Nothing
R/CodonAlphabet.R
In phylosim: Flexible Simulations of Biological Sequence Evolution
##
## Copyright 2009 Botond Sipos
## See the package description for licensing information.
##
##
## CodonAlphabet
##
##########################################################################/**
#
# @RdocClass CodonAlphabet
#
# @title "The CodonAlphabet class"
#
# \description{
# This class implements codon alphabets and handles the translation of codons
# to their corresponding amino acids. Stop codons are excluded from the symbol set,
# thus the symbol set depends on the genetic code table.
# The genetic code table can be specified through the \code{table.id} constructor parameter.
#
# The available genetic code tables:
# \preformatted{
# 1 Standard
# 2 Vertebrate Mitochondrial
# 3 Yeast Mitochondrial
# 4 Mold, Protozoan, and CoelenterateMitochondrial and Mycoplasma/Spiroplasma
# 5 Invertebrate Mitochondrial
# 6 Ciliate, Dasycladacean and Hexamita Nuclear
# 9 Echinoderm Mitochondrial
# 10 Euplotid Nuclear
# 11 Bacterial
# 12 Alternative Yeast Nuclear
# 13 Ascidian Mitochondrial
# 14 Flatworm Mitochondrial
# 15 Blepharisma Nuclear
# 16 Chlorophycean Mitochondrial
# 21 Trematode Mitochondrial
# 22 Scenedesmus obliquus Mitochondrial
# 23 Thraustochytrium Mitochondrial
# }
#
# @classhierarchy
# }
#
# @synopsis
#
# \arguments{
# \item{table.id}{The identifier of the genetic code table.}
# \item{...}{Not used.}
# }
#
# \section{Fields and Methods}{
# @allmethods
# }
#
# \examples{
# # create a CodonAlphabet object
# a<-CodonAlphabet(table.id=2)
# # get object summary
# summary(a)
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setConstructorS3(
"CodonAlphabet",
function(table.id=1,...){
# Genetic code tables, ripped from BioPerl. #
CODON.TABLES<-list(
'1'=list(
'name'='Standard',
'trans'=list(
'TTT'=list(
aa='F',
type='ORDINARY'
),
'TTC'=list(
aa='F',
type='ORDINARY'
),
'TTA'=list(
aa='L',
type='ORDINARY'
),
'TTG'=list(
aa='L',
type='START'
),
'TCT'=list(
aa='S',
type='ORDINARY'
),
'TCC'=list(
aa='S',
type='ORDINARY'
),
'TCA'=list(
aa='S',
type='ORDINARY'
),
'TCG'=list(
aa='S',
type='ORDINARY'
),
'TAT'=list(
aa='Y',
type='ORDINARY'
),
'TAC'=list(
aa='Y',
type='ORDINARY'
),
'TAA'=list(
aa='*',
type='STOP'
),
'TAG'=list(
aa='*',
type='STOP'
),
'TGT'=list(
aa='C',
type='ORDINARY'
),
'TGC'=list(
aa='C',
type='ORDINARY'
),
'TGA'=list(
aa='*',
type='STOP'
),
'TGG'=list(
aa='W',
type='ORDINARY'
),
'CTT'=list(
aa='L',
type='ORDINARY'
),
'CTC'=list(
aa='L',
type='ORDINARY'
),
'CTA'=list(
aa='L',
type='ORDINARY'
),
'CTG'=list(
aa='L',
type='START'
),
'CCT'=list(
aa='P',
type='ORDINARY'
),
'CCC'=list(
aa='P',
type='ORDINARY'
),
'CCA'=list(
aa='P',
type='ORDINARY'
),
'CCG'=list(
aa='P',
type='ORDINARY'
),
'CAT'=list(
aa='H',
type='ORDINARY'
),
'CAC'=list(
aa='H',
type='ORDINARY'
),
'CAA'=list(
aa='Q',
type='ORDINARY'
),
'CAG'=list(
aa='Q',
type='ORDINARY'
),
'CGT'=list(
aa='R',
type='ORDINARY'
),
'CGC'=list(
aa='R',
type='ORDINARY'
),
'CGA'=list(
aa='R',
type='ORDINARY'
),
'CGG'=list(
aa='R',
type='ORDINARY'
),
'ATT'=list(
aa='I',
type='ORDINARY'
),
'ATC'=list(
aa='I',
type='ORDINARY'
),
'ATA'=list(
aa='I',
type='ORDINARY'
),
'ATG'=list(
aa='M',
type='START'
),
'ACT'=list(
aa='T',
type='ORDINARY'
),
'ACC'=list(
aa='T',
type='ORDINARY'
),
'ACA'=list(
aa='T',
type='ORDINARY'
),
'ACG'=list(
aa='T',
type='ORDINARY'
),
'AAT'=list(
aa='N',
type='ORDINARY'
),
'AAC'=list(
aa='N',
type='ORDINARY'
),
'AAA'=list(
aa='K',
type='ORDINARY'
),
'AAG'=list(
aa='K',
type='ORDINARY'
),
'AGT'=list(
aa='S',
type='ORDINARY'
),
'AGC'=list(
aa='S',
type='ORDINARY'
),
'AGA'=list(
aa='R',
type='ORDINARY'
),
'AGG'=list(
aa='R',
type='ORDINARY'
),
'GTT'=list(
aa='V',
type='ORDINARY'
),
'GTC'=list(
aa='V',
type='ORDINARY'
),
'GTA'=list(
aa='V',
type='ORDINARY'
),
'GTG'=list(
aa='V',
type='ORDINARY'
),
'GCT'=list(
aa='A',
type='ORDINARY'
),
'GCC'=list(
aa='A',
type='ORDINARY'
),
'GCA'=list(
aa='A',
type='ORDINARY'
),
'GCG'=list(
aa='A',
type='ORDINARY'
),
'GAT'=list(
aa='D',
type='ORDINARY'
),
'GAC'=list(
aa='D',
type='ORDINARY'
),
'GAA'=list(
aa='E',
type='ORDINARY'
),
'GAG'=list(
aa='E',
type='ORDINARY'
),
'GGT'=list(
aa='G',
type='ORDINARY'
),
'GGC'=list(
aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
'2'=list(
'name'='Vertebrate Mitochondrial',
'trans'=list(
'TTT'=list(
aa='F',
type='ORDINARY'
),
'TTC'=list(
aa='F',
type='ORDINARY'
),
'TTA'=list(
aa='L',
type='ORDINARY'
),
'TTG'=list(
aa='L',
type='ORDINARY'
),
'TCT'=list(
aa='S',
type='ORDINARY'
),
'TCC'=list(
aa='S',
type='ORDINARY'
),
'TCA'=list(
aa='S',
type='ORDINARY'
),
'TCG'=list(
aa='S',
type='ORDINARY'
),
'TAT'=list(
aa='Y',
type='ORDINARY'
),
'TAC'=list(
aa='Y',
type='ORDINARY'
),
'TAA'=list(
aa='*',
type='STOP'
),
'TAG'=list(
aa='*',
type='STOP'
),
'TGT'=list(
aa='C',
type='ORDINARY'
),
'TGC'=list(
aa='C',
type='ORDINARY'
),
'TGA'=list(
aa='W',
type='ORDINARY'
),
'TGG'=list(
aa='W',
type='ORDINARY'
),
'CTT'=list(
aa='L',
type='ORDINARY'
),
'CTC'=list(
aa='L',
type='ORDINARY'
),
'CTA'=list(
aa='L',
type='ORDINARY'
),
'CTG'=list(
aa='L',
type='ORDINARY'
),
'CCT'=list(
aa='P',
type='ORDINARY'
),
'CCC'=list(
aa='P',
type='ORDINARY'
),
'CCA'=list(
aa='P',
type='ORDINARY'
),
'CCG'=list(
aa='P',
type='ORDINARY'
),
'CAT'=list(
aa='H',
type='ORDINARY'
),
'CAC'=list(
aa='H',
type='ORDINARY'
),
'CAA'=list(
aa='Q',
type='ORDINARY'
),
'CAG'=list(
aa='Q',
type='ORDINARY'
),
'CGT'=list(
aa='R',
type='ORDINARY'
),
'CGC'=list(
aa='R',
type='ORDINARY'
),
'CGA'=list(
aa='R',
type='ORDINARY'
),
'CGG'=list(
aa='R',
type='ORDINARY'
),
'ATT'=list(
aa='I',
type='START'
),
'ATC'=list(
aa='I',
type='START'
),
'ATA'=list(
aa='M',
type='START'
),
'ATG'=list(
aa='M',
type='START'
),
'ACT'=list(
aa='T',
type='ORDINARY'
),
'ACC'=list(
aa='T',
type='ORDINARY'
),
'ACA'=list(
aa='T',
type='ORDINARY'
),
'ACG'=list(
aa='T',
type='ORDINARY'
),
'AAT'=list(
aa='N',
type='ORDINARY'
),
'AAC'=list(
aa='N',
type='ORDINARY'
),
'AAA'=list(
aa='K',
type='ORDINARY'
),
'AAG'=list(
aa='K',
type='ORDINARY'
),
'AGT'=list(
aa='S',
type='ORDINARY'
),
'AGC'=list(
aa='S',
type='ORDINARY'
),
'AGA'=list(
aa='*',
type='STOP'
),
'AGG'=list(
aa='*',
type='STOP'
),
'GTT'=list(
aa='V',
type='ORDINARY'
),
'GTC'=list(
aa='V',
type='ORDINARY'
),
'GTA'=list(
aa='V',
type='ORDINARY'
),
'GTG'=list(
aa='V',
type='START'
),
'GCT'=list(
aa='A',
type='ORDINARY'
),
'GCC'=list(
aa='A',
type='ORDINARY'
),
'GCA'=list(
aa='A',
type='ORDINARY'
),
'GCG'=list(
aa='A',
type='ORDINARY'
),
'GAT'=list(
aa='D',
type='ORDINARY'
),
'GAC'=list(
aa='D',
type='ORDINARY'
),
'GAA'=list(
aa='E',
type='ORDINARY'
),
'GAG'=list(
aa='E',
type='ORDINARY'
),
'GGT'=list(
aa='G',
type='ORDINARY'
),
'GGC'=list(
aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
'3'=list(
'name'='Yeast Mitochondrial',
'trans'=list(
'TTT'=list(
aa='F',
type='ORDINARY'
),
'TTC'=list(
aa='F',
type='ORDINARY'
),
'TTA'=list(
aa='L',
type='ORDINARY'
),
'TTG'=list(
aa='L',
type='ORDINARY'
),
'TCT'=list(
aa='S',
type='ORDINARY'
),
'TCC'=list(
aa='S',
type='ORDINARY'
),
'TCA'=list(
aa='S',
type='ORDINARY'
),
'TCG'=list(
aa='S',
type='ORDINARY'
),
'TAT'=list(
aa='Y',
type='ORDINARY'
),
'TAC'=list(
aa='Y',
type='ORDINARY'
),
'TAA'=list(
aa='*',
type='STOP'
),
'TAG'=list(
aa='*',
type='STOP'
),
'TGT'=list(
aa='C',
type='ORDINARY'
),
'TGC'=list(
aa='C',
type='ORDINARY'
),
'TGA'=list(
aa='W',
type='ORDINARY'
),
'TGG'=list(
aa='W',
type='ORDINARY'
),
'CTT'=list(
aa='T',
type='ORDINARY'
),
'CTC'=list(
aa='T',
type='ORDINARY'
),
'CTA'=list(
aa='T',
type='ORDINARY'
),
'CTG'=list(
aa='T',
type='ORDINARY'
),
'CCT'=list(
aa='P',
type='ORDINARY'
),
'CCC'=list(
aa='P',
type='ORDINARY'
),
'CCA'=list(
aa='P',
type='ORDINARY'
),
'CCG'=list(
aa='P',
type='ORDINARY'
),
'CAT'=list(
aa='H',
type='ORDINARY'
),
'CAC'=list(
aa='H',
type='ORDINARY'
),
'CAA'=list(
aa='Q',
type='ORDINARY'
),
'CAG'=list(
aa='Q',
type='ORDINARY'
),
'CGT'=list(
aa='R',
type='ORDINARY'
),
'CGC'=list(
aa='R',
type='ORDINARY'
),
'CGA'=list(
aa='R',
type='ORDINARY'
),
'CGG'=list(
aa='R',
type='ORDINARY'
),
'ATT'=list(
aa='I',
type='ORDINARY'
),
'ATC'=list(
aa='I',
type='ORDINARY'
),
'ATA'=list(
aa='M',
type='START'
),
'ATG'=list(
aa='M',
type='START'
),
'ACT'=list(
aa='T',
type='ORDINARY'
),
'ACC'=list(
aa='T',
type='ORDINARY'
),
'ACA'=list(
aa='T',
type='ORDINARY'
),
'ACG'=list(
aa='T',
type='ORDINARY'
),
'AAT'=list(
aa='N',
type='ORDINARY'
),
'AAC'=list(
aa='N',
type='ORDINARY'
),
'AAA'=list(
aa='K',
type='ORDINARY'
),
'AAG'=list(
aa='K',
type='ORDINARY'
),
'AGT'=list(
aa='S',
type='ORDINARY'
),
'AGC'=list(
aa='S',
type='ORDINARY'
),
'AGA'=list(
aa='R',
type='ORDINARY'
),
'AGG'=list(
aa='R',
type='ORDINARY'
),
'GTT'=list(
aa='V',
type='ORDINARY'
),
'GTC'=list(
aa='V',
type='ORDINARY'
),
'GTA'=list(
aa='V',
type='ORDINARY'
),
'GTG'=list(
aa='V',
type='ORDINARY'
),
'GCT'=list(
aa='A',
type='ORDINARY'
),
'GCC'=list(
aa='A',
type='ORDINARY'
),
'GCA'=list(
aa='A',
type='ORDINARY'
),
'GCG'=list(
aa='A',
type='ORDINARY'
),
'GAT'=list(
aa='D',
type='ORDINARY'
),
'GAC'=list(
aa='D',
type='ORDINARY'
),
'GAA'=list(
aa='E',
type='ORDINARY'
),
'GAG'=list(
aa='E',
type='ORDINARY'
),
'GGT'=list(
aa='G',
type='ORDINARY'
),
'GGC'=list(
aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
'4'=list(
'name'='Mold, Protozoan, and CoelenterateMitochondrial and Mycoplasma/Spiroplasma',
'trans'=list(
'TTT'=list(
aa='F',
type='ORDINARY'
),
'TTC'=list(
aa='F',
type='ORDINARY'
),
'TTA'=list(
aa='L',
type='START'
),
'TTG'=list(
aa='L',
type='START'
),
'TCT'=list(
aa='S',
type='ORDINARY'
),
'TCC'=list(
aa='S',
type='ORDINARY'
),
'TCA'=list(
aa='S',
type='ORDINARY'
),
'TCG'=list(
aa='S',
type='ORDINARY'
),
'TAT'=list(
aa='Y',
type='ORDINARY'
),
'TAC'=list(
aa='Y',
type='ORDINARY'
),
'TAA'=list(
aa='*',
type='STOP'
),
'TAG'=list(
aa='*',
type='STOP'
),
'TGT'=list(
aa='C',
type='ORDINARY'
),
'TGC'=list(
aa='C',
type='ORDINARY'
),
'TGA'=list(
aa='W',
type='ORDINARY'
),
'TGG'=list(
aa='W',
type='ORDINARY'
),
'CTT'=list(
aa='L',
type='ORDINARY'
),
'CTC'=list(
aa='L',
type='ORDINARY'
),
'CTA'=list(
aa='L',
type='ORDINARY'
),
'CTG'=list(
aa='L',
type='START'
),
'CCT'=list(
aa='P',
type='ORDINARY'
),
'CCC'=list(
aa='P',
type='ORDINARY'
),
'CCA'=list(
aa='P',
type='ORDINARY'
),
'CCG'=list(
aa='P',
type='ORDINARY'
),
'CAT'=list(
aa='H',
type='ORDINARY'
),
'CAC'=list(
aa='H',
type='ORDINARY'
),
'CAA'=list(
aa='Q',
type='ORDINARY'
),
'CAG'=list(
aa='Q',
type='ORDINARY'
),
'CGT'=list(
aa='R',
type='ORDINARY'
),
'CGC'=list(
aa='R',
type='ORDINARY'
),
'CGA'=list(
aa='R',
type='ORDINARY'
),
'CGG'=list(
aa='R',
type='ORDINARY'
),
'ATT'=list(
aa='I',
type='START'
),
'ATC'=list(
aa='I',
type='START'
),
'ATA'=list(
aa='I',
type='START'
),
'ATG'=list(
aa='M',
type='START'
),
'ACT'=list(
aa='T',
type='ORDINARY'
),
'ACC'=list(
aa='T',
type='ORDINARY'
),
'ACA'=list(
aa='T',
type='ORDINARY'
),
'ACG'=list(
aa='T',
type='ORDINARY'
),
'AAT'=list(
aa='N',
type='ORDINARY'
),
'AAC'=list(
aa='N',
type='ORDINARY'
),
'AAA'=list(
aa='K',
type='ORDINARY'
),
'AAG'=list(
aa='K',
type='ORDINARY'
),
'AGT'=list(
aa='S',
type='ORDINARY'
),
'AGC'=list(
aa='S',
type='ORDINARY'
),
'AGA'=list(
aa='R',
type='ORDINARY'
),
'AGG'=list(
aa='R',
type='ORDINARY'
),
'GTT'=list(
aa='V',
type='ORDINARY'
),
'GTC'=list(
aa='V',
type='ORDINARY'
),
'GTA'=list(
aa='V',
type='ORDINARY'
),
'GTG'=list(
aa='V',
type='START'
),
'GCT'=list(
aa='A',
type='ORDINARY'
),
'GCC'=list(
aa='A',
type='ORDINARY'
),
'GCA'=list(
aa='A',
type='ORDINARY'
),
'GCG'=list(
aa='A',
type='ORDINARY'
),
'GAT'=list(
aa='D',
type='ORDINARY'
),
'GAC'=list(
aa='D',
type='ORDINARY'
),
'GAA'=list(
aa='E',
type='ORDINARY'
),
'GAG'=list(
aa='E',
type='ORDINARY'
),
'GGT'=list(
aa='G',
type='ORDINARY'
),
'GGC'=list(
aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
'5'=list(
'name'='Invertebrate Mitochondrial',
'trans'=list(
'TTT'=list(
aa='F',
type='ORDINARY'
),
'TTC'=list(
aa='F',
type='ORDINARY'
),
'TTA'=list(
aa='L',
type='ORDINARY'
),
'TTG'=list(
aa='L',
type='START'
),
'TCT'=list(
aa='S',
type='ORDINARY'
),
'TCC'=list(
aa='S',
type='ORDINARY'
),
'TCA'=list(
aa='S',
type='ORDINARY'
),
'TCG'=list(
aa='S',
type='ORDINARY'
),
'TAT'=list(
aa='Y',
type='ORDINARY'
),
'TAC'=list(
aa='Y',
type='ORDINARY'
),
'TAA'=list(
aa='*',
type='STOP'
),
'TAG'=list(
aa='*',
type='STOP'
),
'TGT'=list(
aa='C',
type='ORDINARY'
),
'TGC'=list(
aa='C',
type='ORDINARY'
),
'TGA'=list(
aa='W',
type='ORDINARY'
),
'TGG'=list(
aa='W',
type='ORDINARY'
),
'CTT'=list(
aa='L',
type='ORDINARY'
),
'CTC'=list(
aa='L',
type='ORDINARY'
),
'CTA'=list(
aa='L',
type='ORDINARY'
),
'CTG'=list(
aa='L',
type='ORDINARY'
),
'CCT'=list(
aa='P',
type='ORDINARY'
),
'CCC'=list(
aa='P',
type='ORDINARY'
),
'CCA'=list(
aa='P',
type='ORDINARY'
),
'CCG'=list(
aa='P',
type='ORDINARY'
),
'CAT'=list(
aa='H',
type='ORDINARY'
),
'CAC'=list(
aa='H',
type='ORDINARY'
),
'CAA'=list(
aa='Q',
type='ORDINARY'
),
'CAG'=list(
aa='Q',
type='ORDINARY'
),
'CGT'=list(
aa='R',
type='ORDINARY'
),
'CGC'=list(
aa='R',
type='ORDINARY'
),
'CGA'=list(
aa='R',
type='ORDINARY'
),
'CGG'=list(
aa='R',
type='ORDINARY'
),
'ATT'=list(
aa='I',
type='START'
),
'ATC'=list(
aa='I',
type='START'
),
'ATA'=list(
aa='M',
type='START'
),
'ATG'=list(
aa='M',
type='START'
),
'ACT'=list(
aa='T',
type='ORDINARY'
),
'ACC'=list(
aa='T',
type='ORDINARY'
),
'ACA'=list(
aa='T',
type='ORDINARY'
),
'ACG'=list(
aa='T',
type='ORDINARY'
),
'AAT'=list(
aa='N',
type='ORDINARY'
),
'AAC'=list(
aa='N',
type='ORDINARY'
),
'AAA'=list(
aa='K',
type='ORDINARY'
),
'AAG'=list(
aa='K',
type='ORDINARY'
),
'AGT'=list(
aa='S',
type='ORDINARY'
),
'AGC'=list(
aa='S',
type='ORDINARY'
),
'AGA'=list(
aa='S',
type='ORDINARY'
),
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aa='S',
type='ORDINARY'
),
'GTT'=list(
aa='V',
type='ORDINARY'
),
'GTC'=list(
aa='V',
type='ORDINARY'
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'GTA'=list(
aa='V',
type='ORDINARY'
),
'GTG'=list(
aa='V',
type='START'
),
'GCT'=list(
aa='A',
type='ORDINARY'
),
'GCC'=list(
aa='A',
type='ORDINARY'
),
'GCA'=list(
aa='A',
type='ORDINARY'
),
'GCG'=list(
aa='A',
type='ORDINARY'
),
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aa='D',
type='ORDINARY'
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'GAC'=list(
aa='D',
type='ORDINARY'
),
'GAA'=list(
aa='E',
type='ORDINARY'
),
'GAG'=list(
aa='E',
type='ORDINARY'
),
'GGT'=list(
aa='G',
type='ORDINARY'
),
'GGC'=list(
aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
'6'=list(
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'trans'=list(
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aa='F',
type='ORDINARY'
),
'TTC'=list(
aa='F',
type='ORDINARY'
),
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type='ORDINARY'
),
'TTG'=list(
aa='L',
type='ORDINARY'
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aa='S',
type='ORDINARY'
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'TCC'=list(
