PhyloTree.SequenceSimulation.MutableRateMatrix Class Reference

Represents a rate matrix whose values can be changed after initialisation. More...

Inheritance diagram for PhyloTree.SequenceSimulation.MutableRateMatrix:

Public Member Functions
	MutableRateMatrix (ReadOnlySpan< char > states)
	Creates a new MutableRateMatrix with the specified states . More...
	MutableRateMatrix (ReadOnlySpan< char > states, double[,] rates)
	Creates a new MutableRateMatrix with the specified states and rates . More...

Properties
override ImmutableArray< char >	States [get]
	Gets the states for the character to which the rate matrix applies. More...
new double	this[int from, int to] [get, set]
	Gets or sets the rate of going from state number from to state number to . If from == to , the negative sum of the elements on the row is returned, but this value cannot be set. More...
new double	this[char from, char to] [get, set]
	Gets or sets the rate of going from state from to state to . If from == to , the negative sum of the elements on the row is returned, but this value cannot be set. More...
override ImmutableArray< double >	EquilibriumFrequencies [get]
	Gets the equilibrium frequences of the rate matrix. More...
Properties inherited from PhyloTree.SequenceSimulation.IMutableRateMatrix
sealed override double	this[int from, int to] [get]
	Gets the rate of going from state number from to state number to . If from == to , the negative sum of the elements on the row is returned. More...
sealed override double	this[char from, char to] [get]
	Gets the rate of going from state from to state to . If from == to , the negative sum of the elements on the row is returned. More...
Properties inherited from PhyloTree.SequenceSimulation.RateMatrix
abstract ImmutableArray< char >	States [get]
	Gets the states for the character to which the rate matrix applies. More...
abstract ImmutableArray< double >	EquilibriumFrequencies [get]
	Gets the equilibrium frequences of the rate matrix. More...
abstract double	this[int from, int to] [get]
	Gets the rate of going from state number from to state number to . If from == to , the negative sum of the elements on the row is returned. More...
abstract double	this[char from, char to] [get]
	Gets the rate of going from state from to state to . If from == to , the negative sum of the elements on the row is returned. More...

Detailed Description

Represents a rate matrix whose values can be changed after initialisation.

Definition at line 114 of file RateMatix.cs.

Constructor & Destructor Documentation

MutableRateMatrix() [1/2]

PhyloTree.SequenceSimulation.MutableRateMatrix.MutableRateMatrix

(

ReadOnlySpan< char >

states

)

Creates a new MutableRateMatrix with the specified states .

Parameters

states

The possible states of the character described by the MutableRateMatrix.

Definition at line 297 of file RateMatix.cs.

MutableRateMatrix() [2/2]

PhyloTree.SequenceSimulation.MutableRateMatrix.MutableRateMatrix	(	ReadOnlySpan< char >	states,
		double	rates[,]
	)

Creates a new MutableRateMatrix with the specified states and rates .

Parameters

states	The possible states of the character described by the MutableRateMatrix.
rates	A 2D double> array containing the rates used to initialise the matrix. The number of rows and columns in the array must be equal to the number of states. Diagonal entries are ignored.

Exceptions

ArgumentException

Thrown if the number of rows or columns of the rates matrix does not correspond to the number of states .

Definition at line 313 of file RateMatix.cs.

Property Documentation

EquilibriumFrequencies

override ImmutableArray<double> PhyloTree.SequenceSimulation.MutableRateMatrix.EquilibriumFrequencies

get

Gets the equilibrium frequences of the rate matrix.

Definition at line 264 of file RateMatix.cs.

States

override ImmutableArray<char> PhyloTree.SequenceSimulation.MutableRateMatrix.States

get

Gets the states for the character to which the rate matrix applies.

Definition at line 120 of file RateMatix.cs.

this[char from, char to]

new double PhyloTree.SequenceSimulation.MutableRateMatrix.this[char from, char to]

getset

Gets or sets the rate of going from state from to state to . If from == to , the negative sum of the elements on the row is returned, but this value cannot be set.

Parameters

from	The row state.
to	The column state.

Returns

The rate of going from state from to state to .

Exceptions

ArgumentOutOfRangeException	Thrown if the state is not part of the rate matrix.
ArgumentException	Thrown when attempting to set the value of a diagonal entry.

Definition at line 216 of file RateMatix.cs.

this[int from, int to]

new double PhyloTree.SequenceSimulation.MutableRateMatrix.this[int from, int to]

getset

Gets or sets the rate of going from state number from to state number to . If from == to , the negative sum of the elements on the row is returned, but this value cannot be set.

Parameters

from	The row number.
to	The column number.

Returns

The rate of going from state number from to state number to .

Exceptions

ArgumentOutOfRangeException	Thrown if the state index is < 0 or greater than the number of states in the rate matrix.
ArgumentException	Thrown when attempting to set the value of a diagonal entry.

Definition at line 138 of file RateMatix.cs.

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The documentation for this class was generated from the following file:

• SequenceSimulation/RateMatix.cs