Uses of Class
pal.misc.TimeOrderCharacterData
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Packages that use TimeOrderCharacterData Package Description pal.coalescent Classes to model population genetic processes using the coalescent.pal.eval Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters.pal.gui GUI components for some special objects (e.g., trees).pal.mep Classes for the analysis of "measurably evolving populations" (mep).pal.misc Classes that don't fit elsewhere ;^)pal.substmodel Classes describing substitution models, i.e.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 TimeOrderCharacterData in pal.coalescent
Methods in pal.coalescent with parameters of type TimeOrderCharacterData Modifier and Type Method Description CoalescentIntervals
SerialCoalescentSimulator. simulateIntervals(TimeOrderCharacterData tocd, DemographicModel model, boolean createTree)
Simulates a set of CoalescentIntervals from a genealogy.Constructors in pal.coalescent with parameters of type TimeOrderCharacterData Constructor Description SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate)
Results will not contain alignmentsSerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate, TreeOperation treeFinisher)
Results will not contain alignmentsSerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate, TreeOperation treeFinisher, SimulatedAlignment.Factory alignmentFactory)
SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, TreeOperation treeFinisher, SimulatedAlignment.Factory alignmentFactory)
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Uses of TimeOrderCharacterData in pal.eval
Methods in pal.eval with parameters of type TimeOrderCharacterData Modifier and Type Method Description static Tree
LikelihoodTool. optimiseMRDT(Tree tree, Alignment alignment, SubstitutionModel model, TimeOrderCharacterData tocd, boolean optimiseModel, double[] rateStore)
Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and multiple mutation rate parameters, mu - one for each sampling interval.static Tree
LikelihoodTool. optimiseMRDT(Tree tree, Alignment alignment, SubstitutionModel model, TimeOrderCharacterData tocd, boolean optimiseModel, double[] rateChangeTimes, double[] rateStore)
Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and multiple mutation rate parameters, mu, over general time intervals.static Tree
LikelihoodTool. optimiseSRDT(Tree tree, Alignment alignment, SubstitutionModel model, TimeOrderCharacterData tocd, boolean optimiseModel, double[] rateStore)
Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and a single mutation rate parameter. -
Uses of TimeOrderCharacterData in pal.gui
Methods in pal.gui that return TimeOrderCharacterData Modifier and Type Method Description TimeOrderCharacterData
TreePainter. getTimeOrderCharacterData()
Methods in pal.gui with parameters of type TimeOrderCharacterData Modifier and Type Method Description void
TreePainter. setTimeOrderCharacterData(TimeOrderCharacterData tocd)
Constructors in pal.gui with parameters of type TimeOrderCharacterData Constructor Description TreeComponent(Tree tree, TimeOrderCharacterData tocd, boolean usingSymbols)
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Uses of TimeOrderCharacterData in pal.mep
Methods in pal.mep that return TimeOrderCharacterData Modifier and Type Method Description TimeOrderCharacterData
MutationRateModel. scale(TimeOrderCharacterData toScale)
Methods in pal.mep with parameters of type TimeOrderCharacterData Modifier and Type Method Description DeltaModel.Instance
DeltaModel. generateInstance(TimeOrderCharacterData tocd)
static DeltaModel
DeltaModel.Utils. getDisjointBased(DeltaModel primaryModel, DeltaModel subgroupModel, TimeOrderCharacterData subgroupTOCD)
static MutationRateModel.Factory
SteppedMutationRate. getFactory(double[] muChanges, TimeOrderCharacterData tocd)
Generate a MutationRateModel.Factory class for a SteppedMutationRateTimeOrderCharacterData
MutationRateModel. scale(TimeOrderCharacterData toScale)
Constructors in pal.mep with parameters of type TimeOrderCharacterData Constructor Description SteppedMutationRate(double[] rates, TimeOrderCharacterData timeInfo)
Construct mutation rate model of a give rate in given units.SteppedMutationRate(double[] rates, TimeOrderCharacterData timeInfo, boolean fixed)
Construct mutation rate model of a give rate in given units. -
Uses of TimeOrderCharacterData in pal.misc
Methods in pal.misc that return TimeOrderCharacterData Modifier and Type Method Description static TimeOrderCharacterData
TimeOrderCharacterData. clone(TimeOrderCharacterData tocd)
Returns a clone of the specified TimeOrderCharacterDataTimeOrderCharacterData