aa='S',
type='ORDINARY'
),
'TCA'=list(
aa='S',
type='ORDINARY'
),
'TCG'=list(
aa='S',
type='ORDINARY'
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aa='Y',
type='ORDINARY'
),
'TAC'=list(
aa='Y',
type='ORDINARY'
),
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aa='Q',
type='ORDINARY'
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'TAG'=list(
aa='Q',
type='ORDINARY'
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type='ORDINARY'
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aa='C',
type='ORDINARY'
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aa='*',
type='STOP'
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aa='W',
type='ORDINARY'
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aa='L',
type='ORDINARY'
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'CTC'=list(
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type='ORDINARY'
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aa='L',
type='ORDINARY'
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'CTG'=list(
aa='L',
type='ORDINARY'
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aa='P',
type='ORDINARY'
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'CCC'=list(
aa='P',
type='ORDINARY'
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'CCA'=list(
aa='P',
type='ORDINARY'
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'CCG'=list(
aa='P',
type='ORDINARY'
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'CAT'=list(
aa='H',
type='ORDINARY'
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'CAC'=list(
aa='H',
type='ORDINARY'
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aa='Q',
type='ORDINARY'
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'CAG'=list(
aa='Q',
type='ORDINARY'
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aa='R',
type='ORDINARY'
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aa='R',
type='ORDINARY'
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aa='R',
type='ORDINARY'
),
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aa='R',
type='ORDINARY'
),
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aa='I',
type='ORDINARY'
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'ATC'=list(
aa='I',
type='ORDINARY'
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'ATA'=list(
aa='I',
type='ORDINARY'
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aa='M',
type='START'
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'ACT'=list(
aa='T',
type='ORDINARY'
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'ACC'=list(
aa='T',
type='ORDINARY'
),
'ACA'=list(
aa='T',
type='ORDINARY'
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'ACG'=list(
aa='T',
type='ORDINARY'
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aa='N',
type='ORDINARY'
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'AAC'=list(
aa='N',
type='ORDINARY'
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'AAA'=list(
aa='K',
type='ORDINARY'
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'AAG'=list(
aa='K',
type='ORDINARY'
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'AGT'=list(
aa='S',
type='ORDINARY'
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'AGC'=list(
aa='S',
type='ORDINARY'
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aa='R',
type='ORDINARY'
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'AGG'=list(
aa='R',
type='ORDINARY'
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'GTT'=list(
aa='V',
type='ORDINARY'
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'GTC'=list(
aa='V',
type='ORDINARY'
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'GTA'=list(
aa='V',
type='ORDINARY'
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'GTG'=list(
aa='V',
type='ORDINARY'
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aa='A',
type='ORDINARY'
),
'GCC'=list(
aa='A',
type='ORDINARY'
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'GCA'=list(
aa='A',
type='ORDINARY'
),
'GCG'=list(
aa='A',
type='ORDINARY'
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aa='D',
type='ORDINARY'
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'GAC'=list(
aa='D',
type='ORDINARY'
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aa='E',
type='ORDINARY'
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'GAG'=list(
aa='E',
type='ORDINARY'
),
'GGT'=list(
aa='G',
type='ORDINARY'
),
'GGC'=list(
aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
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aa='F',
type='ORDINARY'
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aa='F',
type='ORDINARY'
),
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aa='L',
type='ORDINARY'
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aa='L',
type='ORDINARY'
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aa='S',
type='ORDINARY'
),
'TCC'=list(
aa='S',
type='ORDINARY'
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'TCA'=list(
aa='S',
type='ORDINARY'
),
'TCG'=list(
aa='S',
type='ORDINARY'
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'TAT'=list(
aa='Y',
type='ORDINARY'
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'TAC'=list(
aa='Y',
type='ORDINARY'
),
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aa='*',
type='STOP'
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'TAG'=list(
aa='*',
type='STOP'
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aa='C',
type='ORDINARY'
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'TGC'=list(
aa='C',
type='ORDINARY'
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aa='W',
type='ORDINARY'
),
'TGG'=list(
aa='W',
type='ORDINARY'
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aa='L',
type='ORDINARY'
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'CTC'=list(
aa='L',
type='ORDINARY'
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'CTA'=list(
aa='L',
type='ORDINARY'
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'CTG'=list(
aa='L',
type='ORDINARY'
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'CCT'=list(
aa='P',
type='ORDINARY'
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'CCC'=list(
aa='P',
type='ORDINARY'
),
'CCA'=list(
aa='P',
type='ORDINARY'
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'CCG'=list(
aa='P',
type='ORDINARY'
),
'CAT'=list(
aa='H',
type='ORDINARY'
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'CAC'=list(
aa='H',
type='ORDINARY'
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aa='Q',
type='ORDINARY'
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'CAG'=list(
aa='Q',
type='ORDINARY'
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aa='R',
type='ORDINARY'
),
'CGC'=list(
aa='R',
type='ORDINARY'
),
'CGA'=list(
aa='R',
type='ORDINARY'
),
'CGG'=list(
aa='R',
type='ORDINARY'
),
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aa='I',
type='ORDINARY'
),
'ATC'=list(
aa='I',
type='ORDINARY'
),
'ATA'=list(
aa='I',
type='ORDINARY'
),
'ATG'=list(
aa='M',
type='START'
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'ACT'=list(
aa='T',
type='ORDINARY'
),
'ACC'=list(
aa='T',
type='ORDINARY'
),
'ACA'=list(
aa='T',
type='ORDINARY'
),
'ACG'=list(
aa='T',
type='ORDINARY'
),
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aa='N',
type='ORDINARY'
),
'AAC'=list(
aa='N',
type='ORDINARY'
),
'AAA'=list(
aa='N',
type='ORDINARY'
),
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aa='K',
type='ORDINARY'
),
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aa='S',
type='ORDINARY'
),
'AGC'=list(
aa='S',
type='ORDINARY'
),
'AGA'=list(
aa='S',
type='ORDINARY'
),
'AGG'=list(
aa='S',
type='ORDINARY'
),
'GTT'=list(
aa='V',
type='ORDINARY'
),
'GTC'=list(
aa='V',
type='ORDINARY'
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'GTA'=list(
aa='V',
type='ORDINARY'
),
'GTG'=list(
aa='V',
type='ORDINARY'
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aa='A',
type='ORDINARY'
),
'GCC'=list(
aa='A',
type='ORDINARY'
),
'GCA'=list(
aa='A',
type='ORDINARY'
),
'GCG'=list(
aa='A',
type='ORDINARY'
),
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aa='D',
type='ORDINARY'
),
'GAC'=list(
aa='D',
type='ORDINARY'
),
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aa='E',
type='ORDINARY'
),
'GAG'=list(
aa='E',
type='ORDINARY'
),
'GGT'=list(
aa='G',
type='ORDINARY'
),
'GGC'=list(
aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
'10'=list(
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aa='F',
type='ORDINARY'
),
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aa='F',
type='ORDINARY'
),
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aa='L',
type='ORDINARY'
),
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type='ORDINARY'
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type='ORDINARY'
),
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aa='S',
type='ORDINARY'
),
'TCA'=list(
aa='S',
type='ORDINARY'
),
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aa='S',
type='ORDINARY'
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type='ORDINARY'
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aa='Y',
type='ORDINARY'
),
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type='STOP'
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aa='*',
type='STOP'
),
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type='ORDINARY'
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type='ORDINARY'
),
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aa='C',
type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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aa='L',
type='ORDINARY'
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aa='P',
type='ORDINARY'
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type='ORDINARY'
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'CCA'=list(
aa='P',
type='ORDINARY'
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aa='P',
type='ORDINARY'
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aa='H',
type='ORDINARY'
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aa='H',
type='ORDINARY'
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type='ORDINARY'
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aa='Q',
type='ORDINARY'
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type='ORDINARY'
),
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type='ORDINARY'
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aa='R',
type='ORDINARY'
),
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aa='R',
type='ORDINARY'
),
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aa='I',
type='ORDINARY'
),
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aa='I',
type='ORDINARY'
),
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aa='I',
type='ORDINARY'
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aa='M',
type='START'
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aa='T',
type='ORDINARY'
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aa='T',
type='ORDINARY'
),
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aa='T',
type='ORDINARY'
),
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aa='T',
type='ORDINARY'
),
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aa='N',
type='ORDINARY'
),
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aa='N',
type='ORDINARY'
),
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aa='K',
type='ORDINARY'
),
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aa='K',
type='ORDINARY'
),
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aa='S',
type='ORDINARY'
),
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aa='S',
type='ORDINARY'
),
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aa='R',
type='ORDINARY'
),
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aa='R',
type='ORDINARY'
),
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aa='V',
type='ORDINARY'
),
'GTC'=list(
aa='V',
type='ORDINARY'
),
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aa='V',
type='ORDINARY'
),
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aa='V',
type='ORDINARY'
),
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aa='A',
type='ORDINARY'
),
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aa='A',
type='ORDINARY'
),
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aa='A',
type='ORDINARY'
),
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aa='A',
type='ORDINARY'
),
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aa='D',
type='ORDINARY'
),
'GAC'=list(
aa='D',
type='ORDINARY'
),
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aa='E',
type='ORDINARY'
),
'GAG'=list(
aa='E',
type='ORDINARY'
),
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aa='G',
type='ORDINARY'
),
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aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
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aa='F',
type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='START'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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aa='S',
type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='STOP'
),
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aa='*',
type='STOP'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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aa='*',
type='STOP'
),
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aa='W',
type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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aa='L',
type='START'
),
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type='ORDINARY'
),
'CCC'=list(
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type='ORDINARY'
),
'CCA'=list(
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type='ORDINARY'
),
'CCG'=list(
aa='P',
type='ORDINARY'
),
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aa='H',
type='ORDINARY'
),
'CAC'=list(
aa='H',
type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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aa='R',
type='ORDINARY'
),
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type='START'
),
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aa='I',
type='START'
),
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aa='I',
type='START'
),
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type='START'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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aa='T',
type='ORDINARY'
),
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aa='T',
type='ORDINARY'
),
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aa='N',
type='ORDINARY'
),
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aa='N',
type='ORDINARY'
),
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aa='K',
type='ORDINARY'
),
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aa='K',
type='ORDINARY'
),
