test/jalview/analysis/DnaTest.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ 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.testng.AssertJUnit.assertEquals;
  24 import static org.testng.AssertJUnit.assertNotNull;
  25 import static org.testng.AssertJUnit.assertTrue;
  26
  27 import jalview.api.AlignViewportI;
  28 import jalview.datamodel.AlignedCodon;
  29 import jalview.datamodel.Alignment;
  30 import jalview.datamodel.AlignmentI;
  31 import jalview.datamodel.HiddenColumns;
  32 import jalview.datamodel.Sequence;
  33 import jalview.datamodel.SequenceI;
  34 import jalview.gui.AlignViewport;
  35 import jalview.gui.JvOptionPane;
  36 import jalview.io.DataSourceType;
  37 import jalview.io.FileFormat;
  38 import jalview.io.FormatAdapter;
  39
  40 import java.io.IOException;
  41 import java.util.Iterator;
  42
  43 import org.testng.annotations.BeforeClass;
  44 import org.testng.annotations.Test;
  45
  46 public class DnaTest
  47 {
  48   @BeforeClass(alwaysRun = true)
  49   public void setUpJvOptionPane()
  50   {
  51     JvOptionPane.setInteractiveMode(false);
  52     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  53   }
  54
  55   // @formatter:off
  56   // AA encoding codons as ordered on the Jalview help page Amino Acid Table
  57   private static String fasta = ">B\n" + "GCT" + "GCC" + "GCA" + "GCG"
  58           + "TGT" + "TGC" + "GAT" + "GAC" + "GAA" + "GAG" + "TTT" + "TTC"
  59           + "GGT" + "GGC" + "GGA" + "GGG" + "CAT" + "CAC" + "ATT" + "ATC"
  60           + "ATA" + "AAA" + "AAG" + "TTG" + "TTA" + "CTT" + "CTC" + "CTA"
  61           + "CTG" + "ATG" + "AAT" + "AAC" + "CCT" + "CCC" + "CCA" + "CCG"
  62           + "CAA" + "CAG" + "CGT" + "CGC" + "CGA" + "CGG" + "AGA" + "AGG"
  63           + "TCT" + "TCC" + "TCA" + "TCG" + "AGT" + "AGC" + "ACT" + "ACC"
  64           + "ACA" + "ACG" + "GTT" + "GTC" + "GTA" + "GTG" + "TGG" + "TAT"
  65           + "TAC" + "TAA" + "TAG" + "TGA";
  66
  67   private static String JAL_1312_example_align_fasta = ">B.FR.83.HXB2_LAI_IIIB_BRU_K03455/45-306\n"
  68           + "ATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
  69           + "GGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACA\n"
  70           + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  71           + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAC\n"
  72           + ">gi|27804621|gb|AY178912.1|/1-259\n"
  73           + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
  74           + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGGACA\n"
  75           + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  76           + "TGTTCATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAT\n"
  77           + ">gi|27804623|gb|AY178913.1|/1-259\n"
  78           + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
  79           + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGAACA\n"
  80           + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  81           + "TGTTCATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
  82           + ">gi|27804627|gb|AY178915.1|/1-260\n"
  83           + "-TGGGAAAA-ATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
  84           + "GGAGCTAGAACGATTCGCAGTTAACCCTGGCCTGTTAGAAACATCAGAAGGTTGTAGACAAATATTGGGACA\n"
  85           + "GCTACAACCATCCCTTGAGACAGGATCAGAAGAACTTAAATCATTATWTAATACCATAGCAGTCCTCTATTG\n"
  86           + "TGTACATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAG\n"
  87           + ">gi|27804631|gb|AY178917.1|/1-261\n"
  88           + "-TGGGAAAAAATTCGGTTGAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
  89           + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACACCAGAAGGCTGTAGACAAATACTGGGACA\n"
