test/jalview/analysis/DnaTest.java

   1 package jalview.analysis;
   2
   3 import static org.junit.Assert.assertEquals;
   4 import static org.junit.Assert.assertNotNull;
   5 import static org.junit.Assert.assertTrue;
   6 import jalview.api.AlignViewportI;
   7 import jalview.datamodel.AlignedCodon;
   8 import jalview.datamodel.Alignment;
   9 import jalview.datamodel.AlignmentI;
  10 import jalview.datamodel.ColumnSelection;
  11 import jalview.datamodel.SequenceI;
  12 import jalview.gui.AlignViewport;
  13 import jalview.io.FormatAdapter;
  14
  15 import java.io.IOException;
  16
  17 import org.junit.Test;
  18
  19 public class DnaTest
  20 {
  21   // @formatter:off
  22   // AA encoding codons as ordered on the Jalview help page Amino Acid Table
  23   private static String fasta = ">B\n" + "GCT" + "GCC" + "GCA" + "GCG"
  24           + "TGT" + "TGC" + "GAT" + "GAC" + "GAA" + "GAG" + "TTT" + "TTC"
  25           + "GGT" + "GGC" + "GGA" + "GGG" + "CAT" + "CAC" + "ATT" + "ATC"
  26           + "ATA" + "AAA" + "AAG" + "TTG" + "TTA" + "CTT" + "CTC" + "CTA"
  27           + "CTG" + "ATG" + "AAT" + "AAC" + "CCT" + "CCC" + "CCA" + "CCG"
  28           + "CAA" + "CAG" + "CGT" + "CGC" + "CGA" + "CGG" + "AGA" + "AGG"
  29           + "TCT" + "TCC" + "TCA" + "TCG" + "AGT" + "AGC" + "ACT" + "ACC"
  30           + "ACA" + "ACG" + "GTT" + "GTC" + "GTA" + "GTG" + "TGG" + "TAT"
  31           + "TAC" + "TAA" + "TAG" + "TGA";
  32
  33   private static String JAL_1312_example_align_fasta = ">B.FR.83.HXB2_LAI_IIIB_BRU_K03455/45-306\n"
  34           + "ATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
  35           + "GGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACA\n"
  36           + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  37           + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAC\n"
  38           + ">gi|27804621|gb|AY178912.1|/1-259\n"
  39           + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
  40           + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGGACA\n"
  41           + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  42           + "TGTTCATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAT\n"
  43           + ">gi|27804623|gb|AY178913.1|/1-259\n"
  44           + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
  45           + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGAACA\n"
  46           + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  47           + "TGTTCATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
  48           + ">gi|27804627|gb|AY178915.1|/1-260\n"
  49           + "-TGGGAAAA-ATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
  50           + "GGAGCTAGAACGATTCGCAGTTAACCCTGGCCTGTTAGAAACATCAGAAGGTTGTAGACAAATATTGGGACA\n"
  51           + "GCTACAACCATCCCTTGAGACAGGATCAGAAGAACTTAAATCATTATWTAATACCATAGCAGTCCTCTATTG\n"
  52           + "TGTACATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAG\n"
  53           + ">gi|27804631|gb|AY178917.1|/1-261\n"
  54           + "-TGGGAAAAAATTCGGTTGAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
  55           + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACACCAGAAGGCTGTAGACAAATACTGGGACA\n"
  56           + "GCTACAACCGTCCCTTCAGACAGGATCGGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  57           + "TGTGCATCAAAGGATAGATGTAAAAGACACCAAGGAGGCTTTAGAC\n"
  58           + ">gi|27804635|gb|AY178919.1|/1-261\n"
  59           + "-TGGGAGAGAATTCGGTTACGGCCAGGAGGAAAGAAAAAATATAAATTGAAACATATAGTATGGGCAGGCAG\n"
  60           + "AGAGCTAGATCGATTCGCAGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAGATATTGGGACA\n"
  61           + "GCTACAACCGTCCCTTAAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  62           + "TGTACATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
  63           + ">gi|27804641|gb|AY178922.1|/1-261\n"
  64           + "-TGGGAGAAAATTCGGTTACGGCCAGGGGGAAAGAAAAGATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
  65           + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAAATACTGGGACA\n"
  66           + "GTTACACCCATCCCTTCATACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  67           + "TGTGCATCAAAGGATAGAAGTAAAAGACACCAAGGAAGCTTTAGAC\n"
