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mutation.h
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/********************************************/
/* mutation.h 17th November 2005 */
/* (c) Danny Wilson. */
/* www.danielwilson.me.uk */
/********************************************/
#ifndef _MUTATION_H_
#define _MUTATION_H_
#include <vector>
#include <myutils.h>
using std::vector;
using namespace myutils;
class Mutation_Matrix {
public:
int n_states;
vector<double> state_freq;
vector<string> state_char;
Random *ran;
Matrix<double> C; /*continuous-time rate matrix*/
Matrix<double> D; /*discrete-time transition matrix*/
vector<double> mutation_rate;
vector<double> mutation_mean;
protected:
/*assumes C_in is a valid rate matrix of size n_states_in*/
void initialize(const int n_states_in, Matrix<double> *C_in) {
n_states = n_states_in;
C = *C_in;
D.resize(n_states,n_states);
mutation_rate.resize(n_states);
mutation_mean.resize(n_states);
int i,j;
for(i=0;i<n_states;i++) {
for(j=0;j<n_states;j++)
D[i][j] = -C[i][j]/C[i][i];
D[i][i] = 0.0;
mutation_rate[i] = -C[i][i];
mutation_mean[i] = -1./C[i][i];
}
}
public:
Mutation_Matrix() {};
Mutation_Matrix(const Mutation_Matrix &M) {
n_states = M.n_states;
state_freq = M.state_freq;
state_char = M.state_char;
ran = M.ran;
C = M.C;
D = M.D;
mutation_rate = M.mutation_rate;
mutation_mean = M.mutation_mean;
}
Mutation_Matrix& operator=(const Mutation_Matrix& M) {
//if(this==&M) return *this;
n_states = M.n_states;
state_freq = M.state_freq;
state_char = M.state_char;
ran = M.ran;
C = M.C;
D = M.D;
mutation_rate = M.mutation_rate;
mutation_mean = M.mutation_mean;
return *this;
}
void set_state_freq(vector<double> state_freq_in) {
if(state_freq_in.size()!=n_states) error("Mutation_Matrix::set_state_freq(state_freq_in): state_freq_in inconsistent in size with n_states");
double tot = 0.0;
int i;
for(i=0;i<n_states;i++) tot += state_freq_in[i];
state_freq.resize(n_states);
for(i=0;i<n_states;i++) state_freq[i]=state_freq_in[i]/tot;
}
void set_state_char(vector<string> state_char_in) {
if(state_char_in.size()!=n_states) error("Mutation_Matrix::set_state_char(state_char_in): state_char_in inconsistent in size with n_states");
state_char = state_char_in;
}
void set_ran(Random *ran_in) {
ran = ran_in;
}
inline double get_rate(const int state) {
if(state<0||state>=n_states) error("Mutation_Matrix::get_rate(state): unknown state");
return mutation_rate[state];
}
int draw() {
int state;
double rp;
double U = ran->U();
for(state=0;state<n_states-1;state++) {
rp = state_freq[state];
if(U < rp) break;
U -= rp;
}
return state;
}
int mutate(const int state) {
if(state<0||state>=n_states) error("Mutation_Matrix::mutate(state): unknown state");
int new_state = state;
double U = ran->U();
double rp;
for(new_state=0;new_state<n_states-1;new_state++) {
