diff --git a/DESCRIPTION b/DESCRIPTION
index 8d7d6f8e8e3f150abe8cf147ec6eb0766117599c..d1df7728709a8ba11316333a950bbce45d527fd1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: sybil
Type: Package
Title: Efficient Constrained Based Modelling
-Version: 2.0.4
-Date: 2017-07-18
+Version: 2.1.1
+Date: 2018-05-14
Authors@R: c(
person(c("C.", "Jonathan"), "Fritzemeier", role = c("cre", "ctb"), email = "clausjonathan.fritzemeier@uni-duesseldorf.de"),
person("Gabriel", "Gelius-Dietrich", role = c("aut")),
@@ -12,7 +12,7 @@ Authors@R: c(
person("Abdelmoneim", "Desouki", role = "ctb"),
person(c("Martin", "J."), "Lercher", role = "ctb"))
Maintainer: C. Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
-Depends: R (>= 2.14.2), Matrix, lattice
+Depends: R (>= 3.2.0), Matrix, lattice
Imports: methods
Suggests: glpkAPI (>= 1.2.8), cplexAPI (>= 1.2.4), clpAPI (>= 1.2.4),
lpSolveAPI (>= 5.5.2.0), parallel, grid
@@ -21,7 +21,8 @@ URL:
Description: This Systems Biology Package (Gelius-Dietrich et. al. (2012) <doi:10.1186/1752-0509-7-125>) implements algorithms for constraint based analyses of metabolic networks, e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis. The package is easily extendable for additional algorithms. Most of the current LP/MILP solvers are supported via additional packages.
LazyLoad: yes
License: GPL-3 | file LICENSE
-Collate: generics.R validmodelorg.R validoptsol.R validreactId.R
+Collate: generics.R validmodelorg.R validoptsol.R validreactId.R validreact.R
+ reactClass.R
validreactId_Exch.R validsysBiolAlg.R addAlgorithm.R
addExchReact.R addReact.R addSolver.R blockedReact.R
bracket_pairs.R ceilValues.R changeBounds.R changeGPR.R
@@ -53,7 +54,8 @@ Collate: generics.R validmodelorg.R validoptsol.R validreactId.R
sysBiolAlg_lmomaClass.R sysBiolAlg_momaClass.R
sysBiolAlg_mtfClass.R sysBiolAlg_mtfEasyConstraintClass.R
sysBiolAlg_roomClass.R sybilLogClass.R upgradeModelorg.R
-Packaged: 2017-07-18 09:34:14 UTC; jonathan
+ mergeReact2Modelorg.R
+Packaged: 2018-05-14 12:34:14 UTC; jonathan
Author: C. Jonathan Fritzemeier [cre, ctb],
Gabriel Gelius-Dietrich [aut],
Rajen Piernikarczyk [ctb],
diff --git a/NAMESPACE b/NAMESPACE
index e782ef4835465a07be574fe5c2c7610ae3cb85da..b750218c1187f48e7e88423bd85e7d3971599a43 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -11,6 +11,7 @@ importFrom("utils", "compareVersion")
exportPattern("^[^\\.]")
+
exportClass(
checksol,
fluxDistribution,
@@ -30,6 +31,7 @@ optsol_robAna,
optsol,
pointerToProb,
ppProc,
+react,
reactId,
sybilError,
sybilLog
diff --git a/R/addReact.R b/R/addReact.R
index 35e6a252a998e9d3147ebc08b7916fbdc6b9b35d..0478d7af32613189fa777a6470d55c2dc1289cca 100644
--- a/R/addReact.R
+++ b/R/addReact.R
@@ -31,19 +31,20 @@
# The algorithm is (more or less) the same.
-addReact <- function(model,
- id,
- met,
- Scoef,
- reversible = FALSE,
- lb = 0,
- ub = SYBIL_SETTINGS("MAXIMUM"),
- obj = 0,
- subSystem = NA,
- gprAssoc = NA,
- reactName = NA,
- metName = NA,
- metComp = NA) {
+setMethod("addReact", signature(model = "modelorg"),
+ function(model,
+ id,
+ met,
+ Scoef,
+ reversible = FALSE,
+ lb = 0,
+ ub = SYBIL_SETTINGS("MAXIMUM"),
+ obj = 0,
+ subSystem = NA,
+ gprAssoc = NA,
+ reactName = NA,
+ metName = NA,
+ metComp = NA) {
# ------------------------------------------------------------------------ #
@@ -185,7 +186,7 @@ addReact <- function(model,
newRows <- Matrix::Matrix(0,
nrow = nNewRows,
ncol = react_num(model))
- newS <- Matrix::rBind(newS, newRows)
+ newS <- rbind(newS, newRows)
# new met attrs
if(ncol(newMetAttr) > 0){
@@ -219,7 +220,7 @@ addReact <- function(model,
newobj_coef <- append(obj_coef(model), obj)
# new column in stoichiometric matrix
- newS <- cBind(newS, rep(0, nrow(newS)))
+ newS <- cbind(newS, rep(0, nrow(newS)))
# new react Attr
# only one new row, /bc we can only add one reaction a time.
@@ -235,23 +236,23 @@ addReact <- function(model,
newsubSys <- ss
}
else {
- newsubSys <- rBind(ss, rep(FALSE, ncol(subSys(model))))
+ newsubSys <- rbind(ss, rep(FALSE, ncol(subSys(model))))
}
}
else {
if (is(subSystem, "logical")) {
- newsubSys <- rBind(subSys(model), subSystem)
+ newsubSys <- rbind(subSys(model), subSystem)
}
else {
nSubsRow <- colnames(subSys(model)) %in% subSystem
- newsubSys <- rBind(subSys(model), nSubsRow)
+ newsubSys <- rbind(subSys(model), nSubsRow)
}
}
# gpr association
if (ncol(rxnGeneMat(model)) > 0) {
- newrxnGeneMat <- rBind(rxnGeneMat(model),
+ newrxnGeneMat <- rbind(rxnGeneMat(model),
rep(FALSE, ncol(rxnGeneMat(model))))
}
else { #if (nrow(rxnGeneMat(model)) > 0) {
@@ -293,7 +294,7 @@ addReact <- function(model,
}
else {
for (i in seq(along = gene_rule[["gene"]][new_gene])) {
- newrxnGeneMat <- cBind(newrxnGeneMat,
+ newrxnGeneMat <- cbind(newrxnGeneMat,
rep(FALSE, nrow(newrxnGeneMat)))
}
}
@@ -410,5 +411,5 @@ addReact <- function(model,
return(mod_out)
-}
+})
diff --git a/R/checksolClass.R b/R/checksolClass.R
index 8659abf9d89d79f9a54084dcd679d4039ae23067..3f8c08ad95f321ec85e9e0f8c2d482bd9ab53ccc 100644
--- a/R/checksolClass.R
+++ b/R/checksolClass.R
@@ -62,7 +62,7 @@ setMethod("num_of_prob", signature(object = "checksol"),
}
)
-setReplaceMethod("num_of_prob", signature = (object = "checksol"),
+setReplaceMethod("num_of_prob", signature(object = "checksol"),
function(object, value) {
object@num_of_prob <- value
return(object)
@@ -77,7 +77,7 @@ setMethod("exit_code", signature(object = "checksol"),
}
)
-setReplaceMethod("exit_code", signature = (object = "checksol"),
+setReplaceMethod("exit_code", signature(object = "checksol"),
function(object, value) {
object@exit_code <- value
return(object)
@@ -92,7 +92,7 @@ setMethod("exit_num", signature(object = "checksol"),
}
)
-setReplaceMethod("exit_num", signature = (object = "checksol"),
+setReplaceMethod("exit_num", signature(object = "checksol"),
function(object, value) {
object@exit_num <- value
return(object)
@@ -107,7 +107,7 @@ setMethod("exit_meaning", signature(object = "checksol"),
}
)
-setReplaceMethod("exit_meaning", signature = (object = "checksol"),
+setReplaceMethod("exit_meaning", signature(object = "checksol"),
function(object, value) {
object@exit_meaning <- value
return(object)
@@ -122,7 +122,7 @@ setMethod("status_code", signature(object = "checksol"),
}
)
-setReplaceMethod("status_code", signature = (object = "checksol"),
+setReplaceMethod("status_code", signature(object = "checksol"),
function(object, value) {
object@status_code <- value
return(object)
@@ -137,7 +137,7 @@ setMethod("status_num", signature(object = "checksol"),
}
)
-setReplaceMethod("status_num", signature = (object = "checksol"),
+setReplaceMethod("status_num", signature(object = "checksol"),
function(object, value) {
object@status_num <- value
return(object)
@@ -153,7 +153,7 @@ setMethod("status_meaning", signature(object = "checksol"),
}
)
-setReplaceMethod("status_meaning", signature = (object = "checksol"),
+setReplaceMethod("status_meaning", signature(object = "checksol"),
function(object, value) {
object@status_meaning <- value
return(object)
diff --git a/R/doubleReact.R b/R/doubleReact.R
index 69b6c5475746d00ae40b9943ebc9d0c977cb4d90..fbf56ab863d7d158ad3e4aa2cf4b2a18b90e920b 100644
--- a/R/doubleReact.R
+++ b/R/doubleReact.R