  68           + ">gi|27804647|gb|AY178925.1|/1-261\n"
  69           + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATCAATTAAAACATGTAGTATGGGCAAGCAG\n"
  70           + "GGAACTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
  71           + "GCTACAACCATCCCTTCAGACAGGATCAGAGGAACTTAAATCATTATTTAATACAGTAGCAGTCCTCTATTG\n"
  72           + "TGTACATCAAAGAATAGATGTAAAAGACACCAAGGAAGCTCTAGAA\n"
  73           + ">gi|27804649|gb|AY178926.1|/1-261\n"
  74           + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
  75           + "GGAGCTAGAACGATTCGCGGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAACTACTGGGACA\n"
  76           + "GTTACAACCATCCCTTCAGACAGGATCAGAAGAACTCAAATCATTATATAATACAATAGCAACCCTCTATTG\n"
  77           + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCCTTAGAT\n"
  78           + ">gi|27804653|gb|AY178928.1|/1-261\n"
  79           + "-TGGGAAAGAATTCGGTTAAGGCCAGGGGGAAAGAAACAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
  80           + "GGAGCTAGACCGATTCGCACTTAACCCCGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
  81           + "GCTACAATCGTCCCTTCAGACAGGATCAGAAGAACTTAGATCACTATATAATACAGTAGCAGTCCTCTATTG\n"
  82           + "TGTGCATCAAAAGATAGATGTAAAAGACACCAAGGAAGCCTTAGAC\n"
  83           + ">gi|27804659|gb|AY178931.1|/1-261\n"
  84           + "-TGGGAAAAAATTCGGTTACGGCCAGGAGGAAAGAAAAGATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
  85           + "GGAGCTAGAACGATTYGCAGTTAATCCTGGCCTTTTAGAAACAGCAGAAGGCTGTAGACAAATACTGGGACA\n"
  86           + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  87           + "TGTACATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAA\n";
  88   // @formatter:on
  89
  90   /**
  91    * Corner case for this test is the presence of codons after codons that were
  92    * not translated.
  93    *
  94    * @throws IOException
  95    */
  96   @Test
  97   public void testTranslateCdna_withUntranslatableCodons()
  98           throws IOException
  99   {
 100     AlignmentI alf = new FormatAdapter().readFile(
 101             JAL_1312_example_align_fasta, jalview.io.FormatAdapter.PASTE,
 102             "FASTA");
 103     ColumnSelection cs = new ColumnSelection();
 104     AlignViewportI av = new AlignViewport(alf, cs);
 105     Dna dna = new Dna(av, new int[]
 106     { 0, alf.getWidth() - 1 });
 107     AlignmentI translated = dna.translateCdna();
 108     assertNotNull("Couldn't do a full width translation of test data.",
 109             translated);
 110   }
 111
 112   /**
 113    * Test variant in which 15 column blocks at a time are translated (the rest
 114    * hidden).
 115    *
 116    * @throws IOException
 117    */
 118   @Test
 119   public void testTranslateCdna_withUntranslatableCodonsAndHiddenColumns()
 120           throws IOException
 121   {
 122     AlignmentI alf = new FormatAdapter().readFile(
 123             JAL_1312_example_align_fasta, jalview.io.FormatAdapter.PASTE,
 124             "FASTA");
 125     int vwidth = 15;
 126     for (int ipos = 0; ipos + vwidth < alf.getWidth(); ipos += vwidth)
 127     {
 128       ColumnSelection cs = new ColumnSelection();
 129       if (ipos > 0)
 130       {
 131         cs.hideColumns(0, ipos - 1);
 132       }
 133       cs.hideColumns(ipos + vwidth, alf.getWidth());
 134       int[] vcontigs = cs.getVisibleContigs(0, alf.getWidth());
 135       AlignViewportI av = new AlignViewport(alf, cs);
 136       Dna dna = new Dna(av, vcontigs);
 137       AlignmentI transAlf = dna.translateCdna();
 138
 139       assertTrue("Translation failed (ipos=" + ipos
 140               + ") No alignment data.", transAlf != null);
 141       assertTrue("Translation failed (ipos=" + ipos + ") Empty alignment.",
 142               transAlf.getHeight() > 0);
 143       assertTrue("Translation failed (ipos=" + ipos + ") Translated "
 144               + transAlf.getHeight() + " sequences from " + alf.getHeight()
 145               + " sequences", alf.getHeight() == transAlf.getHeight());
 146     }
 147   }
 148
 149   /**
 150    * Test simple translation to Amino Acids (with STOP codons translated to X).
