/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
 * Copyright (C) 2014 The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
 *  
 * Jalview is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty 
 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 * PURPOSE.  See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.analysis;

import static org.junit.Assert.*;
import jalview.datamodel.ColumnSelection;

import java.io.IOException;

import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
import org.junit.runner.RunWith;

public class DnaTranslation
{

  private static String JAL_1312_example_align_fasta = ">B.FR.83.HXB2_LAI_IIIB_BRU_K03455/45-306\n"
          + "ATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
          + "GGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACA\n"
          + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTG\n"
          + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAC\n"
          + ">gi|27804621|gb|AY178912.1|/1-259\n"
          + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
          + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGGACA\n"
          + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
          + "TGTTCATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAT\n"
          + ">gi|27804623|gb|AY178913.1|/1-259\n"
          + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
          + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGAACA\n"
          + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
          + "TGTTCATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
          + ">gi|27804627|gb|AY178915.1|/1-260\n"
          + "-TGGGAAAA-ATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
          + "GGAGCTAGAACGATTCGCAGTTAACCCTGGCCTGTTAGAAACATCAGAAGGTTGTAGACAAATATTGGGACA\n"
          + "GCTACAACCATCCCTTGAGACAGGATCAGAAGAACTTAAATCATTATWTAATACCATAGCAGTCCTCTATTG\n"
          + "TGTACATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAG\n"
          + ">gi|27804631|gb|AY178917.1|/1-261\n"
          + "-TGGGAAAAAATTCGGTTGAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
          + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACACCAGAAGGCTGTAGACAAATACTGGGACA\n"
          + "GCTACAACCGTCCCTTCAGACAGGATCGGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
          + "TGTGCATCAAAGGATAGATGTAAAAGACACCAAGGAGGCTTTAGAC\n"
          + ">gi|27804635|gb|AY178919.1|/1-261\n"
          + "-TGGGAGAGAATTCGGTTACGGCCAGGAGGAAAGAAAAAATATAAATTGAAACATATAGTATGGGCAGGCAG\n"
          + "AGAGCTAGATCGATTCGCAGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAGATATTGGGACA\n"
          + "GCTACAACCGTCCCTTAAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
          + "TGTACATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
          + ">gi|27804641|gb|AY178922.1|/1-261\n"
          + "-TGGGAGAAAATTCGGTTACGGCCAGGGGGAAAGAAAAGATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
          + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAAATACTGGGACA\n"
          + "GTTACACCCATCCCTTCATACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
          + "TGTGCATCAAAGGATAGAAGTAAAAGACACCAAGGAAGCTTTAGAC\n"
          + ">gi|27804647|gb|AY178925.1|/1-261\n"
          + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATCAATTAAAACATGTAGTATGGGCAAGCAG\n"
          + "GGAACTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
          + "GCTACAACCATCCCTTCAGACAGGATCAGAGGAACTTAAATCATTATTTAATACAGTAGCAGTCCTCTATTG\n"
          + "TGTACATCAAAGAATAGATGTAAAAGACACCAAGGAAGCTCTAGAA\n"
          + ">gi|27804649|gb|AY178926.1|/1-261\n"
          + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
          + "GGAGCTAGAACGATTCGCGGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAACTACTGGGACA\n"
          + "GTTACAACCATCCCTTCAGACAGGATCAGAAGAACTCAAATCATTATATAATACAATAGCAACCCTCTATTG\n"
          + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCCTTAGAT\n"
          + ">gi|27804653|gb|AY178928.1|/1-261\n"
          + "-TGGGAAAGAATTCGGTTAAGGCCAGGGGGAAAGAAACAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
          + "GGAGCTAGACCGATTCGCACTTAACCCCGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
          + "GCTACAATCGTCCCTTCAGACAGGATCAGAAGAACTTAGATCACTATATAATACAGTAGCAGTCCTCTATTG\n"
          + "TGTGCATCAAAAGATAGATGTAAAAGACACCAAGGAAGCCTTAGAC\n"
          + ">gi|27804659|gb|AY178931.1|/1-261\n"
          + "-TGGGAAAAAATTCGGTTACGGCCAGGAGGAAAGAAAAGATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
          + "GGAGCTAGAACGATTYGCAGTTAATCCTGGCCTTTTAGAAACAGCAGAAGGCTGTAGACAAATACTGGGACA\n"
          + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
          + "TGTACATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAA\n";

  
  @Test
  public void translationWithUntranslatableCodonsTest()
  {
    // Corner case for this test is the presence of codons after codons that
    // were not translated.
    jalview.datamodel.AlignmentI alf = null;
    try
    {
      alf = new jalview.io.FormatAdapter().readFile(JAL_1312_example_align_fasta,
              jalview.io.FormatAdapter.PASTE, "FASTA");
    } catch (IOException x)
    {
      x.printStackTrace();
      fail("Unexpected IOException (" + x.getMessage()
              + ") - check test environment");
    }
    {
      // full translation
      ColumnSelection cs = new jalview.datamodel.ColumnSelection();
      assertNotNull("Couldn't do a full width translation of test data.",
              jalview.analysis.Dna.CdnaTranslate(
                      alf.getSequencesArray(),
                      cs.getVisibleSequenceStrings(0, alf.getWidth(),
                              alf.getSequencesArray()), new int[]
                      { 0, alf.getWidth() - 1 }, alf.getGapCharacter(),
                      null, alf.getWidth(), null));
    }
    int vwidth = 15; // translate in 15 base stretches
    for (int ipos = 0; ipos + vwidth < alf.getWidth(); ipos += vwidth)
    {
      ColumnSelection cs = new jalview.datamodel.ColumnSelection();
      if (ipos > 0)
      {
        cs.hideColumns(0, ipos - 1);
      }
      cs.hideColumns(ipos + vwidth, alf.getWidth());
      int[] vcontigs = cs.getVisibleContigs(0, alf.getWidth());
      String[] sel = cs.getVisibleSequenceStrings(0, alf.getWidth(),
              alf.getSequencesArray());
      jalview.datamodel.AlignmentI transAlf = jalview.analysis.Dna
              .CdnaTranslate(alf.getSequencesArray(), sel, vcontigs,
                      alf.getGapCharacter(), null, alf.getWidth(), null);

      assertTrue("Translation failed (ipos=" + ipos
              + ") No alignment data.", transAlf != null);
      assertTrue("Translation failed (ipos=" + ipos + ") Empty algnment.",
              transAlf.getHeight() > 0);
      assertTrue("Translation failed (ipos=" + ipos + ") Translated "
              + transAlf.getHeight() + " sequences from " + alf.getHeight()
              + " sequences", alf.getHeight() == transAlf.getHeight());
    }

  }
}