test/jalview/analysis/DnaTest.java

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