Description Usage Arguments Fields and Methods Author(s) See Also Examples
This is the class representing a site. Site objects can have one associated Alphabet object and one or more Process objects that act on their states. The associated Process and Site objects must have associated Alphabet objects with the same symbols set, or at least one of the Alphabet objects should inherit from the class AnyAlphabet.
Site objects store the site-process-specific parameters of the attached Process objects.
A site-process-specific parameter is a list containing: the identifier, the name, the value and type of the parameter.
For example the ubiquitous rate multiplier site-process-specific parameter looks like
list(id="rate.multiplier",name="Rate multiplier",value=1,type="numeric")
.
Templates for site-process-specific parameters and their default values are stored in the Process objects and copied into the Site object when the process is attached.
Site objects have fields for associated ancestral Site objects and Sequence objects.
Package:
Class Site
Object
~~|
~~+--
PSRoot
~~~~~~~|
~~~~~~~+--
Site
Directly known subclasses:
public static class Site
extends PSRoot
1 |
state |
A symbol belonging to the specified alphabet. |
alphabet |
An alphabet object. |
ancestral |
The ancestral Site object. |
processes |
A list of Process objects. |
sequence |
The Sequence object to which the Site object belongs. |
... |
Not used. |
Methods:
as.character | - | |
attachProcess | - | |
checkConsistency | - | |
detachProcess | - | |
flagTotalRate | - | |
getAlphabet | - | |
getAncestral | - | |
getEvents | - | |
getProcesses | - | |
getSequence | - | |
getState | - | |
getTotalRate | - | |
is | - | |
isAttached | - | |
setAlphabet | - | |
setAncestral | - | |
setEvents | - | |
setProcesses | - | |
setSequence | - | |
setState | - | |
setTotalRate | - | |
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:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save
Botond Sipos, Gregory Jordan
Alphabet, Process, Event
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | # create a site object
site<-Site();
# print the character representation (state)
print(site);
# get a summary
summary(site);
# create a site with a nucleotide alphabet
site<-Site(state="A",alphabet=NucleotideAlphabet());
# set site state
site$state<-"G"
# manipulate the associated Sequence object
site$sequence<-Sequence()
site$sequence
# attach a substitution process
site$processes<-list(JC69())
# add one more substitution process
attachProcess(site,K80())
# get a list of active Event objects
site$events
# get a summary of the Site object
summary(site);
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