Represents a sequence of characters. More...

Inheritance diagram for PhyloTree.SequenceSimulation.Sequence:

Public Member Functions
	Sequence (ReadOnlySpan< char > sequence)
	Creates a new Sequence. More...

	Sequence (ReadOnlySpan< char > sequence, IReadOnlyList< char > states)
	Creates a new Sequence. More...

	Sequence (ReadOnlySpan< char > sequence, IReadOnlyList< char > states, IReadOnlyList< double > conservation)
	Creates a new Sequence. More...

	Sequence (ReadOnlySpan< char > sequence, IReadOnlyList< char > states, IReadOnlyList< double > conservation, IReadOnlyList< double > indelProfile)
	Creates a new Sequence. More...

override string	ToString ()

IEnumerator< char >	GetEnumerator ()

Sequence	Evolve (RateMatrix rateMatrix, double time)
	Simulates the evolution of the Sequence over the specified amount of time , using the specified rate matrix. No indels are allowed to happen. More...

Sequence	Evolve (RateMatrix rateMatrix, IndelModel indelModel, double time)
	Simulates the evolution of the Sequence over the specified amount of time , using the specified rate matrix. Insertions and deletions happen according to the specified indelModel . More...

Sequence	Evolve (RateMatrix rateMatrix, IndelModel indelModel, double time, out Insertion[] insertions)
	Simulates the evolution of the Sequence over the specified amount of time , using the specified rate matrix. Insertions and deletions happen according to the specified indelModel . More...

Dictionary< string, Sequence >	Evolve (TreeNode tree, RateMatrix rateMatrix, double scale=1, IndelModel indelModel=null)
	Simulates the evolution of the sequence over a phylogenetic tree , with the specified rate matrix, scale factor, and insertion/deletion model. More...

Dictionary< string, Sequence >	EvolveAll (TreeNode tree, RateMatrix rateMatrix, double scale=1, IndelModel indelModel=null)
	Simulates the evolution of the sequence over a phylogenetic tree , with the specified rate matrix, scale factor, and insertion/deletion model. More...

Static Public Member Functions
static implicit	operator string (Sequence sequence)
	Converts a Sequence to a `string` More...

static Sequence	RandomSequence (int length, RateMatrix rateMatrix)
	Create a random sequence with the specified length , using the states and equilibrium frequencies from the rateMatrix . More...

static Sequence	RandomSequence (int length, IReadOnlyList< char > states)
	Create a random sequence with the specified length containing all states with equal probability. More...

static Sequence	RandomSequence (int length, char[] states)
	Create a random sequence with the specified length containing all states with equal probability. More...

static Sequence	RandomSequence (int length, IReadOnlyList< char > states, IReadOnlyList< double > stateFrequencies)
	Create a random sequence with the specified length containing each state with probabilities given by stateFrequencies . More...

static Sequence	RandomSequence (int length, char[] states, double[] stateFrequencies)
	Create a random sequence with the specified length containing each state with probabilities given by stateFrequencies . More...

Properties
ImmutableArray< char >	States `[get]`
	The possible states that make up the sequence. Note that some states may not actually be present in the sequence. More...

ImmutableArray< double >?	Conservation `[get]`
	The conservation profile of the sequence. If this is `null`, all positions in the sequence are equally conserved. More...

ImmutableArray< double >?	IndelProfile `[get]`
	The indel profile of the sequence. If this is `null`, all positions in the sequence have equal probability of being affected by an indel event. More...

string	StringSequence `[get]`
	Returns the sequence as a `string`. More...

int	Length `[get]`
	The length of the sequence. More...

int	Count `[get]`

char	this[int index] `[get]`

Detailed Description

Represents a sequence of characters.

Definition at line 14 of file Sequence.cs.

Constructor & Destructor Documentation

◆ Sequence() [1/4]

PhyloTree.SequenceSimulation.Sequence.Sequence ( ReadOnlySpan< char > sequence )

Creates a new Sequence.

Parameters

sequence The sequence.

Definition at line 64 of file Sequence.cs.

◆ Sequence() [2/4]

PhyloTree.SequenceSimulation.Sequence.Sequence	(	ReadOnlySpan< char >	sequence,
		IReadOnlyList< char >	states
	)

Creates a new Sequence.

Parameters

sequence	The sequence.
states	The possible states for the sequence.

Definition at line 95 of file Sequence.cs.

◆ Sequence() [3/4]

PhyloTree.SequenceSimulation.Sequence.Sequence	(	ReadOnlySpan< char >	sequence,
		IReadOnlyList< char >	states,
		IReadOnlyList< double >	conservation
	)

Creates a new Sequence.

Parameters

sequence	The sequence.
states	The possible states for the sequence.
conservation	The conservation profile for the sequence.

