Uses of Class
pal.misc.TimeOrderCharacterData

Packages that use TimeOrderCharacterData
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. 
 

Uses of TimeOrderCharacterData in pal.coalescent
 

Methods in pal.coalescent with parameters of type TimeOrderCharacterData
 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
SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate)
          Results will not contain alignments
SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate, TreeOperation treeFinisher)
          Results will not contain alignments
SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate, TreeOperation treeFinisher, SimulatedAlignment.Factory alignmentFactory)
           
SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, TreeOperation treeFinisher, SimulatedAlignment.Factory alignmentFactory)
           
 

Uses of TimeOrderCharacterData in pal.eval
 

Methods in pal.eval with parameters of type TimeOrderCharacterData
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
 TimeOrderCharacterData TreePainter.getTimeOrderCharacterData()
           
 

Methods in pal.gui with parameters of type TimeOrderCharacterData
 void TreePainter.setTimeOrderCharacterData(TimeOrderCharacterData tocd)
           
 

Constructors in pal.gui with parameters of type TimeOrderCharacterData
TreeComponent(Tree tree, TimeOrderCharacterData tocd, boolean usingSymbols)
           
 

Uses of TimeOrderCharacterData in pal.mep
 

Methods in pal.mep that return TimeOrderCharacterData
 TimeOrderCharacterData MutationRateModel.scale(TimeOrderCharacterData toScale)
           
 

Methods in pal.mep with parameters of type TimeOrderCharacterData
 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 SteppedMutationRate
 TimeOrderCharacterData MutationRateModel.scale(TimeOrderCharacterData toScale)
           
 

Constructors in pal.mep with parameters of type TimeOrderCharacterData
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
static TimeOrderCharacterData TimeOrderCharacterData.clone(TimeOrderCharacterData tocd)
          Returns a clone of the specified TimeOrderCharacterData
 TimeOrderCharacterData 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
static TimeOrderCharacterData TimeOrderCharacterData.clone(TimeOrderCharacterData tocd)
          Returns a clone of the specified TimeOrderCharacterData
 void 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
TOCDSampleInformation(TimeOrderCharacterData base)
           
 

Uses of TimeOrderCharacterData in pal.substmodel
 

Methods in pal.substmodel with parameters of type TimeOrderCharacterData
static TemporalModelChange TemporalModelChange.Utils.getSpecificTime(double time, TimeOrderCharacterData tocd)
           
 

Uses of TimeOrderCharacterData in pal.supgma
 

Methods in pal.supgma with parameters of type TimeOrderCharacterData
 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 model
 MutationRateModel.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
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, DeltaModel deltaModel, boolean allowNegatives, ClusterTree.ClusteringMethod cm)
          constructor SUPGMA tree
SUPGMATree(DistanceMatrix m, TimeOrderCharacterData tocd, double rate, ClusterTree.ClusteringMethod cm)
          constructor SUPGMA tree
 

Uses of TimeOrderCharacterData in pal.tree
 

Methods in pal.tree that return TimeOrderCharacterData
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
static ParameterizedTree.Factory MutationRateModelTree.getParameterizedTreeFactory(MutationRateModel.Factory rateModel, TimeOrderCharacterData tocd)
          Obtain a ParameterizedTree.Factory for generating Unconstrained trees
 

Constructors in pal.tree with parameters of type TimeOrderCharacterData
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
static TimeOrderCharacterData ElementParser.parseTimeDataElement(org.w3c.dom.Element e)
           
 

Methods in pal.xml with parameters of type TimeOrderCharacterData
static org.w3c.dom.Element ElementFactory.createTimeDataElement(TimeOrderCharacterData tocd, org.w3c.dom.Document document)