@@ -123,7 +123,7 @@ doubleReact <- function(model, checkRev = TRUE, linInd = FALSE) {
# Put the columns of S into a new matrix, which contain the same
# number of metabolites
- Stmp <- cBind(S(model)[, columns[[i]] ])
+ Stmp <- cbind(S(model)[, columns[[i]] ])
# translate Stmp into a matrix with the row indices of the
# non zero elements
diff --git a/R/fluxDistributionClass.R b/R/fluxDistributionClass.R
index d716d5da1082b61923ed360f871e5ce618201b05..ef3e4466e7cf69ae2ac56e6b567d760f14d26711 100644
--- a/R/fluxDistributionClass.R
+++ b/R/fluxDistributionClass.R
@@ -72,7 +72,7 @@ setMethod("fluxes", signature(object = "fluxDistribution"),
}
)
-setReplaceMethod("fluxes", signature = (object = "fluxDistribution"),
+setReplaceMethod("fluxes", signature(object = "fluxDistribution"),
function(object, value) {
object@fluxes <- value
return(object)
diff --git a/R/generics.R b/R/generics.R
index af64b93398d579728264339f40fbcd40d648d6bd..b294389bfb4364df658d908bb0f6cffb79de20bf 100644
--- a/R/generics.R
+++ b/R/generics.R
@@ -38,6 +38,10 @@ setGeneric(name = "addColsToProb",
def = function(lp, ...) { standardGeneric("addColsToProb") }
)
+setGeneric(name = "addReact",
+ def = function(model, ...) { standardGeneric("addReact") }
+)
+
setGeneric(name = "addRows",
def = function(lp, nrows, ...) { standardGeneric("addRows") }
)
@@ -351,6 +355,10 @@ setGeneric(name = "getObjVal",
def = function(lp) { standardGeneric("getObjVal") }
)
+setGeneric(name = "getReaction",
+ def = function(X, ...) { standardGeneric("getReaction") }
+)
+
setGeneric(name = "getRedCosts",
def = function(lp) { standardGeneric("getRedCosts") }
)
@@ -389,6 +397,13 @@ setGeneric(name = "gprRules<-",
def = function(object, value) { standardGeneric("gprRules<-") }
)
+setGeneric(name = "gprRule",
+ def = function(object) { standardGeneric("gprRule") }
+)
+setGeneric(name = "gprRule<-",
+ def = function(object, value) { standardGeneric("gprRule<-") }
+)
+
setGeneric(name = "hasEffect",
def = function(object) { standardGeneric("hasEffect") }
)
@@ -869,6 +884,13 @@ setGeneric(name = "S<-",
def = function(object, value) { standardGeneric("S<-") }
)
+setGeneric(name = "s",
+ def = function(object) { standardGeneric("s") }
+)
+setGeneric(name = "s<-",
+ def = function(object, value) { standardGeneric("s<-") }
+)
+
setGeneric(name = "scaleProb",
def = function(lp, ...) { standardGeneric("scaleProb") }
)
diff --git a/R/mergeReact2Modelorg.R b/R/mergeReact2Modelorg.R
new file mode 100644
index 0000000000000000000000000000000000000000..0c7cb3aab0676b98ee8695a2d4604f2ddae70613
--- /dev/null
+++ b/R/mergeReact2Modelorg.R
@@ -0,0 +1,162 @@
+# mergeReact2Modelorg.R
+# FBA and friends with R.
+#
+# Copyright (C) 2010-2017 Claus Jonathan Fritzemeier, Dpt. for Computational Cell Biology,
+# Institute for Informatics, Heinrich-Heine-University, Duesseldorf, Germany.
+# All right reserved.
+# Email: clausjonathan.fritzemeier@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/>.
+
+
+# mergeReact2Modelorg
+
+
+################################################
+# Function: mergeReact2Modelorg
+#
+# Merge react objects into modelorg object
+#
+# Takes a list of react class instances and returns a modelorg object by
+# merging the reactions into one model.
+
+
+#------------------------------------------------------------------------------#
+# definition of the function mergeReact2Modelorg #
+#------------------------------------------------------------------------------#
+
+
+mergeReact2Modelorg <- function(reactList = NULL, id="newModel", name=""){
+
+ stopifnot(!is.null(reactList))
+
+ morg <- new("modelorg", id=id, name=name)
+
+ reacts <- sapply(reactList, react_id)
+ if(anyDuplicated(reacts)){
+ stop("reaction ids have to be unique.")
+ }
+ react_id(morg) <- reacts
+ react_num(morg) <- length(reacts)
+
+ met_id <- unique(unlist(lapply(reactList, met_id)))
+ met_id(morg) <- met_id
+ met_num(morg) <- length(met_id(morg))
+
+ # collecting metabolite names and verifying identical assignments
+ met_name <- character(length(met_id))
+ names(met_name) <- met_id
+ for(r in reactList){
+ if(!all(met_name[met_id(r)] == "" | met_name[met_id(r)] == met_name(r))){
+ stop("different metabolite names for same met_id")
+ }
+ met_name[met_id(r)] <- met_name(r)
+ }
+ met_name(morg) <- met_name
+
+ # collecting metabolite compartments and verifying identical assignments
+ met_comp <- character(length(met_id))
+ names(met_comp) <- met_id
+ for(r in reactList){
+ stopifnot(all(met_comp[met_id(r)] == "" | met_comp[met_id(r)] == met_comp(r)))
+ met_comp[met_id(r)] <- met_comp(r)
+ }
+ mod_compart(morg) <- unique(met_comp)
+ met_comp(morg) <- match(met_comp, mod_compart(morg))
+
+ S <- Matrix(0, nrow=length(met_id), ncol=length(reacts))
+ for(j in seq(along=reactList)){
+ r <- reactList[[j]]
+ i <- match(met_id(r), met_id)
+ S[i, j] <- s(r)
+ }
+ S(morg) <- S
+
+ subs <- lapply(reactList, subSys)
+ subsUnique <- unique(unlist(subs))
+
+ subSys <- Matrix(F, ncol=length(subsUnique), nrow=length(reacts))
+ for(i in seq(along=reactList)){
+ ss <- setdiff(subSys(r), "")
+ if(length(ss)> 0 ){
+ j <- match(ss, subsUnique)
+ subSys[i, j] <- T
+ }
+ }
+ colnames(subSys) <- subsUnique
+ subSys(morg) <- subSys
+
+ gprRules(morg) <- sapply(reactList, gprRule)
+ gpr(morg) <- sapply(reactList, gpr)
+ genes(morg) <- lapply(reactList, genes)
+ allGenes(morg) <- setdiff(unique(unlist(genes(morg))), "")
+
+
+ # built react_attr frame:
+ if(all(sapply(reactList, function(x) nrow(react_attr(x))==0))){
+ react_attr(morg) <- data.frame()
+ }else{
+ reactAttrList <- lapply(reactList, function(x){
+ df <- react_attr(x)
+ df$react_id <- react_id(x)
+ df
+ })
+ reactAttr <- Reduce(function(x, y) merge(x, y, by=intersect(colnames(x), colnames(y)), suffixes=c("", ""), all=TRUE), reactAttrList)
+ reactAttr <- reactAttr[match(react_id(morg), reactAttr$react_id), ]
+ reactAttr <- reactAttr[, setdiff(colnames(reactAttr), "react_id"), drop=F]
+ react_attr(morg) <- reactAttr
+ }
+
+ # built met_attr frame:
+ if(all(sapply(reactList, function(x) nrow(met_attr(x))==0))){
+ met_attr(morg) <- data.frame()
+ }else{
+ metAttrList <- lapply(reactList, function(x){
+ df <- met_attr(x)
+ df$met_id <- met_id(x)
+ df
+ })
+ metAttr <- Reduce(function(x, y) merge(x, y, by=intersect(colnames(x), colnames(y)), suffixes=c("", ""), all=TRUE), metAttrList)
+ metAttr <- metAttr[match(met_id(morg), metAttr$met_id), ]
+ metAttr <- metAttr[, setdiff(colnames(metAttr), "met_id"), drop=F]
+ met_attr(morg) <- metAttr
+ }
+
+
+ # built comp_attr frame:
+ if(all(sapply(reactList, function(x) nrow(comp_attr(x))==0))){
+ comp_attr(morg) <- data.frame()
+ }else{
+ compAttrList <- lapply(reactList, function(x){
+ df <- comp_attr(x)
+ df
+ })
+ compAttr <- Reduce(function(x, y) merge(x, y, by=intersect(colnames(x), colnames(y)), suffixes=c("", ""), all=TRUE), compAttrList)
+ compAttr <- compAttr[match(mod_compart(morg), compAttr$comp_id), ]
+ compAttr <- compAttr[, setdiff(colnames(compAttr), "comp_id"), drop=F]
+ comp_attr(morg) <- compAttr
+ }
+
+ mod_attr(morg) <- data.frame()
+ stopifnot(validObject(morg, "modelorg"))
+ return(morg)
+}
+
+
+
+
+
+
diff --git a/R/modelorgClass.R b/R/modelorgClass.R
index 5cd4063e5cd24ab01b9f406e35558bea526576d4..4f6bcf46cca68dffdae5fd47d81366924196d3b3 100644
