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Alphabet.R
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Alphabet.R
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##
## Copyright 2009 Botond Sipos
## See the package description for licensing information.
##
##########################################################################/**
#
# @RdocClass Alphabet
#
# @title "The Alphabet class"
#
# \description{
#
# Class representing an alphabet (a set of symbols).
# @classhierarchy
#
# }
#
# @synopsis
#
# \arguments{
# \item{symbols}{A character vector containing the symbols for the alphabet. All elements must have the
# same length and no duplicates are allowed. No element of the vector may contain the dash symbol, which is reserved for gaps.}
# \item{type}{An identifier for the Alphabet object.}
# \item{...}{Not used.}
# }
#
# \section{Fields and Methods}{
# @allmethods
# }
#
# \examples{
# # create an alphabet object
# a<-Alphabet(type="Binary",symbols=c("0","1"));
# # print summary
# summary(a);
# # change the identifier
# a$type<-"Nucleotide";
# # change the symbol set
# a$symbols<-c("A","T","G","C");
# # print summary again
# summary(a);
# # clone the alphabet object
# b<-clone(a);
# # test the equality of the symbol sets
# a == b;
# }
#
# @author
#
#
# \seealso{
# Site Process Event BinaryAlphabet NucleotideAlphabet AminoAcidAlphabet
# }
#
#*/###########################################################################
setConstructorS3(
"Alphabet",
function(
symbols=NA,
type="Generic",
...
){
symbol_length<-NA;
if(!missing(symbols)){
symbols<-as.character(symbols);
symbol_length<-.checkSymbolLengths(symbols);
if(!exists(x="PSIM_FAST")){
.checkSymbolDuplicates(symbols);
}
}
size<-NA;
if(!is.na(symbol_length)){
size<-length(symbols);
}
extend(PSRoot(), "Alphabet",
.symbols=symbols,
.symbolLength=symbol_length,
.size=size,
.type=type,
.write.protected=FALSE,
.is.alphabet=TRUE
);
},
###
enforceRCC=TRUE
);
##
## Method: .checkSymbolLengths
##
setMethodS3(
".checkSymbolLengths",
class="character",
function(
this,
...
){
if(length(this) == 0 ){return(0)}
symbol_lengths<-stringLengthVector(this);
if(length(unique(symbol_lengths)) != 1) {
throw("The symbols must have the same length!");
} else {
symbol_lengths[[1]];
}
},
private=TRUE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: .checkSymbolDuplicates
##
setMethodS3(
".checkSymbolDuplicates",
class="character",
function(
this,
...
){
# Check for the gap character "-", and die if present:
if(length(grep("^-+$",this)) != 0){
throw("The symbol sets cannot contain the character \"-\" as that is reserved as a gap symbol!\n");
}
if(length(this) != length(unique(this))){
throw("The alphabet must not contain duplicated symbols!");
} else {
return(invisible(TRUE));
}
},
###
private=TRUE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: .checkConsistency
##
setMethodS3(
".checkConsistency",
class="character",
function(
this,
...
){
.checkSymbolLengths(this);
.checkSymbolDuplicates(this);
},
private=TRUE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: checkConsistency
##
###########################################################################/**
#
# @RdocMethod checkConsistency
#
# @title "Check object consistency"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{this}{An object.}
# \item{...}{Not used.}
# }
#
# \value{
# Returns an invisible TRUE if no inconsistencies found, throws an error otherwise.
# }
#
# \examples{
# # create an alphabet object
# a<-Alphabet(symbols=c(0,1));
# # check consistency
# print(checkConsistency(a));
# # mess up with the internals
# a$.symbols[1]<-"BAD";
# # NOT run: cosistency check now will throw an error
# \dontrun{ print(checkConsistency(a)); }
#
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"checkConsistency",
class="Alphabet",
function(
this,
...
){
if(is.null(this$.symbols)) {
throw("Alphabet symbols is NULL!\n");
}
else if(is.null(this$.size)) {
throw("Alphabet size is NULL!\n");
}
else if(is.null(this$.symbolLength)) {
throw("Alphabet symbol length is NULL!\n");
}
else if(is.null(this$.type)) {
throw("Alphabet type is NULL!\n");
}
# Disable write protection for a while.
wp<-this$writeProtected;
if(wp) {
this$writeProtected<-FALSE;
}
may.fail<-function(this){
this$symbols<-this$symbols;
if( length(this$symbols) != this$size) {
throw("Alphabet object inconsistent! Length mismatch!\n");
}
}
tryCatch(may.fail(this), finally=this$writeProtected<-wp);
.checkConsistency(this$.symbols);
},
###
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: ==
##
###########################################################################/**
#
# @RdocMethod ==
# \alias{!=.Alphabet}
# @title "Check if two alaphabet objects have the same symbol set"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{e1}{An Alphabet object.}
# \item{e2}{An Alphabet object.}
# \item{...}{Not used.}
# }
#
# \value{
# TRUE or FALSE
# }
#
# \examples{
#
# # create an alpahabet object
# a<-Alphabet(symbols=c(0,1));
# # clone object
# b<-clone(a)
# # compare the two objects
# print(a == b)
# # modify symbol set in b
# b$symbols<-c("AT","GC");
# print(a == b)
#
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"==",
class="Alphabet",
function(
e1,
e2,
...
