Likelihood

Class Probabilities

java.lang.Object

Likelihood.Probabilities

public class Probabilities
extends java.lang.Object

Stores the values of each transition, frequency etc for one set of parameters.

Version:

2.0

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	Probabilities.RateProbabilities Stores the values of each transition, frequency etc for one set of parameters and for a single rate category.

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
java.util.Set<java.lang.String>	getAllStates() Gets the list of all possible states
java.util.Map<java.lang.String,java.lang.Integer>	getMap() Gets an Map linking states to position in an array
Probabilities.RateProbabilities	getP(RateCategory r) Gets a specific probability for a change from one state to another along a specific branch under a specific RateClass
java.util.Set<RateCategory>	getRateCategory() Gets the set of RateClasses that we have calculated probabilities for
double	getRateP(RateCategory r) Gets the probability of a rate class
Root	getRoot(RateCategory r) Get a root object, for the given rate category, that can be used to the total likelihood from the root node likelihoods or provide the frequencies of the various states at the root

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Probabilities

public Probabilities(Model m,
             Tree t,
             Parameters p)
              throws TreeException,
                     RateCategory.RateException,
                     Model.ModelException,
                     Parameters.ParameterException

Constructor

Parameters:

m - The model

t - The tree

p - The parameters

Throws:

TreeException - Thrown if there is a problem with the tree.

RateCategory.RateException - Thrown if there is an issue with a rate category in the model (e.g. a badly formatted rate).

Model.ModelException - Thrown if there is a problem with the model (e.g. the rate categories differ in their states)

Parameters.ParameterException - Thrown if there is a problem with the parameters (e.g. a required parameter is not present)

Method Detail

getRateCategory

public java.util.Set<RateCategory> getRateCategory()

Gets the set of RateClasses that we have calculated probabilities for

Returns:

Set of RateClasses

getAllStates

public java.util.Set<java.lang.String> getAllStates()

Gets the list of all possible states

Returns:

A list of all possible states

getP

public Probabilities.RateProbabilities getP(RateCategory r)

Gets a specific probability for a change from one state to another along a specific branch under a specific RateClass

Parameters:

r - The rate class

Returns:

The probability of a transition from start state to end state along the branch under the specified rate class.

getRoot

public Root getRoot(RateCategory r)

Get a root object, for the given rate category, that can be used to the total likelihood from the root node likelihoods or provide the frequencies of the various states at the root

Parameters:

r - The rate category to get the root object for

Returns:

A root object

getRateP

public double getRateP(RateCategory r)

Gets the probability of a rate class

Parameters:

r - the rate class

Returns:

The probability of the rate class

getMap

public java.util.Map<java.lang.String,java.lang.Integer> getMap()

Gets an Map linking states to position in an array

Returns:

Map linking state to positions