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### =========================================================================
### VCFHeader class methods
### =========================================================================
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Constructor
###
VCFHeader <-
function(reference=character(), samples=character(),
header=DataFrameList(), ...)
{
new("VCFHeader", reference=reference, samples=samples, header=header, ...)
}
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Getters and Setters
###
setMethod("reference", "VCFHeader",
function(x)
{
slot(x, "reference")
})
setMethod("samples", "VCFHeader",
function(object)
{
slot(object, "samples")
})
setMethod("header", "VCFHeader",
function(x)
{
slot(x, "header")
})
## meta
setMethod("meta", "VCFHeader",
function(x)
{
slot(x, "header")$META
})
setReplaceMethod("meta", c("VCFHeader", "DataFrame"),
function(x, value)
{
slot(x, "header")$META <- value
validObject(x)
x
})
## fixed (QUAL, FILTER, ALT, REF)
setMethod("fixed", "VCFHeader",
function(x)
{
fixed <- c("QUAL", "FILTER")
lst <- slot(x, "header")
lst[names(lst) %in% fixed]
})
setReplaceMethod("fixed", c("VCFHeader", "DataFrameList"),
function(x, value)
{
validObject(value)
if (!all(names(value) %in% c("QUAL", "FILTER")))
stop("names for 'fixed' must be 'QUAL' or 'FILTER'")
slot(x, "header")$FILTER <- value$FILTER
slot(x, "header")$QUAL <- value$QUAL
x
})
## info
setMethod("info", "VCFHeader",
function(x)
{
info <- slot(x, "header")$INFO
if (is.null(info))
info <- DataFrame()
info
})
setReplaceMethod("info", c("VCFHeader", "DataFrame"),
function(x, value)
{
slot(x, "header")$INFO <- value
validObject(x)
x
})
## geno
setMethod("geno", "VCFHeader",
function(x)
{
geno <- slot(x, "header")$FORMAT
if (is.null(geno))
geno <- DataFrame()
geno
})
setReplaceMethod("geno", c("VCFHeader", "missing", "DataFrame"),
function(x, i, ..., value)
{
slot(x, "header")$FORMAT <- value
validObject(x)
x
})
setMethod("seqinfo", "VCFHeader",
function(x)
{
contig <- slot(x, "header")$contig
if (is.null(contig))
Seqinfo()
else Seqinfo(rownames(contig),
seqlengths =
if (is.null(contig$length)) NA else as.integer(contig$length),
genome = if (is.null(contig$assembly)) NA else contig$assembly)
})
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Show
###
setMethod(show, "VCFHeader",
function(object)
{
selectSome <- BiocGenerics:::selectSome
scat <- function(fmt, vals=character(), exdent=2, ...)
{
vals <- ifelse(nzchar(vals), vals, "''")
lbls <- paste(selectSome(vals), collapse=" ")
txt <- sprintf(fmt, length(vals), lbls)
cat(strwrap(txt, exdent=exdent, ...), sep="\n")
}
cat("class:", class(object), "\n")
samples <- samples(object)
scat("samples(%d): %s\n", samples)
meta <- rownames(meta(object))
scat("meta(%d): %s\n", meta)
fixed <- names(fixed(object))
scat("fixed(%d): %s\n", fixed)
info <- rownames(info(object))
scat("info(%d): %s\n", info)
geno <- rownames(geno(object))
scat("geno(%d): %s\n", geno)
})
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