class CodonEvoDiscr More...
#include <codonevodiscr.hh>
Inheritance diagram for CodonEvoDiscr:
Public Member Functions | |
| void | setM () |
| int | getM () |
| void | writeRateMatrices (string filename) |
| void | readMatrices (MatrixFormat fmt=fmt_TXT) |
| 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) |
| vector< double > | loglikForCodonTuple (vector< string > &seqtuple, PhyloTree *ctree) |
| vector< double > | loglikForCodonTuple (vector< string > &seqtuple, PhyloTree *ctree, PhyloTree *tree, int &subs) |
| void | addBranchLength (double b) |
| void | produceComb (vector< vector< int > > &config) |
| double | getProb (const vector< double > &lls) |
 Public Member Functions inherited from Evo | |
| Evo (int s) | |
| int | getNumStates () |
| void | setBranchLengths (vector< double > b, int m=-1) |
| void | printBranchLengths () |
| virtual void | getRateMatrices () |
| 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 CodonEvoDiscr
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()
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inlinevirtual |
Implements Evo.
◆ computeLogPmatrices()
|
virtual |
Implements Evo.
The documentation for this class was generated from the following files:
- include/codonevodiscr.hh
- src/codonevodiscr.cc
