diff --git a/NAMESPACE b/NAMESPACE
index 737bebc00403fc8df1f2fa6bd54bc8212dd43a82..e782ef4835465a07be574fe5c2c7610ae3cb85da 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -7,6 +7,7 @@ import(lattice)
importFrom("grDevices", "colorRampPalette", "grey")
importFrom("graphics", "arrows", "hist", "points", "polygon", "segments")
importFrom("utils", "combn", "edit", "read.table", "str", "write.table")
+importFrom("utils", "compareVersion")
exportPattern("^[^\\.]")
diff --git a/R/addReact.R b/R/addReact.R
index 101842d1dd21afc70518a1f98eaec010bce4a061..35e6a252a998e9d3147ebc08b7916fbdc6b9b35d 100644
--- a/R/addReact.R
+++ b/R/addReact.R
@@ -53,6 +53,8 @@ addReact <- function(model,
if (!is(model, "modelorg")) {
stop("needs an object of class modelorg!")
}
+
+ stopifnot(checkVersion(model))
if (length(met) != length(Scoef)) {
stop("arguments 'met' and 'Scoef' must have the same length")
@@ -137,6 +139,11 @@ addReact <- function(model,
newsubSys <- subSys(model)
newS <- S(model)
+
+ newMetAttr <- met_attr(model)
+ newReactAttr <- react_attr(model)
+ newCompAttr <- comp_attr(model)
+ newModAttr <- mod_attr(model)
if (isTRUE(addRow)) {
@@ -179,6 +186,11 @@ addReact <- function(model,
nrow = nNewRows,
ncol = react_num(model))
newS <- Matrix::rBind(newS, newRows)
+
+ # new met attrs
+ if(ncol(newMetAttr) > 0){
+ newMetAttr[nrow(newMetAttr)+1:nNewRows, ] <- NA
+ }
}
if (isTRUE(addCol)) { # we add at most one column
@@ -209,6 +221,12 @@ addReact <- function(model,
# new column in stoichiometric matrix
newS <- cBind(newS, rep(0, nrow(newS)))
+ # new react Attr
+ # only one new row, /bc we can only add one reaction a time.
+ if(ncol(newReactAttr) > 0){
+ newReactAttr[nrow(newReactAttr)+1, ] <- NA
+ }
+
# subsystems
if (any(is.na(subSystem))) {
ss <- subSys(model)
@@ -290,13 +308,14 @@ addReact <- function(model,
# genes per reaction
newgenes <- append(genes(model), list(gene_rule$gene))
newrule <- gene_rule$rule
-
- for (j in 1 : length(geneInd)) {
- pat <- paste("x(", j, ")", sep = "")
- repl <- paste("x[", geneInd[j], "]", sep = "")
-
- newrule <- gsub(pat, repl, newrule, fixed = TRUE)
- }
+
+ # not needed for modelorg version 2.0
+# for (j in 1 : length(geneInd)) {
+# pat <- paste("x(", j, ")", sep = "")
+# repl <- paste("x[", geneInd[j], "]", sep = "")
+#
+# newrule <- gsub(pat, repl, newrule, fixed = TRUE)
+# }
newgprRules <- append(gprRules(model), newrule)
}
@@ -356,6 +375,12 @@ addReact <- function(model,
subSys(mod_out) <- newsubSys
S(mod_out) <- newS
+
+ react_attr(mod_out) <- newReactAttr
+ met_attr(mod_out) <- newMetAttr
+ comp_attr(mod_out) <- newCompAttr
+ mod_attr(mod_out) <- newModAttr
+
}
else {
diff --git a/R/geneDel.R b/R/geneDel.R
index f69dad53e2d81e30d72d10da1367826db1fb6eaf..87811bb55e0474f12665dc6065d0a39c11a10845 100644
--- a/R/geneDel.R
+++ b/R/geneDel.R
@@ -41,6 +41,8 @@ geneDel <- function(model, genes, checkId = FALSE) {
stop("needs an object of class modelorg!")