 151    *
 152    * @throws IOException
 153    */
 154   @Test
 155   public void testTranslateCdna_simple() throws IOException
 156   {
 157     AlignmentI alf = new FormatAdapter().readFile(fasta,
 158             FormatAdapter.PASTE, "FASTA");
 159     ColumnSelection cs = new ColumnSelection();
 160     AlignViewportI av = new AlignViewport(alf, cs);
 161     Dna dna = new Dna(av, new int[]
 162     { 0, alf.getWidth() - 1 });
 163     AlignmentI translated = dna.translateCdna();
 164     String aa = translated.getSequenceAt(0).getSequenceAsString();
 165     assertEquals(
 166             "AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYYXXX",
 167             aa);
 168   }
 169
 170   /**
 171    * Test translation excluding hidden columns.
 172    *
 173    * @throws IOException
 174    */
 175   @Test
 176   public void testTranslateCdna_hiddenColumns() throws IOException
 177   {
 178     AlignmentI alf = new FormatAdapter().readFile(fasta,
 179             FormatAdapter.PASTE, "FASTA");
 180     ColumnSelection cs = new jalview.datamodel.ColumnSelection();
 181     cs.hideColumns(6, 14); // hide codons 3/4/5
 182     cs.hideColumns(24, 35); // hide codons 9-12
 183     cs.hideColumns(177, 191); // hide codons 60-64
 184     AlignViewportI av = new AlignViewport(alf, cs);
 185     Dna dna = new Dna(av, new int[]
 186     { 0, alf.getWidth() - 1 });
 187     AlignmentI translated = dna.translateCdna();
 188     String aa = translated.getSequenceAt(0).getSequenceAsString();
 189     assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa);
 190   }
 191
 192   /**
 193    * Use this test to help debug into any cases of interest.
 194    */
 195   @Test
 196   public void testCompareCodonPos_oneOnly()
 197   {
 198     assertFollows("-AA--A", "G--GG"); // 2 shifted seq2, 3 shifted seq1
 199   }
 200
 201   /**
 202    * Tests for method that compares 'alignment' of two codon position triplets.
 203    */
 204   @Test
 205   public void testCompareCodonPos()
 206   {
 207     /*
 208      * Returns 0 for any null argument
 209      */
 210     assertEquals(0, Dna.compareCodonPos(new AlignedCodon(1, 2, 3), null));
 211     assertEquals(0, Dna.compareCodonPos(null, new AlignedCodon(1, 2, 3)));
 212
 213     /*
 214      * Work through 27 combinations. First 9 cases where first position matches.
 215      */
 216     assertMatches("AAA", "GGG"); // 2 and 3 match
 217     assertFollows("AA-A", "GGG"); // 2 matches, 3 shifted seq1
 218     assertPrecedes("AAA", "GG-G"); // 2 matches, 3 shifted seq2
 219     assertFollows("A-AA", "GG-G"); // 2 shifted seq1, 3 matches
 220     assertFollows("A-A-A", "GG-G"); // 2 shifted seq1, 3 shifted seq1
 221     assertPrecedes("A-AA", "GG--G"); // 2 shifted seq1, 3 shifted seq2
 222     assertPrecedes("AA-A", "G-GG"); // 2 shifted seq2, 3 matches
 223     assertFollows("AA--A", "G-GG"); // 2 shifted seq2, 3 shifted seq1
 224     assertPrecedes("AAA", "G-GG"); // 2 shifted seq2, 3 shifted seq2
 225
 226     /*
 227      * 9 cases where first position is shifted in first sequence.
 228      */
 229     assertFollows("-AAA", "G-GG"); // 2 and 3 match
 230     assertFollows("-AA-A", "G-GG"); // 2 matches, 3 shifted seq1
 231     // 'enclosing' case: pick first to start precedes
 232     assertFollows("-AAA", "G-G-G"); // 2 matches, 3 shifted seq2
 233     assertFollows("-A-AA", "G-G-G"); // 2 shifted seq1, 3 matches
 234     assertFollows("-A-A-A", "G-G-G"); // 2 shifted seq1, 3 shifted seq1
 235     // 'enclosing' case: pick first to start precedes
 236     assertFollows("-A-AA", "G-G--G"); // 2 shifted seq1, 3 shifted seq2
 237     assertFollows("-AA-A", "G--GG"); // 2 shifted seq2, 3 matches
 238     assertFollows("-AA--A", "G--GG"); // 2 shifted seq2, 3 shifted seq1
 239     assertPrecedes("-AAA", "G--GG"); // 2 shifted seq2, 3 shifted seq2
 240
 241     /*
 242      * 9 cases where first position is shifted in second sequence.
