diff --git a/DESCRIPTION b/DESCRIPTION
index e83260ccff9825f98bd0b617dbcf640237cbf981..dba45ba5d2a64f020c77931a75e7d90e3b8efb32 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,22 +1,24 @@
Package: sybilSBML
Type: Package
Title: SBML Integration in Package 'Sybil'
-Version: 2.0.11
-Date: 2016-06-06
+Version: 3.0.1
+Date: 2016-12-16
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", "ctb")),
- person("Deya", "Alzoubi", role = "ctb"))
+ person("Deya", "Alzoubi", role = "ctb"),
+ person("Ardalan", "Habil", role = "ctb"))
Maintainer: C. Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
Depends: R (>= 2.14.2), Matrix, sybil (>= 2.0.0)
Imports: methods
-Description: 'SBML' (Systems Biology Markup Language) integration in 'sybil'. Many constraint based metabolic models are published in 'SBML' format ('*.xml'). Herewith is the ability to read and check 'SBML' files in 'sybil' provided.
+Description: 'SBML' (Systems Biology Markup Language) with FBC (Flux Balance Constraints) integration in 'sybil'. Many constraint based metabolic models are published in 'SBML' format ('*.xml'). Herewith is the ability to read, write, and check 'SBML' files in 'sybil' provided.
License: GPL-3 | file LICENSE
LazyLoad: yes
Collate: generics.R sbmlPtrClass.R sbmlErrorClass.R sybilSBML.R
uglyHack.R readSBMLmod.R zzz.R
-Packaged: 2015-06-06 07:11:55 UTC; jonathan
+Packaged: 2016-12-16 07:11:55 UTC; jonathan
Author: C. Jonathan Fritzemeier [cre, ctb],
Gabriel Gelius-Dietrich [aut, ctb],
- Deya Alzoubi [ctb]
+ Deya Alzoubi [ctb],
+ Ardalan Habil [ctb]
NeedsCompilation: yes
Repository: CRAN
diff --git a/NAMESPACE b/NAMESPACE
index 26d265c425dbe35dfde3dc4f40632a6e2e3d3ef9..ef1a335a79643feaf6af3485646e34b13d8d8eea 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -48,5 +48,9 @@ getSBMLunitDefinitionsList,
getSBMLCompartList,
getSBMLSpeciesList,
getSBMLReactionsList,
-readSBMLmod
+readSBMLmod,
+writeSBML,
+getSBMLFbcversion,
+getSBMLmodNotes,
+getSBMLmodAnnotation
)
diff --git a/R/readSBMLmod.R b/R/readSBMLmod.R
index fe1ebba72355814d7400f3cca3c6660803526007..56e9a4125cef71a77b5a0b31e686bdd60d1e1ea8 100644
--- a/R/readSBMLmod.R
+++ b/R/readSBMLmod.R
@@ -247,7 +247,13 @@ parseNotesReact <- function(notes) {
gpr <- sub("GENE[_ ]?ASSOCIATION: *", "", fields_str[j])
gene_rule <- sybil:::.parseBoolean(gpr)
#print(gene_rule)
- }
+
+ }#Ardalan Habil
+ else if (grepl("GPR[_ ]?ASSOCIATION", fields_str[j])) {
+ gpr <- sub("GPR[_ ]?ASSOCIATION: *", "", fields_str[j])
+ gene_rule <- sybil:::.parseBoolean(gpr)
+ }
+
if (charmatch("SUBSYSTEM", fields_str[j], nomatch = -1) != -1) {
subSyst <- sub("SUBSYSTEM: *", "", fields_str[j])
subSyst <- sub("^S_", "", subSyst, perl = TRUE)
@@ -283,6 +289,14 @@ sbmldoc <- openSBMLfile(filename)
message("OK")
+# warning if new Version/Level/
+SBMLlevel<- getSBMLlevel(sbmldoc)
+SBMLversion<- getSBMLversion(sbmldoc)
+FBCversion<-getSBMLFbcversion(sbmldoc)
+if(SBMLlevel == 3 && SBMLversion > 1)
+ warning(paste("No support for Level 3 Version ",SBMLversion))
+if (FBCversion > 2)
+ warning(paste("No support for Fbc Version ",FBCversion))
#------------------------------------------------------------------------------#
# check the model #
@@ -380,6 +394,7 @@ if (mdesc == filename) {
sybil::mod_desc(mod) <- mdesc
+
#------------------------------------------------------------------------------#
# units #
#------------------------------------------------------------------------------#
@@ -398,7 +413,7 @@ if (is.null(compartmentsList)) {
}
missingId(compartmentsList)
-sybil::mod_compart(mod) <- compartmentsList[["id"]]
+comp_tmp_id <- compartmentsList[["id"]]
#------------------------------------------------------------------------------#
@@ -430,6 +445,7 @@ missingId(metabolitesList)
metSpIds <- metabolitesList[["id"]]
#nummet <- getSBMLnumSpecies(sbmlmod)
+
if (isTRUE(bndCond)) {
metSpBnd <- metabolitesList[["boundaryCondition"]]
met_id_pos <- !metSpBnd
@@ -485,12 +501,20 @@ gpr <- character(numreact)
hasNotes <- FALSE
hasAnnot <- FALSE
+#FBC contraints @Ardalan Habil
+fbclowbnd<-reactionsList[["fbc_lowbnd"]]
+fbcuppbnd<-reactionsList[["fbc_uppbnd"]]
+fbcgprRules<-reactionsList[["fbc_gprRules"]]
+fbcObjectives<-reactionsList[["fbc_Objectives"]]
+
for (i in 1 : numreact) {
# the notes/annotations field
notes <- reactionsList[["notes"]][i]
annot <- reactionsList[["annotation"]][i]
-
+
+ # Notes und Annotation can be null ( @Ardalan Habil)
+ if(!is.null( reactionsList[["notes"]]))
if (nchar(notes) > 0) {
hasNotes <- TRUE
@@ -504,7 +528,7 @@ for (i in 1 : numreact) {
}
else {
-
+ if(!is.null( reactionsList[["annotation"]]))
if (nchar(annot) > 0) {
hasAnnot <- TRUE
pn <- regexpr("Pathway Name: [^<]+", annot, perl = TRUE)
@@ -512,7 +536,18 @@ for (i in 1 : numreact) {
}
}
-
+
+
+
+ fbcgene_rule <- NA
+ if ( !is.null(fbcgprRules))
+ {
+ fbcgene_rule<- sybil:::.parseBoolean(fbcgprRules[i])
+
+ genes[[i]] <- fbcgene_rule$gene # list of genes
+ rules[i] <- fbcgene_rule$rule # rules
+ gpr[i] <- fbcgprRules[i]
+ }
# Check here if reactants and products lists exist, same for the stoichiometry slot
@@ -565,6 +600,16 @@ for (i in 1 : numreact) {
# }
# the constraints
+
+ #FBC contraints @Ardalan Habil
+ if ( !is.null(fbclowbnd) && !is.null(fbcuppbnd))
+ {
+ lbnd[i] <- checkupplowbnd(fbclowbnd[i])
+ ubnd[i] <- checkupplowbnd(fbcuppbnd[i])
+ }
+ #read from kinetic_law if fbc is empty
+ else
+ {
parm <- reactionsList[["kinetic_law"]][[i]]
if (is.null(parm)) {
ubnd[i] <- def_bnd
@@ -591,10 +636,16 @@ for (i in 1 : numreact) {
# reduced cost? (sbml file)
}
}
-
+ }
+ #FBC Objective @Ardalan Habil
+ if(!is.null(fbcObjectives))
+ {
+ ocof[i]<-as.numeric(fbcObjectives[i])
+ }
+
+
}
-
# ---------------------------------------------------------------------------- #
# search for unused metabolites and unused reactions
@@ -877,7 +928,7 @@ else {
rules <- rules[SKIP_REACTION]
gpr <- gpr[SKIP_REACTION]
- if (isTRUE(hasNotes)) {
+ if (isTRUE(hasNotes) || !is.null(fbcgprRules) ) {
message("GPR mapping ... ", appendLF = FALSE)
#allGenes <- unique(allGenes)
@@ -897,14 +948,13 @@ else {
if ( (length(genes[[i]] == 1)) && (genes[[i]] != "") ) {
geneInd <- match(genes[[i]], allGenes)
rxnGeneMat[i, geneInd] <- TRUE
-
- # no use because new gprRule format
-# for (j in 1 : length(geneInd)) {
-# pat <- paste("x(", j, ")", sep = "")
-# repl <- paste("x[", geneInd[j], "]", sep = "")
-#
-# rules[i] <- gsub(pat, repl, rules[i], fixed = TRUE)
-# }
+
+ for (j in 1 : length(geneInd)) {
+ pat <- paste("x(", j, ")", sep = "")
+ repl <- paste("x[", geneInd[j], "]", sep = "")
+
+ rules[i] <- gsub(pat, repl, rules[i], fixed = TRUE)
+ }
}
}
@@ -970,6 +1020,63 @@ react_name_tmp <- sub( "\\s+$", "", react_name_tmp, perl = TRUE)
sybil::react_name(mod) <- react_name_tmp
+#------------------------------------------------------------------------------#
+# Reaction Attr @Ardalan #
+#------------------------------------------------------------------------------#
+# Test for new Slots
+if( .hasSlot(mod,"mod_attr") && .hasSlot(mod,"comp_attr") && .hasSlot(mod,"met_attr") && .hasSlot(mod,"react_attr") )
+ newSybil<-TRUE
+else newSybil<-FALSE
+
+numreact<-nummet <- sum(SKIP_REACTION)
+reactannotation <- reactionsList[["annotation"]][SKIP_REACTION]
+reactnotes <- reactionsList[["notes"]][SKIP_REACTION]
+if(newSybil)
+{
+ sybil::react_attr(mod) <-data.frame(row.names=1:numreact)
+ #Speed optimierung durch notes NULL falls nichts drin steht
+
+ if( !is.null(reactannotation) && length(reactannotation)==numreact )sybil::react_attr(mod)[['annotation']]<-reactannotation
+ if( !is.null(reactnotes) && length(reactnotes)==numreact )sybil::react_attr(mod)[['notes']]<-reactnotes
+}
+
+
+#------------------------------------------------------------------------------#
+# Model Attr @Ardalan #
+#------------------------------------------------------------------------------#
+
+modanno<-getSBMLmodAnnotation(sbmlmod)
+modnotes<-getSBMLmodNotes(sbmlmod)
+if(newSybil)
+{
+ sybil::mod_attr(mod) <-data.frame(row.names=1)
+ if(nchar(modanno)>1)sybil::mod_attr(mod)[['annotation']]<-modanno
+ if(nchar(modnotes)>1)sybil::mod_attr(mod)[['notes']]<-modnotes
+
+}
+
+
+#------------------------------------------------------------------------------#
+# compartments Attr @Ardalan #
+#------------------------------------------------------------------------------#
+# Define SKIP_COMPARTMENT FALSE= HAS NO REFERENCE
+met_comp_tmp <- metabolitesList[["compartment"]][met_id_pos][SKIP_METABOLITE]
+SKIP_COMPARTMENT<- comp_tmp_id %in% unique(met_comp_tmp)
+
+
+sybil::mod_compart(mod) <- comp_tmp_id[SKIP_COMPARTMENT]
+numcom<-length(mod_compart(mod))
+comannotation <- compartmentsList[["annotation"]][SKIP_COMPARTMENT]
+comnotes <- compartmentsList[["notes"]][SKIP_COMPARTMENT]
+if(newSybil)
+{
+ sybil::comp_attr(mod) <-data.frame(row.names=1:numcom)
+ if( !is.null(comannotation) && length(comannotation)==numcom )sybil::comp_attr(mod)[['annotation']]<-comannotation
+ if( !is.null(comnotes) && length(comnotes)==numcom )sybil::comp_attr(mod)[['notes']]<-comnotes
+
+}
+
+
#------------------------------------------------------------------------------#
# metabolite id's #
#------------------------------------------------------------------------------#
@@ -985,7 +1092,7 @@ sybil::met_id(mod) <- gsub("-", "_", met_id_tmp, fixed = TRUE)
# metabolite compartments #
#------------------------------------------------------------------------------#
-met_comp_tmp <- metabolitesList[["compartment"]][met_id_pos][SKIP_METABOLITE]
+#met_comp_tmp <- metabolitesList[["compartment"]][met_id_pos][SKIP_METABOLITE]
sybil::met_comp(mod) <- match(met_comp_tmp, sybil::mod_compart(mod))
@@ -1002,6 +1109,69 @@ met_name_tmp <- sub( "\\s+$", "", met_name_tmp, perl = TRUE)
sybil::met_name(mod) <- met_name_tmp
+#------------------------------------------------------------------------------#
+# metabolite attr @Ardalan Habil #
+#------------------------------------------------------------------------------#
+
+#ChemicalFormula Charge Notes Annotation MetaID @Ardalan Habil
+
+metformula <- metabolitesList[["chemicalFormula"]][met_id_pos][SKIP_METABOLITE]
+metcharge <- metabolitesList[["charge"]][met_id_pos][SKIP_METABOLITE]
+
+metnotes <- metabolitesList[["notes"]][met_id_pos][SKIP_METABOLITE]
+metannotation <- metabolitesList[["annotation"]][met_id_pos][SKIP_METABOLITE]
+
+
+metchargenote<-NULL
+metformulanote<-NULL
+# check metnotes for Formula and Charge
+if( !is.null(metnotes) && length(metnotes==nummet))
+{
+ pn <- regexpr("FORMULA: [^<]+", metnotes, perl = TRUE)
+ metformulanote <- substr(metnotes, (pn+9), pn + ((attr(pn, "match.length"))-1))
+ pn <- regexpr("CHARGE: [^<]+", metnotes, perl = TRUE)
+ metchargenote <- substr(metnotes, (pn+8), pn + ((attr(pn, "match.length"))-1))
+ metchargenote <- as.integer(metchargenote)
+ metchargenote[is.na(metchargenote)] <- 0
+}
+
+
+nummet <- sum(SKIP_METABOLITE)
+if(newSybil)
+{
+ # save attributes to met_attr slot
+ sybil::met_attr(mod) <-data.frame(row.names=1:nummet)
+ if( !is.null(metformula) && length(metformula)==nummet)
+ {sybil::met_attr(mod)[['chemicalFormula']]<-metformula}
+ else{
+ if(length(metformulanote)==nummet)
+ { if(max(nchar(metformulanote)) >0)
+ sybil::met_attr(mod)[['chemicalFormula']]<-metformulanote
+ }
+ }
+ if( !is.null(metcharge) && length(metcharge)==nummet && sum(metcharge)!=0)
+ {sybil::met_attr(mod)[['charge']]<-metcharge}
+ else{
+ if( length(metchargenote)==nummet)
+ { if(max(nchar(metchargenote)) >0)
+ sybil::met_attr(mod)[['charge']]<-metchargenote
+ }
+ }
+ if( !is.null(metnotes) && length(metnotes)==nummet)sybil::met_attr(mod)[['notes']]<-metnotes
+ if( !is.null(metannotation) && length(metannotation)==nummet)sybil::met_attr(mod)[['annotation']]<-metannotation
+
+ # Save boundaryCondition when bndCond=FALSE
+ if (!isTRUE(bndCond)) {
+ metBnd <- metabolitesList[["boundaryCondition"]][met_id_pos][SKIP_METABOLITE]
+ # When all metBnd = False -> metabolite removed by extMetFlag
+ if( !is.null(metBnd) && length(metBnd)==nummet && !all(metBnd == FALSE) )sybil::met_attr(mod)[['boundaryCondition']]<-metBnd
+ }
+
+
+}
+
+
+
#------------------------------------------------------------------------------#
# check reversibilities #
#------------------------------------------------------------------------------#
diff --git a/R/sybilSBML.R b/R/sybilSBML.R
index c76394e29b0bb1cb091909509bc362f977828512..b3eb40bee432ac7871489f4779c8fd2d086de6b1 100644
--- a/R/sybilSBML.R
+++ b/R/sybilSBML.R
@@ -1,280 +1,575 @@
-#------------------------------------------------------------------------------#
-# Link to libSBML for sybil #
-#------------------------------------------------------------------------------#
-
-# sybilSBML.R
-# Link to libSBML for sybil.
-#
-# Copyright (C) 2010-2013 Gabriel Gelius-Dietrich, Dpt. for Bioinformatics,
-# Institute for Informatics, Heinrich-Heine-University, Duesseldorf, Germany.
-# All right reserved.
-# Email: geliudie@uni-duesseldorf.de
-#
-# This file is part of sybilSBML.
-#
-# SybilSBML 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.
-#
-# SybilSBML 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 SybilSBML. If not, see <http://www.gnu.org/licenses/>.
