void SetAAModel(int theAAModel)
{
aaModel = theAAModel;
switch (aaModel) {
case AA_JTT: SetRelativeRates(jttRelativeRates); break;
case AA_WAG: SetRelativeRates(wagRelativeRates); break;
case AA_DAYHOFF78: SetRelativeRates(dayhoffRelativeRates); break;
case AA_BLOSUM62: SetRelativeRates(blosumRelativeRates); break;
case AA_MTREV24: SetRelativeRates(mtrevRelativeRates); break;
case AA_CPREV45: SetRelativeRates(cprevRelativeRates); break;
case AA_GENERAL:
// relative rates set by user
break;
}
if (!aaFreqSet) {
switch (aaModel) {
case AA_JTT: SetFrequencies(jttFrequencies); break;
case AA_WAG: SetFrequencies(wagFrequencies); break;
case AA_DAYHOFF78: SetFrequencies(dayhoffFrequencies); break;
case AA_BLOSUM62: SetFrequencies(blosumFrequencies); break;
case AA_MTREV24: SetFrequencies(mtrevFrequencies); break;
case AA_CPREV45: SetFrequencies(cprevFrequencies); break;
case AA_GENERAL:
// frequencies set by user
break;
}
} else {
// User set or equal frequencies
CheckAAFrequencies();
}
SetupAAMatrix();
}
void RateMatrix::SetAAFreqs(int theModel, inClade *branch)
{
switch (theModel) {
case AA_JTT: SetFrequencies(jttFrequencies, branch); break;
case AA_WAG: SetFrequencies(wagFrequencies, branch); break;
case AA_DAYHOFF78: SetFrequencies(dayhoffFrequencies, branch); break;
case AA_BLOSUM62: SetFrequencies(blosumFrequencies, branch); break;
case AA_MTREV24: SetFrequencies(mtrevFrequencies, branch); break;
case AA_CPREV45: SetFrequencies(cprevFrequencies, branch); break;
default: cerr << "You cannot set the general matrix in lineages." << endl; exit(EXIT_FAILURE);
}
}
void RateMatrix::SetModel(
inClade *branch
)
{
int i;
bool freqSet = true;
double a, b, c, d, e, f, a_, b_, c_, d_, e_, f_, kappa1, kappa2, alpha, beta, gamma, delta;
double sum_freq = 0;
cerr << "Point-> RateMatrix::SetModel(inClade *branch) IN" << endl;
if (isNucModel) stateCharacters = nucleotides;
else stateCharacters = aminoAcids;
//////////
/// freqSet does not matter for nucleotides. It should always be set for nuc models that do
/// not require equal frequencies. For amino acid models, though, need to know if the freqs
/// are set, otherwise they can be overwritten by model-specific pi values.
//////////
if (branch != NULL) {
if ( !(branch->values2Export2Freq.empty()) ) {
for (int j = 0; j < numStates; j++)
pi.at(j) = branch->values2Export2Freq.at(j);
} else freqSet = false;
} else freqSet = false;
for (vector<double>::iterator it = pi.begin(); it != pi.end(); ++it)
sum_freq += (*it);
for (vector<double>::iterator it = pi.begin(); it != pi.end(); ++it)
(*it) /= sum_freq;
//////////
/// Putting model parameters explicitly, easier to understand.
//////////
switch (substitution_model)
{
case NUC_JC69:
////////// OK
/// | * 1 1 1 |
/// Q = | 1 * 1 1 |
/// | 1 1 * 1 |
/// | 1 1 1 * |
//////////
a=b=c=d=e=f=a_=b_=c_=d_=e_=f_=1;
pi.at(A) = pi.at(C) = pi.at(G) = pi.at(T) = 0.25;
break;
case NUC_K80:
////////// OK
/// | * 1 K 1 |
/// Q = | 1 * 1 K |
/// | K 1 * 1 |
/// | 1 K 1 * |
//////////
kappa1 = kappa.front();
b = b_ = e = e_ = kappa1;
a = a_ = c = c_ = d = d_ = f = f_ = 1.0;
pi.at(A) = pi.at(C) = pi.at(G) = pi.at(T) = 0.25;
break;
case NUC_K81:
pi.at(A) = pi.at(C) = pi.at(G) = pi.at(T) = 0.25;
case NUC_K81ne:
////////// OK
/// | * 1 K A |
/// Q = | 1 * A K |
/// | K A * 1 |
/// | A K 1 * |
//////////
kappa1 = kappa.at(0);
alpha = kappa.at(1);
a = 1; b = kappa1; c = alpha; // *fA
a_ = 1; d = alpha; e = kappa1; // *fC
b_ = kappa1; d_ = alpha; f = 1; // *fG
c_ = alpha; e_ = kappa1; f_ = 1; // *fT
break;
case NUC_F81:
////////// OK
/// | * fA fA fA |
/// Q = | fC * fC fC |
/// | fG fG * fG |
/// | fT fT fT * |
//////////
a=b=c=d=e=f=a_=b_=c_=d_=e_=f_=1;
break;
case NUC_HKY:
