test/jalview/schemes/ResiduePropertiesTest.java

   1 package jalview.schemes;
   2
   3 import static org.junit.Assert.assertEquals;
   4 import static org.junit.Assert.assertNull;
   5
   6 import org.junit.Test;
   7
   8 public class ResiduePropertiesTest
   9 {
  10
  11   /**
  12    * Test 'standard' codon translations (no ambiguity codes)
  13    */
  14   @Test
  15   public void testCodonTranslate()
  16   {
  17     // standard translation table order column 1/2/3/4
  18     assertEquals("F", ResidueProperties.codonTranslate("TTT"));
  19     assertEquals("F", ResidueProperties.codonTranslate("TTC"));
  20     assertEquals("L", ResidueProperties.codonTranslate("TTA"));
  21     assertEquals("L", ResidueProperties.codonTranslate("TTG"));
  22     assertEquals("L", ResidueProperties.codonTranslate("CTT"));
  23     assertEquals("L", ResidueProperties.codonTranslate("CTC"));
  24     assertEquals("L", ResidueProperties.codonTranslate("CTA"));
  25     assertEquals("L", ResidueProperties.codonTranslate("CTG"));
  26     assertEquals("I", ResidueProperties.codonTranslate("ATT"));
  27     assertEquals("I", ResidueProperties.codonTranslate("ATC"));
  28     assertEquals("I", ResidueProperties.codonTranslate("ATA"));
  29     assertEquals("M", ResidueProperties.codonTranslate("ATG"));
  30     assertEquals("V", ResidueProperties.codonTranslate("GTT"));
  31     assertEquals("V", ResidueProperties.codonTranslate("GTC"));
  32     assertEquals("V", ResidueProperties.codonTranslate("GTA"));
  33     assertEquals("V", ResidueProperties.codonTranslate("GTG"));
  34     assertEquals("S", ResidueProperties.codonTranslate("TCT"));
  35     assertEquals("S", ResidueProperties.codonTranslate("TCC"));
  36     assertEquals("S", ResidueProperties.codonTranslate("TCA"));
  37     assertEquals("S", ResidueProperties.codonTranslate("TCG"));
  38     assertEquals("P", ResidueProperties.codonTranslate("CCT"));
  39     assertEquals("P", ResidueProperties.codonTranslate("CCC"));
  40     assertEquals("P", ResidueProperties.codonTranslate("CCA"));
  41     assertEquals("P", ResidueProperties.codonTranslate("CCG"));
  42     assertEquals("T", ResidueProperties.codonTranslate("ACT"));
  43     assertEquals("T", ResidueProperties.codonTranslate("ACC"));
  44     assertEquals("T", ResidueProperties.codonTranslate("ACA"));
  45     assertEquals("T", ResidueProperties.codonTranslate("ACG"));
  46     assertEquals("A", ResidueProperties.codonTranslate("GCT"));
  47     assertEquals("A", ResidueProperties.codonTranslate("GCC"));
  48     assertEquals("A", ResidueProperties.codonTranslate("GCA"));
  49     assertEquals("A", ResidueProperties.codonTranslate("GCG"));
  50     assertEquals("Y", ResidueProperties.codonTranslate("TAT"));
  51     assertEquals("Y", ResidueProperties.codonTranslate("TAC"));
  52     assertEquals("STOP", ResidueProperties.codonTranslate("TAA"));
  53     assertEquals("STOP", ResidueProperties.codonTranslate("TAG"));
  54     assertEquals("H", ResidueProperties.codonTranslate("CAT"));
  55     assertEquals("H", ResidueProperties.codonTranslate("CAC"));
  56     assertEquals("Q", ResidueProperties.codonTranslate("CAA"));
  57     assertEquals("Q", ResidueProperties.codonTranslate("CAG"));
  58     assertEquals("N", ResidueProperties.codonTranslate("AAT"));
  59     assertEquals("N", ResidueProperties.codonTranslate("AAC"));
  60     assertEquals("K", ResidueProperties.codonTranslate("AAA"));
  61     assertEquals("K", ResidueProperties.codonTranslate("AAG"));
