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.
    try {
      jalview.datamodel.AlignmentI alf = new jalview.io.FormatAdapter().readFile(JAL_1312_example_align_fasta, jalview.io.FormatAdapter.PASTE, "FASTA");
      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());
      }
    } catch (IOException x)
    {
      x.printStackTrace();
      fail("Unexpected IOException ("+x.getMessage()+") - check test environment");
    }
  }

}