test/jalview/schemes/ResiduePropertiesTest.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.schemes;
  22
  23 import static org.testng.AssertJUnit.assertEquals;
  24 import static org.testng.AssertJUnit.assertNull;
  25
  26 import java.util.Collections;
  27 import java.util.List;
  28
  29 import org.testng.annotations.Test;
  30
  31 public class ResiduePropertiesTest
  32 {
  33
  34   /**
  35    * Test 'standard' codon translations (no ambiguity codes)
  36    */
  37   @Test(groups = { "Functional" })
  38   public void testCodonTranslate()
  39   {
  40     // standard translation table order column 1/2/3/4
  41     assertEquals("F", ResidueProperties.codonTranslate("TTT"));
  42     assertEquals("F", ResidueProperties.codonTranslate("TTC"));
  43     assertEquals("L", ResidueProperties.codonTranslate("TTA"));
  44     assertEquals("L", ResidueProperties.codonTranslate("TTG"));
  45     assertEquals("L", ResidueProperties.codonTranslate("CTT"));
  46     assertEquals("L", ResidueProperties.codonTranslate("CTC"));
  47     assertEquals("L", ResidueProperties.codonTranslate("CTA"));
  48     assertEquals("L", ResidueProperties.codonTranslate("CTG"));
  49     assertEquals("I", ResidueProperties.codonTranslate("ATT"));
  50     assertEquals("I", ResidueProperties.codonTranslate("ATC"));
  51     assertEquals("I", ResidueProperties.codonTranslate("ATA"));
  52     assertEquals("M", ResidueProperties.codonTranslate("ATG"));
  53     assertEquals("V", ResidueProperties.codonTranslate("GTT"));
  54     assertEquals("V", ResidueProperties.codonTranslate("GTC"));
  55     assertEquals("V", ResidueProperties.codonTranslate("GTA"));
  56     assertEquals("V", ResidueProperties.codonTranslate("GTG"));
  57     assertEquals("S", ResidueProperties.codonTranslate("TCT"));
  58     assertEquals("S", ResidueProperties.codonTranslate("TCC"));
  59     assertEquals("S", ResidueProperties.codonTranslate("TCA"));
  60     assertEquals("S", ResidueProperties.codonTranslate("TCG"));
  61     assertEquals("P", ResidueProperties.codonTranslate("CCT"));
  62     assertEquals("P", ResidueProperties.codonTranslate("CCC"));
  63     assertEquals("P", ResidueProperties.codonTranslate("CCA"));
  64     assertEquals("P", ResidueProperties.codonTranslate("CCG"));
  65     assertEquals("T", ResidueProperties.codonTranslate("ACT"));
  66     assertEquals("T", ResidueProperties.codonTranslate("ACC"));
  67     assertEquals("T", ResidueProperties.codonTranslate("ACA"));
  68     assertEquals("T", ResidueProperties.codonTranslate("ACG"));
  69     assertEquals("A", ResidueProperties.codonTranslate("GCT"));
  70     assertEquals("A", ResidueProperties.codonTranslate("GCC"));
  71     assertEquals("A", ResidueProperties.codonTranslate("GCA"));
  72     assertEquals("A", ResidueProperties.codonTranslate("GCG"));
  73     assertEquals("Y", ResidueProperties.codonTranslate("TAT"));
  74     assertEquals("Y", ResidueProperties.codonTranslate("TAC"));
  75     assertEquals("STOP", ResidueProperties.codonTranslate("TAA"));
  76     assertEquals("STOP", ResidueProperties.codonTranslate("TAG"));
  77     assertEquals("H", ResidueProperties.codonTranslate("CAT"));
  78     assertEquals("H", ResidueProperties.codonTranslate("CAC"));
  79     assertEquals("Q", ResidueProperties.codonTranslate("CAA"));
  80     assertEquals("Q", ResidueProperties.codonTranslate("CAG"));
  81     assertEquals("N", ResidueProperties.codonTranslate("AAT"));
  82     assertEquals("N", ResidueProperties.codonTranslate("AAC"));
  83     assertEquals("K", ResidueProperties.codonTranslate("AAA"));
  84     assertEquals("K", ResidueProperties.codonTranslate("AAG"));
  85     assertEquals("D", ResidueProperties.codonTranslate("GAT"));
  86     assertEquals("D", ResidueProperties.codonTranslate("GAC"));
  87     assertEquals("E", ResidueProperties.codonTranslate("GAA"));
  88     assertEquals("E", ResidueProperties.codonTranslate("GAG"));
  89     assertEquals("C", ResidueProperties.codonTranslate("TGT"));
  90     assertEquals("C", ResidueProperties.codonTranslate("TGC"));