-
-
-#------------------------------------------------------------------------------#
-
-versionLibSBML <- function() {
-
- version <- .Call("getLibSBMLversion", PACKAGE = "sybilSBML")
- return(version)
-
-}
-
-
-#------------------------------------------------------------------------------#
-
-openSBMLfile <- function(fname, ptrtype = "sbml_doc") {
-
- if ( file.exists(fname) == FALSE ) {
- stop("file not found: ", sQuote(fname))
- }
-
- sbmlf <- .Call("readSBMLfile", PACKAGE = "sybilSBML",
- as.character(normalizePath(fname)[1]),
- as.character(ptrtype)
- )
-
- sbmlfP <- sbmlDocPointer(sbmlf)
-
- return(sbmlfP)
-}
-
-
-#------------------------------------------------------------------------------#
-
-closeSBMLfile <- function(sbmlf) {
-
- invisible(
- .Call("delDocument", PACKAGE = "sybilSBML",
- sbmlPointer(sbmlf)
- )
- )
-
-}
-
-
-#------------------------------------------------------------------------------#
-
-getSBMLmodel <- function(sbmlf, ptrtype = "sbml_mod") {
-
- sbmlm <- .Call("getSBMLmodel", PACKAGE = "sybilSBML",
- sbmlPointer(sbmlf),
- as.character(ptrtype)
- )
-
- sbmlmP <- sbmlModPointer(sbmlm, sbmlf)
-
- if (isTRUE(isNULLpointerSBML(sbmlmP))) {
- sbmlmP <- NULL
- }
-
- return(sbmlmP)
-}
-
-
-#------------------------------------------------------------------------------#
-
-delSBMLmodel <- function(sbmlm) {
-
- invisible(
- .Call("delModel", PACKAGE = "sybilSBML",
- sbmlPointer(sbmlm)
- )
- )
-
-}
-
-
-#------------------------------------------------------------------------------#
-
-getSBMLlevel <- function(sbmlf) {
-
- level <- .Call("getSBMLlevel", PACKAGE = "sybilSBML",
- sbmlPointer(sbmlf)
- )
-
- return(level)
-}
-
-
-
-#------------------------------------------------------------------------------#
-
-getSBMLversion <- function(sbmlf) {
-
- version <- .Call("getSBMLversion", PACKAGE = "sybilSBML",
- sbmlPointer(sbmlf)
- )
-
- return(version)
-}
-
-
-#------------------------------------------------------------------------------#
-
-validateSBMLdocument <- function(sbmlf) {
-
- if (is(sbmlf, "character")) {
- sbmlff <- openSBMLfile(fname = sbmlf)
- }
- else {
- sbmlff <- sbmlf
- }
-
- val <- .Call("validateDocument", PACKAGE = "sybilSBML",
- sbmlPointer(sbmlff)
- )
-
- if (is(sbmlf, "character")) {
- val <- getSBMLerrors(sbmlff)
- closeSBMLfile(sbmlff)
- }
-
- return(val)
-}
-
-
-#------------------------------------------------------------------------------#
-
-getSBMLerrors <- function(sbmlf) {
-
- err <- .Call("getSBMLerrors", PACKAGE = "sybilSBML",
- sbmlPointer(sbmlf)
- )
-
- err <- sbmlError(err, sbmlf)
-
- return(err)
-}
-
-
-#------------------------------------------------------------------------------#
-
-getSBMLmodId <- function(sbmlm) {
-
- modid <- .Call("getSBMLmodId", PACKAGE = "sybilSBML",
- sbmlPointer(sbmlm)
- )
-
- return(modid)
-}
-
-
-#------------------------------------------------------------------------------#
-
-getSBMLmodName <- function(sbmlm) {
-
- modn <- .Call("getSBMLmodName", PACKAGE = "sybilSBML",
- sbmlPointer(sbmlm)
- )
-
- return(modn)
-}
-
-
-#------------------------------------------------------------------------------#
-
-getSBMLnumCompart <- function(sbmlm) {
-
- num <- .Call("getSBMLnumCompart", PACKAGE = "sybilSBML",
- sbmlPointer(sbmlm)
- )
-
- return(num)
-}
-
-
-#------------------------------------------------------------------------------#
-
-getSBMLnumSpecies <- function(sbmlm) {
-
- num <- .Call("getSBMLnumSpecies", PACKAGE = "sybilSBML",
- sbmlPointer(sbmlm)
- )
-
- return(num)
-}
-
-
-#------------------------------------------------------------------------------#
-
-getSBMLnumReactions <- function(sbmlm) {
-
- num <- .Call("getSBMLnumReactions", PACKAGE = "sybilSBML",
- sbmlPointer(sbmlm)
- )
-
- return(num)
-}
-
-
-#------------------------------------------------------------------------------#
-
-getSBMLunitDefinitionsList <- function(sbmlm) {
-
- units <- .Call("getSBMLunitDefinitionsList", PACKAGE = "sybilSBML",
- sbmlPointer(sbmlm)
- )
-
- return(units)
-}
-
-
-#------------------------------------------------------------------------------#
-
-getSBMLCompartList <- function(sbmlm) {
-
- comp <- .Call("getSBMLCompartList", PACKAGE = "sybilSBML",
- sbmlPointer(sbmlm)
- )
-
- return(comp)
-}
-
-
-#------------------------------------------------------------------------------#
-
-getSBMLSpeciesList <- function(sbmlm) {
-
- spec <- .Call("getSBMLSpeciesList", PACKAGE = "sybilSBML",
- sbmlPointer(sbmlm)
- )
-
- return(spec)
-}
-
-
-#------------------------------------------------------------------------------#
-
-getSBMLReactionsList <- function(sbmlm) {
-
- react <- .Call("getSBMLReactionsList", PACKAGE = "sybilSBML",
- sbmlPointer(sbmlm)
- )
-
- return(react)
-}
-
-
-
-
-
-
-
-
-
+#------------------------------------------------------------------------------#
+# Link to libSBML for sybil #
+#------------------------------------------------------------------------------#
+
+# sybilSBML.R
+# Link to libSBML for sybil.
+#
+# Copyright (C) 2010-2013 Gabriel Gelius-Dietrich, Dpt. for Bioinformatics,
+# Institute for Informatics, Heinrich-Heine-University, Duesseldorf, Germany.
+# All right reserved.
+# Email: geliudie@uni-duesseldorf.de
+#
+# This file is part of sybilSBML.
+#
+# SybilSBML 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.
+#
+# SybilSBML 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 SybilSBML. If not, see <http://www.gnu.org/licenses/>.
+
+
+#------------------------------------------------------------------------------#
+
+versionLibSBML <- function() {
+
+ version <- .Call("getLibSBMLversion", PACKAGE = "sybilSBML")
+ return(version)
+
+}
+
+
+#------------------------------------------------------------------------------#
+
+openSBMLfile <- function(fname, ptrtype = "sbml_doc") {
+
+ if ( file.exists(fname) == FALSE ) {
+ stop("file not found: ", sQuote(fname))
+ }
+
+ sbmlf <- .Call("readSBMLfile", PACKAGE = "sybilSBML",
+ as.character(normalizePath(fname)[1]),
+ as.character(ptrtype)
+ )
+
+ sbmlfP <- sbmlDocPointer(sbmlf)
+
+ return(sbmlfP)
+}
+
+
+#------------------------------------------------------------------------------#
+
+closeSBMLfile <- function(sbmlf) {
+
+ invisible(
+ .Call("delDocument", PACKAGE = "sybilSBML",
+ sbmlPointer(sbmlf)
+ )
+ )
+
+}
+
+
+#------------------------------------------------------------------------------#
+
+getSBMLmodel <- function(sbmlf, ptrtype = "sbml_mod") {
+
+ sbmlm <- .Call("getSBMLmodel", PACKAGE = "sybilSBML",
+ sbmlPointer(sbmlf),
+ as.character(ptrtype)
+ )
+
+ sbmlmP <- sbmlModPointer(sbmlm, sbmlf)
+
+ if (isTRUE(isNULLpointerSBML(sbmlmP))) {
+ sbmlmP <- NULL
+ }
+
+ return(sbmlmP)
+}
+
+
+#------------------------------------------------------------------------------#
+
+delSBMLmodel <- function(sbmlm) {
+
+ invisible(
+ .Call("delModel", PACKAGE = "sybilSBML",
+ sbmlPointer(sbmlm)
+ )
+ )
+
+}
+
+
+#------------------------------------------------------------------------------#
+
+getSBMLlevel <- function(sbmlf) {
+
+ level <- .Call("getSBMLlevel", PACKAGE = "sybilSBML",
+ sbmlPointer(sbmlf)
+ )
+
+ return(level)
+}
+
+
+
+#------------------------------------------------------------------------------#
+
+getSBMLversion <- function(sbmlf) {
+
+ version <- .Call("getSBMLversion", PACKAGE = "sybilSBML",
+ sbmlPointer(sbmlf)
+ )
+
+ return(version)
+}
+
+#------------------------------------------------------------------------------#
+
+getSBMLFbcversion <- function(sbmlf) {
+
+ version <- .Call("getSBMLFbcversion", PACKAGE = "sybilSBML",
+ sbmlPointer(sbmlf)
+ )
+
+ return(version)
+}
+
+
+#------------------------------------------------------------------------------#
+
+validateSBMLdocument <- function(sbmlf) {
+
+ if (is(sbmlf, "character")) {
+ sbmlff <- openSBMLfile(fname = sbmlf)
+ }
+ else {
+ sbmlff <- sbmlf
+ }
+
+ val <- .Call("validateDocument", PACKAGE = "sybilSBML",
+ sbmlPointer(sbmlff)
+ )
+
+ if (is(sbmlf, "character")) {
+ val <- getSBMLerrors(sbmlff)
+ closeSBMLfile(sbmlff)
+ }
+
+ return(val)
+}
+
+
+#------------------------------------------------------------------------------#
+
+getSBMLerrors <- function(sbmlf) {
+
+ err <- .Call("getSBMLerrors", PACKAGE = "sybilSBML",
+ sbmlPointer(sbmlf)
+ )
+
+ err <- sbmlError(err, sbmlf)
+
+ return(err)
+}
+
+
+#------------------------------------------------------------------------------#
+
+getSBMLmodId <- function(sbmlm) {
+
+ modid <- .Call("getSBMLmodId", PACKAGE = "sybilSBML",
+ sbmlPointer(sbmlm)
+ )
+
+ return(modid)
+}
+
+
+#------------------------------------------------------------------------------#
+
+getSBMLmodName <- function(sbmlm) {
+
+ modn <- .Call("getSBMLmodName", PACKAGE = "sybilSBML",
+ sbmlPointer(sbmlm)
+ )
+
+ return(modn)
+}
+
+#------------------------------------------------------------------------------#
+
+getSBMLmodNotes <- function(sbmlm) {
+
+ modnotes <- .Call("getSBMLmodNotes", PACKAGE = "sybilSBML",
+ sbmlPointer(sbmlm)
+ )
+
+ return(modnotes)
+}
+
+#------------------------------------------------------------------------------#
+
+getSBMLmodAnnotation <- function(sbmlm) {
+
+ modanno <- .Call("getSBMLmodAnnotation", PACKAGE = "sybilSBML",
+ sbmlPointer(sbmlm)
+ )
+
+ return(modanno)
+}
+
+
+#------------------------------------------------------------------------------#
+
+getSBMLnumCompart <- function(sbmlm) {
+
+ num <- .Call("getSBMLnumCompart", PACKAGE = "sybilSBML",
+ sbmlPointer(sbmlm)
+ )
+
+ return(num)
+}
+
+
+#------------------------------------------------------------------------------#
+
+getSBMLnumSpecies <- function(sbmlm) {
+
+ num <- .Call("getSBMLnumSpecies", PACKAGE = "sybilSBML",
+ sbmlPointer(sbmlm)
+ )
+
+ return(num)
+}
+
+
+#------------------------------------------------------------------------------#
+
+getSBMLnumReactions <- function(sbmlm) {
+
+ num <- .Call("getSBMLnumReactions", PACKAGE = "sybilSBML",
+ sbmlPointer(sbmlm)
+ )
+
+ return(num)
+}
+
+
+#------------------------------------------------------------------------------#
+
+getSBMLunitDefinitionsList <- function(sbmlm) {
+
+ units <- .Call("getSBMLunitDefinitionsList", PACKAGE = "sybilSBML",
+ sbmlPointer(sbmlm)
+ )
+
+ return(units)
+}
+
+
+#------------------------------------------------------------------------------#
+
+getSBMLCompartList <- function(sbmlm) {
+
+ comp <- .Call("getSBMLCompartList", PACKAGE = "sybilSBML",
+ sbmlPointer(sbmlm)
+ )
+
+ return(comp)
+}
+
+
+#------------------------------------------------------------------------------#
+
+getSBMLSpeciesList <- function(sbmlm) {
+
+ spec <- .Call("getSBMLSpeciesList", PACKAGE = "sybilSBML",
+ sbmlPointer(sbmlm)
+ )
+
+ return(spec)
+}
+
+
+#------------------------------------------------------------------------------#
+
+getSBMLReactionsList <- function(sbmlm) {
+
+ react <- .Call("getSBMLReactionsList", PACKAGE = "sybilSBML",
+ sbmlPointer(sbmlm)
+ )
+
+ return(react)
+}
+
+
+#------------------------------------------------------------------------------#
+#export mod to SBML
+deformatSBMLid <- function(idstr) {
+ idstr <- gsub("-", "_DASH_", idstr, fixed = TRUE)
+ idstr <- gsub("(", "_LPAREN_", idstr, fixed = TRUE)
+ idstr <- gsub(")", "_RPAREN_", idstr, fixed = TRUE)
+ idstr <- gsub("[", "_", idstr, fixed = TRUE)
+ idstr <- gsub("]", "", idstr, fixed = TRUE)
+ idstr <- gsub(",", "_COMMA_", idstr, fixed = TRUE)
+ idstr <- gsub(".", "_PERIOD_", idstr, fixed = TRUE)
+ idstr <- gsub("'", "_APOS_", idstr, fixed = TRUE)
+ idstr <- sub("\\(e\\)$", "_e_", idstr)
+ idstr <- gsub("-", "_", idstr, fixed = TRUE)
+ return(idstr)
+}
+
+deformatGene<-function(idstr) {
+ idstr<-gsub("\\((\\S+)\\)", "\\1", idstr)
+ #idstr <- gsub("( ", "(", idstr, fixed = TRUE)
+ #idstr <- gsub(" (", "(", idstr, fixed = TRUE)
+ #idstr <- gsub(") ", ")", idstr, fixed = TRUE)
+ #idstr <- gsub(" )", ")", idstr, fixed = TRUE)
+ idstr <- gsub(":", "_", idstr, fixed = TRUE)
+ return(idstr)
+}
+
+writeSBML<- function(morg=NULL,level=2,version=4,fbcLevel=0,filename="export.xml",recoverExtMet=FALSE,printNotes=TRUE,printAnnos=TRUE,validation=FALSE ){
+ if(class(morg)!="modelorg"){
+ stop("morg has to be of class modelorg\n")
+ }
+
+ ###right
+ if(level==1)
+ {
+ # test if Matrix has no double values
+ if( !all( S(morg) == floor(S(morg))) ) warning("Level 1 does not support double values")
+ fbcLevel=0
+ if(version != 2)
+ {
+ warning("just Level 1 Version 2 will be supported")
+ version=2
+ }
+ }else if (level==2)
+ {
+ fbcLevel=0
+ if(version >5)
+ {
+ warning("Level 2 Version 5 will be supported")
+ version=5
+ }
+ if(version < 1)
+ {
+ warning("Level 2 Version 1 will be supported")
+ version=1
+ }
+ }
+ else if (level==3)
+ { if(fbcLevel >2)fbcLevel=2
+ if(version != 1)
+ {
+ print("Level 3 Version 1 will be supported")
+ version=1
+ }
+
+ }else {
+ stop(" Support just for Level 1,2 and 3 \n")
+ }
+
+ ##All GENES###
+ allgenes<- unique(unlist(genes(morg)))
+ allgenes<-allgenes[allgenes != ""]
+
+
+ ##EXCHANGE REACTIONS##
+ ex <- findExchReact(morg)
+ ex_react<-NULL
+ # if recoverExtMet== FALSE => null for ex_react
+ if( (!is.null(ex)) && (recoverExtMet) )
+ {
+ if(!(all(diag(S(morg)[met_pos(ex), react_pos(ex)])==-1)))
+ stop("exchange reactions with Scoeff different than -1\n")
+ ex_react<-as.integer(react_pos(ex))
+ }
+
+ ### Build wrapper for C Function #####
+
+
+ ##Met Attribute###
+ com_meta_id<- NULL
+ met_meta_id<- NULL
+ com_notes <- NULL
+ com_annotation<- NULL
+ met_notes<- NULL
+ met_anno<- NULL
+ met_bnd<- NULL
+ met_charge<-NULL
+ met_formula<-NULL
+
+ react_notes<-NULL
+ react_anno<-NULL
+
+ mod_notes<-NULL
+ mod_anno<-NULL
+
+ #subsystem
+ # is subsystem Empty
+ if(length( colnames(subSys(morg)))==1 && colnames(subSys(morg))[1]=="" ) modhasubSys<-FALSE
+ else modhasubSys<-TRUE
+
+ newsubS<- NULL
+
+ if( .hasSlot(morg,"mod_attr") && .hasSlot(morg,"comp_attr") && .hasSlot(morg,"met_attr") && .hasSlot(morg,"react_attr") )
+ newSybil<-TRUE
+ else newSybil<-FALSE
+ ### Start newSybil attr
+ if(newSybil)
+ {
+ if(("notes" %in% colnames(mod_attr(morg))) && (printNotes) ) mod_notes<-as.character(mod_attr(morg)[['notes']])
+ if(("annotation" %in% colnames(mod_attr(morg))) && (printAnnos) ) mod_annotation<-as.character(mod_attr(morg)[['annotation']])
+
+ if(("notes" %in% colnames(comp_attr(morg))) && (printNotes) ) com_notes<-as.character(as.list((comp_attr(morg)[['notes']])))
+ if(("annotation" %in% colnames(comp_attr(morg))) && (printAnnos) ) com_annotation<-as.character(as.list((comp_attr(morg)[['annotation']])))
+
+ if("charge" %in% colnames(met_attr(morg))) met_charge<- as.integer(as.list((met_attr(morg)[['charge']])))
+ if("chemicalFormula" %in% colnames(met_attr(morg))) met_formula<-as.character(as.list((met_attr(morg)[['chemicalFormula']])))
+ if(("annotation" %in% colnames(met_attr(morg))) && (printAnnos)) met_anno<-as.character(as.list((met_attr(morg)[['annotation']])))
+ if("boundaryCondition" %in% colnames(met_attr(morg))) met_bnd<-as.logical(as.list((met_attr(morg)[['boundaryCondition']])))
+
+ if(("notes" %in% colnames(met_attr(morg))) && (printNotes) )
+ { # delete Formular and charge from notes to do
+ met_notes<-as.character(as.list((met_attr(morg)[['notes']])))
+ if (!is.null(met_charge) || !is.null(met_formula))
+ {
+ for ( i in 1:met_num(morg))
+ {
+
+ if(nchar(met_notes[i])> 8)
+ {
+ # Have Assocation in Notes?yes: replace no: append
+
+ if (regexpr("html:p", met_notes[i], fixed = TRUE) == -1)tag <- "p"
+ else tag <- "html:p"
+
+
+ if (!is.null(met_formula))
+ {
+ haveform<-grepl("FORMULA: [^<]+",met_notes[i])
+ #Have Gene if not ->no need to write in FBC2
