#include <codonevo.hh>
Inheritance diagram for CodonEvo:
Public Member Functions | |
| void | setKappa (double kappa) |
| void | setPi (double *pi) |
| void | setOmegas (int k) |
| void | setPrior (double sigma=0.2) |
| double | getPrior (int u) |
| vector< double > * | getOmegas () |
| double | getOmega (int u) |
| int | getK () |
| void | printOmegas () |
| void | setAAPostProbs () |
| void | getRateMatrices () |
| void | writeRateMatrices (string filename) |
| void | readRateMatrices (string filename) |
| void | computeLogPmatrices () |
| gsl_matrix * | getSubMatrixLogP (double omega, double t) |
| double | subLogProb (int from, int to, double omega, double t) |
| double | logLik (const char *e1, const char *e2, int u, double t) |
| double | estOmegaOnSeqPair (const char *e1, const char *e2, double t, int &numAliCodons, int &numSynSubst, int &numNonSynSubst) |
| double | estOmegaOnSeqTuple (vector< string > &seqtuple, PhyloTree *tree, int &subst) |
| vector< double > | loglikForCodonTuple (vector< string > &seqtuple, PhyloTree *ctree) |
| vector< double > | loglikForCodonTuple (vector< string > &seqtuple, PhyloTree *ctree, PhyloTree *tree, int &subs) |
| double | graphOmegaOnCodonAli (vector< string > &seqtuple, PhyloTree *tree, int refSpeciesIdx=0) |
| void | addBranchLength (double b) |
 Public Member Functions inherited from Evo | |
| Evo (int s) | |
| int | getNumStates () |
| void | setBranchLengths (vector< double > b, int m=-1) |
| void | printBranchLengths () |
| double | getPi (int i) const |
| double | getLogPi (int i) const |
| gsl_matrix * | getSubMatrixQ (int u) |
| gsl_matrix * | getSubMatrixP (int u, double t) |
| gsl_matrix * | getSubMatrixLogP (int u, double t) |
| gsl_matrix * | expQt (double t, gsl_vector *lambda, gsl_matrix *U, gsl_matrix *Uinv) |
Additional Inherited Members | |
| Protected Member Functions inherited from Evo | |
| int | findClosestIndex (vector< double > &v, double val) |
| Protected Attributes inherited from Evo | |
| const int | states |
| int | m |
| double * | pi |
| vector< double > | times |
| vector< gsl_matrix * > | allQs |
| Matrix< gsl_matrix * > | allPs |
| Matrix< gsl_matrix * > | allLogPs |
Detailed Description
class CodonEvo
Computes and stores 64x64 codon substitution probability matrices P(t,omega,kappa,pi) = exp(Q(omega,kappa,pi)*t) for a sample of values for t and omega (dN/dS, selection) and a fixed given value of kappa (transition/transversion ratio) and vector pi (codon usage). Matrices are precomputed and retrieval of P(t,omega) is then a constant time lookup as this is needed very often during estimation of omega for a given tree.
Member Function Documentation
◆ addBranchLength()
|
inlinevirtual |
Implements Evo.
◆ computeLogPmatrices()
|
virtual |
Implements Evo.
◆ getRateMatrices()
|
virtual |
Reimplemented from Evo.
The documentation for this class was generated from the following files:
- include/codonevo.hh
- src/codonevo.cc