--- a/R/modelorgClass.R
+++ b/R/modelorgClass.R
@@ -105,7 +105,7 @@ modelorg <- function(id, name, subSys = NULL, compartment = NULL) {
#------------------------------------------------------------------------------#
setMethod(f = "initialize",
- signature = "modelorg",
+ signature("modelorg"),
definition = function(.Object, id, name,
subSys = NULL, compartment = NULL) {
@@ -147,7 +147,7 @@ setMethod("mod_id", signature(object = "modelorg"),
}
)
-setReplaceMethod("mod_id", signature = (object = "modelorg"),
+setReplaceMethod("mod_id", signature(object = "modelorg"),
function(object, value) {
object@mod_id <- value
return(object)
@@ -162,7 +162,7 @@ setMethod("mod_key", signature(object = "modelorg"),
}
)
-setReplaceMethod("mod_key", signature = (object = "modelorg"),
+setReplaceMethod("mod_key", signature(object = "modelorg"),
function(object, value) {
object@mod_key <- value
return(object)
@@ -177,7 +177,7 @@ setMethod("mod_name", signature(object = "modelorg"),
}
)
-setReplaceMethod("mod_name", signature = (object = "modelorg"),
+setReplaceMethod("mod_name", signature(object = "modelorg"),
function(object, value) {
object@mod_name <- value
return(object)
@@ -192,7 +192,7 @@ setMethod("mod_desc", signature(object = "modelorg"),
}
)
-setReplaceMethod("mod_desc", signature = (object = "modelorg"),
+setReplaceMethod("mod_desc", signature(object = "modelorg"),
function(object, value) {
object@mod_desc <- value
return(object)
@@ -965,7 +965,68 @@ setMethod("printMetabolite", signature(object = "modelorg"),
}
)
+#------------------------------------------------------------------------------#
+setMethod("getReaction", signature(X = "modelorg"),
+ function(X, j = NULL, drop=T, tol = SYBIL_SETTINGS("TOLERANCE")) {
+ # translate reaction id's to indices
+ cj <- checkReactId(X, react = j)
+ if (!is(cj, "reactId")) {
+ stop("check argument j")
+ }
+ else {
+ cn <- react_pos(cj)
+ }
+ rl <- lapply(cn, function(r){
+ s <- S(X)[,r]
+
+ if(nrow(met_attr(X))>0){
+ ma <- met_attr(X)[abs(s) > tol, , drop=F]
+ }else{
+ ma <- data.frame()
+ }
+ if(nrow(react_attr(X))>0){
+ ra <- react_attr(X)[r, , drop=F]
+ }else{
+ ra <- data.frame()
+ }
+ if(nrow(comp_attr(X))>0){
+ comp <- unique(met_comp(X)[abs(s) > tol])
+ ca <- comp_attr(X)[comp, , drop=F]
+ ca$comp_id <- mod_compart(X)[comp]
+ }else{
+ ca <- data.frame()
+ }
+
+ new("react",
+ id=react_id(X)[r],
+ name=react_name(X)[r],
+ rev=react_rev(X)[r],
+ met_id=met_id(X)[abs(s) > tol],
+ met_name=met_name(X)[abs(s) > tol],
+ met_comp=mod_compart(X)[met_comp(X)[abs(s) > tol]],
+ s=s[abs(s) > tol],
+ lowbnd=lowbnd(X)[r],
+ uppbnd=uppbnd(X)[r],
+ obj_coef=obj_coef(X)[r],
+ gprRule=gprRules(X)[r],
+ genes=genes(X)[[r]],
+ gpr = gpr(X)[r],
+ subSys = colnames(subSys(X))[subSys(X)[r,]],
+ met_attr = ma,
+ react_attr = ra,
+ comp_attr = ca
+ )
+ })
+
+ if(length(rl) == 1 && drop){
+ return(rl[[1]])
+ }
+
+ names(rl) <- react_id(X)[cn]
+ return(rl)
+ }
+)
#------------------------------------------------------------------------------#
diff --git a/R/modelorg_irrevClass.R b/R/modelorg_irrevClass.R
index 9c1850bf56295974228f01cd2a9dc903b6e69852..673ffe6f3d29e722eeb3b22c278260846bb1d9d7 100644
--- a/R/modelorg_irrevClass.R
+++ b/R/modelorg_irrevClass.R
@@ -83,7 +83,7 @@ setMethod("irrev", signature(object = "modelorg_irrev"),
}
)
-setReplaceMethod("irrev", signature = (object = "modelorg_irrev"),
+setReplaceMethod("irrev", signature(object = "modelorg_irrev"),
function(object, value) {
object@irrev <- value
return(object)
@@ -98,7 +98,7 @@ setMethod("matchrev", signature(object = "modelorg_irrev"),
}
)
-setReplaceMethod("matchrev", signature = (object = "modelorg_irrev"),
+setReplaceMethod("matchrev", signature(object = "modelorg_irrev"),
function(object, value) {
object@matchrev <- value
return(object)
@@ -113,7 +113,7 @@ setMethod("rev2irrev", signature(object = "modelorg_irrev"),
}
)
-setReplaceMethod("rev2irrev", signature = (object = "modelorg_irrev"),
+setReplaceMethod("rev2irrev", signature(object = "modelorg_irrev"),
function(object, value) {
object@rev2irrev <- value
return(object)
@@ -128,7 +128,7 @@ setMethod("irrev2rev", signature(object = "modelorg_irrev"),
}
)
-setReplaceMethod("irrev2rev", signature = (object = "modelorg_irrev"),
+setReplaceMethod("irrev2rev", signature(object = "modelorg_irrev"),
function(object, value) {
object@irrev2rev<- value
return(object)
diff --git a/R/netFluxClass.R b/R/netFluxClass.R
index 624bf6cabdd3177cea41ad2e7d3568649856abb6..4f9d281d5e79c27af5311617adb452b8a92c9365 100644
--- a/R/netFluxClass.R
+++ b/R/netFluxClass.R
@@ -75,7 +75,7 @@ setMethod("react_id", signature(object = "netFlux"),
}
)
-setReplaceMethod("react_id", signature = (object = "netFlux"),
+setReplaceMethod("react_id", signature(object = "netFlux"),
function(object, value) {
object@react_id <- value
return(object)
diff --git a/R/optsolClass.R b/R/optsolClass.R
index 1311b7127d07ae6b558e00d0badea6d79c4c854c..bf550387a659023f4d1e601dbd5ad772ea0ac59e 100644
--- a/R/optsolClass.R
+++ b/R/optsolClass.R
@@ -78,7 +78,7 @@ setMethod("mod_id", signature(object = "optsol"),
}
)
-setReplaceMethod("mod_id", signature = (object = "optsol"),
+setReplaceMethod("mod_id", signature(object = "optsol"),
function(object, value) {
object@mod_id <- value
return(object)
@@ -93,7 +93,7 @@ setMethod("mod_key", signature(object = "optsol"),
}
)
-setReplaceMethod("mod_key", signature = (object = "optsol"),
+setReplaceMethod("mod_key", signature(object = "optsol"),
function(object, value) {
object@mod_key <- value
return(object)
@@ -108,7 +108,7 @@ setMethod("solver", signature(object = "optsol"),
}
)
-setReplaceMethod("solver", signature = (object = "optsol"),
+setReplaceMethod("solver", signature(object = "optsol"),
function(object, value) {
object@solver <- value
return(object)
@@ -123,7 +123,7 @@ setMethod("method", signature(object = "optsol"),
}
)
-setReplaceMethod("method", signature = (object = "optsol"),
+setReplaceMethod("method", signature(object = "optsol"),
function(object, value) {
object@method <- value
return(object)
@@ -138,7 +138,7 @@ setMethod("algorithm", signature(object = "optsol"),
}
)
-setReplaceMethod("algorithm", signature = (object = "optsol"),
+setReplaceMethod("algorithm", signature(object = "optsol"),
function(object, value) {
object@algorithm <- value
return(object)
@@ -153,7 +153,7 @@ setMethod("num_of_prob", signature(object = "optsol"),
}
)
-setReplaceMethod("num_of_prob", signature = (object = "optsol"),
+setReplaceMethod("num_of_prob", signature(object = "optsol"),
function(object, value) {
object@num_of_prob <- value
return(object)
@@ -168,7 +168,7 @@ setMethod("lp_num_cols", signature(object = "optsol"),
}
)
-setReplaceMethod("lp_num_cols", signature = (object = "optsol"),
+setReplaceMethod("lp_num_cols", signature(object = "optsol"),
function(object, value) {
object@lp_num_cols <- value
return(object)
@@ -183,7 +183,7 @@ setMethod("lp_num_rows", signature(object = "optsol"),
}
)
-setReplaceMethod("lp_num_rows", signature = (object = "optsol"),
+setReplaceMethod("lp_num_rows", signature(object = "optsol"),
function(object, value) {
object@lp_num_rows <- value
return(object)
@@ -240,7 +240,7 @@ setMethod("lp_obj", signature(object = "optsol"),
}
)