}
+ stopifnot(checkVersion(model))
+
if (isTRUE(checkId)) {
if (is(genes, "character")) {
# Check if all genes are there
@@ -95,9 +97,10 @@ geneDel <- function(model, genes, checkId = FALSE) {
#print(reactInd)
#x <- logical(length(allGenes(model)))
- x <- rep(TRUE, length(allGenes(model)))
+ xAll <- rep(TRUE, length(allGenes(model)))
#print(x)
- x[geneInd] <- FALSE
+ xAll[geneInd] <- FALSE
+ names(xAll) <- allGenes(model)
constReact <- logical(length(reactInd))
#print(constReact)
@@ -108,10 +111,15 @@ geneDel <- function(model, genes, checkId = FALSE) {
# If that's the case, the reaction needs gene bla.
ru <- gprRules(model)[reactInd]
+ ge <- genes(model)[reactInd]
for(i in 1:length(reactInd)) {
#print(reactInd[i])
#print(ru[i])
#ev <- eval(parse(text = ru[i]))
+
+ #define x for eval:
+ x <- xAll[ge[[i]]]
+
ev <- tryCatch(eval(parse(text = ru[i])), error = function(e) e)
if (is(ev, "simpleError")) {
stop("wrong gene association:",
diff --git a/R/generics.R b/R/generics.R
index e249177a90f6bd4c028d15b46d8cf90591daf192..af64b93398d579728264339f40fbcd40d648d6bd 100644
--- a/R/generics.R
+++ b/R/generics.R
@@ -126,6 +126,10 @@ setGeneric(name = "checkStat",
def = function(opt) { standardGeneric("checkStat") }
)
+setGeneric(name = "checkVersion",
+ def = function(object, ...) { standardGeneric("checkVersion") }
+)
+
setGeneric(name = "chlb",
def = function(object) { standardGeneric("chlb") }
)
@@ -147,6 +151,13 @@ setGeneric(name = "cmd<-",
def = function(object, value) { standardGeneric("cmd<-") }
)
+setGeneric(name = "comp_attr",
+ def = function(object) { standardGeneric("comp_attr") }
+)
+setGeneric(name = "comp_attr<-",
+ def = function(object, value) { standardGeneric("comp_attr<-") }
+)
+
setGeneric(name = "ctrlfl",
def = function(object) { standardGeneric("ctrlfl") }
)
@@ -536,6 +547,13 @@ setGeneric(name = "maxSol",
def = function(object, ...) { standardGeneric("maxSol") }
)
+setGeneric(name = "met_attr",
+ def = function(object) { standardGeneric("met_attr") }
+)
+setGeneric(name = "met_attr<-",
+ def = function(object, value) { standardGeneric("met_attr<-") }
+)
+
setGeneric(name = "met_comp",
def = function(object) { standardGeneric("met_comp") }
)
@@ -596,6 +614,13 @@ setGeneric(name = "minSol",
def = function(object, ...) { standardGeneric("minSol") }
)
+setGeneric(name = "mod_attr",
+ def = function(object) { standardGeneric("mod_attr") }
+)
+setGeneric(name = "mod_attr<-",
+ def = function(object, value) { standardGeneric("mod_attr<-") }
+)
+
setGeneric(name = "mod_compart",
def = function(object) { standardGeneric("mod_compart") }
)
@@ -759,6 +784,13 @@ setGeneric(name = "react<-",
def = function(object, value) { standardGeneric("react<-") }
)
+setGeneric(name = "react_attr",
+ def = function(object) { standardGeneric("react_attr") }
+)
+setGeneric(name = "react_attr<-",
+ def = function(object, value) { standardGeneric("react_attr<-") }
+)
+
setGeneric(name = "react_de",
def = function(object) { standardGeneric("react_de") }
)
@@ -945,6 +977,13 @@ setGeneric(name = "verblevel<-",
def = function(object, value) { standardGeneric("verblevel<-") }
)
+setGeneric(name = "version",
+ def = function(object) { standardGeneric("version") }
+)
+setGeneric(name = "version<-",
+ def = function(object, value) { standardGeneric("version<-") }
+)
+
setGeneric(name = "writeProb",
def = function(lp, fname, ff = "lp", ...) { standardGeneric("writeProb") }
)
diff --git a/R/mod2irrev.R b/R/mod2irrev.R