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aa='S',
type='ORDINARY'
),
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aa='S',
type='ORDINARY'
),
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aa='R',
type='ORDINARY'
),
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aa='R',
type='ORDINARY'
),
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aa='V',
type='ORDINARY'
),
'GTC'=list(
aa='V',
type='ORDINARY'
),
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aa='V',
type='ORDINARY'
),
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aa='V',
type='START'
),
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aa='A',
type='ORDINARY'
),
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type='ORDINARY'
),
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aa='A',
type='ORDINARY'
),
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aa='A',
type='ORDINARY'
),
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type='ORDINARY'
),
'GAC'=list(
aa='D',
type='ORDINARY'
),
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aa='E',
type='ORDINARY'
),
'GAG'=list(
aa='E',
type='ORDINARY'
),
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aa='G',
type='ORDINARY'
),
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aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
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aa='F',
type='ORDINARY'
),
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aa='F',
type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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aa='S',
type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='STOP'
),
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aa='*',
type='STOP'
),
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type='ORDINARY'
),
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aa='C',
type='ORDINARY'
),
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aa='*',
type='STOP'
),
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aa='W',
type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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aa='L',
type='ORDINARY'
),
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aa='S',
type='START'
),
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aa='P',
type='ORDINARY'
),
'CCC'=list(
aa='P',
type='ORDINARY'
),
'CCA'=list(
aa='P',
type='ORDINARY'
),
'CCG'=list(
aa='P',
type='ORDINARY'
),
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aa='H',
type='ORDINARY'
),
'CAC'=list(
aa='H',
type='ORDINARY'
),
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aa='Q',
type='ORDINARY'
),
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aa='Q',
type='ORDINARY'
),
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aa='R',
type='ORDINARY'
),
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type='ORDINARY'
),
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aa='R',
type='ORDINARY'
),
'CGG'=list(
aa='R',
type='ORDINARY'
),
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aa='I',
type='ORDINARY'
),
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aa='I',
type='ORDINARY'
),
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aa='I',
type='ORDINARY'
),
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aa='M',
type='START'
),
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aa='T',
type='ORDINARY'
),
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aa='T',
type='ORDINARY'
),
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aa='T',
type='ORDINARY'
),
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aa='T',
type='ORDINARY'
),
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aa='N',
type='ORDINARY'
),
'AAC'=list(
aa='N',
type='ORDINARY'
),
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aa='K',
type='ORDINARY'
),
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aa='K',
type='ORDINARY'
),
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aa='S',
type='ORDINARY'
),
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aa='S',
type='ORDINARY'
),
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aa='R',
type='ORDINARY'
),
'AGG'=list(
aa='R',
type='ORDINARY'
),
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aa='V',
type='ORDINARY'
),
'GTC'=list(
aa='V',
type='ORDINARY'
),
'GTA'=list(
aa='V',
type='ORDINARY'
),
'GTG'=list(
aa='V',
type='ORDINARY'
),
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aa='A',
type='ORDINARY'
),
'GCC'=list(
aa='A',
type='ORDINARY'
),
'GCA'=list(
aa='A',
type='ORDINARY'
),
'GCG'=list(
aa='A',
type='ORDINARY'
),
'GAT'=list(
aa='D',
type='ORDINARY'
),
'GAC'=list(
aa='D',
type='ORDINARY'
),
'GAA'=list(
aa='E',
type='ORDINARY'
),
'GAG'=list(
aa='E',
type='ORDINARY'
),
'GGT'=list(
aa='G',
type='ORDINARY'
),
'GGC'=list(
aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
'13'=list(
'name'='Ascidian Mitochondrial',
'trans'=list(
'TTT'=list(
aa='F',
type='ORDINARY'
),
'TTC'=list(
aa='F',
type='ORDINARY'
),
'TTA'=list(
aa='L',
type='ORDINARY'
),
'TTG'=list(
aa='L',
type='ORDINARY'
),
'TCT'=list(
aa='S',
type='ORDINARY'
),
'TCC'=list(
aa='S',
type='ORDINARY'
),
'TCA'=list(
aa='S',
type='ORDINARY'
),
'TCG'=list(
aa='S',
type='ORDINARY'
),
'TAT'=list(
aa='Y',
type='ORDINARY'
),
'TAC'=list(
aa='Y',
type='ORDINARY'
),
'TAA'=list(
aa='*',
type='STOP'
),
'TAG'=list(
aa='*',
type='STOP'
),
'TGT'=list(
aa='C',
type='ORDINARY'
),
'TGC'=list(
aa='C',
type='ORDINARY'
),
'TGA'=list(
aa='W',
type='ORDINARY'
),
'TGG'=list(
aa='W',
type='ORDINARY'
),
'CTT'=list(
aa='L',
type='ORDINARY'
),
'CTC'=list(
aa='L',
type='ORDINARY'
),
'CTA'=list(
aa='L',
type='ORDINARY'
),
'CTG'=list(
aa='L',
type='ORDINARY'
),
'CCT'=list(
aa='P',
type='ORDINARY'
),
'CCC'=list(
aa='P',
type='ORDINARY'
),
'CCA'=list(
aa='P',
type='ORDINARY'
),
'CCG'=list(
aa='P',
type='ORDINARY'
),
'CAT'=list(
aa='H',
type='ORDINARY'
),
'CAC'=list(
aa='H',
type='ORDINARY'
),
'CAA'=list(
aa='Q',
type='ORDINARY'
),
'CAG'=list(
aa='Q',
type='ORDINARY'
),
'CGT'=list(
aa='R',
type='ORDINARY'
),
'CGC'=list(
aa='R',
type='ORDINARY'
),
'CGA'=list(
aa='R',
type='ORDINARY'
),
'CGG'=list(
aa='R',
type='ORDINARY'
),
'ATT'=list(
aa='I',
type='ORDINARY'
),
'ATC'=list(
aa='I',
type='ORDINARY'
),
'ATA'=list(
aa='M',
type='ORDINARY'
),
'ATG'=list(
aa='M',
type='START'
),
'ACT'=list(
aa='T',
type='ORDINARY'
),
'ACC'=list(
aa='T',
type='ORDINARY'
),
'ACA'=list(
aa='T',
type='ORDINARY'
),
'ACG'=list(
aa='T',
type='ORDINARY'
),
'AAT'=list(
aa='N',
type='ORDINARY'
),
'AAC'=list(
aa='N',
type='ORDINARY'
),
'AAA'=list(
aa='K',
type='ORDINARY'
),
'AAG'=list(
aa='K',
type='ORDINARY'
),
'AGT'=list(
aa='S',
type='ORDINARY'
),
'AGC'=list(
aa='S',
type='ORDINARY'
),
'AGA'=list(
aa='G',
type='ORDINARY'
),
'AGG'=list(
aa='G',
type='ORDINARY'
),
'GTT'=list(
aa='V',
type='ORDINARY'
),
'GTC'=list(
aa='V',
type='ORDINARY'
),
'GTA'=list(
aa='V',
type='ORDINARY'
),
'GTG'=list(
aa='V',
type='ORDINARY'
),
'GCT'=list(
aa='A',
type='ORDINARY'
),
'GCC'=list(
aa='A',
type='ORDINARY'
),
'GCA'=list(
aa='A',
type='ORDINARY'
),
'GCG'=list(
aa='A',
type='ORDINARY'
),
'GAT'=list(
aa='D',
type='ORDINARY'
),
'GAC'=list(
aa='D',
type='ORDINARY'
),
'GAA'=list(
aa='E',
type='ORDINARY'
),
'GAG'=list(
aa='E',
type='ORDINARY'
),
'GGT'=list(
aa='G',
type='ORDINARY'
),
'GGC'=list(
aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
'14'=list(
'name'='Flatworm Mitochondrial',
'trans'=list(
'TTT'=list(
aa='F',
type='ORDINARY'
),
'TTC'=list(
aa='F',
type='ORDINARY'
),
'TTA'=list(
aa='L',
type='ORDINARY'
),
'TTG'=list(
aa='L',
type='ORDINARY'
),
'TCT'=list(
aa='S',
type='ORDINARY'
),
'TCC'=list(
aa='S',
type='ORDINARY'
),
'TCA'=list(
aa='S',
type='ORDINARY'
),
'TCG'=list(
aa='S',
type='ORDINARY'
),
'TAT'=list(
aa='Y',
type='ORDINARY'
),
'TAC'=list(
aa='Y',
type='ORDINARY'
),
'TAA'=list(
aa='Y',
type='ORDINARY'
),
'TAG'=list(
aa='*',
type='STOP'
),
'TGT'=list(
aa='C',
type='ORDINARY'
),
'TGC'=list(
aa='C',
type='ORDINARY'
),
'TGA'=list(
aa='W',
type='ORDINARY'
),
'TGG'=list(
aa='W',
type='ORDINARY'
),
'CTT'=list(
aa='L',
type='ORDINARY'
),
'CTC'=list(
aa='L',
type='ORDINARY'
),
'CTA'=list(
aa='L',
type='ORDINARY'
),
'CTG'=list(
aa='L',
type='ORDINARY'
),
'CCT'=list(
aa='P',
type='ORDINARY'
),
'CCC'=list(
aa='P',
type='ORDINARY'
),
'CCA'=list(
aa='P',
type='ORDINARY'
),
'CCG'=list(
aa='P',
type='ORDINARY'
),
'CAT'=list(
aa='H',
type='ORDINARY'
),
'CAC'=list(
aa='H',
type='ORDINARY'
),
'CAA'=list(
aa='Q',
type='ORDINARY'
),
'CAG'=list(
aa='Q',
type='ORDINARY'
),
'CGT'=list(
aa='R',
type='ORDINARY'
),
'CGC'=list(
aa='R',
type='ORDINARY'
),
'CGA'=list(
aa='R',
type='ORDINARY'
),
'CGG'=list(
aa='R',
type='ORDINARY'
),
'ATT'=list(
aa='I',
type='ORDINARY'
),
'ATC'=list(
aa='I',
type='ORDINARY'
),
'ATA'=list(
aa='I',
type='ORDINARY'
),
'ATG'=list(
aa='M',
type='START'
),
'ACT'=list(
aa='T',
type='ORDINARY'
),
'ACC'=list(
aa='T',
type='ORDINARY'
),
'ACA'=list(
aa='T',
type='ORDINARY'
),
'ACG'=list(
aa='T',
type='ORDINARY'
),
'AAT'=list(
aa='N',
type='ORDINARY'
),
'AAC'=list(
aa='N',
type='ORDINARY'
),
'AAA'=list(
aa='N',
type='ORDINARY'
),
'AAG'=list(
aa='K',
type='ORDINARY'
),
'AGT'=list(
aa='S',
type='ORDINARY'
),
'AGC'=list(
aa='S',
type='ORDINARY'
),
'AGA'=list(
aa='S',
type='ORDINARY'
),
'AGG'=list(
aa='S',
type='ORDINARY'
),
'GTT'=list(
aa='V',
type='ORDINARY'
),
'GTC'=list(
aa='V',
type='ORDINARY'
),
'GTA'=list(
aa='V',
type='ORDINARY'
),
'GTG'=list(
aa='V',
type='ORDINARY'
),
'GCT'=list(
aa='A',
type='ORDINARY'
),
'GCC'=list(
aa='A',
type='ORDINARY'
),
'GCA'=list(
aa='A',
type='ORDINARY'
),
'GCG'=list(
aa='A',
type='ORDINARY'
),
'GAT'=list(
aa='D',
type='ORDINARY'
),
'GAC'=list(
aa='D',
type='ORDINARY'
),
'GAA'=list(
aa='E',
type='ORDINARY'
),
'GAG'=list(
aa='E',
type='ORDINARY'
),
'GGT'=list(
aa='G',
type='ORDINARY'
),
'GGC'=list(
aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
'15'=list(
'name'='Blepharisma Nuclear',
'trans'=list(
'TTT'=list(
aa='F',
type='ORDINARY'
),
'TTC'=list(
aa='F',
type='ORDINARY'
),
'TTA'=list(
aa='L',
type='ORDINARY'
),
'TTG'=list(
aa='L',
type='ORDINARY'
),
'TCT'=list(
aa='S',
type='ORDINARY'
),
'TCC'=list(
aa='S',
type='ORDINARY'
),
'TCA'=list(
aa='S',
type='ORDINARY'
),
'TCG'=list(
aa='S',
type='ORDINARY'
),
'TAT'=list(
aa='Y',
type='ORDINARY'
),
'TAC'=list(
aa='Y',
type='ORDINARY'
),
'TAA'=list(
aa='*',
type='STOP'
),
'TAG'=list(
aa='Q',
type='ORDINARY'
),
'TGT'=list(
aa='C',
type='ORDINARY'
),
'TGC'=list(
aa='C',
type='ORDINARY'
),
'TGA'=list(
aa='*',
type='STOP'
),
'TGG'=list(
aa='W',
type='ORDINARY'
),
'CTT'=list(
aa='L',
type='ORDINARY'
),
'CTC'=list(
aa='L',
type='ORDINARY'
),
'CTA'=list(
aa='L',
type='ORDINARY'
),
'CTG'=list(
aa='L',
type='ORDINARY'
),
'CCT'=list(
aa='P',
type='ORDINARY'
),
'CCC'=list(
aa='P',
type='ORDINARY'
),
'CCA'=list(
aa='P',
type='ORDINARY'
),
'CCG'=list(
aa='P',
type='ORDINARY'
),
'CAT'=list(
aa='H',
type='ORDINARY'
),
'CAC'=list(
aa='H',
type='ORDINARY'
),
'CAA'=list(
aa='Q',
type='ORDINARY'
),
'CAG'=list(
aa='Q',
type='ORDINARY'
),
'CGT'=list(
aa='R',
type='ORDINARY'
),
'CGC'=list(
aa='R',
type='ORDINARY'
),
'CGA'=list(
aa='R',
type='ORDINARY'
),
'CGG'=list(
aa='R',
type='ORDINARY'
),
'ATT'=list(
aa='I',
type='ORDINARY'
),
'ATC'=list(
aa='I',
type='ORDINARY'
),
'ATA'=list(
aa='I',
type='ORDINARY'
),
'ATG'=list(
aa='M',
type='START'
),
'ACT'=list(
aa='T',
type='ORDINARY'
),
'ACC'=list(
aa='T',
type='ORDINARY'
),
'ACA'=list(
aa='T',
type='ORDINARY'
),
'ACG'=list(
aa='T',
type='ORDINARY'
),
'AAT'=list(
aa='N',
type='ORDINARY'
),
'AAC'=list(
aa='N',
type='ORDINARY'
),
'AAA'=list(
aa='K',
type='ORDINARY'
),
'AAG'=list(
aa='K',
type='ORDINARY'
),
'AGT'=list(
aa='S',
type='ORDINARY'
),
'AGC'=list(
aa='S',
type='ORDINARY'
),
'AGA'=list(
aa='R',
type='ORDINARY'
),
'AGG'=list(
aa='R',
type='ORDINARY'
),
'GTT'=list(
aa='V',
type='ORDINARY'
),
'GTC'=list(
aa='V',
type='ORDINARY'
),
'GTA'=list(
aa='V',
type='ORDINARY'
),
'GTG'=list(
aa='V',
type='ORDINARY'
),
'GCT'=list(
aa='A',
type='ORDINARY'
),
'GCC'=list(
aa='A',
type='ORDINARY'
),
'GCA'=list(
aa='A',
type='ORDINARY'
),
'GCG'=list(
aa='A',
type='ORDINARY'
),
'GAT'=list(
aa='D',
type='ORDINARY'
),
'GAC'=list(
aa='D',
type='ORDINARY'
),
'GAA'=list(
aa='E',
type='ORDINARY'
),
'GAG'=list(
aa='E',
type='ORDINARY'
),
'GGT'=list(
aa='G',
type='ORDINARY'
),
'GGC'=list(
aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
'16'=list(
'name'='Chlorophycean Mitochondrial',
'trans'=list(
'TTT'=list(
aa='F',
type='ORDINARY'
),
'TTC'=list(
aa='F',
type='ORDINARY'
),
'TTA'=list(
aa='L',
type='ORDINARY'
),
'TTG'=list(
aa='L',
type='ORDINARY'
),
'TCT'=list(
aa='S',
type='ORDINARY'
),
'TCC'=list(
aa='S',
type='ORDINARY'
),
'TCA'=list(
aa='S',
type='ORDINARY'
),
'TCG'=list(
aa='S',
type='ORDINARY'
),
'TAT'=list(
aa='Y',
type='ORDINARY'
),
'TAC'=list(
aa='Y',
type='ORDINARY'
),
'TAA'=list(
aa='*',
type='STOP'
),
'TAG'=list(
aa='L',
type='ORDINARY'
),
'TGT'=list(
aa='C',
type='ORDINARY'
),
'TGC'=list(
aa='C',
type='ORDINARY'
),
'TGA'=list(
aa='*',
type='STOP'
),
'TGG'=list(
aa='W',
type='ORDINARY'
),
'CTT'=list(
aa='L',
type='ORDINARY'
),
'CTC'=list(
aa='L',
type='ORDINARY'
),
'CTA'=list(
aa='L',
type='ORDINARY'
),
'CTG'=list(
aa='L',
type='ORDINARY'
),
'CCT'=list(
aa='P',
type='ORDINARY'
),
'CCC'=list(
aa='P',
type='ORDINARY'
),
'CCA'=list(
aa='P',
type='ORDINARY'
),
'CCG'=list(
aa='P',
type='ORDINARY'
),
'CAT'=list(
aa='H',
type='ORDINARY'
),
'CAC'=list(
aa='H',
type='ORDINARY'
),
'CAA'=list(
aa='Q',
type='ORDINARY'
),
'CAG'=list(
aa='Q',
type='ORDINARY'
),
'CGT'=list(
aa='R',
type='ORDINARY'
),
'CGC'=list(
aa='R',
type='ORDINARY'
),
'CGA'=list(
aa='R',
type='ORDINARY'
),
'CGG'=list(
aa='R',
type='ORDINARY'
),
'ATT'=list(
aa='I',
type='ORDINARY'
),
'ATC'=list(
aa='I',
type='ORDINARY'
),
'ATA'=list(
aa='I',
type='ORDINARY'
),
'ATG'=list(
aa='M',
type='START'
),
'ACT'=list(
aa='T',
type='ORDINARY'
),
'ACC'=list(
aa='T',
type='ORDINARY'
),
'ACA'=list(
aa='T',
type='ORDINARY'
),
'ACG'=list(
aa='T',
type='ORDINARY'
),
'AAT'=list(
aa='N',
type='ORDINARY'
),
'AAC'=list(
aa='N',
type='ORDINARY'
),
'AAA'=list(
aa='K',
type='ORDINARY'
),
'AAG'=list(
aa='K',
type='ORDINARY'
),
'AGT'=list(
aa='S',
type='ORDINARY'
),
'AGC'=list(
aa='S',
type='ORDINARY'
),
'AGA'=list(
aa='R',
type='ORDINARY'
),
'AGG'=list(
aa='R',
type='ORDINARY'
),
'GTT'=list(
aa='V',
type='ORDINARY'
),
'GTC'=list(
aa='V',
type='ORDINARY'
),
'GTA'=list(
aa='V',
type='ORDINARY'
),
'GTG'=list(
aa='V',
type='ORDINARY'
),
'GCT'=list(
aa='A',
type='ORDINARY'
),
'GCC'=list(
aa='A',
type='ORDINARY'
),
'GCA'=list(
aa='A',
type='ORDINARY'
),
'GCG'=list(
aa='A',
type='ORDINARY'
),
'GAT'=list(
aa='D',
type='ORDINARY'
),
'GAC'=list(
aa='D',
type='ORDINARY'
),
'GAA'=list(
aa='E',
type='ORDINARY'
),
'GAG'=list(
aa='E',
type='ORDINARY'
),
'GGT'=list(
aa='G',
type='ORDINARY'
),
'GGC'=list(
aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