-setReplaceMethod("lp_obj", signature = (object = "optsol"),
+setReplaceMethod("lp_obj", signature(object = "optsol"),
function(object, value) {
object@lp_obj <- value
return(object)
@@ -255,7 +255,7 @@ setMethod("lp_ok", signature(object = "optsol"),
}
)
-setReplaceMethod("lp_ok", signature = (object = "optsol"),
+setReplaceMethod("lp_ok", signature(object = "optsol"),
function(object, value) {
object@lp_ok <- value
return(object)
@@ -270,7 +270,7 @@ setMethod("lp_stat", signature(object = "optsol"),
}
)
-setReplaceMethod("lp_stat", signature = (object = "optsol"),
+setReplaceMethod("lp_stat", signature(object = "optsol"),
function(object, value) {
object@lp_stat <- value
return(object)
@@ -315,7 +315,7 @@ setMethod("fldind", signature(object = "optsol"),
}
)
-setReplaceMethod("fldind", signature = (object = "optsol"),
+setReplaceMethod("fldind", signature(object = "optsol"),
function(object, value) {
object@fldind <- value
return(object)
@@ -330,7 +330,7 @@ setMethod("fluxdist", signature(object = "optsol"),
}
)
-setReplaceMethod("fluxdist", signature = (object = "optsol"),
+setReplaceMethod("fluxdist", signature(object = "optsol"),
function(object, value) {
object@fluxdist <- value
return(object)
@@ -345,7 +345,7 @@ setMethod("fluxes", signature(object = "optsol"),
}
)
-setReplaceMethod("fluxes", signature = (object = "optsol"),
+setReplaceMethod("fluxes", signature(object = "optsol"),
function(object, value) {
fluxes(object@fluxdist) <- value
return(object)
@@ -360,7 +360,7 @@ setMethod("alg_par", signature(object = "optsol"),
}
)
-setReplaceMethod("alg_par", signature = (object = "optsol"),
+setReplaceMethod("alg_par", signature(object = "optsol"),
function(object, value) {
object@alg_par <- value
return(object)
diff --git a/R/optsol_blockedReactClass.R b/R/optsol_blockedReactClass.R
index 37e6970abe2d71f21858c7666aea2209683c6046..e50af4a78659450e0b7e96c1769d50e5cb28b374 100644
--- a/R/optsol_blockedReactClass.R
+++ b/R/optsol_blockedReactClass.R
@@ -50,7 +50,7 @@ setMethod("blocked", signature(object = "optsol_blockedReact"),
}
)
-setReplaceMethod("blocked", signature = (object = "optsol_blockedReact"),
+setReplaceMethod("blocked", signature(object = "optsol_blockedReact"),
function(object, value) {
object@blocked <- value
return(object)
@@ -65,7 +65,7 @@ setMethod("react", signature(object = "optsol_blockedReact"),
}
)
-setReplaceMethod("react", signature = (object = "optsol_blockedReact"),
+setReplaceMethod("react", signature(object = "optsol_blockedReact"),
function(object, value) {
object@react <- value
return(object)
diff --git a/R/optsol_fluxVarClass.R b/R/optsol_fluxVarClass.R
index 5ad34c5814348395e36515d48da4e9473a0cb5c9..cc8399415b03c6e34eb5e7b2e46795ac500bd5b3 100644
--- a/R/optsol_fluxVarClass.R
+++ b/R/optsol_fluxVarClass.R
@@ -48,7 +48,7 @@ setMethod("react", signature(object = "optsol_fluxVar"),
}
)
-setReplaceMethod("react", signature = (object = "optsol_fluxVar"),
+setReplaceMethod("react", signature(object = "optsol_fluxVar"),
function(object, value) {
object@react <- value
return(object)
diff --git a/R/optsol_fluxdelClass.R b/R/optsol_fluxdelClass.R
index 1017db274df1fcc453c6dc1bc0fc4f8890dad984..e59efea8aa28661b093ed915fc275c3e2762a5e4 100644
--- a/R/optsol_fluxdelClass.R
+++ b/R/optsol_fluxdelClass.R
@@ -50,7 +50,7 @@ setMethod("chlb", signature(object = "optsol_fluxdel"),
}
)
-setReplaceMethod("chlb", signature = (object = "optsol_fluxdel"),
+setReplaceMethod("chlb", signature(object = "optsol_fluxdel"),
function(object, value) {
object@chlb <- value
return(object)
@@ -65,7 +65,7 @@ setMethod("chub", signature(object = "optsol_fluxdel"),
}
)
-setReplaceMethod("chub", signature = (object = "optsol_fluxdel"),
+setReplaceMethod("chub", signature(object = "optsol_fluxdel"),
function(object, value) {
object@chub <- value
return(object)
@@ -80,7 +80,7 @@ setMethod("dels", signature(object = "optsol_fluxdel"),
}
)
-setReplaceMethod("dels", signature = (object = "optsol_fluxdel"),
+setReplaceMethod("dels", signature(object = "optsol_fluxdel"),
function(object, value) {
object@dels <- value
return(object)
@@ -111,7 +111,7 @@ setMethod("lethal", signature(object = "optsol_fluxdel"),
)
-#setMethod("ind2id", signature = (object = "optsol_fluxdel"),
+#setMethod("ind2id", signature(object = "optsol_fluxdel"),
# function(object, slotN) {
# out <- NULL
# switch (slotN,
@@ -136,7 +136,7 @@ setMethod("lethal", signature(object = "optsol_fluxdel"),
#)
-setMethod("deleted", signature = (object = "optsol_fluxdel"),
+setMethod("deleted", signature(object = "optsol_fluxdel"),
function(object, i) {
value <- dels(object)[i, ]
return(value)
diff --git a/R/optsol_genedelClass.R b/R/optsol_genedelClass.R
index d58f040bd1a54a271dce4f0573bcaa30f30db48d..eba63cc64d5737ee216120797f784818c5235f46 100644
--- a/R/optsol_genedelClass.R
+++ b/R/optsol_genedelClass.R
@@ -49,7 +49,7 @@ setMethod("fluxdels", signature(object = "optsol_genedel"),
}
)
-setReplaceMethod("fluxdels", signature = (object = "optsol_genedel"),
+setReplaceMethod("fluxdels", signature(object = "optsol_genedel"),
function(object, value) {
object@fluxdels <- value
return(object)
@@ -64,7 +64,7 @@ setMethod("hasEffect", signature(object = "optsol_genedel"),
}
)
-setReplaceMethod("hasEffect", signature = (object = "optsol_genedel"),
+setReplaceMethod("hasEffect", signature(object = "optsol_genedel"),
function(object, value) {
object@hasEffect <- value
return(object)
@@ -76,7 +76,7 @@ setReplaceMethod("hasEffect", signature = (object = "optsol_genedel"),
# other methods #
#------------------------------------------------------------------------------#
-#setMethod("ind2id", signature = (object = "optsol_genedel"),
+#setMethod("ind2id", signature(object = "optsol_genedel"),
# function(object, slotN) {
# out <- NULL
# switch (slotN,
@@ -107,7 +107,7 @@ setReplaceMethod("hasEffect", signature = (object = "optsol_genedel"),
#)
-setMethod("deleted", signature = (object = "optsol_genedel"),
+setMethod("deleted", signature(object = "optsol_genedel"),
function(object, i) {
value <- fluxdels(object)[[i]]
return(value)
diff --git a/R/optsol_optimizeProbClass.R b/R/optsol_optimizeProbClass.R
index 3c45d48cab9220c839a5dbae593153fc0ccf9e01..ca7880b28e75f12bf5dc59662c59bd30566fd289 100644
--- a/R/optsol_optimizeProbClass.R
+++ b/R/optsol_optimizeProbClass.R
@@ -92,7 +92,7 @@ setMethod("preProc", signature(object = "optsol_optimizeProb"),
}
)
-setReplaceMethod("preProc", signature = (object = "optsol_optimizeProb"),
+setReplaceMethod("preProc", signature(object = "optsol_optimizeProb"),
function(object, value) {
object@preProc <- value
return(object)
@@ -107,7 +107,7 @@ setMethod("postProc", signature(object = "optsol_optimizeProb"),
}
)
-setReplaceMethod("postProc", signature = (object = "optsol_optimizeProb"),
+setReplaceMethod("postProc", signature(object = "optsol_optimizeProb"),
function(object, value) {
object@postProc <- value
return(object)
diff --git a/R/optsol_phppClass.R b/R/optsol_phppClass.R
index 9d788ff27d711534eb78f92107d77680613d5a76..e8a6ae4c25eaed6d84a1cfa91b8dab3781b327eb 100644
--- a/R/optsol_phppClass.R
+++ b/R/optsol_phppClass.R
@@ -50,7 +50,7 @@ setMethod("ctrlfl", signature(object = "optsol_phpp"),
}
)
-setReplaceMethod("ctrlfl", signature = (object = "optsol_phpp"),
