Uses of Class
Exceptions.GeneralException

Packages that use GeneralException

Package	Description
Alignments	Provides class for dealing with "alignments" and the sites in an alignment.
Ancestors	Provides classed to calculate ancestral reconstruction.
Exceptions	Provides exceptions that are common across the package.
Likelihood	Provides classes for calculating the likelihood of a tree given a model and an alignment.
Models	Provides classes for defining a phylogenetic model.
ModelTest
Optimizers	Provides classes for optimising a likelihood.
Parameters	Provides classes for defining parameters used in the various calculations.
Simulations	Provides a class to create simulated data.
Trees	Provides classes to define a tree.

Uses of GeneralException in Alignments

Subclasses of GeneralException in Alignments

Modifier and Type	Class and Description
class	AlignmentException Exception related to an alignment (currently only input errors)

Uses of GeneralException in Ancestors

Subclasses of GeneralException in Ancestors

Modifier and Type	Class and Description
class	AncestralException Exception related to ancestral reconstruction

Uses of GeneralException in Exceptions

Subclasses of GeneralException in Exceptions

Modifier and Type	Class and Description
class	InputException General exception for an exception in or about an input file
class	OutputException Exception for problems writing an output file

Uses of GeneralException in Likelihood

Subclasses of GeneralException in Likelihood

Modifier and Type	Class and Description
static class	Calculator.CalculatorException Exception thrown when there is a problem with the calculation
static class	SiteLikelihood.LikelihoodException Exception related to a likelihood calculation

Uses of GeneralException in Models

Subclasses of GeneralException in Models

Modifier and Type	Class and Description
static class	Model.ModelException Exception thrown when there is a problem with the model
static class	RateCategory.RateException Exception thrown if there is a problem within a RateClass

Uses of GeneralException in ModelTest

Methods in ModelTest that throw GeneralException

Modifier and Type	Method and Description
double	HypothesisTest.test(java.util.Map<java.lang.String,Tree> t, Alignment a, Alignment unobserved, Parameters nullParams, Parameters altParams) Does a hypothesis test on the given data and gives a p-value
double	HypothesisTest.test(java.util.Map<java.lang.String,Tree> t, Alignment a, Alignment unobserved, Parameters nullParams, Parameters altParams, java.util.Map<java.lang.String,java.lang.String> recode) Does a hypothesis test on the given data and gives a p-value
double	HypothesisTest.test(Tree t, Alignment a, Alignment unobserved, Parameters nullParams, Parameters altParams) Does a hypothesis test on the given data and gives a p-value
double	HypothesisTest.test(Tree t, Alignment a, Alignment unobserved, Parameters nullParams, Parameters altParams, java.util.Map<java.lang.String,java.lang.String> recode) Does a hypothesis test on the given data and gives a p-value

Constructors in ModelTest that throw GeneralException

Constructor and Description
AIC(java.util.List<TestInstance> instances, Optimizer o) Creates an object containing the AIC for several test instances
BIC(java.util.List<TestInstance> instances, Optimizer o) Creates an object containing the BIC for several test instances

Uses of GeneralException in Optimizers

Subclasses of GeneralException in Optimizers

Modifier and Type	Class and Description
static class	Optimizer.OptimizerException Exception for when there is a problem with an optimiser.

Methods in Optimizers that throw GeneralException

Modifier and Type	Method and Description
R	Optimizable.calculate(Parameters p) The optimisable likelihood function.
<R extends Likelihood> R	ConjugateGradient.maximise(Optimizable<R> c, Parameters p)
<R extends Likelihood> R	GoldenSection.maximise(Optimizable<R> l, Parameters params)
<R extends Likelihood> R	NelderMead.maximise(Optimizable<R> l, Parameters params)
<R extends Likelihood> R	Optimizer.maximise(Optimizable<R> l, Parameters p) Maximises the likelihood, logging to screen.
<R extends Likelihood> R	ConjugateGradient.maximise(Optimizable<R> c, Parameters p, java.io.File log)
<R extends Likelihood> R	GoldenSection.maximise(Optimizable<R> l, Parameters params, java.io.File log)
<R extends Likelihood> R	NelderMead.maximise(Optimizable<R> l, Parameters params, java.io.File log)
<R extends Likelihood> R	Optimizer.maximise(Optimizable<R> l, Parameters params, java.io.File log) Maximises the likelihood, logging to a file.
<R extends Likelihood> R	ConjugateGradient.restart(Optimizable<R> l, java.io.File checkPoint)
<R extends Likelihood> R	GoldenSection.restart(Optimizable<R> l, java.io.File checkPoint)
<R extends Likelihood> R	NelderMead.restart(Optimizable<R> l, java.io.File checkPoint)
<R extends Likelihood> R	Optimizer.restart(Optimizable<R> l, java.io.File checkPoint) Maximises the likelihood starting from a checkpoint file (see Optimizer.setCheckPointFile(java.io.File), logging to the screen.
<R extends Likelihood> R	ConjugateGradient.restart(Optimizable<R> l, java.io.File checkPoint, java.io.File log)
<R extends Likelihood> R	GoldenSection.restart(Optimizable<R> l, java.io.File checkPoint, java.io.File log)
<R extends Likelihood> R	NelderMead.restart(Optimizable<R> l, java.io.File checkPoint, java.io.File log)
<R extends Likelihood> R	Optimizer.restart(Optimizable<R> l, java.io.File checkPoint, java.io.File log) Maximises the likelihood starting from a checkpoint file (see Optimizer.setCheckPointFile(java.io.File), logging to a file.

Uses of GeneralException in Parameters

Subclasses of GeneralException in Parameters

Modifier and Type	Class and Description
static class	Parameters.ParameterException Exception related to the parameters

Uses of GeneralException in Simulations

Subclasses of GeneralException in Simulations

Modifier and Type	Class and Description
class	Simulate.SimulationException Exception for when there is a problem with the simulation

Uses of GeneralException in Trees

Subclasses of GeneralException in Trees

Modifier and Type	Class and Description
class	TreeException Exception thrown when there is a problem with a tree