Uses of Interface
pal.eval.LHCalculator.Factory

Packages that use LHCalculator.Factory
pal.eval Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters. 
pal.treesearch   
 

Uses of LHCalculator.Factory in pal.eval
 

Methods in pal.eval that return LHCalculator.Factory
static LHCalculator.Factory SimpleModelFastFourStateLHCalculator.getFactory()
           
static LHCalculator.Factory SimpleLHCalculator.getFactory()
           
static LHCalculator.Factory FastFourStateLHCalculator.getFactory()
           
static LHCalculator.Factory SimpleModelFastFourStateLHCalculator.getFactory(LHCalculator.Factory fallbackFactory)
           
static LHCalculator.Factory FastFourStateLHCalculator.getFactory(LHCalculator.Factory fallbackFactory)
           
 

Methods in pal.eval with parameters of type LHCalculator.Factory
static MolecularClockLikelihoodModel.Instance SimpleMolecularClockLikelihoodModel.createInstance(LHCalculator.Factory baseFactory, SubstitutionModel model)
           
static UnconstrainedLikelihoodModel.Instance SimpleUnconstrainedLikelihoodModel.createInstance(LHCalculator.Factory base, SubstitutionModel model)
          Create a SimpleUnconstrainedLikelihoodModel instance
static MolecularClockLikelihoodModel.Instance SingleSplitMolecularClockLikelihoodModel.createInstance(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, SingleSplitDistribution probabilityModel, LHCalculator.Factory baseFactory, double splitTime)
           
static LHCalculator.Factory SimpleModelFastFourStateLHCalculator.getFactory(LHCalculator.Factory fallbackFactory)
           
static LHCalculator.Factory FastFourStateLHCalculator.getFactory(LHCalculator.Factory fallbackFactory)
           
 

Uses of LHCalculator.Factory in pal.treesearch
 

Constructors in pal.treesearch with parameters of type LHCalculator.Factory
UnrootedMLSearcher(Alignment alignment, SubstitutionModel model, LHCalculator.Factory calcFactory)
           
UnrootedMLSearcher(Node root, Alignment alignment, SubstitutionModel model, LHCalculator.Factory calcFactory)