+setReplaceMethod("ctrlfl", signature(object = "optsol_phpp"),
function(object, value) {
object@ctrlflm <- value
return(object)
diff --git a/R/optsol_robAnaClass.R b/R/optsol_robAnaClass.R
index 18ca6899a69ea4d2862ee6ccb6aafa2b28f63674..b1baf8c83c0fd301edbc12b699943cdc79f10634 100644
--- a/R/optsol_robAnaClass.R
+++ b/R/optsol_robAnaClass.R
@@ -49,7 +49,7 @@ setMethod("ctrlr", signature(object = "optsol_robAna"),
}
)
-setReplaceMethod("ctrlr", signature = (object = "optsol_robAna"),
+setReplaceMethod("ctrlr", signature(object = "optsol_robAna"),
function(object, value) {
object@ctrlr <- value
return(object)
@@ -64,7 +64,7 @@ setMethod("ctrlfl", signature(object = "optsol_robAna"),
}
)
-setReplaceMethod("ctrlfl", signature = (object = "optsol_robAna"),
+setReplaceMethod("ctrlfl", signature(object = "optsol_robAna"),
function(object, value) {
object@ctrlfl <- value
return(object)
diff --git a/R/ppProcClass.R b/R/ppProcClass.R
index a38a12228c8beb0fb9f0be83aefa803c101ceb65..b9282cbeb3b5bd3f7a0824ad5c0547e731a9cdb6 100644
--- a/R/ppProcClass.R
+++ b/R/ppProcClass.R
@@ -68,7 +68,7 @@ setMethod("cmd", signature(object = "ppProc"),
}
)
-setReplaceMethod("cmd", signature = (object = "ppProc"),
+setReplaceMethod("cmd", signature(object = "ppProc"),
function(object, value) {
object@cmd <- value
return(object)
@@ -83,7 +83,7 @@ setMethod("pa", signature(object = "ppProc"),
}
)
-setReplaceMethod("pa", signature = (object = "ppProc"),
+setReplaceMethod("pa", signature(object = "ppProc"),
function(object, value) {
object@pa <- value
return(object)
@@ -98,7 +98,7 @@ setMethod("ind", signature(object = "ppProc"),
}
)
-setReplaceMethod("ind", signature = (object = "ppProc"),
+setReplaceMethod("ind", signature(object = "ppProc"),
function(object, value) {
object@ind <- value
return(object)
diff --git a/R/reactClass.R b/R/reactClass.R
new file mode 100644
index 0000000000000000000000000000000000000000..29ac5e840e90261bfc93e37b90ee5cbf099a7c07
--- /dev/null
+++ b/R/reactClass.R
@@ -0,0 +1,487 @@
+# reactClass.R
+# FBA and friends with R.
+#
+# Copyright (C) 2010-2017 Claus Jonathan Fritzemeier, Dpt. for Computational Cell Biology,
+# Institute for Informatics, Heinrich-Heine-University, Duesseldorf, Germany.
+# All right reserved.
+# Email: clausjonathan.fritzemeier@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/>.
+
+
+# reactClass
+
+
+#------------------------------------------------------------------------------#
+# definition of the class react #
+#------------------------------------------------------------------------------#
+
+setClass("react",
+ representation(
+ react_rev = "logical", # vector reversibilities
+ react_id = "character", # reaction id
+ react_name = "character", # reaction name
+ react_single = "logical", # reaction using metabolites appearing only once in S
+ react_de = "logical", # reaction using dead end metabolites
+ react_attr = "data.frame", # reaction attributes
+ met_id = "character", # metabolites used in this reaction
+ met_comp = "character", # compartments of metabolites
+ met_name = "character", # metabolite names
+ met_attr = "data.frame", # metabolite attributes
+ comp_attr = "data.frame", # compartment attributes
+ s = "numeric", # matrix S
+ lowbnd = "numeric", # reaction lower bound
+ uppbnd = "numeric", # reaction upper bound
+ obj_coef = "numeric", # objective coefficient
+ gprRule = "character",
+ genes = "character",
+ gpr = "character",
+ subSys = "character"
+
+ ),
+ validity = .validreact
+)
+
+
+#------------------------------------------------------------------------------#
+# default constructor #
+#------------------------------------------------------------------------------#
+
+setMethod(f = "initialize",
+ signature = "react",
+ definition = function(.Object,
+ id,
+ name="",
+ rev=TRUE,
+ single=NA,
+ de=NA,
+ met_id,
+ met_name=NULL,
+ met_comp=NULL,
+ s,
+ lowbnd=-1000,
+ uppbnd=1000,
+ obj_coef=0,
+ gprRule="",
+ genes="",
+ gpr = "",
+ subSys = "",
+ met_attr = data.frame(),
+ react_attr = data.frame(),
+ comp_attr = data.frame()
+ ) {
+ stopifnot(!missing(id))
+ stopifnot(!missing(met_id))
+ stopifnot(!missing(s))
+
+ .Object@react_id <- id
+ .Object@react_name <- name
+ .Object@react_rev <- rev
+ .Object@react_single <- single
+ .Object@react_de <- de
+ .Object@met_id <- met_id
+ .Object@met_comp <- met_comp
+ .Object@met_name <- met_name
+ .Object@s <- s
+ .Object@lowbnd <- lowbnd
+ .Object@uppbnd <- uppbnd
+ .Object@obj_coef <- obj_coef
+ .Object@gprRule <- gprRule
+ .Object@genes <- genes
+ .Object@gpr <- gpr
+ .Object@subSys <- subSys
+
+ .Object@met_attr <- met_attr
+ .Object@react_attr <- react_attr
+ .Object@comp_attr <- comp_attr
+ return(.Object)
+ }
+)
+
+
+#------------------------------------------------------------------------------#
+# setters and getters #
+#------------------------------------------------------------------------------#
+
+# metabolite id's
+setMethod("met_id", signature(object = "react"),
+ function(object) {
+ return(object@met_id)
+ }
+)
+
+setReplaceMethod("met_id", signature(object = "react"),
+ function(object, value) {
+ object@met_id <- value
+ return(object)
+ }
+)
+
+
+# metabolite names
+setMethod("met_name", signature(object = "react"),
+ function(object) {
+ return(object@met_name)
+ }
+)
+
+setReplaceMethod("met_name", signature(object = "react"),
+ function(object, value) {
+ object@met_name <- value
+ return(object)
+ }
+)
+
+
+# metabolites compartments
+setMethod("met_comp", signature(object = "react"),
+ function(object) {
+ return(object@met_comp)
+ }
+)
+
+setReplaceMethod("met_comp", signature(object = "react"),
+ function(object, value) {
+ object@met_comp <- value
+ return(object)
+ }
+)
+
+
+# reversibilities
+setMethod("react_rev", signature(object = "react"),
+ function(object) {
+ return(object@react_rev)
+ }
+)
+
+setReplaceMethod("react_rev", signature(object = "react"),
+ function(object, value) {
+ object@react_rev <- value
+ return(object)
+ }
+)
+
+
+# reaction id's
+setMethod("react_id", signature(object = "react"),
+ function(object) {
+ return(object@react_id)
+ }
+)
+
+setReplaceMethod("react_id", signature(object = "react"),
+ function(object, value) {
+ object@react_id <- value
+ return(object)
+ }
+)
+
+
+# reaction names
+setMethod("react_name", signature(object = "react"),
+ function(object) {
+ return(object@react_name)
+ }
+)
+
+setReplaceMethod("react_name", signature(object = "react"),
+ function(object, value) {
+ object@react_name <- value
+ return(object)
+ }
+)
+
+
+# singletons
+setMethod("react_single", signature(object = "react"),
+ function(object) {
+ return(object@react_single)
+ }
+)
+
+setReplaceMethod("react_single", signature(object = "react"),
+ function(object, value) {
+ object@react_single <- value
+ return(object)
+ }
+)
+
+
+# dead ends
+setMethod("react_de", signature(object = "react"),
+ function(object) {
+ return(object@react_de)
+ }
+)
+
+setReplaceMethod("react_de", signature(object = "react"),
+ function(object, value) {
+ object@react_de <- value
+ return(object)
+ }
+)
+
+
+# stoichiometric matrix
+setMethod("s", signature(object = "react"),
+ function(object) {
+ return(object@s)
+ }
+)
+
+setReplaceMethod("s", signature(object = "react"),