  91     assertEquals("STOP", ResidueProperties.codonTranslate("TGA"));
  92     assertEquals("W", ResidueProperties.codonTranslate("TGG"));
  93     assertEquals("R", ResidueProperties.codonTranslate("CGT"));
  94     assertEquals("R", ResidueProperties.codonTranslate("CGC"));
  95     assertEquals("R", ResidueProperties.codonTranslate("CGA"));
  96     assertEquals("R", ResidueProperties.codonTranslate("CGG"));
  97     assertEquals("S", ResidueProperties.codonTranslate("AGT"));
  98     assertEquals("S", ResidueProperties.codonTranslate("AGC"));
  99     assertEquals("R", ResidueProperties.codonTranslate("AGA"));
 100     assertEquals("R", ResidueProperties.codonTranslate("AGG"));
 101     assertEquals("G", ResidueProperties.codonTranslate("GGT"));
 102     assertEquals("G", ResidueProperties.codonTranslate("GGC"));
 103     assertEquals("G", ResidueProperties.codonTranslate("GGA"));
 104     assertEquals("G", ResidueProperties.codonTranslate("GGG"));
 105   }
 106
 107   /**
 108    * Test a sample of codon translations involving ambiguity codes. Should
 109    * return a protein value where the ambiguity does not affect the translation.
 110    */
 111   @Test(groups = { "Functional" })
 112   public void testCodonTranslate_ambiguityCodes()
 113   {
 114     // Y is C or T
 115     assertEquals("C", ResidueProperties.codonTranslate("TGY"));
 116     // Phenylalanine first base variation
 117     assertEquals("L", ResidueProperties.codonTranslate("YTA"));
 118
 119     // W is A or T
 120     assertEquals("L", ResidueProperties.codonTranslate("CTW"));
 121     assertNull(ResidueProperties.codonTranslate("TTW"));
 122
 123     // S is G or C
 124     assertEquals("G", ResidueProperties.codonTranslate("GGS"));
 125     assertNull(ResidueProperties.codonTranslate("ATS"));
 126
 127     // K is T or G
 128     assertEquals("S", ResidueProperties.codonTranslate("TCK"));
 129     assertNull(ResidueProperties.codonTranslate("ATK"));
 130
 131     // M is C or A
 132     assertEquals("T", ResidueProperties.codonTranslate("ACM"));
 133     // Arginine first base variation
 134     assertEquals("R", ResidueProperties.codonTranslate("MGA"));
 135     assertEquals("R", ResidueProperties.codonTranslate("MGG"));
 136     assertNull(ResidueProperties.codonTranslate("TAM"));
 137
 138     // D is A, G or T
 139     assertEquals("P", ResidueProperties.codonTranslate("CCD"));
 140     assertNull(ResidueProperties.codonTranslate("AAD"));
 141
 142     // V is A, C or G
 143     assertEquals("V", ResidueProperties.codonTranslate("GTV"));
 144     assertNull(ResidueProperties.codonTranslate("TTV"));
 145
 146     // H is A, C or T
 147     assertEquals("A", ResidueProperties.codonTranslate("GCH"));
 148     assertEquals("I", ResidueProperties.codonTranslate("ATH"));
 149     assertNull(ResidueProperties.codonTranslate("AGH"));
 150
 151     // B is C, G or T
 152     assertEquals("P", ResidueProperties.codonTranslate("CCB"));
 153     assertNull(ResidueProperties.codonTranslate("TAB"));
 154
 155     // R is A or G
 156     // additional tests for JAL-1685 (resolved)
 157     assertEquals("L", ResidueProperties.codonTranslate("CTR"));
 158     assertEquals("V", ResidueProperties.codonTranslate("GTR"));
 159     assertEquals("S", ResidueProperties.codonTranslate("TCR"));
 160     assertEquals("P", ResidueProperties.codonTranslate("CCR"));
 161     assertEquals("T", ResidueProperties.codonTranslate("ACR"));
 162     assertEquals("A", ResidueProperties.codonTranslate("GCR"));
 163     assertEquals("R", ResidueProperties.codonTranslate("CGR"));
 164     assertEquals("G", ResidueProperties.codonTranslate("GGR"));
 165     assertEquals("R", ResidueProperties.codonTranslate("AGR"));
 166     assertEquals("E", ResidueProperties.codonTranslate("GAR"));
 167     assertEquals("K", ResidueProperties.codonTranslate("AAR"));
 168     assertEquals("L", ResidueProperties.codonTranslate("TTR"));
 169     assertEquals("Q", ResidueProperties.codonTranslate("CAR"));