rp = D[state][new_state];
if(U < rp) break;
U -= rp;
}
return new_state;
};
int mutate_edge(const int state, const double time) {
int old_state = state;
if(old_state<0||old_state>=n_states) error("Mutation_Matrix::mutate_edge(state,time): unknown state");
if(time<0.0) error("Mutation_Matrix::mutate_edge(state,time): time must be non-negative");
double time_remaining = time;
double next_mutation = ran->exponential(mutation_mean[old_state]);
double U,rp;
int new_state = state;
while(next_mutation<time_remaining) {
U = ran->U();
for(new_state=0;new_state<n_states-1;new_state++) {
rp = D[old_state][new_state];
if(U < rp) break;
U -= rp;
}
time_remaining -= next_mutation;
next_mutation = ran->exponential(mutation_mean[old_state]);
}
return new_state;
}
int mutate_edge(const int state, const double time, int &nmut) {
int old_state = state;
if(old_state<0||old_state>=n_states) error("Mutation_Matrix::mutate_edge(state,time): unknown state");
if(time<0.0) error("Mutation_Matrix::mutate_edge(state,time): time must be non-negative");
double time_remaining = time;
double next_mutation = ran->exponential(mutation_mean[old_state]);
double U,rp;
int new_state = state;
while(next_mutation<time_remaining) {
U = ran->U();
for(new_state=0;new_state<n_states-1;new_state++) {
rp = D[old_state][new_state];
if(U < rp) break;
U -= rp;
}
time_remaining -= next_mutation;
next_mutation = ran->exponential(mutation_mean[old_state]);
++nmut;
}
return new_state;
}
double expected_rate() {
double result = 0.0;
int i;
for(i=0;i<n_states;i++)
result -= state_freq[i] * C[i][i];
return result;
}
};
class Nucleotide_Mutation_Matrix : public Mutation_Matrix {
public:
void set_defaults() {
n_states = 4;
state_freq.resize(n_states,0.25);
state_char.resize(n_states);
state_char[0] = string(1,'A');
state_char[1] = string(1,'G');
state_char[2] = string(1,'C');
state_char[3] = string(1,'T');
}
};
class JC69 : public Nucleotide_Mutation_Matrix {
public:
JC69(const double lambda, Random *ran_in) {
set_defaults();
ran = ran_in;
C.resize(n_states,n_states);
int i,j;
for(i=0;i<4;i++) {
C[i][i] = 0.0;
for(j=0;j<4;j++)
if(i!=j) {
C[i][j] = lambda/4.;
C[i][i] -= C[i][j];
}
}
initialize(n_states,&C);
}
int fast_mutate(const int state, const double time) {
double lambda = 4.*C[0][1];
double p0 = .25 + .75*exp(-lambda*time);
double p1 = .25 - .25*exp(-lambda*time);
double p2 = p1;
p1 += p0;
p2 += p1;
double U = ran->U();
switch(state) {
case 0:
if(U<p0) return 0;
if(U<p1) return 2;
if(U<p2) return 3;
return 1;
case 1:
if(U<p0) return 1;
if(U<p1) return 2;
if(U<p2) return 3;
return 0;
case 2:
if(U<p0) return 2;
if(U<p1) return 0;
if(U<p2) return 1;
return 3;
case 3:
if(U<p0) return 3;
if(U<p1) return 0;
if(U<p2) return 1;
return 2;
}
error("JC69::fast_mutate(): state not recognised");
return -1;
}
};
class F81 : public Nucleotide_Mutation_Matrix {