index 0d63548ea770aac241023adae18bac0b8a0fb997..658b10a26d9cf460c4634ce8b494caab90e85ca0 100644
--- a/R/mod2irrev.R
+++ b/R/mod2irrev.R
@@ -245,7 +245,7 @@ mod2irrev <- function(model, exex = FALSE) {
allGenes(modelIr) <- allGenes(model)
rxnG_temp <- rxnGeneMat(model)
- rxnG_temp <- rxnG_temp[irrev2rev(modelIr),]
+ rxnG_temp <- rxnG_temp[irrev2rev(modelIr), ,drop=FALSE]
#rxnG_temp <- rxnG_temp[irrev2rev,]
rxnGeneMat(modelIr) <- rxnG_temp
diff --git a/R/modelorgClass.R b/R/modelorgClass.R
index 9f8702a5f2d758b418d0111498ec3af373625243..5cd4063e5cd24ab01b9f406e35558bea526576d4 100644
--- a/R/modelorgClass.R
+++ b/R/modelorgClass.R
@@ -39,22 +39,27 @@ setClass("modelorg",
mod_id = "character", # model id
mod_key = "character", # model key (unique character string)
mod_compart = "character", # vector compartments
+ mod_attr = "data.frame", # dataframe to store attributes of the model
+ comp_attr = "data.frame", # dataframe to store attributes of the compartments
met_num = "integer", # number of metabolites
met_id = "character", # vector metabolite id's
met_name = "character", # vector metabolite names
met_comp = "integer", # vector the metabolites compartment
met_single = "logical", # metabolites appearing only once in S
met_de = "logical", # dead end metabolites
+ met_attr = "data.frame", # dataframe to store attributes of the metabolites
react_num = "integer", # number of reactions
react_rev = "logical", # vector reversibilities
react_id = "character", # vector reaction id's
react_name = "character", # vector reaction names
react_single = "logical", # reactions using metabolites appearing only once in S
react_de = "logical", # reactions using dead end metabolites
+ react_attr = "data.frame", # dataframe to store attributes of the reactions
S = "Matrix", # matrix S
lowbnd = "numeric", # vector reactions lower bounds
uppbnd = "numeric", # vector reactions upper bounds
obj_coef = "numeric", # vector objective coefficients
+ version = "character", # version to be compatible with changes in the class
gprRules = "character",
genes = "list",
gpr = "character",
@@ -110,9 +115,14 @@ setMethod(f = "initialize",
.Object@mod_key <- as.character(.generateModKey())
.Object@react_num <- as.integer(0)
.Object@met_num <- as.integer(0)
+ .Object@react_attr <- data.frame()
+ .Object@met_attr <- data.frame()
+ .Object@mod_attr <- data.frame()
+ .Object@comp_attr <- data.frame()
.Object@S <- Matrix::Matrix(0, 0, 0)
.Object@rxnGeneMat <- Matrix::Matrix(0, 0, 0)
.Object@subSys <- Matrix::Matrix(0, 0, length(subSys))
+ .Object@version <- SYBIL_SETTINGS("MODELORG_VERSION")
if (!is.null(subSys)) {
colnames(.Object@subSys) <- as.character(subSys)
}
@@ -204,7 +214,6 @@ setReplaceMethod("mod_compart", signature(object = "modelorg"),
}
)
-
# number of metabolites
setMethod("met_num", signature(object = "modelorg"),
function(object) {
@@ -548,6 +557,79 @@ setReplaceMethod("subSys", signature(object = "modelorg"),
}
)
+# reaction sub systems
+setMethod("version", signature(object = "modelorg"),
+ function(object) {
+ return(object@version)
+ }
+)
+
+setReplaceMethod("version", signature(object = "modelorg"),
+ function(object, value) {
+ object@version <- value
+ stopifnot(validObject(object))
+ return(object)
+ }
+)
+
+# metabolites attributes
+setMethod("met_attr", signature(object = "modelorg"),
+ function(object) {
+ return(object@met_attr)
+ }
+)
+
+setReplaceMethod("met_attr", signature(object = "modelorg"),
+ function(object, value) {
