Uses of Class
Models.RateCategory.RateException

Packages that use RateCategory.RateException

Package	Description
Ancestors	Provides classed to calculate ancestral reconstruction.
Likelihood	Provides classes for calculating the likelihood of a tree given a model and an alignment.
Models	Provides classes for defining a phylogenetic model.
Simulations	Provides a class to create simulated data.

Uses of RateCategory.RateException in Ancestors

Methods in Ancestors that throw RateCategory.RateException

Modifier and Type	Method and Description
abstract Alignment	AncestralJoint.calculate(Parameters params) Calculates the reconstruction
Alignment	AncestralJointBB.calculate(Parameters p)
Alignment	AncestralJointDP.calculate(Parameters params)
AncestralMarginal.Result	AncestralMarginal.calculate(Parameters params) Calculates the reconstruction

Uses of RateCategory.RateException in Likelihood

Methods in Likelihood that throw RateCategory.RateException

Modifier and Type	Method and Description
R	Calculator.calculate(Parameters p) Abstract method for actually calculating the likelihood
abstract R	Calculator.combineSites(java.util.Map<Site,SiteLikelihood> sites, Parameters p) Combines the likelihood from each site into a alignment likelihood
Range	ConfidenceInterval.getCI(Parameter param, double conf) Calculates the confidence interval for a single parameter
double	FitzJohnRoot.getFreq(java.lang.String state)
double	Root.getFreq(java.lang.String state) Get the frequency of the given state at the root
protected java.util.Map<Site,SiteLikelihood>	Calculator.siteCalculate(Parameters p) Calculates the likelihood for each site

Constructors in Likelihood that throw RateCategory.RateException

Constructor and Description
Probabilities(Model m, Tree t, Parameters p) Constructor

Uses of RateCategory.RateException in Models

Methods in Models that throw RateCategory.RateException

Modifier and Type	Method and Description
static Model	Model.fromFile(java.io.File f) Creates a new model from a file.
static RateCategory	RateCategory.fromFile(java.io.File mfile) Creates an instance from the information in a file.
SquareMatrix	RateCategory.getP(double length) Gets the P-matrix for a given length
RateCategory	RateCategory.multiplyBy(java.lang.String mult) Returns a new RateCategory where every position in the rate matrix is multiplied by a given value
void	Model.setParameters(Parameters p) Sets the parameters of a model to the values contained in the Parameters data structure.
void	RateCategory.setParameters(Parameters p) Updates the parameters in the RateCategory and recalculates matrices / frequencies if necessary.

Constructors in Models that throw RateCategory.RateException

Constructor and Description
RateCategory(java.lang.String[][] rates, RateCategory.FrequencyType freqType, java.util.HashMap<java.lang.String,java.lang.Integer> map) Constructor for when the root distribution is defined as the stationary or quasi-stationary distribution.
RateCategory(java.lang.String[][] rates, java.lang.String[] freq, java.util.Map<java.lang.String,java.lang.Integer> map) Constructor for when the root distribution is defined.

Uses of RateCategory.RateException in Simulations

Methods in Simulations that throw RateCategory.RateException

Modifier and Type	Method and Description
Alignment	Simulate.getAlignment(int length) Gets a simulated alignment, not returning the state of internal nodes
Alignment	Simulate.getAlignment(int length, boolean internal) Gets a simulated alignment
Alignment	Simulate.getAlignment(int length, boolean internal, java.util.Map<java.lang.String,java.lang.String> recode) Gets a simulated alignment.
Alignment	Simulate.getAlignment(int length, java.util.Map<java.lang.String,java.lang.String> recode) Gets a simulated alignment, not returning the state of internal nodes.
Alignment	Simulate.getAlignment(java.util.List<java.lang.String> siteClasses) Gets a simulated alignment, not returning the state of the internal nodes.
Alignment	Simulate.getAlignment(java.util.List<java.lang.String> siteClasses, boolean internal) Gets a simulated alignment.
Alignment	Simulate.getAlignment(java.util.List<java.lang.String> siteClasses, boolean internal, java.util.Map<java.lang.String,java.lang.String> recode) Gets a simulated alignment.
Alignment	Simulate.getAlignment(java.util.List<java.lang.String> siteClasses, java.util.Map<java.lang.String,java.lang.String> recode) Gets a simulated alignment, not returning the state of the internal nodes.
Site	Simulate.getSite() Gets a simulated site without returning the state of the internal nodes
Site	Simulate.getSite(boolean internal) Gets a simulated site
Site	Simulate.getSite(boolean internal, java.util.Map<java.lang.String,java.lang.String> recode) Gets a simulated site.
Site	Simulate.getSite(boolean internal, java.util.Map<java.lang.String,java.lang.String> recode, java.lang.String siteClass) Gets a simulated site.
Site	Simulate.getSite(boolean internal, java.lang.String siteClass) Gets a simulated site
Site	Simulate.getSite(java.util.Map<java.lang.String,java.lang.String> recode) Gets a simulated site without returning the state of the internal nodes.
Site	Simulate.getSite(java.util.Map<java.lang.String,java.lang.String> recode, java.lang.String siteClass) Gets a simulated site without returning the state of the internal nodes.
Site	Simulate.getSite(java.lang.String siteClass) Gets a simulated site without returning the state of the internal nodes

Constructors in Simulations that throw RateCategory.RateException

Constructor and Description
Simulate(java.util.Map<java.lang.String,Model> m, java.util.Map<java.lang.String,Tree> t, Parameters p) Creates an object to simulate data for a given set of models and trees, parameters and unobserved states.
Simulate(java.util.Map<java.lang.String,Model> m, java.util.Map<java.lang.String,Tree> t, Parameters p, Alignment unobserved) Creates an object to simulate data for a given set of models and trees, parameters and unobserved states.
Simulate(java.util.Map<java.lang.String,Model> m, Tree t, Parameters p) Creates an object to simulate data for a given set of models, a tree and parameters.
Simulate(java.util.Map<java.lang.String,Model> m, Tree t, Parameters p, Alignment unobserved) Creates an object to simulate data for a given set of models, a tree, parameters and unobserved states.
Simulate(Model m, java.util.Map<java.lang.String,Tree> t, Parameters p) Creates an object to simulate data for a given model, set of trees, parameters and unobserved states.
Simulate(Model m, java.util.Map<java.lang.String,Tree> t, Parameters p, Alignment unobserved) Creates an object to simulate data for a given model, set of trees, parameters and unobserved states.
Simulate(Model m, Tree t, Parameters p) Creates an object to simulate data for a given model, tree and parameters.
Simulate(Model m, Tree t, Parameters p, Alignment unobserved) Creates an object to simulate data for a given model, tree, parameters and unobserved states.