test/jalview/analysis/DnaTest.java

   1 package jalview.analysis;
   2
   3 import static org.junit.Assert.assertEquals;
   4 import jalview.datamodel.AlignmentI;
   5 import jalview.datamodel.ColumnSelection;
   6 import jalview.io.FormatAdapter;
   7
   8 import java.io.IOException;
   9
  10 import org.junit.Test;
  11
  12 public class DnaTest
  13 {
  14   // AA encoding codons as ordered on the Jalview help page Amino Acid Table
  15   private static String fasta = ">B\n" + "GCT" + "GCC" + "GCA" + "GCG"
  16           + "TGT" + "TGC" + "GAT" + "GAC" + "GAA" + "GAG" + "TTT" + "TTC"
  17           + "GGT" + "GGC" + "GGA" + "GGG" + "CAT" + "CAC" + "ATT" + "ATC"
  18           + "ATA" + "AAA" + "AAG" + "TTG" + "TTA" + "CTT" + "CTC" + "CTA"
  19           + "CTG" + "ATG" + "AAT" + "AAC" + "CCT" + "CCC" + "CCA" + "CCG"
  20           + "CAA" + "CAG" + "CGT" + "CGC" + "CGA" + "CGG" + "AGA" + "AGG"
  21           + "TCT" + "TCC" + "TCA" + "TCG" + "AGT" + "AGC" + "ACT" + "ACC"
  22           + "ACA" + "ACG" + "GTT" + "GTC" + "GTA" + "GTG" + "TGG" + "TAT"
  23           + "TAC" + "TAA" + "TAG" + "TGA";
  24
  25   /**
  26    * Test simple translation to Amino Acids (with STOP codons translated to X).
  27    *
  28    * @throws IOException
  29    */
  30   @Test
  31   public void testCdnaTranslate_simple() throws IOException
  32   {
  33     AlignmentI alf = new FormatAdapter().readFile(fasta,
  34             FormatAdapter.PASTE, "FASTA");
  35     final String sequenceAsString = alf
  36                 .getSequenceAt(0).getSequenceAsString();
  37     AlignmentI translated = Dna.CdnaTranslate(alf.getSequencesArray(),
  38             new String[]
  39             { sequenceAsString }, new int[]
  40             { 0, alf.getWidth() - 1 }, alf.getGapCharacter(), null,
  41             alf.getWidth(), null);
  42     String aa = translated.getSequenceAt(0).getSequenceAsString();
  43     assertEquals(
  44             "AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYYXXX",
  45             aa);
  46   }
  47
  48   /**
  49    * Test translation excluding hidden columns.
  50    *
  51    * @throws IOException
  52    */
  53   @Test
  54   public void testCdnaTranslate_hiddenColumns() throws IOException
  55   {
  56     AlignmentI alf = new FormatAdapter().readFile(fasta,
  57             FormatAdapter.PASTE, "FASTA");
  58     ColumnSelection cs = new jalview.datamodel.ColumnSelection();
  59     cs.hideColumns(6, 14); // hide codons 3/4/5
  60     cs.hideColumns(24, 35); // hide codons 9-12
  61     cs.hideColumns(177, 191); // hide codons 60-64
  62     AlignmentI translated = Dna.CdnaTranslate(alf.getSequencesArray(),
  63             cs.getVisibleSequenceStrings(0, alf.getWidth(),
  64                     alf.getSequencesArray()), new int[]
  65             { 0, alf.getWidth() - 1 }, alf.getGapCharacter(), null,
  66             alf.getWidth(), null);
  67     String aa = translated.getSequenceAt(0).getSequenceAsString();
  68     assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa);
  69   }
  70 }