_abstract | markovChain | protected |
_abstractNbre | markovChain | protected |
_debug | markovChain | protected |
_format | markovChain | protected |
_generator | markovChain | protected |
_initDistribution | markovChain | protected |
_isAbstract | markovChain | protected |
_modelName | markovChain | protected |
_size | felsenstein81 | protected |
_stateSpace | felsenstein81 | protected |
_stateSpaceSize | markovChain | protected |
_transDistrib | felsenstein81 | protected |
_transSpeed | felsenstein81 | protected |
_type | markovChain | protected |
abstract() | markovChain | inline |
abstract() | markovChain | inline |
abstractNbre() | markovChain | inline |
abstractNbre() | markovChain | inline |
averageHittingTime(bool *hittingSet) | felsenstein81 | |
averageHittingTime(bool *hittingSet) | felsenstein81 | |
averageHittingTimeDT(bool *hitSetIndicator) | markovChain | |
averageHittingTimeDT(bool *hitSetIndicator) | markovChain | |
averageHittingTimeDT_iterative(bool *hitSetIndicator) | markovChain | |
averageHittingTimeDT_iterative(bool *hitSetIndicator) | markovChain | |
copy() | markovChain | virtual |
copy() | markovChain | virtual |
felsenstein81(double p[4], double mu) | felsenstein81 | |
felsenstein81(discreteDistribution *d, double mu) | felsenstein81 | |
felsenstein81(double p[4], double mu) | felsenstein81 | |
felsenstein81(discreteDistribution *d, double mu) | felsenstein81 | |
format() | markovChain | inline |
format() | markovChain | inline |
generator() | markovChain | inline |
generator() | markovChain | inline |
hittingTimeDistribution(int iState, bool *hittingSet) | felsenstein81 | |
hittingTimeDistribution(int iState, bool *hittingSet) | felsenstein81 | |
makeMarkovChain() | felsenstein81 | |
makeMarkovChain() | felsenstein81 | |
markovChain(int sz, timeType t) | markovChain | |
markovChain(transitionStructure *tr) | markovChain | |
markovChain(string format, string param[], int nbreParam, string modelName, bool isAbstract) | markovChain | |
markovChain(int sz, timeType t) | markovChain | |
markovChain(transitionStructure *tr) | markovChain | |
markovChain(string format, string param[], int nbreParam, string modelName, bool isAbstract) | markovChain | |
modelName() | markovChain | inline |
modelName() | markovChain | inline |
read() | markovChain | |
read() | markovChain | |
setAbstract(string abstract[]) | markovChain | |
setAbstract(string abstract[]) | markovChain | |
setAbstractNbre(int abstractNbre) | markovChain | inline |
setAbstractNbre(int abstractNbre) | markovChain | inline |
setFormat(string format) | markovChain | inline |
setFormat(string format) | markovChain | inline |
setGenerator(transitionStructure *tr) | markovChain | inline |
setGenerator(transitionStructure *tr) | markovChain | inline |
setInitDistribution(discreteDistribution *d) | markovChain | inline |
setInitDistribution(discreteDistribution *d) | markovChain | inline |
setModelName(string modelName) | markovChain | inline |
setModelName(string modelName) | markovChain | inline |
setSizeType(const string path) | markovChain | |
setSizeType(const string path) | markovChain | |
simulateChain(double tMax, bool stats, bool traj, bool withIncrements, bool trace) | felsenstein81 | virtual |
simulateChain(double tMax, bool stats, bool traj, bool withIncrements, bool trace) | felsenstein81 | virtual |
simulateChainCT(double tMax, bool stats, bool traj, bool withIncrements, bool trace) | markovChain | virtual |
simulateChainCT(double tMax, bool stats, bool traj, bool withIncrements, bool trace) | markovChain | virtual |
simulateChainDT(int tMax, bool stats, bool traj, bool trace) | markovChain | virtual |
simulateChainDT(int tMax, bool stats, bool traj, bool trace) | markovChain | virtual |
simulateHittingTime(int iState, bool *hittingSet, int nbSamples, int tMax) | markovChain | |
simulateHittingTime(int iState, bool *hittingSet, int nbSamples, int tMax) | markovChain | |
simulatePSI(int tMax, bool stats, bool Traj, bool Print) | markovChain | |
simulatePSI(int tMax, bool stats, bool Traj, bool Print) | markovChain | |
stateSpaceSize() | markovChain | inline |
stateSpaceSize() | markovChain | inline |
stationaryDistribution() | felsenstein81 | |
stationaryDistribution() | felsenstein81 | |
markovChain::stationaryDistribution(bool progress) | markovChain | virtual |
stationaryDistributionCT(bool progress) | markovChain | virtual |
stationaryDistributionCT(bool progress) | markovChain | virtual |
stationaryDistributionDT(bool progress) | markovChain | virtual |
stationaryDistributionDT(bool progress) | markovChain | virtual |
stationaryDistributionGthLD() | markovChain | |
stationaryDistributionGthLD() | markovChain | |
stationaryDistributionSample(int nbSamples) | markovChain | |
stationaryDistributionSample(int nbSamples) | markovChain | |
stationaryDistributionSOR() | markovChain | |
stationaryDistributionSOR() | markovChain | |
transientDistribution(double) | felsenstein81 | |
transientDistribution(double) | felsenstein81 | |
uniformize() | markovChain | virtual |
uniformize() | markovChain | virtual |
write(FILE *out, bool withReward) | markovChain | virtual |
write(string format, string modelName) (defined in markovChain) | markovChain | virtual |
write(FILE *out, bool withReward) | markovChain | virtual |
write(string format, string modelName) (defined in markovChain) | markovChain | virtual |
~felsenstein81() | felsenstein81 | |
~felsenstein81() | felsenstein81 | |
~markovChain() | markovChain | virtual |
~markovChain() | markovChain | virtual |