+ function(object, value) {
+ object@s <- value
+ return(object)
+ }
+)
+
+# lower bounds
+setMethod("lowbnd", signature(object = "react"),
+ function(object) {
+ return(object@lowbnd)
+ }
+)
+
+setReplaceMethod("lowbnd", signature(object = "react"),
+ function(object, value) {
+ object@lowbnd <- value
+ return(object)
+ }
+)
+
+# upper bounds
+setMethod("uppbnd", signature(object = "react"),
+ function(object) {
+ return(object@uppbnd)
+ }
+)
+
+setReplaceMethod("uppbnd", signature(object = "react"),
+ function(object, value) {
+ object@uppbnd <- value
+ return(object)
+ }
+)
+
+
+# objective coefficient
+setMethod("obj_coef", signature(object = "react"),
+ function(object) {
+ return(object@obj_coef)
+ }
+)
+
+setReplaceMethod("obj_coef", signature(object = "react"),
+ function(object, value) {
+ object@obj_coef <- value
+ return(object)
+ }
+)
+
+
+# gprRules
+setMethod("gprRule", signature(object = "react"),
+ function(object) {
+ return(object@gprRule)
+ }
+)
+
+setReplaceMethod("gprRule", signature(object = "react"),
+ function(object, value) {
+ object@gprRule <- value
+ return(object)
+ }
+)
+
+
+# genes
+setMethod("genes", signature(object = "react"),
+ function(object) {
+ return(object@genes)
+ }
+)
+
+setReplaceMethod("genes", signature(object = "react"),
+ function(object, value) {
+ object@genes <- value
+ return(object)
+ }
+)
+
+
+# gpr associations
+setMethod("gpr", signature(object = "react"),
+ function(object) {
+ return(object@gpr)
+ }
+)
+
+setReplaceMethod("gpr", signature(object = "react"),
+ function(object, value) {
+ object@gpr <- value
+ return(object)
+ }
+)
+
+
+# reaction sub systems
+setMethod("subSys", signature(object = "react"),
+ function(object) {
+ return(object@subSys)
+ }
+)
+
+setReplaceMethod("subSys", signature(object = "react"),
+ function(object, value) {
+ object@subSys <- value
+ return(object)
+ }
+)
+
+
+# metabolites attributes
+setMethod("met_attr", signature(object = "react"),
+ function(object) {
+ return(object@met_attr)
+ }
+)
+
+setReplaceMethod("met_attr", signature(object = "react"),
+ function(object, value) {
+ object@met_attr <- value
+ return(object)
+ }
+)
+
+# reaction attributes
+setMethod("react_attr", signature(object = "react"),
+ function(object) {
+ return(object@react_attr)
+ }
+)
+
+setReplaceMethod("react_attr", signature(object = "react"),
+ function(object, value) {
+ object@react_attr <- value
+ return(object)
+ }
+)
+
+# compartment attributes
+setMethod("comp_attr", signature(object = "react"),
+ function(object) {
+ return(object@comp_attr)
+ }
+)
+
+setReplaceMethod("comp_attr", signature(object = "react"),
+ function(object, value) {
+ object@comp_attr <- value
+ return(object)
+ }
+)
+
+# model attributes
+setMethod("mod_attr", signature(object = "react"),
+ function(object) {
+ return(object@mod_attr)
+ }
+)
+
+setReplaceMethod("mod_attr", signature(object = "react"),
+ function(object, value) {
+ object@mod_attr <- value
+ return(object)
+ }
+)
+
+
+
+#------------------------------------------------------------------------------#
+# other methods #
+#------------------------------------------------------------------------------#
+
+setMethod("show", signature(object = "react"),
+ function(object) {
+ cat("react id: ", react_id(object), "\n")
+ cat("react name: ", react_name(object), "\n")
+ cat("stoichiometry:\n")
+ print(data.frame(met_id=met_id(object), s_coef=s(object)))
+ cat("lower bound: ", lowbnd(object), "\n")
+ cat("upper bound: ", uppbnd(object), "\n")
+ cat("objective function: ", obj_coef(object), "\n")
+ }
+)
+
+
+#------------------------------------------------------------------------------#
+
+# print reactions
+setMethod("printReaction", signature(object = "react"),
+ function(object, printOut = TRUE, ...) {
+
+ mat <- s(object)
+ reaction <- character(1)
+
+
+ met <- met_id(object)
+ nzv <- mat
+
+ ed <- nzv < 0
+ pd <- nzv > 0
+
+ if (sum(ed) > 0) {
+ educt <- paste(paste("(", abs(nzv[ed]), ")", sep = ""),
+ met[ed], collapse = " + ")
+ }
+ else {
+ educt = ""
+ }
+
+ if (sum(pd) > 0) {
+ product <- paste(paste("(", nzv[pd], ")", sep = ""),
+ met[pd], collapse = " + ")
+ }
+ else {
+ product = ""
+ }
+
+ arrow <- ifelse(react_rev(object), " <==> ", " --> ")
+
+ reaction <- paste(react_id(object),
+ paste(educt, product, sep = arrow), sep = "\t")
+
+ if (isTRUE(printOut)) {
+ cat("abbreviation\tequation", reaction, sep = "\n", ...)
+ }
+
+ return(invisible(reaction))
+
+ }
+)
+
+
+
+
+
+
+
+
+
+
+
diff --git a/R/reactIdClass.R b/R/reactIdClass.R
index ca6b6d5783a80a4b80988c941ffd1ce14d30dbd1..eadcfe4f423000e65743150f3c841d6d92a952ef 100644
--- a/R/reactIdClass.R
+++ b/R/reactIdClass.R
@@ -77,7 +77,7 @@ setMethod("mod_id", signature(object = "reactId"),
}
)
-setReplaceMethod("mod_id", signature = (object = "reactId"),
+setReplaceMethod("mod_id", signature(object = "reactId"),
function(object, value) {
object@mod_id <- value
return(object)
@@ -92,7 +92,7 @@ setMethod("mod_key", signature(object = "reactId"),
}
)
-setReplaceMethod("mod_key", signature = (object = "reactId"),
+setReplaceMethod("mod_key", signature(object = "reactId"),
function(object, value) {
object@mod_key <- value
return(object)
@@ -107,7 +107,7 @@ setMethod("react_pos", signature(object = "reactId"),
}
)
-setReplaceMethod("react_pos", signature = (object = "reactId"),
+setReplaceMethod("react_pos", signature(object = "reactId"),
function(object, value) {
object@react_pos <- value
return(object)
@@ -122,7 +122,7 @@ setMethod("react_id", signature(object = "reactId"),
}
)
-setReplaceMethod("react_id", signature = (object = "reactId"),
+setReplaceMethod("react_id", signature(object = "reactId"),
function(object, value) {
object@react_id <- value
return(object)
diff --git a/R/reactId_ExchClass.R b/R/reactId_ExchClass.R
index a09be51c779fa9ecddc50d599593ee6e3d0d2156..cb7669cafed8a54b8c1503b9d4bf6c4af9fc8d51 100644
--- a/R/reactId_ExchClass.R
+++ b/R/reactId_ExchClass.R
@@ -92,7 +92,7 @@ setMethod("met_pos", signature(object = "reactId_Exch"),
}
)
-setReplaceMethod("met_pos", signature = (object = "reactId_Exch"),
+setReplaceMethod("met_pos", signature(object = "reactId_Exch"),
function(object, value) {
object@met_pos <- value
return(object)
@@ -107,7 +107,7 @@ setMethod("met_id", signature(object = "reactId_Exch"),
}
)
-setReplaceMethod("met_id", signature = (object = "reactId_Exch"),
+setReplaceMethod("met_id", signature(object = "reactId_Exch"),
function(object, value) {
object@met_id <- value
return(object)
@@ -122,7 +122,7 @@ setMethod("lowbnd", signature(object = "reactId_Exch"),
}
)
-setReplaceMethod("lowbnd", signature = (object = "reactId_Exch"),
+setReplaceMethod("lowbnd", signature(object = "reactId_Exch"),
function(object, value) {
object@lowbnd <- value
return(object)
@@ -137,7 +137,7 @@ setMethod("uppbnd", signature(object = "reactId_Exch"),
}
)
-setReplaceMethod("uppbnd", signature = (object = "reactId_Exch"),
+setReplaceMethod("uppbnd", signature(object = "reactId_Exch"),
function(object, value) {
object@uppbnd <- value
return(object)
@@ -152,7 +152,7 @@ setMethod("uptake", signature(object = "reactId_Exch"),
}
)
-setReplaceMethod("uptake", signature = (object = "reactId_Exch"),
+setReplaceMethod("uptake", signature(object = "reactId_Exch"),