){
# First check by reference:
if ( equals(e1,e2) ) {return(TRUE)}
# Check if both objects inherit from Alphabet:
if(!exists(x="PSIM_FAST")){
if (!length(intersect(intersect(class(e1),class(e2)),c("Alphabet")))){
throw("Alphabet object compared to something else!");
}
}
# Check ANY flag:
if(!is.null(e1$.any.flag) | !is.null(e2$.any.flag)) { return(TRUE) }
# then check by value:
setequal(e1$.symbols,e2$.symbols);
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: !=
##
setMethodS3(
"!=",
class="Alphabet",
function(
e1,
e2,
...
){
!'=='(e1,e2);
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: getSymbols
##
###########################################################################/**
#
# @RdocMethod getSymbols
#
# @title "Get the symbol set from an Alphabet object"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{this}{An Alphabet object.}
# \item{...}{Not used.}
# }
#
# \value{
# A character vector containing the symbol set of the Alphabet object.
# }
#
# \examples{
#
# # create a new alphabet object
# a<-Alphabet(symbols=c("AC","GT"));
# # get the symbols
# getSymbols(a)
# # get the symbols by using the virtual field
# a$symbols
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"getSymbols",
class="Alphabet",
function(
this,
...
){
as.character(this$.symbols);
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: setSymbols
##
###########################################################################/**
#
# @RdocMethod setSymbols
#
# @title "Specify a new symbol set for an Alphabet object"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{this}{An Alphabet object.}
# \item{set}{The vector containing the new symbols set, automatically converted
# into a character vector.}
# \item{...}{Not used.}
# }
#
# \value{
# The new symbol set as a character vector.
# }
#
# \examples{
#
# # create a new alphabet object
# a<-Alphabet()
# a
# # specify a new symbol set
# setSymbols(a,c(0,1))
# a
# # the same, but now use the virtual field
# a$symbols<-c("A","T","G","C")
# a
#
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"setSymbols",
class="Alphabet",
function(
this,
set, # the new symbol set
...
){
if (is.null(set)) {
throw("Cannot set NULL as symbols!\n");
}
.checkWriteProtection(this);
set<-as.character(set);
if(!exists(x="PSIM_FAST")){
.checkSymbolDuplicates(set)
}
this$.symbolLength<-.checkSymbolLengths(set);
this$.size<-length(set);
this$.symbols<-set;
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: getSymbolLength
##
###########################################################################/**
#
# @RdocMethod getSymbolLength
#
# @title "Get the length of the symbols in a given alphabet object"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{this}{An Alphabet object.}
# \item{...}{Not used.}
# }
#
# \value{
# A numeric vector of length one.
# }
#
# \examples{
#
# # create an alphabet object
# a<-Alphabet(symbols=c("AAA","AAC"));
# # get symbol length
# getSymbolLength(a);
# # get symbol length via virtual field
# a$symbolLength
#
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"getSymbolLength",
class="Alphabet",
function(
this,
...
){
this$.symbolLength;
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: setSymbolLength
##
###########################################################################/**
#
# @RdocMethod setSymbolLength
#
# @title "Forbidden action: setting the symbol length for an Alphabet object"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{this}{An Alphabet object.}
# \item{value}{Not used.}
# \item{...}{Not used.}
# }
#
# \value{
# Throws an error.
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"setSymbolLength",
class="Alphabet",
function(
this,
value,
...
){
virtualAssignmentForbidden(this);
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: getSize
##
###########################################################################/**
#
# @RdocMethod getSize
#
# @title "Get the number of symbols in an Alphabet object"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{this}{An Alphabet object.}
# \item{...}{Not used.}
# }
#
# \value{
# An integer vector of length one.
# }
#
# \examples{
#
# # create an alphabet object
# a<-Alphabet(symbols=c(0,1,2,3,4,5))
# a
# # get alphabet size
# getSize(a)
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"getSize",
class="Alphabet",
function(
this,
...
