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### =========================================================================
### CollapsedVCF class methods
### =========================================================================
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Constructor
###
### See VCF(..., collapsed=TRUE) in methods-VCF-class.R
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Getters and Setters
### alt() setter
setReplaceMethod("alt", c("CollapsedVCF", "DNAStringSetList"),
function(x, value)
{
if (length(value) != length(rowData(x)))
stop("length(value) must equal length(rowData(x))")
slot(x, "fixed")$ALT <- value
x
})
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### isSNV family
###
.logicalListToVector <- function(res, alt, singleAltOnly) {
lst <- relist(res, alt)
if (singleAltOnly)
all(lst) & elementLengths(lst) == 1
else
any(lst)
}
.dispatchSNV_CollapsedVCF <- function(FUN, x, singleAltOnly)
{
if (is(alt <- alt(x), "CharacterList"))
stop("'alt' must be non-structural nucleotide values")
res <- FUN(rep(ref(x), elementLengths(alt)),
unlist(alt, use.names=FALSE))
.logicalListToVector(res, alt, singleAltOnly)
}
setMethod("isSNV", "CollapsedVCF",
function(x, ..., singleAltOnly=TRUE)
.dispatchSNV_CollapsedVCF(.isSNV, x, singleAltOnly)
)
setMethod("isInsertion", "CollapsedVCF",
function(x, ..., singleAltOnly=TRUE)
.dispatchSNV_CollapsedVCF(.isInsertion, x, singleAltOnly)
)
setMethod("isDeletion", "CollapsedVCF",
function(x, ..., singleAltOnly=TRUE)
.dispatchSNV_CollapsedVCF(.isDeletion, x, singleAltOnly)
)
setMethod("isIndel", "CollapsedVCF",
function(x, ..., singleAltOnly=TRUE)
.dispatchSNV_CollapsedVCF(.isIndel, x, singleAltOnly)
)
setMethod("isTransition", "CollapsedVCF",
function(x, ..., singleAltOnly=TRUE)
.dispatchSNV_CollapsedVCF(.isTransition, x, singleAltOnly)
)
setMethod("isSubstitution", "CollapsedVCF",
function(x, ..., singleAltOnly=TRUE)
.dispatchSNV_CollapsedVCF(.isSubstitution, x, singleAltOnly)
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### show
###
setMethod(show, "CollapsedVCF",
function(object)
{
.showVCFSubclass(object)
})
|