+ if(haveform)
+ {
+ if(fbcLevel==0)met_notes[i]<-sub("FORMULA: [^<]+",paste("FORMULA: ",met_formula[i], sep = ""), met_notes[i], perl = TRUE)
+ else met_notes[i]<-sub(paste("<",tag,">","FORMULA: [^<]+","</",tag,">",sep = ""),"",met_notes[i], perl = TRUE)
+ }
+ else if(fbcLevel==0) met_notes[i]<-gsub("</notes>",paste("<",tag,">","FORMULA: ",met_formula[i],"</",tag,">","\n</notes>",sep = ""),met_notes[i])
+ }
+ if (!is.null(met_charge))
+ {
+ havecharge<-grepl("CHARGE: [^<]+",met_notes[i])
+ #Have Subsystem
+ if(havecharge)
+ {
+ if(fbcLevel !=0 || (level==2 && version==1 ))
+ met_notes[i]<-sub(paste("<",tag,">","CHARGE: [^<]+","</",tag,">",sep = ""),"",met_notes[i], perl = TRUE)
+ else met_notes[i]<-sub("CHARGE: [^<]+",paste("CHARGE: ",met_charge[i], sep = ""), met_notes[i], perl = TRUE)
+
+
+ }
+ else if(fbcLevel==0) if(level!=2 && version!=1) met_notes[i]<-gsub("</notes>",paste("<",tag,">","CHARGE: ",met_charge[i],"</",tag,">","\n</notes>",sep = ""),met_notes[i])
+ }
+ }
+ }
+ }
+
+ }
+ if(("annotation" %in% colnames(react_attr(morg))) && (printAnnos)) react_anno<-as.character(as.list((react_attr(morg)[['annotation']])))
+
+ # Merge Notes with "our" Notes and make sure gpr Rules from gpr
+ if(("notes" %in% colnames(react_attr(morg))) && (printNotes))
+ {
+ react_notes<-as.character(as.list((react_attr(morg)[['notes']])))
+ # using
+ # SubSystem EXISTIERT nicht colnames(subSys(ec))
+
+ for ( i in 1:react_num(morg))
+ {
+ # using the for loop
+ if(modhasubSys)newsubS[i]<- paste(names(which(subSys(morg)[i,])), collapse=", ")
+ if(nchar(react_notes[i])> 8)
+ {
+ # Have Association in Notes? yes: replace no: append
+
+ if (regexpr("html:p", react_notes[i], fixed = TRUE) == -1)tag <- "p"
+ else tag <- "html:p"
+
+ havegene<-grepl("GENE[_ ]?ASSOCIATION: [^<]+",react_notes[i])
+ havesub<-grepl("SUBSYSTEM: [^<]+",react_notes[i])
+
+ #Have Gene if not ->no need to write in FBC2
+ if(havegene)
+ {
+ if(fbcLevel==2) react_notes[i]<-sub(paste("<",tag,">","GENE[_ ]?ASSOCIATION: [^<]+","</",tag,">",sep = ""),"",react_notes[i], perl = TRUE)
+ else react_notes[i]<-sub("GENE[_ ]?ASSOCIATION: [^<]+",paste("GENE_ASSOCIATION: ",gpr(morg)[i], sep = ""), react_notes[i], perl = TRUE)
+ }
+ else if(fbcLevel!=2)react_notes[i]<-gsub("</notes>",paste("<",tag,">","GENE_ASSOCIATION: ",gpr(morg)[i],"</",tag,">","\n</notes>",sep = ""),react_notes[i])
+
+ #Have Subsystem
+ if(havesub)react_notes[i]<-sub("SUBSYSTEM: [^<]+",paste("SUBSYSTEM: ",newsubS[i], sep = ""), react_notes[i], perl = TRUE)
+ else if(modhasubSys) react_notes[i]<-gsub("</notes>",paste("<",tag,">","SUBSYSTEM: ",newsubS[i],"</",tag,">","\n</notes>",sep = ""),react_notes[i])
+ }
+ }
+ }
+
+
+ } ####END newSybil attr
+
+ # Subsystem
+ if(is.null(newsubS) && !(modhasubSys) ) for ( i in 1:react_num(morg)) {newsubS[i]<- paste(names(which(subSys(morg)[i,])), collapse=", ")}
+
+ newmet_id <- paste0("M_", (deformatSBMLid(met_id(morg))))
+ #newmet_id <- sub("\\[(\\w)\\]$", "_\\1", newmet_id) # append compartment id, if in postfix with square brkts
+
+ newreact_id <- paste0("R_", deformatSBMLid(react_id(morg)))
+ newmet_comp<-mod_compart(morg)[met_comp(morg)]
+
+
+ success <-.Call("exportSBML", PACKAGE = "sybilSBML",
+ as.integer(version),
+ as.integer(level),
+ as.integer(fbcLevel),
+ as.character(filename),
+ SYBIL_SETTINGS("MAXIMUM"),
+ as.character(mod_desc(morg)),
+ as.character(mod_name(morg)),
+ as.character(mod_compart(morg)),
+ as.character(newmet_id),
+ as.character(met_name(morg)),
+ as.character(newmet_comp),
+ met_formula,
+ met_charge,
+ as.character(newreact_id),
+ as.character(react_name(morg)),
+ as.logical(react_rev(morg)),
+ as.numeric(lowbnd(morg)),
+ as.numeric(uppbnd(morg)),
+ as.integer(obj_coef(morg)),
+ as.character(newsubS),
+ as.character(deformatGene(gpr(morg))),
+ as.numeric(shrinkMatrix(morg,j=1:react_num(morg))),
+ mod_notes,
+ mod_anno,
+ com_notes,
+ com_annotation,
+ met_notes,
+ met_anno,
+ met_bnd,
+ react_notes,
+ react_anno,
+ ex_react,
+ as.character(deformatGene(allgenes))
+ )
+# SUCESS MESSAGES
+ if(success)
+ {
+ message(paste("Wrote file ",filename,"\n",sep=""), appendLF = FALSE);
+ if (validation)print(validateSBMLdocument(filename));
+ }
+ else message(paste("Could not write file ",filename,"\n",sep=""), appendLF = FALSE);
+ return (success)
+}
\ No newline at end of file
diff --git a/build/vignette.rds b/build/vignette.rds
new file mode 100644
index 0000000000000000000000000000000000000000..217b014b3aaa3d2181c33fc96a7045116045540b
Binary files /dev/null and b/build/vignette.rds differ
diff --git a/configure b/configure
index c935bad4b88e8c1b54ffc657c001f9f52a23033a..ba94dc2b4ec2da43b77e94e9fe8036692a4e4aab 100755
--- a/configure
+++ b/configure
@@ -1,8 +1,8 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for sybilSBML 2.0.8.
+# Generated by GNU Autoconf 2.69 for sybilSBML 3.0.0.
#
-# Report bugs to <geliudie@uni-duesseldorf.de>.
+# Report bugs to <clausjonathan.fritzemeier@uni-duesseldorf.de>.
#
#
# Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
@@ -267,8 +267,8 @@ fi
$as_echo "$0: be upgraded to zsh 4.3.4 or later."
else
$as_echo "$0: Please tell bug-autoconf@gnu.org and
-$0: geliudie@uni-duesseldorf.de about your system,
-$0: including any error possibly output before this
+$0: clausjonathan.fritzemeier@uni-duesseldorf.de about your
+$0: system, including any error possibly output before this
$0: message. Then install a modern shell, or manually run
$0: the script under such a shell if you do have one."
fi
@@ -580,9 +580,9 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='sybilSBML'
PACKAGE_TARNAME='sybilsbml'
-PACKAGE_VERSION='2.0.8'
-PACKAGE_STRING='sybilSBML 2.0.8'
-PACKAGE_BUGREPORT='geliudie@uni-duesseldorf.de'
+PACKAGE_VERSION='3.0.0'
+PACKAGE_STRING='sybilSBML 3.0.0'
+PACKAGE_BUGREPORT='clausjonathan.fritzemeier@uni-duesseldorf.de'
PACKAGE_URL=''
# Factoring default headers for most tests.
@@ -1230,7 +1230,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
-\`configure' configures sybilSBML 2.0.8 to adapt to many kinds of systems.
+\`configure' configures sybilSBML 3.0.0 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1291,7 +1291,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of sybilSBML 2.0.8:";;
+ short | recursive ) echo "Configuration of sybilSBML 3.0.0:";;
esac
cat <<\_ACEOF
@@ -1315,7 +1315,7 @@ Some influential environment variables:
Use these variables to override the choices made by `configure' or to help
it to find libraries and programs with nonstandard names/locations.
-Report bugs to <geliudie@uni-duesseldorf.de>.
+Report bugs to <clausjonathan.fritzemeier@uni-duesseldorf.de>.
_ACEOF
ac_status=$?
fi
@@ -1378,7 +1378,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-sybilSBML configure 2.0.8
+sybilSBML configure 3.0.0
generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1537,9 +1537,9 @@ $as_echo "$as_me: WARNING: $2: see the Autoconf documentation" >&2;}
$as_echo "$as_me: WARNING: $2: section \"Present But Cannot Be Compiled\"" >&2;}
{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: proceeding with the compiler's result" >&5
$as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;}
-( $as_echo "## ------------------------------------------ ##
-## Report this to geliudie@uni-duesseldorf.de ##
-## ------------------------------------------ ##"
+( $as_echo "## ----------------------------------------------------------- ##
+## Report this to clausjonathan.fritzemeier@uni-duesseldorf.de ##
+## ----------------------------------------------------------- ##"
) | sed "s/^/$as_me: WARNING: /" >&2
;;
esac
@@ -1676,11 +1676,78 @@ fi
as_fn_set_status $ac_retval
} # ac_fn_c_try_link
+
+# ac_fn_c_check_func LINENO FUNC VAR
+# ----------------------------------
+# Tests whether FUNC exists, setting the cache variable VAR accordingly
+ac_fn_c_check_func ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if eval \${$3+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+/* Define $2 to an innocuous variant, in case <limits.h> declares $2.
+ For example, HP-UX 11i <limits.h> declares gettimeofday. */
+#define $2 innocuous_$2
+
+/* System header to define __stub macros and hopefully few prototypes,
+ which can conflict with char $2 (); below.
+ Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ <limits.h> exists even on freestanding compilers. */
+
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+
+#undef $2
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char $2 ();
+/* The GNU C library defines this for functions which it implements
+ to always fail with ENOSYS. Some functions are actually named
+ something starting with __ and the normal name is an alias. */
+#if defined __stub_$2 || defined __stub___$2
+choke me
+#endif
+
+int
+main ()
+{
+return $2 ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ eval "$3=yes"
+else
+ eval "$3=no"
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+ eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+
+} # ac_fn_c_check_func
cat >config.log <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
-It was created by sybilSBML $as_me 2.0.8, which was
+It was created by sybilSBML $as_me 3.0.0, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
@@ -3528,6 +3595,101 @@ else
fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for readSBML in -lsbml" >&5
+$as_echo_n "checking for readSBML in -lsbml... " >&6; }
+if ${ac_cv_lib_sbml_readSBML+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-lsbml $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char readSBML ();
+int
+main ()
+{
+return readSBML ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ ac_cv_lib_sbml_readSBML=yes
+else
+ ac_cv_lib_sbml_readSBML=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_sbml_readSBML" >&5
+$as_echo "$ac_cv_lib_sbml_readSBML" >&6; }
+if test "x$ac_cv_lib_sbml_readSBML" = xyes; then :
+ cat >>confdefs.h <<_ACEOF
+#define HAVE_LIBSBML 1
+_ACEOF
+
+ LIBS="-lsbml $LIBS"
+
+else
+ as_fn_error $? "Could not link to libSBML:
+ use --with-sbml-lib or PKG_LIBS to specify the library path and the libraries to pass to the linker." "$LINENO" 5
+fi
+
+
+ac_fn_c_check_header_compile "$LINENO" "sbml/packages/fbc/common/FbcExtensionTypes.h" "ac_cv_header_sbml_packages_fbc_common_FbcExtensionTypes_h" "#include <sbml/SBMLTypes.h>
+"
+if test "x$ac_cv_header_sbml_packages_fbc_common_FbcExtensionTypes_h" = xyes; then :
+
+else
+ as_fn_error $? "Could not find specific FBC header of libSBML:
+ make sure your libSBML version is >= 5.13." "$LINENO" 5
+fi
+
+
+
+#AC_CHECK_LIB([sbml], [SBMLExtensionRegistry_getRegisteredPackages], ,
+# AC_MSG_ERROR([Could not find specific FBC function of libSBML:
+# make sure your libSBML version is >= 5.13.]))
+
+for ac_func in SBase_getPlugin SBMLExtensionRegistry_getRegisteredPackages GeneProductAssociation_setAssociation FbcReactionPlugin_getLowerFluxBound
+do :
+ as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
+ac_fn_c_check_func "$LINENO" "$ac_func" "$as_ac_var"
+if eval test \"x\$"$as_ac_var"\" = x"yes"; then :
+ cat >>confdefs.h <<_ACEOF
+#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1
+_ACEOF
+
+else
+ as_fn_error $? "Could not find specific FBC function of libSBML:
+ make sure your libSBML version is >= 5.13." "$LINENO" 5
+fi
+done
+
+
+#AC_SEARCH_LIBS([SBase_getPlugin], [sbml], ,
+# AC_MSG_ERROR([Could not find specific FBC function of libSBML:
+# make sure your libSBML version is >= 5.13.]))
+
+#AC_SEARCH_LIBS([SBMLExtensionRegistry_getRegisteredPackages], [sbml], ,
+# AC_MSG_ERROR([Could not find specific FBC function of libSBML:
+# make sure your libSBML version is >= 5.13.]))
+
+
+
+#AC_SEARCH_LIBS([GeneProductAssociation_setAssociation], [sbml], ,
+# AC_MSG_ERROR([Could not find specific FBC function of libSBML:
+# make sure your libSBML version is >= 5.13.]))
+
+
@@ -4077,7 +4239,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
-This file was extended by sybilSBML $as_me 2.0.8, which was
+This file was extended by sybilSBML $as_me 3.0.0, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -4124,13 +4286,13 @@ Usage: $0 [OPTION]... [TAG]...
Configuration files:
$config_files
-Report bugs to <geliudie@uni-duesseldorf.de>."
+Report bugs to <clausjonathan.fritzemeier@uni-duesseldorf.de>."
_ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
-sybilSBML config.status 2.0.8
+sybilSBML config.status 3.0.0
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
diff --git a/configure.ac b/configure.ac
index c75e9c7e0a8012cf7e0f97754609a57bea301223..08faede40197a400f9e86fc8520a65aa90f60143 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,4 +1,4 @@
-AC_INIT([sybilSBML], [2.0.8], [geliudie@uni-duesseldorf.de])
+AC_INIT([sybilSBML], [3.0.0], [clausjonathan.fritzemeier@uni-duesseldorf.de])
dnl # --------------------------------------------------------------------
dnl # global (environment) variables
@@ -236,6 +236,38 @@ AC_SEARCH_LIBS([readSBML], [sbml], ,
AC_MSG_ERROR([Could not link to libSBML:
use --with-sbml-lib or PKG_LIBS to specify the library path and the libraries to pass to the linker.]))
+AC_CHECK_LIB([sbml], [readSBML], ,
+ AC_MSG_ERROR([Could not link to libSBML:
+ use --with-sbml-lib or PKG_LIBS to specify the library path and the libraries to pass to the linker.]))
+
+AC_CHECK_HEADER([sbml/packages/fbc/common/FbcExtensionTypes.h], ,
+ AC_MSG_ERROR([Could not find specific FBC header of libSBML:
+ make sure your libSBML version is >= 5.13.]),
+ [#include <sbml/SBMLTypes.h>])
+
+#AC_CHECK_LIB([sbml], [SBMLExtensionRegistry_getRegisteredPackages], ,
+# AC_MSG_ERROR([Could not find specific FBC function of libSBML:
+# make sure your libSBML version is >= 5.13.]))
+
+AC_CHECK_FUNCS([SBase_getPlugin SBMLExtensionRegistry_getRegisteredPackages GeneProductAssociation_setAssociation FbcReactionPlugin_getLowerFluxBound], ,
+ AC_MSG_ERROR([Could not find specific FBC function of libSBML:
+ make sure your libSBML version is >= 5.13.]))
+
+#AC_SEARCH_LIBS([SBase_getPlugin], [sbml], ,
+# AC_MSG_ERROR([Could not find specific FBC function of libSBML:
+# make sure your libSBML version is >= 5.13.]))
+
+#AC_SEARCH_LIBS([SBMLExtensionRegistry_getRegisteredPackages], [sbml], ,
+# AC_MSG_ERROR([Could not find specific FBC function of libSBML:
+# make sure your libSBML version is >= 5.13.]))
+
+
+
+#AC_SEARCH_LIBS([GeneProductAssociation_setAssociation], [sbml], ,
+# AC_MSG_ERROR([Could not find specific FBC function of libSBML:
+# make sure your libSBML version is >= 5.13.]))
+
+
dnl # --------------------------------------------------------------------
dnl # substitute src/Makevars
diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
index 6f08e633b3cc7acf365879f5cd7a815bfa64fadf..043c9615087a4614204fb3a54940ca80891369c3 100644
--- a/inst/NEWS.Rd
+++ b/inst/NEWS.Rd
@@ -4,7 +4,24 @@
\title{sybilSBML News}
\encoding{UTF-8}
-\newcommand{\CRANpkg}{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}}
+\newcommand{\CRANpkg}{\href{https://cran.r-project.org/package=#1}{\pkg{#1}}}
+
+% ---------------------------------------------------------------------------- %
+\section{Changes in version 3.0.1 2016-12-16}{
+ \itemize{
+ \item sybilSBML now supports writing of SBML files.
+ \item The new FBC additional package for SBML is now fully integrated.
+ \item Urls in NEWS file are now in default style.
+ }
+}
+
+% ---------------------------------------------------------------------------- %
+\section{Changes in version 2.0.11 2015-07-03}{
+ \itemize{
+ \item \code{gprRules}-Slot in \code{modelorg} has changed. Thus
+ \code{readSBMLmod} had to be updated.
