phylosim (version 3.0.5)

CodonSequence: The CodonSequence class

Description

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

Package: Class CodonSequence

Object ~~| ~~+--PSRoot ~~~~~~~| ~~~~~~~+--Sequence ~~~~~~~~~~~~| ~~~~~~~~~~~~+--CodonSequence

Directly known subclasses:

public static class CodonSequence extends Sequence

Usage

CodonSequence(name=NA, string=NA, length=NA, table.id=1, 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".

table.id

The genetic code table to use in the attached CodonAlphabet object ("Standard" by default).

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:

	Translate	-
	checkConsistency	-
	getOmegas	-
	omegaHist	-
	omegaVarM0	-
	omegaVarM1	-
	omegaVarM2	-
	omegaVarM3	-
	omegaVarM4	-
	setOmegas	-

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

For more information see CodonSequence.

Examples

# NOT RUN {
       # create an empty CodonSequence object
       s<-CodonSequence(length=50)
       s
       # set states
       s$states<-c("ATG","CGA","TTT","CTA")
       s
       # create a sequence object by specifying a string
       s<-CodonSequence(string="ATCTTTCGAATG")
       s
 
# }