function(object, value) {
object@uptake <- value
return(object)
diff --git a/R/summaryOptsolClass.R b/R/summaryOptsolClass.R
index ef779e9a1c0eb936b2ca2a55013ddc699e05ca37..66d61113d03af391fcc3201bb0116c27a33b9ade 100644
--- a/R/summaryOptsolClass.R
+++ b/R/summaryOptsolClass.R
@@ -108,7 +108,7 @@ setMethod("mod_id", signature(object = "summaryOptsol"),
}
)
-setReplaceMethod("mod_id", signature = (object = "summaryOptsol"),
+setReplaceMethod("mod_id", signature(object = "summaryOptsol"),
function(object, value) {
object@mod_id <- value
return(object)
@@ -123,7 +123,7 @@ setMethod("mod_key", signature(object = "summaryOptsol"),
}
)
-setReplaceMethod("mod_key", signature = (object = "summaryOptsol"),
+setReplaceMethod("mod_key", signature(object = "summaryOptsol"),
function(object, value) {
object@mod_key <- value
return(object)
@@ -138,7 +138,7 @@ setMethod("mod_obj", signature(object = "summaryOptsol"),
}
)
-setReplaceMethod("mod_obj", signature = (object = "summaryOptsol"),
+setReplaceMethod("mod_obj", signature(object = "summaryOptsol"),
function(object, value) {
object@mod_obj <- value
return(object)
diff --git a/R/sysBiolAlgClass.R b/R/sysBiolAlgClass.R
index 44a6b565456a4f54fb49138c45262d798c00f55e..882ad7897a3fb07a41cba6e83ee1760ae560770a 100644
--- a/R/sysBiolAlgClass.R
+++ b/R/sysBiolAlgClass.R
@@ -186,7 +186,7 @@ setMethod("algorithm", signature(object = "sysBiolAlg"),
}
)
-setReplaceMethod("algorithm", signature = (object = "sysBiolAlg"),
+setReplaceMethod("algorithm", signature(object = "sysBiolAlg"),
function(object, value) {
object@algorithm <- value
return(object)
@@ -201,7 +201,7 @@ setMethod("nr", signature(object = "sysBiolAlg"),
}
)
-setReplaceMethod("nr", signature = (object = "sysBiolAlg"),
+setReplaceMethod("nr", signature(object = "sysBiolAlg"),
function(object, value) {
object@nr <- value
return(object)
@@ -216,7 +216,7 @@ setMethod("nc", signature(object = "sysBiolAlg"),
}
)
-setReplaceMethod("nc", signature = (object = "sysBiolAlg"),
+setReplaceMethod("nc", signature(object = "sysBiolAlg"),
function(object, value) {
object@nc <- value
return(object)
@@ -231,7 +231,7 @@ setMethod("fldind", signature(object = "sysBiolAlg"),
}
)
-setReplaceMethod("fldind", signature = (object = "sysBiolAlg"),
+setReplaceMethod("fldind", signature(object = "sysBiolAlg"),
function(object, value) {
object@fldind <- value
return(object)
@@ -246,7 +246,7 @@ setMethod("alg_par", signature(object = "sysBiolAlg"),
}
)
-setReplaceMethod("alg_par", signature = (object = "sysBiolAlg"),
+setReplaceMethod("alg_par", signature(object = "sysBiolAlg"),
function(object, value) {
object@alg_par <- value
return(object)
diff --git a/R/sysBiolAlg_lmomaClass.R b/R/sysBiolAlg_lmomaClass.R
index cba013b5e1402d942bf0ecc2028cec16840fb916..7d6944b1f809311edb07d70620344991cc56ab8c 100644
--- a/R/sysBiolAlg_lmomaClass.R
+++ b/R/sysBiolAlg_lmomaClass.R
@@ -154,7 +154,7 @@ setMethod(f = "initialize",
sparse = TRUE)
# the final contraint matrix
- LHS <- rBind(LHSwt, LHS, crow)
+ LHS <- rbind(LHSwt, LHS, crow)
subalg <- "lmoma_cobra"
}
diff --git a/R/validreact.R b/R/validreact.R
new file mode 100644
index 0000000000000000000000000000000000000000..0036dd2923c5e198c89c3f2053862ee09d1a6752
--- /dev/null
+++ b/R/validreact.R
@@ -0,0 +1,112 @@
+# validreact.R
+# FBA and friends with R.
+#
+# Copyright (C) 2010-2017 Claus Jonathan Fritzemeier, Dpt. for Computational Cell Biology,
+# Institute for Informatics, Heinrich-Heine-University, Duesseldorf, Germany.
+# All right reserved.
+# Email: clausjonathan.fritzemeier@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/>.
+
+
+# validreact
+
+
+################################################
+# Function: .validreact
+#
+# Validity checking of an object of class react.
+#
+# Returns TRUE if the model is valid, otherwise
+# a character String containing a description of
+# the error.
+
+
+.validreact <- function(object) {
+ # data has to have the same length or to be NULL
+ if(!is(object, "react")){
+ "object is not of react class"
+ }
+
+ if(length(object@id) != 1){
+ return("id has to be length 1")
+ }
+ if(length(object@name) != 1){
+ return("id has to be length 1")
+ }
+
+ met_count <- length(object@s)
+ if(met_comp < 1){
+ return("reactions have to have at least one metabolite")
+ }
+ if(length(object@met_id) == met_count){
+ return("s, met_id, met_name, and met_comp have to have the same length")
+ }
+ if(length(object@met_name) == met_count && !is.null(object@met_name)){
+ return("s, met_id, met_name, and met_comp have to have the same length")
+ }
+ if(length(object@met_comp) == met_count && !is.null(object@met_comp)){
+ return("s, met_id, met_name, and met_comp have to have the same length")
+ }
+
+ if(length(object@id)!=1){
+ return("length of id has to be 1")
+ }
+ if(length(object@rev)!=1){
+ return("length of rev has to be 1")
+ }
+ if(length(object@name)!=1){
+ return("length of name has to be 1")
+ }
+ if(length(object@lowbnd)!=1){
+ return("length of lowbnd has to be 1")
+ }
+ if(length(object@uppbnd)!=1){
+ return("length of uppbnd has to be 1")
+ }
+ if(length(object@obj_coef)!=1){
+ return("length of obj_coef has to be 1")
+ }
+
+ if(!is.null(gprRule) && length(object@gprRule)!=1){
+ return("if not NULL, the length of gprRule has to be 1")
+ }
+ if(!is.null(genes) && length(object@genes)!=1){
+ return("if not NULL, the length of genes has to be 1")
+ }
+ if(!is.null(gpr) && length(object@gpr)!=1){
+ return("if not NULL, the length of gpr has to be 1")
+ }
+ if(!is.null(subSys) && length(object@subSys)!=1){
+ return("if not NULL, the length of subSys has to be 1")
+ }
+
+ return(TRUE)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
index 8dd55d7d241dc3478fcd7f363f433c54ecdf6422..2608cff2ce707c391637840c237cfe6f084026c5 100644
--- a/inst/NEWS.Rd
+++ b/inst/NEWS.Rd
@@ -5,15 +5,38 @@
\encoding{UTF-8}
\newcommand{\CRANpkg}{\href{https://CRAN.R-project.org/package=#1}{\pkg{#1}}}
+% ---------------------------------------------------------------------------- %
+
+\section{Changes in version 2.1.1 2018-07-17}{
+ \itemize{
+ \item Package sybilSBML gets rejected on CRAN, but can be downloaded
+ at \url{http://www.cs.hhu.de/en/research-groups/computational-cell-biology/software.html}.
+ \item Documentation for \code{react-class} and related methods.
+ \
+ }
+}
+% ---------------------------------------------------------------------------- %
+
+\section{Changes in version 2.1.0 2017-07-17}{
+ \itemize{
+ \item \code{addReact} is now a method of the \code{modelorg} class.
+ \item Preparation for \code{sybilNLO}.
+ \item New reaction object for easy merging and splitting of models. See \code{reactClass}.
+ \item Typo in setting methods generated an character vector \code{object}.
+ \
+ }
+}
+% ---------------------------------------------------------------------------- %
+
\section{Changes in version 2.0.4 2017-07-18}{
\itemize{
\item Minor changes for CRAN submission.
}
}
-% ---------------------------------------------------------------------------- %
-\section{Changes in version 2.0.3 2017-07-12}{
+
+\section{Changes in version 2.0.3 2017-04-20}{
\itemize{
\item The function \code{genrateWT} caused a problem when setting only \code{solverParm} and no solver.
