+++ /dev/null
-package jalview.analysis;
-
-import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertFalse;
-import static org.testng.Assert.assertNull;
-import static org.testng.Assert.assertSame;
-
-import java.util.Iterator;
-
-import org.testng.annotations.Test;
-
-public class GeneticCodesTest
-{
- @Test(groups = "Functional")
- public void testGetCodeTable()
- {
- assertEquals(GeneticCodes.getStandardCodeTable().getName(), "Standard");
- assertEquals(GeneticCodes.getStandardCodeTable().getId(), "1");
- assertSame(GeneticCodes.getStandardCodeTable(),
- GeneticCodes.getCodeTable("1"));
- assertEquals(GeneticCodes.getCodeTable("2").getName(),
- "Vertebrate Mitochondrial");
- assertEquals(GeneticCodes.getCodeTable("11").getName(),
- "Bacterial, Archaeal and Plant Plastid");
- assertEquals(GeneticCodes.getCodeTable("31").getName(),
- "Blastocrithidia Nuclear");
- }
-
- @Test(groups = "Functional")
- public void testGetCodeTables()
- {
- Iterator<GeneticCodeI> tableIterator = GeneticCodes.getCodeTables()
- .iterator();
- String[] ids = new String[] { "1", "2", "3", "4", "5", "6", "9", "10",
- "11", "12", "13", "14", "15", "16", "21", "22", "23", "24", "25",
- "26", "27", "28", "29", "30", "31" };
- for (int i = 0; i < ids.length; i++)
- {
- assertEquals(tableIterator.next().getId(), ids[i]);
- }
- assertFalse(tableIterator.hasNext());
- }
-
- @Test(groups = "Functional")
- public void testTranslate()
- {
- GeneticCodeI gc = GeneticCodes.getCodeTable("1");
- assertNull(gc.translate("XYZ"));
- assertEquals(gc.translate("AGA"), "R");
-
- gc = GeneticCodes.getCodeTable("2");
- assertEquals(gc.translate("AGA"), "*"); // variant
- assertEquals(gc.translate("ttc"), "F"); // non-variant
-
- // table 11 has no variant translations - should serve the standard values
- gc = GeneticCodes.getCodeTable("11");
- assertEquals(gc.translate("ttc"), "F");
-
- gc = GeneticCodes.getCodeTable("31");
- assertEquals(gc.translate("TGA"), "W"); // variant
- assertEquals(gc.translate("tag"), "E"); // variant
- assertEquals(gc.translate("AGC"), "S"); // non-variant
- }
-
- /**
- * Test 'standard' codon translations (no ambiguity codes)
- */
- @Test(groups = { "Functional" })
- public void testTranslate_standardTable()
- {
- GeneticCodeI st = GeneticCodes.getStandardCodeTable();
- assertEquals("F", st.translate("TTT"));
- assertEquals("F", st.translate("TTC"));
- assertEquals("L", st.translate("TTA"));
- assertEquals("L", st.translate("TTG"));
- assertEquals("L", st.translate("CTT"));
- assertEquals("L", st.translate("CTC"));
- assertEquals("L", st.translate("CTA"));
- assertEquals("L", st.translate("CTG"));
- assertEquals("I", st.translate("ATT"));
- assertEquals("I", st.translate("ATC"));
- assertEquals("I", st.translate("ATA"));
- assertEquals("M", st.translate("ATG"));
- assertEquals("V", st.translate("GTT"));
- assertEquals("V", st.translate("GTC"));
- assertEquals("V", st.translate("GTA"));
- assertEquals("V", st.translate("GTG"));
- assertEquals("S", st.translate("TCT"));
- assertEquals("S", st.translate("TCC"));
- assertEquals("S", st.translate("TCA"));
- assertEquals("S", st.translate("TCG"));
- assertEquals("P", st.translate("CCT"));
- assertEquals("P", st.translate("CCC"));
- assertEquals("P", st.translate("CCA"));
- assertEquals("P", st.translate("CCG"));
- assertEquals("T", st.translate("ACT"));
- assertEquals("T", st.translate("ACC"));