Definition at line 125 of file Sequence.cs.

◆ Sequence() [4/4]

PhyloTree.SequenceSimulation.Sequence.Sequence	(	ReadOnlySpan< char >	sequence,
		IReadOnlyList< char >	states,
		IReadOnlyList< double >	conservation,
		IReadOnlyList< double >	indelProfile
	)

Creates a new Sequence.

Parameters

sequence	The sequence.
states	The possible states for the sequence.
conservation	The conservation profile for the sequence.
indelProfile	The indel profile for the sequence.

Definition at line 161 of file Sequence.cs.

Member Function Documentation

◆ Evolve() [1/4]

Sequence PhyloTree.SequenceSimulation.Sequence.Evolve	(	RateMatrix	rateMatrix,
		double	time
	)

Simulates the evolution of the Sequence over the specified amount of time , using the specified rate matrix. No indels are allowed to happen.

Parameters

rateMatrix	The rate matrix to simulate sequence evolution.
time	The length of time over which the sequence evolves.

Returns: The evolved sequence.

Definition at line 288 of file Sequence.cs.

◆ Evolve() [2/4]

Sequence PhyloTree.SequenceSimulation.Sequence.Evolve	(	RateMatrix	rateMatrix,
		IndelModel	indelModel,
		double	time
	)

Simulates the evolution of the Sequence over the specified amount of time , using the specified rate matrix. Insertions and deletions happen according to the specified indelModel .

Parameters

rateMatrix	The rate matrix to simulate sequence evolution.
indelModel	The insertion/deletion model.
time	The length of time over which the sequence evolves.

Returns: The evolved sequence.

Definition at line 303 of file Sequence.cs.

◆ Evolve() [3/4]

Sequence PhyloTree.SequenceSimulation.Sequence.Evolve	(	RateMatrix	rateMatrix,
		IndelModel	indelModel,
		double	time,
		out Insertion[]	insertions
	)

Simulates the evolution of the Sequence over the specified amount of time , using the specified rate matrix. Insertions and deletions happen according to the specified indelModel .

Parameters

rateMatrix	The rate matrix to simulate sequence evolution.
indelModel	The insertion/deletion model.
time	The length of time over which the sequence evolves.
insertions	An array containing all the insertion events that have occurred during the evolution of the sequence (useful to map the evolved sequence back onto the ancestral sequence).

Returns: The evolved sequence and an array containing all the insertion events that happened during its evolution.

Definition at line 320 of file Sequence.cs.

◆ Evolve() [4/4]

Dictionary< string, Sequence > PhyloTree.SequenceSimulation.Sequence.Evolve	(	TreeNode	tree,
		RateMatrix	rateMatrix,
		double	scale = `1`,
		IndelModel	indelModel = `null`
	)

Simulates the evolution of the sequence over a phylogenetic tree , with the specified rate matrix, scale factor, and insertion/deletion model.

Parameters

tree	The tree over which the sequence evolves. This is assumed to be rooted (i.e., the ancestral sequence is placed at the root of the tree).
rateMatrix	The rate matrix that governs the evolution of the sequence.
scale	A scaling factor. If this is different from 1, the effect is the same as multiplying the branch lengths of the tree or the rate matrix by the supplied value.
indelModel	The model for insertions/deletions. If this is null, no insertions/deletions are allowed to happen.

Returns: A Dictionary<String, Sequence> containing entries for all the nodes in the tree that have names. For each entry, the key is a string containing the TreeNode.Name of the node, and the value is a Sequence containing the sequence. The sequences are all aligned.

Definition at line 351 of file Sequence.cs.

◆ EvolveAll()

Dictionary< string, Sequence > PhyloTree.SequenceSimulation.Sequence.EvolveAll	(	TreeNode	tree,
		RateMatrix	rateMatrix,
		double	scale = `1`,
		IndelModel	indelModel = `null`
	)

Simulates the evolution of the sequence over a phylogenetic tree , with the specified rate matrix, scale factor, and insertion/deletion model.

Parameters

tree	The tree over which the sequence evolves. This is assumed to be rooted (i.e., the ancestral sequence is placed at the root of the tree).
rateMatrix	The rate matrix that governs the evolution of the sequence.
scale	A scaling factor. If this is different from 1, the effect is the same as multiplying the branch lengths of the tree or the rate matrix by the supplied value.
indelModel	The model for insertions/deletions. If this is null, no insertions/deletions are allowed to happen.

Returns: A Dictionary<String, Sequence> containing entries for all the nodes in the tree. For each entry, the key is a string containing the TreeNode.Id of the node, and the value is a Sequence containing the sequence. The sequences are all aligned.

Definition at line 367 of file Sequence.cs.

