package jalview.schemes;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNull;

import org.junit.Test;

public class ResiduePropertiesTest
{

  /**
   * Test 'standard' codon translations (no ambiguity codes)
   */
  @Test
  public void testCodonTranslate()
  {
    // standard translation table order column 1/2/3/4
    assertEquals("F", ResidueProperties.codonTranslate("TTT"));
    assertEquals("F", ResidueProperties.codonTranslate("TTC"));
    assertEquals("L", ResidueProperties.codonTranslate("TTA"));
    assertEquals("L", ResidueProperties.codonTranslate("TTG"));
    assertEquals("L", ResidueProperties.codonTranslate("CTT"));
    assertEquals("L", ResidueProperties.codonTranslate("CTC"));
    assertEquals("L", ResidueProperties.codonTranslate("CTA"));
    assertEquals("L", ResidueProperties.codonTranslate("CTG"));
    assertEquals("I", ResidueProperties.codonTranslate("ATT"));
    assertEquals("I", ResidueProperties.codonTranslate("ATC"));
    assertEquals("I", ResidueProperties.codonTranslate("ATA"));
    assertEquals("M", ResidueProperties.codonTranslate("ATG"));
    assertEquals("V", ResidueProperties.codonTranslate("GTT"));
    assertEquals("V", ResidueProperties.codonTranslate("GTC"));
    assertEquals("V", ResidueProperties.codonTranslate("GTA"));
    assertEquals("V", ResidueProperties.codonTranslate("GTG"));
    assertEquals("S", ResidueProperties.codonTranslate("TCT"));
    assertEquals("S", ResidueProperties.codonTranslate("TCC"));
    assertEquals("S", ResidueProperties.codonTranslate("TCA"));
    assertEquals("S", ResidueProperties.codonTranslate("TCG"));
    assertEquals("P", ResidueProperties.codonTranslate("CCT"));
    assertEquals("P", ResidueProperties.codonTranslate("CCC"));
    assertEquals("P", ResidueProperties.codonTranslate("CCA"));
    assertEquals("P", ResidueProperties.codonTranslate("CCG"));
    assertEquals("T", ResidueProperties.codonTranslate("ACT"));
    assertEquals("T", ResidueProperties.codonTranslate("ACC"));
    assertEquals("T", ResidueProperties.codonTranslate("ACA"));
    assertEquals("T", ResidueProperties.codonTranslate("ACG"));
    assertEquals("A", ResidueProperties.codonTranslate("GCT"));
    assertEquals("A", ResidueProperties.codonTranslate("GCC"));
    assertEquals("A", ResidueProperties.codonTranslate("GCA"));
    assertEquals("A", ResidueProperties.codonTranslate("GCG"));
    assertEquals("Y", ResidueProperties.codonTranslate("TAT"));
    assertEquals("Y", ResidueProperties.codonTranslate("TAC"));
    assertEquals("STOP", ResidueProperties.codonTranslate("TAA"));
    assertEquals("STOP", ResidueProperties.codonTranslate("TAG"));
    assertEquals("H", ResidueProperties.codonTranslate("CAT"));
    assertEquals("H", ResidueProperties.codonTranslate("CAC"));
    assertEquals("Q", ResidueProperties.codonTranslate("CAA"));
    assertEquals("Q", ResidueProperties.codonTranslate("CAG"));
    assertEquals("N", ResidueProperties.codonTranslate("AAT"));
    assertEquals("N", ResidueProperties.codonTranslate("AAC"));
    assertEquals("K", ResidueProperties.codonTranslate("AAA"));
    assertEquals("K", ResidueProperties.codonTranslate("AAG"));
    assertEquals("D", ResidueProperties.codonTranslate("GAT"));
    assertEquals("D", ResidueProperties.codonTranslate("GAC"));
    assertEquals("E", ResidueProperties.codonTranslate("GAA"));
    assertEquals("E", ResidueProperties.codonTranslate("GAG"));
    assertEquals("C", ResidueProperties.codonTranslate("TGT"));
    assertEquals("C", ResidueProperties.codonTranslate("TGC"));
    assertEquals("STOP", ResidueProperties.codonTranslate("TGA"));
    assertEquals("W", ResidueProperties.codonTranslate("TGG"));
    assertEquals("R", ResidueProperties.codonTranslate("CGT"));
    assertEquals("R", ResidueProperties.codonTranslate("CGC"));
    assertEquals("R", ResidueProperties.codonTranslate("CGA"));
    assertEquals("R", ResidueProperties.codonTranslate("CGG"));
    assertEquals("S", ResidueProperties.codonTranslate("AGT"));
    assertEquals("S", ResidueProperties.codonTranslate("AGC"));
    assertEquals("R", ResidueProperties.codonTranslate("AGA"));
    assertEquals("R", ResidueProperties.codonTranslate("AGG"));
    assertEquals("G", ResidueProperties.codonTranslate("GGT"));
    assertEquals("G", ResidueProperties.codonTranslate("GGC"));
    assertEquals("G", ResidueProperties.codonTranslate("GGA"));
    assertEquals("G", ResidueProperties.codonTranslate("GGG"));
  }

  /**
   * Test a sample of codon translations involving ambiguity codes. Should
   * return a protein value where the ambiguity does not affect the translation.
   */
  @Test
  public void testCodonTranslate_ambiguityCodes()
  {
    // Y is C or T
    assertEquals("C", ResidueProperties.codonTranslate("TGY"));
    assertEquals("L", ResidueProperties.codonTranslate("YTA"));

    // W is A or T
    assertEquals("L", ResidueProperties.codonTranslate("CTW"));
    assertNull(ResidueProperties.codonTranslate("TTW"));

    // S is G or C
    assertEquals("G", ResidueProperties.codonTranslate("GGS"));
    assertNull(ResidueProperties.codonTranslate("ATS"));

    // K is T or G
    assertEquals("S", ResidueProperties.codonTranslate("TCS"));
    assertNull(ResidueProperties.codonTranslate("ATK"));

    // M is C or A
    assertEquals("T", ResidueProperties.codonTranslate("ACM"));
    assertNull(ResidueProperties.codonTranslate("TAM"));

    // D is A, G or T
    assertEquals("P", ResidueProperties.codonTranslate("CCD"));
    assertNull(ResidueProperties.codonTranslate("AAD"));

    // V is A, C or G
    assertEquals("V", ResidueProperties.codonTranslate("GTV"));
    assertNull(ResidueProperties.codonTranslate("TTV"));

    // H is A, C or T
    assertEquals("A", ResidueProperties.codonTranslate("GCH"));
    assertEquals("I", ResidueProperties.codonTranslate("ATH"));
    assertNull(ResidueProperties.codonTranslate("AGH"));

    // B is C, G or T
    assertEquals("P", ResidueProperties.codonTranslate("CCB"));
    assertNull(ResidueProperties.codonTranslate("TAB"));

    // R is A or G
    assertEquals("R", ResidueProperties.codonTranslate("AGR"));
    assertEquals("STOP", ResidueProperties.codonTranslate("TAR"));
    assertEquals("STOP", ResidueProperties.codonTranslate("TRA"));
    assertNull(ResidueProperties.codonTranslate("ATR"));

  }
}