 243      */
 244     assertPrecedes("A-AA", "-GGG"); // 2 and 3 match
 245     assertPrecedes("A-A-A", "-GGG"); // 2 matches, 3 shifted seq1
 246     assertPrecedes("A-AA", "-GG-G"); // 2 matches, 3 shifted seq2
 247     assertPrecedes("A--AA", "-GG-G"); // 2 shifted seq1, 3 matches
 248     // 'enclosing' case with middle base deciding:
 249     assertFollows("A--AA", "-GGG"); // 2 shifted seq1, 3 shifted seq1
 250     assertPrecedes("A--AA", "-GG--G"); // 2 shifted seq1, 3 shifted seq2
 251     assertPrecedes("AA-A", "-GGG"); // 2 shifted seq2, 3 matches
 252     assertPrecedes("AA--A", "-GGG"); // 2 shifted seq2, 3 shifted seq1
 253     assertPrecedes("AAA", "-GGG"); // 2 shifted seq2, 3 shifted seq2
 254   }
 255
 256   /**
 257    * This test generates a random cDNA alignment and its translation, then
 258    * reorders the cDNA and retranslates, and verifies that the translations are
 259    * the same (apart from ordering).
 260    */
 261   @Test
 262   public void testTranslateCdna_sequenceOrderIndependent()
 263   {
 264     /*
 265      * Generate cDNA - 8 sequences of 12 bases each.
 266      */
 267     AlignmentI cdna = new DnaAlignmentGenerator().generate(12, 8, 97, 5, 5);
 268     ColumnSelection cs = new ColumnSelection();
 269     AlignViewportI av = new AlignViewport(cdna, cs);
 270     Dna dna = new Dna(av, new int[]
 271     { 0, cdna.getWidth() - 1 });
 272     AlignmentI translated = dna.translateCdna();
 273
 274     /*
 275      * Jumble the cDNA sequences and translate.
 276      */
 277     SequenceI[] sorted = new SequenceI[cdna.getHeight()];
 278     final int[] jumbler = new int[]
 279     { 6, 7, 3, 4, 2, 0, 1, 5 };
 280     int seqNo = 0;
 281     for (int i : jumbler)
 282     {
 283       sorted[seqNo++] = cdna.getSequenceAt(i);
 284     }
 285     AlignmentI cdnaReordered = new Alignment(sorted);
 286     av = new AlignViewport(cdnaReordered, cs);
 287     dna = new Dna(av, new int[]
 288     { 0, cdna.getWidth() - 1 });
 289     AlignmentI translated2 = dna.translateCdna();
 290
 291     /*
 292      * Check translated sequences are the same in both alignments.
 293      */
 294     System.out.println("Original");
 295     System.out.println(translated.toString());
 296     System.out.println("Sorted");
 297     System.out.println(translated2.toString());
 298
 299     int sortedSequenceIndex = 0;
 300     for (int originalSequenceIndex : jumbler)
 301     {
 302       final String translation1 = translated.getSequenceAt(
 303               originalSequenceIndex).getSequenceAsString();
 304       final String translation2 = translated2.getSequenceAt(sortedSequenceIndex)
 305               .getSequenceAsString();
 306       assertEquals(translation2, translation1);
 307       sortedSequenceIndex++;
 308     }
 309   }
 310
 311   /**
 312    * Test that all the cases in testCompareCodonPos have a 'symmetric'
 313    * comparison (without checking the actual comparison result).
