Uses of Class
pal.mep.MutationRateModel
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Packages that use MutationRateModel Package Description pal.coalescent Classes to model population genetic processes using the coalescent.pal.mep Classes for the analysis of "measurably evolving populations" (mep).pal.supgma pal.tree Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint).pal.xml Utility classes for converting PAL objects to and from XML documents. -
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Uses of MutationRateModel in pal.coalescent
Methods in pal.coalescent with parameters of type MutationRateModel Modifier and Type Method Description static CoalescentIntervals
IntervalsExtractor. extractFromTree(Tree tree, MutationRateModel muModel)
extracts intervals in generation times from serial clock tree (in mutation times) after taking into account mutation rate model. -
Uses of MutationRateModel in pal.mep
Subclasses of MutationRateModel in pal.mep Modifier and Type Class Description class
ConstantMutationRate
This class models a constant mutation rate (parameter: mu = mutation rate).class
SteppedMutationRate
This class models a step-wise mutation rate.class
WindowedMutationRate
This class models a windowed mutation rate (parameter: mu = mutation rate).Methods in pal.mep that return MutationRateModel Modifier and Type Method Description MutationRateModel
MutationRateModel.Factory. generateNewModel()
Request a new MutationRateModel instanceMutationRateModel
ConstantMutationRate. getCopy()
abstract MutationRateModel
MutationRateModel. getCopy()
MutationRateModel
SteppedMutationRate. getCopy()
MutationRateModel
WindowedMutationRate. getCopy()
Constructors in pal.mep with parameters of type MutationRateModel Constructor Description MutationRateModel(MutationRateModel toCopy)
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Uses of MutationRateModel in pal.supgma
Methods in pal.supgma with parameters of type MutationRateModel Modifier and Type Method Description static RateHandler
RateHandler.Utils. getSetRateHandler(MutationRateModel model)
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Uses of MutationRateModel in pal.tree
Methods in pal.tree that return MutationRateModel Modifier and Type Method Description MutationRateModel
MutationRateModelTree. getMutationRateModel()
returns muMethods in pal.tree with parameters of type MutationRateModel Modifier and Type Method Description static Tree
TreeUtils. generationsToMutations(Tree generationTree, MutationRateModel muModel)
Takes a tree (in generation units) and returns a scaled version of it (in mutation units).static Tree
TreeUtils. generationsToMutations(Tree generationTree, MutationRateModel muModel, double generationTime)
Takes a tree (in generation units) and returns a scaled version of it (in mutation units).static Tree
TreeUtils. getScaled(Tree mutationRateTree, MutationRateModel muModel)
Takes a tree and returns a scaled version of it.static Tree
TreeUtils. getScaled(Tree mutationRateTree, MutationRateModel muModel, int newUnits)
Takes a tree and returns a scaled version of it.static Tree
TreeUtils. mutationsToGenerations(Tree mutationTree, MutationRateModel muModel)
Takes a tree (in mutation units) and returns a scaled version of it (in generation units).static Tree
TreeUtils. scale(Tree mutationRateTree, MutationRateModel muModel)
Deprecated.use getScaled()static Tree
TreeUtils. scale(Tree mutationRateTree, MutationRateModel muModel, int newUnits)
Deprecated.use getScaled()Constructors in pal.tree with parameters of type MutationRateModel Constructor Description MutationRateModelTree(Tree t, TimeOrderCharacterData tocd, MutationRateModel model)
take any tree and afford it with an interface suitable for a clock-like tree (parameters are the minimal node height differences at each internal node).MutationRateModelTree(Tree t, TimeOrderCharacterData tocd, MutationRateModel model, boolean includeModelParameters)
take any tree and afford it with an interface suitable for a clock-like tree (parameters are the minimal node height differences at each internal node). -
Uses of MutationRateModel in pal.xml
Methods in pal.xml that return MutationRateModel Modifier and Type Method Description static MutationRateModel
ElementParser. parseMutationRateModel(org.w3c.dom.Element e)
Reads a mutation rate model from a DOM Document element.Methods in pal.xml with parameters of type MutationRateModel Modifier and Type Method Description static org.w3c.dom.Element
ElementFactory. createMutationRateModelElement(MutationRateModel muModel, org.w3c.dom.Document document)
Creates an XML element representing a mutation rate model.
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