public:
F81(const double lambda, const vector<double> state_freq_in, Random *ran_in) {
set_defaults();
ran = ran_in;
set_state_freq(state_freq_in);
C.resize(n_states,n_states);
int i,j;
for(i=0;i<4;i++) {
C[i][i] = 0.0;
for(j=0;j<4;j++)
if(i!=j) {
C[i][j] = lambda*state_freq[j];
C[i][i] -= C[i][j];
}
}
initialize(n_states,&C);
}
};
class K80 : public Nucleotide_Mutation_Matrix {
public:
K80(const double lambda, const double kappa, Random *ran_in) {
set_defaults();
ran = ran_in;
C.resize(n_states,n_states);
update(lambda,kappa);
}
K80& update(const double lambda, const double kappa) {
int i,j;
for(i=0;i<4;i++)
for(j=0;j<4;j++)
C[i][j] = (i==j) ? 0.0 : lambda/4.;
C[0][1]*=kappa;C[1][0]*=kappa;
C[2][3]*=kappa;C[3][2]*=kappa;
for(i=0;i<4;i++)
for(j=0;j<4;j++)
if(i!=j)
C[i][i] -= C[i][j];
initialize(n_states,&C);
return *this;
}
int fast_mutate(const int state, const double time) {
double lambda = 4.*C[0][2];
double kappa = C[0][1]/C[0][2];
double p0 = .25 + .25*exp(-2.*lambda*time) + .5*exp(-lambda*time*(1.+kappa));
double p1 = p0 + .25 - .25*exp(-2.*lambda*time);
double p2 = p1 + .25 - .25*exp(-2.*lambda*time);
double U = ran->U();
switch(state) {
case 0:
if(U<p0) return 0;
if(U<p1) return 2;
if(U<p2) return 3;
return 1;
case 1:
if(U<p0) return 1;
if(U<p1) return 2;
if(U<p2) return 3;
return 0;
case 2:
if(U<p0) return 2;
if(U<p1) return 0;
if(U<p2) return 1;
return 3;
case 3:
if(U<p0) return 3;
if(U<p1) return 0;
if(U<p2) return 1;
return 2;
}
error("K80::fast_mutate(): state not recognised");
return -1;
}
};
class HKY85 : public Nucleotide_Mutation_Matrix {
public:
HKY85(const double lambda, const double kappa, const vector<double> state_freq_in, Random *ran_in) {
set_defaults();
ran = ran_in;
set_state_freq(state_freq_in);
C.resize(n_states,n_states);
int i,j;
for(i=0;i<4;i++)
for(j=0;j<4;j++)
C[i][j] = (i==j) ? 0.0 : lambda*state_freq[j];
C[0][1]*=kappa;C[1][0]*=kappa;
C[2][3]*=kappa;C[3][2]*=kappa;
for(i=0;i<4;i++)
for(j=0;j<4;j++)
if(i!=j)
C[i][i] -= C[i][j];
initialize(n_states,&C);
}
};
class TN93 : public Nucleotide_Mutation_Matrix {
public:
TN93(const double lambda, const double kappa_R, const double kappa_Y, const vector<double> state_freq_in, Random *ran_in) {
set_defaults();
ran = ran_in;
set_state_freq(state_freq_in);
C.resize(n_states,n_states);
int i,j;
for(i=0;i<4;i++)
for(j=0;j<4;j++)
C[i][j] = (i==j) ? 0.0 : lambda*state_freq[j];
C[0][1]*=kappa_R;C[1][0]*=kappa_R;
C[2][3]*=kappa_Y;C[3][2]*=kappa_Y;
for(i=0;i<4;i++)
for(j=0;j<4;j++)
if(i!=j)
C[i][i] -= C[i][j];
initialize(n_states,&C);
}
};
class Codon_Mutation_Matrix : public Mutation_Matrix {
public:
void set_defaults() {
n_states = 64;
state_freq.resize(n_states,1./61.);
state_freq[10]=state_freq[11]=state_freq[14]=0.0;
string default_char = string(3,'-');
state_char.resize(n_states,default_char);
int i,j,k,l;
