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### =========================================================================
### VariantType class methods
### =========================================================================
### 'show' methods
setMethod("show", "VariantType",
function(object)
{
cat("class:", class(object), "\n")
}
)
setMethod("show", "AllVariants",
function(object)
{
cat("class:", class(object), "\n")
cat("promoter: \n")
cat(" upstream: ", upstream(promoter(object)), "\n")
cat(" downstream: ", downstream(promoter(object)), "\n")
cat("intergenic: \n")
cat(" upstream: ", upstream(intergenic(object)), "\n")
cat(" downstream: ", downstream(intergenic(object)), "\n")
}
)
setMethod("show", "PromoterVariants",
function(object)
{
cat("class:", class(object), "\n")
cat("upstream:", upstream(object), "\n")
cat("downstream:", downstream(object), "\n")
}
)
setMethod("show", "IntergenicVariants",
function(object)
{
cat("class:", class(object), "\n")
cat("upstream:", upstream(object), "\n")
cat("downstream:", downstream(object), "\n")
}
)
### constructors
CodingVariants <- function() new("CodingVariants")
IntronVariants <- function() new("IntronVariants")
UTRVariants <- function() new("UTRVariants")
ThreeUTRVariants <- function() new("ThreeUTRVariants")
FiveUTRVariants <- function() new("FiveUTRVariants")
SpliceSiteVariants <- function() new("SpliceSiteVariants")
### .checkArgs() takes the place of a validity method.
### 'upstream' and 'downstream' are forced to integers
### which changes the object and can't be done a validity
### method.
.checkArgs <- function(x, argName)
{
if (!isSingleNumber(x) | x < 0)
stop(paste0("'", argName, "'", " must be a single integer >= 0"))
if (!is.integer(x))
as.integer(x)
else
x
}
IntergenicVariants <- function(upstream=1e+06L, downstream=1e+06L)
{
upstream <- .checkArgs(upstream, "upstream")
downstream <- .checkArgs(downstream, "downstream")
new("IntergenicVariants", upstream=upstream,
downstream=downstream)
}
PromoterVariants <- function(upstream=2000L, downstream=200L)
{
upstream <- .checkArgs(upstream, "upstream")
downstream <- .checkArgs(downstream, "downstream")
new("PromoterVariants", upstream=upstream,
downstream=downstream)
}
AllVariants <- function(promoter=PromoterVariants(),
intergenic=IntergenicVariants())
{
new("AllVariants", promoter=promoter, intergenic=intergenic)
}
### getters and setters
setMethod("upstream", "PromoterVariants",
function(x) slot(x, "upstream"))
setReplaceMethod("upstream", "PromoterVariants",
function(x, value)
{
slot(x, "upstream") <- .checkArgs(value, "upstream")
x
})
setMethod("downstream", "PromoterVariants",
function(x) slot(x, "downstream"))
setReplaceMethod("downstream", "PromoterVariants",
function(x, value)
{
slot(x, "downstream") <- .checkArgs(value, "downstream")
x
})
setMethod("upstream", "IntergenicVariants",
function(x) slot(x, "upstream"))
setReplaceMethod("upstream", "IntergenicVariants",
function(x, value)
{
slot(x, "upstream") <- .checkArgs(value, "upstream")
x
})
setMethod("downstream", "IntergenicVariants",
function(x) slot(x, "downstream"))
setReplaceMethod("downstream", "IntergenicVariants",
function(x, value)
{
slot(x, "downstream") <- .checkArgs(value, "downstream")
x
})
setMethod("promoter", "AllVariants",
function(x) slot(x, "promoter"))
setReplaceMethod("promoter", "AllVariants",
function(x, value)
{
if (class(value) != "PromoterVariants")
stop("'value' must be a 'PromoterVariants' object")
slot(x, "promoter") <- value
x
})
setMethod("intergenic", "AllVariants",
function(x) slot(x, "intergenic"))
setReplaceMethod("intergenic", "AllVariants",
function(x, value)
{
if (class(value) != "IntergenicVariants")
stop("'value' must be a 'IntergenicVariants' object")
slot(x, "intergenic") <- value
x
})
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