Nothing
## new generics
setGeneric(".throw",
function(object, call=NULL, ...) standardGeneric(".throw"),
signature=c("object"))
setGeneric("renewable", function(x, ...) standardGeneric("renewable"))
setGeneric("renew", function(x, ...) standardGeneric("renew"))
countLines <- function(dirPath, pattern=character(0), ..., useFullName=FALSE)
{
src <- .file_names(path.expand(dirPath), pattern, ...)
nLines <- .Call(.count_lines, src)
names(nLines) <-
if (useFullName) src
else basename(src)
nLines
}
setGeneric("countLines", signature="dirPath")
alphabetByCycle <-
function(stringSet, alphabet, ...)
{
if (missing(alphabet))
alphabet <- Biostrings::alphabet(stringSet)
w <- max(0L, width(stringSet))
.Call(.alphabet_by_cycle, stringSet, w, alphabet)
}
setGeneric("alphabetByCycle", signature="stringSet")
setGeneric("dustyScore", function(x, batchSize=NA, ...)
standardGeneric("dustyScore"),
signature="x")
setGeneric("srorder", function(x, ...) standardGeneric("srorder"))
setGeneric("srduplicated",
function(x, ...) standardGeneric("srduplicated"))
setGeneric("srsort", function(x, ...) standardGeneric("srsort"))
setGeneric("srrank", function(x, ...) standardGeneric("srrank"))
setGeneric("tables", function(x, n=50, ...)
standardGeneric("tables"),
signature="x")
## Intensities
setGeneric("readIntensities",
function(dirPath, pattern=character(0), ...)
standardGeneric("readIntensities"),
signature="dirPath")
## QualityScore
setGeneric("FastqQuality", function(quality, ...)
standardGeneric("FastqQuality"))
setGeneric("SFastqQuality", function(quality, ...)
standardGeneric("SFastqQuality"))
setGeneric("readPrb", function(dirPath, pattern=character(0), ...)
standardGeneric("readPrb"), signature="dirPath")
## ShortRead / ShortReadQ
setGeneric("ShortRead", function(sread, id, ...)
standardGeneric("ShortRead"))
setGeneric("sread", function(object, ...) standardGeneric("sread"))
setGeneric("writeFasta", function(object, file, mode="w", ...)
standardGeneric("writeFasta"),
signature=signature("object"))
setGeneric("ShortReadQ", function(sread, quality, id, ...)
standardGeneric("ShortReadQ"))
setGeneric("readFastq", function(dirPath, pattern=character(0), ...)
standardGeneric("readFastq"), signature="dirPath")
setGeneric("writeFastq",
function(object, file, mode="w", full=FALSE, compress=TRUE, ...)
standardGeneric("writeFastq"), signature=c("object", "file"))
setGeneric("countFastq",
function(dirPath, pattern = character(0), ...)
standardGeneric("countFastq"), signature = "dirPath")
setGeneric("readFasta",
function(dirPath, pattern=character(0), ...,
nrec=-1L, skip=0L)
standardGeneric("readFasta"),
signature="dirPath")
setGeneric("readQual",
function(dirPath, pattern=character(0), ...)
standardGeneric("readQual"))
setGeneric("read454",
function(dirPath, ...)
standardGeneric("read454"))
setGeneric("readFastaQual",
function(dirPath, ...)
standardGeneric("readFastaQual"))
setGeneric("readBaseQuality",
function(dirPath, ...)
standardGeneric("readBaseQuality"))
setGeneric("readQseq", function(dirPath, pattern=character(0), ...,
as=c("ShortReadQ", "DataFrame",
"XDataFrame"),
filtered=FALSE, verbose=FALSE)
standardGeneric("readQseq"), signature="dirPath")
setGeneric("trimTails",
function(object, k, a, successive=FALSE, ..., ranges=FALSE)
standardGeneric("trimTails"), signature="object")
setGeneric("trimTailw",
function(object, k, a, halfwidth, ..., ranges=FALSE)
standardGeneric("trimTailw"), signature="object")
setGeneric("trimEnds",
function(object, a, left=TRUE, right=TRUE, relation=c("<=", "=="),
..., ranges=FALSE)
standardGeneric("trimEnds"),
signature="object")
setGeneric("clean", function(object, ...) standardGeneric("clean"))
setGeneric("srdistance", function(pattern, subject, ...)
standardGeneric("srdistance"), signature=c("pattern", "subject"))
setGeneric("alphabetScore",
function(object, ...) standardGeneric("alphabetScore"))
## SRFilter
setGeneric("name", function(x, ...) standardGeneric("name"))
setGeneric("stats", function(x, ...) standardGeneric("stats"))
setGeneric("srFilter", function(fun, name=NA_character_, ...)