'21'=list(
'name'='Trematode Mitochondrial',
'trans'=list(
'TTT'=list(
aa='F',
type='ORDINARY'
),
'TTC'=list(
aa='F',
type='ORDINARY'
),
'TTA'=list(
aa='L',
type='ORDINARY'
),
'TTG'=list(
aa='L',
type='ORDINARY'
),
'TCT'=list(
aa='S',
type='ORDINARY'
),
'TCC'=list(
aa='S',
type='ORDINARY'
),
'TCA'=list(
aa='S',
type='ORDINARY'
),
'TCG'=list(
aa='S',
type='ORDINARY'
),
'TAT'=list(
aa='Y',
type='ORDINARY'
),
'TAC'=list(
aa='Y',
type='ORDINARY'
),
'TAA'=list(
aa='*',
type='STOP'
),
'TAG'=list(
aa='*',
type='STOP'
),
'TGT'=list(
aa='C',
type='ORDINARY'
),
'TGC'=list(
aa='C',
type='ORDINARY'
),
'TGA'=list(
aa='W',
type='ORDINARY'
),
'TGG'=list(
aa='W',
type='ORDINARY'
),
'CTT'=list(
aa='L',
type='ORDINARY'
),
'CTC'=list(
aa='L',
type='ORDINARY'
),
'CTA'=list(
aa='L',
type='ORDINARY'
),
'CTG'=list(
aa='L',
type='ORDINARY'
),
'CCT'=list(
aa='P',
type='ORDINARY'
),
'CCC'=list(
aa='P',
type='ORDINARY'
),
'CCA'=list(
aa='P',
type='ORDINARY'
),
'CCG'=list(
aa='P',
type='ORDINARY'
),
'CAT'=list(
aa='H',
type='ORDINARY'
),
'CAC'=list(
aa='H',
type='ORDINARY'
),
'CAA'=list(
aa='Q',
type='ORDINARY'
),
'CAG'=list(
aa='Q',
type='ORDINARY'
),
'CGT'=list(
aa='R',
type='ORDINARY'
),
'CGC'=list(
aa='R',
type='ORDINARY'
),
'CGA'=list(
aa='R',
type='ORDINARY'
),
'CGG'=list(
aa='R',
type='ORDINARY'
),
'ATT'=list(
aa='I',
type='ORDINARY'
),
'ATC'=list(
aa='I',
type='ORDINARY'
),
'ATA'=list(
aa='M',
type='ORDINARY'
),
'ATG'=list(
aa='M',
type='START'
),
'ACT'=list(
aa='T',
type='ORDINARY'
),
'ACC'=list(
aa='T',
type='ORDINARY'
),
'ACA'=list(
aa='T',
type='ORDINARY'
),
'ACG'=list(
aa='T',
type='ORDINARY'
),
'AAT'=list(
aa='N',
type='ORDINARY'
),
'AAC'=list(
aa='N',
type='ORDINARY'
),
'AAA'=list(
aa='N',
type='ORDINARY'
),
'AAG'=list(
aa='K',
type='ORDINARY'
),
'AGT'=list(
aa='S',
type='ORDINARY'
),
'AGC'=list(
aa='S',
type='ORDINARY'
),
'AGA'=list(
aa='S',
type='ORDINARY'
),
'AGG'=list(
aa='S',
type='ORDINARY'
),
'GTT'=list(
aa='V',
type='ORDINARY'
),
'GTC'=list(
aa='V',
type='ORDINARY'
),
'GTA'=list(
aa='V',
type='ORDINARY'
),
'GTG'=list(
aa='V',
type='START'
),
'GCT'=list(
aa='A',
type='ORDINARY'
),
'GCC'=list(
aa='A',
type='ORDINARY'
),
'GCA'=list(
aa='A',
type='ORDINARY'
),
'GCG'=list(
aa='A',
type='ORDINARY'
),
'GAT'=list(
aa='D',
type='ORDINARY'
),
'GAC'=list(
aa='D',
type='ORDINARY'
),
'GAA'=list(
aa='E',
type='ORDINARY'
),
'GAG'=list(
aa='E',
type='ORDINARY'
),
'GGT'=list(
aa='G',
type='ORDINARY'
),
'GGC'=list(
aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
'22'=list(
'name'='Scenedesmus obliquus Mitochondrial',
'trans'=list(
'TTT'=list(
aa='F',
type='ORDINARY'
),
'TTC'=list(
aa='F',
type='ORDINARY'
),
'TTA'=list(
aa='L',
type='ORDINARY'
),
'TTG'=list(
aa='L',
type='ORDINARY'
),
'TCT'=list(
aa='S',
type='ORDINARY'
),
'TCC'=list(
aa='S',
type='ORDINARY'
),
'TCA'=list(
aa='*',
type='STOP'
),
'TCG'=list(
aa='S',
type='ORDINARY'
),
'TAT'=list(
aa='Y',
type='ORDINARY'
),
'TAC'=list(
aa='Y',
type='ORDINARY'
),
'TAA'=list(
aa='*',
type='STOP'
),
'TAG'=list(
aa='L',
type='ORDINARY'
),
'TGT'=list(
aa='C',
type='ORDINARY'
),
'TGC'=list(
aa='C',
type='ORDINARY'
),
'TGA'=list(
aa='*',
type='STOP'
),
'TGG'=list(
aa='W',
type='ORDINARY'
),
'CTT'=list(
aa='L',
type='ORDINARY'
),
'CTC'=list(
aa='L',
type='ORDINARY'
),
'CTA'=list(
aa='L',
type='ORDINARY'
),
'CTG'=list(
aa='L',
type='ORDINARY'
),
'CCT'=list(
aa='P',
type='ORDINARY'
),
'CCC'=list(
aa='P',
type='ORDINARY'
),
'CCA'=list(
aa='P',
type='ORDINARY'
),
'CCG'=list(
aa='P',
type='ORDINARY'
),
'CAT'=list(
aa='H',
type='ORDINARY'
),
'CAC'=list(
aa='H',
type='ORDINARY'
),
'CAA'=list(
aa='Q',
type='ORDINARY'
),
'CAG'=list(
aa='Q',
type='ORDINARY'
),
'CGT'=list(
aa='R',
type='ORDINARY'
),
'CGC'=list(
aa='R',
type='ORDINARY'
),
'CGA'=list(
aa='R',
type='ORDINARY'
),
'CGG'=list(
aa='R',
type='ORDINARY'
),
'ATT'=list(
aa='I',
type='ORDINARY'
),
'ATC'=list(
aa='I',
type='ORDINARY'
),
'ATA'=list(
aa='I',
type='ORDINARY'
),
'ATG'=list(
aa='M',
type='START'
),
'ACT'=list(
aa='T',
type='ORDINARY'
),
'ACC'=list(
aa='T',
type='ORDINARY'
),
'ACA'=list(
aa='T',
type='ORDINARY'
),
'ACG'=list(
aa='T',
type='ORDINARY'
),
'AAT'=list(
aa='N',
type='ORDINARY'
),
'AAC'=list(
aa='N',
type='ORDINARY'
),
'AAA'=list(
aa='K',
type='ORDINARY'
),
'AAG'=list(
aa='K',
type='ORDINARY'
),
'AGT'=list(
aa='S',
type='ORDINARY'
),
'AGC'=list(
aa='S',
type='ORDINARY'
),
'AGA'=list(
aa='R',
type='ORDINARY'
),
'AGG'=list(
aa='R',
type='ORDINARY'
),
'GTT'=list(
aa='V',
type='ORDINARY'
),
'GTC'=list(
aa='V',
type='ORDINARY'
),
'GTA'=list(
aa='V',
type='ORDINARY'
),
'GTG'=list(
aa='V',
type='ORDINARY'
),
'GCT'=list(
aa='A',
type='ORDINARY'
),
'GCC'=list(
aa='A',
type='ORDINARY'
),
'GCA'=list(
aa='A',
type='ORDINARY'
),
'GCG'=list(
aa='A',
type='ORDINARY'
),
'GAT'=list(
aa='D',
type='ORDINARY'
),
'GAC'=list(
aa='D',
type='ORDINARY'
),
'GAA'=list(
aa='E',
type='ORDINARY'
),
'GAG'=list(
aa='E',
type='ORDINARY'
),
'GGT'=list(
aa='G',
type='ORDINARY'
),
'GGC'=list(
aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
'23'=list(
'name'='Thraustochytrium Mitochondrial',
'trans'=list(
'TTT'=list(
aa='F',
type='ORDINARY'
),
'TTC'=list(
aa='F',
type='ORDINARY'
),
'TTA'=list(
aa='*',
type='STOP'
),
'TTG'=list(
aa='L',
type='ORDINARY'
),
'TCT'=list(
aa='S',
type='ORDINARY'
),
'TCC'=list(
aa='S',
type='ORDINARY'
),
'TCA'=list(
aa='S',
type='ORDINARY'
),
'TCG'=list(
aa='S',
type='ORDINARY'
),
'TAT'=list(
aa='Y',
type='ORDINARY'
),
'TAC'=list(
aa='Y',
type='ORDINARY'
),
'TAA'=list(
aa='*',
type='STOP'
),
'TAG'=list(
aa='*',
type='STOP'
),
'TGT'=list(
aa='C',
type='ORDINARY'
),
'TGC'=list(
aa='C',
type='ORDINARY'
),
'TGA'=list(
aa='*',
type='STOP'
),
'TGG'=list(
aa='W',
type='ORDINARY'
),
'CTT'=list(
aa='L',
type='ORDINARY'
),
'CTC'=list(
aa='L',
type='ORDINARY'
),
'CTA'=list(
aa='L',
type='ORDINARY'
),
'CTG'=list(
aa='L',
type='ORDINARY'
),
'CCT'=list(
aa='P',
type='ORDINARY'
),
'CCC'=list(
aa='P',
type='ORDINARY'
),
'CCA'=list(
aa='P',
type='ORDINARY'
),
'CCG'=list(
aa='P',
type='ORDINARY'
),
'CAT'=list(
aa='H',
type='ORDINARY'
),
'CAC'=list(
aa='H',
type='ORDINARY'
),
'CAA'=list(
aa='Q',
type='ORDINARY'
),
'CAG'=list(
aa='Q',
type='ORDINARY'
),
'CGT'=list(
aa='R',
type='ORDINARY'
),
'CGC'=list(
aa='R',
type='ORDINARY'
),
'CGA'=list(
aa='R',
type='ORDINARY'
),
'CGG'=list(
aa='R',
type='ORDINARY'
),
'ATT'=list(
aa='I',
type='START'
),
'ATC'=list(
aa='I',
type='ORDINARY'
),
'ATA'=list(
aa='I',
type='ORDINARY'
),
'ATG'=list(
aa='M',
type='START'
),
'ACT'=list(
aa='T',
type='ORDINARY'
),
'ACC'=list(
aa='T',
type='ORDINARY'
),
'ACA'=list(
aa='T',
type='ORDINARY'
),
'ACG'=list(
aa='T',
type='ORDINARY'
),
'AAT'=list(
aa='N',
type='ORDINARY'
),
'AAC'=list(
aa='N',
type='ORDINARY'
),
'AAA'=list(
aa='K',
type='ORDINARY'
),
'AAG'=list(
aa='K',
type='ORDINARY'
),
'AGT'=list(
aa='S',
type='ORDINARY'
),
'AGC'=list(
aa='S',
type='ORDINARY'
),
'AGA'=list(
aa='R',
type='ORDINARY'
),
'AGG'=list(
aa='R',
type='ORDINARY'
),
'GTT'=list(
aa='V',
type='ORDINARY'
),
'GTC'=list(
aa='V',
type='ORDINARY'
),
'GTA'=list(
aa='V',
type='ORDINARY'
),
'GTG'=list(
aa='V',
type='START'
),
'GCT'=list(
aa='A',
type='ORDINARY'
),
'GCC'=list(
aa='A',
type='ORDINARY'
),
'GCA'=list(
aa='A',
type='ORDINARY'
),
'GCG'=list(
aa='A',
type='ORDINARY'
),
'GAT'=list(
aa='D',
type='ORDINARY'
),
'GAC'=list(
aa='D',
type='ORDINARY'
),
'GAA'=list(
aa='E',
type='ORDINARY'
),
'GAG'=list(
aa='E',
type='ORDINARY'
),
'GGT'=list(
aa='G',
type='ORDINARY'
),
'GGC'=list(
aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
)
);
# end of genetic code tables #
table.id<-as.character(table.id);
# Figure out the symbols set by excluding stop codons:
symbols<-character();
for (codon in names(CODON.TABLES[[table.id]]$trans)) {
if(CODON.TABLES[[table.id]]$trans[[codon]]$type != "STOP") {
symbols<-c(symbols,codon);
}
}
this<-Alphabet(
type=CODON.TABLES[[table.id]]$name,
symbols=symbols
);
this<-extend(this,
"CodonAlphabet",
.table.id=table.id,
.trans.table=CODON.TABLES[[table.id]]$trans,
.is.codon.alphabet=TRUE
);
return(this);
},
enforceRCC=TRUE
);
##
## Method: checkConsistency
##
###########################################################################/**
#
# @RdocMethod checkConsistency
#
# @title "Check object consistency"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{this}{An object.}
# \item{...}{Not used.}
# }
#
#
# \value{
# Returns an invisible TRUE if no inconsistencies found in the object, throws
# an error otherwise.
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"checkConsistency",
class="CodonAlphabet",
function(
this,
...
){
wp<-this$writeProtected;
if (wp) {
this$writeProtected<-FALSE;
}
may.fail<-function(this) {
if(!is.character(this$.table.id) | (length(this$.table.id) != 1) ) {
throw(".table.id inconsistency!\n");
}
if(!is.list(this$.trans.table)){
throw("Translation table is not a list!\n");
}
for (tmp in this$.trans.table){
if (length(intersect(names(tmp),c("aa","type"))) != 2){
throw("Translation table contains invalid entries!\n");
}
}
}
tryCatch(may.fail(this),finally=this$writeProtected<-wp);
NextMethod();
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: getTableId
##
###########################################################################/**
#
# @RdocMethod getTableId
#
# @title "Get the genetic code id"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{this}{A CodonAlphabet object.}
# \item{...}{Not used.}
# }
#
# \value{
# A numeric vector of length one.
# }
#
# \examples{
# # create CodonAlphabet object
# a<-CodonAlphabet()
# # get genetic code id
# getTableId(a)
# # get genetic code id via virtual field
# a$tableId
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"getTableId",
class="CodonAlphabet",
function(
this,
...
){
this$.table.id;
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: setTableId
##
###########################################################################/**
#
# @RdocMethod setTableId
#
# @title "Forbidden action: setting the genetic code id"
#
# \description{
# @get "title".
# Use the \code{table.id} constructor argument to set the genetic code.
# }
#
# @synopsis
#
# \arguments{
# \item{this}{An object.}
# \item{value}{Not used.}
# \item{...}{Not used.}
# }
#
# \value{
# Throws an error.
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"setTableId",
class="CodonAlphabet",
function(
this,
value,
...
){
virtualAssignmentForbidden(this);
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: translateCodon
##
###########################################################################/**
#
# @RdocMethod translateCodon
#
# @title "Translate a codon"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{this}{A CodonAlphabet object.}
# \item{codon}{The codon to be translated.}
# \item{...}{Not used.}
# }
#
# \value{
# A character vector containing an amino acid IUPAC code.
# }
#
# \examples{
# # create a CodonAlphabet object
# a<-CodonAlphabet()
# # translate a codon
# translateCodon(a,"AGG")
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"translateCodon",
class="CodonAlphabet",
function(
this,
codon,
...
){
if(!exists(x="PSIM_FAST")){
if(missing(codon)){
throw("No codon given!\n");
}
else if (!is.character(codon) | (length(codon) != 1)){
throw("The codon argument must be a character vector of size 1!\n");
}
else if (length(intersect(names(this$.trans.table),codon)) != 1){
throw("Codon not in translation table!\n");
}
else if (this$.trans.table[[codon]]$type == "STOP"){
return("*");
}
else {
return(this$.trans.table[[codon]]$aa);
}
} else {
return(this$.trans.table[[codon]]$aa);
}
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: isStopCodon
##
###########################################################################/**
#
# @RdocMethod isStopCodon
#
# @title "Check if a codon is a stop codon"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{this}{A CodonAlphabet object.}
# \item{codon}{The codon to be checked.}
# \item{...}{Not used.}
# }
#
# \value{
# TRUE or FALSE.
# }
#
# \examples{
# # create a CodonAlphabet object
# a<-CodonAlphabet()
# # check some codons
# isStopCodon(a,"ATG")
# isStopCodon(a,"TGA")
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"isStopCodon",
class="CodonAlphabet",
function(
this,
codon,
...
){
if(!exists(x="PSIM_FAST")){
if(missing(codon)){
throw("No codon given!\n");
}
else if (!is.character(codon) | (length(codon) != 1)){
throw("The codon argument must be a character vector of size 1!\n");
}
else if (length(intersect(names(this$.trans.table),codon)) != 1){
throw("Codon not in translation table!\n");
}
}
if (this$.trans.table[[codon]]$type == "STOP"){
return(TRUE);
}
else {
return(FALSE);
}
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: isStartCodon
##
###########################################################################/**
#
# @RdocMethod isStartCodon
#
# @title "Check if a codon is a start codon"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{this}{A CodonAlphabet object.}
# \item{codon}{The codon to be checked.}
# \item{...}{Not used.}
# }
#
# \value{
# TRUE or FALSE.
# }
#
# \examples{
# # create a CodonAlphabet object
# a<-CodonAlphabet()
# # check some codons
# isStartCodon(a,"ATG")
# isStartCodon(a,"TGA")
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"isStartCodon",
class="CodonAlphabet",
function(
this,
codon,
...
){
if(!exists(x="PSIM_FAST")){
if(missing(codon)){
throw("No codon given!\n");
}
else if (!is.character(codon) | (length(codon) != 1)){
throw("The codon argument must be a character vector of size 1!\n");
}
else if (length(intersect(names(this$.trans.table),codon)) != 1){
throw("Codon not in translation table!\n");
}
}
if (this$.trans.table[[codon]]$type == "START"){
return(TRUE);
}
else {
return(FALSE);
}
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: areSynonymous
##
###########################################################################/**
#
# @RdocMethod areSynonymous
#
# @title "Check whether two codons are synonymous"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{this}{A CodonAlphabet object.}
# \item{codons}{A vector containing two codons.}
# \item{...}{Not used.}
# }
#
# \value{
# TRUE or FALSE.
# }
#
# \examples{
# # create a CodonAlphabet object
# a<-CodonAlphabet()
# areSynonymous(a,c("TCC","TCT"))
# areSynonymous(a,c("TCC","CCT"))
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"areSynonymous",
class="CodonAlphabet",
function(
this,
codons,
...
){
if(!exists(x="PSIM_FAST")){
if(missing(codons)){
throw("No codons given!\n");
}
else if (!is.character(codons) | (length(codons) != 2)){
throw("The codons argument must be a character vector of size 2!\n");
}
}
if (translateCodon(this,codons[1]) == translateCodon(this,codons[2])){
return(TRUE);
}
else {
return(FALSE);
}
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: .codonDiff
##
setMethodS3(
".codonDiff",
class="CodonAlphabet",
function(
this,
codons,
...
