test/jalview/analysis/DnaTranslation.java

   1 package jalview.analysis;
   2
   3 import static org.junit.Assert.*;
   4 import jalview.datamodel.ColumnSelection;
   5
   6 import java.io.IOException;
   7
   8 import org.junit.AfterClass;
   9 import org.junit.BeforeClass;
  10 import org.junit.Test;
  11 import org.junit.runner.RunWith;
  12
  13 public class DnaTranslation
  14 {
  15
  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";
  71
  72
  73   @Test
  74   public void translationWithUntranslatableCodonsTest()
  75   {
  76     // Corner case for this test is the presence of codons after codons that
  77     // were not translated.
  78     jalview.datamodel.AlignmentI alf = null;
  79     try
  80     {
  81       alf = new jalview.io.FormatAdapter().readFile(JAL_1312_example_align_fasta,
  82               jalview.io.FormatAdapter.PASTE, "FASTA");
  83     } catch (IOException x)
  84     {
  85       x.printStackTrace();
  86       fail("Unexpected IOException (" + x.getMessage()
  87               + ") - check test environment");
  88     }
  89     {
  90       // full translation
  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));
  99     }
 100     int vwidth = 15; // translate in 15 base stretches
 101     for (int ipos = 0; ipos + vwidth < alf.getWidth(); ipos += vwidth)
 102     {
 103       ColumnSelection cs = new jalview.datamodel.ColumnSelection();
 104       if (ipos > 0)
 105       {
 106         cs.hideColumns(0, ipos - 1);
 107       }
 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);
 115
 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());
 123     }
 124
 125   }
 126 }