@Test public void testSetDescription() { SubstitutionMatrix<AminoAcidCompound> matrix = SimpleSubstitutionMatrix.getBlosum62(); assertEquals(matrix.getDescription().substring(0, 2), "# "); matrix.setDescription("blah"); assertEquals(matrix.getDescription().substring(0, 2), "bl"); }
@Test public void testSetName() { SubstitutionMatrix<AminoAcidCompound> matrix = SimpleSubstitutionMatrix.getBlosum62(); assertEquals(matrix.getName(), "blosum62"); matrix.setName("blah"); assertEquals(matrix.getName(), "blah"); }
@Test public void testSimpleSubstitutionMatrixCompoundSetOfCShortShort() { SubstitutionMatrix<AminoAcidCompound> matrix = new SimpleSubstitutionMatrix<AminoAcidCompound>( AminoAcidCompoundSet.getAminoAcidCompoundSet(), (short) 5, (short) 1); assertEquals(matrix.getName(), "IDENTITY_5_1"); }
@Test() public void testSimpleSubstitutionMatrix() { SubstitutionMatrix<AminoAcidCompound> matrix = SimpleSubstitutionMatrix.getBlosum62(); assertEquals(matrix.getCompoundSet(), AminoAcidCompoundSet.getAminoAcidCompoundSet()); assertEquals(matrix.getName(), "blosum62"); assertEquals(matrix.getMaxValue(), 11); assertEquals(matrix.getMinValue(), -4); }
@Test public void testToString() { SubstitutionMatrix<NucleotideCompound> matrix = new SimpleSubstitutionMatrix<NucleotideCompound>( DNACompoundSet.getDNACompoundSet(), "# Test\nA C G T\nA 5 0 0 0\nC 0 5 0 0 \nG 0 0 5 0\n T 0 0 0 1\n", "DNAtest"); assertEquals(matrix.toString().substring(0, 6), "# Test"); assertEquals( matrix.toString(), String.format("# Test%n A C G T%nA 5 0 0 0%nC 0 5 0 0%nG 0 0 5 0%nT 0 0 0 1%n")); }
@Test public void test() throws CompoundNotFoundException { NucleotideCompound A = new DNASequence("A").getCompoundAt(1); NucleotideCompound a = new DNASequence("a").getCompoundAt(1); NucleotideCompound c = new DNASequence("c").getCompoundAt(1); SubstitutionMatrix<NucleotideCompound> matrix = new SimpleSubstitutionMatrix<NucleotideCompound>( DNACompoundSet.getDNACompoundSet(), (short) 1, (short) 0); assertEquals(1, (matrix.getValue(A, A))); assertEquals(1, (matrix.getValue(a, a))); assertEquals(1, (matrix.getValue(A, a))); assertEquals(0, (matrix.getValue(a, c))); }
@Test public void testSimpleSubstitutionMatrixCompoundSetOfCStringString() { DNACompoundSet dnacs = DNACompoundSet.getDNACompoundSet(); SubstitutionMatrix<NucleotideCompound> dnaTest = new SimpleSubstitutionMatrix<NucleotideCompound>( dnacs, "# Test\nA C G T\nA 5 0 0 0\nC 0 5 0 0\nG 0 0 5 0\nT 0 0 0 1\n", "DNA Test"); short[][] matrix = dnaTest.getMatrix(); assertEquals(matrix[1][1], 5); assertEquals(matrix[3][3], 1); assertEquals(matrix[3][1], 0); assertEquals(dnaTest.getMatrixAsString().substring(2, 9), "A C G T"); assertEquals( dnaTest.getValue(dnacs.getCompoundForString("G"), dnacs.getCompoundForString("G")), 5); assertEquals( dnaTest.getValue(dnacs.getCompoundForString("A"), dnacs.getCompoundForString("G")), 0); }
/* * Author: Daniel Cameron */ @Test public void testCaseEquivalence() { DNACompoundSet dnacs = DNACompoundSet.getDNACompoundSet(); SubstitutionMatrix<NucleotideCompound> dnaTest = new SimpleSubstitutionMatrix<NucleotideCompound>( dnacs, "# Test\nA C G T\nA 5 0 0 0\nC 0 5 0 0\nG 0 0 5 0\nT 0 0 0 1\n", "DNA Test"); @SuppressWarnings("unused") short[][] matrix = dnaTest.getMatrix(); assertEquals( dnaTest.getValue(dnacs.getCompoundForString("G"), dnacs.getCompoundForString("g")), 5); assertEquals( dnaTest.getValue(dnacs.getCompoundForString("A"), dnacs.getCompoundForString("g")), 0); assertEquals( dnaTest.getValue(dnacs.getCompoundForString("g"), dnacs.getCompoundForString("G")), 5); assertEquals( dnaTest.getValue(dnacs.getCompoundForString("g"), dnacs.getCompoundForString("A")), 0); }