NucleotideSequence: The NucleotideSequence class

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

Sequence objects aggregating Site objects having a NucleotideAlphabet attached by default.

Package:
Class NucleotideSequence

Object
~~|
~~+--PSRoot
~~~~~~~|
~~~~~~~+--Sequence
~~~~~~~~~~~~|
~~~~~~~~~~~~+--NucleotideSequence

Directly known subclasses:

public static class NucleotideSequence
extends Sequence

Usage

NucleotideSequence(name=NA, string=NA, length=NA, processes=NA, ancestral.obj=NA, ...)

Arguments

name	Name of the Sequence object.
string	A string specifying the length and the states of the Sequence object.
length	The length of the sequence. Mutually exclusive with "string".
processes	A list of lists of Process objects, to be attached to the aggregated Site objects. Recycled if shorter than the length of the sequence.
ancestral.obj	The ancestral object of the Sequence object (a valid Sequence or Process object).
...	Not used.

Fields and Methods

Methods:

	revComp	-

Methods inherited from Sequence:
as.character, attachProcess, checkConsistency, clearStates, clone, copySubSequence, deleteSubSequence, detachProcess, getAlphabets, getAncestral, getBigRate, getCumulativeRates, getCumulativeRatesFromRange, getDeletionTolerance, getEvents, getId, getInsertionTolerance, getLength, getName, getOmegas, getParameterAtSites, getProcesses, getRateMultipliers, getSites, getStates, getString, getSymbolFreqs, getTotalRates, getTotalRatesFromRange, getUniqueAlphabets, getUniqueProcesses, getWriteProtected, insertSequence, is, plot, plotParametersAtSites, plusGamma, plusInvGamma, sampleStates, setAlphabets, setAncestral, setBigRate, setCumulativeRates, setDeletionTolerance, setId, setInsertionTolerance, setLength, setName, setOmegas, setParameterAtSites, setProcesses, setRateMultipliers, setStates, setString, setTotalRates, setUniqueAlphabets, setUniqueProcesses, setWriteProtected, summary

Methods inherited from PSRoot:
checkConsistency, enableVirtual, getComments, getMethodsList, globalConsistencyCheck, intersect.list, is, is.na, ll, my.all.equal, plot, setComments, setMethodsList, summary, virtualAssignmentForbidden

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save

Author(s)

Botond Sipos, Gregory Jordan

See Also

Sequence NucleotideAlphabet

Examples

	# create an empty NucleotideSequence object
	s<-NucleotideSequence(length=50)
	s
	# set states
	s$states<-c("A","A","G","T")
	s
	# create a sequence object by specifying a string
	s<-NucleotideSequence(string="ATGCCGATTAGCAAA")
	s
 

phylosim documentation built on Nov. 22, 2019, 1:07 a.m.