+ }
+}
% ---------------------------------------------------------------------------- %
\section{Changes in version 2.0.11 2015-07-03}{
diff --git a/inst/doc/sybilSBML.R b/inst/doc/sybilSBML.R
new file mode 100644
index 0000000000000000000000000000000000000000..3b366b5520db2fc39b7fab091b74bf5767cf5bbf
--- /dev/null
+++ b/inst/doc/sybilSBML.R
@@ -0,0 +1,30 @@
+### R code from vignette source 'sybilSBML.Rnw'
+### Encoding: UTF-8
+
+###################################################
+### code chunk number 1: sybilSBML.Rnw:85-87 (eval = FALSE)
+###################################################
+## library(sybilSBML)
+## model <- readSBMLmod("<model>.xml")
+
+
+###################################################
+### code chunk number 2: sybilSBML.Rnw:103-106
+###################################################
+library(sybilSBML)
+mp <- system.file(package = "sybilSBML", "extdata")
+ec_mod <- file.path(mp, "ecoli_core_model.xml")
+
+
+###################################################
+### code chunk number 3: sybilSBML.Rnw:109-110
+###################################################
+mod <- readSBMLmod(ec_mod, bndCond = FALSE)
+
+
+###################################################
+### code chunk number 4: sybilSBML.Rnw:123-124
+###################################################
+err <- validateSBMLdocument(ec_mod)
+
+
diff --git a/inst/doc/sybilSBML.Rnw b/inst/doc/sybilSBML.Rnw
new file mode 100644
index 0000000000000000000000000000000000000000..5d11fdf9e2ba00c73f9684559b42fd8f93fc0e5e
--- /dev/null
+++ b/inst/doc/sybilSBML.Rnw
@@ -0,0 +1,132 @@
+\documentclass[a4paper,headings=small]{scrartcl}
+\usepackage[english]{babel}
+\usepackage[T1]{fontenc}
+\usepackage[utf8]{inputenc}
+\usepackage{textcomp,lmodern}
+\typearea[current]{last}
+\usepackage{fixltx2e,mparhack,mathdots}
+
+\usepackage{natbib}
+%\usepackage{hyperref}
+
+\usepackage{microtype}
+
+\newcommand{\Comp}[1]{\texttt{#1}}
+% bash command prompt
+\DeclareRobustCommand{\PROMPTL}{\Comp{\$}}
+
+% just a bash command
+\DeclareRobustCommand{\COML}[1]{%
+ \small{\PROMPTL\Comp{ #1}}
+}
+% bash command with quote environment
+\DeclareRobustCommand{\COMML}[1]{%
+ \begin{quote}%
+ \small{\PROMPTL\Comp{ #1}}
+ \end{quote}
+}
+
+\addtolength{\skip\footins}{0.5\baselineskip}
+\usepackage{fnpos}
+
+
+% \hypersetup{
+% pdftitle = {sybilSBML -- Quick Start},
+% pdfauthor = {Gabriel Gelius-Dietrich},
+% pdfsubject = {SBML support for SyBiL},
+% pdfkeywords = {SBML},
+% pdfborder = {0 0 0},
+% pdfhighlight = {/N}
+% }
+
+
+\newcommand{\pkg}[1]{\emph{#1}}
+\newcommand{\CRANpkg}[1]{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}}
+%\newcommand{\pkgname}{\CRANpkg{sybilSBML}}
+\newcommand{\pkgname}{\emph{sybilSBML}}
+\newcommand{\prgname}[1]{\textsc{#1}}
+
+
+\begin{document}
+\title{sybilSBML -- Quick Start}
+%\VignetteIndexEntry{Package sybilSBML -- Quick Start}
+%\VignettePackage{sybilSBML}
+\author{Gabriel Gelius-Dietrich}
+
+\maketitle
+
+
+\section{Introduction}
+
+The package \pkgname{} is an addition to package
+\pkg{sybil}\footnote{\texttt{http://CRAN.R-project.org/package=sybil}}
+providing support for
+metabolic networks written in SBML (Systems Biology Markup Language), in
+particular those developed by Bernhard \O. Palsson's
+lab\footnote{\texttt{http://gcrg.ucsd.edu/}} and those from the BiGG
+database\footnote{\texttt{http://bigg.ucsd.edu/}} \citep{Schellenberger:2010fk}.
+\nocite{Becker:2007uq,Schellenberger:2011fk}
+
+
+\section{Installation}
+
+The package \pkgname{} depends on a working installation of
+LibSBML \citep{Bornstein:2008uq} available from the SBML
+homepage\footnote{\texttt{http://www.sbml.org/}, libSBML version 5.6.0 or higher}
+(in particular libraries and header files).
+See \Comp{INSTALL} for installation instructions and platform specific details.
+
+
+\section{Usage}
+
+The package \pkgname{} provides the command \Comp{readSBMLmod()} which reads
+SBML formated files and returns instances of class \Comp{modelorg}.
+
+<<eval=FALSE>>=
+library(sybilSBML)
+model <- readSBMLmod("<model>.xml")
+@
+
+
+\section{Input files}
+
+The function \Comp{readSBMLmod()} reads metabolic network models written in
+SBML format (Systems Biology Markup Language). Among the models available in
+this de-facto standard format are in particular those developed by
+Bernhard \O. Palsson's lab.
+
+The file \Comp{ecoli\_core\_model.xml} (in \Comp{extdata/}) contains an
+exemplarily metabolic network written in SBML for the core energy metabolism
+of \emph{E.~coli} \citep{Palsson:2006fk,Orth:2010fk}.
+The exact location of the file can be retrieved with the \Comp{system.file()}
+command:
+<<>>=
+library(sybilSBML)
+mp <- system.file(package = "sybilSBML", "extdata")
+ec_mod <- file.path(mp, "ecoli_core_model.xml")
+@
+The model can be read in by using the command \Comp{readSBMLmod()}:
+<<print=true>>=
+mod <- readSBMLmod(ec_mod, bndCond = FALSE)
+@
+The metabolite id's of the SBML files are written in the format
+\Comp{M\_<metabolite abbreviation>\_<compartment abbreviation>}. The compartment
+abbreviation is a one letter abbreviation, e.\,g. \Comp{c} for cytosol. All
+metabolites outside the system boundary belong to compartment \Comp{b}. Those
+metabolites are transported into or outside the system. As long as they are
+mentioned, the network is closed. The function \Comp{readSBMLmod()} will remove
+them in order to produce an open network.
+
+\section{Validation of input files}
+
+SBML files can be validated by using the command \Comp{validateSBMLdocument()}:
+<<>>=
+err <- validateSBMLdocument(ec_mod)
+@
+The variable \Comp{err} is of class \Comp{sbmlError}, storing error messages
+generated by the validation procedure.
+
+\bibliographystyle{abbrvnat}
+\bibliography{sybilSBML}
+
+\end{document}
diff --git a/inst/doc/sybilSBML.pdf b/inst/doc/sybilSBML.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..fd54c3f9672b2e542000cb87bca02a4e8f84429a
Binary files /dev/null and b/inst/doc/sybilSBML.pdf differ
diff --git a/man/getSBMLFbcversion.Rd b/man/getSBMLFbcversion.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..5fadfd5f13a5ae2b2c8cf8c69fb975fde943bb29
--- /dev/null
+++ b/man/getSBMLFbcversion.Rd
@@ -0,0 +1,44 @@
+\name{getSBMLFbcversion}
+\alias{getSBMLFbcversion}
+
+\title{
+ Get SBML Version
+}
+
+\description{
+ Retrieve SBML FBC version of SBML file.
+}
+
+\usage{
+ getSBMLFbcversion(sbmlf)
+}
+
+\arguments{
+ \item{sbmlf}{
+ An object of class \code{\linkS4class{sbmlPtr}} as returned by
+ \code{\link{openSBMLfile}}. This is basically a pointer to a SBML document.
+ }
+}
+
+\value{
+ A single integer value containing the SBML FBC version of the SBML file.
+}
+
+\references{
+ Bornstein, B. J., Keating, S. M., Jouraku, A., and Hucka M. (2008)
+ LibSBML: An API Library for SBML. \emph{Bioinformatics} \bold{24},
+ 880--881.
+}
+
+\author{
+ Gabriel Gelius-Dietrich <geliudie@uni-duesseldorf.de>
+
+ Maintainer: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
+}
+
+
+\seealso{
+ \code{\link{openSBMLfile}}, \code{\linkS4class{sbmlPtr}}
+}
+
+\keyword{ IO }
\ No newline at end of file
diff --git a/man/getSBMLmodAnnotation.Rd b/man/getSBMLmodAnnotation.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..342af4fec419b91762dd801c1e036353171f8ee2
--- /dev/null
+++ b/man/getSBMLmodAnnotation.Rd
@@ -0,0 +1,44 @@
+\name{getSBMLmodAnnotation}
+\alias{getSBMLmodAnnotation}
+
+\title{
+ Get Model Annotation
+}
+
+\description{
+ Retrieve model annotation of a SBML model
+}
+
+\usage{
+ getSBMLmodAnnotation(sbmlm)
+}
+
+\arguments{
+ \item{sbmlm}{
+ An object of class \code{\linkS4class{sbmlPtr}} as returned by
+ \code{\link{getSBMLmodel}}. This is basically a pointer to a SBML model.
+ }
+}
+
+\value{
+ A single character string containing the model annotation of the SBML model.
+}
+
+\references{
+ Bornstein, B. J., Keating, S. M., Jouraku, A., and Hucka M. (2008)
+ LibSBML: An API Library for SBML. \emph{Bioinformatics} \bold{24},
+ 880--881.
+}
+
+\author{
+ Gabriel Gelius-Dietrich <geliudie@uni-duesseldorf.de>
+
+ Maintainer: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
+}
+
+
+\seealso{
+ \code{\link{getSBMLmodel}}, \code{\linkS4class{sbmlPtr}}
+}
+
+\keyword{ IO }
\ No newline at end of file
diff --git a/man/getSBMLmodNotes.Rd b/man/getSBMLmodNotes.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..005e8cf649ad9a0fd441d9cbe81eafa53a3bfb98
--- /dev/null
+++ b/man/getSBMLmodNotes.Rd
@@ -0,0 +1,44 @@
+\name{getSBMLmodNotes}
+\alias{getSBMLmodNotes}
+
+\title{
+ Get Model Note
+}
+
+\description{
+ Retrieve model notes of a SBML model
+}
+
+\usage{
+ getSBMLmodNotes(sbmlm)
+}
+
+\arguments{
+ \item{sbmlm}{
+ An object of class \code{\linkS4class{sbmlPtr}} as returned by
+ \code{\link{getSBMLmodel}}. This is basically a pointer to a SBML model.
+ }
+}
+
+\value{
+ A single character string containing the model notes of the SBML model.
+}
+
+\references{
+ Bornstein, B. J., Keating, S. M., Jouraku, A., and Hucka M. (2008)
+ LibSBML: An API Library for SBML. \emph{Bioinformatics} \bold{24},
+ 880--881.
+}
+
+\author{
+ Gabriel Gelius-Dietrich <geliudie@uni-duesseldorf.de>
+
+ Maintainer: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
+}
+
+
+\seealso{
+ \code{\link{getSBMLmodel}}, \code{\linkS4class{sbmlPtr}}
+}
+
+\keyword{ IO }
\ No newline at end of file
diff --git a/man/writeSBML.Rd b/man/writeSBML.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..6b94b13ab1ee793c32447acbbe8764ac526885a6
--- /dev/null
+++ b/man/writeSBML.Rd
@@ -0,0 +1,118 @@
+\name{writeSBML}
+\alias{writeSBML}
+
+\encoding{utf8}
+
+\title{Exports a Metabolic Network in SBML Format}
+
+\description{
+ The function exports a metabolic network from S4 object of the class \code{\link{modelorg}} in SBML format. The function returns TRUE if the SBML file is successfully built.
+}
+
+\usage{
+ writeSBML(morg=NULL,level=2,version=4,fbcLevel=0,
+ filename="export.xml",
+ recoverExtMet=FALSE,
+ printNotes=TRUE,
+ printAnnos=TRUE,
+ validation=FALSE)
+
+}
+
+\arguments{
+ \item{morg}{
+ An S4 object of the class \code{\link[sybil]{modelorg}}.
+ }
+ \item{level}{
+ A single integer value containing the SBML level for the exporting SBML file. \cr
+ Default: \code{2}.
+ }
+ \item{version}{
+ A single integer value containing the SBML version for the exporting SBML file. \cr
+ Default: \code{4}.
+ }
+ \item{fbcLevel}{
+ A single integer value containing the fbc package version for the exporting SBML file. \cr
+ Default: \code{2}.
+ }
+ \item{filename}{
+ SBML filename for exporting the model.
+ Default: \code{"export.xml"}.
+ }
+ \item{recoverExtMet}{
+ Boolean: recover external metabolites and refer them to compartment \code{"BOUNDARY"}.\cr
+ Default: \code{FALSE}.
+ }
+ \item{printNotes}{
+ Boolean: print Notes from original SBML file .\cr
+ Default: \code{TRUE}.
+ }
+ \item{printAnnos}{
+ Boolean: print Annotations from original SBML file .\cr
+ Default: \code{TRUE}.
+ }
+ \item{validation}{
+ Boolean: print containing errors for xml file .\cr
+ Default: \code{TRUE}.
+ }
+
+}
+
+\details{
+ The library \code{libSBML} is used to export a \code{\link[sybil]{modelorg}}
+ to a SBML file.
+
+}
+
+\value{
+ A single boolean value for a successful export .
+}
+
+\references{
+ The BiGG database \url{http://bigg.ucsd.edu/}.
+
+ Bornstein, B. J., Keating, S. M., Jouraku, A., and Hucka M. (2008)
+ LibSBML: An API Library for SBML. \emph{Bioinformatics} \bold{24},
+ 880--881.
+
+ Schellenberger, J., Park, J. O., Conrad, T. C., and Palsson, B. Ø., (2010)
+ BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic
+ reconstructions. \emph{BMC Bioinformatics} \bold{11}, 213.
+
+ Becker, S. A., Feist, A. M., Mo, M. L., Hannum, G., Palsson, B. Ø. and
+ Herrgard, M. J. (2007) Quantitative prediction of cellular metabolism with
+ constraint-based models: the COBRA Toolbox. \emph{Nat Protoc} \bold{2},
+ 727--738.
+
+ Schellenberger, J., Que, R., Fleming, R. M. T., Thiele, I., Orth, J. D.,
+ Feist, A. M., Zielinski, D. C., Bordbar, A., Lewis, N. E., Rahmanian, S.,
+ Kang, J., Hyduke, D. R. and Palsson, B. Ø. (2011) Quantitative prediction of
+ cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.
+ \emph{Nat Protoc} \bold{6}, 1290--1307.
+}
+
+\author{
+ Gabriel Gelius-Dietrich <geliudie@uni-duesseldorf.de>
+
+ Maintainer: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
+}
+
+
+\note{
+ The function \code{writeSBML} makes use of the library
+ \code{libSBML} (\url{http://www.sbml.org}).
+}
+
+\seealso{
+ \code{\link{readSBMLmod}}
+}
+
+\examples{
+ dir <- system.file(package = "sybilSBML", "extdata")
+ file <- file.path(dir, "ecoli_core_model.xml")
+ mod <- readSBMLmod(file, bndCond = FALSE)
+ writeSBML(mod,level=3,version=1,fbcLevel=2)
+}
+
+\keyword{ IO }
+
diff --git a/src/init.c b/src/init.c
index 59a802a9e413e5c3ea02eab24e95b474ba715580..7e4b174aafb9654417111f7c416117caf8ca2610 100644
--- a/src/init.c
+++ b/src/init.c
@@ -1,66 +1,68 @@
-/* init.c
- Link to libSBML for sybil.
-
- Copyright (C) 2010-2013 Gabriel Gelius-Dietrich, Dpt. for Bioinformatics,
- Institute for Informatics, Heinrich-Heine-University, Duesseldorf, Germany.
- All right reserved.
- Email: geliudie@uni-duesseldorf.de
-
- This file is part of sybilSBML.
-
- SybilSBML 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.
-
- SybilSBML 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 sybilSBML. If not, see <http://www.gnu.org/licenses/>.
-*/
-
-#include <R.h>
-#include <Rinternals.h>
-
-#include "sybilSBML.h"
-
-#include <R_ext/Rdynload.h>
-
-static const R_CallMethodDef callMethods[] = {
- {"isSBMLdocptr", (DL_FUNC) &isSBMLdocptr, 1},
- {"isSBMLmodptr", (DL_FUNC) &isSBMLmodptr, 1},
- {"isNULLptr", (DL_FUNC) &isNULLptr, 1},
- {"getLibSBMLversion", (DL_FUNC) &getLibSBMLversion, 0},
- {"initSBML", (DL_FUNC) &initSBML, 0},
- {"delDocument", (DL_FUNC) &delDocument, 1},
- {"delModel", (DL_FUNC) &delModel, 1},
- {"readSBMLfile", (DL_FUNC) &readSBMLfile, 2},
- {"getSBMLlevel", (DL_FUNC) &getSBMLlevel, 1},
- {"getSBMLversion", (DL_FUNC) &getSBMLversion, 1},
- {"validateDocument", (DL_FUNC) &validateDocument, 1},
- {"getSBMLerrors", (DL_FUNC) &getSBMLerrors, 1},
- {"getSBMLmodel", (DL_FUNC) &getSBMLmodel, 2},
- {"getSBMLmodId", (DL_FUNC) &getSBMLmodId, 1},
- {"getSBMLmodName", (DL_FUNC) &getSBMLmodName, 1},
- {"getSBMLnumCompart", (DL_FUNC) &getSBMLnumCompart, 1},
- {"getSBMLnumSpecies", (DL_FUNC) &getSBMLnumSpecies, 1},
- {"getSBMLnumReactions", (DL_FUNC) &getSBMLnumReactions, 1},
- {"getSBMLunitDefinitionsList", (DL_FUNC) &getSBMLunitDefinitionsList, 1},
- {"getSBMLCompartList", (DL_FUNC) &getSBMLCompartList, 1},
- {"getSBMLSpeciesList", (DL_FUNC) &getSBMLSpeciesList, 1},
- {"getSBMLReactionsList", (DL_FUNC) &getSBMLReactionsList, 1},
- {NULL, NULL, 0}
-};
-
-
-/* -------------------------------------------------------------------------- */
-
-void R_init_sybilSBML(DllInfo *info) {
- R_registerRoutines(info, NULL, callMethods, NULL, NULL);
- R_useDynamicSymbols(info, FALSE);
-}
-
-
+/* init.c
+ Link to libSBML for sybil.
+
+ Copyright (C) 2010-2013 Gabriel Gelius-Dietrich, Dpt. for Bioinformatics,
+ Institute for Informatics, Heinrich-Heine-University, Duesseldorf, Germany.
+ All right reserved.