////////// OK
/// | * fA KfA fA |
/// Q = | fC * fC KfC |
/// | KfG fG * fG |
/// | fT KfT fT * |
//////////
kappa1 = kappa.at(0);
a = c = 1; b = kappa1; // *fA
a_ = d = 1; e = kappa1; // *fC
b_ = kappa1; d_ = f = 1; // *fG
c_ = f_ = 1; e_ = kappa1; // *fT
break;
case NUC_F84:
////////// OK
/// INPUT: kappa
/// | * fA (1+K/(fA+fG))fA fA |
/// Q = | fC * fC (1+K/(fC+fT))fC |
/// | (1+K/(fA+fG))fG fG * fG |
/// | fT (1+K/(fC+fT))fT fT * |
//////////
kappa1 = kappa.at(0);
a = c = 1; b = (1.0+kappa1/(pi.at(A)+pi.at(G))); // *fA
a_ = d = 1; e = (1.0+kappa1/(pi.at(C)+pi.at(T))); // *fC
b_ = (1.0+kappa1/(pi.at(A)+pi.at(G))); d_ = f = 1; // *fG
c_ = f_ = 1; e_ = (1.0+kappa1/(pi.at(C)+pi.at(T))); // *fT
break;
case NUC_T92:
//////////
/// INPUT: kappa
/// | * (1-(fG+fC))/2 K(1-(fG+fC))/2 (1-(fG+fC))/2 |
/// Q = | (fG+fC)/2 * (fG+fC)/2 K(fG+fC)/2 |
/// | K(fG+fC)/2 (fG+fC)/2 * (fG+fC)/2 |
/// | (1-(fG+fC))/2 K(1-(fG+fC))/2 (1-(fG+fC))/2 * |
//////////
break;
case NUC_TN93eq:
pi.at(A) = pi.at(C) = pi.at(G) = pi.at(T) = 0.25;
case NUC_TN93:
//////////
/// INPUT: kappa, kappa2;
/// | * fA K1fA fA |
/// Q = | fC * fC K2fC |
/// | K1fG fG * fG |
/// | fT K2fT fT * |
//////////
kappa1 = kappa.at(0);
kappa2 = kappa.at(1);
a = c = 1; b = kappa1; // *fA
a_ = d = 1; e = kappa2; // *fC
b_ = kappa1; d_ = f = 1; // *fG
c_ = f_ = 1; e_ = kappa2; // *fT
break;
case NUC_TIMeq:
pi.at(A) = pi.at(C) = pi.at(G) = pi.at(T) = 0.25;
case NUC_TIM:
//////////
/// INPUT: alpha, beta, gamma
/// | * fA AfA BfA |
/// Q = | fC * BfC GfC |
/// | AfG BfG * fG |
/// | BfT GfT fT * |
///////////
alpha = kappa.at(0);
beta = kappa.at(1);
gamma = kappa.at(2);
a = 1; b = alpha; c = beta; // *fA
a_ = 1; d = beta; e = gamma; // *fC
b_ = alpha; d_ = beta; f = 1; // *fG
c_ = beta; e_ = gamma; f_ = 1; // *fT
break;
case NUC_TVMeq:
pi.at(A) = pi.at(C) = pi.at(G) = pi.at(T) = 0.25;
case NUC_TVM:
//////////
/// INPUT: alpha, beta, gamma, delta
/// | * fA AfA BfA |
/// Q = | fC * GfC AfC |
/// | AfG GfG * DfG |
/// | BfT AfT DfT * |
///////////
alpha = kappa.at(0);
beta = kappa.at(1);
gamma = kappa.at(2);
delta = kappa.at(3);
a = 1; b = alpha; c = beta; // *fA
a_ = 1; c = gamma; d = alpha; // *fC
b_ = alpha; d_ = gamma; f = delta; // *fG
c_ = beta; e_ = alpha; f_ = delta; // *fT
break;
case NUC_SYM:
pi.at(A) = pi.at(C) = pi.at(G) = pi.at(T) = 0.25;
/// SYM and GTR are same, except SYM has equal nucleotide frequencies. No break.
case NUC_GTR:
//////////
/// INPUT: relative rates abcdef
/// | * rACfC rAGfA rATfA |
/// Q = | rACfC * rCGfG rCTfC |
/// | rAGfG rCGfG * rGTfG |
/// | rATfT rCTfT rGTfT * |
//////////
a = Sij.at(0); b = Sij.at(1); c = Sij.at(2); // *fA
a_ = Sij.at(0); d = Sij.at(3); e = Sij.at(4); // *fC
b_ = Sij.at(1); d_ = Sij.at(3); f = Sij.at(5); // *fG
c_ = Sij.at(2); e_ = Sij.at(4); d_ = Sij.at(5); // *fT
break;
case AA_JTT:
SetRelativeRates(jttRelativeRates);
if (!freqSet) SetFrequencies(jttFrequencies);
break;
case AA_WAG:
SetRelativeRates(wagRelativeRates);
if (!freqSet) SetFrequencies(wagFrequencies);
break;
case AA_DAYHOFF78:
SetRelativeRates(dayhoffRelativeRates);
if (!freqSet) SetFrequencies(dayhoffFrequencies);
break;
case AA_BLOSUM62:
SetRelativeRates(blosumRelativeRates);
if (!freqSet) SetFrequencies(blosumFrequencies);
break;
case AA_MTREV24:
SetRelativeRates(mtrevRelativeRates);
if (!freqSet) SetFrequencies(mtrevFrequencies);
break;
case AA_CPREV45:
SetRelativeRates(cprevRelativeRates);
if (!freqSet) SetFrequencies(cprevFrequencies);
break;
default:
cerr << "Do not know what to do with your model." << endl;
exit(EXIT_FAILURE);
}
if (numStates == NUM_NUC) {
Sij.at(0) = a;
Sij.at(1) = b;
Sij.at(2) = c;
Sij.at(3) = d;
Sij.at(4) = e;
Sij.at(5) = f;
}
SetupMatrix(true);
}
