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## "pubRepo" is from Bioconductor "AnnBuilder" package
## other subClass of "pubRepo" are defined by Hong Li, 2008
## A generic class that reads or downloads data from public data repositories.
## srcUrl - the url for the cgi script that initiates a query against
## the databse. The value at the time of coding is:
## "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?"
##
setClass("pubRepo", representation(srcUrl = "character",
parser = "character",
baseFile = "character",
built = "character",
fromWeb = "logical"))
## Set the get methods
setGeneric("srcUrl", function(object) standardGeneric("srcUrl"))
setMethod("srcUrl", "pubRepo", function(object) object@srcUrl)
setGeneric("builtInfo", function(object) standardGeneric("builtInfo"))
setMethod("builtInfo", "pubRepo", function(object) object@built)
setGeneric("fromWeb", function(object) standardGeneric("fromWeb"))
setMethod("fromWeb", "pubRepo", function(object) object@fromWeb)
setGeneric("baseFile", function(object) standardGeneric("baseFile"))
setMethod("baseFile", "pubRepo", function(object) object@baseFile)
setGeneric("parser", function(object) standardGeneric("parser"))
setMethod("parser", "pubRepo", function(object) object@parser)
# Define the replace methods
setGeneric("srcUrl<-", function(object, value)
standardGeneric("srcUrl<-"))
setReplaceMethod("srcUrl", "pubRepo", function(object, value){
object@srcUrl <- value; object})
setGeneric("baseFile<-", function(object, value) standardGeneric("baseFile<-"))
setReplaceMethod("baseFile", "pubRepo", function(object, value){
object@baseFile <- value; object})
setGeneric("fromWeb<-", function(object, value) standardGeneric("fromWeb<-"))
setReplaceMethod("fromWeb", "pubRepo", function(object, value){
object@fromWeb <- value; object})
setGeneric("parser<-", function(object, value) standardGeneric("parser<-"))
setReplaceMethod("parser", "pubRepo", function(object, value){
object@parser <- value; object})
# Defines functions
setGeneric("readData",
function(object, ...)
standardGeneric("readData"))
setMethod("readData", "pubRepo",
function(object, ...){
if(fromWeb(object)){
conn <- url(srcUrl(object))
}else{
conn <- file(srcUrl(object))
}
temp <- readLines(conn)
close(conn)
return(temp)})
setGeneric("downloadData",
function(object, dist)
standardGeneric("downloadData"))
setMethod("downloadData", "pubRepo",
function(object, dist)
return(loadFromUrl(srcUrl(object), dist)))
setGeneric("parseData", function(object, ...)
standardGeneric("parseData"))
setMethod("parseData", "pubRepo",
function(object, sep = "\t",
ncol = 2, mergeKey = TRUE){
if(fromWeb(object)){
srcData <- downloadData(object, "")
}else{
srcData <- srcUrl(object)
}
tempOut <- tempfile("tempOut")
obtained <- matrix(scan(fileMuncher(tempOut, baseFile(object),
srcData, parser(object)), what = "character",
sep = sep, quote = "", quiet = TRUE,
strip.white = TRUE, comment.char = ""),
ncol = ncol, byrow = TRUE)
if(fromWeb(object)){
unlink(srcData)
}
unlink(tempOut)
if(nrow(obtained) <= 1 || !mergeKey){
return(obtained)
}else{
return(mergeRowByKey(obtained))
}} )
# getClass("pubRepo")
## sub class of "pubRepo"
## "pBase" class for SwissProt, TREMBL, IPI, NCBI RefSeq data
setClass("pBase", contains = "pubRepo",
representation(organism = "character"))
setGeneric("organism", function(object) standardGeneric("organism"))
setMethod("organism", "pBase", function(object) object@organism)
setGeneric("organism<-", function(object, value)
standardGeneric("organism<-"))
setReplaceMethod("organism", "pBase", function(object, value){
object@organism <- value; object})
setMethod("parseData", "pBase", function(object, sep = "\t", mergeKey = TRUE){
if(fromWeb(object)){
srcData <- downloadData(object, "")
}else{
srcData <- srcUrl(object)
}
tempOut <- tempfile("tempOut")
obtained <- as.matrix(read.csv(fileMuncher(tempOut,
srcData, parser(object),organism(object) ), header=T, sep = sep ) )
if(fromWeb(object)){
unlink(srcData)
}
unlink(tempOut)
if(nrow(obtained) <= 1 || !mergeKey){
return(obtained)
}else{
return(mergeRowByKey(obtained))
}} )
pBase <- function(srcUrl, parser, built="", fromWeb=TRUE, organism ) {
new("pBase", srcUrl = srcUrl, parser = parser,
built = built, fromWeb = fromWeb, organism = organism)
}
## "GOTermsAnnDbBimap" is from Bioconductor "AnnotationDbi" package.
## setMethod("as.list", "GOTermsAnnDbBimap",
## function(x, ...)
## {
## y <- AnnotationDbi:::flatten(x, fromKeys.only=TRUE)
## AnnotationDbi:::.toListOfLists(y, mode=1)
## }
## )
##
##
##
##setClass("PtmAnnDbBimap",contains="AnnDbBimap",where)
##setMethod("as.list", "PtmAnnDbBimap",
## function(x, ...)
## {
## y <- AnnotationDbi:::flatten(x, fromKeys.only=TRUE)
## AnnotationDbi:::.toListOfLists(y, mode=1)
## }
##)
##
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