+ object@met_attr <- value
+ return(object)
+ }
+)
+
+# reaction attributes
+setMethod("react_attr", signature(object = "modelorg"),
+ function(object) {
+ return(object@react_attr)
+ }
+)
+
+setReplaceMethod("react_attr", signature(object = "modelorg"),
+ function(object, value) {
+ object@react_attr <- value
+ return(object)
+ }
+)
+
+# compartment attributes
+setMethod("comp_attr", signature(object = "modelorg"),
+ function(object) {
+ return(object@comp_attr)
+ }
+)
+
+setReplaceMethod("comp_attr", signature(object = "modelorg"),
+ function(object, value) {
+ object@comp_attr <- value
+ return(object)
+ }
+)
+
+# model attributes
+setMethod("mod_attr", signature(object = "modelorg"),
+ function(object) {
+ return(object@mod_attr)
+ }
+)
+
+setReplaceMethod("mod_attr", signature(object = "modelorg"),
+ function(object, value) {
+ object@mod_attr <- value
+ return(object)
+ }
+)
+
+
+
#------------------------------------------------------------------------------#
# other methods #
@@ -587,6 +669,7 @@ setMethod("optimizeProb", signature(object = "modelorg"),
prCmd = NA, poCmd = NA,
prCil = NA, poCil = NA, ...) {
+ stopifnot(checkVersion(object))
if (!is.null(gene)) {
if (!is.null(react)) {
@@ -1073,11 +1156,22 @@ setMethod("singletonMetabolites", signature(object = "modelorg"),
}
)
+#------------------------------------------------------------------------------#
-
-
+setMethod("checkVersion", signature(object = "modelorg"),
+ function(object) {
+ if(!.hasSlot(object, "version")){
+ return("No version slot found. Please use upgradeModelorg with object")
+ }
+
+ if(compareVersion(version(object), SYBIL_SETTINGS("MODELORG_VERSION")) == 0){
+ return(TRUE)
+ }
+ return(paste0("modelorg has version ", version(object), ", but you need at least version ", version))
+ }
+)
diff --git a/R/parseBoolean.R b/R/parseBoolean.R
index 653aecc2e37b9de4f45c91a9fc7737693cdc3eb8..4546b26b778bcd49ff2c08ff4d31cb58a54af7bd 100644
--- a/R/parseBoolean.R
+++ b/R/parseBoolean.R
@@ -31,6 +31,7 @@
# The algorithm is the same.
#
# 2015-06-17 CJF: added handling for emtpy gprRule like "( )"
+# 2016-05-18 CJF: format of gprRules was changed.
.parseBoolean <- function(gprRule, tokens = "()&|~") {
@@ -88,7 +89,7 @@
gene_uniq <- unique(genes)
newTok <- match(genes, gene_uniq)
- newTok <- sapply(newTok, function(x) paste("x(", x, ")", sep = ""))
+ newTok <- sapply(newTok, function(x) paste("x[", x, "]", sep = ""))
# rule <-
diff --git a/R/readTEXTmod.R b/R/readTEXTmod.R
index 8746664f786c00533e700bddd0dd2369addfb059..00e71cc53f663309af0f43c89334aa1032b263d0 100644
--- a/R/readTEXTmod.R
+++ b/R/readTEXTmod.R
@@ -24,9 +24,9 @@
################################################
# Function: readTEXTmod
-#
-#
#
+# 2016-05-18 CJF: format of gprRules was changed.
+
readTEXTmod <- function(filename,
description,
@@ -112,7 +112,10 @@ parse_genes <- function(gene) {
}
# for the gpr slot and gprRules slot
- gene_pos <- which(allGenes %in% gene)
+ #gene_pos <- which(allGenes %in% gene)
+ #new gprRules:
+ gene_pos <- seq(along=gene)
+
if (length(gene) > 1) {
gpr_string <- paste("(", paste(gene, sep = "", collapse = " and "), ")")
rules_string <- paste("x[", gene_pos, "]", sep = "")
diff --git a/R/readTSVmod.R b/R/readTSVmod.R
index f66c1bda4435b43d10a4b502b9f47db00ae40b81..032e82fd6b5af3e7cb00c652ab8de4cba175114d 100644
--- a/R/readTSVmod.R
+++ b/R/readTSVmod.R
@@ -26,7 +26,7 @@
# Function: readTSVmod
#
#
-#
+# 2016-05-18 CJF: format of gprRules was changed.
