test/jalview/schemes/ResiduePropertiesTest.java

   1 package jalview.schemes;
   2
   3 import static org.testng.AssertJUnit.assertEquals;
   4 import static org.testng.AssertJUnit.assertNull;
   5
   6 import java.util.Collections;
   7 import java.util.List;
   8
   9 import org.testng.annotations.Test;
  10
  11 public class ResiduePropertiesTest
  12 {
  13
  14   /**
  15    * Test 'standard' codon translations (no ambiguity codes)
  16    */
  17   @Test
  18   public void testCodonTranslate()
  19   {
  20     // standard translation table order column 1/2/3/4
  21     assertEquals("F", ResidueProperties.codonTranslate("TTT"));
  22     assertEquals("F", ResidueProperties.codonTranslate("TTC"));
  23     assertEquals("L", ResidueProperties.codonTranslate("TTA"));
  24     assertEquals("L", ResidueProperties.codonTranslate("TTG"));
  25     assertEquals("L", ResidueProperties.codonTranslate("CTT"));
  26     assertEquals("L", ResidueProperties.codonTranslate("CTC"));
  27     assertEquals("L", ResidueProperties.codonTranslate("CTA"));
  28     assertEquals("L", ResidueProperties.codonTranslate("CTG"));
  29     assertEquals("I", ResidueProperties.codonTranslate("ATT"));
  30     assertEquals("I", ResidueProperties.codonTranslate("ATC"));
  31     assertEquals("I", ResidueProperties.codonTranslate("ATA"));
  32     assertEquals("M", ResidueProperties.codonTranslate("ATG"));
  33     assertEquals("V", ResidueProperties.codonTranslate("GTT"));
  34     assertEquals("V", ResidueProperties.codonTranslate("GTC"));
  35     assertEquals("V", ResidueProperties.codonTranslate("GTA"));
  36     assertEquals("V", ResidueProperties.codonTranslate("GTG"));
  37     assertEquals("S", ResidueProperties.codonTranslate("TCT"));
  38     assertEquals("S", ResidueProperties.codonTranslate("TCC"));
  39     assertEquals("S", ResidueProperties.codonTranslate("TCA"));
  40     assertEquals("S", ResidueProperties.codonTranslate("TCG"));
  41     assertEquals("P", ResidueProperties.codonTranslate("CCT"));
  42     assertEquals("P", ResidueProperties.codonTranslate("CCC"));
  43     assertEquals("P", ResidueProperties.codonTranslate("CCA"));
  44     assertEquals("P", ResidueProperties.codonTranslate("CCG"));
  45     assertEquals("T", ResidueProperties.codonTranslate("ACT"));
  46     assertEquals("T", ResidueProperties.codonTranslate("ACC"));
  47     assertEquals("T", ResidueProperties.codonTranslate("ACA"));
  48     assertEquals("T", ResidueProperties.codonTranslate("ACG"));
  49     assertEquals("A", ResidueProperties.codonTranslate("GCT"));
  50     assertEquals("A", ResidueProperties.codonTranslate("GCC"));
  51     assertEquals("A", ResidueProperties.codonTranslate("GCA"));
  52     assertEquals("A", ResidueProperties.codonTranslate("GCG"));
  53     assertEquals("Y", ResidueProperties.codonTranslate("TAT"));
  54     assertEquals("Y", ResidueProperties.codonTranslate("TAC"));
  55     assertEquals("STOP", ResidueProperties.codonTranslate("TAA"));
  56     assertEquals("STOP", ResidueProperties.codonTranslate("TAG"));
  57     assertEquals("H", ResidueProperties.codonTranslate("CAT"));
  58     assertEquals("H", ResidueProperties.codonTranslate("CAC"));
  59     assertEquals("Q", ResidueProperties.codonTranslate("CAA"));
  60     assertEquals("Q", ResidueProperties.codonTranslate("CAG"));
  61     assertEquals("N", ResidueProperties.codonTranslate("AAT"));
  62     assertEquals("N", ResidueProperties.codonTranslate("AAC"));
  63     assertEquals("K", ResidueProperties.codonTranslate("AAA"));
  64     assertEquals("K", ResidueProperties.codonTranslate("AAG"));
  65     assertEquals("D", ResidueProperties.codonTranslate("GAT"));