\item \code{rmReact} handles now \code{react_attr} and \code{met_attr} corretly, if there is just one column.
diff --git a/man/addReact.Rd b/man/addReact.Rd
index 2470300238be767f106697b71ef271d54d8a27dc..597e0788d64c35b03d416e9527f0121559009a2c 100644
--- a/man/addReact.Rd
+++ b/man/addReact.Rd
@@ -1,8 +1,12 @@
-\name{addReact}
-\alias{addReact}
-
+\name{addReact,modelorg-method}
+\docType{methods}
\encoding{utf8}
+
+\alias{addReact}
+\alias{addReact,modelorg-method}
+\alias{addReact,modelorg,ANY-method}
+
\title{
Add/Change Reactions in a Model
}
@@ -11,9 +15,15 @@
The function \code{addReact} adds one reaction to a metabolic model, or
changes one reaction in a metabolic model.
}
-
+\section{Methods}{
+ \describe{
+ \item{\code{addReact}:}{
+ \code{signature(object = "modelorg")}: adds a new reaction to a \code{modelorg} object.
+ }
+ }
+}
\usage{
- addReact(model,
+\S4method{addReact}{modelorg}(model,
id,
met,
Scoef,
diff --git a/man/mergeReact2Modelorg.Rd b/man/mergeReact2Modelorg.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..f451a94ae504fb66306288acbd9ffe717f55e57e
--- /dev/null
+++ b/man/mergeReact2Modelorg.Rd
@@ -0,0 +1,69 @@
+\name{mergeReact2Modelorg}
+
+\docType{methods}
+\encoding{utf8}
+
+\alias{mergeReact2Modelorg}
+\alias{getReaction}
+\alias{getReaction,modelorg-method}
+\alias{getReaction,modelorg,ANY-method}
+
+\title{
+ Functions to subset and merge modelorg objects.
+}
+\description{
+ The function \code{getReaction} can extract singe \code{react} objects from
+ a modelorg object. If those \code{react} objects are saved in a list, they
+ can be passed to the function \code{mergeReact2Modelorg} to combine them to
+ one new model.
+}
+\usage{
+mergeReact2Modelorg(reactList = NULL, id = "newModel", name = "")
+\S4method{getReaction}{modelorg,ANY}(X, j = NULL, drop = T, tol = SYBIL_SETTINGS("TOLERANCE"))
+}
+\arguments{
+ \item{reactList}{
+ list of \code{react} objects
+}
+ \item{id}{
+ id for the new \code{modelorg}
+}
+ \item{name}{
+ name for the new \code{modelorg}
+}
+\item{j}{
+ defines the reaction numbers or IDs to extract from the model.
+}
+\item{drop}{
+ If FALSE, a list of length 1 is returned.
+}
+\item{tol}{
+ Threshold for coefficients to be unequal zero.
+}
+\item{X}{
+ \code{modelorg} object to extract reactions from.
+}
+}
+\value{
+ mergeReact2Modelorg returns a \code{modelorg} object.
+
+ getReaction returns a \code{react} object if \code{length(j) = 1} and \code{drop = TRUE}. Otherwise
+ a list of \code{react} objects.
+}
+\author{
+ Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
+}
+
+\seealso{
+ \code{\link{modelorg}}, \code{\link{react}}
+}
+\examples{
+ data(Ec_core)
+ l <- getReaction(Ec_core, j=1:3)
+ print(l)
+ m <- mergeReact2Modelorg(l)
+ print(m)
+
+}
+\keyword{ subset }
+\keyword{ merge }
diff --git a/man/modelorg-class.Rd b/man/modelorg-class.Rd
index dfeb47d779bbd9cd0189f77d9ff4c2d13b05cad5..ad83d5f1a42ccdfe626c48f9eeefdcebd06f715f 100644
--- a/man/modelorg-class.Rd
+++ b/man/modelorg-class.Rd
@@ -139,6 +139,90 @@
\alias{version<-}
\alias{version}
+\alias{react-class}
+\alias{react}
+\alias{comp_attr,react-method}
+\alias{comp_attr}
+\alias{comp_attr<-,react-method}
+\alias{comp_attr<-}
+\alias{genes,react-method}
+\alias{genes}
+\alias{genes<-,react-method}
+\alias{genes<-}
+\alias{gpr,react-method}
+\alias{gpr}
+\alias{gpr<-,react-method}
+\alias{gpr<-}
+\alias{gprRule,react-method}
+\alias{gprRule}
+\alias{gprRule<-,react-method}
+\alias{gprRule<-}
+\alias{lowbnd,react-method}
+\alias{lowbnd}
+\alias{lowbnd<-,react-method}
+\alias{lowbnd<-}
+\alias{met_attr,react-method}
+\alias{met_attr}
+\alias{met_attr<-,react-method}
+\alias{met_attr<-}
+\alias{met_comp,react-method}
+\alias{met_comp}
+\alias{met_comp<-,react-method}
+\alias{met_comp<-}
+\alias{met_id,react-method}
+\alias{met_id}
+\alias{met_id<-,react-method}
+\alias{met_id<-}
+\alias{met_name,react-method}
+\alias{met_name}
+\alias{met_name<-,react-method}
+\alias{met_name<-}
+\alias{mod_attr,react-method}
+\alias{mod_attr}
+\alias{mod_attr<-,react-method}
+\alias{mod_attr<-}
+\alias{obj_coef,react-method}
+\alias{obj_coef}
+\alias{obj_coef<-,react-method}
+\alias{obj_coef<-}
+\alias{react_attr,react-method}
+\alias{react_attr}
+\alias{react_attr<-,react-method}
+\alias{react_attr<-}
+\alias{react_de,react-method}
+\alias{react_de}
+\alias{react_de<-,react-method}
+\alias{react_de<-}
+\alias{react_id,react-method}
+\alias{react_id}
+\alias{react_id<-,react-method}
+\alias{react_id<-}
+\alias{react_name,react-method}
+\alias{react_name}
+\alias{react_name<-,react-method}
+\alias{react_name<-}
+\alias{react_rev,react-method}
+\alias{react_rev}
+\alias{react_rev<-,react-method}
+\alias{react_rev<-}
+\alias{react_single,react-method}
+\alias{react_single}
+\alias{react_single<-,react-method}
+\alias{react_single<-}
+\alias{s,react-method}
+\alias{s}
+\alias{s<-,react-method}
+\alias{s<-}
+\alias{subSys,react-method}
+\alias{subSys}
+\alias{subSys<-,react-method}
+\alias{subSys<-}
+\alias{uppbnd,react-method}
+\alias{uppbnd}
+\alias{uppbnd<-,react-method}
+\alias{uppbnd<-}
+
+
\encoding{utf8}
\title{Structure of Class "modelorg"}
@@ -146,6 +230,10 @@
\description{
Structure of the class \code{"modelorg"}. Objects of that class are
returned by functions like \code{\link{readTSVmod}}.
+
+ Structure of the class \code{"react"}. This depicts a subset of a metabolic model
+ that contains only one reaction. Multiple \code{react} objects can be combined to an
+ \code{"modelorg"} object.
}
\section{Objects from the Class}{
diff --git a/man/optsol_blockedReact-class.Rd b/man/optsol_blockedReact-class.Rd
index 4f0450be7700183b3a2be87f953bd530aee89247..2a611e2c419d6ed29dccbd9e158a207b21fa2e6e 100644
--- a/man/optsol_blockedReact-class.Rd
+++ b/man/optsol_blockedReact-class.Rd
@@ -11,7 +11,6 @@
\alias{blocked<-}
\alias{react,optsol_blockedReact-method}
\alias{react<-,optsol_blockedReact-method}
-\alias{react}
\alias{react<-}
\alias{maxSol,optsol_blockedReact-method}
\alias{minSol,optsol_blockedReact-method}
diff --git a/man/printReaction-methods.Rd b/man/printReaction-methods.Rd
index 715779ac2661ba3eca2a3e1f10a78952a0ceae79..e4e1880af15664da340698ef9bcccd3feea8d61e 100644
--- a/man/printReaction-methods.Rd
+++ b/man/printReaction-methods.Rd
@@ -7,6 +7,7 @@
\alias{printReaction-methods}
\alias{printReaction,modelorg,ANY-method}
\alias{printReaction,summaryOptsol,modelorg-method}
+\alias{printReaction,react,ANY-method}
\title{Print Columns of the Stoichiometric Matrix}
@@ -17,6 +18,7 @@
\usage{
\S4method{printReaction}{modelorg,ANY}(object, react, printOut = TRUE, ...)
\S4method{printReaction}{summaryOptsol,modelorg}(object, mod, j, ...)
+\S4method{printReaction}{react,ANY}(object, printOut = TRUE, ...)
}
\section{Methods}{
@@ -27,6 +29,9 @@
\item{\code{signature(object = "summaryOptsol", mod = "modelorg")}}{
method to use with objects of class \code{\linkS4class{summaryOptsol}}.
}
+ \item{\code{signature(object = "react", ...)}}{
+ method to use with objects of class \code{\linkS4class{react}}.
+ }
}
}