readTSVmod <- function(prefix, suffix,
reactList, metList = NA, modDesc = NA,
@@ -949,13 +949,14 @@ readTSVmod <- function(prefix, suffix,
if (isTRUE(RruleL[i])) {
geneInd <- match(Rgenes[[i]], allGenes)
rxnGeneMat[i, geneInd] <- TRUE
+
+ # not needed for version 2.0 modelorg gprRules
+# for (j in 1 : length(geneInd)) {
+# pat <- paste("x(", j, ")", sep = "")
+# repl <- paste("x[", geneInd[j], "]", sep = "")
- for (j in 1 : length(geneInd)) {
- pat <- paste("x(", j, ")", sep = "")
- repl <- paste("x[", geneInd[j], "]", sep = "")
-
- Rrules[i] <- gsub(pat, repl, Rrules[i], fixed = TRUE)
- }
+# Rrules[i] <- gsub(pat, repl, Rrules[i], fixed = TRUE)
+# }
}
}
diff --git a/R/rmReact.R b/R/rmReact.R
index 9b30a44388c8af1c7788484aa72fc8ea773e845e..c420d70941bb3161316ccfcf208bf212cbbf25f3 100644
--- a/R/rmReact.R
+++ b/R/rmReact.R
@@ -38,30 +38,31 @@ rmReact <- function(model, react, rm_met = TRUE) {
# check model and react #
#------------------------------------------------------------------------------#
- if (!is(model, "modelorg")) {
- stop("needs an object of class modelorg!")
- }
-
-
- # check this, propably working wrong
- if (is.na(match(is(react)[1], c("reactId", "numeric", "integer", "character")))) {
- stop("argument react must be numeric, character, or of class reactId. Use checkReactId!")
- }
-
- # argument react comes from the function checkReactId()
- if (is(react, "reactId")) {
- rmReact <- react_pos(react)
- }
- else {
- checked_react <- checkReactId(model, react)
- #print(is(checked_react))
- if (!is(checked_react, "reactId")) {
- stop("Check your reaction Id's")
- }
- else {
- rmReact <- react_pos(checked_react)
- }
- }
+ if (!is(model, "modelorg")) {
+ stop("needs an object of class modelorg!")
+ }
+
+ stopifnot(checkVersion(model))
+
+ # check this, propably working wrong
+ if (is.na(match(is(react)[1], c("reactId", "numeric", "integer", "character")))) {
+ stop("argument react must be numeric, character, or of class reactId. Use checkReactId!")
+ }
+
+ # argument react comes from the function checkReactId()
+ if (is(react, "reactId")) {
+ rmReact <- react_pos(react)
+ }
+ else {
+ checked_react <- checkReactId(model, react)
+ #print(is(checked_react))
+ if (!is(checked_react, "reactId")) {
+ stop("Check your reaction Id's")
+ }
+ else {
+ rmReact <- react_pos(checked_react)
+ }
+ }
# if ((is(react, "numeric")) || (is(react, "integer"))) {
@@ -132,6 +133,10 @@ rmReact <- function(model, react, rm_met = TRUE) {
obj_coef(mod_out) <- obj_coef(model)[keepReact]
react_single(mod_out) <- react_single(model)[keepReact]
react_de(mod_out) <- react_de(model)[keepReact]
+
+ if(ncol(react_attr(model))>0){
+ react_attr(mod_out) <- react_attr(model)[keepReact, ]
+ }
react_num(mod_out) <- length(react_id(mod_out))
@@ -158,19 +163,8 @@ rmReact <- function(model, react, rm_met = TRUE) {
allGenes(mod_out) <- ag
}
-
- # reaction to gene mapping
- #SrGMbin <- rxnGeneMat(mod_out) != 0
-
- #SrGMbindiag <- diag(crossprod(SrGMbin))
-
- #keepGenes <- ifelse(SrGMbindiag == 0, FALSE, TRUE)
- keepGenes <- sapply(allGenes(model), function(x) match(x, allGenes(mod_out)))
- keepGenes <- ifelse(is.na(keepGenes), FALSE, TRUE)
- #print(keepGenes)
-
- rxnGeneMat(mod_out) <- rxnGeneMat(mod_out)[, keepGenes, drop = FALSE]
- #print(dim(rxnGeneMat))
+ newGeneOrder <- match(allGenes(mod_out), allGenes(model))
+ rxnGeneMat(mod_out) <- rxnGeneMat(mod_out)[, newGeneOrder, drop = FALSE]
}
@@ -208,6 +202,10 @@ rmReact <- function(model, react, rm_met = TRUE) {
met_comp(mod_out) <- met_comp(model)[keepMet]
met_single(mod_out) <- met_single(model)[keepMet]
met_de(mod_out) <- met_de(model)[keepMet]
+
+ if(ncol(met_attr(model))>0){
+ met_attr(mod_out) <- met_attr(model)[keepMet, ]
+ }
}
else {
met_num(mod_out) <- met_num(model)
diff --git a/R/settings.R b/R/settings.R
index da9dc9e2b7cfe67fe69098ad86a0c9014a14c8d3..7cff1f7780be6984028825ea650bbe7f098bda2e 100644
--- a/R/settings.R
+++ b/R/settings.R
@@ -42,6 +42,9 @@ SYBIL_SETTINGS <- function(parm, value, ...) {
}
switch(parm,
+ "MODELORG_VERSION" = {
+ stop("this value must not be set by the user!")