  90           + "GCTACAACCGTCCCTTCAGACAGGATCGGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  91           + "TGTGCATCAAAGGATAGATGTAAAAGACACCAAGGAGGCTTTAGAC\n"
  92           + ">gi|27804635|gb|AY178919.1|/1-261\n"
  93           + "-TGGGAGAGAATTCGGTTACGGCCAGGAGGAAAGAAAAAATATAAATTGAAACATATAGTATGGGCAGGCAG\n"
  94           + "AGAGCTAGATCGATTCGCAGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAGATATTGGGACA\n"
  95           + "GCTACAACCGTCCCTTAAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  96           + "TGTACATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
  97           + ">gi|27804641|gb|AY178922.1|/1-261\n"
  98           + "-TGGGAGAAAATTCGGTTACGGCCAGGGGGAAAGAAAAGATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
  99           + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAAATACTGGGACA\n"
 100           + "GTTACACCCATCCCTTCATACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
 101           + "TGTGCATCAAAGGATAGAAGTAAAAGACACCAAGGAAGCTTTAGAC\n"
 102           + ">gi|27804647|gb|AY178925.1|/1-261\n"
 103           + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATCAATTAAAACATGTAGTATGGGCAAGCAG\n"
 104           + "GGAACTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
 105           + "GCTACAACCATCCCTTCAGACAGGATCAGAGGAACTTAAATCATTATTTAATACAGTAGCAGTCCTCTATTG\n"
 106           + "TGTACATCAAAGAATAGATGTAAAAGACACCAAGGAAGCTCTAGAA\n"
 107           + ">gi|27804649|gb|AY178926.1|/1-261\n"
 108           + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
 109           + "GGAGCTAGAACGATTCGCGGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAACTACTGGGACA\n"
 110           + "GTTACAACCATCCCTTCAGACAGGATCAGAAGAACTCAAATCATTATATAATACAATAGCAACCCTCTATTG\n"
 111           + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCCTTAGAT\n"
 112           + ">gi|27804653|gb|AY178928.1|/1-261\n"
 113           + "-TGGGAAAGAATTCGGTTAAGGCCAGGGGGAAAGAAACAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
 114           + "GGAGCTAGACCGATTCGCACTTAACCCCGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
 115           + "GCTACAATCGTCCCTTCAGACAGGATCAGAAGAACTTAGATCACTATATAATACAGTAGCAGTCCTCTATTG\n"
 116           + "TGTGCATCAAAAGATAGATGTAAAAGACACCAAGGAAGCCTTAGAC\n"
 117           + ">gi|27804659|gb|AY178931.1|/1-261\n"
 118           + "-TGGGAAAAAATTCGGTTACGGCCAGGAGGAAAGAAAAGATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
 119           + "GGAGCTAGAACGATTYGCAGTTAATCCTGGCCTTTTAGAAACAGCAGAAGGCTGTAGACAAATACTGGGACA\n"
 120           + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
 121           + "TGTACATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAA\n";
 122   // @formatter:on
 123
 124   /**
 125    * Corner case for this test is the presence of codons after codons that were
 126    * not translated.
 127    *
 128    * @throws IOException
 129    */
 130   @Test(groups = { "Functional" })
 131   public void testTranslateCdna_withUntranslatableCodons()
 132           throws IOException
 133   {
 134     AlignmentI alf = new FormatAdapter().readFile(
 135             JAL_1312_example_align_fasta, DataSourceType.PASTE,
 136             FileFormat.Fasta);
 137     HiddenColumns cs = new HiddenColumns();
 138     AlignViewportI av = new AlignViewport(alf, cs);
 139     Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
 140             false);
 141     Dna dna = new Dna(av, contigs);
 142     AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
 143             .getStandardCodeTable());
 144     assertNotNull("Couldn't do a full width translation of test data.",
 145             translated);
 146   }
 147
 148   /**
 149    * Test variant in which 15 column blocks at a time are translated (the rest
 150    * hidden).
