Uses of Interface
Maths.Real

Packages that use Real

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.
Maths	Provides maths classes.

Uses of Real in Ancestors

Methods in Ancestors that return Real

Modifier and Type	Method and Description
Real	AncestralMarginal.SiteResult.getProbability(java.lang.String node, java.lang.String state) Gets thr probability of a given state at a given node

Uses of Real in Likelihood

Methods in Likelihood that return Real

Modifier and Type	Method and Description
Real	FitzJohnRoot.calculate(SiteLikelihood.NodeLikelihood root)
Real	Root.calculate(SiteLikelihood.NodeLikelihood root) Calculate the total likelihood from the root node likelihood
Real	StandardRoot.calculate(SiteLikelihood.NodeLikelihood root)
Real	SiteLikelihood.getLikelihood() Get the likelihood
Real	SiteLikelihood.RateLikelihood.getLikelihood() Returns the likelihood.
Real	SiteLikelihood.NodeLikelihood.getLikelihood(int i) Returns the partial likelihood for the state at position i.
Real	SiteLikelihood.NodeLikelihood.getLikelihood(java.lang.String state) Returns the partial likelihood for a given state
Real[]	SiteLikelihood.NodeLikelihood.getLikelihoods() Returns the partial likelihood for each state as an array.
Real	SiteLikelihood.getRateCategoryProbability(RateCategory rc) Gets the probability of being in a rate category

Methods in Likelihood with parameters of type Real

Modifier and Type	Method and Description
void	SiteLikelihood.NodeLikelihood.multiply(java.lang.String state, Real by) This is a fudge to stop to allow this code to be reused in some of the ancestor classes.

Constructors in Likelihood with parameters of type Real

Constructor and Description
SiteLikelihood.RateLikelihood(Real l, java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood> nodeLikelihoods) Default constructor

Uses of Real in Maths

Classes in Maths that implement Real

Modifier and Type	Class and Description
class	SmallDouble Represents a real number.
class	StandardDouble Represents a real.

Methods in Maths that return Real

Modifier and Type	Method and Description
Real	Real.add(double o) Adds this Real to a double
Real	Real.add(Real o) Adds this Real to another
Real	Real.divide(double o) Divides this Real by a double
Real	Real.divide(Real o) Divides this Real by another one
static Real	RealFactory.getReal(RealFactory.RealType type, double d) Returns a new real of the given type and value
static Real	RealFactory.getSmallestReal(RealFactory.RealType type) Returns the smallest possible real of the given type
Real	Real.inverse() Returns the inverse of this real (i.e.
Real	Real.multiply(double o) Multiplies this Real by a double
Real	Real.multiply(Real o) Multiplies this Real by another
Real	Real.negate() Negates this real.
Real	Real.subtract(double o) Subtracts a double from this Real
Real	Real.subtract(Real o) Subtracts another Real from this one

Methods in Maths with parameters of type Real

Modifier and Type	Method and Description
Real	Real.add(Real o) Adds this Real to another
SmallDouble	SmallDouble.add(Real r)
StandardDouble	StandardDouble.add(Real o)
void	Real.addip(Real o) Adds a Real to this Real in place.
void	SmallDouble.addip(Real o)
void	StandardDouble.addip(Real o)
void	Real.addproductip(Real o1, double o2) Adds the product of a Real and a double to this Real in place.
void	SmallDouble.addproductip(Real o1, double o2)
void	StandardDouble.addproductip(Real o1, double o2)
Real	Real.divide(Real o) Divides this Real by another one
SmallDouble	SmallDouble.divide(Real o)
StandardDouble	StandardDouble.divide(Real o)
boolean	Real.greaterThan(Real o) Compares this real to another
boolean	SmallDouble.greaterThan(Real r)
boolean	StandardDouble.greaterThan(Real o)
Real	Real.multiply(Real o) Multiplies this Real by another
SmallDouble	SmallDouble.multiply(Real r)
StandardDouble	StandardDouble.multiply(Real o)
void	Real.multiplyip(Real o) Multiplies this Real by another Real in place.
void	SmallDouble.multiplyip(Real o)
void	StandardDouble.multiplyip(Real o)
Real	Real.subtract(Real o) Subtracts another Real from this one
SmallDouble	SmallDouble.subtract(Real o)
StandardDouble	StandardDouble.subtract(Real o)