+ },
"SOLVER" = {
diff --git a/R/validmodelorg.R b/R/validmodelorg.R
index aba3fc6994dd245b0cb5f67f0cf60e6b1fc9a1fb..9ac0dd23a00480b5c75ccb056b4314aea16bc9e7 100644
--- a/R/validmodelorg.R
+++ b/R/validmodelorg.R
@@ -38,6 +38,12 @@
return("needs an object of class modelorg!")
}
+ versionCheck <- checkVersion(object)
+
+ if(!isTRUE(versionCheck)){
+ return(versionCheck)
+ }
+
if ((length(mod_id(object)) != 1) || (length(mod_name(object)) != 1)) {
return("mod_id and mod_name must have a length of 1!")
}
@@ -163,6 +169,30 @@
return("Wrong dimension of rxnGeneMat!")
}
}
+
+ # attributes
+
+ if(0 < ncol(met_attr(object))){
+ if(nrow(met_attr(object)) != met){
+ return("Wrong nrow of metabolite attributes")
+ }
+ }
+ if(0 < ncol(react_attr(object))){
+ if(nrow(react_attr(object)) != react){
+ return("Wrong nrow of reaction attributes")
+ }
+ }
+ if(0 < ncol(comp_attr(object))){
+ if(nrow(comp_attr(object)) != length(mod_compart(object))){
+ return("Wrong nrow of compartment attributes")
+ }
+ }
+ if(0 < ncol(mod_attr(object))){
+ if(nrow(mod_attr(object)) != 1){
+ return("Wrong nrow of model attributes")
+ }
+ }
+
}
return(TRUE)
}
diff --git a/R/zzz.R b/R/zzz.R
index 864d5d0f63c78a07d6a8149ca40ea8f17aa2489c..0dc683d56bcb26be60ced5f674ee03c8236bf822 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -36,6 +36,7 @@
# settings in sybil
.SYBILenv$settings <- list(
+ MODELORG_VERSION = "2.0",
SOLVER = "glpkAPI",
METHOD = "simplex",
TOLERANCE = 1E-6,
diff --git a/data/Ec_core.RData b/data/Ec_core.RData
index 4030d203e277531c772fa49364dc271910625cde..93dd81cd5a51117c39246a8701d39073edb12bbb 100644
Binary files a/data/Ec_core.RData and b/data/Ec_core.RData differ
diff --git a/man/SYBIL_SETTINGS.Rd b/man/SYBIL_SETTINGS.Rd
index 75810ed08aa3174c7c8ecfe5d64584fb2dc4b8b2..471edb62f3f9d383641693f7fe44faff2ba42965 100644
--- a/man/SYBIL_SETTINGS.Rd
+++ b/man/SYBIL_SETTINGS.Rd
@@ -93,14 +93,15 @@
for a particular \code{"SOLVER"}, the corresponding default value will
be used in such a case.
}
- \item{\code{"TOLERANCE"}}{
- Tolerance value.\cr
- Default: \code{1E-6}.
- }
\item{\code{"MAXIMUM"}}{
Absolute maximum value.\cr
Default: \code{1000}.
}
+ \item{\code{"MODELORG_VERSION"}}{
+ Currtent version of \code{modelorg}-Class.\cr
+ Value: \code{"2.0"}.\cr
+ This value must not be changed.
+ }
\item{\code{"ALGORITHM"}}{
Algorithm to use in order to analyze metabolic networks.
