test/jalview/analysis/DnaTranslation.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
   3  * Copyright (C) 2014 The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   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.
  11  *
  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.
  16  *
  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.
  20  */
  21 package jalview.analysis;
  22
  23 import static org.junit.Assert.*;
  24 import jalview.datamodel.ColumnSelection;
  25
  26 import java.io.IOException;
  27
  28 import org.junit.AfterClass;
  29 import org.junit.BeforeClass;
  30 import org.junit.Test;
  31 import org.junit.runner.RunWith;
  32
  33 public class DnaTranslation
  34 {
  35
  36   private static String JAL_1312_example_align_fasta = ">B.FR.83.HXB2_LAI_IIIB_BRU_K03455/45-306\n"
  37           + "ATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
  38           + "GGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACA\n"
  39           + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  40           + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAC\n"
  41           + ">gi|27804621|gb|AY178912.1|/1-259\n"
  42           + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
  43           + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGGACA\n"
  44           + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  45           + "TGTTCATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAT\n"
  46           + ">gi|27804623|gb|AY178913.1|/1-259\n"
  47           + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
  48           + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGAACA\n"
  49           + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  50           + "TGTTCATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
  51           + ">gi|27804627|gb|AY178915.1|/1-260\n"
  52           + "-TGGGAAAA-ATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
  53           + "GGAGCTAGAACGATTCGCAGTTAACCCTGGCCTGTTAGAAACATCAGAAGGTTGTAGACAAATATTGGGACA\n"
  54           + "GCTACAACCATCCCTTGAGACAGGATCAGAAGAACTTAAATCATTATWTAATACCATAGCAGTCCTCTATTG\n"
  55           + "TGTACATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAG\n"
  56           + ">gi|27804631|gb|AY178917.1|/1-261\n"
  57           + "-TGGGAAAAAATTCGGTTGAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
  58           + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACACCAGAAGGCTGTAGACAAATACTGGGACA\n"
  59           + "GCTACAACCGTCCCTTCAGACAGGATCGGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  60           + "TGTGCATCAAAGGATAGATGTAAAAGACACCAAGGAGGCTTTAGAC\n"
  61           + ">gi|27804635|gb|AY178919.1|/1-261\n"
  62           + "-TGGGAGAGAATTCGGTTACGGCCAGGAGGAAAGAAAAAATATAAATTGAAACATATAGTATGGGCAGGCAG\n"
  63           + "AGAGCTAGATCGATTCGCAGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAGATATTGGGACA\n"
  64           + "GCTACAACCGTCCCTTAAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  65           + "TGTACATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
  66           + ">gi|27804641|gb|AY178922.1|/1-261\n"
  67           + "-TGGGAGAAAATTCGGTTACGGCCAGGGGGAAAGAAAAGATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
  68           + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAAATACTGGGACA\n"
  69           + "GTTACACCCATCCCTTCATACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  70           + "TGTGCATCAAAGGATAGAAGTAAAAGACACCAAGGAAGCTTTAGAC\n"
  71           + ">gi|27804647|gb|AY178925.1|/1-261\n"
  72           + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATCAATTAAAACATGTAGTATGGGCAAGCAG\n"
  73           + "GGAACTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
  74           + "GCTACAACCATCCCTTCAGACAGGATCAGAGGAACTTAAATCATTATTTAATACAGTAGCAGTCCTCTATTG\n"
  75           + "TGTACATCAAAGAATAGATGTAAAAGACACCAAGGAAGCTCTAGAA\n"
  76           + ">gi|27804649|gb|AY178926.1|/1-261\n"
  77           + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
  78           + "GGAGCTAGAACGATTCGCGGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAACTACTGGGACA\n"
  79           + "GTTACAACCATCCCTTCAGACAGGATCAGAAGAACTCAAATCATTATATAATACAATAGCAACCCTCTATTG\n"
  80           + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCCTTAGAT\n"
  81           + ">gi|27804653|gb|AY178928.1|/1-261\n"
  82           + "-TGGGAAAGAATTCGGTTAAGGCCAGGGGGAAAGAAACAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
  83           + "GGAGCTAGACCGATTCGCACTTAACCCCGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
  84           + "GCTACAATCGTCCCTTCAGACAGGATCAGAAGAACTTAGATCACTATATAATACAGTAGCAGTCCTCTATTG\n"
  85           + "TGTGCATCAAAAGATAGATGTAAAAGACACCAAGGAAGCCTTAGAC\n"
  86           + ">gi|27804659|gb|AY178931.1|/1-261\n"
  87           + "-TGGGAAAAAATTCGGTTACGGCCAGGAGGAAAGAAAAGATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
  88           + "GGAGCTAGAACGATTYGCAGTTAATCCTGGCCTTTTAGAAACAGCAGAAGGCTGTAGACAAATACTGGGACA\n"
  89           + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  90           + "TGTACATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAA\n";
  91
  92   @Test
  93   public void translationWithUntranslatableCodonsTest()
  94   {
  95     // Corner case for this test is the presence of codons after codons that
  96     // were not translated.
  97     jalview.datamodel.AlignmentI alf = null;
  98     try
  99     {
 100       alf = new jalview.io.FormatAdapter().readFile(
 101               JAL_1312_example_align_fasta, jalview.io.FormatAdapter.PASTE,
 102               "FASTA");
 103     } catch (IOException x)
 104     {
 105       x.printStackTrace();
 106       fail("Unexpected IOException (" + x.getMessage()
 107               + ") - check test environment");
 108     }
 109     {
 110       // full translation
 111       ColumnSelection cs = new jalview.datamodel.ColumnSelection();
 112       assertNotNull("Couldn't do a full width translation of test data.",
 113               jalview.analysis.Dna.CdnaTranslate(
 114                       alf.getSequencesArray(),
 115                       cs.getVisibleSequenceStrings(0, alf.getWidth(),
 116                               alf.getSequencesArray()), new int[]
 117                       { 0, alf.getWidth() - 1 }, alf.getGapCharacter(),
 118                       null, alf.getWidth(), null));
 119     }
 120     int vwidth = 15; // translate in 15 base stretches
 121     for (int ipos = 0; ipos + vwidth < alf.getWidth(); ipos += vwidth)
 122     {
 123       ColumnSelection cs = new jalview.datamodel.ColumnSelection();
 124       if (ipos > 0)
 125       {
 126         cs.hideColumns(0, ipos - 1);
 127       }
 128       cs.hideColumns(ipos + vwidth, alf.getWidth());
 129       int[] vcontigs = cs.getVisibleContigs(0, alf.getWidth());
 130       String[] sel = cs.getVisibleSequenceStrings(0, alf.getWidth(),
 131               alf.getSequencesArray());
 132       jalview.datamodel.AlignmentI transAlf = jalview.analysis.Dna
 133               .CdnaTranslate(alf.getSequencesArray(), sel, vcontigs,
 134                       alf.getGapCharacter(), null, alf.getWidth(), null);
 135
 136       assertTrue("Translation failed (ipos=" + ipos
 137               + ") No alignment data.", transAlf != null);
 138       assertTrue("Translation failed (ipos=" + ipos + ") Empty algnment.",
 139               transAlf.getHeight() > 0);
 140       assertTrue("Translation failed (ipos=" + ipos + ") Translated "
 141               + transAlf.getHeight() + " sequences from " + alf.getHeight()
 142               + " sequences", alf.getHeight() == transAlf.getHeight());
 143     }
 144
 145   }
 146 }