- assertEquals("T", st.translate("ACA"));
- assertEquals("T", st.translate("ACG"));
- assertEquals("A", st.translate("GCT"));
- assertEquals("A", st.translate("GCC"));
- assertEquals("A", st.translate("GCA"));
- assertEquals("A", st.translate("GCG"));
- assertEquals("Y", st.translate("TAT"));
- assertEquals("Y", st.translate("TAC"));
- assertEquals("*", st.translate("TAA"));
- assertEquals("*", st.translate("TAG"));
- assertEquals("H", st.translate("CAT"));
- assertEquals("H", st.translate("CAC"));
- assertEquals("Q", st.translate("CAA"));
- assertEquals("Q", st.translate("CAG"));
- assertEquals("N", st.translate("AAT"));
- assertEquals("N", st.translate("AAC"));
- assertEquals("K", st.translate("AAA"));
- assertEquals("K", st.translate("AAG"));
- assertEquals("D", st.translate("GAT"));
- assertEquals("D", st.translate("GAC"));
- assertEquals("E", st.translate("GAA"));
- assertEquals("E", st.translate("GAG"));
- assertEquals("C", st.translate("TGT"));
- assertEquals("C", st.translate("TGC"));
- assertEquals("*", st.translate("TGA"));
- assertEquals("W", st.translate("TGG"));
- assertEquals("R", st.translate("CGT"));
- assertEquals("R", st.translate("CGC"));
- assertEquals("R", st.translate("CGA"));
- assertEquals("R", st.translate("CGG"));
- assertEquals("S", st.translate("AGT"));
- assertEquals("S", st.translate("AGC"));
- assertEquals("R", st.translate("AGA"));
- assertEquals("R", st.translate("AGG"));
- assertEquals("G", st.translate("GGT"));
- assertEquals("G", st.translate("GGC"));
- assertEquals("G", st.translate("GGA"));
- assertEquals("G", st.translate("GGG"));
- }
-
- /**
- * Test a sample of codon translations involving ambiguity codes. Should
- * return a protein value where the ambiguity does not affect the translation.
- */
- @Test(groups = { "Functional" })
- public void testTranslate_standardTableAmbiguityCodes()
- {
- GeneticCodeI st = GeneticCodes.getStandardCodeTable();
- // Y is C or T
- assertEquals("C", st.translate("TGY"));
- // Phenylalanine first base variation
- assertEquals("L", st.translate("YTA"));
-
- // W is A or T
- assertEquals("L", st.translate("CTW"));
- assertNull(st.translate("TTW"));
-
- // S is G or C
- assertEquals("G", st.translate("GGS"));
- assertNull(st.translate("ATS"));
-
- // K is T or G
- assertEquals("S", st.translate("TCK"));
- assertNull(st.translate("ATK"));
-
- // M is C or A
- assertEquals("T", st.translate("ACM"));
- // Arginine first base variation
- assertEquals("R", st.translate("MGA"));
- assertEquals("R", st.translate("MGG"));
- assertNull(st.translate("TAM"));
-
- // D is A, G or T
- assertEquals("P", st.translate("CCD"));
- assertNull(st.translate("AAD"));
-
- // V is A, C or G
- assertEquals("V", st.translate("GTV"));
- assertNull(st.translate("TTV"));
-
- // H is A, C or T
- assertEquals("A", st.translate("GCH"));
- assertEquals("I", st.translate("ATH"));
- assertNull(st.translate("AGH"));
-
- // B is C, G or T
- assertEquals("P", st.translate("CCB"));
- assertNull(st.translate("TAB"));
-
- // R is A or G
- // additional tests for JAL-1685 (resolved)
- assertEquals("L", st.translate("CTR"));
- assertEquals("V", st.translate("GTR"));
- assertEquals("S", st.translate("TCR"));
- assertEquals("P", st.translate("CCR"));
- assertEquals("T", st.translate("ACR"));
- assertEquals("A", st.translate("GCR"));
- assertEquals("R", st.translate("CGR"));
- assertEquals("G", st.translate("GGR"));
