R/fromPsimi.R

In BioPAX/paxtoolsr: Access Pathways from Multiple Databases Through BioPAX and Pathway Commons

# #' Read PSIMI file
# #' 
# #' This function reads in a PSIMI file. 
# #' 
# #' @param inputFile a string of the name of the input PSIMI file
# #' @param outputFile a string of the name of the output BioPAX OWL file
# #' @param bpLevelArg a string representing the BioPAX level for the output file
# #'   (default: NULL)
# #' @return an XMLInternalDocument representing a BioPAX OWL file
# #' 
# #' @details The Proteomics Standard Initiative (PSIMI) format is described at 
# #' https://code.google.com/p/psimi/wiki/PsimiTabFormat
# #' 
# #' This function has been removed from Paxtools as of 4.3.1
# #' 
# #' @examples
# #' outFile <- tempfile()
# #' results <- fromPsimi(system.file("extdata", "10523676-compact.xml", package="paxtoolsr"), 
# #'                                  outFile, 
# #'                                  "3")
# #'                                  
# #' @concept paxtoolsr
# fromPsimi <- function(inputFile, outputFile=NULL, bpLevelArg=3) {
#     command <- "fromPsimi"
#     
#     outputFile <- checkOutputFile(outputFile)
#     bpLevelArg <- as.character(bpLevelArg)
#     
#     commandJStr <- .jnew("java/lang/String", command)
#     inputJStr <- .jnew("java/lang/String", inputFile)
#     outputJStr <- .jnew("java/lang/String", outputFile)
#     bpLevelArgJStr <- .jnew("java/lang/String", bpLevelArg)
#     
#     argsList <- list(commandJStr, bpLevelArgJStr, inputJStr, outputJStr) 
#     
#     .jcall("org/biopax/paxtools/PaxtoolsMain","V",command,.jarray(argsList, "java/lang/String"))
#     .jcheck()
#     
#     results <- xmlTreeParse(outputFile, useInternalNodes=TRUE)
#     return(results) 
#     
# }