 151    *
 152    * @throws IOException
 153    */
 154   @Test(groups = { "Functional" })
 155   public void testTranslateCdna_withUntranslatableCodonsAndHiddenColumns()
 156           throws IOException
 157   {
 158     AlignmentI alf = new FormatAdapter().readFile(
 159             JAL_1312_example_align_fasta, DataSourceType.PASTE,
 160             FileFormat.Fasta);
 161     int vwidth = 15;
 162     for (int ipos = 0; ipos + vwidth < alf.getWidth(); ipos += vwidth)
 163     {
 164       HiddenColumns cs = new HiddenColumns();
 165       if (ipos > 0)
 166       {
 167         cs.hideColumns(0, ipos - 1);
 168       }
 169       cs.hideColumns(ipos + vwidth, alf.getWidth());
 170       Iterator<int[]> vcontigs = cs.getVisContigsIterator(0,
 171               alf.getWidth(), false);
 172       AlignViewportI av = new AlignViewport(alf, cs);
 173       Dna dna = new Dna(av, vcontigs);
 174       AlignmentI transAlf = dna.translateCdna(GeneticCodes.getInstance()
 175               .getStandardCodeTable());
 176
 177       assertTrue("Translation failed (ipos=" + ipos
 178               + ") No alignment data.", transAlf != null);
 179       assertTrue("Translation failed (ipos=" + ipos + ") Empty alignment.",
 180               transAlf.getHeight() > 0);
 181       assertTrue("Translation failed (ipos=" + ipos + ") Translated "
 182               + transAlf.getHeight() + " sequences from " + alf.getHeight()
 183               + " sequences", alf.getHeight() == transAlf.getHeight());
 184     }
 185   }
 186
 187   /**
 188    * Test simple translation to Amino Acids (with STOP codons translated to *).
 189    *
 190    * @throws IOException
 191    */
 192   @Test(groups = { "Functional" })
 193   public void testTranslateCdna_simple() throws IOException
 194   {
 195     AlignmentI alf = new FormatAdapter().readFile(fasta,
 196             DataSourceType.PASTE, FileFormat.Fasta);
 197     HiddenColumns cs = new HiddenColumns();
 198     AlignViewportI av = new AlignViewport(alf, cs);
 199     Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
 200             false);
 201     Dna dna = new Dna(av, contigs);
 202     AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
 203             .getStandardCodeTable());
 204     String aa = translated.getSequenceAt(0).getSequenceAsString();
 205     assertEquals(
 206             "AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYY***",
 207             aa);
 208   }
 209
 210   /**
 211    * Test translation excluding hidden columns.
 212    *
 213    * @throws IOException
 214    */
 215   @Test(groups = { "Functional" })
 216   public void testTranslateCdna_hiddenColumns() throws IOException
 217   {
 218     AlignmentI alf = new FormatAdapter().readFile(fasta,
 219             DataSourceType.PASTE, FileFormat.Fasta);
 220     HiddenColumns cs = new HiddenColumns();
 221     cs.hideColumns(6, 14); // hide codons 3/4/5
 222     cs.hideColumns(24, 35); // hide codons 9-12
 223     cs.hideColumns(177, 191); // hide codons 60-64
 224     AlignViewportI av = new AlignViewport(alf, cs);
 225     Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
 226             false);
 227     Dna dna = new Dna(av, contigs);
 228     AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
 229             .getStandardCodeTable());
 230     String aa = translated.getSequenceAt(0).getSequenceAsString();
 231     assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa);
 232   }
 233
 234   /**
 235    * Use this test to help debug into any cases of interest.
 236    */
 237   @Test(groups = { "Functional" })
 238   public void testCompareCodonPos_oneOnly()
 239   {
 240     assertFollows("-AA--A", "G--GG"); // 2 shifted seq2, 3 shifted seq1
 241   }
 242
 243   /**
 244    * Tests for method that compares 'alignment' of two codon position triplets.