vector<char> base(4,'-');
base[0] = 'U'; base[1] = 'C'; base[2] = 'A'; base[3] = 'G';
for(i=0,l=0;i<4;i++)
for(j=0;j<4;j++)
for(k=0;k<4;k++,l++) {
state_char[l][0] = base[i];
state_char[l][1] = base[j];
state_char[l][2] = base[k];
}
//for(i=0;i<64;i++) state_char[i] = i+1;
}
virtual Codon_Mutation_Matrix& update(const double mu, const double kappa, const double omega) = 0;
virtual Codon_Mutation_Matrix& update(const double mu, const double kappa, const double omega, const vector<double> &pi) = 0;
virtual Codon_Mutation_Matrix& build_C(const double mu, const double kappa, const double omega, const vector<double> &pi) = 0;
};
class NY98 : public Codon_Mutation_Matrix {
protected:
NY98() {}
public:
NY98(Random *ran_in) {
set_defaults();
ran = ran_in;
C.resize(n_states,n_states);
D.resize(n_states,n_states);
}
NY98(const double mu, const double kappa, const double omega, Random *ran_in) {
set_defaults();
ran = ran_in;
C.resize(n_states,n_states);
D.resize(n_states,n_states);
update(mu,kappa,omega,state_freq);
}
NY98(const double mu, const double kappa, const double omega, const vector<double> &pi, Random *ran_in) {
set_defaults();
ran = ran_in;
set_state_freq(pi);
C.resize(n_states,n_states);
D.resize(n_states,n_states);
update(mu,kappa,omega,state_freq);
}
Codon_Mutation_Matrix& update(const double mu, const double kappa, const double omega) {
build_C(mu,kappa,omega,state_freq);
initialize(n_states,&C);
return *this;
}
Codon_Mutation_Matrix& update(const double mu, const double kappa, const double omega, const vector<double> &pi) {
set_state_freq(pi);
build_C(mu,kappa,omega,state_freq);
initialize(n_states,&C);
return *this;
}
Codon_Mutation_Matrix& build_C(const double mu, const double kappa, const double omega, const vector<double> &pi)
{
int i,j;
/*Initialize to zero*/
for(i=0;i<64;i++){for(j=0;j<64;j++)C[i][j]=0.0;}
C[0][1]=kappa*mu;
C[0][2]=omega*mu;
C[0][3]=omega*mu;
C[0][4]=kappa*omega*mu;
C[0][8]=omega*mu;
C[0][12]=omega*mu;
C[0][16]=kappa*omega*mu;
C[0][32]=omega*mu;
C[0][48]=omega*mu;
C[1][2]=omega*mu;
C[1][3]=omega*mu;
C[1][5]=kappa*omega*mu;
C[1][9]=omega*mu;
C[1][13]=omega*mu;
C[1][17]=kappa*omega*mu;
C[1][33]=omega*mu;
C[1][49]=omega*mu;
C[2][3]=kappa*mu;
C[2][6]=kappa*omega*mu;
C[2][10]=omega*mu;
C[2][14]=omega*mu;
C[2][18]=kappa*mu; /*Synonymous!*/
C[2][34]=omega*mu;
C[2][50]=omega*mu;
C[3][7]=kappa*omega*mu;
C[3][11]=omega*mu;
C[3][15]=omega*mu;
C[3][19]=kappa*mu; /*Synonymous!*/
C[3][35]=omega*mu;
C[3][51]=omega*mu;
C[4][5]=kappa*mu;
C[4][6]=mu;
C[4][7]=mu;
C[4][8]=omega*mu;
C[4][12]=omega*mu;
C[4][20]=kappa*omega*mu;
C[4][36]=omega*mu;
C[4][52]=omega*mu;
C[5][6]=mu;
C[5][7]=mu;
C[5][9]=omega*mu;
C[5][13]=omega*mu;
C[5][21]=kappa*omega*mu;
C[5][37]=omega*mu;
C[5][53]=omega*mu;
C[6][7]=kappa*mu;
C[6][10]=omega*mu;
C[6][14]=omega*mu;
C[6][22]=kappa*omega*mu;
C[6][38]=omega*mu;