 314    */
 315   @Test
 316   public void testCompareCodonPos_isSymmetric()
 317   {
 318     assertSymmetric("AAA", "GGG");
 319     assertSymmetric("AA-A", "GGG");
 320     assertSymmetric("AAA", "GG-G");
 321     assertSymmetric("A-AA", "GG-G");
 322     assertSymmetric("A-A-A", "GG-G");
 323     assertSymmetric("A-AA", "GG--G");
 324     assertSymmetric("AA-A", "G-GG");
 325     assertSymmetric("AA--A", "G-GG");
 326     assertSymmetric("AAA", "G-GG");
 327     assertSymmetric("-AAA", "G-GG");
 328     assertSymmetric("-AA-A", "G-GG");
 329     assertSymmetric("-AAA", "G-G-G");
 330     assertSymmetric("-A-AA", "G-G-G");
 331     assertSymmetric("-A-A-A", "G-G-G");
 332     assertSymmetric("-A-AA", "G-G--G");
 333     assertSymmetric("-AA-A", "G--GG");
 334     assertSymmetric("-AA--A", "G--GG");
 335     assertSymmetric("-AAA", "G--GG");
 336     assertSymmetric("A-AA", "-GGG");
 337     assertSymmetric("A-A-A", "-GGG");
 338     assertSymmetric("A-AA", "-GG-G");
 339     assertSymmetric("A--AA", "-GG-G");
 340     assertSymmetric("A--AA", "-GGG");
 341     assertSymmetric("A--AA", "-GG--G");
 342     assertSymmetric("AA-A", "-GGG");
 343     assertSymmetric("AA--A", "-GGG");
 344     assertSymmetric("AAA", "-GGG");
 345   }
 346
 347   private void assertSymmetric(String codon1, String codon2)
 348   {
 349     assertEquals("Comparison of '" + codon1 + "' and '" + codon2
 350             + " not symmetric", Integer.signum(compare(codon1, codon2)),
 351             -Integer.signum(compare(codon2, codon1)));
 352   }
 353
 354   /**
 355    * Assert that the first sequence should map to the same position as the
 356    * second in a translated alignment. Also checks that this is true if the
 357    * order of the codons is reversed.
 358    *
 359    * @param codon1
 360    * @param codon2
 361    */
 362   private void assertMatches(String codon1, String codon2)
 363   {
 364     assertEquals("Expected '" + codon1 + "' matches '" + codon2 + "'", 0,
 365             compare(codon1, codon2));
 366     assertEquals("Expected '" + codon2 + "' matches '" + codon1 + "'", 0,
 367             compare(codon2, codon1));
 368   }
 369
 370   /**
 371    * Assert that the first sequence should precede the second in a translated
 372    * alignment
 373    *
 374    * @param codon1
 375    * @param codon2
 376    */
 377   private void assertPrecedes(String codon1, String codon2)
 378   {
 379     assertEquals("Expected '" + codon1 + "'  precedes '" + codon2 + "'",
 380             -1, compare(codon1, codon2));
 381   }
 382
 383   /**
 384    * Assert that the first sequence should follow the second in a translated
 385    * alignment
 386    *
 387    * @param codon1
 388    * @param codon2
 389    */
 390   private void assertFollows(String codon1, String codon2)
 391   {
 392     assertEquals("Expected '" + codon1 + "'  follows '" + codon2 + "'", 1,
 393             compare(codon1, codon2));
 394   }
 395
 396   /**
 397    * Convert two nucleotide strings to base positions and pass to
 398    * Dna.compareCodonPos, return the result.
 399    *
 400    * @param s1
 401    * @param s2
 402    * @return
 403    */
 404   private int compare(String s1, String s2)
 405   {
 406     final AlignedCodon cd1 = convertCodon(s1);
 407     final AlignedCodon cd2 = convertCodon(s2);
 408     System.out.println("K: " + s1 + "  " + cd1.toString());
 409     System.out.println("G: " + s2 + "  " + cd2.toString());
 410     System.out.println();
 411     return Dna.compareCodonPos(cd1, cd2);
 412   }
 413
 414   /**
 415    * Convert a string e.g. "-GC-T" to base positions e.g. [1, 2, 4]. The string
 416    * should have exactly 3 non-gap characters, and use '-' for gaps.
 417    *
 418    * @param s
 419    * @return
 420    */
 421   private AlignedCodon convertCodon(String s)
 422   {
 423     int[] codon = new int[3];
 424     int i = 0;
 425     for (int j = 0; j < s.length(); j++)
 426     {
 427       if (s.charAt(j) != '-')
 428       {
 429         codon[i++] = j;
 430       }
 431     }
 432     return new AlignedCodon(codon[0], codon[1], codon[2]);
 433   }
 434
 435   /**
 436    * Weirdly, maybe worth a test to prove the helper method of this test class.
 437    */
 438   @Test
 439   public void testConvertCodon()
 440   {
 441     assertEquals("[0, 1, 2]", convertCodon("AAA").toString());
 442     assertEquals("[0, 2, 5]", convertCodon("A-A--A").toString());
 443     assertEquals("[1, 3, 4]", convertCodon("-A-AA-").toString());
 444   }
 445 }