){
if(!exists(x="PSIM_FAST")){
if(missing(codons)){
throw("No codons given!\n");
}
else if (!is.character(codons) | (length(codons) != 2)){
throw("The codons argument must be a character vector of size 2!\n");
}
else if (length(intersect(names(this$.trans.table),codons[1])) != 1){
throw("Codon 1 is not in translation table!\n");
}
else if (length(intersect(names(this$.trans.table),codons[2])) != 1){
throw("Codon 2 is not in translation table!\n");
}
}
purines<-c("A","G");
pyrimidines<-c("C","T");
res<-character();
codon1<-strsplit(codons[1],"",fixed=TRUE)[[1]];
codon2<-strsplit(codons[2],"",fixed=TRUE)[[1]];
for(i in c(1,2,3)){
if(codon1[i] == codon2[i]) {
res[i]<-0;
}
else if ( length(intersect(purines,c(codon1[i],codon2[i]))) == 2 | length(intersect(pyrimidines,c(codon1[i],codon2[i]))) == 2 ){
res[i]<-"TI";
} else {
res[i]<-"TV";
}
}
return(res);
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: summary
##
###########################################################################/**
#
# @RdocMethod summary
#
# @title "Summarize the properties of an object"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{object}{An object}
# \item{...}{Not used.}
# }
#
# \value{
# Returns a PSRootSummary object.
# }
#
# \examples{
#
# # create an object
# a<-CodonAlphabet()
# # get a summary
# summary(a)
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"summary",
class="CodonAlphabet",
function(
object,
...
){
NextMethod();
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: getTransTable
##
###########################################################################/**
#
# @RdocMethod getTransTable
#
# @title "Get the list storing the genetic code table"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{this}{A CodonAlphabet object.}
# \item{...}{Not used.}
# }
#
# \value{
# A list.
# }
#
# \examples{
# # create object
# a<-CodonAlphabet()
# # get genetic code table
# getTransTable(a)
# # get genetic code table via virtual field
# a$transTable
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"getTransTable",
class="CodonAlphabet",
function(
this,
...
){
this$.trans.table
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: setTransTable
##
###########################################################################/**
#
# @RdocMethod setTransTable
#
# @title "Forbidden action: setting the genetic code table for a CodonAlphabet object"
#
# \description{
# @get "title".
# Use the \code{table.id} constructor argument to set the genetic code.
# }
#
# @synopsis
#
# \arguments{
# \item{this}{An object.}
# \item{value}{Not used.}
# \item{...}{Not used.}
# }
#
# \value{
# Throws an error.
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"setTransTable",
class="CodonAlphabet",
function(
this,
value,
...
){
virtualAssignmentForbidden(this);
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: is.CodonAlphabet
##
###########################################################################/**
#
# @RdocDefault is.CodonAlphabet
#
# @title "Check if an object inherits from CodonAlphabet"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{this}{An object.}
# \item{...}{Not used.}
#
# }
#
# \value{
# TRUE of FALSE.
# }
#
# \examples{
# # create some objects
# a<-CodonAlphabet()
# p<-Process()
# # check if they inherit from CodonAlphabet
# is.CodonAlphabet(a)
# is.CodonAlphabet(p)
# }
#
# @author
#
#*/###########################################################################
setMethodS3(
"is.CodonAlphabet",
class="default",
function(
this,
...
){
if(!is.PSRoot(this)) {return(FALSE)}
else if(!is.null(this$.is.codon.alphabet)){return(TRUE)}
else if ( inherits(this, "CodonAlphabet")) {
this$.is.codon.alphabet<-TRUE;
return(TRUE);
} else {
return(FALSE)
}
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
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##
## Copyright 2009 Botond Sipos
## See the package description for licensing information.
##
##
## CodonAlphabet
##
##########################################################################/**
#
# @RdocClass CodonAlphabet
#
# @title "The CodonAlphabet class"
#
# \description{
# This class implements codon alphabets and handles the translation of codons
# to their corresponding amino acids. Stop codons are excluded from the symbol set,
# thus the symbol set depends on the genetic code table.
# The genetic code table can be specified through the \code{table.id} constructor parameter.
#
# The available genetic code tables:
# \preformatted{
# 1 Standard
# 2 Vertebrate Mitochondrial
# 3 Yeast Mitochondrial
# 4 Mold, Protozoan, and CoelenterateMitochondrial and Mycoplasma/Spiroplasma
# 5 Invertebrate Mitochondrial
# 6 Ciliate, Dasycladacean and Hexamita Nuclear
# 9 Echinoderm Mitochondrial
# 10 Euplotid Nuclear
# 11 Bacterial
# 12 Alternative Yeast Nuclear
# 13 Ascidian Mitochondrial
# 14 Flatworm Mitochondrial
# 15 Blepharisma Nuclear
# 16 Chlorophycean Mitochondrial
# 21 Trematode Mitochondrial
# 22 Scenedesmus obliquus Mitochondrial
# 23 Thraustochytrium Mitochondrial
# }
#
# @classhierarchy
# }
#
# @synopsis
#
# \arguments{
# \item{table.id}{The identifier of the genetic code table.}
# \item{...}{Not used.}
# }
#
# \section{Fields and Methods}{
# @allmethods
# }
#
# \examples{
# # create a CodonAlphabet object
# a<-CodonAlphabet(table.id=2)
# # get object summary
# summary(a)
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setConstructorS3(
"CodonAlphabet",
function(table.id=1,...){
# Genetic code tables, ripped from BioPerl. #
CODON.TABLES<-list(
'1'=list(
'name'='Standard',
'trans'=list(
'TTT'=list(
aa='F',
type='ORDINARY'
),
'TTC'=list(
aa='F',
type='ORDINARY'
),
'TTA'=list(
aa='L',
type='ORDINARY'
),
'TTG'=list(
aa='L',
type='START'
),
'TCT'=list(
aa='S',
type='ORDINARY'
),
'TCC'=list(
aa='S',
type='ORDINARY'
),
'TCA'=list(
aa='S',
type='ORDINARY'
),
'TCG'=list(
aa='S',
type='ORDINARY'
),
'TAT'=list(
aa='Y',
type='ORDINARY'
),
'TAC'=list(
aa='Y',
type='ORDINARY'
),
'TAA'=list(
aa='*',
type='STOP'
),
'TAG'=list(
aa='*',
type='STOP'
),
'TGT'=list(
aa='C',
type='ORDINARY'
),
'TGC'=list(
aa='C',
type='ORDINARY'
),
'TGA'=list(
aa='*',
type='STOP'
),
'TGG'=list(
aa='W',
type='ORDINARY'
),
'CTT'=list(
aa='L',
type='ORDINARY'
),
'CTC'=list(
aa='L',
type='ORDINARY'
),
'CTA'=list(
aa='L',
type='ORDINARY'
),
'CTG'=list(
aa='L',
type='START'
),
'CCT'=list(
aa='P',
type='ORDINARY'
),
'CCC'=list(
aa='P',
type='ORDINARY'
),
'CCA'=list(
aa='P',
type='ORDINARY'
),
'CCG'=list(
aa='P',
type='ORDINARY'
),
'CAT'=list(
aa='H',
type='ORDINARY'
),
'CAC'=list(
aa='H',
type='ORDINARY'
),
'CAA'=list(
aa='Q',
type='ORDINARY'
),
'CAG'=list(
aa='Q',
type='ORDINARY'
),
'CGT'=list(
aa='R',
type='ORDINARY'
),
'CGC'=list(
aa='R',
type='ORDINARY'
),
'CGA'=list(
aa='R',
type='ORDINARY'
),
'CGG'=list(
aa='R',
type='ORDINARY'
),
'ATT'=list(
aa='I',
type='ORDINARY'
),
'ATC'=list(
aa='I',
type='ORDINARY'
),
'ATA'=list(
aa='I',
type='ORDINARY'
),
'ATG'=list(
aa='M',
type='START'
),
'ACT'=list(
aa='T',
type='ORDINARY'
),
'ACC'=list(
aa='T',
type='ORDINARY'
),
'ACA'=list(
aa='T',
type='ORDINARY'
),
'ACG'=list(
aa='T',
type='ORDINARY'
),
'AAT'=list(
aa='N',
type='ORDINARY'
),
'AAC'=list(
aa='N',
type='ORDINARY'
),
'AAA'=list(
aa='K',
type='ORDINARY'
),
'AAG'=list(
aa='K',
type='ORDINARY'
),
'AGT'=list(
aa='S',
type='ORDINARY'
),
'AGC'=list(
aa='S',
type='ORDINARY'
),
'AGA'=list(
aa='R',
type='ORDINARY'
),
'AGG'=list(
aa='R',
type='ORDINARY'
),
'GTT'=list(
aa='V',
type='ORDINARY'
),
'GTC'=list(
aa='V',
type='ORDINARY'
),
'GTA'=list(
aa='V',
type='ORDINARY'
),
'GTG'=list(
aa='V',
type='ORDINARY'
),
'GCT'=list(
aa='A',
type='ORDINARY'
),
'GCC'=list(
aa='A',
type='ORDINARY'
),
'GCA'=list(
aa='A',
type='ORDINARY'
),
'GCG'=list(
aa='A',
type='ORDINARY'
),
'GAT'=list(
aa='D',
type='ORDINARY'
),
'GAC'=list(
aa='D',
type='ORDINARY'
),
'GAA'=list(
aa='E',
type='ORDINARY'
),
'GAG'=list(
aa='E',
type='ORDINARY'
),
'GGT'=list(
aa='G',
type='ORDINARY'
),
'GGC'=list(
aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
'2'=list(
'name'='Vertebrate Mitochondrial',
'trans'=list(
'TTT'=list(
aa='F',
type='ORDINARY'
),
'TTC'=list(
aa='F',
type='ORDINARY'
),
'TTA'=list(
aa='L',
type='ORDINARY'
),
'TTG'=list(
aa='L',
type='ORDINARY'
),
'TCT'=list(
aa='S',
type='ORDINARY'
),
'TCC'=list(
aa='S',
type='ORDINARY'
),
'TCA'=list(
aa='S',
type='ORDINARY'
),
'TCG'=list(
aa='S',
type='ORDINARY'
),
'TAT'=list(
aa='Y',
type='ORDINARY'
),
'TAC'=list(
aa='Y',
type='ORDINARY'
),
'TAA'=list(
aa='*',
type='STOP'
),
'TAG'=list(
aa='*',
type='STOP'
),
'TGT'=list(
aa='C',
type='ORDINARY'
),
'TGC'=list(
aa='C',
type='ORDINARY'
),
'TGA'=list(
aa='W',
type='ORDINARY'
),
'TGG'=list(
aa='W',
type='ORDINARY'
),
'CTT'=list(
aa='L',
type='ORDINARY'
),
'CTC'=list(
aa='L',
type='ORDINARY'
),
'CTA'=list(
aa='L',
type='ORDINARY'
),
'CTG'=list(
aa='L',
type='ORDINARY'
),
'CCT'=list(
aa='P',
type='ORDINARY'
),
'CCC'=list(
aa='P',
type='ORDINARY'
),
'CCA'=list(
aa='P',
type='ORDINARY'
),
'CCG'=list(
aa='P',
type='ORDINARY'
),
'CAT'=list(
aa='H',
type='ORDINARY'
),
'CAC'=list(
aa='H',
type='ORDINARY'
),
'CAA'=list(
aa='Q',
type='ORDINARY'
),
'CAG'=list(
aa='Q',
type='ORDINARY'
),
'CGT'=list(
aa='R',
type='ORDINARY'
),
'CGC'=list(
aa='R',
type='ORDINARY'
),
'CGA'=list(
aa='R',
type='ORDINARY'
),
'CGG'=list(
aa='R',
type='ORDINARY'
),
'ATT'=list(
aa='I',
type='START'
),
'ATC'=list(
aa='I',
type='START'
),
'ATA'=list(
aa='M',
type='START'
),
'ATG'=list(
aa='M',
type='START'
),
'ACT'=list(
aa='T',
type='ORDINARY'
),
'ACC'=list(
aa='T',
type='ORDINARY'
),
'ACA'=list(
aa='T',
type='ORDINARY'
),
'ACG'=list(
aa='T',
type='ORDINARY'
),
'AAT'=list(
aa='N',
type='ORDINARY'
),
'AAC'=list(
aa='N',
type='ORDINARY'
),
'AAA'=list(
aa='K',
type='ORDINARY'
),
'AAG'=list(
aa='K',
type='ORDINARY'
),
'AGT'=list(
aa='S',
type='ORDINARY'
),
'AGC'=list(
aa='S',
type='ORDINARY'
),
'AGA'=list(
aa='*',
type='STOP'
),
'AGG'=list(
aa='*',
type='STOP'
),
'GTT'=list(
aa='V',
type='ORDINARY'
),
'GTC'=list(
aa='V',
type='ORDINARY'
),
'GTA'=list(
aa='V',
type='ORDINARY'
),
'GTG'=list(
aa='V',
type='START'
),
'GCT'=list(
aa='A',
type='ORDINARY'
),
'GCC'=list(
aa='A',
type='ORDINARY'
),
'GCA'=list(
aa='A',
type='ORDINARY'
),
'GCG'=list(
aa='A',
type='ORDINARY'
),
'GAT'=list(
aa='D',
type='ORDINARY'
),
'GAC'=list(
aa='D',
type='ORDINARY'
),
'GAA'=list(
aa='E',
type='ORDINARY'
),
'GAG'=list(
aa='E',
type='ORDINARY'
),
'GGT'=list(
aa='G',
type='ORDINARY'
),
'GGC'=list(
aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
'3'=list(
'name'='Yeast Mitochondrial',
'trans'=list(
'TTT'=list(
aa='F',
type='ORDINARY'
),
'TTC'=list(
aa='F',
type='ORDINARY'
),
'TTA'=list(
aa='L',
type='ORDINARY'
),
'TTG'=list(
aa='L',
type='ORDINARY'
),
'TCT'=list(
aa='S',
type='ORDINARY'
),
'TCC'=list(
aa='S',
type='ORDINARY'
),
'TCA'=list(
aa='S',
type='ORDINARY'
),
'TCG'=list(
aa='S',
type='ORDINARY'
),
'TAT'=list(
aa='Y',
type='ORDINARY'
),
'TAC'=list(
aa='Y',
type='ORDINARY'
),
'TAA'=list(
aa='*',
type='STOP'
),
'TAG'=list(
aa='*',
type='STOP'
),
'TGT'=list(
aa='C',
type='ORDINARY'
),
'TGC'=list(
aa='C',
type='ORDINARY'
),
'TGA'=list(
aa='W',
type='ORDINARY'
),
'TGG'=list(
aa='W',
type='ORDINARY'
),
'CTT'=list(
aa='T',
type='ORDINARY'
),
'CTC'=list(
aa='T',
type='ORDINARY'
),
'CTA'=list(
aa='T',
type='ORDINARY'
),
'CTG'=list(
aa='T',
type='ORDINARY'
),
'CCT'=list(
aa='P',
type='ORDINARY'
),
'CCC'=list(
aa='P',
type='ORDINARY'
),
'CCA'=list(
aa='P',
type='ORDINARY'
),
'CCG'=list(
aa='P',
type='ORDINARY'
),
'CAT'=list(
aa='H',
type='ORDINARY'
),
'CAC'=list(
aa='H',
type='ORDINARY'
),
'CAA'=list(
aa='Q',
type='ORDINARY'
),
'CAG'=list(
aa='Q',
type='ORDINARY'
),
'CGT'=list(
aa='R',
type='ORDINARY'
),
'CGC'=list(
aa='R',
type='ORDINARY'
),
'CGA'=list(
aa='R',
type='ORDINARY'
),
'CGG'=list(
aa='R',
type='ORDINARY'
),
'ATT'=list(
aa='I',
type='ORDINARY'
),
'ATC'=list(
aa='I',
type='ORDINARY'
),
'ATA'=list(
aa='M',
type='START'
),
'ATG'=list(
aa='M',
type='START'
),
'ACT'=list(
aa='T',
type='ORDINARY'
),
'ACC'=list(
aa='T',
type='ORDINARY'
),
'ACA'=list(
aa='T',
type='ORDINARY'
),
'ACG'=list(
aa='T',
type='ORDINARY'
),
'AAT'=list(
aa='N',
type='ORDINARY'
),
'AAC'=list(
aa='N',
type='ORDINARY'
),
'AAA'=list(
aa='K',
type='ORDINARY'
),
'AAG'=list(
aa='K',
type='ORDINARY'
),
'AGT'=list(
aa='S',
type='ORDINARY'
),
'AGC'=list(
aa='S',
type='ORDINARY'
),
'AGA'=list(
aa='R',
type='ORDINARY'
),
'AGG'=list(
aa='R',
type='ORDINARY'
),
'GTT'=list(
aa='V',
type='ORDINARY'
),
'GTC'=list(
aa='V',
type='ORDINARY'
),
'GTA'=list(
aa='V',
type='ORDINARY'
),
'GTG'=list(
aa='V',
type='ORDINARY'
),
'GCT'=list(
aa='A',
type='ORDINARY'
),
'GCC'=list(
aa='A',
type='ORDINARY'
),
'GCA'=list(
aa='A',
type='ORDINARY'
),
'GCG'=list(
aa='A',
type='ORDINARY'
),
'GAT'=list(
aa='D',
type='ORDINARY'
),
'GAC'=list(
aa='D',
type='ORDINARY'
),
'GAA'=list(
aa='E',
type='ORDINARY'
),
'GAG'=list(
aa='E',
type='ORDINARY'
),
'GGT'=list(
aa='G',
type='ORDINARY'
),
'GGC'=list(
aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
'4'=list(
'name'='Mold, Protozoan, and CoelenterateMitochondrial and Mycoplasma/Spiroplasma',
'trans'=list(
'TTT'=list(
aa='F',
type='ORDINARY'
),
'TTC'=list(
aa='F',
type='ORDINARY'
),
'TTA'=list(
aa='L',
type='START'
),
'TTG'=list(
aa='L',
type='START'
),
'TCT'=list(
aa='S',
type='ORDINARY'
),
'TCC'=list(
aa='S',
type='ORDINARY'
),
'TCA'=list(
aa='S',
type='ORDINARY'
),
'TCG'=list(
aa='S',
type='ORDINARY'
),
'TAT'=list(
aa='Y',
type='ORDINARY'
),
'TAC'=list(
aa='Y',
type='ORDINARY'
),
'TAA'=list(
aa='*',
type='STOP'
),
'TAG'=list(
aa='*',
type='STOP'
),
'TGT'=list(
aa='C',
type='ORDINARY'
),
'TGC'=list(
aa='C',
type='ORDINARY'
),
'TGA'=list(
aa='W',
type='ORDINARY'
),
'TGG'=list(
aa='W',
type='ORDINARY'
),
'CTT'=list(
aa='L',
type='ORDINARY'
),
'CTC'=list(
aa='L',
type='ORDINARY'
),
'CTA'=list(
aa='L',
type='ORDINARY'
),
'CTG'=list(
aa='L',
type='START'
),
'CCT'=list(
aa='P',
type='ORDINARY'
),
'CCC'=list(
aa='P',
type='ORDINARY'
),
'CCA'=list(
aa='P',
type='ORDINARY'
),
'CCG'=list(
aa='P',
type='ORDINARY'
),
'CAT'=list(
aa='H',
type='ORDINARY'
),
'CAC'=list(
aa='H',
type='ORDINARY'
),
'CAA'=list(
aa='Q',
type='ORDINARY'
),
'CAG'=list(
aa='Q',
type='ORDINARY'
),
'CGT'=list(
aa='R',
type='ORDINARY'
),
'CGC'=list(
aa='R',
type='ORDINARY'
),
'CGA'=list(
aa='R',
type='ORDINARY'
),
'CGG'=list(
aa='R',
type='ORDINARY'
),
'ATT'=list(
aa='I',
type='START'
),
'ATC'=list(
aa='I',
type='START'
),
'ATA'=list(
aa='I',
type='START'
),
'ATG'=list(
aa='M',
type='START'
),
'ACT'=list(
aa='T',
type='ORDINARY'
),
'ACC'=list(
aa='T',
type='ORDINARY'
),
'ACA'=list(
aa='T',
type='ORDINARY'
),
'ACG'=list(
aa='T',
type='ORDINARY'
),
'AAT'=list(
aa='N',
type='ORDINARY'
),
'AAC'=list(
aa='N',
type='ORDINARY'
),
'AAA'=list(
aa='K',
type='ORDINARY'
),
'AAG'=list(
aa='K',
type='ORDINARY'
),
'AGT'=list(
aa='S',
type='ORDINARY'
),
'AGC'=list(
aa='S',
type='ORDINARY'
),
'AGA'=list(
aa='R',
type='ORDINARY'
),
'AGG'=list(
aa='R',
type='ORDINARY'
),
'GTT'=list(
aa='V',
type='ORDINARY'
),
'GTC'=list(
aa='V',
type='ORDINARY'
),
'GTA'=list(
aa='V',
type='ORDINARY'
),
'GTG'=list(
aa='V',
type='START'
),
'GCT'=list(
aa='A',
type='ORDINARY'
),
'GCC'=list(
aa='A',
type='ORDINARY'
),
'GCA'=list(
aa='A',
type='ORDINARY'
),
'GCG'=list(
aa='A',
type='ORDINARY'
),
'GAT'=list(
aa='D',
type='ORDINARY'
),
'GAC'=list(
aa='D',
type='ORDINARY'
),
'GAA'=list(
aa='E',
type='ORDINARY'
),
'GAG'=list(
aa='E',
type='ORDINARY'
),
'GGT'=list(
aa='G',
type='ORDINARY'
),
'GGC'=list(
aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
'5'=list(
'name'='Invertebrate Mitochondrial',
'trans'=list(
'TTT'=list(
aa='F',
type='ORDINARY'
),
'TTC'=list(
aa='F',
type='ORDINARY'
),
'TTA'=list(
aa='L',
type='ORDINARY'
),
