Nothing
##
## Copyright 2009 Botond Sipos
## See the package description for licensing information.
##
##
## AnyAlphabet
##
##########################################################################/**
#
# @RdocClass AnyAlphabet
#
# @title "The AnyAlphabet class"
#
# \description{
# This is a special Alphabet class which matches any alphabet.
# The '=='.Alphabet method always returns TRUE when one of the
# compared objects inherits from AnyAlphabet. This behaviour is
# handy when creating processes that have no alphabet preference
# (like a deletion process).
#
# @classhierarchy
# }
#
# @synopsis
#
# \arguments{
# \item{...}{Not used.}
# }
#
# \section{Fields and Methods}{
# @allmethods
# }
#
# \examples{
# # create some alphabet objects
# a<-BinaryAlphabet()
# b<-NucleotideAlphabet()
# any<-AnyAlphabet()
# # compare objects
# a == b
# any == a
# any == b
# }
#
# @author
#
# \seealso{
# Alphabet
# }
#
#*/###########################################################################
setConstructorS3(
"AnyAlphabet",
function(... ){
this<-Alphabet(type="*ANY*",symbols=c());
extend(this,
"AnyAlphabet",
.any.flag=TRUE
);
},
enforceRCC=TRUE
);
##
## BinaryAlphabet
##
##########################################################################/**
#
# @RdocClass BinaryAlphabet
#
# @title "The BinaryAlphabet class"
#
# \description{
# Class of Alphabet objects with the c("0","1") symbol set.
#
# @classhierarchy
# }
#
# @synopsis
#
# \arguments{
# \item{...}{Not used.}
# }
#
# \section{Fields and Methods}{
# @allmethods
# }
#
# \examples{
# # create a binary alphabet
# b<-BinaryAlphabet()
# # get alphabet summary
# summary(b)
# }
#
# @author
#
# \seealso{
# Alphabet
# }
#
#*/###########################################################################
setConstructorS3(
"BinaryAlphabet",
function(... ){
this<-Alphabet(type="Binary",symbols=c("0","1"));
extend(this,"BinaryAlphabet");
},
enforceRCC=TRUE
);
##
## NucleotideAlphabet
##
##########################################################################/**
#
# @RdocClass NucleotideAlphabet
#
# @title "The NucleotideAlphabet class"
#
# \description{
# Class of Alphabet objects with the c("T","C","A","G") symbol
# set, representing nucleotides.
#
# @classhierarchy
# }
#
# @synopsis
#
# \arguments{
# \item{...}{Not used.}
# }
#
# \section{Fields and Methods}{
# @allmethods
# }
#
# \examples{
# # create a nucleotide alphabet
# b<-NucleotideAlphabet()
# # get alphabet summary
# summary(b)
# }
#
# @author
#
# \seealso{
# Alphabet
# }
#
#*/###########################################################################
setConstructorS3(
"NucleotideAlphabet",
function(... ){
this<-Alphabet(type="Nucleotide",symbols=c("T","C","A","G"));
extend(this,"NucleotideAlphabet");
},
enforceRCC=TRUE
);
##
## AminoAcidAlphabet
##
##########################################################################/**
#
# @RdocClass AminoAcidAlphabet
#
# @title "The AminoAcidAlphabet class"
#
# \description{
# Class of Alphabet objects representing amino acids, using the
# one-letter IUPAC amino acid codes as symbol set:
# \preformatted{
# IUPAC code Amino acid
#
# A Alanine
# C Cysteine
# D Aspartic Acid
# E Glutamic Acid
# F Phenylalanine
# G Glycine
# H Histidine
# I Isoleucine
# K Lysine
# L Leucine
# M Methionine
# N Asparagine
# P Proline
# Q Glutamine
# R Arginine
# S Serine
# T Threonine
# V Valine
# W Tryptophan
# Y Tyrosine
#}
#
# @classhierarchy
# }
#
# @synopsis
#
# \arguments{
# \item{...}{Not used.}
# }
#
# \section{Fields and Methods}{
# @allmethods
# }
#
# \examples{
# a<-AminoAcidAlphabet();
# # get object summary
# summary(a)
# }
#
# @author
#
# \seealso{
# Alphabet
# }
#
#*/###########################################################################
setConstructorS3(
"AminoAcidAlphabet",
function(... ){
this<-Alphabet(
type="Amino acid",
symbols=c(
"A",
"R",
"N",
"D",
"C",
"Q",
"E",
"G",
"H",
"I",
"L",
"K",
"M",
"F",
"P",
"S",
"T",
"W",
"Y",
"V"
)
);
extend(this,"AminoAcidAlphabet");
},
enforceRCC=TRUE
);
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.