Uses of Class
Maths.SquareMatrix

Packages that use SquareMatrix

Package	Description
Likelihood	Provides classes for calculating the likelihood of a tree given a model and an alignment.
Maths	Provides maths classes.
Models	Provides classes for defining a phylogenetic model.

Uses of SquareMatrix in Likelihood

Methods in Likelihood that return SquareMatrix

Modifier and Type	Method and Description
SquareMatrix	Probabilities.RateProbabilities.getP(Branch b) Gets the probability matrix for a single branch

Uses of SquareMatrix in Maths

Methods in Maths that return SquareMatrix

Modifier and Type	Method and Description
SquareMatrix	SquareMatrix.add(SquareMatrix o) Adds a matrix to this one and returns a new matrix as the result
SquareMatrix	SquareMatrix.divide(SquareMatrix B) Divides this matrix by another (this / B) and returns a new matrix as the result
SquareMatrix	SquareMatrix.eigValuesDiag() Calculates the Eigenvalues.
SquareMatrix	SquareMatrix.eigVectors() Calculates the Eigenvectors.
SquareMatrix	SquareMatrix.exp() Calculates e^A where A is the current matrix and returns a new matrix as the result
SquareMatrix	SquareMatrix.expMult(double x) Calculates e^Ax where A is this matrix and returns a new matrix as the result.
SquareMatrix	EigenvalueDecomposition.getD() Return the block diagonal eigenvalue matrix
SquareMatrix	LUDecomposition.getL() Return lower triangular factor
SquareMatrix	LUDecomposition.getU() Return upper triangular factor
SquareMatrix	EigenvalueDecomposition.getV() Return the eigenvector matrix
SquareMatrix	SquareMatrix.inverse() Calculates the inverse of this matrix and returns a new matrix as the result.
SquareMatrix	SquareMatrix.multiply(SquareMatrix o) Multiplies this matrix by another (this × o) and returns a new matrix as a result
SquareMatrix	SquareMatrix.scalarDivide(double n) Divides the matrix by a scalar and returns a new matrix as the result
SquareMatrix	SquareMatrix.scalarMultiply(double n) Multiplies the matrix by a scalar and returns a new matrix as the result
SquareMatrix	LUDecomposition.solve(SquareMatrix B) Solve A*X = B
SquareMatrix	SquareMatrix.square() Sqaures the matrix and returns a new Matrix that is the result
SquareMatrix	SquareMatrix.transpose() Transposes the matrix and returns a new matrix as the result

Methods in Maths with parameters of type SquareMatrix

Modifier and Type	Method and Description
SquareMatrix	SquareMatrix.add(SquareMatrix o) Adds a matrix to this one and returns a new matrix as the result
SquareMatrix	SquareMatrix.divide(SquareMatrix B) Divides this matrix by another (this / B) and returns a new matrix as the result
SquareMatrix	SquareMatrix.multiply(SquareMatrix o) Multiplies this matrix by another (this × o) and returns a new matrix as a result
SquareMatrix	LUDecomposition.solve(SquareMatrix B) Solve A*X = B

Constructors in Maths with parameters of type SquareMatrix

Constructor and Description
EigenvalueDecomposition(SquareMatrix Arg) Check for symmetry, then construct the eigenvalue decomposition
LUDecomposition(SquareMatrix A) LU Decomposition

Uses of SquareMatrix in Models

Methods in Models that return SquareMatrix

Modifier and Type	Method and Description
SquareMatrix	RateCategory.getP(double length) Gets the P-matrix for a given length
SquareMatrix	RateCategory.getScaledMatrix() Gets the scaled rate matrix

Methods in Models with parameters of type SquareMatrix

Modifier and Type	Method and Description
static double[]	Distributions.quasiStationary(SquareMatrix m) Calculates a quasi-stationary distribution from a given rate matrix.
static double[]	Distributions.stationary(SquareMatrix m) Calculates a stationary distribution from a given rate matrix.