//Function to return the calculate substitution matrix for the given length
double* F84Model::GetSubstitutionMatrix(double length) {
//Multiply Rate Matrix by time (length)
double RateMatrixTemp[16];
for (int i=0;i<16;i++){
RateMatrixTemp[i] = RateMatrix[i]*length;
}
//Estimate Matrix Exponential of RateMatrixTemp
double *MatrixExponential = expm2 ( 4, RateMatrixTemp );
return MatrixExponential;
}
//Function to estimate the substitution probability between the given nucleotides at length time
double F84Model::GetProbability(Alphabet a, Alphabet b, double length) const{
//Multiply Rate Matrix by time (length)
double RateMatrixTemp[16];
for (int i=0;i<16;i++){
RateMatrixTemp[i] = RateMatrix[i]*length;
}
//Estimate Matrix Exponential of RateMatrixTemp
double *MatrixExponential = expm2 ( 4, RateMatrixTemp );
return MatrixExponential[GetAlphabetPair(a, b)];
}
//Function to set the length of the model and calculate substitution matrix
void F84Model::SetLength(double length) {
//Multiply Rate Matrix by time (length)
double RateMatrixTemp[16];
for (int i=0;i<16;i++){
RateMatrixTemp[i] = RateMatrix[i]*length;
}
//Estimate Matrix Exponential of RateMatrixTemp
double *MatrixExponential = expm2 ( 4, RateMatrixTemp );
for (int i=0;i<16;i++){
SubMatrix[i] = MatrixExponential[i];
}
}
void matrix_exponential_test01 ( void )
/******************************************************************************/
/*
Purpose:
MATRIX_EXPONENTIAL_TEST01 compares matrix exponential algorithms.
Licensing:
This code is distributed under the GNU LGPL license.
Modified:
02 December 2011
Author:
John Burkardt
*/
{
double *a;
double *a_exp;
int n;
int test;
int test_num;
printf ( "\n" );
printf ( "MATRIX_EXPONENTIAL_TEST01:\n" );
printf ( " EXPM is MATLAB's matrix exponential function\n" );
printf ( " EXPM11 is an equivalent to EXPM\n" );
printf ( " EXPM2 uses a Taylor series approach\n" );
printf ( " EXPM3 relies on an eigenvalue calculation.\n" );
test_num = mexp_test_num ( );
for ( test = 1; test <= test_num; test++ )
{
printf ( "\n" );
printf ( " Test #%d\n", test );
mexp_story ( test );
n = mexp_n ( test );
printf ( " Matrix order N = %d\n", n );
a = mexp_a ( test, n );
r8mat_print ( n, n, a, " Matrix:" );
a_exp = expm11 ( n, a );
r8mat_print ( n, n, a_exp, " EXPM1(A):" );
free ( a_exp );
a_exp = expm2 ( n, a );
r8mat_print ( n, n, a_exp, " EXPM2(A):" );
free ( a_exp );
/*
a_exp = expm3 ( n, a );
r8mat_print ( n, n, a_exp, " EXPM3(A):" );
free ( a_exp );
*/
a_exp = mexp_expa ( test, n );
r8mat_print ( n, n, a_exp, " Exact Exponential:" );
free ( a_exp );
free ( a );
}
return;
}