C[6][54]=omega*mu;
C[7][11]=omega*mu;
C[7][15]=omega*mu;
C[7][23]=kappa*omega*mu;
C[7][39]=omega*mu;
C[7][55]=omega*mu;
C[8][9]=kappa*mu;
C[8][10]=omega*mu;
C[8][11]=omega*mu;
C[8][12]=kappa*omega*mu;
C[8][24]=kappa*omega*mu;
C[8][40]=omega*mu;
C[8][56]=omega*mu;
C[9][10]=omega*mu;
C[9][11]=omega*mu;
C[9][13]=kappa*omega*mu;
C[9][25]=kappa*omega*mu;
C[9][41]=omega*mu;
C[9][57]=omega*mu;
C[10][11]=kappa*mu;
C[10][14]=kappa*mu;
C[10][26]=kappa*omega*mu;
C[10][42]=omega*mu;
C[10][58]=omega*mu;
C[11][15]=kappa*omega*mu;
C[11][27]=kappa*omega*mu;
C[11][43]=omega*mu;
C[11][59]=omega*mu;
C[12][13]=kappa*mu;
C[12][14]=omega*mu;
C[12][15]=omega*mu;
C[12][28]=kappa*omega*mu;
C[12][44]=omega*mu;
C[12][60]=omega*mu;
C[13][14]=omega*mu;
C[13][15]=omega*mu;
C[13][29]=kappa*omega*mu;
C[13][45]=omega*mu;
C[13][61]=omega*mu;
C[14][15]=kappa*omega*mu;
C[14][30]=kappa*omega*mu;
C[14][46]=omega*mu;
C[14][62]=omega*mu;
C[15][31]=kappa*omega*mu;
C[15][47]=omega*mu;
C[15][63]=omega*mu;
C[16][17]=kappa*mu;
C[16][18]=mu;
C[16][19]=mu;
C[16][20]=kappa*omega*mu;
C[16][24]=omega*mu;
C[16][28]=omega*mu;
C[16][32]=omega*mu;
C[16][48]=omega*mu;
C[17][18]=mu;
C[17][19]=mu;
C[17][21]=kappa*omega*mu;
C[17][25]=omega*mu;
C[17][29]=omega*mu;
C[17][33]=omega*mu;
C[17][49]=omega*mu;
C[18][19]=kappa*mu;
C[18][22]=kappa*omega*mu;
C[18][26]=omega*mu;
C[18][30]=omega*mu;
C[18][34]=omega*mu;
C[18][50]=omega*mu;
C[19][23]=kappa*omega*mu;
C[19][27]=omega*mu;
C[19][31]=omega*mu;
C[19][35]=omega*mu;
C[19][51]=omega*mu;
C[20][21]=kappa*mu;
C[20][22]=mu;
C[20][23]=mu;
C[20][24]=omega*mu;
C[20][28]=omega*mu;
C[20][36]=omega*mu;
C[20][52]=omega*mu;
C[21][22]=mu;
C[21][23]=mu;
C[21][25]=omega*mu;
C[21][29]=omega*mu;
C[21][37]=omega*mu;
C[21][53]=omega*mu;
C[22][23]=kappa*mu;
C[22][26]=omega*mu;
C[22][30]=omega*mu;
C[22][38]=omega*mu;
C[22][54]=omega*mu;
C[23][27]=omega*mu;
C[23][31]=omega*mu;
C[23][39]=omega*mu;
C[23][55]=omega*mu;
C[24][25]=kappa*mu;
C[24][26]=omega*mu;
C[24][27]=omega*mu;
C[24][28]=kappa*omega*mu;
C[24][40]=omega*mu;
C[24][56]=omega*mu;
C[25][26]=omega*mu;
C[25][27]=omega*mu;
C[25][29]=kappa*omega*mu;
C[25][41]=omega*mu;
C[25][57]=omega*mu;
C[26][27]=kappa*mu;
C[26][30]=kappa*omega*mu;
C[26][42]=omega*mu;
C[26][58]=omega*mu;
C[27][31]=kappa*omega*mu;
C[27][43]=omega*mu;
C[27][59]=omega*mu;
C[28][29]=kappa*mu;
C[28][30]=mu;
C[28][31]=mu;
C[28][44]=omega*mu;
C[28][60]=omega*mu;
C[29][30]=mu;
C[29][31]=mu;
C[29][45]=omega*mu;
C[29][61]=omega*mu;
C[30][31]=kappa*mu;
C[30][46]=mu;
C[30][62]=omega*mu;
C[31][47]=mu;
C[31][63]=omega*mu;
C[32][33]=kappa*mu;
C[32][34]=mu;
C[32][35]=omega*mu;
C[32][36]=kappa*omega*mu;
C[32][40]=omega*mu;
C[32][44]=omega*mu;
C[32][48]=kappa*omega*mu;
C[33][34]=mu;
C[33][35]=omega*mu;
C[33][37]=kappa*omega*mu;
C[33][41]=omega*mu;
C[33][45]=omega*mu;
C[33][49]=kappa*omega*mu;
C[34][35]=kappa*omega*mu;
