R/UniprotEntry.R
In pkrog/biodbUniprot: biodbUniprot, a library for connecting to the Uniprot Database
#' Uniprot entry class.
#'
#' This is the entry class for Uniprot database.
#'
#' @examples
#' # Create an instance with default settings:
#' mybiodb <- biodb::newInst()
#'
#' # Create a connector
#' conn <- mybiodb$getFactory()$createConn('uniprot')
#'
#' # Get an entry
#' e <- conn$getEntry('P01011')
#'
#' # Terminate instance.
#' mybiodb$terminate()
#'
#' @importFrom R6 R6Class
#' @export
UniprotEntry <- R6::R6Class("UniprotEntry",
inherit=BiodbXmlEntry,
public=list(
),
private=list(
doCheckContent=function(content) {
return( ! grepl("^<!DOCTYPE html ", content, perl=TRUE))
},
doParseFieldsStep2=function(parsed.content) {
# Remove new lines from sequence string
if (self$hasField('aa.seq'))
self$setFieldValue('aa.seq',
gsub("\\n", "", self$getFieldValue('aa.seq')))
# Get synonyms
ns <- self$getParent()$getPropertyValue('xml.ns')
synonyms <- XML::xpathSApply(parsed.content,
"//uniprot:protein//uniprot:fullName", XML::xmlValue, namespaces=ns)
if (length(synonyms) > 0)
self$appendFieldValue('name', synonyms)
}
))
pkrog/biodbUniprot documentation built on Sept. 26, 2022, 3:50 p.m.
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#' Uniprot entry class.
#'
#' This is the entry class for Uniprot database.
#'
#' @examples
#' # Create an instance with default settings:
#' mybiodb <- biodb::newInst()
#'
#' # Create a connector
#' conn <- mybiodb$getFactory()$createConn('uniprot')
#'
#' # Get an entry
#' e <- conn$getEntry('P01011')
#'
#' # Terminate instance.
#' mybiodb$terminate()
#'
#' @importFrom R6 R6Class
#' @export
UniprotEntry <- R6::R6Class("UniprotEntry",
inherit=BiodbXmlEntry,
public=list(
),
private=list(
doCheckContent=function(content) {
return( ! grepl("^<!DOCTYPE html ", content, perl=TRUE))
},
doParseFieldsStep2=function(parsed.content) {
# Remove new lines from sequence string
if (self$hasField('aa.seq'))
self$setFieldValue('aa.seq',
gsub("\\n", "", self$getFieldValue('aa.seq')))
# Get synonyms
ns <- self$getParent()$getPropertyValue('xml.ns')
synonyms <- XML::xpathSApply(parsed.content,
"//uniprot:protein//uniprot:fullName", XML::xmlValue, namespaces=ns)
if (length(synonyms) > 0)
self$appendFieldValue('name', synonyms)
}
))
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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