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Packages that use TimeOrderCharacterData | |
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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 |
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Methods in pal.coalescent with parameters of type TimeOrderCharacterData | |
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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 | |
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SerialCoalescentGenerator(TimeOrderCharacterData tocd,
DemographicModel demographicModel,
int numberOfTreesToGenerate)
Results will not contain alignments |
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SerialCoalescentGenerator(TimeOrderCharacterData tocd,
DemographicModel demographicModel,
int numberOfTreesToGenerate,
TreeOperation treeFinisher)
Results will not contain alignments |
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SerialCoalescentGenerator(TimeOrderCharacterData tocd,
DemographicModel demographicModel,
int numberOfTreesToGenerate,
TreeOperation treeFinisher,
SimulatedAlignment.Factory alignmentFactory)
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SerialCoalescentGenerator(TimeOrderCharacterData tocd,
DemographicModel demographicModel,
TreeOperation treeFinisher,
SimulatedAlignment.Factory alignmentFactory)
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Uses of TimeOrderCharacterData in pal.eval |
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Methods in pal.eval with parameters of type TimeOrderCharacterData | |
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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 |
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Methods in pal.gui that return TimeOrderCharacterData | |
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TimeOrderCharacterData |
TreePainter.getTimeOrderCharacterData()
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Methods in pal.gui with parameters of type TimeOrderCharacterData | |
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void |
TreePainter.setTimeOrderCharacterData(TimeOrderCharacterData tocd)
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Constructors in pal.gui with parameters of type TimeOrderCharacterData | |
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TreeComponent(Tree tree,
TimeOrderCharacterData tocd,
boolean usingSymbols)
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Uses of TimeOrderCharacterData in pal.mep |
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Methods in pal.mep that return TimeOrderCharacterData | |
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TimeOrderCharacterData |
MutationRateModel.scale(TimeOrderCharacterData toScale)
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Methods in pal.mep with parameters of type TimeOrderCharacterData | |
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DeltaModel.Instance |
DeltaModel.generateInstance(TimeOrderCharacterData tocd)
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static DeltaModel |
DeltaModel.Utils.getDisjointBased(DeltaModel primaryModel,
DeltaModel subgroupModel,
TimeOrderCharacterData subgroupTOCD)
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static MutationRateModel.Factory |
SteppedMutationRate.getFactory(double[] muChanges,
TimeOrderCharacterData tocd)
Generate a MutationRateModel.Factory class for a SteppedMutationRate |
TimeOrderCharacterData |
MutationRateModel.scale(TimeOrderCharacterData toScale)
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Constructors in pal.mep with parameters of type TimeOrderCharacterData | |
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SteppedMutationRate(double[] rates,
TimeOrderCharacterData timeInfo)
Construct mutation rate model of a give rate in given units. |
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SteppedMutationRate(double[] rates,
TimeOrderCharacterData timeInfo,
boolean fixed)
Construct mutation rate model of a give rate in given units. |
Uses of TimeOrderCharacterData in pal.misc |
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Methods in pal.misc that return TimeOrderCharacterData | |
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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)
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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)
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TimeOrderCharacterData |
TimeOrderCharacterData.subset(IdGroup staxa)
Extracts a subset of a TimeOrderCharacterData. |
Methods in pal.misc with parameters of type TimeOrderCharacterData | |
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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)
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Constructors in pal.misc with parameters of type TimeOrderCharacterData | |
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TOCDSampleInformation(TimeOrderCharacterData base)
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Uses of TimeOrderCharacterData in pal.substmodel |
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Methods in pal.substmodel with parameters of type TimeOrderCharacterData | |
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static TemporalModelChange |
TemporalModelChange.Utils.getSpecificTime(double time,
TimeOrderCharacterData tocd)
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Uses of TimeOrderCharacterData in pal.supgma |
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Methods in pal.supgma with parameters of type TimeOrderCharacterData | |
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void |
RateHandler.adjustDistances(double[][] matrix,
TimeOrderCharacterData tocd)
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void |
ThetaHandler.adjustDistances(double[][] matrix,
TimeOrderCharacterData tocd)
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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)
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int |
RateHandler.getNumberOfParameters(TimeOrderCharacterData tocd)
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int |
ThetaHandler.getNumberOfParameters(TimeOrderCharacterData tocd)
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Constructors in pal.supgma with parameters of type TimeOrderCharacterData | |
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SUPGMABase(DistanceMatrixAccess distanceAccess,
DistanceMatrixGenerator replicateGenerator,
TimeOrderCharacterData tocd)
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SUPGMADistanceMatrix(DistanceMatrix raw,
TimeOrderCharacterData tocd,
DeltaModel deltaModel)
Uses date/time information and a constant rate to correct distance matrices. |
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SUPGMATree(DistanceMatrix m,
TimeOrderCharacterData tocd,
DeltaModel deltaModel,
boolean allowNegatives,
ClusterTree.ClusteringMethod cm)
constructor SUPGMA tree |
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SUPGMATree(DistanceMatrix m,
TimeOrderCharacterData tocd,
double rate,
ClusterTree.ClusteringMethod cm)
constructor SUPGMA tree |
Uses of TimeOrderCharacterData in pal.tree |
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Methods in pal.tree that return TimeOrderCharacterData | |
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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 | |
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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 | |
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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). |
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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 |
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Methods in pal.xml that return TimeOrderCharacterData | |
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static TimeOrderCharacterData |
ElementParser.parseTimeDataElement(org.w3c.dom.Element e)
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Methods in pal.xml with parameters of type TimeOrderCharacterData | |
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static org.w3c.dom.Element |
ElementFactory.createTimeDataElement(TimeOrderCharacterData tocd,
org.w3c.dom.Document document)
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