+ Email: geliudie@uni-duesseldorf.de
+
+ This file is part of sybilSBML.
+
+ SybilSBML 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.
+
+ SybilSBML 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 sybilSBML. If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#include <R.h>
+#include <Rinternals.h>
+
+#include "sybilSBML.h"
+
+#include <R_ext/Rdynload.h>
+
+static const R_CallMethodDef callMethods[] = {
+ {"isSBMLdocptr", (DL_FUNC) &isSBMLdocptr, 1},
+ {"isSBMLmodptr", (DL_FUNC) &isSBMLmodptr, 1},
+ {"isNULLptr", (DL_FUNC) &isNULLptr, 1},
+ {"getLibSBMLversion", (DL_FUNC) &getLibSBMLversion, 0},
+ {"initSBML", (DL_FUNC) &initSBML, 0},
+ {"delDocument", (DL_FUNC) &delDocument, 1},
+ {"delModel", (DL_FUNC) &delModel, 1},
+ {"readSBMLfile", (DL_FUNC) &readSBMLfile, 2},
+ {"getSBMLlevel", (DL_FUNC) &getSBMLlevel, 1},
+ {"getSBMLversion", (DL_FUNC) &getSBMLversion, 1},
+ {"validateDocument", (DL_FUNC) &validateDocument, 1},
+ {"getSBMLerrors", (DL_FUNC) &getSBMLerrors, 1},
+ {"getSBMLmodel", (DL_FUNC) &getSBMLmodel, 2},
+ {"getSBMLmodId", (DL_FUNC) &getSBMLmodId, 1},
+ {"getSBMLmodName", (DL_FUNC) &getSBMLmodName, 1},
+ {"getSBMLmodNotes", (DL_FUNC) &getSBMLmodNotes, 1},
+ {"getSBMLmodAnnotation", (DL_FUNC) &getSBMLmodAnnotation, 1},
+ {"getSBMLnumCompart", (DL_FUNC) &getSBMLnumCompart, 1},
+ {"getSBMLnumSpecies", (DL_FUNC) &getSBMLnumSpecies, 1},
+ {"getSBMLnumReactions", (DL_FUNC) &getSBMLnumReactions, 1},
+ {"getSBMLunitDefinitionsList", (DL_FUNC) &getSBMLunitDefinitionsList, 1},
+ {"getSBMLCompartList", (DL_FUNC) &getSBMLCompartList, 1},
+ {"getSBMLSpeciesList", (DL_FUNC) &getSBMLSpeciesList, 1},
+ {"getSBMLReactionsList", (DL_FUNC) &getSBMLReactionsList, 1},
+ {"exportSBML", (DL_FUNC) &exportSBML, 33},
+ {"getSBMLFbcversion", (DL_FUNC) &getSBMLFbcversion, 1},
+ {NULL, NULL, 0}
+};
+
+
+/* -------------------------------------------------------------------------- */
+
+void R_init_sybilSBML(DllInfo *info) {
+ R_registerRoutines(info, NULL, callMethods, NULL, NULL);
+ R_useDynamicSymbols(info, FALSE);
+}
\ No newline at end of file
diff --git a/src/sybilSBML.c b/src/sybilSBML.c
index 2c89694af10869e8047f21fd5620d9e43c0c2be2..0eee3b09a9bb8259d8c3b962876ff95f36bf043c 100644
--- a/src/sybilSBML.c
+++ b/src/sybilSBML.c
@@ -1,1047 +1,2290 @@
-/* sybilSBML.c
- Link to libSBML for sybil.
-
- Copyright (C) 2010-2013 Gabriel Gelius-Dietrich, Dpt. for Bioinformatics,
- Institute for Informatics, Heinrich-Heine-University, Duesseldorf, Germany.
- All right reserved.
- Email: geliudie@uni-duesseldorf.de
-
- This file is part of sybilSBML.
-
- SybilSBML 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.
-
- SybilSBML 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 sybilSBML. If not, see <http://www.gnu.org/licenses/>.
-*/
-
-
-#include "sybilSBML.h"
-
-
-static SEXP tagSBMLmodel;
-static SEXP tagSBMLdocument;
-
-
-/* -------------------------------------------------------------------------- */
-/* Finalizer */
-/* -------------------------------------------------------------------------- */
-
-/* -------------------------------------------------------------------------- */
-/* finalizer for sbml document objects */
-static void sbmlDocumentFinalizer (SEXP sbmldoc) {
- if (!R_ExternalPtrAddr(sbmldoc)) {
- return;
- }
- else {
- delDocument(sbmldoc);
- }
-}
-
-
-/* -------------------------------------------------------------------------- */
-/* finalizer for sbml model objects */
-/*
-static void sbmlModelFinalizer (SEXP sbmlmodel) {
- if (!R_ExternalPtrAddr(sbmlmodel)) {
- return;
- }
- else {
- delModel(sbmlmodel);
- }
-}
-*/
-
-
-/* -------------------------------------------------------------------------- */
-/* help functions */
-/* -------------------------------------------------------------------------- */
-
-/* check for pointer to sbml document */
-SEXP isSBMLdocptr(SEXP ptr) {
-
- SEXP out = R_NilValue;
-
- if ( (TYPEOF(ptr) == EXTPTRSXP) &&
- (R_ExternalPtrTag(ptr) == tagSBMLdocument) ) {
- out = Rf_ScalarLogical(1);
- }
- else {
- out = Rf_ScalarLogical(0);
- }
-
- return out;
-}
-
-/* check for pointer to sbml model */
-SEXP isSBMLmodptr(SEXP ptr) {
-
- SEXP out = R_NilValue;
-
- if ( (TYPEOF(ptr) == EXTPTRSXP) &&
- (R_ExternalPtrTag(ptr) == tagSBMLmodel) ) {
- out = Rf_ScalarLogical(1);
- }
- else {
- out = Rf_ScalarLogical(0);
- }
-
- return out;
-}
-
-/* check for NULL pointer */
-SEXP isNULLptr(SEXP ptr) {
-
- SEXP out = R_NilValue;
-
- if ( (TYPEOF(ptr) == EXTPTRSXP) &&
- (R_ExternalPtrAddr(ptr) == NULL) ) {
- out = Rf_ScalarLogical(1);
- }
- else {
- out = Rf_ScalarLogical(0);
- }
-
- return out;
-}
-
-
-/* -------------------------------------------------------------------------- */
-/* API-Functions */
-/* -------------------------------------------------------------------------- */
-
-/* -------------------------------------------------------------------------- */
-/* initialize sybilSBML */
-SEXP initSBML(void) {
- tagSBMLmodel = Rf_install("TYPE_SBML_MODEL");
- tagSBMLdocument = Rf_install("TYPE_SBML_DOCUMENT");
- return R_NilValue;
-}
-
-
-/* -------------------------------------------------------------------------- */
-/* get libsbml version number (dotted version) */
-SEXP getLibSBMLversion() {
-
- SEXP out = R_NilValue;
-
- const char *vstr = getLibSBMLDottedVersion();
-
- out = Rf_mkString(vstr);
-
- return out;
-
-}
-
-
-/* -------------------------------------------------------------------------- */
-/* remove sbml document pointer */
-SEXP delDocument(SEXP sbmldoc) {
-
- SEXP out = R_NilValue;
- SBMLDocument_t *del = NULL;
-
- checkDocument(sbmldoc);
-
- del = R_ExternalPtrAddr(sbmldoc);
-
- SBMLDocument_free(del);
- R_ClearExternalPtr(sbmldoc);
-
- return out;
-}
-
-
-/* -------------------------------------------------------------------------- */
-/* remove model pointer */
-SEXP delModel(SEXP sbmlmodel) {
-
- SEXP out = R_NilValue;
- /* Model_t *del = NULL; */
-
- checkModel(sbmlmodel);
-
- /* del = R_ExternalPtrAddr(sbmlmodel); */
-
- /* Model_free(del); */
- R_ClearExternalPtr(sbmlmodel);
-
- return out;
-}
-
-
-/* -------------------------------------------------------------------------- */
-/* read SBML file */
-SEXP readSBMLfile(SEXP fname, SEXP ptrtype) {
-
- SEXP sfext = R_NilValue;
- SEXP ptr, class, file;
- const char *rfname = CHAR(STRING_ELT(fname, 0));
-
- SBMLDocument_t *sbmldoc;
-
- /* create sbml document pointer */
- PROTECT(ptr = Rf_allocVector(STRSXP, 1));
- SET_STRING_ELT(ptr, 0, STRING_ELT(ptrtype, 0));
-
- PROTECT(class = Rf_allocVector(STRSXP, 1));
- SET_STRING_ELT(class, 0, Rf_mkChar("sbml_doc_ptr"));
-
- PROTECT(file = Rf_allocVector(STRSXP, 1));
- SET_STRING_ELT(file, 0, Rf_mkChar("file_name"));
-
- /* read the model xml file */
- sbmldoc = readSBML(rfname);
-
- sfext = R_MakeExternalPtr(sbmldoc, tagSBMLdocument, R_NilValue);
- PROTECT(sfext);
- R_RegisterCFinalizerEx(sfext, sbmlDocumentFinalizer, TRUE);
- Rf_setAttrib(ptr, class, sfext);
- Rf_setAttrib(ptr, file, fname);
- Rf_classgets(ptr, class);
-
- UNPROTECT(4);
-
- return ptr;
-}
-
-
-/* -------------------------------------------------------------------------- */
-/* get sbml document level */
-SEXP getSBMLlevel(SEXP sbmldoc) {
-
- SEXP out = R_NilValue;
- unsigned int level;
-
- checkDocument(sbmldoc);
-
- level = SBMLDocument_getLevel(R_ExternalPtrAddr(sbmldoc));
-
- out = Rf_ScalarInteger(level);
-
- return out;
-}
-
-
-/* -------------------------------------------------------------------------- */
-/* get sbml document version */
-SEXP getSBMLversion(SEXP sbmldoc) {
-
- SEXP out = R_NilValue;
- unsigned int version;
-
- checkDocument(sbmldoc);
-
- version = SBMLDocument_getVersion(R_ExternalPtrAddr(sbmldoc));
-
- out = Rf_ScalarInteger(version);
-
- return out;
-}
-
-
-/* -------------------------------------------------------------------------- */
-/* validate SBML document */
-SEXP validateDocument(SEXP sbmldoc) {
-
- /*
- this is adopted from Michael Lawrence: rsbml
- Michael Lawrence (). rsbml: R support for SBML, using libsbml.
- R package version 2.18.0. http://www.sbml.org
- http://www.bioconductor.org/packages/release/bioc/html/rsbml.html
- */
-
- SEXP out = R_NilValue;
-
- unsigned int validation;
-
- checkDocument(sbmldoc);
-
- /* number or errors logged when reading SBML file */
- validation = SBMLDocument_getNumErrors(R_ExternalPtrAddr(sbmldoc));
- /* number or errors from structural and mathematical tests */
- validation += SBMLDocument_checkConsistency(R_ExternalPtrAddr(sbmldoc));
-
- if (validation > 0) {
- out = Rf_ScalarLogical(0);
- }
- else {
- out = Rf_ScalarLogical(1);
- }
-
- return out;
-}
-
-
-/* -------------------------------------------------------------------------- */
-/* get SBML errors */
-SEXP getSBMLerrors(SEXP sbmldoc) {
-
- /*
- this is adopted from Michael Lawrence: rsbml
- Michael Lawrence (). rsbml: R support for SBML, using libsbml.
- R package version 2.18.0. http://www.sbml.org
- http://www.bioconductor.org/packages/release/bioc/html/rsbml.html
- */
-
- SEXP out = R_NilValue;
- SEXP listv = R_NilValue;
- SEXP info = R_NilValue;
- SEXP warn = R_NilValue;
- SEXP error = R_NilValue;
- SEXP fatal = R_NilValue;
- SEXP class = R_NilValue;
- SEXP el = R_NilValue;
-
- XMLError_t *sbml_err;
-
- unsigned int nprob, i, ind;
- int ninfo = 0, nwarn = 0, nerror = 0, nfatal = 0, nunknown = 0;
-
- checkDocument(sbmldoc);
-
- nprob = SBMLDocument_getNumErrors(R_ExternalPtrAddr(sbmldoc));
-
- /*
- Rprintf("Model Errors: %i\n", nprob);
- */
-
- if (nprob > 0) {
-
- /* check how many infos, warnings, errors and fatals we have */
- for (i = 0; i < nprob; i++) {
- sbml_err = (XMLError_t *) SBMLDocument_getError(R_ExternalPtrAddr(sbmldoc), i);
- if (XMLError_isInfo(sbml_err)) {
- ninfo++;
- }
- else if (XMLError_isWarning(sbml_err)) {
- nwarn++;
- }
- else if (XMLError_isError(sbml_err)) {
- nerror++;
- }
- else if (XMLError_isFatal(sbml_err)) {
- nfatal++;
- }
- else {
- nunknown++;
- }
- }
-
- /*
- Rprintf("number of infos: %i, warnings: %i, errors: %i, falals: %i, unknowns: %i\n",
- ninfo, nwarn, nerror, nfatal, nunknown);
- */
-
- /*
- out will be a list of four elements:
- infos
- warnings
- errors
- fatals
- each of them is a list of three elements:
- id
- line
- column
- msg
- */
-
- PROTECT(out = Rf_allocVector(VECSXP, 4));
-
- /* allocate space for each error list */
- PROTECT(info = Rf_allocVector(VECSXP, ninfo));
- PROTECT(warn = Rf_allocVector(VECSXP, nwarn));
- PROTECT(error = Rf_allocVector(VECSXP, nerror));
- PROTECT(fatal = Rf_allocVector(VECSXP, nfatal));
-
- SET_VECTOR_ELT(out, 0, info);
- SET_VECTOR_ELT(out, 1, warn);
- SET_VECTOR_ELT(out, 2, error);
- SET_VECTOR_ELT(out, 3, fatal);
-
- PROTECT(listv = Rf_allocVector(STRSXP, 4));
- SET_STRING_ELT(listv, 0, Rf_mkChar("infos"));
- SET_STRING_ELT(listv, 1, Rf_mkChar("warnings"));
- SET_STRING_ELT(listv, 2, Rf_mkChar("errors"));
- SET_STRING_ELT(listv, 3, Rf_mkChar("fatals"));
- Rf_setAttrib(out, R_NamesSymbol, listv);
-
- /* get the error messages */
- ninfo = 0, nwarn = 0, nerror = 0, nfatal = 0, nunknown = 0;
- for (i = 0; i < nprob; i++) {
- sbml_err = (XMLError_t *) SBMLDocument_getError(R_ExternalPtrAddr(sbmldoc), i);
- el = R_NilValue;
- ind = 0;
- if (XMLError_isInfo(sbml_err)) {
- ind = ninfo++;
- el = info;
- }
- else if (XMLError_isWarning(sbml_err)) {
- ind = nwarn++;
- el = warn;
- }
- else if (XMLError_isError(sbml_err)) {
- ind = nerror++;
- el = error;
- }
- else if (XMLError_isFatal(sbml_err)) {
- ind = nfatal++;
- el = fatal;
- }
- else {
- nunknown++;
- }
- SET_VECTOR_ELT(el, ind, generateProblemMsg(sbml_err));
- }
-
- /* make the list to be an instance of 'sbml_error' */
- PROTECT(class = Rf_allocVector(STRSXP, 1));
- SET_STRING_ELT(class, 0, Rf_mkChar("sbml_error"));
- Rf_classgets(out, class);
-
- UNPROTECT(7);
-
- } /* end if nprob > 0 */
- else {
- out = Rf_ScalarLogical(1);
- }
-
- return out;
-}
-
-
-/* -------------------------------------------------------------------------- */
-/* get sbml model from sbml document */
-SEXP getSBMLmodel(SEXP sbmldoc, SEXP ptrtype) {
-
- SEXP smext = R_NilValue;
- SEXP ptr, class;
-
- Model_t *sbmlmodel;
-
- checkDocument(sbmldoc);
-
- /* create model pointer */
- PROTECT(ptr = Rf_allocVector(STRSXP, 1));
- SET_STRING_ELT(ptr, 0, STRING_ELT(ptrtype, 0));
-
- PROTECT(class = Rf_allocVector(STRSXP, 1));
- SET_STRING_ELT(class, 0, Rf_mkChar("sbml_model_ptr"));
-
- /* get sbml model */
- sbmlmodel = SBMLDocument_getModel(R_ExternalPtrAddr(sbmldoc));
-
- smext = R_MakeExternalPtr(sbmlmodel, tagSBMLmodel, R_NilValue);
- PROTECT(smext);
- /* R_RegisterCFinalizerEx(smext, sbmlModelFinalizer, TRUE); */
- Rf_setAttrib(ptr, class, smext);
- Rf_classgets(ptr, class);
-
- UNPROTECT(3);
-
- return ptr;
-}
-
-
-/* -------------------------------------------------------------------------- */
-/* get model id */
-SEXP getSBMLmodId(SEXP sbmlmod) {
-
- SEXP out = R_NilValue;
- const char *mid;
-
- checkModel(sbmlmod);
-
- if (Model_isSetId(R_ExternalPtrAddr(sbmlmod))) {
- mid = Model_getId(R_ExternalPtrAddr(sbmlmod));
- }
- else {
- mid = "no_id";
- }
-
- out = Rf_mkString(mid);
-
- return out;
-}
-
-
-/* -------------------------------------------------------------------------- */
-/* get model name */
-SEXP getSBMLmodName(SEXP sbmlmod) {
-
- SEXP out = R_NilValue;
- const char *mnm;
-
- checkModel(sbmlmod);
-
- if (Model_isSetName(R_ExternalPtrAddr(sbmlmod))) {
- mnm = Model_getName(R_ExternalPtrAddr(sbmlmod));
- }
- else {
- mnm = "";
- }
-
- out = Rf_mkString(mnm);
-
- return out;
-}
-
-
-/* -------------------------------------------------------------------------- */
-/* get number of compartments */
-SEXP getSBMLnumCompart(SEXP sbmlmod) {
-
- SEXP out = R_NilValue;
- unsigned int nc;
-
- checkModel(sbmlmod);
-
- nc = Model_getNumCompartments(R_ExternalPtrAddr(sbmlmod));
-
- out = Rf_ScalarInteger(nc);
-
- return out;
-}
-
-
-/* -------------------------------------------------------------------------- */
-/* get number of species (metabolites) */