 170     assertEquals("STOP", ResidueProperties.codonTranslate("TAR"));
 171     assertEquals("STOP", ResidueProperties.codonTranslate("TRA"));
 172     // Arginine first and third base ambiguity
 173     assertEquals("R", ResidueProperties.codonTranslate("MGR"));
 174     assertNull(ResidueProperties.codonTranslate("ATR"));
 175
 176     // N is any base; 8 proteins accept any base in 3rd position
 177     assertEquals("L", ResidueProperties.codonTranslate("CTN"));
 178     assertEquals("V", ResidueProperties.codonTranslate("GTN"));
 179     assertEquals("S", ResidueProperties.codonTranslate("TCN"));
 180     assertEquals("P", ResidueProperties.codonTranslate("CCN"));
 181     assertEquals("T", ResidueProperties.codonTranslate("ACN"));
 182     assertEquals("A", ResidueProperties.codonTranslate("GCN"));
 183     assertEquals("R", ResidueProperties.codonTranslate("CGN"));
 184     assertEquals("G", ResidueProperties.codonTranslate("GGN"));
 185     assertNull(ResidueProperties.codonTranslate("ATN"));
 186     assertNull(ResidueProperties.codonTranslate("ANT"));
 187     assertNull(ResidueProperties.codonTranslate("NAT"));
 188     assertNull(ResidueProperties.codonTranslate("ANN"));
 189     assertNull(ResidueProperties.codonTranslate("NNA"));
 190     assertNull(ResidueProperties.codonTranslate("NNN"));
 191
 192     // some random stuff
 193     assertNull(ResidueProperties.codonTranslate("YWB"));
 194     assertNull(ResidueProperties.codonTranslate("VHD"));
 195     assertNull(ResidueProperties.codonTranslate("WSK"));
 196   }
 197
 198   @Test(groups = { "Functional" })
 199   public void testGetResidues_nucleotide()
 200   {
 201     /*
 202      * Non-ambiguous only; we don't care about the order of the list, it is just
 203      * sorted here to make assertions reliable
 204      */
 205     List<String> residues = ResidueProperties.getResidues(true, false);
 206     Collections.sort(residues);
 207     assertEquals("[A, C, G, T, U]", residues.toString());
 208
 209     /*
 210      * Including ambiguity codes I N R X Y
 211      */
 212     residues = ResidueProperties.getResidues(true, true);
 213     Collections.sort(residues);
 214     assertEquals("[A, C, G, I, N, R, T, U, X, Y]", residues.toString());
 215   }
 216
 217   @Test(groups = { "Functional" })
 218   public void testGetResidues_peptide()
 219   {
 220     /*
 221      * Non-ambiguous only; we don't care about the order of the list, it is just
 222      * sorted here to make assertions reliable
 223      */
 224     List<String> residues = ResidueProperties.getResidues(false, false);
 225     Collections.sort(residues);
 226     assertEquals(
 227             "[ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL]",
 228             residues.toString());
 229
 230     /*
 231      * Including ambiguity codes ASX, GLX, XAA
 232      */
 233     residues = ResidueProperties.getResidues(false, true);
 234     Collections.sort(residues);
 235     assertEquals(
 236             "[ALA, ARG, ASN, ASP, ASX, CYS, GLN, GLU, GLX, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, XAA]",
 237             residues.toString());
 238   }
 239
 240   @Test(groups = { "Functional" })
 241   public void testGetCanonicalAminoAcid()
 242   {
 243     assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MET"));
 244     assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MSE"));
 245     assertEquals(null, ResidueProperties.getCanonicalAminoAcid(null));
 246   }
 247
 248   @Test(groups = { "Functional" })
 249   public void testGetSingleCharacterCode()
 250   {
 251     assertEquals('0', ResidueProperties.getSingleCharacterCode(null));
 252     assertEquals('0', ResidueProperties.getSingleCharacterCode(null));
 253     assertEquals('0', ResidueProperties.getSingleCharacterCode(""));
 254     assertEquals('Q', ResidueProperties.getSingleCharacterCode("GLN"));
 255     assertEquals('Q', ResidueProperties.getSingleCharacterCode("Gln"));
 256     assertEquals('Q', ResidueProperties.getSingleCharacterCode("gln"));
 257   }
 258 }