C[34][38]=kappa*omega*mu;
C[34][42]=omega*mu;
C[34][46]=omega*mu;
C[34][50]=kappa*omega*mu;
C[35][39]=kappa*omega*mu;
C[35][43]=omega*mu;
C[35][47]=omega*mu;
C[35][51]=kappa*omega*mu;
C[36][37]=kappa*mu;
C[36][38]=mu;
C[36][39]=mu;
C[36][40]=omega*mu;
C[36][44]=omega*mu;
C[36][52]=kappa*omega*mu;
C[37][38]=mu;
C[37][39]=mu;
C[37][41]=omega*mu;
C[37][45]=omega*mu;
C[37][53]=kappa*omega*mu;
C[38][39]=kappa*mu;
C[38][42]=omega*mu;
C[38][46]=omega*mu;
C[38][54]=kappa*omega*mu;
C[39][43]=omega*mu;
C[39][47]=omega*mu;
C[39][55]=kappa*omega*mu;
C[40][41]=kappa*mu;
C[40][42]=omega*mu;
C[40][43]=omega*mu;
C[40][44]=kappa*omega*mu;
C[40][56]=kappa*omega*mu;
C[41][42]=omega*mu;
C[41][43]=omega*mu;
C[41][45]=kappa*omega*mu;
C[41][57]=kappa*omega*mu;
C[42][43]=kappa*mu;
C[42][46]=kappa*omega*mu;
C[42][58]=kappa*omega*mu;
C[43][47]=kappa*omega*mu;
C[43][59]=kappa*omega*mu;
C[44][45]=kappa*mu;
C[44][46]=omega*mu;
C[44][47]=omega*mu;
C[44][60]=kappa*omega*mu;
C[45][46]=omega*mu;
C[45][47]=omega*mu;
C[45][61]=kappa*omega*mu;
C[46][47]=kappa*mu;
C[46][62]=kappa*omega*mu;
C[47][63]=kappa*omega*mu;
C[48][49]=kappa*mu;
C[48][50]=mu;
C[48][51]=mu;
C[48][52]=kappa*omega*mu;
C[48][56]=omega*mu;
C[48][60]=omega*mu;
C[49][50]=mu;
C[49][51]=mu;
C[49][53]=kappa*omega*mu;
C[49][57]=omega*mu;
C[49][61]=omega*mu;
C[50][51]=kappa*mu;
C[50][54]=kappa*omega*mu;
C[50][58]=omega*mu;
C[50][62]=omega*mu;
C[51][55]=kappa*omega*mu;
C[51][59]=omega*mu;
C[51][63]=omega*mu;
C[52][53]=kappa*mu;
C[52][54]=mu;
C[52][55]=mu;
C[52][56]=omega*mu;
C[52][60]=omega*mu;
C[53][54]=mu;
C[53][55]=mu;
C[53][57]=omega*mu;
C[53][61]=omega*mu;
C[54][55]=kappa*mu;
C[54][58]=omega*mu;
C[54][62]=omega*mu;
C[55][59]=omega*mu;
C[55][63]=omega*mu;
C[56][57]=kappa*mu;
C[56][58]=omega*mu;
C[56][59]=omega*mu;
C[56][60]=kappa*omega*mu;
C[57][58]=omega*mu;
C[57][59]=omega*mu;
C[57][61]=kappa*omega*mu;
C[58][59]=kappa*mu;
C[58][62]=kappa*omega*mu;
C[59][63]=kappa*omega*mu;
C[60][61]=kappa*mu;
C[60][62]=mu;
C[60][63]=mu;
C[61][62]=mu;
C[61][63]=mu;
C[62][63]=kappa*mu;
/*Remove the STOP codons from the scheme*/
for(i=0;i<64;i++){
C[10][i]=0.0; C[i][10]=0.0;
C[11][i]=0.0; C[i][11]=0.0;
C[14][i]=0.0; C[i][14]=0.0;
}
/*Fill in the lower triangle*/
for(i=0;i<64;i++){
for(j=i+1;j<64;j++)C[j][i]=C[i][j];}
/*Apply the equilibrium frequencies*/
for(i=0;i<64;i++)
for(j=0;j<64;j++)
C[i][j]*=pi[j];
/*Compute the diagonal*/
for(i=0;i<64;i++)
{
double rowsum=0.0;
for(j=0;j<64;j++) rowsum+=C[i][j];
C[i][i]=-rowsum;
}
return *this;
}
};
class NY98_61 : public NY98 {
public:
void set_defaults() {
n_states = 61;
state_freq.resize(n_states,1./61.);
string default_char = string(3,'-');
state_char.resize(n_states,default_char);
int i,j,k,l,m;
vector<char> base(4,'-');
base[0] = 'U'; base[1] = 'C'; base[2] = 'A'; base[3] = 'G';
for(i=0,l=0,m=0;i<4;i++)
for(j=0;j<4;j++)
for(k=0;k<4;k++,l++,m++) {
