SimpleSubstitutionMatrix implements SubstitutionMatrix<C> { @Override public String getName() { return name; } @SuppressWarnings("unchecked") // TODO proper generic type checking instead of possible ClassCastException  SimpleSubstitutionMatrix();  SimpleSubstitutionMatrix(CompoundSet<C> compoundSet, File fileInput);  SimpleSubstitutionMatrix(CompoundSet<C> compoundSet, Reader input, String name);  SimpleSubstitutionMatrix(CompoundSet<C> compoundSet, String matrixInput, String name);  SimpleSubstitutionMatrix(CompoundSet<C> compoundSet, short match, short replace); private  SimpleSubstitutionMatrix(CompoundSet<C> compoundSet, Scanner input, String name); @Override CompoundSet<C> getCompoundSet(); @Override String getDescription(); @Override short[][] getMatrix(); @Override String getMatrixAsString(); @Override short getMaxValue(); @Override short getMinValue(); @Override String getName(); @Override short getValue(C from, C to); @Override SubstitutionMatrix<C> normalizeMatrix(short scale); @Override void setDescription(String description); @Override void setName(String name); @Override String toString();  }
@Test public void testSimpleSubstitutionMatrixCompoundSetOfCShortShort() { SubstitutionMatrix<AminoAcidCompound> matrix = new SimpleSubstitutionMatrix<AminoAcidCompound>( AminoAcidCompoundSet.getAminoAcidCompoundSet(), (short) 5, (short) 1); assertEquals(matrix.getName(), "IDENTITY_5_1"); }