ContinuousInsertor: The ContinuousInsertor class

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

This class implements a process which performs insertions with lengths sampled from a user-specified R expression returning a numeric value. See GeneralInsertor for the how the insertion process works.

Package:
Class ContinuousInsertor

Object
~~|
~~+--PSRoot
~~~~~~~|
~~~~~~~+--Process
~~~~~~~~~~~~|
~~~~~~~~~~~~+--GeneralInDel
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--GeneralInsertor
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--ContinuousInsertor

Directly known subclasses:

public static class ContinuousInsertor
extends GeneralInsertor

Usage

ContinuousInsertor(name="Anonymous", rate=NA, dist=NA, max.length=NA, ...)

Arguments

name	The name of the object.
rate	The general rate.
dist	The length sampling expression.
max.length	Maximum event length.
...	Additional arguments.

Fields and Methods

Methods:

	checkConsistency	-
	getDist	-
	getMaxLength	-
	plot	-
	setDist	-
	setMaxLength	-
	summary	-

Methods inherited from GeneralInsertor:
checkConsistency, generateInsert, getAcceptWin, getEventsAtSite, getGenerateBy, getInsertHook, getTemplateSeq, is, setAcceptWin, setGenerateBy, setInsertHook, setTemplateSeq, summary

Methods inherited from GeneralInDel:
checkConsistency, getAcceptBy, getProposeBy, getRate, hasUndefinedRate, is, proposeLength, setAcceptBy, setProposeBy, setRate, summary

Methods inherited from Process:
!=, ==, as.character, checkConsistency, clone, getAlphabet, getEventsAtSite, getId, getName, getParameterAtSite, getSiteSpecificParamIds, getSiteSpecificParamList, getWriteProtected, hasSiteSpecificParameter, hasUndefinedRate, is, setAlphabet, setId, setName, setParameterAtSite, setSiteSpecificParamIds, setSiteSpecificParamList, 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

GeneralInsertor DiscreteInsertor GeneralInDel

Examples

       # create a ContinuousInsertor process
       o<-ContinuousInsertor(
               name="Conty",
               rate=0.1,
               dist=expression(1),
               max.length=2
       )
	# set template sequence
	o$templateSeq<-NucleotideSequence(string="CAC")
       # get object summary
       summary(o)
       # set/get length sampling expression
       o$dist<-expression(rnorm(1,mean=3,sd=3))
       o$dist
       # set/get maximum event length
       o$maxLength<-4
       o$maxLength
       # plot length density
       plot(o)
     
       # The following code illustrates how to use
       # a ContinuousInsertor process in a simulation
     
       # create a sequence object, attach process o
       s<-NucleotideSequence(string="AAAAAAAAAAGGGGAAAAAAAAAA",processes=list(list(o)))
       # set the insertion tolerance to zero in range 11:15
       # creating a region rejecting all insertions
       setInsertionTolerance(s,o,0,11:15)     
       # get insertion tolerances
       getInsertionTolerance(s,o)
       # create a simulation object
       sim<-PhyloSim(root.seq=s,phylo=rcoal(2))
       # simulate
       Simulate(sim)
       # print resulting alignment
       sim$alignment
 

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