Possible values are:
@@ -145,6 +146,10 @@
(e.g. GLPK).\cr
Default: \code{as.data.frame(NA)}.
}
+ \item{\code{"TOLERANCE"}}{
+ Tolerance value.\cr
+ Default: \code{1E-6}.
+ }
}
}
diff --git a/man/checkOptSol-methods.Rd b/man/checkOptSol-methods.Rd
index ae86bd489f38114ee5221b54a4b25853de497a4f..35afd4ea948825f05f81074f0a58705968084906 100644
--- a/man/checkOptSol-methods.Rd
+++ b/man/checkOptSol-methods.Rd
@@ -50,7 +50,7 @@
}
\value{
- TRUE or FALSE if \code{onlywarn} is set to TRUE, otherwisw an object of class
+ TRUE or FALSE if \code{onlywarn} is set to TRUE, otherwise an object of class
\code{\linkS4class{checksol}}.
}
diff --git a/man/checkVersion-methods.Rd b/man/checkVersion-methods.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..528c2759f9ab2de289c4dd38d15e0ec436efce55
--- /dev/null
+++ b/man/checkVersion-methods.Rd
@@ -0,0 +1,58 @@
+\name{checkVersion-methods}
+
+\docType{methods}
+\encoding{utf8}
+
+\alias{checkVersion}
+\alias{checkVersion-methods}
+\alias{checkVersion,modelorg}
+\alias{checkVersion,modelorg-method}
+
+\title{checks Version of modelorg}
+
+\description{
+ Checks the Version of the modelorg.
+}
+
+\usage{
+\S4method{checkVersion}{modelorg}(object)
+}
+
+\section{Methods}{
+ \describe{
+ \item{\code{signature(object = "modelorg")}}{
+ method to use with objects of class \code{\linkS4class{modelorg}}.
+ }
+ }
+}
+
+\arguments{
+ \item{object}{
+ An object of class \code{\linkS4class{modelorg}} or of class
+ \code{\linkS4class{summaryOptsol}}.
+ }
+}
+
+\details{
+ This method checks whether this instance of a modelorg-Class is of the currently
+ used version. All methods of sybil create the correct version of modelorg, but
+ if objects saved to disk may be of an older version. Current version can be
+ obtained by \code{SYBIL_SETTINGS("VERSION")}.
+}
+
+\author{
+ Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
+}
+
+
+\value{
+ Returns \code{TRUE} if the version is correct. Otherwise returns a character
+ stating the reason.
+}
+
+\seealso{
+ Class \code{\linkS4class{modelorg}},
+ method \code{\link{upgradeModelorg}} and \code{\link{SYBIL_SETTINGS}}
+}
+
+\keyword{methods}
diff --git a/man/modelorg-class.Rd b/man/modelorg-class.Rd
index 2b34679cdd15c76cc57bf68f1f1b1baf6445bab1..dfeb47d779bbd9cd0189f77d9ff4c2d13b05cad5 100644
--- a/man/modelorg-class.Rd
+++ b/man/modelorg-class.Rd
@@ -8,6 +8,10 @@
\alias{allGenes,modelorg-method}
\alias{allGenes<-}
\alias{allGenes}
+\alias{comp_attr<-,modelorg-method}
+\alias{comp_attr,modelorg-method}
+\alias{comp_attr<-}
+\alias{comp_attr}
\alias{dim,modelorg-method}
\alias{genes<-,modelorg-method}
\alias{genes,modelorg-method}
@@ -25,6 +29,10 @@
\alias{lowbnd,modelorg-method}
\alias{lowbnd<-}
\alias{lowbnd}
+\alias{met_attr<-,modelorg-method}
+\alias{met_attr,modelorg-method}
+\alias{met_attr<-}
+\alias{met_attr}
\alias{met_comp<-,modelorg-method}
\alias{met_comp,modelorg-method}
\alias{met_comp<-}
@@ -49,6 +57,10 @@
\alias{met_single,modelorg-method}
\alias{met_single<-}
\alias{met_single}
+\alias{mod_attr<-,modelorg-method}
+\alias{mod_attr,modelorg-method}
+\alias{mod_attr<-}
+\alias{mod_attr}
\alias{mod_compart<-,modelorg-method}
\alias{mod_compart,modelorg-method}
\alias{mod_compart<-}
@@ -75,6 +87,10 @@
\alias{obj_coef}
\alias{printObjFunc,modelorg-method}
\alias{printObjFunc}
+\alias{react_attr<-,modelorg-method}
+\alias{react_attr,modelorg-method}
+\alias{react_attr<-}
+\alias{react_attr}
\alias{react_de<-,modelorg-method}
\alias{react_de,modelorg-method}
\alias{react_de<-}
@@ -118,6 +134,10 @@
\alias{uppbnd,modelorg-method}
\alias{uppbnd<-}
\alias{uppbnd}
+\alias{version<-,modelorg-method}
+\alias{version,modelorg-method}
+\alias{version<-}
+\alias{version}
\encoding{utf8}
@@ -160,6 +180,9 @@
\item{\code{mod_name}:}{
Object of class \code{"character"} indicating the model name.