  66     assertEquals("D", ResidueProperties.codonTranslate("GAC"));
  67     assertEquals("E", ResidueProperties.codonTranslate("GAA"));
  68     assertEquals("E", ResidueProperties.codonTranslate("GAG"));
  69     assertEquals("C", ResidueProperties.codonTranslate("TGT"));
  70     assertEquals("C", ResidueProperties.codonTranslate("TGC"));
  71     assertEquals("STOP", ResidueProperties.codonTranslate("TGA"));
  72     assertEquals("W", ResidueProperties.codonTranslate("TGG"));
  73     assertEquals("R", ResidueProperties.codonTranslate("CGT"));
  74     assertEquals("R", ResidueProperties.codonTranslate("CGC"));
  75     assertEquals("R", ResidueProperties.codonTranslate("CGA"));
  76     assertEquals("R", ResidueProperties.codonTranslate("CGG"));
  77     assertEquals("S", ResidueProperties.codonTranslate("AGT"));
  78     assertEquals("S", ResidueProperties.codonTranslate("AGC"));
  79     assertEquals("R", ResidueProperties.codonTranslate("AGA"));
  80     assertEquals("R", ResidueProperties.codonTranslate("AGG"));
  81     assertEquals("G", ResidueProperties.codonTranslate("GGT"));
  82     assertEquals("G", ResidueProperties.codonTranslate("GGC"));
  83     assertEquals("G", ResidueProperties.codonTranslate("GGA"));
  84     assertEquals("G", ResidueProperties.codonTranslate("GGG"));
  85   }
  86
  87   /**
  88    * Test a sample of codon translations involving ambiguity codes. Should
  89    * return a protein value where the ambiguity does not affect the translation.
  90    */
  91   @Test
  92   public void testCodonTranslate_ambiguityCodes()
  93   {
  94     // Y is C or T
  95     assertEquals("C", ResidueProperties.codonTranslate("TGY"));
  96     // Phenylalanine first base variation
  97     assertEquals("L", ResidueProperties.codonTranslate("YTA"));
  98
  99     // W is A or T
 100     assertEquals("L", ResidueProperties.codonTranslate("CTW"));
 101     assertNull(ResidueProperties.codonTranslate("TTW"));
 102
 103     // S is G or C
 104     assertEquals("G", ResidueProperties.codonTranslate("GGS"));
 105     assertNull(ResidueProperties.codonTranslate("ATS"));
 106
 107     // K is T or G
 108     assertEquals("S", ResidueProperties.codonTranslate("TCK"));
 109     assertNull(ResidueProperties.codonTranslate("ATK"));
 110
 111     // M is C or A
 112     assertEquals("T", ResidueProperties.codonTranslate("ACM"));
 113     // Arginine first base variation
 114     assertEquals("R", ResidueProperties.codonTranslate("MGA"));
 115     assertEquals("R", ResidueProperties.codonTranslate("MGG"));
 116     assertNull(ResidueProperties.codonTranslate("TAM"));
 117
 118     // D is A, G or T
 119     assertEquals("P", ResidueProperties.codonTranslate("CCD"));
 120     assertNull(ResidueProperties.codonTranslate("AAD"));
 121
 122     // V is A, C or G
 123     assertEquals("V", ResidueProperties.codonTranslate("GTV"));
 124     assertNull(ResidueProperties.codonTranslate("TTV"));
 125
 126     // H is A, C or T
 127     assertEquals("A", ResidueProperties.codonTranslate("GCH"));
 128     assertEquals("I", ResidueProperties.codonTranslate("ATH"));
 129     assertNull(ResidueProperties.codonTranslate("AGH"));
 130
 131     // B is C, G or T
 132     assertEquals("P", ResidueProperties.codonTranslate("CCB"));
 133     assertNull(ResidueProperties.codonTranslate("TAB"));
 134
 135     // R is A or G
 136     // additional tests for JAL-1685 (resolved)
 137     assertEquals("L", ResidueProperties.codonTranslate("CTR"));
 138     assertEquals("V", ResidueProperties.codonTranslate("GTR"));
 139     assertEquals("S", ResidueProperties.codonTranslate("TCR"));
 140     assertEquals("P", ResidueProperties.codonTranslate("CCR"));
