Uses of Interface
pal.misc.NeoParameterized

Packages that use NeoParameterized
pal.eval Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters. 
pal.misc Classes that don't fit elsewhere ;^) 
pal.substmodel Classes describing substitution models, i.e. 
pal.treesearch   
 

Uses of NeoParameterized in pal.eval
 

Methods in pal.eval that return NeoParameterized
 NeoParameterized MolecularClockLikelihoodModel.Instance.getParameterAccess()
           
 NeoParameterized UnconstrainedLikelihoodModel.Instance.getParameterAccess()
           
 

Methods in pal.eval with parameters of type NeoParameterized
static MolecularClockLikelihoodModel.Instance SingleSplitMolecularClockLikelihoodModel.createInstance(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, double splitTime)
           
static MolecularClockLikelihoodModel.Instance SingleSplitMolecularClockLikelihoodModel.createInstance(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, double[] classProbabilities, double splitTime)
           
static MolecularClockLikelihoodModel.Instance SingleSplitMolecularClockLikelihoodModel.createInstance(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, SingleSplitDistribution probabilityModel, double splitTime)
           
static MolecularClockLikelihoodModel.Instance SingleSplitMolecularClockLikelihoodModel.createInstance(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, SingleSplitDistribution probabilityModel, LHCalculator.Factory baseFactory, double splitTime)
           
 

Uses of NeoParameterized in pal.misc
 

Classes in pal.misc that implement NeoParameterized
 class ParameterizedDoubleBundle
          Title: ParameterizedDoubleBundle
 class ParameterizedNeoWrapper
          Title: ParameterizedNeoWrapper
 

Uses of NeoParameterized in pal.substmodel
 

Subinterfaces of NeoParameterized in pal.substmodel
 interface SingleSplitDistribution
           
 

Classes in pal.substmodel that implement NeoParameterized
 class ConstantIndependentSingleSplitDistribution
          Title: ConstantIndependentSingleSplitDistribution
 class MultiRateMatrixHandler
           
 class SaturatedSingleSplitDistribution
          Title: SaturatedSingleSplitDistribution
 class VariableIndependentSingleSplitDistribution
          Title: VariableIndependentSingleSplitDistribution
 

Uses of NeoParameterized in pal.treesearch
 

Classes in pal.treesearch that implement NeoParameterized
 class FixedBSRDTGlobalClockModel
           
 class GlobalClockModel
           
 class MRDTGlobalClockModel
           
 class SRDTGlobalClockModel
           
 

Methods in pal.treesearch that return NeoParameterized
 NeoParameterized MRDTGlobalClockModel.getAllGroupRelatedParameterAccess()
           
 NeoParameterized ConstraintModel.GroupManager.getAllGroupRelatedParameterAccess()
           
 NeoParameterized SRDTGlobalClockModel.getAllGroupRelatedParameterAccess()
           
 NeoParameterized FixedBSRDTGlobalClockModel.getAllGroupRelatedParameterAccess()
           
 NeoParameterized FixedSRDTGlobalClockModel.getAllGroupRelatedParameterAccess()
           
 NeoParameterized GlobalClockModel.getAllGroupRelatedParameterAccess()
           
 NeoParameterized MRDTGlobalClockModel.getGlobalParameterAccess()
           
 NeoParameterized ConstraintModel.getGlobalParameterAccess()
           
 NeoParameterized SRDTGlobalClockModel.getGlobalParameterAccess()
           
 NeoParameterized FixedBSRDTGlobalClockModel.getGlobalParameterAccess()
           
 NeoParameterized FixedSRDTGlobalClockModel.getGlobalParameterAccess()
           
 NeoParameterized GlobalClockModel.getGlobalParameterAccess()
           
 NeoParameterized UnconstrainedModel.getGlobalParameterAccess()
           
 NeoParameterized MRDTGlobalClockModel.getPrimaryGroupRelatedParameterAccess()
           
 NeoParameterized ConstraintModel.GroupManager.getPrimaryGroupRelatedParameterAccess()
           
 NeoParameterized SRDTGlobalClockModel.getPrimaryGroupRelatedParameterAccess()
           
 NeoParameterized FixedBSRDTGlobalClockModel.getPrimaryGroupRelatedParameterAccess()
           
 NeoParameterized FixedSRDTGlobalClockModel.getPrimaryGroupRelatedParameterAccess()
           
 NeoParameterized GlobalClockModel.getPrimaryGroupRelatedParameterAccess()
           
 NeoParameterized MRDTGlobalClockModel.getSecondaryGroupRelatedParameterAccess()
           
 NeoParameterized ConstraintModel.GroupManager.getSecondaryGroupRelatedParameterAccess()
           
 NeoParameterized SRDTGlobalClockModel.getSecondaryGroupRelatedParameterAccess()
           
 NeoParameterized FixedBSRDTGlobalClockModel.getSecondaryGroupRelatedParameterAccess()
           
 NeoParameterized FixedSRDTGlobalClockModel.getSecondaryGroupRelatedParameterAccess()
           
 NeoParameterized GlobalClockModel.getSecondaryGroupRelatedParameterAccess()