Represents a rate matrix for a continuous-type Markov chain model. This type cannot be instantiated directly, please use MutableRateMatrix or ImmutableRateMatrix instead, or access the static members for some pre-baked common rate matrices for DNA and protein evolution. More...

Inheritance diagram for PhyloTree.SequenceSimulation.RateMatrix:

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Classes
class	DNA
	Contains rate matrices for DNA sequence evolution. More...

class	Protein
	Contains rate matrices for protein sequence evolution. More...

Properties
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 for a continuous-type Markov chain model. This type cannot be instantiated directly, please use MutableRateMatrix or ImmutableRateMatrix instead, or access the static members for some pre-baked common rate matrices for DNA and protein evolution.

Definition at line 14 of file RateMatix.cs.

Property Documentation

◆ EquilibriumFrequencies

abstract ImmutableArray<double> PhyloTree.SequenceSimulation.RateMatrix.EquilibriumFrequencies

get

Gets the equilibrium frequences of the rate matrix.

Definition at line 30 of file RateMatix.cs.

◆ States

abstract ImmutableArray<char> PhyloTree.SequenceSimulation.RateMatrix.States

get

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

Definition at line 25 of file RateMatix.cs.

◆ this[char from, char to]

abstract double PhyloTree.SequenceSimulation.RateMatrix.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.

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.

Definition at line 53 of file RateMatix.cs.

◆ this[int from, int to]

abstract double PhyloTree.SequenceSimulation.RateMatrix.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.

Parameters

from	The row number.
to	The column number.

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

Definition at line 41 of file RateMatix.cs.

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

SequenceSimulation/RateMatix.cs