Uses of Class
Maths.SquareMatrix

Packages that use SquareMatrix
Likelihood Provides classes for calculating the likelihood of a tree given a model and an alignment. 
Maths Provides maths classes. 
Models Provides classes for defing a phylogenetic model. 
 

Uses of SquareMatrix in Likelihood
 

Methods in Likelihood that return SquareMatrix
 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
 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
 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
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
 SquareMatrix RateCategory.getP(double length)
          Gets the P-matrix for a given length
 

Methods in Models with parameters of type SquareMatrix
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.