){
this$.size;
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: getType
##
###########################################################################/**
#
# @RdocMethod getType
#
# @title "Get Alphabet obejct type"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{this}{An Alphabet object.}
# \item{...}{Not used.}
# }
#
# \value{
# A character vector of length one.
# }
#
# \examples{
#
# # create alphabet object
# a<-Alphabet(symbols=c(0,1),type="Binary");
# # get alphabet type
# getType(a)
# a$type
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"getType",
class="Alphabet",
function(
this,
...
){
this$.type;
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: setType
##
###########################################################################/**
#
# @RdocMethod setType
#
# @title "Set Alphabet object type"
#
# \description{
# @get "title".
# }
#
# @synopsis
#
# \arguments{
# \item{this}{An Alphabet object.}
# \item{new_type}{A character vector of length one.}
# \item{...}{Not used.}
# }
#
# \value{
# The new type (invisible).
# }
#
# \examples{
# # create an alphabet object
# a<-Alphabet(symbols=c(1,2,3))
# # set a new type
# setType(a,"MyAlphabet")
# a$type
# # set type via virtual field
# a$type<-"MorphChars"
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"setType",
class="Alphabet",
function(
this,
new_type,
...
){
.checkWriteProtection(this);
if(!exists(x="PSIM_FAST")){
if (length(new_type) != 1) {throw("The new type must be a character vector of length 1!")}
if (new_type == "" ){ throw("Cannot set empty type!")}
}
this$.type<-new_type;
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: hasSymbols
##
###########################################################################/**
#
# @RdocMethod hasSymbols
#
# @title "Check if an Alphabet object has a given set of symbols"
#
# \description{
# @get "title".
# Returns true if the class of the object is "AnyAlphabet".
# }
#
# @synopsis
#
# \arguments{
# \item{this}{An Alphabet object.}
# \item{sym}{A character vector.}
# \item{...}{Not used.}
# }
#
# \value{
# TRUE or FALSE
# }
#
# \examples{
#
# # create alphabet object
# a<-Alphabet(symbols=c("A","T","G","C"));
# # check if it has the symbols "A" and "G"
# hasSymbols(a,c("A","G"))
# # check if has the symbol "X"
# hasSymbols(a,"X")
# # any alphabet returns true for every symbol
# b<-AnyAlphabet();
# hasSymbols(b,"X")
#
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"hasSymbols",
class="Alphabet",
function(
this,
sym,
...
){
sym<-unique(as.character(sym));
if (length(intersect(this$.symbols,sym)) == length(sym)){
return(TRUE);
}
# Check ANY flag:
else if(!is.null(this$.any.flag)) { return(TRUE) }
else {
return(FALSE);
}
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: getWriteProtected
##
###########################################################################/**
#
# @RdocMethod getWriteProtected
#
# @title "Check if the object is write protected"
#
# \description{
# @get "title".
# Write protected objects cannot be modified through get/set methods and virtual fields.
# }
#
# @synopsis
#
# \arguments{
# \item{this}{An object.}
# \item{...}{Not used.}
# }
#
# \value{
# TRUE or FALSE.
# }
#
# \examples{
#
# # create an object
# o<-Alphabet()
# # toggle write protection
# o$writeProtected<-TRUE
# # check if it's write protected
# getWriteProtected(o)
# # check write protection via virtual field
# o$writeProtected
#
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"getWriteProtected",
class="Alphabet",
function(
this,
...
){
this$.write.protected;
},
private=FALSE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: setWriteProtected
##
###########################################################################/**
#
# @RdocMethod setWriteProtected
#
# @title "Set the write protection field for an object"
#
# \description{
# @get "title".
# Write protected objects cannot be modified through get/set methods and virtual fields.
# }
#
# @synopsis
#
# \arguments{
# \item{this}{An object.}
# \item{value}{A logical vector of size one.}
# \item{...}{Not used.}
# }
#
# \value{
# Invisible TRUE or FALSE.
# }
#
# \examples{
#
# # create an object
# o<-Alphabet()
# # toggle write protection
# setWriteProtected(o,TRUE)
# # check write protection
# o$writeProtected
# # set write protection via virtual field
# o$writeProtected<-FALSE
# o$writeProtected
#
#
# }
#
# @author
#
# \seealso{
# @seeclass
# }
#
#*/###########################################################################
setMethodS3(
"setWriteProtected",
class="Alphabet",
function(
this,
value,
...
){
if(!is.logical(value)) {throw("The new value must be logical!\n")}
else {
this$.write.protected<-value;
}
},
private=TRUE,
protected=FALSE,
overwrite=FALSE,
conflict="warning",
validators=getOption("R.methodsS3:validators:setMethodS3")
);
##
## Method: .checkWriteProtection
##
setMethodS3(
".checkWriteProtection",
class="Alphabet",
function(
this,
...
){
if(exists(x="PSIM_FAST")){ return(FALSE) }