broad.core.siphy.EvolutionaryModelParameters Member List

This is the complete list of members for broad.core.siphy.EvolutionaryModelParameters, including all inherited members.

copy()	broad.core.siphy.EvolutionaryModelParameters
EvolutionaryModelParameters(Phylogeny tree, double kappa, double mu, Matrix Q, Matrix pi)	broad.core.siphy.EvolutionaryModelParameters
EvolutionaryModelParameters(File sourceFile)	broad.core.siphy.EvolutionaryModelParameters
EvolutionaryModelParameters(double kappa, double[] bg, double mu)	broad.core.siphy.EvolutionaryModelParameters
generateHKYQMatrix(double kappa, double scalingFactor)	broad.core.siphy.EvolutionaryModelParameters
getBackgroundNucleotideFreqs()	broad.core.siphy.EvolutionaryModelParameters
getRateMatrix()	broad.core.siphy.EvolutionaryModelParameters
getTree()	broad.core.siphy.EvolutionaryModelParameters
setBackgroundNucleotideFreqs(Matrix dist)	broad.core.siphy.EvolutionaryModelParameters
setRateMatrix(Matrix Q)	broad.core.siphy.EvolutionaryModelParameters
setTree(Phylogeny tree)	broad.core.siphy.EvolutionaryModelParameters
toString()	broad.core.siphy.EvolutionaryModelParameters
write(BufferedWriter bw)	broad.core.siphy.EvolutionaryModelParameters