- assertEquals("R", st.translate("AGR"));
- assertEquals("E", st.translate("GAR"));
- assertEquals("K", st.translate("AAR"));
- assertEquals("L", st.translate("TTR"));
- assertEquals("Q", st.translate("CAR"));
- assertEquals("*", st.translate("TAR"));
- assertEquals("*", st.translate("TRA"));
- // Arginine first and third base ambiguity
- assertEquals("R", st.translate("MGR"));
- assertNull(st.translate("ATR"));
-
- // N is any base; 8 proteins accept any base in 3rd position
- assertEquals("L", st.translate("CTN"));
- assertEquals("V", st.translate("GTN"));
- assertEquals("S", st.translate("TCN"));
- assertEquals("P", st.translate("CCN"));
- assertEquals("T", st.translate("ACN"));
- assertEquals("A", st.translate("GCN"));
- assertEquals("R", st.translate("CGN"));
- assertEquals("G", st.translate("GGN"));
- assertNull(st.translate("ATN"));
- assertNull(st.translate("ANT"));
- assertNull(st.translate("NAT"));
- assertNull(st.translate("ANN"));
- assertNull(st.translate("NNA"));
- assertNull(st.translate("NNN"));
-
- // some random stuff
- assertNull(st.translate("YWB"));
- assertNull(st.translate("VHD"));
- assertNull(st.translate("WSK"));
- }
-
- /**
- * Test a sample of codon translations involving ambiguity codes. Should
- * return a protein value where the ambiguity does not affect the translation.
- */
- @Test(groups = { "Functional" })
- public void testTranslate_nonStandardTableAmbiguityCodes()
- {
- GeneticCodeI standard = GeneticCodes
- .getStandardCodeTable();
-
- /*
- * Vertebrate Mitochondrial (Table 2)
- */
- GeneticCodeI gc = GeneticCodes.getCodeTable("2");
- // AGR is AGA or AGG - R in standard code, * in table 2
- assertEquals(gc.translate("AGR"), "*");
- assertEquals(standard.translate("AGR"), "R");
- // TGR is TGA or TGG - ambiguous in standard code, W in table 2
- assertEquals(gc.translate("TGR"), "W");
- assertNull(standard.translate("TGR"));
-
- /*
- * Yeast Mitochondrial (Table 3)
- */
- gc = GeneticCodes.getCodeTable("3");
- // CTN is L in standard code, T in table 3
- assertEquals(gc.translate("ctn"), "T");
- assertEquals(standard.translate("CTN"), "L");
-
- /*
- * Alternative Yeast Nuclear (Table 12)
- */
- gc = GeneticCodes.getCodeTable("12");
- // CTG is S; in the standard code CTN is L
- assertEquals(gc.translate("CTG"), "S");
- assertNull(gc.translate("CTK")); // K is G or T -> S or L
- assertEquals(standard.translate("CTK"), "L");
- assertEquals(gc.translate("CTH"), "L"); // H is anything other than G
- assertEquals(standard.translate("CTH"), "L");
- assertEquals(standard.translate("CTN"), "L");
-
- /*
- * Trematode Mitochondrial (Table 21)
- */
- gc = GeneticCodes.getCodeTable("21");
- // AAR is K in standard code, ambiguous in table 21 as AAA=N not K
- assertNull(gc.translate("AAR"));
- assertEquals(standard.translate("AAR"), "K");
- }
-
- @Test(groups = "Functional")
- public void testTranslateCanonical()
- {
- GeneticCodeI gc = GeneticCodes.getCodeTable("1");
- assertNull(gc.translateCanonical("XYZ"));
- assertEquals(gc.translateCanonical("AGA"), "R");
- // translateCanonical should not resolve ambiguity codes
- assertNull(gc.translateCanonical("TGY"));
-
- gc = GeneticCodes.getCodeTable("2");
- assertNull(gc.translateCanonical("AGR"));
- assertEquals(gc.translateCanonical("AGA"), "*"); // variant
- assertEquals(gc.translateCanonical("ttc"), "F"); // non-variant
- }
-}
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