CodonEvo Member List
This is the complete list of members for CodonEvo, including all inherited members.
| addBranchLength(double b) (defined in CodonEvo) | CodonEvo | inlinevirtual |
| allLogPs (defined in Evo) | Evo | protected |
| allPs (defined in Evo) | Evo | protected |
| allQs (defined in Evo) | Evo | protected |
| CodonEvo() (defined in CodonEvo) | CodonEvo | inline |
| computeLogPmatrices() (defined in CodonEvo) | CodonEvo | virtual |
| estOmegaOnSeqPair(const char *e1, const char *e2, double t, int &numAliCodons, int &numSynSubst, int &numNonSynSubst) (defined in CodonEvo) | CodonEvo | |
| estOmegaOnSeqTuple(vector< string > &seqtuple, PhyloTree *tree, int &subst) (defined in CodonEvo) | CodonEvo | |
| Evo(int s) (defined in Evo) | Evo | inline |
| expQt(double t, gsl_vector *lambda, gsl_matrix *U, gsl_matrix *Uinv) (defined in Evo) | Evo | |
| findClosestIndex(vector< double > &v, double val) (defined in Evo) | Evo | protected |
| getK() (defined in CodonEvo) | CodonEvo | inline |
| getLogPi(int i) const (defined in Evo) | Evo | inline |
| getNumStates() (defined in Evo) | Evo | inline |
| getOmega(int u) (defined in CodonEvo) | CodonEvo | inline |
| getOmegas() (defined in CodonEvo) | CodonEvo | inline |
| getPi(int i) const (defined in Evo) | Evo | inline |
| getPrior(int u) (defined in CodonEvo) | CodonEvo | inline |
| getRateMatrices() (defined in CodonEvo) | CodonEvo | virtual |
| getSubMatrixLogP(double omega, double t) (defined in CodonEvo) | CodonEvo | |
| getSubMatrixLogP(int u, double t) (defined in Evo) | Evo | |
| getSubMatrixP(int u, double t) (defined in Evo) | Evo | |
| getSubMatrixQ(int u) (defined in Evo) | Evo | inline |
| graphOmegaOnCodonAli(vector< string > &seqtuple, PhyloTree *tree, int refSpeciesIdx=0) (defined in CodonEvo) | CodonEvo | |
| logLik(const char *e1, const char *e2, int u, double t) (defined in CodonEvo) | CodonEvo | |
| loglikForCodonTuple(vector< string > &seqtuple, PhyloTree *ctree) (defined in CodonEvo) | CodonEvo | inline |
| loglikForCodonTuple(vector< string > &seqtuple, PhyloTree *ctree, PhyloTree *tree, int &subs) (defined in CodonEvo) | CodonEvo | |
| m (defined in Evo) | Evo | protected |
| pi (defined in Evo) | Evo | protected |
| printBranchLengths() (defined in Evo) | Evo | |
| printOmegas() (defined in CodonEvo) | CodonEvo | |
| readRateMatrices(string filename) (defined in CodonEvo) | CodonEvo | |
| setAAPostProbs() (defined in CodonEvo) | CodonEvo | |
| setBranchLengths(vector< double > b, int m=-1) (defined in Evo) | Evo | |
| setKappa(double kappa) (defined in CodonEvo) | CodonEvo | inline |
| setOmegas(int k) (defined in CodonEvo) | CodonEvo | |
| setPi(double *pi) (defined in CodonEvo) | CodonEvo | |
| setPrior(double sigma=0.2) (defined in CodonEvo) | CodonEvo | |
| states (defined in Evo) | Evo | protected |
| subLogProb(int from, int to, double omega, double t) (defined in CodonEvo) | CodonEvo | inline |
| times (defined in Evo) | Evo | protected |
| writeRateMatrices(string filename) (defined in CodonEvo) | CodonEvo | |
| ~CodonEvo() (defined in CodonEvo) | CodonEvo | |
| ~Evo() (defined in Evo) | Evo | virtual |
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