 245    */
 246   @Test(groups = { "Functional" })
 247   public void testCompareCodonPos()
 248   {
 249     /*
 250      * Returns 0 for any null argument
 251      */
 252     assertEquals(0, Dna.compareCodonPos(new AlignedCodon(1, 2, 3), null));
 253     assertEquals(0, Dna.compareCodonPos(null, new AlignedCodon(1, 2, 3)));
 254
 255     /*
 256      * Work through 27 combinations. First 9 cases where first position matches.
 257      */
 258     assertMatches("AAA", "GGG"); // 2 and 3 match
 259     assertFollows("AA-A", "GGG"); // 2 matches, 3 shifted seq1
 260     assertPrecedes("AAA", "GG-G"); // 2 matches, 3 shifted seq2
 261     assertFollows("A-AA", "GG-G"); // 2 shifted seq1, 3 matches
 262     assertFollows("A-A-A", "GG-G"); // 2 shifted seq1, 3 shifted seq1
 263     assertPrecedes("A-AA", "GG--G"); // 2 shifted seq1, 3 shifted seq2
 264     assertPrecedes("AA-A", "G-GG"); // 2 shifted seq2, 3 matches
 265     assertFollows("AA--A", "G-GG"); // 2 shifted seq2, 3 shifted seq1
 266     assertPrecedes("AAA", "G-GG"); // 2 shifted seq2, 3 shifted seq2
 267
 268     /*
 269      * 9 cases where first position is shifted in first sequence.
 270      */
 271     assertFollows("-AAA", "G-GG"); // 2 and 3 match
 272     assertFollows("-AA-A", "G-GG"); // 2 matches, 3 shifted seq1
 273     // 'enclosing' case: pick first to start precedes
 274     assertFollows("-AAA", "G-G-G"); // 2 matches, 3 shifted seq2
 275     assertFollows("-A-AA", "G-G-G"); // 2 shifted seq1, 3 matches
 276     assertFollows("-A-A-A", "G-G-G"); // 2 shifted seq1, 3 shifted seq1
 277     // 'enclosing' case: pick first to start precedes
 278     assertFollows("-A-AA", "G-G--G"); // 2 shifted seq1, 3 shifted seq2
 279     assertFollows("-AA-A", "G--GG"); // 2 shifted seq2, 3 matches
 280     assertFollows("-AA--A", "G--GG"); // 2 shifted seq2, 3 shifted seq1
 281     assertPrecedes("-AAA", "G--GG"); // 2 shifted seq2, 3 shifted seq2
 282
 283     /*
 284      * 9 cases where first position is shifted in second sequence.
 285      */
 286     assertPrecedes("A-AA", "-GGG"); // 2 and 3 match
 287     assertPrecedes("A-A-A", "-GGG"); // 2 matches, 3 shifted seq1
 288     assertPrecedes("A-AA", "-GG-G"); // 2 matches, 3 shifted seq2
 289     assertPrecedes("A--AA", "-GG-G"); // 2 shifted seq1, 3 matches
 290     // 'enclosing' case with middle base deciding:
 291     assertFollows("A--AA", "-GGG"); // 2 shifted seq1, 3 shifted seq1
 292     assertPrecedes("A--AA", "-GG--G"); // 2 shifted seq1, 3 shifted seq2
 293     assertPrecedes("AA-A", "-GGG"); // 2 shifted seq2, 3 matches
 294     assertPrecedes("AA--A", "-GGG"); // 2 shifted seq2, 3 shifted seq1
 295     assertPrecedes("AAA", "-GGG"); // 2 shifted seq2, 3 shifted seq2
 296   }
 297
 298   /**
 299    * This test generates a random cDNA alignment and its translation, then
 300    * reorders the cDNA and retranslates, and verifies that the translations are
 301    * the same (apart from ordering).
 302    */
 303   @Test(groups = { "Functional" })
 304   public void testTranslateCdna_sequenceOrderIndependent()
 305   {
 306     /*
 307      * Generate cDNA - 8 sequences of 12 bases each.