}
+ \item{\code{version}:}{
+ Object of class \code{"character"} indicating the model version.
+ }
\item{\code{mod_id}:}{
Object of class \code{"character"} indicating the model id.
}
@@ -167,9 +190,16 @@
Object of class \code{"character"} containing a single character string
functioning as a unique key to a model object.
}
+ \item{\code{mod_attr}:}{
+ Object of class \code{"data.frame"} to store additional attributes of the model.
+ }
\item{\code{mod_compart}:}{
Object of class \code{"character"} containing the model compartments.
}
+ \item{\code{comp_attr}:}{
+ Object of class \code{"data.frame"} to store additional attributes for
+ each compartment.
+ }
\item{\code{met_num}:}{
Object of class \code{"integer"} indicating the number of metabolites.
}
@@ -182,6 +212,10 @@
\item{\code{met_comp}:}{
Object of class \code{"integer"} containing the metabolites compartment.
}
+ \item{\code{met_attr}:}{
+ Object of class \code{"data.frame"} to store additional attributes for
+ each metabolite.
+ }
\item{\code{met_single}:}{
Object of class \code{"logical"} with length \code{met_num}. Element
\code{i} is \code{TRUE}, if metabolite \code{i} appears only once in S.
@@ -203,6 +237,10 @@
\item{\code{react_name}:}{
Object of class \code{"character"} containing the reaction names.
}
+ \item{\code{react_attr}:}{
+ Object of class \code{"data.frame"} to store additional attributes for
+ each reaction.
+ }
\item{\code{react_single}:}{
Object of class \code{"logical"} with length \code{react_num}. Element
\code{i} is \code{TRUE}, if reaction \code{i} uses metabolites appearing
@@ -430,6 +468,12 @@
\item{\code{uppbnd}:}{
\code{signature(object = "modelorg")}: gets the \code{uppbnd} slot.
}
+ \item{\code{version<-}:}{
+ \code{signature(object = "modelorg")}: sets the \code{version} slot.
+ }
+ \item{\code{version}:}{
+ \code{signature(object = "modelorg")}: gets the \code{version} slot.
+ }
}
}
diff --git a/man/upgradeModelorg.Rd b/man/upgradeModelorg.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..45073b33772fd8409c22d26c177bb3267f2c8ece
--- /dev/null
+++ b/man/upgradeModelorg.Rd
@@ -0,0 +1,46 @@
+\name{upgradeModelorg}
+\alias{upgradeModelorg}
+
+\encoding{utf8}
+
+\title{
+ Upgrade modelorg to newer version.
+}
+\description{
+ Performs necessary changes to the object to promote it to a newer version.
+}
+\usage{
+ upgradeModelorg(object)
+}
+
+\arguments{
+ \item{object}{
+ An object of class \code{\linkS4class{modelorg}}.
+ }
+}
+
+\details{
+ This method performs the necessary changes on a modelorg object to promote
+ it to a newer version.
+
+ Changes from previous modelorg version (no version slot set) to version 2.0:
+ Representation in the gprRules slot is now incompatible to the earlier versions.
+}
+
+\value{
+ An object of class \code{\linkS4class{modelorg}}, matching the current
+ version requirements used by sybil.
+}
+
+\author{
+ Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
+}
+
+
+\examples{
+ data(Ec_core)
+ upgradeModelorg(Ec_core)
+}
+
+\keyword{upgrade, version}
+