standardGeneric("srFilter"),
signature="fun")
## AlignedRead
setGeneric("readAligned",
function(dirPath, pattern=character(0), ...)
standardGeneric("readAligned"), signature="dirPath")
setGeneric("chromosome",
function(object, ...) standardGeneric("chromosome"))
setGeneric("id",
function(object, ...) standardGeneric("id"))
setGeneric("position",
function(object, ...) standardGeneric("position"))
## ExperimentPath
experimentPath <- function(object, ...) {
slot(object, "basePath")
}
setGeneric("experimentPath")
## *Set
setGeneric("qa", function(dirPath, ...) standardGeneric("qa"))
report <-
function (x, ..., dest = tempfile(), type="html")
{
func <- switch(type, html=report_html, pdf=.report_pdf,
.report_any)
func(x, dest, type, ...)
}
setGeneric("report", signature="x")
.report_any <-
function (x, dest, type, ...)
{
.throw(SRError("UserArgumentMismatch",
"'%s, type=\"%s\"' not implemented for class '%s'",
"report", type, class(x)))
}
setGeneric("report_html", function(x, dest, type, ...)
standardGeneric("report_html"),
signature="x", useAsDefault=.report_any)
setGeneric(".report_pdf", function(x, dest, type, ...)
standardGeneric(".report_pdf"),
signature="x", useAsDefault=.report_any)
## SolexaSet
setGeneric("SolexaSet", function(path, ...)
standardGeneric("SolexaSet"))
setGeneric("laneNames", function(object, ...) {
standardGeneric("laneNames")
})
## Roche
setGeneric("RocheSet", function(path, ...)
standardGeneric("RocheSet"))
setGeneric("runNames", function(object, ...)
standardGeneric("runNames"))
## Snapshot
setGeneric("Snapshot",
function(files, range, ...) standardGeneric("Snapshot"))
setGeneric("SnapshotFunctionList",
function(...) standardGeneric("SnapshotFunctionList"))
setGeneric("files", function(x, ...) standardGeneric("files"))
setGeneric("vrange", function(x, ...) standardGeneric("vrange"))
setGeneric("functions", function(x, ...) standardGeneric("functions"))
setGeneric("annTrack", function(x, ...) standardGeneric("annTrack"))
setGeneric("ignore.strand", function(x, ...) standardGeneric("ignore.strand"))
setGeneric("fac", function(x, ...) standardGeneric("fac"))
setGeneric("getTrellis", function(x, ...) standardGeneric("getTrellis"))
setGeneric("togglez", function(x, ...) standardGeneric("togglez"))
setGeneric("togglep", function(x, ...) standardGeneric("togglep"))
setGeneric("togglefun", function(x, name, ...) standardGeneric("togglefun"))
setGeneric("zoom", function(x, range, ...) standardGeneric("zoom"))
setGeneric("pan", function(x, ...) standardGeneric("pan"))
setGeneric("view", function(x, ...) standardGeneric("view"))
setGeneric("zi", function(x, ...) standardGeneric("zi"))
setGeneric("zo", function(x, ...) standardGeneric("zo"))
setGeneric("left", function(x, ...) standardGeneric("left"))
setGeneric("right", function(x, ...) standardGeneric("right"))
setGeneric("restore", function(x, ...) standardGeneric("restore"))
## ShortReadFile
setGeneric(".ShortReadFile", function(g, path, ...)
standardGeneric(".ShortReadFile"), signature="path")
setGeneric("FastqFileList",
function(..., class="FastqFile")
standardGeneric("FastqFileList"),
signature="...")
BiocGenerics:::apply_hotfix73465(getGeneric("FastqFileList"))
setGeneric("FastqStreamer",
function(con, n, readerBlockSize=1e8, verbose=FALSE)
standardGeneric("FastqStreamer"),
signature=c("con", "n"))
setGeneric("FastqStreamerList",
function(..., n, readerBlockSize=1e8, verbose=FALSE)
standardGeneric("FastqStreamerList"),
signature="...")
BiocGenerics:::apply_hotfix73465(getGeneric("FastqStreamerList"))
setGeneric("FastqSamplerList",
function(..., n=1e6, readerBlockSize=1e8, verbose=FALSE,
ordered = FALSE)
standardGeneric("FastqSamplerList"),
signature="...")
BiocGenerics:::apply_hotfix73465(getGeneric("FastqSamplerList"))
setGeneric("yield", function(x, ...) standardGeneric("yield"))
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