CodonEvoDiscr Member List
This is the complete list of members for CodonEvoDiscr, including all inherited members.
| addBranchLength(double b) (defined in CodonEvoDiscr) | CodonEvoDiscr | inlinevirtual |
| allLogPs (defined in Evo) | Evo | protected |
| allPs (defined in Evo) | Evo | protected |
| allQs (defined in Evo) | Evo | protected |
| CodonEvoDiscr() (defined in CodonEvoDiscr) | CodonEvoDiscr | inline |
| computeLogPmatrices() (defined in CodonEvoDiscr) | CodonEvoDiscr | virtual |
| 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 |
| getLogPi(int i) const (defined in Evo) | Evo | inline |
| getM() (defined in CodonEvoDiscr) | CodonEvoDiscr | inline |
| getNumStates() (defined in Evo) | Evo | inline |
| getPi(int i) const (defined in Evo) | Evo | inline |
| getProb(const vector< double > &lls) (defined in CodonEvoDiscr) | CodonEvoDiscr | |
| getRateMatrices() (defined in Evo) | Evo | inlinevirtual |
| getSubMatrixLogP(double omega, double t) (defined in CodonEvoDiscr) | CodonEvoDiscr | |
| 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 |
| logLik(const char *e1, const char *e2, int u, double t) (defined in CodonEvoDiscr) | CodonEvoDiscr | |
| loglikForCodonTuple(vector< string > &seqtuple, PhyloTree *ctree) (defined in CodonEvoDiscr) | CodonEvoDiscr | inline |
| loglikForCodonTuple(vector< string > &seqtuple, PhyloTree *ctree, PhyloTree *tree, int &subs) (defined in CodonEvoDiscr) | CodonEvoDiscr | |
| m (defined in Evo) | Evo | protected |
| pi (defined in Evo) | Evo | protected |
| printBranchLengths() (defined in Evo) | Evo | |
| produceComb(vector< vector< int > > &config) (defined in CodonEvoDiscr) | CodonEvoDiscr | inline |
| readMatrices(MatrixFormat fmt=fmt_TXT) (defined in CodonEvoDiscr) | CodonEvoDiscr | |
| setBranchLengths(vector< double > b, int m=-1) (defined in Evo) | Evo | |
| setM() (defined in CodonEvoDiscr) | CodonEvoDiscr | |
| states (defined in Evo) | Evo | protected |
| subLogProb(int from, int to, double omega, double t) (defined in CodonEvoDiscr) | CodonEvoDiscr | inline |
| times (defined in Evo) | Evo | protected |
| writeRateMatrices(string filename) (defined in CodonEvoDiscr) | CodonEvoDiscr | |
| ~CodonEvoDiscr() (defined in CodonEvoDiscr) | CodonEvoDiscr | |
| ~Evo() (defined in Evo) | Evo | virtual |
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