-SEXP getSBMLnumSpecies(SEXP sbmlmod) {
-
- SEXP out = R_NilValue;
- unsigned int nsp;
-
- checkModel(sbmlmod);
-
- nsp = Model_getNumSpecies(R_ExternalPtrAddr(sbmlmod));
-
- out = Rf_ScalarInteger(nsp);
-
- return out;
-}
-
-
-/* -------------------------------------------------------------------------- */
-/* get number of reactions */
-SEXP getSBMLnumReactions(SEXP sbmlmod) {
-
- SEXP out = R_NilValue;
- unsigned int nr;
-
- checkModel(sbmlmod);
-
- nr = Model_getNumReactions(R_ExternalPtrAddr(sbmlmod));
-
- out = Rf_ScalarInteger(nr);
-
- return out;
-}
-
-
-/* -------------------------------------------------------------------------- */
-/* get list of unit definitions */
-SEXP getSBMLunitDefinitionsList(SEXP sbmlmod) {
-
- SEXP out = R_NilValue;
- SEXP class = R_NilValue;
- SEXP unl = R_NilValue;
- SEXP listv = R_NilValue;
- SEXP listn = R_NilValue;
-
- SEXP unitdefid = R_NilValue;
- SEXP unitdef = R_NilValue;
-
- SEXP unitkind = R_NilValue;
- SEXP unitscale = R_NilValue;
- SEXP unitexp = R_NilValue;
- SEXP unitmult = R_NilValue;
-
- unsigned int nud, nu, i, j;
-
- /* ListOf_t *udl; */
- UnitDefinition_t *udlel;
- Unit_t *uel;
-
- checkModel(sbmlmod);
-
- /* udl = Model_getListOfUnitDefinitions(R_ExternalPtrAddr(sbmlmod)); */
- nud = Model_getNumUnitDefinitions(R_ExternalPtrAddr(sbmlmod));
-
- if (nud > 0) {
- PROTECT(unitdefid = Rf_allocVector(STRSXP, nud));
- PROTECT(unitdef = Rf_allocVector(VECSXP, nud));
- for (i = 0; i < nud; i++) {
- /* udlel = (UnitDefinition_t *) ListOf_get(udl, i); */
- udlel = Model_getUnitDefinition(R_ExternalPtrAddr(sbmlmod), i);
-
- /* id and unit */
- if (UnitDefinition_isSetId(udlel)) {
- SET_STRING_ELT(unitdefid, i, Rf_mkChar(UnitDefinition_getId(udlel)));
-
- nu = UnitDefinition_getNumUnits(udlel);
-
- PROTECT(unitkind = Rf_allocVector(STRSXP, nu));
- PROTECT(unitscale = Rf_allocVector(INTSXP, nu));
- PROTECT(unitexp = Rf_allocVector(INTSXP, nu));
- PROTECT(unitmult = Rf_allocVector(REALSXP, nu));
-
- for (j = 0; j < nu; j++) {
- uel = UnitDefinition_getUnit(udlel, j);
-
- /* kind */
- if (Unit_isSetKind(uel)) {
- SET_STRING_ELT(unitkind, j, Rf_mkChar(UnitKind_toString(Unit_getKind(uel))));
- }
- else {
- SET_STRING_ELT(unitkind, j, Rf_mkChar("no_kind"));
- }
-
- /* scale */
- if (Unit_isSetScale(uel)) {
- INTEGER(unitscale)[j] = Unit_getScale(uel);
- }
- else {
- INTEGER(unitscale)[j] = 0;
- }
-
- /* exponent */
- if (Unit_isSetExponent(uel)) {
- INTEGER(unitexp)[j] = Unit_getExponent(uel);
- }
- else {
- INTEGER(unitexp)[j] = 1;
- }
-
- /* multiplier */
- if (Unit_isSetMultiplier(uel)) {
- REAL(unitmult)[j] = Unit_getMultiplier(uel);
- }
- else {
- REAL(unitmult)[j] = 1;
- }
-
- }
-
- PROTECT(unl = Rf_allocVector(VECSXP, 4));
- SET_VECTOR_ELT(unl, 0, unitkind);
- SET_VECTOR_ELT(unl, 1, unitscale);
- SET_VECTOR_ELT(unl, 2, unitexp);
- SET_VECTOR_ELT(unl, 3, unitmult);
-
- PROTECT(listn = Rf_allocVector(STRSXP, 4));
- SET_STRING_ELT(listn, 0, Rf_mkChar("kind"));
- SET_STRING_ELT(listn, 1, Rf_mkChar("scale"));
- SET_STRING_ELT(listn, 2, Rf_mkChar("exponent"));
- SET_STRING_ELT(listn, 3, Rf_mkChar("multiplier"));
- Rf_setAttrib(unl, R_NamesSymbol, listn);
-
- SET_VECTOR_ELT(unitdef, i, unl);
-
- UNPROTECT(6);
-
- }
- else {
- SET_STRING_ELT(unitdefid, i, Rf_mkChar("no_id"));
- }
- }
-
- PROTECT(out = Rf_allocVector(VECSXP, 2));
- SET_VECTOR_ELT(out, 0, unitdefid);
- SET_VECTOR_ELT(out, 1, unitdef);
-
- PROTECT(listv = Rf_allocVector(STRSXP, 2));
- SET_STRING_ELT(listv, 0, Rf_mkChar("definition_id"));
- SET_STRING_ELT(listv, 1, Rf_mkChar("definition"));
-
- Rf_setAttrib(out, R_NamesSymbol, listv);
-
- /* make the list to be an instance of 'unit_definition' */
- PROTECT(class = Rf_allocVector(STRSXP, 1));
- SET_STRING_ELT(class, 0, Rf_mkChar("unit_definition"));
- Rf_classgets(out, class);
-
- UNPROTECT(5);
- }
- else {
- out = R_NilValue;
- }
-
- return out;
-}
-
-
-/* -------------------------------------------------------------------------- */
-/* get list of compartments */
-SEXP getSBMLCompartList(SEXP sbmlmod) {
-
- SEXP out = R_NilValue;
- SEXP class = R_NilValue;
- SEXP listv = R_NilValue;
- SEXP compid = R_NilValue;
- SEXP compname = R_NilValue;
- SEXP compout = R_NilValue;
-
- unsigned int nc, i;
-
- /* ListOf_t *cl; */
- Compartment_t *clel;
-
- checkModel(sbmlmod);
-
- /* cl = Model_getListOfCompartments(R_ExternalPtrAddr(sbmlmod)); */
- nc = Model_getNumCompartments(R_ExternalPtrAddr(sbmlmod));
-
- if (nc > 0) {
- PROTECT(compid = Rf_allocVector(STRSXP, nc));
- PROTECT(compname = Rf_allocVector(STRSXP, nc));
- PROTECT(compout = Rf_allocVector(STRSXP, nc));
-
- for (i = 0; i < nc; i++) {
- /* clel = (Compartment_t *) ListOf_get(cl, i); */
- clel = Model_getCompartment(R_ExternalPtrAddr(sbmlmod), i);
- /* id */
- if (Compartment_isSetId(clel)) {
- SET_STRING_ELT(compid, i, Rf_mkChar(Compartment_getId(clel)));
- }
- else {
- SET_STRING_ELT(compid, i, Rf_mkChar("no_id"));
- }
- /* name */
- if (Compartment_isSetName(clel)) {
- SET_STRING_ELT(compname, i, Rf_mkChar(Compartment_getName(clel)));
- }
- else {
- SET_STRING_ELT(compname, i, Rf_mkChar(""));
- }
- /* outside */
- if (Compartment_isSetOutside(clel)) {
- SET_STRING_ELT(compout, i, Rf_mkChar(Compartment_getOutside(clel)));
- }
- else {
- SET_STRING_ELT(compout, i, Rf_mkChar(""));
- }
- }
-
- PROTECT(out = Rf_allocVector(VECSXP, 3));
- SET_VECTOR_ELT(out, 0, compid);
- SET_VECTOR_ELT(out, 1, compname);
- SET_VECTOR_ELT(out, 2, compout);
-
- PROTECT(listv = Rf_allocVector(STRSXP, 3));
- SET_STRING_ELT(listv, 0, Rf_mkChar("id"));
- SET_STRING_ELT(listv, 1, Rf_mkChar("name"));
- SET_STRING_ELT(listv, 2, Rf_mkChar("outside"));
-
- Rf_setAttrib(out, R_NamesSymbol, listv);
-
- /* make the list to be an instance of 'compartments_list' */
- PROTECT(class = Rf_allocVector(STRSXP, 1));
- SET_STRING_ELT(class, 0, Rf_mkChar("compartments_list"));
- Rf_classgets(out, class);
-
- UNPROTECT(6);
- }
- else {
- out = R_NilValue;
- }
-
- return out;
-}
-
-
-/* -------------------------------------------------------------------------- */
-/* get list of species (metabolites) */
-SEXP getSBMLSpeciesList(SEXP sbmlmod) {
-
- SEXP out = R_NilValue;
- SEXP class = R_NilValue;
- SEXP listv = R_NilValue;
- SEXP metid = R_NilValue;
- SEXP metname = R_NilValue;
- SEXP metcomp = R_NilValue;
- SEXP metcharge = R_NilValue;
- SEXP metbndcnd = R_NilValue;
-
- unsigned int nsp, i;
-
- /* ListOf_t *spl; */
- Species_t *splel;
-
- checkModel(sbmlmod);
-
- /* spl = Model_getListOfSpecies(R_ExternalPtrAddr(sbmlmod)); */
- nsp = Model_getNumSpecies(R_ExternalPtrAddr(sbmlmod));
-
- if (nsp > 0) {
- PROTECT(metid = Rf_allocVector(STRSXP, nsp));
- PROTECT(metname = Rf_allocVector(STRSXP, nsp));
- PROTECT(metcomp = Rf_allocVector(STRSXP, nsp));
- PROTECT(metcharge = Rf_allocVector(INTSXP, nsp));
- PROTECT(metbndcnd = Rf_allocVector(LGLSXP, nsp));
-
- for (i = 0; i < nsp; i++) {
- /* splel = (Species_t *) ListOf_get(spl, i); */
- splel = Model_getSpecies(R_ExternalPtrAddr(sbmlmod), i);
- /* id */
- if (Species_isSetId(splel)) {
- SET_STRING_ELT(metid, i, Rf_mkChar(Species_getId(splel)));
- }
- else {
- SET_STRING_ELT(metid, i, Rf_mkChar("no_id"));
- }
- /* name */
- if (Species_isSetName(splel)) {
- SET_STRING_ELT(metname, i, Rf_mkChar(Species_getName(splel)));
- }
- else {
- SET_STRING_ELT(metname, i, Rf_mkChar(""));
- }
- /* compartment */
- if (Species_isSetCompartment(splel)) {
- SET_STRING_ELT(metcomp, i, Rf_mkChar(Species_getCompartment(splel)));
- }
- else {
- SET_STRING_ELT(metcomp, i, Rf_mkChar(""));
- }
- /* charge */
- if (Species_isSetCharge(splel)) {
- INTEGER(metcharge)[i] = Species_getCharge(splel);
- }
- else {
- INTEGER(metcharge)[i] = 0;
- }
- /* boundary condition */
- if (Species_isSetBoundaryCondition(splel)) {
- LOGICAL(metbndcnd)[i] = Species_getBoundaryCondition(splel);
- }
- else {
- LOGICAL(metbndcnd)[i] = 0;
- }
- }
-
- PROTECT(out = Rf_allocVector(VECSXP, 5));
- SET_VECTOR_ELT(out, 0, metid);
- SET_VECTOR_ELT(out, 1, metname);
- SET_VECTOR_ELT(out, 2, metcomp);
- SET_VECTOR_ELT(out, 3, metcharge);
- SET_VECTOR_ELT(out, 4, metbndcnd);
-
- PROTECT(listv = Rf_allocVector(STRSXP, 5));
- SET_STRING_ELT(listv, 0, Rf_mkChar("id"));
- SET_STRING_ELT(listv, 1, Rf_mkChar("name"));
- SET_STRING_ELT(listv, 2, Rf_mkChar("compartment"));
- SET_STRING_ELT(listv, 3, Rf_mkChar("charge"));
- SET_STRING_ELT(listv, 4, Rf_mkChar("boundaryCondition"));
-
- Rf_setAttrib(out, R_NamesSymbol, listv);
-
- /* make the list to be an instance of 'species_list' */
- PROTECT(class = Rf_allocVector(STRSXP, 1));
- SET_STRING_ELT(class, 0, Rf_mkChar("species_list"));
- Rf_classgets(out, class);
-
- UNPROTECT(8);
- }
- else {
- out = R_NilValue;
- }
-
- return out;
-}
-
-
-/* -------------------------------------------------------------------------- */
-/* get list of reactions */
-SEXP getSBMLReactionsList(SEXP sbmlmod) {
-
- SEXP out = R_NilValue;
- SEXP class = R_NilValue;
- SEXP listv = R_NilValue;
- SEXP reactid = R_NilValue;
- SEXP reactname = R_NilValue;
- SEXP reactrev = R_NilValue;
- SEXP reactnotes = R_NilValue;
- SEXP reactannot = R_NilValue;
- SEXP reactreact = R_NilValue;
- SEXP reactprod = R_NilValue;
- SEXP reactkl = R_NilValue;
-
- SEXP parml = R_NilValue;
- SEXP parmn = R_NilValue;
- SEXP parmid = R_NilValue;
- SEXP parmval = R_NilValue;
- SEXP parmunit = R_NilValue;
-
- unsigned int nre, i, j, nreactant, nproduct, nparm;
-
- /* ListOf_t *rel; */
- Reaction_t *relel;
- KineticLaw_t *kl;
- Parameter_t *parm;
-
- checkModel(sbmlmod);
-
- /* rel = Model_getListOfReactions(R_ExternalPtrAddr(sbmlmod)); */
- nre = Model_getNumReactions(R_ExternalPtrAddr(sbmlmod));
-
- if (nre > 0) {
- PROTECT(reactid = Rf_allocVector(STRSXP, nre));
- PROTECT(reactname = Rf_allocVector(STRSXP, nre));
- PROTECT(reactrev = Rf_allocVector(LGLSXP, nre));
- PROTECT(reactnotes = Rf_allocVector(STRSXP, nre));
- PROTECT(reactannot = Rf_allocVector(STRSXP, nre));
- PROTECT(reactreact = Rf_allocVector(VECSXP, nre));
- PROTECT(reactprod = Rf_allocVector(VECSXP, nre));
- PROTECT(reactkl = Rf_allocVector(VECSXP, nre));
-
- for (i = 0; i < nre; i++) {
- /* relel = (Reaction_t *) ListOf_get(rel, i); */
- relel = Model_getReaction(R_ExternalPtrAddr(sbmlmod), i);
-
- nreactant = Reaction_getNumReactants(relel);
- nproduct = Reaction_getNumProducts(relel);
-
- /* id */
- if (Reaction_isSetId(relel)) {
- SET_STRING_ELT(reactid, i, Rf_mkChar(Reaction_getId(relel)));
- }
- else {
- SET_STRING_ELT(reactid, i, Rf_mkChar("no_id"));
- }
- /* name */
- if (Reaction_isSetName(relel)) {
- SET_STRING_ELT(reactname, i, Rf_mkChar(Reaction_getName(relel)));
- }
- else {
- SET_STRING_ELT(reactname, i, Rf_mkChar(""));
- }
- /* reversible */
- if (Reaction_isSetReversible(relel)) {
- LOGICAL(reactrev)[i] = Reaction_getReversible(relel);
- }
- else {
- LOGICAL(reactrev)[i] = 0;
- }
- /* notes */
- if (SBase_isSetNotes((SBase_t *) relel)) {
- SET_STRING_ELT(reactnotes, i, Rf_mkChar(SBase_getNotesString((SBase_t *) relel)));
- }
- else {
- SET_STRING_ELT(reactnotes, i, Rf_mkChar(""));
- }
- /* annotation */
- if (SBase_isSetAnnotation((SBase_t *) relel)) {
- SET_STRING_ELT(reactannot, i, Rf_mkChar(SBase_getAnnotationString((SBase_t *) relel)));
- }
- else {
- SET_STRING_ELT(reactannot, i, Rf_mkChar(""));
- }
-
- /* reactants */
- SET_VECTOR_ELT(reactreact, i, getSpeciesReference(relel, nreactant, 0));
-
- /* products */
- SET_VECTOR_ELT(reactprod, i, getSpeciesReference(relel, nproduct, 1));
-
- /* kineticLaw */
- if (Reaction_isSetKineticLaw(relel)) {
- kl = Reaction_getKineticLaw(relel);
- nparm = KineticLaw_getNumParameters(kl);
-
- if (nparm > 0) {
- PROTECT(parmid = Rf_allocVector(STRSXP, nparm));
- PROTECT(parmval = Rf_allocVector(REALSXP, nparm));
- PROTECT(parmunit = Rf_allocVector(STRSXP, nparm));
-
- for (j = 0; j < nparm; j++) {
- parm = KineticLaw_getParameter(kl, j);
-
- /* id */
- if (Parameter_isSetId(parm)) {
- SET_STRING_ELT(parmid, j, Rf_mkChar(Parameter_getId(parm)));
- }
- else {
- SET_STRING_ELT(parmid, j, Rf_mkChar("no_id"));
- }
- /* value */
- if (Parameter_isSetValue(parm)) {
- REAL(parmval)[j] = Parameter_getValue(parm);
- }
- else {
- REAL(parmval)[j] = 0;
- }
- /* units */
- if (Parameter_isSetUnits(parm)) {
- SET_STRING_ELT(parmunit, j, Rf_mkChar(Parameter_getUnits(parm)));
- }
- else {
- SET_STRING_ELT(parmunit, j, Rf_mkChar(""));
- }
- }
-
- PROTECT(parml = Rf_allocVector(VECSXP, 3));
- SET_VECTOR_ELT(parml, 0, parmid);
- SET_VECTOR_ELT(parml, 1, parmval);
- SET_VECTOR_ELT(parml, 2, parmunit);
-
- PROTECT(parmn = Rf_allocVector(STRSXP, 3));
- SET_STRING_ELT(parmn, 0, Rf_mkChar("id"));
- SET_STRING_ELT(parmn, 1, Rf_mkChar("value"));
- SET_STRING_ELT(parmn, 2, Rf_mkChar("units"));
- Rf_setAttrib(parml, R_NamesSymbol, parmn);
-
- UNPROTECT(5);
- }
- else {
- parml = R_NilValue;
- }
- SET_VECTOR_ELT(reactkl, i, parml);
- }
- else {
- SET_VECTOR_ELT(reactkl, i, R_NilValue);
- }
-
- }
-
- PROTECT(out = Rf_allocVector(VECSXP, 8));
- SET_VECTOR_ELT(out, 0, reactid);
- SET_VECTOR_ELT(out, 1, reactname);
- SET_VECTOR_ELT(out, 2, reactrev);
- SET_VECTOR_ELT(out, 3, reactnotes);
- SET_VECTOR_ELT(out, 4, reactannot);
- SET_VECTOR_ELT(out, 5, reactreact);
- SET_VECTOR_ELT(out, 6, reactprod);
- SET_VECTOR_ELT(out, 7, reactkl);
-
- PROTECT(listv = Rf_allocVector(STRSXP, 8));
- SET_STRING_ELT(listv, 0, Rf_mkChar("id"));
- SET_STRING_ELT(listv, 1, Rf_mkChar("name"));
- SET_STRING_ELT(listv, 2, Rf_mkChar("reversible"));
- SET_STRING_ELT(listv, 3, Rf_mkChar("notes"));
- SET_STRING_ELT(listv, 4, Rf_mkChar("annotation"));
- SET_STRING_ELT(listv, 5, Rf_mkChar("reactants"));
- SET_STRING_ELT(listv, 6, Rf_mkChar("products"));
- SET_STRING_ELT(listv, 7, Rf_mkChar("kinetic_law"));
-
- Rf_setAttrib(out, R_NamesSymbol, listv);
-
- /* make the list to be an instance of 'reactions_list' */
- PROTECT(class = Rf_allocVector(STRSXP, 1));
- SET_STRING_ELT(class, 0, Rf_mkChar("reactions_list"));
- Rf_classgets(out, class);
-
- UNPROTECT(11);
- }
- else {
- out = R_NilValue;
- }
-
- return out;
-}
+/* sybilSBML.c
+ Link to libSBML for sybil.
