sequences from " + alf.getHeight()
140 + " sequences", alf.getHeight() == transAlf.getHeight());