Uses of Class
pal.mep.MutationRateModel

Packages that use MutationRateModel
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. 
 

Uses of MutationRateModel in pal.coalescent
 

Methods in pal.coalescent with parameters of type MutationRateModel
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
 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
 MutationRateModel MutationRateModel.Factory.generateNewModel()
          Request a new MutationRateModel instance
 MutationRateModel SteppedMutationRate.getCopy()
           
abstract  MutationRateModel MutationRateModel.getCopy()
           
 MutationRateModel ConstantMutationRate.getCopy()
           
 MutationRateModel WindowedMutationRate.getCopy()
           
 

Constructors in pal.mep with parameters of type MutationRateModel
MutationRateModel(MutationRateModel toCopy)
           
 

Uses of MutationRateModel in pal.supgma
 

Methods in pal.supgma with parameters of type MutationRateModel
static RateHandler RateHandler.Utils.getSetRateHandler(MutationRateModel model)
           
 

Uses of MutationRateModel in pal.tree
 

Methods in pal.tree that return MutationRateModel
 MutationRateModel MutationRateModelTree.getMutationRateModel()
          returns mu
 

Methods in pal.tree with parameters of type MutationRateModel
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
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
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
static org.w3c.dom.Element ElementFactory.createMutationRateModelElement(MutationRateModel muModel, org.w3c.dom.Document document)
          Creates an XML element representing a mutation rate model.