+
+ Copyright (C) 2010-2013 Gabriel Gelius-Dietrich, Dpt. for Bioinformatics,
+Institute for Informatics, Heinrich-Heine-University, Duesseldorf, Germany.
+All right reserved.
+Email: geliudie@uni-duesseldorf.de
+
+This file is part of sybilSBML.
+
+SybilSBML 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.
+
+SybilSBML 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 sybilSBML. If not, see <http://www.gnu.org/licenses/>.
+*/
+
+
+#include "sybilSBML.h"
+
+//new includes @Ardalan Habil
+#include <stdlib.h>
+#include <string.h>
+#include <sbml/xml/XMLTriple.h>
+#include <sbml/annotation/CVTerm.h>
+#include <sbml/annotation/RDFAnnotationParser.h>
+#include <sbml/annotation/ModelHistory.h>
+#include <sbml/math/ASTNode.h>
+#include <math.h>
+
+/* FBCv1includes */
+
+#include <sbml/extension/SBMLExtensionRegister.h>
+#include <sbml/extension/SBMLDocumentPlugin.h>
+
+#include <sbml/packages/fbc/common/fbcfwd.h>
+
+/* FBC PLUGINS*/
+#include <sbml/packages/fbc/extension/FbcSBMLDocumentPlugin.h>
+#include <sbml/packages/fbc/extension/FbcModelPlugin.h>
+#include <sbml/packages/fbc/extension/FbcReactionPlugin.h>
+#include <sbml/packages/fbc/extension/FbcSpeciesPlugin.h>
+
+#include <sbml/packages/fbc/sbml/FluxBound.h>
+#include <sbml/packages/fbc/sbml/Objective.h>
+#include <sbml/packages/fbc/sbml/FluxObjective.h>
+#include <sbml/packages/fbc/sbml/GeneProduct.h>
+#include <sbml/packages/fbc/sbml/GeneProductRef.h>
+#include <sbml/packages/fbc/sbml/GeneProductAssociation.h>
+#include <sbml/packages/fbc/sbml/FbcAssociation.h>
+#include <sbml/packages/fbc/sbml/FbcAnd.h>
+#include <sbml/packages/fbc/sbml/FbcOr.h>
+
+
+static SEXP tagSBMLmodel;
+static SEXP tagSBMLdocument;
+
+
+/* -------------------------------------------------------------------------- */
+/* Finalizer */
+/* -------------------------------------------------------------------------- */
+
+/* -------------------------------------------------------------------------- */
+/* finalizer for sbml document objects */
+static void sbmlDocumentFinalizer (SEXP sbmldoc) {
+ if (!R_ExternalPtrAddr(sbmldoc)) {
+ return;
+ }
+ else {
+ delDocument(sbmldoc);
+ }
+}
+
+
+/* -------------------------------------------------------------------------- */
+/* finalizer for sbml model objects */
+/*
+static void sbmlModelFinalizer (SEXP sbmlmodel) {
+if (!R_ExternalPtrAddr(sbmlmodel)) {
+return;
+}
+else {
+delModel(sbmlmodel);
+}
+}
+*/
+
+
+/* -------------------------------------------------------------------------- */
+/* help functions */
+/* -------------------------------------------------------------------------- */
+
+/* check for pointer to sbml document */
+SEXP isSBMLdocptr(SEXP ptr) {
+
+ SEXP out = R_NilValue;
+
+ if ( (TYPEOF(ptr) == EXTPTRSXP) &&
+ (R_ExternalPtrTag(ptr) == tagSBMLdocument) ) {
+ out = Rf_ScalarLogical(1);
+ }
+ else {
+ out = Rf_ScalarLogical(0);
+ }
+
+ return out;
+}
+
+/* check for pointer to sbml model */
+SEXP isSBMLmodptr(SEXP ptr) {
+
+ SEXP out = R_NilValue;
+
+ if ( (TYPEOF(ptr) == EXTPTRSXP) &&
+ (R_ExternalPtrTag(ptr) == tagSBMLmodel) ) {
+ out = Rf_ScalarLogical(1);
+ }
+ else {
+ out = Rf_ScalarLogical(0);
+ }
+
+ return out;
+}
+
+/* check for NULL pointer */
+SEXP isNULLptr(SEXP ptr) {
+
+ SEXP out = R_NilValue;
+
+ if ( (TYPEOF(ptr) == EXTPTRSXP) &&
+ (R_ExternalPtrAddr(ptr) == NULL) ) {
+ out = Rf_ScalarLogical(1);
+ }
+ else {
+ out = Rf_ScalarLogical(0);
+ }
+
+ return out;
+}
+
+
+/* -------------------------------------------------------------------------- */
+/* Helper functions */
+/* -------------------------------------------------------------------------- */
+
+
+// append two string
+char * append_strings(const char * old, const char * new, const char* delim)
+{
+ // find the size of the string to allocate
+ size_t len = strlen(old) + strlen(new) + strlen(delim) + 1;
+
+ // allocate a pointer to the new string
+ char *out = malloc(len);
+
+ // concat both strings and return
+ sprintf(out, "%s%s%s", old, delim , new);
+
+ return out;
+}
+
+
+
+// Parse Anntatation to modelorg
+const char* parseAnnotationTomorg(XMLNode_t* xml)
+{
+ const XMLNode_t* rdf =NULL;
+ const XMLNode_t* desc = NULL;
+ rdf = XMLNode_getChildForName(xml,"RDF");
+ if(rdf !=NULL) desc= XMLNode_getChildForName(rdf,"Description");
+ const char* annoString = "";
+ int firstelement=1;
+ if (desc!=NULL)
+ {
+
+ int num=0;
+ for(num=0;num<XMLNode_getNumChildren(desc);num++)
+ {
+ const char* pref= XMLNode_getPrefix(XMLNode_getChild(desc,num));
+
+ if( strcmp(pref,"bqbiol")==0 || strcmp(pref,"bqmodel")==0 )
+ {
+ CVTerm_t* cv= CVTerm_createFromNode(XMLNode_getChild(desc,num));
+ if( CVTerm_getNumResources(cv)>0 )
+ {
+ int numR=0;
+ if(strcmp(pref,"bqbiol")==0)
+ {
+ const char* bioQual = append_strings("bqbiol",BiolQualifierType_toString( CVTerm_getBiologicalQualifierType(cv)),"_");
+ if(firstelement==0) annoString = append_strings(annoString,bioQual,";");
+ else
+ {
+ annoString = append_strings(annoString,bioQual,"");
+ firstelement=0;
+ }
+
+ }
+ if(strcmp(pref,"bqmodel")==0)
+ {
+ const char* modQual = append_strings("bqmodel",ModelQualifierType_toString( CVTerm_getModelQualifierType(cv)),"_");
+ if(firstelement==0)annoString = append_strings(annoString,modQual,";");
+
+ else
+ {
+ annoString = append_strings(annoString,modQual,"");
+ firstelement=0;
+ }
+ }
+
+ for(numR=0;numR<CVTerm_getNumResources(cv);numR++)
+ {
+ // sprintf(annoString+strlen(annoString),"__%s", CVTerm_getResourceURI(cv,numR));
+ annoString = append_strings(annoString,CVTerm_getResourceURI(cv,numR),";");
+ }
+
+ }
+ }
+
+
+ }
+ return annoString;
+ }
+ else
+ {
+ return "";
+ }
+
+
+ return "";
+}
+
+
+
+/* -------------------------------------------------------------------------- */
+/* API-Functions */
+/* -------------------------------------------------------------------------- */
+
+/* -------------------------------------------------------------------------- */
+/* initialize sybilSBML */
+SEXP initSBML(void) {
+ tagSBMLmodel = Rf_install("TYPE_SBML_MODEL");
+ tagSBMLdocument = Rf_install("TYPE_SBML_DOCUMENT");
+ return R_NilValue;
+}
+
+
+/* -------------------------------------------------------------------------- */
+/* get libsbml version number (dotted version) */
+SEXP getLibSBMLversion() {
+
+ SEXP out = R_NilValue;
+
+ const char *vstr = getLibSBMLDottedVersion();
+
+ out = Rf_mkString(vstr);
+
+ return out;
+
+}
+
+
+/* -------------------------------------------------------------------------- */
+/* remove sbml document pointer */
+SEXP delDocument(SEXP sbmldoc) {
+
+ SEXP out = R_NilValue;
+ SBMLDocument_t *del = NULL;
+
+ checkDocument(sbmldoc);
+
+ del = R_ExternalPtrAddr(sbmldoc);
+
+ SBMLDocument_free(del);
+ R_ClearExternalPtr(sbmldoc);
+
+ return out;
+}
+
+
+/* -------------------------------------------------------------------------- */
+/* remove model pointer */
+SEXP delModel(SEXP sbmlmodel) {
+
+ SEXP out = R_NilValue;
+ /* Model_t *del = NULL; */
+
+ checkModel(sbmlmodel);
+
+ /* del = R_ExternalPtrAddr(sbmlmodel); */
+
+ /* Model_free(del); */
+ R_ClearExternalPtr(sbmlmodel);
+
+ return out;
+}
+
+
+/* -------------------------------------------------------------------------- */
+/* read SBML file */
+SEXP readSBMLfile(SEXP fname, SEXP ptrtype) {
+
+ SEXP sfext = R_NilValue;
+ SEXP ptr, class, file;
+ const char *rfname = CHAR(STRING_ELT(fname, 0));
+
+ SBMLDocument_t *sbmldoc;
+
+ /* create sbml document pointer */
+ PROTECT(ptr = Rf_allocVector(STRSXP, 1));
+ SET_STRING_ELT(ptr, 0, STRING_ELT(ptrtype, 0));
+
+ PROTECT(class = Rf_allocVector(STRSXP, 1));
+ SET_STRING_ELT(class, 0, Rf_mkChar("sbml_doc_ptr"));
+
+ PROTECT(file = Rf_allocVector(STRSXP, 1));
+ SET_STRING_ELT(file, 0, Rf_mkChar("file_name"));
+
+ /* read the model xml file */
+ sbmldoc = readSBML(rfname);
+
+ sfext = R_MakeExternalPtr(sbmldoc, tagSBMLdocument, R_NilValue);
+ PROTECT(sfext);
+ R_RegisterCFinalizerEx(sfext, sbmlDocumentFinalizer, TRUE);
+ Rf_setAttrib(ptr, class, sfext);
+ Rf_setAttrib(ptr, file, fname);
+ Rf_classgets(ptr, class);
+
+ UNPROTECT(4);
+
+ return ptr;
+}
+
+
+/* -------------------------------------------------------------------------- */
+/* get sbml document level */
+SEXP getSBMLlevel(SEXP sbmldoc) {
+
+ SEXP out = R_NilValue;
+ unsigned int level;
+
+ checkDocument(sbmldoc);
+
+ level = SBMLDocument_getLevel(R_ExternalPtrAddr(sbmldoc));
+
+ out = Rf_ScalarInteger(level);
+
+ return out;
+}
+
+
+/* -------------------------------------------------------------------------- */
+/* get sbml document version */
+SEXP getSBMLversion(SEXP sbmldoc) {
+
+ SEXP out = R_NilValue;
+ unsigned int version;
+
+ checkDocument(sbmldoc);
+
+ version = SBMLDocument_getVersion(R_ExternalPtrAddr(sbmldoc));
+
+ out = Rf_ScalarInteger(version);
+
+ return out;
+}
+
+
+/* -------------------------------------------------------------------------- */
+
+/* get sbml document FBC version */
+SEXP getSBMLFbcversion(SEXP sbmldoc) {
+
+ SEXP out = R_NilValue;
+ unsigned int version;
+
+ checkDocument(sbmldoc);
+ //hierher
+ SBasePlugin_t * modelPlug= NULL;
+ modelPlug = SBase_getPlugin((SBase_t *)(R_ExternalPtrAddr(sbmldoc)), "fbc");
+ if( modelPlug != NULL)
+ {
+ if(strcmp("fbc",SBasePlugin_getPackageName(modelPlug) ) ==0)
+ version = SBasePlugin_getPackageVersion(modelPlug);
+ else version=0;
+ } else version=0;
+
+ out = Rf_ScalarInteger(version);
+
+ return out;
+}
+
+
+/* -------------------------------------------------------------------------- */
+
+
+/* validate SBML document */
+SEXP validateDocument(SEXP sbmldoc) {
+
+ /*
+ this is adopted from Michael Lawrence: rsbml
+ Michael Lawrence (). rsbml: R support for SBML, using libsbml.
+ R package version 2.18.0. http://www.sbml.org
+ http://www.bioconductor.org/packages/release/bioc/html/rsbml.html
+ */
+
+ SEXP out = R_NilValue;
+
+ unsigned int validation;
+
+ checkDocument(sbmldoc);
+
+ /* number or errors logged when reading SBML file */
+ validation = SBMLDocument_getNumErrors(R_ExternalPtrAddr(sbmldoc));
+ /* number or errors from structural and mathematical tests */
+ validation += SBMLDocument_checkConsistency(R_ExternalPtrAddr(sbmldoc));
+
+ if (validation > 0) {
+ out = Rf_ScalarLogical(0);
+ }
+ else {
+ out = Rf_ScalarLogical(1);
+ }
+
+ return out;
+}
+
+
+/* -------------------------------------------------------------------------- */
+/* get SBML errors */
+SEXP getSBMLerrors(SEXP sbmldoc) {
+
+ /*
+ this is adopted from Michael Lawrence: rsbml
+ Michael Lawrence (). rsbml: R support for SBML, using libsbml.