 308      */
 309     AlignmentI cdna = new AlignmentGenerator(true)
 310             .generate(12, 8, 97, 5, 5);
 311     HiddenColumns cs = new HiddenColumns();
 312     AlignViewportI av = new AlignViewport(cdna, cs);
 313     Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth(),
 314             false);
 315     Dna dna = new Dna(av, contigs);
 316     AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
 317             .getStandardCodeTable());
 318
 319     /*
 320      * Jumble the cDNA sequences and translate.
 321      */
 322     SequenceI[] sorted = new SequenceI[cdna.getHeight()];
 323     final int[] jumbler = new int[] { 6, 7, 3, 4, 2, 0, 1, 5 };
 324     int seqNo = 0;
 325     for (int i : jumbler)
 326     {
 327       sorted[seqNo++] = cdna.getSequenceAt(i);
 328     }
 329     AlignmentI cdnaReordered = new Alignment(sorted);
 330     av = new AlignViewport(cdnaReordered, cs);
 331     contigs = cs.getVisContigsIterator(0, cdna.getWidth(), false);
 332     dna = new Dna(av, contigs);
 333     AlignmentI translated2 = dna.translateCdna(GeneticCodes.getInstance()
 334             .getStandardCodeTable());
 335
 336     /*
 337      * Check translated sequences are the same in both alignments.
 338      */
 339     System.out.println("Original");
 340     System.out.println(translated.toString());
 341     System.out.println("Sorted");
 342     System.out.println(translated2.toString());
 343
 344     int sortedSequenceIndex = 0;
 345     for (int originalSequenceIndex : jumbler)
 346     {
 347       final String translation1 = translated.getSequenceAt(
 348               originalSequenceIndex).getSequenceAsString();
 349       final String translation2 = translated2.getSequenceAt(
 350               sortedSequenceIndex).getSequenceAsString();
 351       assertEquals(translation2, translation1);
 352       sortedSequenceIndex++;
 353     }
 354   }
 355
 356   /**
 357    * Test that all the cases in testCompareCodonPos have a 'symmetric'
 358    * comparison (without checking the actual comparison result).
 359    */
 360   @Test(groups = { "Functional" })
 361   public void testCompareCodonPos_isSymmetric()
 362   {
 363     assertSymmetric("AAA", "GGG");
 364     assertSymmetric("AA-A", "GGG");
 365     assertSymmetric("AAA", "GG-G");
 366     assertSymmetric("A-AA", "GG-G");
 367     assertSymmetric("A-A-A", "GG-G");
 368     assertSymmetric("A-AA", "GG--G");
 369     assertSymmetric("AA-A", "G-GG");
 370     assertSymmetric("AA--A", "G-GG");
 371     assertSymmetric("AAA", "G-GG");
 372     assertSymmetric("-AAA", "G-GG");
 373     assertSymmetric("-AA-A", "G-GG");
 374     assertSymmetric("-AAA", "G-G-G");
 375     assertSymmetric("-A-AA", "G-G-G");
 376     assertSymmetric("-A-A-A", "G-G-G");
 377     assertSymmetric("-A-AA", "G-G--G");
 378     assertSymmetric("-AA-A", "G--GG");
 379     assertSymmetric("-AA--A", "G--GG");
 380     assertSymmetric("-AAA", "G--GG");
 381     assertSymmetric("A-AA", "-GGG");
 382     assertSymmetric("A-A-A", "-GGG");
 383     assertSymmetric("A-AA", "-GG-G");
 384     assertSymmetric("A--AA", "-GG-G");
 385     assertSymmetric("A--AA", "-GGG");
 386     assertSymmetric("A--AA", "-GG--G");
 387     assertSymmetric("AA-A", "-GGG");
 388     assertSymmetric("AA--A", "-GGG");
 389     assertSymmetric("AAA", "-GGG");
 390   }
 391
 392   private void assertSymmetric(String codon1, String codon2)
 393   {
 394     assertEquals("Comparison of '" + codon1 + "' and '" + codon2
 395             + " not symmetric", Integer.signum(compare(codon1, codon2)),
 396             -Integer.signum(compare(codon2, codon1)));
 397   }
 398
 399   /**
 400    * Assert that the first sequence should map to the same position as the
 401    * second in a translated alignment. Also checks that this is true if the
 402    * order of the codons is reversed.
