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# ppProcessing.R
# FBA and friends with R.
#
# Copyright (C) 2010-2014 Gabriel Gelius-Dietrich, Dpt. for Bioinformatics,
# Institute for Informatics, Heinrich-Heine-University, Duesseldorf, Germany.
# All right reserved.
# Email: geliudie@uni-duesseldorf.de
#
# This file is part of sybil.
#
# Sybil is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Sybil is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with sybil. If not, see <http://www.gnu.org/licenses/>.
################################################
# Function: ppProcessing
#
# do some kind of post or pre processing
#
#
.ppProcessing <- function(lpprob, ppCmd, loopvar = NA) {
#----------------------------------------------------------------------#
# run the pre/post processing command
#----------------------------------------------------------------------#
.runPPcommand <- function(ppCommand) {
pAnaR <- NA
if(!is(ppCommand, "character")) {
warning("Each command must be passed as character vector.")
ppC <- NA
}
if (nchar(ppCommand[1]) < 1) {
warning("The first element of 'ppC' must contain a function name.")
ppC <- NA
}
else {
ppC <- ppCommand
}
# else {
# if(!isTRUE(is.function(eval(parse(text = ppC[1]))))) {
# warning(paste("The first element of 'ppC' must contain a valid",
# "function name."
# )
# )
# ppC <- NA
# }
# }
if (!is.na(ppC[1])) {
narg <- length(ppC)
if (narg == 1) {
ppC <- paste(ppC, "(lpprob)", sep = "")
}
else {
if (!is.na(loopvar)) {
ppC <- gsub("LOOP_VAR", loopvar, ppC, fixed = TRUE)
}
ppC <- gsub("LP_PROB", "lpprob", ppC, fixed = TRUE)
ppC <- paste(ppC[1], "(",
paste(ppC[-1], collapse = ", "),
")", sep = ""
)
}
# run the command
pAnaR <- tryCatch(eval(parse(text = ppC)), error = function(x) x)
if (is(pAnaR, "simpleError")) {
pAnaR <- sybilError(pAnaR)
}
ppC <- gsub("lpprob", "LP_PROB", ppC, fixed = TRUE)
if (!is.na(loopvar)) {
ppC <- gsub(loopvar, "LOOP_VAR", ppC, fixed = TRUE)
}
}
return(list(com = ppC, res = pAnaR))
}
#------------------------------------------------------------------------------#
# cmdList: list of commands
# resList: list of results for each command
# instance of class ppProc, if successfull, otherwise NA
cmdList <- list(NA)
resList <- list(NA)
pAna <- NA
if (all(!is.na(ppCmd))) {
if (!is(ppCmd, "list")) {
warning("Argument 'ppCmd' must be a list.")
}
else {
tmp_res <- NULL
nCmd <- length(ppCmd)
resList <- vector(mode = "list", length = nCmd)
cmdList <- vector(mode = "list", length = nCmd)
for (i in seq(along = ppCmd)) {
tmp_res <- .runPPcommand(ppCmd[[i]])
resList[[i]] <- tmp_res[["res"]]
cmdList[[i]] <- tmp_res[["com"]]
tmp_res <- NULL
}
}
pAna <- ppProc(cmdList)
pa(pAna) <- resList
}
return(pAna)
}
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