◆ GetEnumerator()

IEnumerator< char > PhyloTree.SequenceSimulation.Sequence.GetEnumerator ( )

Definition at line 228 of file Sequence.cs.

◆ operator string()

static implicit PhyloTree.SequenceSimulation.Sequence.operator string ( Sequence sequence )

static

Converts a Sequence to a string

Parameters

sequence The Sequence to convert.

Definition at line 216 of file Sequence.cs.

◆ RandomSequence() [1/5]

static Sequence PhyloTree.SequenceSimulation.Sequence.RandomSequence	(	int	length,
		char[]	states
	)

static

Create a random sequence with the specified length containing all states with equal probability.

Parameters

length	The length of the sequence.
states	The character states to use for the sequence.

Returns: A random sequence

◆ RandomSequence() [2/5]

static Sequence PhyloTree.SequenceSimulation.Sequence.RandomSequence	(	int	length,
		char[]	states,
		double[]	stateFrequencies
	)

static

Create a random sequence with the specified length containing each state with probabilities given by stateFrequencies .

Parameters

length	The length of the sequence.
states	The character states to use for the sequence.
stateFrequencies	The frequency for each state.

Returns: A random sequence

◆ RandomSequence() [3/5]

static Sequence PhyloTree.SequenceSimulation.Sequence.RandomSequence	(	int	length,
		IReadOnlyList< char >	states
	)

static

Create a random sequence with the specified length containing all states with equal probability.

Parameters

length	The length of the sequence.
states	The character states to use for the sequence.

Returns: A random sequence

◆ RandomSequence() [4/5]

static Sequence PhyloTree.SequenceSimulation.Sequence.RandomSequence	(	int	length,
		IReadOnlyList< char >	states,
		IReadOnlyList< double >	stateFrequencies
	)

static

Create a random sequence with the specified length containing each state with probabilities given by stateFrequencies .

Parameters

length	The length of the sequence.
states	The character states to use for the sequence.
stateFrequencies	The frequency for each state.

Returns: A random sequence

◆ RandomSequence() [5/5]

static Sequence PhyloTree.SequenceSimulation.Sequence.RandomSequence	(	int	length,
		RateMatrix	rateMatrix
	)

static

Create a random sequence with the specified length , using the states and equilibrium frequencies from the rateMatrix .

Parameters

length	The length of the sequence.
rateMatrix	The rate matrix.

Returns: A random sequence.

◆ ToString()

override string PhyloTree.SequenceSimulation.Sequence.ToString ( )

Definition at line 222 of file Sequence.cs.

Property Documentation

◆ Conservation

ImmutableArray<double>? PhyloTree.SequenceSimulation.Sequence.Conservation

get

The conservation profile of the sequence. If this is null, all positions in the sequence are equally conserved.

Definition at line 27 of file Sequence.cs.

◆ Count

int PhyloTree.SequenceSimulation.Sequence.Count

get

Definition at line 55 of file Sequence.cs.

◆ IndelProfile

ImmutableArray<double>? PhyloTree.SequenceSimulation.Sequence.IndelProfile

get

The indel profile of the sequence. If this is null, all positions in the sequence have equal probability of being affected by an indel event.

Definition at line 33 of file Sequence.cs.

◆ Length

int PhyloTree.SequenceSimulation.Sequence.Length

get

The length of the sequence.

Definition at line 49 of file Sequence.cs.

◆ States

ImmutableArray<char> PhyloTree.SequenceSimulation.Sequence.States

get

The possible states that make up the sequence. Note that some states may not actually be present in the sequence.

Definition at line 22 of file Sequence.cs.

◆ StringSequence

string PhyloTree.SequenceSimulation.Sequence.StringSequence

get

Returns the sequence as a string.

Definition at line 38 of file Sequence.cs.

◆ this[int index]

char PhyloTree.SequenceSimulation.Sequence.this[int index]

get

Definition at line 58 of file Sequence.cs.

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

SequenceSimulation/Sequence.cs

Public Member Functions

Static Public Member Functions

Properties

Detailed Description

Constructor & Destructor Documentation

◆ Sequence() [1/4]

◆ Sequence() [2/4]

◆ Sequence() [3/4]

◆ Sequence() [4/4]

Member Function Documentation

◆ Evolve() [1/4]

◆ Evolve() [2/4]

◆ Evolve() [3/4]

◆ Evolve() [4/4]

◆ EvolveAll()

◆ GetEnumerator()

◆ operator string()

◆ RandomSequence() [1/5]

◆ RandomSequence() [2/5]

◆ RandomSequence() [3/5]

◆ RandomSequence() [4/5]

◆ RandomSequence() [5/5]

◆ ToString()

Property Documentation

◆ Conservation

◆ Count

◆ IndelProfile

◆ Length

◆ States

◆ StringSequence

◆ this[int index]