TimeOrderCharacterData. createSubgroup(int subgroupNumber)
Creates a TimeOrderCharacterData which is a subset of this sub group.TimeOrderCharacterData
TimeOrderCharacterData. generateDummyTimedTOCD(double[] sampleRates)
TimeOrderCharacterData
TimeOrderCharacterData. generateExpectedSubsitutionsTimedTOCD(double[] sampleRates)
Given an array of rates between samples (matching exactly the samples in order) then produces a TimeOrderCharacterData object that is timed by Expected Substitutions.TimeOrderCharacterData
TimeOrderCharacterData. getReordered(IdGroup base)
Creates a new TimeOrderCharacterData object with the same properites as this one but the identifier positions match that of base (ie whichIdNumber(Name) returns the same as for base)TimeOrderCharacterData
TimeOrderCharacterData. scale(double rate, int newUnits)
TimeOrderCharacterData
TimeOrderCharacterData. subset(IdGroup staxa)
Extracts a subset of a TimeOrderCharacterData.Methods in pal.misc with parameters of type TimeOrderCharacterData Modifier and Type Method Description static TimeOrderCharacterData
TimeOrderCharacterData. clone(TimeOrderCharacterData tocd)
Returns a clone of the specified TimeOrderCharacterDatavoid
TimeOrderCharacterData. setOrdinals(TimeOrderCharacterData tocd)
Set time ordinals from another TimeOrderCharacterData.void
TimeOrderCharacterData. setOrdinals(TimeOrderCharacterData tocd, IdGroup standard, boolean doTimes)
Set time ordinals from another TimeOrderCharacterData.void
TimeOrderCharacterData. setTimesAndOrdinals(TimeOrderCharacterData tocd)
Constructors in pal.misc with parameters of type TimeOrderCharacterData Constructor Description TOCDSampleInformation(TimeOrderCharacterData base)
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Uses of TimeOrderCharacterData in pal.substmodel
Methods in pal.substmodel with parameters of type TimeOrderCharacterData Modifier and Type Method Description static TemporalModelChange
TemporalModelChange.Utils. getSpecificTime(double time, TimeOrderCharacterData tocd)
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Uses of TimeOrderCharacterData in pal.supgma
Methods in pal.supgma with parameters of type TimeOrderCharacterData Modifier and Type Method Description void
RateHandler. adjustDistances(double[][] matrix, TimeOrderCharacterData tocd)
void
ThetaHandler. adjustDistances(double[][] matrix, TimeOrderCharacterData tocd)
DemographicModel
ThetaHandler. generateDemographicModel(double[] deltas, double[] thetas, TimeOrderCharacterData tocd)
May return null if not possible to infer demographic modelMutationRateModel.Factory
RateHandler. generateRateModelFactory(double[] deltas, TimeOrderCharacterData tocd)
int
RateHandler. getNumberOfParameters(TimeOrderCharacterData tocd)
int
ThetaHandler. getNumberOfParameters(TimeOrderCharacterData tocd)
Constructors in pal.supgma with parameters of type TimeOrderCharacterData Constructor Description SUPGMABase(DistanceMatrixAccess distanceAccess, DistanceMatrixGenerator replicateGenerator, TimeOrderCharacterData tocd)
SUPGMADistanceMatrix(DistanceMatrix raw, TimeOrderCharacterData tocd, DeltaModel deltaModel)
Uses date/time information and a constant rate to correct distance matrices.SUPGMATree(DistanceMatrix m, TimeOrderCharacterData tocd, double rate, ClusterTree.ClusteringMethod cm)
constructor SUPGMA treeSUPGMATree(DistanceMatrix m, TimeOrderCharacterData tocd, DeltaModel deltaModel, boolean allowNegatives, ClusterTree.ClusteringMethod cm)
constructor SUPGMA tree -
Uses of TimeOrderCharacterData in pal.tree
Methods in pal.tree that return TimeOrderCharacterData Modifier and Type Method Description static TimeOrderCharacterData
TreeUtils. extractTimeOrderCharacterData(Tree tree, int units)
Extracts a time order character data from a tree.Methods in pal.tree with parameters of type TimeOrderCharacterData Modifier and Type Method Description static ParameterizedTree.Factory
MutationRateModelTree. getParameterizedTreeFactory(MutationRateModel.Factory rateModel, TimeOrderCharacterData tocd)
Obtain a ParameterizedTree.Factory for generating Unconstrained treesConstructors in pal.tree with parameters of type TimeOrderCharacterData 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 TimeOrderCharacterData in pal.xml
Methods in pal.xml that return TimeOrderCharacterData Modifier and Type Method Description static TimeOrderCharacterData
ElementParser. parseTimeDataElement(org.w3c.dom.Element e)
Methods in pal.xml with parameters of type TimeOrderCharacterData Modifier and Type Method Description static org.w3c.dom.Element
ElementFactory. createTimeDataElement(TimeOrderCharacterData tocd, org.w3c.dom.Document document)
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