state_char[m][0] = base[i];
state_char[m][1] = base[j];
state_char[m][2] = base[k];
if(l==10 || l==11 || l==14) --m;
}
//for(i=0;i<61;i++) state_char[i] = i+1;
}
NY98_61(Random *ran_in) {
set_defaults();
ran = ran_in;
C.resize(n_states,n_states);
D.resize(n_states,n_states);
}
NY98_61(const double mu, const double kappa, const double omega, Random *ran_in) {
set_defaults();
ran = ran_in;
C.resize(n_states,n_states);
D.resize(n_states,n_states);
update(mu,kappa,omega,state_freq);
}
NY98_61(const double mu, const double kappa, const double omega, const vector<double> &pi, Random *ran_in) {
set_defaults();
ran = ran_in;
set_state_freq(pi);
C.resize(n_states,n_states);
D.resize(n_states,n_states);
update(mu,kappa,omega,state_freq);
}
Codon_Mutation_Matrix& update(const double mu, const double kappa, const double omega) {
build_C(mu,kappa,omega,state_freq);
initialize(n_states,&C);
return *this;
}
Codon_Mutation_Matrix& update(const double mu, const double kappa, const double omega, const vector<double> &pi) {
set_state_freq(pi);
build_C(mu,kappa,omega,state_freq);
initialize(n_states,&C);
return *this;
}
Codon_Mutation_Matrix& build_C(const double mu, const double kappa, const double omega, const vector<double> &pi)
{
int i,j;
/*Initialize to zero*/
for(i=0;i<61;i++){for(j=0;j<61;j++)C[i][j]=0.0;}
C[0][1]=kappa*mu;
C[0][2]=omega*mu;
C[0][3]=omega*mu;
C[0][4]=kappa*omega*mu;
C[0][8]=omega*mu;
C[0][10]=omega*mu;
C[0][13]=kappa*omega*mu;
C[0][29]=omega*mu;
C[0][45]=omega*mu;
C[1][2]=omega*mu;
C[1][3]=omega*mu;
C[1][5]=kappa*omega*mu;
C[1][9]=omega*mu;
C[1][11]=omega*mu;
C[1][14]=kappa*omega*mu;
C[1][30]=omega*mu;
C[1][46]=omega*mu;
C[2][3]=kappa*mu;
C[2][6]=kappa*omega*mu;
C[2][15]=kappa*mu;
C[2][31]=omega*mu;
C[2][47]=omega*mu;
C[3][7]=kappa*omega*mu;
C[3][12]=omega*mu;
C[3][16]=kappa*mu;
C[3][32]=omega*mu;
C[3][48]=omega*mu;
C[4][5]=kappa*mu;
C[4][6]=mu;
C[4][7]=mu;
C[4][8]=omega*mu;
C[4][10]=omega*mu;
C[4][17]=kappa*omega*mu;
C[4][33]=omega*mu;
C[4][49]=omega*mu;
C[5][6]=mu;
C[5][7]=mu;
C[5][9]=omega*mu;
C[5][11]=omega*mu;
C[5][18]=kappa*omega*mu;
C[5][34]=omega*mu;
C[5][50]=omega*mu;
C[6][7]=kappa*mu;
C[6][19]=kappa*omega*mu;
C[6][35]=omega*mu;
C[6][51]=omega*mu;
C[7][12]=omega*mu;
C[7][20]=kappa*omega*mu;
C[7][36]=omega*mu;
C[7][52]=omega*mu;
C[8][9]=kappa*mu;
C[8][10]=kappa*omega*mu;
C[8][21]=kappa*omega*mu;
C[8][37]=omega*mu;
C[8][53]=omega*mu;
C[9][11]=kappa*omega*mu;
C[9][22]=kappa*omega*mu;
C[9][38]=omega*mu;
C[9][54]=omega*mu;
C[10][11]=kappa*mu;
C[10][12]=omega*mu;
C[10][25]=kappa*omega*mu;
C[10][41]=omega*mu;
C[10][57]=omega*mu;
C[11][12]=omega*mu;
C[11][26]=kappa*omega*mu;
C[11][42]=omega*mu;
C[11][58]=omega*mu;
C[12][28]=kappa*omega*mu;
C[12][44]=omega*mu;
C[12][60]=omega*mu;
C[13][14]=kappa*mu;
C[13][15]=mu;
C[13][16]=mu;
C[13][17]=kappa*omega*mu;
C[13][21]=omega*mu;