'TTG'=list(
aa='L',
type='START'
),
'TCT'=list(
aa='S',
type='ORDINARY'
),
'TCC'=list(
aa='S',
type='ORDINARY'
),
'TCA'=list(
aa='S',
type='ORDINARY'
),
'TCG'=list(
aa='S',
type='ORDINARY'
),
'TAT'=list(
aa='Y',
type='ORDINARY'
),
'TAC'=list(
aa='Y',
type='ORDINARY'
),
'TAA'=list(
aa='*',
type='STOP'
),
'TAG'=list(
aa='*',
type='STOP'
),
'TGT'=list(
aa='C',
type='ORDINARY'
),
'TGC'=list(
aa='C',
type='ORDINARY'
),
'TGA'=list(
aa='W',
type='ORDINARY'
),
'TGG'=list(
aa='W',
type='ORDINARY'
),
'CTT'=list(
aa='L',
type='ORDINARY'
),
'CTC'=list(
aa='L',
type='ORDINARY'
),
'CTA'=list(
aa='L',
type='ORDINARY'
),
'CTG'=list(
aa='L',
type='ORDINARY'
),
'CCT'=list(
aa='P',
type='ORDINARY'
),
'CCC'=list(
aa='P',
type='ORDINARY'
),
'CCA'=list(
aa='P',
type='ORDINARY'
),
'CCG'=list(
aa='P',
type='ORDINARY'
),
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aa='H',
type='ORDINARY'
),
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aa='H',
type='ORDINARY'
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aa='Q',
type='ORDINARY'
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aa='Q',
type='ORDINARY'
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aa='R',
type='ORDINARY'
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aa='R',
type='ORDINARY'
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aa='R',
type='ORDINARY'
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aa='R',
type='ORDINARY'
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aa='I',
type='START'
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aa='I',
type='START'
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aa='M',
type='START'
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aa='M',
type='START'
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aa='T',
type='ORDINARY'
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'ACC'=list(
aa='T',
type='ORDINARY'
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'ACA'=list(
aa='T',
type='ORDINARY'
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aa='T',
type='ORDINARY'
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aa='N',
type='ORDINARY'
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'AAC'=list(
aa='N',
type='ORDINARY'
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aa='K',
type='ORDINARY'
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'AAG'=list(
aa='K',
type='ORDINARY'
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'AGT'=list(
aa='S',
type='ORDINARY'
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'AGC'=list(
aa='S',
type='ORDINARY'
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'AGA'=list(
aa='S',
type='ORDINARY'
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'AGG'=list(
aa='S',
type='ORDINARY'
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type='ORDINARY'
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'GTC'=list(
aa='V',
type='ORDINARY'
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'GTA'=list(
aa='V',
type='ORDINARY'
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'GTG'=list(
aa='V',
type='START'
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aa='A',
type='ORDINARY'
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'GCC'=list(
aa='A',
type='ORDINARY'
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'GCA'=list(
aa='A',
type='ORDINARY'
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'GCG'=list(
aa='A',
type='ORDINARY'
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aa='D',
type='ORDINARY'
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'GAC'=list(
aa='D',
type='ORDINARY'
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aa='E',
type='ORDINARY'
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'GAG'=list(
aa='E',
type='ORDINARY'
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'GGT'=list(
aa='G',
type='ORDINARY'
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'GGC'=list(
aa='G',
type='ORDINARY'
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'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
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aa='F',
type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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aa='S',
type='ORDINARY'
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aa='S',
type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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aa='Y',
type='ORDINARY'
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type='ORDINARY'
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aa='Q',
type='ORDINARY'
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type='ORDINARY'
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aa='C',
type='ORDINARY'
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aa='*',
type='STOP'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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aa='L',
type='ORDINARY'
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type='ORDINARY'
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aa='P',
type='ORDINARY'
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'CCA'=list(
aa='P',
type='ORDINARY'
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aa='P',
type='ORDINARY'
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aa='H',
type='ORDINARY'
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'CAC'=list(
aa='H',
type='ORDINARY'
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aa='Q',
type='ORDINARY'
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aa='Q',
type='ORDINARY'
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aa='R',
type='ORDINARY'
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aa='R',
type='ORDINARY'
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aa='R',
type='ORDINARY'
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aa='R',
type='ORDINARY'
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aa='I',
type='ORDINARY'
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aa='I',
type='ORDINARY'
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aa='I',
type='ORDINARY'
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aa='M',
type='START'
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aa='T',
type='ORDINARY'
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aa='T',
type='ORDINARY'
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'ACA'=list(
aa='T',
type='ORDINARY'
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aa='T',
type='ORDINARY'
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aa='N',
type='ORDINARY'
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'AAC'=list(
aa='N',
type='ORDINARY'
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aa='K',
type='ORDINARY'
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aa='K',
type='ORDINARY'
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aa='S',
type='ORDINARY'
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aa='S',
type='ORDINARY'
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aa='R',
type='ORDINARY'
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'AGG'=list(
aa='R',
type='ORDINARY'
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aa='V',
type='ORDINARY'
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'GTC'=list(
aa='V',
type='ORDINARY'
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aa='V',
type='ORDINARY'
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aa='V',
type='ORDINARY'
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type='ORDINARY'
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'GCC'=list(
aa='A',
type='ORDINARY'
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aa='A',
type='ORDINARY'
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aa='A',
type='ORDINARY'
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aa='D',
type='ORDINARY'
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aa='D',
type='ORDINARY'
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aa='E',
type='ORDINARY'
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'GAG'=list(
aa='E',
type='ORDINARY'
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aa='G',
type='ORDINARY'
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aa='G',
type='ORDINARY'
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'GGA'=list(
aa='G',
type='ORDINARY'
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'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
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aa='F',
type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='STOP'
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type='STOP'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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'CCA'=list(
aa='P',
type='ORDINARY'
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aa='P',
type='ORDINARY'
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aa='H',
type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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aa='R',
type='ORDINARY'
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type='ORDINARY'
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aa='R',
type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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aa='I',
type='ORDINARY'
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aa='M',
type='START'
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aa='T',
type='ORDINARY'
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type='ORDINARY'
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aa='T',
type='ORDINARY'
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aa='T',
type='ORDINARY'
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aa='N',
type='ORDINARY'
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aa='N',
type='ORDINARY'
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'AAA'=list(
aa='N',
type='ORDINARY'
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aa='K',
type='ORDINARY'
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aa='S',
type='ORDINARY'
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type='ORDINARY'
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aa='S',
type='ORDINARY'
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aa='S',
type='ORDINARY'
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type='ORDINARY'
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'GTC'=list(
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type='ORDINARY'
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type='ORDINARY'
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aa='V',
type='ORDINARY'
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type='ORDINARY'
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aa='A',
type='ORDINARY'
),
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aa='A',
type='ORDINARY'
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aa='A',
type='ORDINARY'
),
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aa='D',
type='ORDINARY'
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aa='D',
type='ORDINARY'
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type='ORDINARY'
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aa='E',
type='ORDINARY'
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aa='G',
type='ORDINARY'
),
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aa='G',
type='ORDINARY'
),
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aa='G',
type='ORDINARY'
),
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aa='G',
type='ORDINARY'
)
)
),
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aa='F',
type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='STOP'
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type='STOP'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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type='ORDINARY'
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aa='R',
type='ORDINARY'
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aa='I',
type='ORDINARY'
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type='ORDINARY'
),
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type='ORDINARY'
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type='START'
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aa='T',
type='ORDINARY'
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aa='T',
type='ORDINARY'
),
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type='ORDINARY'
),
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aa='T',
type='ORDINARY'
),
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aa='N',
type='ORDINARY'
),
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aa='N',
type='ORDINARY'
),
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type='ORDINARY'
),
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aa='K',
type='ORDINARY'
),
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type='ORDINARY'
),
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aa='S',
type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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aa='V',
type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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aa='D',
type='ORDINARY'
),
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type='ORDINARY'
),
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aa='E',
type='ORDINARY'
),
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aa='G',
type='ORDINARY'
),
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type='ORDINARY'
),
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aa='G',
type='ORDINARY'
),
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aa='G',
type='ORDINARY'
)
)
),
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aa='F',
type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='START'
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='STOP'
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type='STOP'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='STOP'
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type='ORDINARY'
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='START'
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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aa='P',
type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='START'
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type='START'
),
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type='START'
),
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type='START'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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aa='N',
type='ORDINARY'
),
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aa='N',
type='ORDINARY'
),
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type='ORDINARY'
),
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aa='K',
type='ORDINARY'
),
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type='ORDINARY'
),
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aa='S',
type='ORDINARY'
),
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type='ORDINARY'
),
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aa='R',
type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='START'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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aa='A',
type='ORDINARY'
),
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aa='A',
type='ORDINARY'
),
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type='ORDINARY'
),
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aa='D',
type='ORDINARY'
),
