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     // Phenylalanine first base variation
  94     assertEquals("L", ResidueProperties.codonTranslate("YTA"));
  95
  96     // W is A or T
  97     assertEquals("L", ResidueProperties.codonTranslate("CTW"));
  98     assertNull(ResidueProperties.codonTranslate("TTW"));
  99
 100     // S is G or C
 101     assertEquals("G", ResidueProperties.codonTranslate("GGS"));
 102     assertNull(ResidueProperties.codonTranslate("ATS"));
 103
 104     // K is T or G
 105     assertEquals("S", ResidueProperties.codonTranslate("TCK"));
 106     assertNull(ResidueProperties.codonTranslate("ATK"));
 107
 108     // M is C or A
 109     assertEquals("T", ResidueProperties.codonTranslate("ACM"));
 110     // Arginine first base variation
 111     assertEquals("R", ResidueProperties.codonTranslate("MGA"));
 112     assertEquals("R", ResidueProperties.codonTranslate("MGG"));
 113     assertNull(ResidueProperties.codonTranslate("TAM"));
 114
 115     // D is A, G or T
 116     assertEquals("P", ResidueProperties.codonTranslate("CCD"));
 117     assertNull(ResidueProperties.codonTranslate("AAD"));
 118
 119     // V is A, C or G
 120     assertEquals("V", ResidueProperties.codonTranslate("GTV"));
 121     assertNull(ResidueProperties.codonTranslate("TTV"));
 122
 123     // H is A, C or T
 124     assertEquals("A", ResidueProperties.codonTranslate("GCH"));
 125     assertEquals("I", ResidueProperties.codonTranslate("ATH"));
 126     assertNull(ResidueProperties.codonTranslate("AGH"));
 127
 128     // B is C, G or T
 129     assertEquals("P", ResidueProperties.codonTranslate("CCB"));
 130     assertNull(ResidueProperties.codonTranslate("TAB"));
 131
 132     // R is A or G
 133     // additional tests for JAL-1685 (resolved)
 134     assertEquals("L", ResidueProperties.codonTranslate("CTR"));
 135     assertEquals("V", ResidueProperties.codonTranslate("GTR"));
 136     assertEquals("S", ResidueProperties.codonTranslate("TCR"));
 137     assertEquals("P", ResidueProperties.codonTranslate("CCR"));
 138     assertEquals("T", ResidueProperties.codonTranslate("ACR"));
 139     assertEquals("A", ResidueProperties.codonTranslate("GCR"));
 140     assertEquals("R", ResidueProperties.codonTranslate("CGR"));
 141     assertEquals("G", ResidueProperties.codonTranslate("GGR"));
 142     assertEquals("R", ResidueProperties.codonTranslate("AGR"));
 143     assertEquals("E", ResidueProperties.codonTranslate("GAR"));
 144     assertEquals("K", ResidueProperties.codonTranslate("AAR"));
 145     assertEquals("L", ResidueProperties.codonTranslate("TTR"));
 146     assertEquals("Q", ResidueProperties.codonTranslate("CAR"));
 147     assertEquals("STOP", ResidueProperties.codonTranslate("TAR"));
 148     assertEquals("STOP", ResidueProperties.codonTranslate("TRA"));
 149     // Arginine first and third base ambiguity
 150     assertEquals("R", ResidueProperties.codonTranslate("MGR"));
 151     assertNull(ResidueProperties.codonTranslate("ATR"));
 152
 153     // N is any base; 8 proteins accept any base in 3rd position
 154     assertEquals("L", ResidueProperties.codonTranslate("CTN"));
 155     assertEquals("V", ResidueProperties.codonTranslate("GTN"));
 156     assertEquals("S", ResidueProperties.codonTranslate("TCN"));
 157     assertEquals("P", ResidueProperties.codonTranslate("CCN"));
 158     assertEquals("T", ResidueProperties.codonTranslate("ACN"));
 159     assertEquals("A", ResidueProperties.codonTranslate("GCN"));
 160     assertEquals("R", ResidueProperties.codonTranslate("CGN"));
 161     assertEquals("G", ResidueProperties.codonTranslate("GGN"));
 162     assertNull(ResidueProperties.codonTranslate("ATN"));
 163     assertNull(ResidueProperties.codonTranslate("ANT"));
 164     assertNull(ResidueProperties.codonTranslate("NAT"));
 165     assertNull(ResidueProperties.codonTranslate("ANN"));
 166     assertNull(ResidueProperties.codonTranslate("NNA"));
 167     assertNull(ResidueProperties.codonTranslate("NNN"));
 168
 169     // some random stuff
 170     assertNull(ResidueProperties.codonTranslate("YWB"));
 171     assertNull(ResidueProperties.codonTranslate("VHD"));
 172     assertNull(ResidueProperties.codonTranslate("WSK"));
 173   }
 174 }