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Augustus 3.4.0
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This is the complete list of members for ExonEvo, including all inherited members.
| addBranchLength(double b) (defined in ExonEvo) | ExonEvo | virtual |
| allLogPs (defined in Evo) | Evo | protected |
| allPs (defined in Evo) | Evo | protected |
| allQs (defined in Evo) | Evo | protected |
| computeLogPmatrices() (defined in ExonEvo) | ExonEvo | virtual |
| eigendecompose(gsl_matrix *Q) (defined in ExonEvo) | ExonEvo | |
| Evo(int s) (defined in Evo) | Evo | inline |
| ExonEvo(int num_states=2) (defined in ExonEvo) | ExonEvo | inline |
| ExonEvo(int num_states, double lambda, double mu, double ali_error) (defined in ExonEvo) | ExonEvo | inline |
| expQt(double t) (defined in ExonEvo) | ExonEvo | 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 |
| getAliErr() const (defined in ExonEvo) | ExonEvo | inline |
| getExonRateMatrix() (defined in ExonEvo) | ExonEvo | |
| getLambda() const (defined in ExonEvo) | ExonEvo | inline |
| getLogPi(int i) const (defined in Evo) | Evo | inline |
| getMu() const (defined in ExonEvo) | ExonEvo | inline |
| getNumStates() (defined in Evo) | Evo | inline |
| getPi(int i) const (defined in Evo) | Evo | inline |
| getRateMatrices() (defined in ExonEvo) | ExonEvo | virtual |
| 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 |
| m (defined in Evo) | Evo | protected |
| minBranchLength() const (defined in ExonEvo) | ExonEvo | inline |
| pi (defined in Evo) | Evo | protected |
| printBranchLengths() (defined in Evo) | Evo | |
| setAliErr(double ali_error=0.1, bool propsOverride=true) (defined in ExonEvo) | ExonEvo | |
| setBranchLengths(vector< double > b, int m=-1) (defined in Evo) | Evo | |
| setLambda(double lambda=0.0001, bool propsOverride=true) (defined in ExonEvo) | ExonEvo | |
| setMu(double mu=0.0001, bool propsOverride=true) (defined in ExonEvo) | ExonEvo | |
| setPi() (defined in ExonEvo) | ExonEvo | |
| states (defined in Evo) | Evo | protected |
| times (defined in Evo) | Evo | protected |
| validateEigenDecomp(gsl_matrix *Q) (defined in ExonEvo) | ExonEvo | inline |
| ~Evo() (defined in Evo) | Evo | virtual |
| ~ExonEvo() (defined in ExonEvo) | ExonEvo | inline |
1.9.8