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type='ORDINARY'
),
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aa='E',
type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
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aa='F',
type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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aa='S',
type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='STOP'
),
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aa='*',
type='STOP'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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aa='*',
type='STOP'
),
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aa='W',
type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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aa='S',
type='START'
),
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aa='P',
type='ORDINARY'
),
'CCC'=list(
aa='P',
type='ORDINARY'
),
'CCA'=list(
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type='ORDINARY'
),
'CCG'=list(
aa='P',
type='ORDINARY'
),
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type='ORDINARY'
),
'CAC'=list(
aa='H',
type='ORDINARY'
),
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aa='Q',
type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
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type='ORDINARY'
),
'CGG'=list(
aa='R',
type='ORDINARY'
),
'ATT'=list(
aa='I',
type='ORDINARY'
),
'ATC'=list(
aa='I',
type='ORDINARY'
),
'ATA'=list(
aa='I',
type='ORDINARY'
),
'ATG'=list(
aa='M',
type='START'
),
'ACT'=list(
aa='T',
type='ORDINARY'
),
'ACC'=list(
aa='T',
type='ORDINARY'
),
'ACA'=list(
aa='T',
type='ORDINARY'
),
'ACG'=list(
aa='T',
type='ORDINARY'
),
'AAT'=list(
aa='N',
type='ORDINARY'
),
'AAC'=list(
aa='N',
type='ORDINARY'
),
'AAA'=list(
aa='K',
type='ORDINARY'
),
'AAG'=list(
aa='K',
type='ORDINARY'
),
'AGT'=list(
aa='S',
type='ORDINARY'
),
'AGC'=list(
aa='S',
type='ORDINARY'
),
'AGA'=list(
aa='R',
type='ORDINARY'
),
'AGG'=list(
aa='R',
type='ORDINARY'
),
'GTT'=list(
aa='V',
type='ORDINARY'
),
'GTC'=list(
aa='V',
type='ORDINARY'
),
'GTA'=list(
aa='V',
type='ORDINARY'
),
'GTG'=list(
aa='V',
type='ORDINARY'
),
'GCT'=list(
aa='A',
type='ORDINARY'
),
'GCC'=list(
aa='A',
type='ORDINARY'
),
'GCA'=list(
aa='A',
type='ORDINARY'
),
'GCG'=list(
aa='A',
type='ORDINARY'
),
'GAT'=list(
aa='D',
type='ORDINARY'
),
'GAC'=list(
aa='D',
type='ORDINARY'
),
'GAA'=list(
aa='E',
type='ORDINARY'
),
'GAG'=list(
aa='E',
type='ORDINARY'
),
'GGT'=list(
aa='G',
type='ORDINARY'
),
'GGC'=list(
aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
'13'=list(
'name'='Ascidian Mitochondrial',
'trans'=list(
'TTT'=list(
aa='F',
type='ORDINARY'
),
'TTC'=list(
aa='F',
type='ORDINARY'
),
'TTA'=list(
aa='L',
type='ORDINARY'
),
'TTG'=list(
aa='L',
type='ORDINARY'
),
'TCT'=list(
aa='S',
type='ORDINARY'
),
'TCC'=list(
aa='S',
type='ORDINARY'
),
'TCA'=list(
aa='S',
type='ORDINARY'
),
'TCG'=list(
aa='S',
type='ORDINARY'
),
'TAT'=list(
aa='Y',
type='ORDINARY'
),
'TAC'=list(
aa='Y',
type='ORDINARY'
),
'TAA'=list(
aa='*',
type='STOP'
),
'TAG'=list(
aa='*',
type='STOP'
),
'TGT'=list(
aa='C',
type='ORDINARY'
),
'TGC'=list(
aa='C',
type='ORDINARY'
),
'TGA'=list(
aa='W',
type='ORDINARY'
),
'TGG'=list(
aa='W',
type='ORDINARY'
),
'CTT'=list(
aa='L',
type='ORDINARY'
),
'CTC'=list(
aa='L',
type='ORDINARY'
),
'CTA'=list(
aa='L',
type='ORDINARY'
),
'CTG'=list(
aa='L',
type='ORDINARY'
),
'CCT'=list(
aa='P',
type='ORDINARY'
),
'CCC'=list(
aa='P',
type='ORDINARY'
),
'CCA'=list(
aa='P',
type='ORDINARY'
),
'CCG'=list(
aa='P',
type='ORDINARY'
),
'CAT'=list(
aa='H',
type='ORDINARY'
),
'CAC'=list(
aa='H',
type='ORDINARY'
),
'CAA'=list(
aa='Q',
type='ORDINARY'
),
'CAG'=list(
aa='Q',
type='ORDINARY'
),
'CGT'=list(
aa='R',
type='ORDINARY'
),
'CGC'=list(
aa='R',
type='ORDINARY'
),
'CGA'=list(
aa='R',
type='ORDINARY'
),
'CGG'=list(
aa='R',
type='ORDINARY'
),
'ATT'=list(
aa='I',
type='ORDINARY'
),
'ATC'=list(
aa='I',
type='ORDINARY'
),
'ATA'=list(
aa='M',
type='ORDINARY'
),
'ATG'=list(
aa='M',
type='START'
),
'ACT'=list(
aa='T',
type='ORDINARY'
),
'ACC'=list(
aa='T',
type='ORDINARY'
),
'ACA'=list(
aa='T',
type='ORDINARY'
),
'ACG'=list(
aa='T',
type='ORDINARY'
),
'AAT'=list(
aa='N',
type='ORDINARY'
),
'AAC'=list(
aa='N',
type='ORDINARY'
),
'AAA'=list(
aa='K',
type='ORDINARY'
),
'AAG'=list(
aa='K',
type='ORDINARY'
),
'AGT'=list(
aa='S',
type='ORDINARY'
),
'AGC'=list(
aa='S',
type='ORDINARY'
),
'AGA'=list(
aa='G',
type='ORDINARY'
),
'AGG'=list(
aa='G',
type='ORDINARY'
),
'GTT'=list(
aa='V',
type='ORDINARY'
),
'GTC'=list(
aa='V',
type='ORDINARY'
),
'GTA'=list(
aa='V',
type='ORDINARY'
),
'GTG'=list(
aa='V',
type='ORDINARY'
),
'GCT'=list(
aa='A',
type='ORDINARY'
),
'GCC'=list(
aa='A',
type='ORDINARY'
),
'GCA'=list(
aa='A',
type='ORDINARY'
),
'GCG'=list(
aa='A',
type='ORDINARY'
),
'GAT'=list(
aa='D',
type='ORDINARY'
),
'GAC'=list(
aa='D',
type='ORDINARY'
),
'GAA'=list(
aa='E',
type='ORDINARY'
),
'GAG'=list(
aa='E',
type='ORDINARY'
),
'GGT'=list(
aa='G',
type='ORDINARY'
),
'GGC'=list(
aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
'14'=list(
'name'='Flatworm Mitochondrial',
'trans'=list(
'TTT'=list(
aa='F',
type='ORDINARY'
),
'TTC'=list(
aa='F',
type='ORDINARY'
),
'TTA'=list(
aa='L',
type='ORDINARY'
),
'TTG'=list(
aa='L',
type='ORDINARY'
),
'TCT'=list(
aa='S',
type='ORDINARY'
),
'TCC'=list(
aa='S',
type='ORDINARY'
),
'TCA'=list(
aa='S',
type='ORDINARY'
),
'TCG'=list(
aa='S',
type='ORDINARY'
),
'TAT'=list(
aa='Y',
type='ORDINARY'
),
'TAC'=list(
aa='Y',
type='ORDINARY'
),
'TAA'=list(
aa='Y',
type='ORDINARY'
),
'TAG'=list(
aa='*',
type='STOP'
),
'TGT'=list(
aa='C',
type='ORDINARY'
),
'TGC'=list(
aa='C',
type='ORDINARY'
),
'TGA'=list(
aa='W',
type='ORDINARY'
),
'TGG'=list(
aa='W',
type='ORDINARY'
),
'CTT'=list(
aa='L',
type='ORDINARY'
),
'CTC'=list(
aa='L',
type='ORDINARY'
),
'CTA'=list(
aa='L',
type='ORDINARY'
),
'CTG'=list(
aa='L',
type='ORDINARY'
),
'CCT'=list(
aa='P',
type='ORDINARY'
),
'CCC'=list(
aa='P',
type='ORDINARY'
),
'CCA'=list(
aa='P',
type='ORDINARY'
),
'CCG'=list(
aa='P',
type='ORDINARY'
),
'CAT'=list(
aa='H',
type='ORDINARY'
),
'CAC'=list(
aa='H',
type='ORDINARY'
),
'CAA'=list(
aa='Q',
type='ORDINARY'
),
'CAG'=list(
aa='Q',
type='ORDINARY'
),
'CGT'=list(
aa='R',
type='ORDINARY'
),
'CGC'=list(
aa='R',
type='ORDINARY'
),
'CGA'=list(
aa='R',
type='ORDINARY'
),
'CGG'=list(
aa='R',
type='ORDINARY'
),
'ATT'=list(
aa='I',
type='ORDINARY'
),
'ATC'=list(
aa='I',
type='ORDINARY'
),
'ATA'=list(
aa='I',
type='ORDINARY'
),
'ATG'=list(
aa='M',
type='START'
),
'ACT'=list(
aa='T',
type='ORDINARY'
),
'ACC'=list(
aa='T',
type='ORDINARY'
),
'ACA'=list(
aa='T',
type='ORDINARY'
),
'ACG'=list(
aa='T',
type='ORDINARY'
),
'AAT'=list(
aa='N',
type='ORDINARY'
),
'AAC'=list(
aa='N',
type='ORDINARY'
),
'AAA'=list(
aa='N',
type='ORDINARY'
),
'AAG'=list(
aa='K',
type='ORDINARY'
),
'AGT'=list(
aa='S',
type='ORDINARY'
),
'AGC'=list(
aa='S',
type='ORDINARY'
),
'AGA'=list(
aa='S',
type='ORDINARY'
),
'AGG'=list(
aa='S',
type='ORDINARY'
),
'GTT'=list(
aa='V',
type='ORDINARY'
),
'GTC'=list(
aa='V',
type='ORDINARY'
),
'GTA'=list(
aa='V',
type='ORDINARY'
),
'GTG'=list(
aa='V',
type='ORDINARY'
),
'GCT'=list(
aa='A',
type='ORDINARY'
),
'GCC'=list(
aa='A',
type='ORDINARY'
),
'GCA'=list(
aa='A',
type='ORDINARY'
),
'GCG'=list(
aa='A',
type='ORDINARY'
),
'GAT'=list(
aa='D',
type='ORDINARY'
),
'GAC'=list(
aa='D',
type='ORDINARY'
),
'GAA'=list(
aa='E',
type='ORDINARY'
),
'GAG'=list(
aa='E',
type='ORDINARY'
),
'GGT'=list(
aa='G',
type='ORDINARY'
),
'GGC'=list(
aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
'15'=list(
'name'='Blepharisma Nuclear',
'trans'=list(
'TTT'=list(
aa='F',
type='ORDINARY'
),
'TTC'=list(
aa='F',
type='ORDINARY'
),
'TTA'=list(
aa='L',
type='ORDINARY'
),
'TTG'=list(
aa='L',
type='ORDINARY'
),
'TCT'=list(
aa='S',
type='ORDINARY'
),
'TCC'=list(
aa='S',
type='ORDINARY'
),
'TCA'=list(
aa='S',
type='ORDINARY'
),
'TCG'=list(
aa='S',
type='ORDINARY'
),
'TAT'=list(
aa='Y',
type='ORDINARY'
),
'TAC'=list(
aa='Y',
type='ORDINARY'
),
'TAA'=list(
aa='*',
type='STOP'
),
'TAG'=list(
aa='Q',
type='ORDINARY'
),
'TGT'=list(
aa='C',
type='ORDINARY'
),
'TGC'=list(
aa='C',
type='ORDINARY'
),
'TGA'=list(
aa='*',
type='STOP'
),
'TGG'=list(
aa='W',
type='ORDINARY'
),
'CTT'=list(
aa='L',
type='ORDINARY'
),
'CTC'=list(
aa='L',
type='ORDINARY'
),
'CTA'=list(
aa='L',
type='ORDINARY'
),
'CTG'=list(
aa='L',
type='ORDINARY'
),
'CCT'=list(
aa='P',
type='ORDINARY'
),
'CCC'=list(
aa='P',
type='ORDINARY'
),
'CCA'=list(
aa='P',
type='ORDINARY'
),
'CCG'=list(
aa='P',
type='ORDINARY'
),
'CAT'=list(
aa='H',
type='ORDINARY'
),
'CAC'=list(
aa='H',
type='ORDINARY'
),
'CAA'=list(
aa='Q',
type='ORDINARY'
),
'CAG'=list(
aa='Q',
type='ORDINARY'
),
'CGT'=list(
aa='R',
type='ORDINARY'
),
'CGC'=list(
aa='R',
type='ORDINARY'
),
'CGA'=list(
aa='R',
type='ORDINARY'
),
'CGG'=list(
aa='R',
type='ORDINARY'
),
'ATT'=list(
aa='I',
type='ORDINARY'
),
'ATC'=list(
aa='I',
type='ORDINARY'
),
'ATA'=list(
aa='I',
type='ORDINARY'
),
'ATG'=list(
aa='M',
type='START'
),
'ACT'=list(
aa='T',
type='ORDINARY'
),
'ACC'=list(
aa='T',
type='ORDINARY'
),
'ACA'=list(
aa='T',
type='ORDINARY'
),
'ACG'=list(
aa='T',
type='ORDINARY'
),
'AAT'=list(
aa='N',
type='ORDINARY'
),
'AAC'=list(
aa='N',
type='ORDINARY'
),
'AAA'=list(
aa='K',
type='ORDINARY'
),
'AAG'=list(
aa='K',
type='ORDINARY'
),
'AGT'=list(
aa='S',
type='ORDINARY'
),
'AGC'=list(
aa='S',
type='ORDINARY'
),
'AGA'=list(
aa='R',
type='ORDINARY'
),
'AGG'=list(
aa='R',
type='ORDINARY'
),
'GTT'=list(
aa='V',
type='ORDINARY'
),
'GTC'=list(
aa='V',
type='ORDINARY'
),
'GTA'=list(
aa='V',
type='ORDINARY'
),
'GTG'=list(
aa='V',
type='ORDINARY'
),
'GCT'=list(
aa='A',
type='ORDINARY'
),
'GCC'=list(
aa='A',
type='ORDINARY'
),
'GCA'=list(
aa='A',
type='ORDINARY'
),
'GCG'=list(
aa='A',
type='ORDINARY'
),
'GAT'=list(
aa='D',
type='ORDINARY'
),
'GAC'=list(
aa='D',
type='ORDINARY'
),
'GAA'=list(
aa='E',
type='ORDINARY'
),
'GAG'=list(
aa='E',
type='ORDINARY'
),
'GGT'=list(
aa='G',
type='ORDINARY'
),
'GGC'=list(
aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
'16'=list(
'name'='Chlorophycean Mitochondrial',
'trans'=list(
'TTT'=list(
aa='F',
type='ORDINARY'
),
'TTC'=list(
aa='F',
type='ORDINARY'
),
'TTA'=list(
aa='L',
type='ORDINARY'
),
'TTG'=list(
aa='L',
type='ORDINARY'
),
'TCT'=list(
aa='S',
type='ORDINARY'
),
'TCC'=list(
aa='S',
type='ORDINARY'
),
'TCA'=list(
aa='S',
type='ORDINARY'
),
'TCG'=list(
aa='S',
type='ORDINARY'
),
'TAT'=list(
aa='Y',
type='ORDINARY'
),
'TAC'=list(
aa='Y',
type='ORDINARY'
),
'TAA'=list(
aa='*',
type='STOP'
),
'TAG'=list(
aa='L',
type='ORDINARY'
),
'TGT'=list(
aa='C',
type='ORDINARY'
),
'TGC'=list(
aa='C',
type='ORDINARY'
),
'TGA'=list(
aa='*',
type='STOP'
),
'TGG'=list(
aa='W',
type='ORDINARY'
),
'CTT'=list(
aa='L',
type='ORDINARY'
),
'CTC'=list(
aa='L',
type='ORDINARY'
),
'CTA'=list(
aa='L',
type='ORDINARY'
),
'CTG'=list(
aa='L',
type='ORDINARY'
),
'CCT'=list(
aa='P',
type='ORDINARY'
),
'CCC'=list(
aa='P',
type='ORDINARY'
),
'CCA'=list(
aa='P',
type='ORDINARY'
),
'CCG'=list(
aa='P',
type='ORDINARY'
),
'CAT'=list(
aa='H',
type='ORDINARY'
),
'CAC'=list(
aa='H',
type='ORDINARY'
),
'CAA'=list(
aa='Q',
type='ORDINARY'
),
'CAG'=list(
aa='Q',
type='ORDINARY'
),
'CGT'=list(
aa='R',
type='ORDINARY'
),
'CGC'=list(
aa='R',
type='ORDINARY'
),
'CGA'=list(
aa='R',
type='ORDINARY'
),
'CGG'=list(
aa='R',
type='ORDINARY'
),
'ATT'=list(
aa='I',
type='ORDINARY'
),
'ATC'=list(
aa='I',
type='ORDINARY'
),
'ATA'=list(
aa='I',
type='ORDINARY'
),
'ATG'=list(
aa='M',
type='START'
),
'ACT'=list(
aa='T',
type='ORDINARY'
),
'ACC'=list(
aa='T',
type='ORDINARY'
),
'ACA'=list(
aa='T',
type='ORDINARY'
),
'ACG'=list(
aa='T',
type='ORDINARY'
),
'AAT'=list(
aa='N',
type='ORDINARY'
),
'AAC'=list(
aa='N',
type='ORDINARY'
),
'AAA'=list(
aa='K',
type='ORDINARY'
),
'AAG'=list(
aa='K',
type='ORDINARY'
),
'AGT'=list(
aa='S',
type='ORDINARY'
),
'AGC'=list(
aa='S',
type='ORDINARY'
),
'AGA'=list(
aa='R',
type='ORDINARY'
),
'AGG'=list(
aa='R',
type='ORDINARY'
),
'GTT'=list(
aa='V',
type='ORDINARY'
),
'GTC'=list(
aa='V',
type='ORDINARY'
),
'GTA'=list(
aa='V',
type='ORDINARY'
),
'GTG'=list(
aa='V',
type='ORDINARY'
),
'GCT'=list(
aa='A',
type='ORDINARY'
),
'GCC'=list(
aa='A',
type='ORDINARY'
),
'GCA'=list(
aa='A',
type='ORDINARY'
),
'GCG'=list(
aa='A',
type='ORDINARY'
),
'GAT'=list(
aa='D',
type='ORDINARY'
),
'GAC'=list(
aa='D',
type='ORDINARY'
),
'GAA'=list(
aa='E',
type='ORDINARY'
),
'GAG'=list(
aa='E',
type='ORDINARY'
),
'GGT'=list(
aa='G',
type='ORDINARY'
),
'GGC'=list(
aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
'21'=list(
'name'='Trematode Mitochondrial',
'trans'=list(
'TTT'=list(
aa='F',
type='ORDINARY'
),
'TTC'=list(
aa='F',
type='ORDINARY'
),
'TTA'=list(
aa='L',
type='ORDINARY'
),
'TTG'=list(
aa='L',
type='ORDINARY'
),
'TCT'=list(
aa='S',
type='ORDINARY'
),
'TCC'=list(
aa='S',
type='ORDINARY'
),
'TCA'=list(
aa='S',
type='ORDINARY'
),
'TCG'=list(
aa='S',
type='ORDINARY'
),
'TAT'=list(
aa='Y',
type='ORDINARY'
),
'TAC'=list(
aa='Y',
type='ORDINARY'
),
'TAA'=list(
aa='*',
type='STOP'
),
'TAG'=list(
aa='*',
type='STOP'
),
'TGT'=list(
aa='C',
type='ORDINARY'
),
'TGC'=list(
aa='C',
type='ORDINARY'
),
'TGA'=list(
aa='W',
type='ORDINARY'
),
'TGG'=list(
aa='W',
type='ORDINARY'
),
'CTT'=list(
aa='L',
type='ORDINARY'
),
'CTC'=list(
aa='L',
type='ORDINARY'
),
'CTA'=list(
aa='L',
type='ORDINARY'
),
'CTG'=list(
aa='L',
type='ORDINARY'
),
'CCT'=list(
aa='P',
type='ORDINARY'
),
'CCC'=list(
aa='P',
type='ORDINARY'
),
'CCA'=list(
aa='P',
type='ORDINARY'
),
'CCG'=list(
aa='P',
type='ORDINARY'
),
'CAT'=list(
aa='H',
type='ORDINARY'
),
'CAC'=list(
aa='H',
type='ORDINARY'
),
'CAA'=list(
aa='Q',
type='ORDINARY'
),
'CAG'=list(
aa='Q',
type='ORDINARY'
),
'CGT'=list(
aa='R',
type='ORDINARY'
),
'CGC'=list(
aa='R',
type='ORDINARY'
),
'CGA'=list(
aa='R',
type='ORDINARY'
),
'CGG'=list(
aa='R',
type='ORDINARY'
),
'ATT'=list(
aa='I',
type='ORDINARY'
),
'ATC'=list(
aa='I',
type='ORDINARY'
),
'ATA'=list(
aa='M',
type='ORDINARY'
),
'ATG'=list(
aa='M',
type='START'
),
'ACT'=list(
aa='T',
type='ORDINARY'
),
'ACC'=list(
aa='T',
type='ORDINARY'
),
'ACA'=list(
aa='T',
type='ORDINARY'
),
'ACG'=list(
aa='T',
type='ORDINARY'
),
'AAT'=list(
aa='N',
type='ORDINARY'
),
'AAC'=list(
aa='N',
type='ORDINARY'
),
'AAA'=list(
aa='N',
type='ORDINARY'
),
'AAG'=list(
aa='K',
type='ORDINARY'
),
'AGT'=list(
aa='S',
type='ORDINARY'
),
'AGC'=list(
aa='S',
type='ORDINARY'
),
'AGA'=list(
aa='S',
type='ORDINARY'
),
'AGG'=list(
aa='S',
type='ORDINARY'
),
'GTT'=list(
aa='V',
type='ORDINARY'
),
'GTC'=list(
aa='V',
type='ORDINARY'
),
'GTA'=list(
aa='V',
type='ORDINARY'
),
'GTG'=list(
aa='V',
type='START'
),
'GCT'=list(
aa='A',
type='ORDINARY'
),
'GCC'=list(
aa='A',
type='ORDINARY'
),
'GCA'=list(
aa='A',
type='ORDINARY'
),
'GCG'=list(
aa='A',
type='ORDINARY'
),
'GAT'=list(
aa='D',
type='ORDINARY'
),
'GAC'=list(
aa='D',
type='ORDINARY'
),
'GAA'=list(
aa='E',
type='ORDINARY'
),
'GAG'=list(
aa='E',
type='ORDINARY'
),
'GGT'=list(
aa='G',
type='ORDINARY'
),
'GGC'=list(
aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
'22'=list(
'name'='Scenedesmus obliquus Mitochondrial',
'trans'=list(
'TTT'=list(
aa='F',
type='ORDINARY'
),
'TTC'=list(
aa='F',
type='ORDINARY'
),
'TTA'=list(
aa='L',
type='ORDINARY'
),
'TTG'=list(
aa='L',
type='ORDINARY'
),
'TCT'=list(
aa='S',
type='ORDINARY'
),
'TCC'=list(
aa='S',
type='ORDINARY'
),
'TCA'=list(
aa='*',
type='STOP'
),
'TCG'=list(
aa='S',
type='ORDINARY'
),
'TAT'=list(
aa='Y',
type='ORDINARY'
),
'TAC'=list(
aa='Y',
type='ORDINARY'
),
'TAA'=list(
aa='*',
type='STOP'
),
'TAG'=list(
aa='L',
type='ORDINARY'
),
'TGT'=list(
aa='C',
type='ORDINARY'
