diff --git a/R/addReact.R b/R/addReact.R
index 31a8c66d93b1e230ff5cfad7f88b0e497da948a5..35e6a252a998e9d3147ebc08b7916fbdc6b9b35d 100644
--- a/R/addReact.R
+++ b/R/addReact.R
@@ -139,6 +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)) {
@@ -181,6 +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
@@ -211,6 +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)
@@ -359,6 +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/generics.R b/R/generics.R
index 3c393a8a8b4959a34676de49fddf99dc658848a8..af64b93398d579728264339f40fbcd40d648d6bd 100644
--- a/R/generics.R
+++ b/R/generics.R
@@ -151,6 +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") }
)
@@ -540,6 +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") }
)
@@ -600,6 +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") }
)
@@ -763,6 +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") }
)
diff --git a/R/modelorgClass.R b/R/modelorgClass.R
index d44d5489a14303b13bd60cbc264f5a08b1beec59..5cd4063e5cd24ab01b9f406e35558bea526576d4 100644
--- a/R/modelorgClass.R
+++ b/R/modelorgClass.R
@@ -39,18 +39,22 @@ 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
@@ -111,6 +115,10 @@ 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))
@@ -206,7 +214,6 @@ setReplaceMethod("mod_compart", signature(object = "modelorg"),
}
)
-
# number of metabolites
setMethod("met_num", signature(object = "modelorg"),
function(object) {
@@ -565,6 +572,64 @@ setReplaceMethod("version", signature(object = "modelorg"),
}
)
+# 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 #
diff --git a/R/parseBoolean.R b/R/parseBoolean.R
index b10a46d4233ab51d2145a2d4db5ae4860a5c39c3..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 = "()&|~") {
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 0bd26047b9f48a5f650c781535aa5bed8c065c2f..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,
@@ -950,7 +950,7 @@ readTSVmod <- function(prefix, suffix,
geneInd <- match(Rgenes[[i]], allGenes)
rxnGeneMat[i, geneInd] <- TRUE
- # not needed for version 2.0 modelorgs
+ # 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 = "")
diff --git a/R/rmReact.R b/R/rmReact.R
index 45ab6ed9e8df8089510449bcf0ebc8d047b8c576..0efb32c1de032df7a56bbabf84caed276379fd94 100644
--- a/R/rmReact.R
+++ b/R/rmReact.R
@@ -133,6 +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))
@@ -210,6 +214,10 @@ 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/upgradeModelorg.R b/R/upgradeModelorg.R
index 54031c1c9d74d78afd4b53fe48076125a36311f4..a10cdfd16b9025d30aa34c9a5da0c8c0b81c0ba9 100644
--- a/R/upgradeModelorg.R
+++ b/R/upgradeModelorg.R
@@ -33,16 +33,24 @@
upgradeModelorg <- function(object){
stopifnot(is(object, "modelorg"))
- if(!.hasSlot(object, "version")){
+ if(!.hasSlot(object, "version") || compareVersion(version(object), "2.0") == -1){
# object is from a time before versions were introduced.
- # just add version slot and run again.
+
+ # just add version slot
object@version <- "2.0"
+ # update gprRules to new format
rules <- lapply(gpr(object), .parseBoolean)
genes(object) <- sapply(rules, "[[", "gene")
gprRules(object) <- sapply(rules, "[[", "rule")
- #recursively upgrad to latest version.
+ # set attribute slots
+ react_attr(object) <- data.frame()
+ comp_attr(object) <- data.frame()
+ met_attr(object) <- data.frame()
+ mod_attr(object) <- data.frame()
+
+ #recursively upgrade to latest version.
return(upgradeModelorg(object))
}
diff --git a/R/validmodelorg.R b/R/validmodelorg.R
index 2aaee840fa48f230f3f41a35f9c2a14be6a076d3..9ac0dd23a00480b5c75ccb056b4314aea16bc9e7 100644
--- a/R/validmodelorg.R
+++ b/R/validmodelorg.R
@@ -169,6 +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/data/Ec_core.RData b/data/Ec_core.RData
index ebf33613cc778356128bc432ac0ee3f02d95b12f..93dd81cd5a51117c39246a8701d39073edb12bbb 100644
Binary files a/data/Ec_core.RData and b/data/Ec_core.RData differ
diff --git a/man/modelorg-class.Rd b/man/modelorg-class.Rd
index c76921ddff8c0d4242f96dd316b6a86bcfb46d9f..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<-}
@@ -174,9 +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.
}
@@ -189,6 +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.
@@ -210,6 +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