  62     assertEquals("D", ResidueProperties.codonTranslate("GAT"));
  63     assertEquals("D", ResidueProperties.codonTranslate("GAC"));
  64     assertEquals("E", ResidueProperties.codonTranslate("GAA"));
  65     assertEquals("E", ResidueProperties.codonTranslate("GAG"));
  66     assertEquals("C", ResidueProperties.codonTranslate("TGT"));
  67     assertEquals("C", ResidueProperties.codonTranslate("TGC"));
  68     assertEquals("STOP", ResidueProperties.codonTranslate("TGA"));
  69     assertEquals("W", ResidueProperties.codonTranslate("TGG"));
  70     assertEquals("R", ResidueProperties.codonTranslate("CGT"));
  71     assertEquals("R", ResidueProperties.codonTranslate("CGC"));
  72     assertEquals("R", ResidueProperties.codonTranslate("CGA"));
  73     assertEquals("R", ResidueProperties.codonTranslate("CGG"));
  74     assertEquals("S", ResidueProperties.codonTranslate("AGT"));
  75     assertEquals("S", ResidueProperties.codonTranslate("AGC"));
  76     assertEquals("R", ResidueProperties.codonTranslate("AGA"));
  77     assertEquals("R", ResidueProperties.codonTranslate("AGG"));
  78     assertEquals("G", ResidueProperties.codonTranslate("GGT"));
  79     assertEquals("G", ResidueProperties.codonTranslate("GGC"));
  80     assertEquals("G", ResidueProperties.codonTranslate("GGA"));
  81     assertEquals("G", ResidueProperties.codonTranslate("GGG"));
  82   }
  83
  84   /**
  85    * Test a sample of codon translations involving ambiguity codes. Should
  86    * return a protein value where the ambiguity does not affect the translation.
  87    */
  88   @Test
  89   public void testCodonTranslate_ambiguityCodes()
  90   {
  91     // Y is C or T
  92     assertEquals("C", ResidueProperties.codonTranslate("TGY"));
  93     assertEquals("L", ResidueProperties.codonTranslate("YTA"));
  94
  95     // W is A or T
  96     assertEquals("L", ResidueProperties.codonTranslate("CTW"));
  97     assertNull(ResidueProperties.codonTranslate("TTW"));
  98
  99     // S is G or C
 100     assertEquals("G", ResidueProperties.codonTranslate("GGS"));
 101     assertNull(ResidueProperties.codonTranslate("ATS"));
 102
 103     // K is T or G
 104     assertEquals("S", ResidueProperties.codonTranslate("TCS"));
 105     assertNull(ResidueProperties.codonTranslate("ATK"));
 106
 107     // M is C or A
 108     assertEquals("T", ResidueProperties.codonTranslate("ACM"));
 109     assertNull(ResidueProperties.codonTranslate("TAM"));
 110
 111     // D is A, G or T
 112     assertEquals("P", ResidueProperties.codonTranslate("CCD"));
 113     assertNull(ResidueProperties.codonTranslate("AAD"));
 114
 115     // V is A, C or G
 116     assertEquals("V", ResidueProperties.codonTranslate("GTV"));
 117     assertNull(ResidueProperties.codonTranslate("TTV"));
 118
 119     // H is A, C or T
 120     assertEquals("A", ResidueProperties.codonTranslate("GCH"));
 121     assertEquals("I", ResidueProperties.codonTranslate("ATH"));
 122     assertNull(ResidueProperties.codonTranslate("AGH"));
 123
 124     // B is C, G or T
 125     assertEquals("P", ResidueProperties.codonTranslate("CCB"));
 126     assertNull(ResidueProperties.codonTranslate("TAB"));
 127
 128     // R is A or G
 129     assertEquals("R", ResidueProperties.codonTranslate("AGR"));
 130     assertEquals("STOP", ResidueProperties.codonTranslate("TAR"));
 131     assertEquals("STOP", ResidueProperties.codonTranslate("TRA"));
 132     assertNull(ResidueProperties.codonTranslate("ATR"));
 133
 134   }
 135 }