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### homoData objects are used by homoPkgBuilder to represent homology data
setClass("homoData", representation(homoOrg = "character",
homoLL = "numeric",
homoType = "character",
homoPS = "numeric",
homoURL = "character",
homoACC = "character",
homoHGID = "numeric"))
# Set the get methods
setGeneric("homoOrg",
function(object) standardGeneric("homoOrg"))
setMethod("homoOrg", "homoData",
function(object) object@homoOrg)
setGeneric("homoLL",
function(object) standardGeneric("homoLL"))
setMethod("homoLL", "homoData",
function(object) object@homoLL)
setGeneric("homoType",
function(object) standardGeneric("homoType"))
setMethod("homoType", "homoData",
function(object) object@homoType)
setGeneric("homoPS",
function(object) standardGeneric("homoPS"))
setMethod("homoPS", "homoData",
function(object) object@homoPS)
setGeneric("homoURL",
function(object) standardGeneric("homoURL"))
setMethod("homoURL", "homoData",
function(object) object@homoURL)
setGeneric("homoACC",
function(object) standardGeneric("homoACC"))
setMethod("homoACC", "homoData",
function(object) object@homoACC)
setGeneric("homoHGID",
function(object) standardGeneric("homoHGID"))
setMethod("homoHGID", "homoData",
function(object) object@homoHGID)
setMethod("show", "homoData",
function(object) {
if(length(homoOrg(object)) > 0 && !is.na(homoOrg(object))){
cat(paste("homoOrg:", homoOrg(object)), fill = TRUE)
}
if(length(homoLL(object)) > 0 && !is.na(homoLL(object))){
cat(paste("\nhomoLL:", homoLL(object)), fill = TRUE)
}
if(length(homoHGID(object)) > 0 && !is.na(homoHGID(object))){
cat(paste("\nhomoHGID:", homoHGID(object)), fill = TRUE)
}
if(length(homoACC(object)) > 0 && !is.na(homoACC(object))){
cat(paste("\nhomoACC:", homoACC(object)), fill = TRUE)
}
if(length(homoType(object)) > 0 && !is.na(homoType(object))){
cat(paste("\nhomoType:", homoType(object)), fill = TRUE)
}
if(length(homoPS(object)) > 0 && !is.na(homoPS(object))){
cat(paste("\nhomoPS:", homoPS(object)), fill = TRUE)
}
if(length(homoURL(object)) > 0 && !is.na(homoURL(object))){
cat(paste("\nhomoURL:", homoURL(object)), fill = TRUE)
}
cat("\n")
})
mapOrgs <- function(toMap, what = c("code", "name")){
fun <- function(x){
if(what == "code"){
return(orgs[[x]])
}else{
return(names(orgs[orgs == x]))
}
}
what <- match.arg(what)
orgs <- getOrgNameNCode()
if(is.null(toMap) || is.na(toMap)){
return(NA)
}
if(length(toMap) == 1){
return(fun(toMap))
}else{
return(sapply(toMap, fun))
}
}
getOrgNameNCode <- function(){
return(list("3055" = "Chlamydomonas reinhardtii",
"3702" = "Arabidopsis thaliana",
"3847" = "Glycine max",
"3880" = "Medicago truncatula",
"4081" = "Lycopersicon esculentum",
"4513" = "Hordeum vulgare",
"4530" = "Oryza sativa",
"4565" = "Triticum aestivum",
"4577" = "Zea mays",
"4896" = "Schizosaccharomyces pombe",
"4932" = "Saccharomyces cerevisiae",
"5141" = "Neurospora crassa",
"5833" = "Plasmodium falciparum",
"6239" = "Caenorhabditis elegans",
"7165" = "Anopheles gambiae",
"7227" = "Drosophila melanogaster",
"7719" = "Ciona intestinalis",
"7955" = "Danio rerio",
"8022" = "Oncorhynchus mykiss",
"8090" = "Oryzias latipes",
"8355" = "Xenopus laevis",
"8364" = "Xenopus tropicalis",
"9031" = "Gallus gallus",
"9606" = "Homo sapiens",
"9615" = "Canis familiaris",
"9598" = "Pan troglodytes",
"9823" = "Sus scrofa",
"9913" = "Bos taurus",
"10090" = "Mus musculus",
"10116" = "Rattus norvegicus",
"28985" = "Kluyveromyces, lactis",
"29760" = "Vitis vinifera",
"33169" = "Eremothecium gossypii",
"44689" = "Dictyostelium discoideum",
"148305" = "Magnaporthe grisea"
))
}
homoData <- function(organism, LL, type, PS, ACC, HGID, URL){
return(new("homoData", homoOrg = mapOrgs(organism),
homoLL = LL, homoType = type,
homoPS = PS, homoURL = URL,
homoACC = ACC, homoHGID = HGID))
}
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