 403    *
 404    * @param codon1
 405    * @param codon2
 406    */
 407   private void assertMatches(String codon1, String codon2)
 408   {
 409     assertEquals("Expected '" + codon1 + "' matches '" + codon2 + "'", 0,
 410             compare(codon1, codon2));
 411     assertEquals("Expected '" + codon2 + "' matches '" + codon1 + "'", 0,
 412             compare(codon2, codon1));
 413   }
 414
 415   /**
 416    * Assert that the first sequence should precede the second in a translated
 417    * alignment
 418    *
 419    * @param codon1
 420    * @param codon2
 421    */
 422   private void assertPrecedes(String codon1, String codon2)
 423   {
 424     assertEquals("Expected '" + codon1 + "'  precedes '" + codon2 + "'",
 425             -1, compare(codon1, codon2));
 426   }
 427
 428   /**
 429    * Assert that the first sequence should follow the second in a translated
 430    * alignment
 431    *
 432    * @param codon1
 433    * @param codon2
 434    */
 435   private void assertFollows(String codon1, String codon2)
 436   {
 437     assertEquals("Expected '" + codon1 + "'  follows '" + codon2 + "'", 1,
 438             compare(codon1, codon2));
 439   }
 440
 441   /**
 442    * Convert two nucleotide strings to base positions and pass to
 443    * Dna.compareCodonPos, return the result.
 444    *
 445    * @param s1
 446    * @param s2
 447    * @return
 448    */
 449   private int compare(String s1, String s2)
 450   {
 451     final AlignedCodon cd1 = convertCodon(s1);
 452     final AlignedCodon cd2 = convertCodon(s2);
 453     System.out.println("K: " + s1 + "  " + cd1.toString());
 454     System.out.println("G: " + s2 + "  " + cd2.toString());
 455     System.out.println();
 456     return Dna.compareCodonPos(cd1, cd2);
 457   }
 458
 459   /**
 460    * Convert a string e.g. "-GC-T" to base positions e.g. [1, 2, 4]. The string
 461    * should have exactly 3 non-gap characters, and use '-' for gaps.
 462    *
 463    * @param s
 464    * @return
 465    */
 466   private AlignedCodon convertCodon(String s)
 467   {
 468     int[] codon = new int[3];
 469     int i = 0;
 470     for (int j = 0; j < s.length(); j++)
 471     {
 472       if (s.charAt(j) != '-')
 473       {
 474         codon[i++] = j;
 475       }
 476     }
 477     return new AlignedCodon(codon[0], codon[1], codon[2]);
 478   }
 479
 480   /**
 481    * Weirdly, maybe worth a test to prove the helper method of this test class.