),
'TGC'=list(
aa='C',
type='ORDINARY'
),
'TGA'=list(
aa='*',
type='STOP'
),
'TGG'=list(
aa='W',
type='ORDINARY'
),
'CTT'=list(
aa='L',
type='ORDINARY'
),
'CTC'=list(
aa='L',
type='ORDINARY'
),
'CTA'=list(
aa='L',
type='ORDINARY'
),
'CTG'=list(
aa='L',
type='ORDINARY'
),
'CCT'=list(
aa='P',
type='ORDINARY'
),
'CCC'=list(
aa='P',
type='ORDINARY'
),
'CCA'=list(
aa='P',
type='ORDINARY'
),
'CCG'=list(
aa='P',
type='ORDINARY'
),
'CAT'=list(
aa='H',
type='ORDINARY'
),
'CAC'=list(
aa='H',
type='ORDINARY'
),
'CAA'=list(
aa='Q',
type='ORDINARY'
),
'CAG'=list(
aa='Q',
type='ORDINARY'
),
'CGT'=list(
aa='R',
type='ORDINARY'
),
'CGC'=list(
aa='R',
type='ORDINARY'
),
'CGA'=list(
aa='R',
type='ORDINARY'
),
'CGG'=list(
aa='R',
type='ORDINARY'
),
'ATT'=list(
aa='I',
type='ORDINARY'
),
'ATC'=list(
aa='I',
type='ORDINARY'
),
'ATA'=list(
aa='I',
type='ORDINARY'
),
'ATG'=list(
aa='M',
type='START'
),
'ACT'=list(
aa='T',
type='ORDINARY'
),
'ACC'=list(
aa='T',
type='ORDINARY'
),
'ACA'=list(
aa='T',
type='ORDINARY'
),
'ACG'=list(
aa='T',
type='ORDINARY'
),
'AAT'=list(
aa='N',
type='ORDINARY'
),
'AAC'=list(
aa='N',
type='ORDINARY'
),
'AAA'=list(
aa='K',
type='ORDINARY'
),
'AAG'=list(
aa='K',
type='ORDINARY'
),
'AGT'=list(
aa='S',
type='ORDINARY'
),
'AGC'=list(
aa='S',
type='ORDINARY'
),
'AGA'=list(
aa='R',
type='ORDINARY'
),
'AGG'=list(
aa='R',
type='ORDINARY'
),
'GTT'=list(
aa='V',
type='ORDINARY'
),
'GTC'=list(
aa='V',
type='ORDINARY'
),
'GTA'=list(
aa='V',
type='ORDINARY'
),
'GTG'=list(
aa='V',
type='ORDINARY'
),
'GCT'=list(
aa='A',
type='ORDINARY'
),
'GCC'=list(
aa='A',
type='ORDINARY'
),
'GCA'=list(
aa='A',
type='ORDINARY'
),
'GCG'=list(
aa='A',
type='ORDINARY'
),
'GAT'=list(
aa='D',
type='ORDINARY'
),
'GAC'=list(
aa='D',
type='ORDINARY'
),
'GAA'=list(
aa='E',
type='ORDINARY'
),
'GAG'=list(
aa='E',
type='ORDINARY'
),
'GGT'=list(
aa='G',
type='ORDINARY'
),
'GGC'=list(
aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
),
'23'=list(
'name'='Thraustochytrium Mitochondrial',
'trans'=list(
'TTT'=list(
aa='F',
type='ORDINARY'
),
'TTC'=list(
aa='F',
type='ORDINARY'
),
'TTA'=list(
aa='*',
type='STOP'
),
'TTG'=list(
aa='L',
type='ORDINARY'
),
'TCT'=list(
aa='S',
type='ORDINARY'
),
'TCC'=list(
aa='S',
type='ORDINARY'
),
'TCA'=list(
aa='S',
type='ORDINARY'
),
'TCG'=list(
aa='S',
type='ORDINARY'
),
'TAT'=list(
aa='Y',
type='ORDINARY'
),
'TAC'=list(
aa='Y',
type='ORDINARY'
),
'TAA'=list(
aa='*',
type='STOP'
),
'TAG'=list(
aa='*',
type='STOP'
),
'TGT'=list(
aa='C',
type='ORDINARY'
),
'TGC'=list(
aa='C',
type='ORDINARY'
),
'TGA'=list(
aa='*',
type='STOP'
),
'TGG'=list(
aa='W',
type='ORDINARY'
),
'CTT'=list(
aa='L',
type='ORDINARY'
),
'CTC'=list(
aa='L',
type='ORDINARY'
),
'CTA'=list(
aa='L',
type='ORDINARY'
),
'CTG'=list(
aa='L',
type='ORDINARY'
),
'CCT'=list(
aa='P',
type='ORDINARY'
),
'CCC'=list(
aa='P',
type='ORDINARY'
),
'CCA'=list(
aa='P',
type='ORDINARY'
),
'CCG'=list(
aa='P',
type='ORDINARY'
),
'CAT'=list(
aa='H',
type='ORDINARY'
),
'CAC'=list(
aa='H',
type='ORDINARY'
),
'CAA'=list(
aa='Q',
type='ORDINARY'
),
'CAG'=list(
aa='Q',
type='ORDINARY'
),
'CGT'=list(
aa='R',
type='ORDINARY'
),
'CGC'=list(
aa='R',
type='ORDINARY'
),
'CGA'=list(
aa='R',
type='ORDINARY'
),
'CGG'=list(
aa='R',
type='ORDINARY'
),
'ATT'=list(
aa='I',
type='START'
),
'ATC'=list(
aa='I',
type='ORDINARY'
),
'ATA'=list(
aa='I',
type='ORDINARY'
),
'ATG'=list(
aa='M',
type='START'
),
'ACT'=list(
aa='T',
type='ORDINARY'
),
'ACC'=list(
aa='T',
type='ORDINARY'
),
'ACA'=list(
aa='T',
type='ORDINARY'
),
'ACG'=list(
aa='T',
type='ORDINARY'
),
'AAT'=list(
aa='N',
type='ORDINARY'
),
'AAC'=list(
aa='N',
type='ORDINARY'
),
'AAA'=list(
aa='K',
type='ORDINARY'
),
'AAG'=list(
aa='K',
type='ORDINARY'
),
'AGT'=list(
aa='S',
type='ORDINARY'
),
'AGC'=list(
aa='S',
type='ORDINARY'
),
'AGA'=list(
aa='R',
type='ORDINARY'
),
'AGG'=list(
aa='R',
type='ORDINARY'
),
'GTT'=list(
aa='V',
type='ORDINARY'
),
'GTC'=list(
aa='V',
type='ORDINARY'
),
'GTA'=list(
aa='V',
type='ORDINARY'
),
'GTG'=list(
aa='V',
type='START'
),
'GCT'=list(
aa='A',
type='ORDINARY'
),
'GCC'=list(
aa='A',
type='ORDINARY'
),
'GCA'=list(
aa='A',
type='ORDINARY'
),
'GCG'=list(
aa='A',
type='ORDINARY'
),
'GAT'=list(
aa='D',
type='ORDINARY'
),
'GAC'=list(
aa='D',
type='ORDINARY'
),
'GAA'=list(
aa='E',
type='ORDINARY'
),
'GAG'=list(
aa='E',
type='ORDINARY'
),
'GGT'=list(
aa='G',
type='ORDINARY'
),
'GGC'=list(
aa='G',
type='ORDINARY'
),
'GGA'=list(
aa='G',
type='ORDINARY'
),
'GGG'=list(
aa='G',
type='ORDINARY'
)
)
)
);
# end of genetic code tables #
table.id<-as.character(table.id);
# Figure out the symbols set by excluding stop codons:
symbols<-character();
for (codon in names(CODON.TABLES[[table.id]]$trans)) {
if(CODON.TABLES[[table.id]]$trans[[codon]]$type != "STOP") {
symbols<-c(symbols,codon);
}
}
this<-Alphabet(
type=CODON.TABLES[[table.id]]$name,
symbols=symbols
);
this<-extend(this,
"CodonAlphabet",
.table.id=table.id,
.trans.table=CODON.TABLES[[table.id]]$trans,
.is.codon.alphabet=TRUE
);
return(this);
},
enforceRCC=TRUE
);
##
## Method: checkConsistency
##
###########################################################################/**
#
# @RdocMethod checkConsistency
#
# @title "Check object consistency"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{this}{An object.}
# \item{...}{Not used.}
# }
#
#
# \value{
# Returns an invisible TRUE if no inconsistencies found in the object, throws
# an error otherwise.
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"checkConsistency",
class="CodonAlphabet",
function(
this,
...
){
wp<-this$writeProtected;
if (wp) {
this$writeProtected<-FALSE;
}
may.fail<-function(this) {
if(!is.character(this$.table.id) | (length(this$.table.id) != 1) ) {
throw(".table.id inconsistency!\n");
}
if(!is.list(this$.trans.table)){
throw("Translation table is not a list!\n");
}
for (tmp in this$.trans.table){
if (length(intersect(names(tmp),c("aa","type"))) != 2){
throw("Translation table contains invalid entries!\n");
}
}
}
tryCatch(may.fail(this),finally=this$writeProtected<-wp);
NextMethod();
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: getTableId
##
###########################################################################/**
#
# @RdocMethod getTableId
#
# @title "Get the genetic code id"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{this}{A CodonAlphabet object.}
# \item{...}{Not used.}
# }
#
# \value{
# A numeric vector of length one.
# }
#
# \examples{
# # create CodonAlphabet object
# a<-CodonAlphabet()
# # get genetic code id
# getTableId(a)
# # get genetic code id via virtual field
# a$tableId
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"getTableId",
class="CodonAlphabet",
function(
this,
...
){
this$.table.id;
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: setTableId
##
###########################################################################/**
#
# @RdocMethod setTableId
#
# @title "Forbidden action: setting the genetic code id"
#
# \description{
# @get "title".
# Use the \code{table.id} constructor argument to set the genetic code.
# }
#
# @synopsis
#
# \arguments{
# \item{this}{An object.}
# \item{value}{Not used.}
# \item{...}{Not used.}
# }
#
# \value{
# Throws an error.
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"setTableId",
class="CodonAlphabet",
function(
this,
value,
...
){
virtualAssignmentForbidden(this);
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: translateCodon
##
###########################################################################/**
#
# @RdocMethod translateCodon
#
# @title "Translate a codon"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{this}{A CodonAlphabet object.}
# \item{codon}{The codon to be translated.}
# \item{...}{Not used.}
# }
#
# \value{
# A character vector containing an amino acid IUPAC code.
# }
#
# \examples{
# # create a CodonAlphabet object
# a<-CodonAlphabet()
# # translate a codon
# translateCodon(a,"AGG")
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"translateCodon",
class="CodonAlphabet",
function(
this,
codon,
...
){
if(!exists(x="PSIM_FAST")){
if(missing(codon)){
throw("No codon given!\n");
}
else if (!is.character(codon) | (length(codon) != 1)){
throw("The codon argument must be a character vector of size 1!\n");
}
else if (length(intersect(names(this$.trans.table),codon)) != 1){
throw("Codon not in translation table!\n");
}
else if (this$.trans.table[[codon]]$type == "STOP"){
return("*");
}
else {
return(this$.trans.table[[codon]]$aa);
}
} else {
return(this$.trans.table[[codon]]$aa);
}
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: isStopCodon
##
###########################################################################/**
#
# @RdocMethod isStopCodon
#
# @title "Check if a codon is a stop codon"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{this}{A CodonAlphabet object.}
# \item{codon}{The codon to be checked.}
# \item{...}{Not used.}
# }
#
# \value{
# TRUE or FALSE.
# }
#
# \examples{
# # create a CodonAlphabet object
# a<-CodonAlphabet()
# # check some codons
# isStopCodon(a,"ATG")
# isStopCodon(a,"TGA")
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"isStopCodon",
class="CodonAlphabet",
function(
this,
codon,
...
){
if(!exists(x="PSIM_FAST")){
if(missing(codon)){
throw("No codon given!\n");
}
else if (!is.character(codon) | (length(codon) != 1)){
throw("The codon argument must be a character vector of size 1!\n");
}
else if (length(intersect(names(this$.trans.table),codon)) != 1){
throw("Codon not in translation table!\n");
}
}
if (this$.trans.table[[codon]]$type == "STOP"){
return(TRUE);
}
else {
return(FALSE);
}
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: isStartCodon
##
###########################################################################/**
#
# @RdocMethod isStartCodon
#
# @title "Check if a codon is a start codon"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{this}{A CodonAlphabet object.}
# \item{codon}{The codon to be checked.}
# \item{...}{Not used.}
# }
#
# \value{
# TRUE or FALSE.
# }
#
# \examples{
# # create a CodonAlphabet object
# a<-CodonAlphabet()
# # check some codons
# isStartCodon(a,"ATG")
# isStartCodon(a,"TGA")
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"isStartCodon",
class="CodonAlphabet",
function(
this,
codon,
...
){
if(!exists(x="PSIM_FAST")){
if(missing(codon)){
throw("No codon given!\n");
}
else if (!is.character(codon) | (length(codon) != 1)){
throw("The codon argument must be a character vector of size 1!\n");
}
else if (length(intersect(names(this$.trans.table),codon)) != 1){
throw("Codon not in translation table!\n");
}
}
if (this$.trans.table[[codon]]$type == "START"){
return(TRUE);
}
else {
return(FALSE);
}
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: areSynonymous
##
###########################################################################/**
#
# @RdocMethod areSynonymous
#
# @title "Check whether two codons are synonymous"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{this}{A CodonAlphabet object.}
# \item{codons}{A vector containing two codons.}
# \item{...}{Not used.}
# }
#
# \value{
# TRUE or FALSE.
# }
#
# \examples{
# # create a CodonAlphabet object
# a<-CodonAlphabet()
# areSynonymous(a,c("TCC","TCT"))
# areSynonymous(a,c("TCC","CCT"))
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"areSynonymous",
class="CodonAlphabet",
function(
this,
codons,
...
){
if(!exists(x="PSIM_FAST")){
if(missing(codons)){
throw("No codons given!\n");
}
else if (!is.character(codons) | (length(codons) != 2)){
throw("The codons argument must be a character vector of size 2!\n");
}
}
if (translateCodon(this,codons[1]) == translateCodon(this,codons[2])){
return(TRUE);
}
else {
return(FALSE);
}
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: .codonDiff
##
setMethodS3(
".codonDiff",
class="CodonAlphabet",
function(
this,
codons,
...
){
if(!exists(x="PSIM_FAST")){
if(missing(codons)){
throw("No codons given!\n");
}
else if (!is.character(codons) | (length(codons) != 2)){
throw("The codons argument must be a character vector of size 2!\n");
}
else if (length(intersect(names(this$.trans.table),codons[1])) != 1){
throw("Codon 1 is not in translation table!\n");
}
else if (length(intersect(names(this$.trans.table),codons[2])) != 1){
throw("Codon 2 is not in translation table!\n");
}
}
purines<-c("A","G");
pyrimidines<-c("C","T");
res<-character();
codon1<-strsplit(codons[1],"",fixed=TRUE)[[1]];
codon2<-strsplit(codons[2],"",fixed=TRUE)[[1]];
for(i in c(1,2,3)){
if(codon1[i] == codon2[i]) {
res[i]<-0;
}
else if ( length(intersect(purines,c(codon1[i],codon2[i]))) == 2 | length(intersect(pyrimidines,c(codon1[i],codon2[i]))) == 2 ){
res[i]<-"TI";
} else {
res[i]<-"TV";
}
}
return(res);
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: summary
##
###########################################################################/**
#
# @RdocMethod summary
#
# @title "Summarize the properties of an object"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{object}{An object}
# \item{...}{Not used.}
# }
#
# \value{
# Returns a PSRootSummary object.
# }
#
# \examples{
#
# # create an object
# a<-CodonAlphabet()
# # get a summary
# summary(a)
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"summary",
class="CodonAlphabet",
function(
object,
...
){
NextMethod();
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: getTransTable
##
###########################################################################/**
#
# @RdocMethod getTransTable
#
# @title "Get the list storing the genetic code table"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{this}{A CodonAlphabet object.}
# \item{...}{Not used.}
# }
#
# \value{
# A list.
# }
#
# \examples{
# # create object
# a<-CodonAlphabet()
# # get genetic code table
# getTransTable(a)
# # get genetic code table via virtual field
# a$transTable
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"getTransTable",
class="CodonAlphabet",
function(
this,
...
){
this$.trans.table
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: setTransTable
##
###########################################################################/**
#
# @RdocMethod setTransTable
#
# @title "Forbidden action: setting the genetic code table for a CodonAlphabet object"
#
# \description{
# @get "title".
# Use the \code{table.id} constructor argument to set the genetic code.
# }
#
# @synopsis
#
# \arguments{
# \item{this}{An object.}
# \item{value}{Not used.}
# \item{...}{Not used.}
# }
#
# \value{
# Throws an error.
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"setTransTable",
class="CodonAlphabet",
function(
this,
value,
...
){
virtualAssignmentForbidden(this);
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: is.CodonAlphabet
##
###########################################################################/**
#
# @RdocDefault is.CodonAlphabet
#
# @title "Check if an object inherits from CodonAlphabet"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{this}{An object.}
# \item{...}{Not used.}
#
# }
#
# \value{
# TRUE of FALSE.
# }
#
# \examples{
# # create some objects
# a<-CodonAlphabet()
# p<-Process()
# # check if they inherit from CodonAlphabet
# is.CodonAlphabet(a)
# is.CodonAlphabet(p)
# }
#
# @author
#
#*/###########################################################################
setMethodS3(
"is.CodonAlphabet",
class="default",
function(
this,
...
){
if(!is.PSRoot(this)) {return(FALSE)}
else if(!is.null(this$.is.codon.alphabet)){return(TRUE)}
else if ( inherits(this, "CodonAlphabet")) {
this$.is.codon.alphabet<-TRUE;
return(TRUE);
} else {
return(FALSE)
}
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
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