diff --git a/DESCRIPTION b/DESCRIPTION
index bc9378415e2a4755981a70877eb2d2f264014e2c..f31336a01503bc6b8eed349b22ff4400843a53dc 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: sybil
Type: Package
Title: Efficient Constrained Based Modelling in R
-Version: 1.3.4
-Date: 2015-04-18
+Version: 2.0.0
+Date: 2016-05-12
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")),
@@ -52,8 +52,8 @@ Collate: generics.R validmodelorg.R validoptsol.R validreactId.R
sysBiolAlg_fbaEasyConstraintClass.R sysBiolAlg_fvClass.R
sysBiolAlg_lmomaClass.R sysBiolAlg_momaClass.R
sysBiolAlg_mtfClass.R sysBiolAlg_mtfEasyConstraintClass.R
- sysBiolAlg_roomClass.R sybilLogClass.R
-Packaged: 2016-01-27 12:34:14 UTC; jonathan
+ sysBiolAlg_roomClass.R sybilLogClass.R upgradeModelorg.R
+Packaged: 2016-05-12 12:34:14 UTC; jonathan
Author: C. Jonathan Fritzemeier [cre, ctb],
Gabriel Gelius-Dietrich [aut],
Rajen Piernikarczyk [ctb],
diff --git a/R/addReact.R b/R/addReact.R
index 101842d1dd21afc70518a1f98eaec010bce4a061..c99b64caf4e061719f39edeb9dc112d0bd896fda 100644
--- a/R/addReact.R
+++ b/R/addReact.R
@@ -53,6 +53,10 @@ addReact <- function(model,
if (!is(model, "modelorg")) {
stop("needs an object of class modelorg!")
}
+
+ if(!.hasSlot(model, "version")){
+ validObject(model)
+ }
if (length(met) != length(Scoef)) {
stop("arguments 'met' and 'Scoef' must have the same length")
@@ -290,13 +294,14 @@ 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)
}
diff --git a/R/geneDel.R b/R/geneDel.R
index f69dad53e2d81e30d72d10da1367826db1fb6eaf..874bb63b25c45afdb81f3a2b7c7864c53c733967 100644
--- a/R/geneDel.R
+++ b/R/geneDel.R
@@ -41,6 +41,10 @@ geneDel <- function(model, genes, checkId = FALSE) {
stop("needs an object of class modelorg!")
}
+ if(!.hasSlot(model, "version")){
+ validObject(model)
+ }
+
if (isTRUE(checkId)) {
if (is(genes, "character")) {
# Check if all genes are there
diff --git a/R/generics.R b/R/generics.R
index e249177a90f6bd4c028d15b46d8cf90591daf192..3c393a8a8b4959a34676de49fddf99dc658848a8 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") }
)
@@ -945,6 +949,13 @@ 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/modelorgClass.R b/R/modelorgClass.R
index 9f8702a5f2d758b418d0111498ec3af373625243..8f8343ad72c5e8e56772e43151c96e8615d0ba8a 100644
--- a/R/modelorgClass.R
+++ b/R/modelorgClass.R
@@ -55,6 +55,7 @@ setClass("modelorg",
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",
@@ -113,6 +114,7 @@ setMethod(f = "initialize",
.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)
}
@@ -548,6 +550,21 @@ 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)
+ }
+)
+
#------------------------------------------------------------------------------#
# other methods #
@@ -1073,11 +1090,22 @@ setMethod("singletonMetabolites", signature(object = "modelorg"),
}
)
+#------------------------------------------------------------------------------#
-
-
+setMethod("checkVersion", signature(object = "modelorg"),
+ function(object) {
+ if(!.hasSlot(object, "version")){
+ stop("No version slot found. Please use upgradeModelorg on object")
+ }
+
+ if(compareVersion(version(object), SYBIL_SETTINGS("MODELORG_VERSION")) == 0){
+ return(TRUE)
+ }
+ stop(paste0("modelorg has version ", object(version), ", but you need at least version ", version))
+ }
+)
diff --git a/R/parseBoolean.R b/R/parseBoolean.R
index 653aecc2e37b9de4f45c91a9fc7737693cdc3eb8..b10a46d4233ab51d2145a2d4db5ae4860a5c39c3 100644
--- a/R/parseBoolean.R
+++ b/R/parseBoolean.R
@@ -88,7 +88,7 @@
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/readTSVmod.R b/R/readTSVmod.R
index f66c1bda4435b43d10a4b502b9f47db00ae40b81..0bd26047b9f48a5f650c781535aa5bed8c065c2f 100644
--- a/R/readTSVmod.R
+++ b/R/readTSVmod.R
@@ -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 modelorgs
+# 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 bacbd822b7be08940bbb53aabcb9df37a80a08bc..6e13204f342e6e07a36bf88107a8fdab6daeb5b7 100644
--- a/R/rmReact.R
+++ b/R/rmReact.R
@@ -38,30 +38,33 @@ 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!")
+ }
+
+ if(!.hasSlot(model, "version")){
+ validObject(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"))) {
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/upgradeModelorg.R b/R/upgradeModelorg.R
new file mode 100644
index 0000000000000000000000000000000000000000..f85fa69ca8ca2724bf63cac4a80ed7a86969b879
--- /dev/null
+++ b/R/upgradeModelorg.R
@@ -0,0 +1,70 @@
+# upgradeModelorg.R
+# FBA and friends with R.
+#
+# Copyright (C) 2010-2016 Claus Jonathan Fritzemeier, Dpt. for Bioinformatics,
+# 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/>.
+
+
+################################################
+# Function: upgradeModelorg
+#
+# Takes an instance of a old modelorg version and returns one updated to the
+# current version.
+#
+
+
+upgradeModelorg <- function(object){
+ stopifnot(is(object, "modelorg"))
+
+ if(!.hasSlot(object, "version")){
+ # object is from a time before versions were introduced.
+ # just add version slot and run again.
+ object@version <- "2.0"
+
+ rules <- lapply(gpr(object), sybil:::.parseBoolean)
+ genes(object) <- sapply(rules, "[[", "gene")
+ gprRules(object) <- sapply(rules, "[[", "rule")
+
+ #recursively upgrad to latest version.
+ return(upgradeModelorg(object))
+ }
+
+ if(compareVersion(version(object), SYBIL_SETTINGS("MODELORG_VERSION")) == 0){
+ stopifnot(validObject(object))
+ return(object)
+ }
+
+ stop("unsupported version of modelorg")
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/R/validmodelorg.R b/R/validmodelorg.R
index aba3fc6994dd245b0cb5f67f0cf60e6b1fc9a1fb..0be179668724efeca658e9e3f2856d708594229e 100644
--- a/R/validmodelorg.R
+++ b/R/validmodelorg.R
@@ -38,6 +38,15 @@
return("needs an object of class modelorg!")
}
+ if(compareVersion(version(object), SYBIL_SETTINGS("MODELORG_VERSION")) != 0){
+ if(compareVersion(version(object), SYBIL_SETTINGS("MODELORG_VERSION")) == -1){
+ return("You are using an old version of the modelorg-Class. Use upgradeModelorg to get a compatible object!")
+ }
+ if(compareVersion(version(object), SYBIL_SETTINGS("MODELORG_VERSION")) == 1){
+ return("You are using a new version of the modelorg-Class. Plase upgrade your sybil package!")
+ }
+ }
+
if ((length(mod_id(object)) != 1) || (length(mod_name(object)) != 1)) {
return("mod_id and mod_name must have a length of 1!")
}
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,