 482    */
 483   @Test(groups = { "Functional" })
 484   public void testConvertCodon()
 485   {
 486     assertEquals("[0, 1, 2]", convertCodon("AAA").toString());
 487     assertEquals("[0, 2, 5]", convertCodon("A-A--A").toString());
 488     assertEquals("[1, 3, 4]", convertCodon("-A-AA-").toString());
 489   }
 490
 491   /**
 492    * Test dna complementing
 493    */
 494   @Test(groups = "Functional")
 495   public void testGetComplement()
 496   {
 497     assertEquals('t', Dna.getComplement('a'));
 498     assertEquals('T', Dna.getComplement('A'));
 499     assertEquals('a', Dna.getComplement('t'));
 500     assertEquals('A', Dna.getComplement('T'));
 501     assertEquals('c', Dna.getComplement('g'));
 502     assertEquals('C', Dna.getComplement('G'));
 503     assertEquals('g', Dna.getComplement('c'));
 504     assertEquals('G', Dna.getComplement('C'));
 505     // note uU --> aA but not vice versa
 506     assertEquals('a', Dna.getComplement('u'));
 507     assertEquals('A', Dna.getComplement('U'));
 508     // ambiguity codes, see http://www.bioinformatics.org/sms/iupac.html
 509     assertEquals('r', Dna.getComplement('y'));
 510     assertEquals('R', Dna.getComplement('Y'));
 511     assertEquals('y', Dna.getComplement('r'));
 512     assertEquals('Y', Dna.getComplement('R'));
 513     assertEquals('k', Dna.getComplement('m'));
 514     assertEquals('K', Dna.getComplement('M'));
 515     assertEquals('m', Dna.getComplement('k'));
 516     assertEquals('M', Dna.getComplement('K'));
 517     assertEquals('b', Dna.getComplement('v'));
 518     assertEquals('B', Dna.getComplement('V'));
 519     assertEquals('v', Dna.getComplement('b'));
 520     assertEquals('V', Dna.getComplement('B'));
 521     assertEquals('d', Dna.getComplement('h'));
 522     assertEquals('D', Dna.getComplement('H'));
 523     assertEquals('h', Dna.getComplement('d'));
 524     assertEquals('H', Dna.getComplement('D'));
 525     assertEquals('Q', Dna.getComplement('Q'));
 526   }
 527
 528   @Test(groups = "Functional")
 529   public void testReverseSequence()
 530   {
 531     String seq = "-Ac-GtU--rYkMbVdHNX-";
 532     String seqRev = new StringBuilder(seq).reverse().toString();
 533
 534     // reverse:
 535     SequenceI reversed = Dna.reverseSequence("Seq1", seq, false);
 536     assertEquals(1, reversed.getStart());
 537     assertEquals(15, reversed.getEnd());
 538     assertEquals(20, reversed.getLength());
 539     assertEquals(seqRev, reversed.getSequenceAsString());
 540     assertEquals("Seq1|rev", reversed.getName());
 541
 542     // reverse complement:
 543     SequenceI revcomp = Dna.reverseSequence("Seq1", seq, true);
 544     assertEquals("-XNDhBvKmRy--AaC-gT-", revcomp.getSequenceAsString());
 545     assertEquals("Seq1|revcomp", revcomp.getName());
 546   }
 547
 548   @Test(groups = "Functional")
 549   public void testReverseCdna()
 550   {
 551     String seq = "-Ac-GtU--rYkMbVdHNX-";
 552     String seqRev = new StringBuilder(seq).reverse().toString();
 553     String seqDs = seq.replaceAll("-", "");
 554     String seqDsRev = new StringBuilder(seqDs).reverse().toString();
 555
 556     SequenceI dna = new Sequence("Seq1", seq);
 557     Alignment al = new Alignment(new SequenceI[] { dna });
 558     al.createDatasetAlignment();
 559     assertEquals(seqDs, al.getSequenceAt(0).getDatasetSequence()
 560             .getSequenceAsString());
 561
 562     HiddenColumns cs = new HiddenColumns();
 563     AlignViewportI av = new AlignViewport(al, cs);
 564     Iterator<int[]> contigs = cs.getVisContigsIterator(0, al.getWidth(),
 565             false);
 566     Dna testee = new Dna(av, contigs);
 567     AlignmentI reversed = testee.reverseCdna(false);
 568     assertEquals(1, reversed.getHeight());
 569     assertEquals(seqRev, reversed.getSequenceAt(0).getSequenceAsString());
 570     assertEquals(seqDsRev, reversed.getSequenceAt(0).getDatasetSequence()
 571             .getSequenceAsString());
 572   }
 573 }