phylosim (version 3.0.5)

NucleotideSequence: The NucleotideSequence class

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

See Also

Sequence NucleotideAlphabet

Examples

# NOT RUN {
	# 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
 
# }