C[13][25]=omega*mu;
C[13][29]=omega*mu;
C[13][45]=omega*mu;
C[14][15]=mu;
C[14][16]=mu;
C[14][18]=kappa*omega*mu;
C[14][22]=omega*mu;
C[14][26]=omega*mu;
C[14][30]=omega*mu;
C[14][46]=omega*mu;
C[15][16]=kappa*mu;
C[15][19]=kappa*omega*mu;
C[15][23]=omega*mu;
C[15][27]=omega*mu;
C[15][31]=omega*mu;
C[15][47]=omega*mu;
C[16][20]=kappa*omega*mu;
C[16][24]=omega*mu;
C[16][28]=omega*mu;
C[16][32]=omega*mu;
C[16][48]=omega*mu;
C[17][18]=kappa*mu;
C[17][19]=mu;
C[17][20]=mu;
C[17][21]=omega*mu;
C[17][25]=omega*mu;
C[17][33]=omega*mu;
C[17][49]=omega*mu;
C[18][19]=mu;
C[18][20]=mu;
C[18][22]=omega*mu;
C[18][26]=omega*mu;
C[18][34]=omega*mu;
C[18][50]=omega*mu;
C[19][20]=kappa*mu;
C[19][23]=omega*mu;
C[19][27]=omega*mu;
C[19][35]=omega*mu;
C[19][51]=omega*mu;
C[20][24]=omega*mu;
C[20][28]=omega*mu;
C[20][36]=omega*mu;
C[20][52]=omega*mu;
C[21][22]=kappa*mu;
C[21][23]=omega*mu;
C[21][24]=omega*mu;
C[21][25]=kappa*omega*mu;
C[21][37]=omega*mu;
C[21][53]=omega*mu;
C[22][23]=omega*mu;
C[22][24]=omega*mu;
C[22][26]=kappa*omega*mu;
C[22][38]=omega*mu;
C[22][54]=omega*mu;
C[23][24]=kappa*mu;
C[23][27]=kappa*omega*mu;
C[23][39]=omega*mu;
C[23][55]=omega*mu;
C[24][28]=kappa*omega*mu;
C[24][40]=omega*mu;
C[24][56]=omega*mu;
C[25][26]=kappa*mu;
C[25][27]=mu;
C[25][28]=mu;
C[25][41]=omega*mu;
C[25][57]=omega*mu;
C[26][27]=mu;
C[26][28]=mu;
C[26][42]=omega*mu;
C[26][58]=omega*mu;
C[27][28]=kappa*mu;
C[27][43]=mu;
C[27][59]=omega*mu;
C[28][44]=mu;
C[28][60]=omega*mu;
C[29][30]=kappa*mu;
C[29][31]=mu;
C[29][32]=omega*mu;
C[29][33]=kappa*omega*mu;
C[29][37]=omega*mu;
C[29][41]=omega*mu;
C[29][45]=kappa*omega*mu;
C[30][31]=mu;
C[30][32]=omega*mu;
C[30][34]=kappa*omega*mu;
C[30][38]=omega*mu;
C[30][42]=omega*mu;
C[30][46]=kappa*omega*mu;
C[31][32]=kappa*omega*mu;
C[31][35]=kappa*omega*mu;
C[31][39]=omega*mu;
C[31][43]=omega*mu;
C[31][47]=kappa*omega*mu;
C[32][36]=kappa*omega*mu;
C[32][40]=omega*mu;
C[32][44]=omega*mu;
C[32][48]=kappa*omega*mu;
C[33][34]=kappa*mu;
C[33][35]=mu;
C[33][36]=mu;
C[33][37]=omega*mu;
C[33][41]=omega*mu;
C[33][49]=kappa*omega*mu;
C[34][35]=mu;
C[34][36]=mu;
C[34][38]=omega*mu;
C[34][42]=omega*mu;
C[34][50]=kappa*omega*mu;
C[35][36]=kappa*mu;
C[35][39]=omega*mu;
C[35][43]=omega*mu;
C[35][51]=kappa*omega*mu;
C[36][40]=omega*mu;
C[36][44]=omega*mu;
C[36][52]=kappa*omega*mu;
C[37][38]=kappa*mu;
C[37][39]=omega*mu;
C[37][40]=omega*mu;
C[37][41]=kappa*omega*mu;
C[37][53]=kappa*omega*mu;
C[38][39]=omega*mu;
C[38][40]=omega*mu;
C[38][42]=kappa*omega*mu;
C[38][54]=kappa*omega*mu;
C[39][40]=kappa*mu;
C[39][43]=kappa*omega*mu;
C[39][55]=kappa*omega*mu;
C[40][44]=kappa*omega*mu;
C[40][56]=kappa*omega*mu;
C[41][42]=kappa*mu;
C[41][43]=omega*mu;
C[41][44]=omega*mu;
C[41][57]=kappa*omega*mu;
C[42][43]=omega*mu;
C[42][44]=omega*mu;
C[42][58]=kappa*omega*mu;
C[43][44]=kappa*mu;
C[43][59]=kappa*omega*mu;