 141     assertEquals("T", ResidueProperties.codonTranslate("ACR"));
 142     assertEquals("A", ResidueProperties.codonTranslate("GCR"));
 143     assertEquals("R", ResidueProperties.codonTranslate("CGR"));
 144     assertEquals("G", ResidueProperties.codonTranslate("GGR"));
 145     assertEquals("R", ResidueProperties.codonTranslate("AGR"));
 146     assertEquals("E", ResidueProperties.codonTranslate("GAR"));
 147     assertEquals("K", ResidueProperties.codonTranslate("AAR"));
 148     assertEquals("L", ResidueProperties.codonTranslate("TTR"));
 149     assertEquals("Q", ResidueProperties.codonTranslate("CAR"));
 150     assertEquals("STOP", ResidueProperties.codonTranslate("TAR"));
 151     assertEquals("STOP", ResidueProperties.codonTranslate("TRA"));
 152     // Arginine first and third base ambiguity
 153     assertEquals("R", ResidueProperties.codonTranslate("MGR"));
 154     assertNull(ResidueProperties.codonTranslate("ATR"));
 155
 156     // N is any base; 8 proteins accept any base in 3rd position
 157     assertEquals("L", ResidueProperties.codonTranslate("CTN"));
 158     assertEquals("V", ResidueProperties.codonTranslate("GTN"));
 159     assertEquals("S", ResidueProperties.codonTranslate("TCN"));
 160     assertEquals("P", ResidueProperties.codonTranslate("CCN"));
 161     assertEquals("T", ResidueProperties.codonTranslate("ACN"));
 162     assertEquals("A", ResidueProperties.codonTranslate("GCN"));
 163     assertEquals("R", ResidueProperties.codonTranslate("CGN"));
 164     assertEquals("G", ResidueProperties.codonTranslate("GGN"));
 165     assertNull(ResidueProperties.codonTranslate("ATN"));
 166     assertNull(ResidueProperties.codonTranslate("ANT"));
 167     assertNull(ResidueProperties.codonTranslate("NAT"));
 168     assertNull(ResidueProperties.codonTranslate("ANN"));
 169     assertNull(ResidueProperties.codonTranslate("NNA"));
 170     assertNull(ResidueProperties.codonTranslate("NNN"));
 171
 172     // some random stuff
 173     assertNull(ResidueProperties.codonTranslate("YWB"));
 174     assertNull(ResidueProperties.codonTranslate("VHD"));
 175     assertNull(ResidueProperties.codonTranslate("WSK"));
 176   }
 177
 178   @Test
 179   public void testGetResidues_nucleotide()
 180   {
 181     /*
 182      * Non-ambiguous only; we don't care about the order of the list, it is just
 183      * sorted here to make assertions reliable
 184      */
 185     List<String> residues = ResidueProperties.getResidues(true, false);
 186     Collections.sort(residues);
 187     assertEquals("[A, C, G, T, U]", residues.toString());
 188
 189     /*
 190      * Including ambiguity codes I N R X Y
 191      */
 192     residues = ResidueProperties.getResidues(true, true);
 193     Collections.sort(residues);
 194     assertEquals("[A, C, G, I, N, R, T, U, X, Y]", residues.toString());
 195   }
 196
 197   @Test
 198   public void testGetResidues_peptide()
 199   {
 200     /*
 201      * Non-ambiguous only; we don't care about the order of the list, it is just
 202      * sorted here to make assertions reliable
 203      */
 204     List<String> residues = ResidueProperties.getResidues(false, false);
 205     Collections.sort(residues);
 206     assertEquals(
 207             "[ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL]",
 208             residues.toString());
 209
 210     /*
 211      * Including ambiguity codes ASX, GLX, XAA
 212      */
 213     residues = ResidueProperties.getResidues(false, true);
 214     Collections.sort(residues);
 215     assertEquals(
 216             "[ALA, ARG, ASN, ASP, ASX, CYS, GLN, GLU, GLX, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, XAA]",
 217             residues.toString());
 218   }
 219 }