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