+ R package version 2.18.0. http://www.sbml.org
+ http://www.bioconductor.org/packages/release/bioc/html/rsbml.html
+ */
+
+ SEXP out = R_NilValue;
+ SEXP listv = R_NilValue;
+ SEXP info = R_NilValue;
+ SEXP warn = R_NilValue;
+ SEXP error = R_NilValue;
+ SEXP fatal = R_NilValue;
+ SEXP class = R_NilValue;
+ SEXP el = R_NilValue;
+
+ XMLError_t *sbml_err;
+
+ unsigned int nprob, i, ind;
+ int ninfo = 0, nwarn = 0, nerror = 0, nfatal = 0, nunknown = 0;
+
+ checkDocument(sbmldoc);
+
+ nprob = SBMLDocument_getNumErrors(R_ExternalPtrAddr(sbmldoc));
+
+ /*
+ Rprintf("Model Errors: %i\n", nprob);
+ */
+
+ if (nprob > 0) {
+
+ /* check how many infos, warnings, errors and fatals we have */
+ for (i = 0; i < nprob; i++) {
+ sbml_err = (XMLError_t *) SBMLDocument_getError(R_ExternalPtrAddr(sbmldoc), i);
+ if (XMLError_isInfo(sbml_err)) {
+ ninfo++;
+ }
+ else if (XMLError_isWarning(sbml_err)) {
+ nwarn++;
+ }
+ else if (XMLError_isError(sbml_err)) {
+ nerror++;
+ }
+ else if (XMLError_isFatal(sbml_err)) {
+ nfatal++;
+ }
+ else {
+ nunknown++;
+ }
+ }
+
+ /*
+ Rprintf("number of infos: %i, warnings: %i, errors: %i, falals: %i, unknowns: %i\n",
+ ninfo, nwarn, nerror, nfatal, nunknown);
+ */
+
+ /*
+ out will be a list of four elements:
+ infos
+ warnings
+ errors
+ fatals
+ each of them is a list of three elements:
+ id
+ line
+ column
+ msg
+ */
+
+ PROTECT(out = Rf_allocVector(VECSXP, 4));
+
+ /* allocate space for each error list */
+ PROTECT(info = Rf_allocVector(VECSXP, ninfo));
+ PROTECT(warn = Rf_allocVector(VECSXP, nwarn));
+ PROTECT(error = Rf_allocVector(VECSXP, nerror));
+ PROTECT(fatal = Rf_allocVector(VECSXP, nfatal));
+
+ SET_VECTOR_ELT(out, 0, info);
+ SET_VECTOR_ELT(out, 1, warn);
+ SET_VECTOR_ELT(out, 2, error);
+ SET_VECTOR_ELT(out, 3, fatal);
+
+ PROTECT(listv = Rf_allocVector(STRSXP, 4));
+ SET_STRING_ELT(listv, 0, Rf_mkChar("infos"));
+ SET_STRING_ELT(listv, 1, Rf_mkChar("warnings"));
+ SET_STRING_ELT(listv, 2, Rf_mkChar("errors"));
+ SET_STRING_ELT(listv, 3, Rf_mkChar("fatals"));
+ Rf_setAttrib(out, R_NamesSymbol, listv);
+
+ /* get the error messages */
+ ninfo = 0, nwarn = 0, nerror = 0, nfatal = 0, nunknown = 0;
+ for (i = 0; i < nprob; i++) {
+ sbml_err = (XMLError_t *) SBMLDocument_getError(R_ExternalPtrAddr(sbmldoc), i);
+ el = R_NilValue;
+ ind = 0;
+ if (XMLError_isInfo(sbml_err)) {
+ ind = ninfo++;
+ el = info;
+ }
+ else if (XMLError_isWarning(sbml_err)) {
+ ind = nwarn++;
+ el = warn;
+ }
+ else if (XMLError_isError(sbml_err)) {
+ ind = nerror++;
+ el = error;
+ }
+ else if (XMLError_isFatal(sbml_err)) {
+ ind = nfatal++;
+ el = fatal;
+ }
+ else {
+ nunknown++;
+ }
+ SET_VECTOR_ELT(el, ind, generateProblemMsg(sbml_err));
+ }
+
+ /* make the list to be an instance of 'sbml_error' */
+ PROTECT(class = Rf_allocVector(STRSXP, 1));
+ SET_STRING_ELT(class, 0, Rf_mkChar("sbml_error"));
+ Rf_classgets(out, class);
+
+ UNPROTECT(7);
+
+ } /* end if nprob > 0 */
+ else {
+ out = Rf_ScalarLogical(1);
+ }
+
+ return out;
+}
+
+
+/* -------------------------------------------------------------------------- */
+/* get sbml model from sbml document */
+SEXP getSBMLmodel(SEXP sbmldoc, SEXP ptrtype) {
+
+ SEXP smext = R_NilValue;
+ SEXP ptr, class;
+
+ Model_t *sbmlmodel;
+
+ checkDocument(sbmldoc);
+
+ /* create model pointer */
+ PROTECT(ptr = Rf_allocVector(STRSXP, 1));
+ SET_STRING_ELT(ptr, 0, STRING_ELT(ptrtype, 0));
+
+ PROTECT(class = Rf_allocVector(STRSXP, 1));
+ SET_STRING_ELT(class, 0, Rf_mkChar("sbml_model_ptr"));
+
+ /* get sbml model */
+ sbmlmodel = SBMLDocument_getModel(R_ExternalPtrAddr(sbmldoc));
+
+ smext = R_MakeExternalPtr(sbmlmodel, tagSBMLmodel, R_NilValue);
+ PROTECT(smext);
+ /* R_RegisterCFinalizerEx(smext, sbmlModelFinalizer, TRUE); */
+ Rf_setAttrib(ptr, class, smext);
+ Rf_classgets(ptr, class);
+
+ UNPROTECT(3);
+
+ return ptr;
+}
+
+
+/* -------------------------------------------------------------------------- */
+/* get model id */
+SEXP getSBMLmodId(SEXP sbmlmod) {
+
+ SEXP out = R_NilValue;
+ const char *mid;
+
+ checkModel(sbmlmod);
+
+ if (Model_isSetId(R_ExternalPtrAddr(sbmlmod))) {
+ mid = Model_getId(R_ExternalPtrAddr(sbmlmod));
+ }
+ else {
+ mid = "no_id";
+ }
+
+ out = Rf_mkString(mid);
+
+ return out;
+}
+
+
+/* -------------------------------------------------------------------------- */
+/* get model name */
+SEXP getSBMLmodName(SEXP sbmlmod) {
+
+ SEXP out = R_NilValue;
+ const char *mnm;
+
+ checkModel(sbmlmod);
+
+ if (Model_isSetName(R_ExternalPtrAddr(sbmlmod))) {
+ mnm = Model_getName(R_ExternalPtrAddr(sbmlmod));
+ }
+ else {
+ mnm = "";
+ }
+
+ out = Rf_mkString(mnm);
+
+ return out;
+}
+
+
+/* -------------------------------------------------------------------------- */
+/* get model notes */
+SEXP getSBMLmodNotes(SEXP sbmlmod) {
+
+ SEXP out = R_NilValue;
+ const char *mnotes;
+
+ checkModel(sbmlmod);
+
+ if (SBase_isSetNotes((SBase_t *) R_ExternalPtrAddr(sbmlmod))) {
+ mnotes = SBase_getNotesString((SBase_t *) R_ExternalPtrAddr(sbmlmod));
+ }
+ else {
+ mnotes = "";
+ }
+
+ out = Rf_mkString(mnotes);
+
+ return out;
+}
+
+/* -------------------------------------------------------------------------- */
+/* get model name */
+SEXP getSBMLmodAnnotation(SEXP sbmlmod) {
+
+ SEXP out = R_NilValue;
+ const char *manno;
+
+ checkModel(sbmlmod);
+
+ if (SBase_isSetAnnotation((SBase_t *) R_ExternalPtrAddr(sbmlmod))) {
+ XMLNode_t* xml = SBase_getAnnotation((SBase_t *) R_ExternalPtrAddr(sbmlmod));
+ manno = parseAnnotationTomorg(xml);
+ }
+ else {
+ manno = "";
+ }
+
+ out = Rf_mkString(manno);
+
+ return out;
+}
+
+
+
+/* -------------------------------------------------------------------------- */
+/* get number of compartments */
+SEXP getSBMLnumCompart(SEXP sbmlmod) {
+
+ SEXP out = R_NilValue;
+ unsigned int nc;
+
+ checkModel(sbmlmod);
+
+ nc = Model_getNumCompartments(R_ExternalPtrAddr(sbmlmod));
+
+ out = Rf_ScalarInteger(nc);
+
+ return out;
+}
+
+
+/* -------------------------------------------------------------------------- */
+/* get number of species (metabolites) */
+SEXP getSBMLnumSpecies(SEXP sbmlmod) {
+
+ SEXP out = R_NilValue;
+ unsigned int nsp;
+
+ checkModel(sbmlmod);
+
+ nsp = Model_getNumSpecies(R_ExternalPtrAddr(sbmlmod));
+
+ out = Rf_ScalarInteger(nsp);
+
+ return out;
+}
+
+
+/* -------------------------------------------------------------------------- */
+/* get number of reactions */
+SEXP getSBMLnumReactions(SEXP sbmlmod) {
+
+ SEXP out = R_NilValue;
+ unsigned int nr;
+
+ checkModel(sbmlmod);
+
+ nr = Model_getNumReactions(R_ExternalPtrAddr(sbmlmod));
+
+ out = Rf_ScalarInteger(nr);
+
+ return out;
+}
+
+
+/* -------------------------------------------------------------------------- */
+/* get list of unit definitions */
+SEXP getSBMLunitDefinitionsList(SEXP sbmlmod) {
+
+ SEXP out = R_NilValue;
+ SEXP class = R_NilValue;
+ SEXP unl = R_NilValue;
+ SEXP listv = R_NilValue;
+ SEXP listn = R_NilValue;
+
+ SEXP unitdefid = R_NilValue;
+ SEXP unitdef = R_NilValue;
+
+ SEXP unitkind = R_NilValue;
+ SEXP unitscale = R_NilValue;
+ SEXP unitexp = R_NilValue;
+ SEXP unitmult = R_NilValue;
+
+ unsigned int nud, nu, i, j;
+
+ /* ListOf_t *udl; */
+ UnitDefinition_t *udlel;
+ Unit_t *uel;
+
+ checkModel(sbmlmod);
+
+ /* udl = Model_getListOfUnitDefinitions(R_ExternalPtrAddr(sbmlmod)); */
+ nud = Model_getNumUnitDefinitions(R_ExternalPtrAddr(sbmlmod));
+
+ if (nud > 0) {
+ PROTECT(unitdefid = Rf_allocVector(STRSXP, nud));
+ PROTECT(unitdef = Rf_allocVector(VECSXP, nud));
+ for (i = 0; i < nud; i++) {
+ /* udlel = (UnitDefinition_t *) ListOf_get(udl, i); */
+ udlel = Model_getUnitDefinition(R_ExternalPtrAddr(sbmlmod), i);
+
+ /* id and unit */
+ if (UnitDefinition_isSetId(udlel)) {
+ SET_STRING_ELT(unitdefid, i, Rf_mkChar(UnitDefinition_getId(udlel)));
+
+ nu = UnitDefinition_getNumUnits(udlel);
+
+ PROTECT(unitkind = Rf_allocVector(STRSXP, nu));
+ PROTECT(unitscale = Rf_allocVector(INTSXP, nu));
+ PROTECT(unitexp = Rf_allocVector(INTSXP, nu));
+ PROTECT(unitmult = Rf_allocVector(REALSXP, nu));
+
+ for (j = 0; j < nu; j++) {
+ uel = UnitDefinition_getUnit(udlel, j);
+
+ /* kind */
+ if (Unit_isSetKind(uel)) {
+ SET_STRING_ELT(unitkind, j, Rf_mkChar(UnitKind_toString(Unit_getKind(uel))));
+ }
+ else {
+ SET_STRING_ELT(unitkind, j, Rf_mkChar("no_kind"));
+ }
+
+ /* scale */
+ if (Unit_isSetScale(uel)) {
+ INTEGER(unitscale)[j] = Unit_getScale(uel);
+ }
+ else {
+ INTEGER(unitscale)[j] = 0;
+ }
+
+ /* exponent */
+ if (Unit_isSetExponent(uel)) {
+ INTEGER(unitexp)[j] = Unit_getExponent(uel);
+ }
+ else {
+ INTEGER(unitexp)[j] = 1;
+ }
+
+ /* multiplier */
+ if (Unit_isSetMultiplier(uel)) {
+ REAL(unitmult)[j] = Unit_getMultiplier(uel);
+ }
+ else {
+ REAL(unitmult)[j] = 1;
+ }
+
+ }
+
+ PROTECT(unl = Rf_allocVector(VECSXP, 4));
+ SET_VECTOR_ELT(unl, 0, unitkind);
+ SET_VECTOR_ELT(unl, 1, unitscale);
+ SET_VECTOR_ELT(unl, 2, unitexp);
+ SET_VECTOR_ELT(unl, 3, unitmult);
+
+ PROTECT(listn = Rf_allocVector(STRSXP, 4));
+ SET_STRING_ELT(listn, 0, Rf_mkChar("kind"));
+ SET_STRING_ELT(listn, 1, Rf_mkChar("scale"));
+ SET_STRING_ELT(listn, 2, Rf_mkChar("exponent"));
+ SET_STRING_ELT(listn, 3, Rf_mkChar("multiplier"));
+ Rf_setAttrib(unl, R_NamesSymbol, listn);
+
+ SET_VECTOR_ELT(unitdef, i, unl);
+
+ UNPROTECT(6);
+
+ }
+ else {
+ SET_STRING_ELT(unitdefid, i, Rf_mkChar("no_id"));
+ }
+ }
+
+ PROTECT(out = Rf_allocVector(VECSXP, 2));
+ SET_VECTOR_ELT(out, 0, unitdefid);
+ SET_VECTOR_ELT(out, 1, unitdef);
+
+ PROTECT(listv = Rf_allocVector(STRSXP, 2));
+ SET_STRING_ELT(listv, 0, Rf_mkChar("definition_id"));
+ SET_STRING_ELT(listv, 1, Rf_mkChar("definition"));
+
+ Rf_setAttrib(out, R_NamesSymbol, listv);
+
+ /* make the list to be an instance of 'unit_definition' */
+ PROTECT(class = Rf_allocVector(STRSXP, 1));
+ SET_STRING_ELT(class, 0, Rf_mkChar("unit_definition"));
+ Rf_classgets(out, class);
+
+ UNPROTECT(5);
+ }
+ else {
+ out = R_NilValue;
+ }
+
+ return out;
+}
+
+
+/* -------------------------------------------------------------------------- */
+/* get list of compartments */
+SEXP getSBMLCompartList(SEXP sbmlmod) {
+
+ SEXP out = R_NilValue;
+ SEXP class = R_NilValue;
+ SEXP listv = R_NilValue;
+ SEXP compid = R_NilValue;
+ SEXP compname = R_NilValue;
+ SEXP compannot = R_NilValue;
+ SEXP compnotes = R_NilValue;
+ SEXP compout = R_NilValue;
+
+ unsigned int nc, i;
+
+ /* ListOf_t *cl; */
+ Compartment_t *clel;
+
+ checkModel(sbmlmod);
+
+ /* cl = Model_getListOfCompartments(R_ExternalPtrAddr(sbmlmod)); */
+ nc = Model_getNumCompartments(R_ExternalPtrAddr(sbmlmod));
+
+ if (nc > 0) {
+ PROTECT(compid = Rf_allocVector(STRSXP, nc));
+ PROTECT(compname = Rf_allocVector(STRSXP, nc));
+ PROTECT(compannot = Rf_allocVector(STRSXP, nc));
+ PROTECT(compnotes = Rf_allocVector(STRSXP, nc));
+
+ // Counter Variables
+ int annocount=0;
+ int notescount=0;
+
+ PROTECT(compout = Rf_allocVector(STRSXP, nc));
+
+ for (i = 0; i < nc; i++) {
+ clel = Model_getCompartment(R_ExternalPtrAddr(sbmlmod), i);
+ /* id */
+ if (Compartment_isSetId(clel)) {
+ SET_STRING_ELT(compid, i, Rf_mkChar(Compartment_getId(clel)));
+ }
+ else {
+ SET_STRING_ELT(compid, i, Rf_mkChar("no_id"));
+ }
+ /* name */
+ if (Compartment_isSetName(clel)) {
+ SET_STRING_ELT(compname, i, Rf_mkChar(Compartment_getName(clel)));
+ }
+ else {
+ SET_STRING_ELT(compname, i, Rf_mkChar(""));
+ }
+ /* outside */
+ if (Compartment_isSetOutside(clel)) {
+ SET_STRING_ELT(compout, i, Rf_mkChar(Compartment_getOutside(clel)));
+ }
+ else {
+ SET_STRING_ELT(compout, i, Rf_mkChar(""));
+ }
+
+ /* NEW INFORMATIONS*/
+ /* notes */
+ if (SBase_isSetNotes((SBase_t *) clel)) {
+ SET_STRING_ELT(compnotes, i, Rf_mkChar(SBase_getNotesString((SBase_t *) clel)));
+ notescount=notescount+1;
+ }
+ else {
+ SET_STRING_ELT(compnotes, i, Rf_mkChar(""));
+ }
+
+ /* annotation */
+ if (SBase_isSetAnnotation((SBase_t *) clel)) {
+ XMLNode_t* xml = SBase_getAnnotation((SBase_t *) clel);
+ SET_STRING_ELT(compannot, i, Rf_mkChar(parseAnnotationTomorg(xml)));
+ annocount=annocount+1;
+ }
+ else {
+ SET_STRING_ELT(compannot, i, Rf_mkChar(""));
+ }
+
+
+ }
+
+ // NULL if empty
+ if (annocount==0) compannot = R_NilValue;
+ if (notescount==0) compnotes = R_NilValue;
+
+ PROTECT(out = Rf_allocVector(VECSXP, 5));
+ SET_VECTOR_ELT(out, 0, compid);
+ SET_VECTOR_ELT(out, 1, compname);
+ SET_VECTOR_ELT(out, 2, compout);
+ SET_VECTOR_ELT(out, 3, compannot);
+ SET_VECTOR_ELT(out, 4, compnotes);
+
+
+ PROTECT(listv = Rf_allocVector(STRSXP, 5));
+ SET_STRING_ELT(listv, 0, Rf_mkChar("id"));
+ SET_STRING_ELT(listv, 1, Rf_mkChar("name"));
+ SET_STRING_ELT(listv, 2, Rf_mkChar("outside"));
+ SET_STRING_ELT(listv, 3, Rf_mkChar("annotation"));
+ SET_STRING_ELT(listv, 4, Rf_mkChar("notes"));
+
+
+
+ Rf_setAttrib(out, R_NamesSymbol, listv);
+
+ /* make the list to be an instance of 'compartments_list' */
+ PROTECT(class = Rf_allocVector(STRSXP, 1));
+ SET_STRING_ELT(class, 0, Rf_mkChar("compartments_list"));
+ Rf_classgets(out, class);
+
+ UNPROTECT(8);
+ }
+ else {
+ out = R_NilValue;
+ }
+
+ return out;
+}
+
+/* -------------------------------------------------------------------------- */
+/* get list of species (metabolites) */
+SEXP getSBMLSpeciesList(SEXP sbmlmod) {
+
+ SEXP out = R_NilValue;
+ SEXP class = R_NilValue;
+ SEXP listv = R_NilValue;
+ SEXP metid = R_NilValue;
+ SEXP metname = R_NilValue;
+ SEXP metcomp = R_NilValue;
+ SEXP metcharge = R_NilValue;
+ SEXP metchemic = R_NilValue;
+ SEXP metbndcnd = R_NilValue;
+ SEXP metannot = R_NilValue;
+ SEXP metnotes = R_NilValue;
+
+ unsigned int nsp, i;
+
+ /* ListOf_t *spl; */
+ Species_t *splel;
+
+ checkModel(sbmlmod);
+
+ /* spl = Model_getListOfSpecies(R_ExternalPtrAddr(sbmlmod)); */
+ nsp = Model_getNumSpecies(R_ExternalPtrAddr(sbmlmod));
+
+
+ if (nsp > 0) {
+ PROTECT(metid = Rf_allocVector(STRSXP, nsp));
+ PROTECT(metname = Rf_allocVector(STRSXP, nsp));
+ PROTECT(metcomp = Rf_allocVector(STRSXP, nsp));
+ PROTECT(metcharge = Rf_allocVector(INTSXP, nsp));
+ PROTECT(metchemic = Rf_allocVector(STRSXP, nsp));
+ PROTECT(metbndcnd = Rf_allocVector(LGLSXP, nsp));
+ PROTECT(metannot = Rf_allocVector(STRSXP, nsp));
+ PROTECT(metnotes = Rf_allocVector(STRSXP, nsp));
+
+ int chcount=0;
+ int notescount=0;
+ int annotcount=0;
+
+ for (i = 0; i < nsp; i++) {
+ /* splel = (Species_t *) ListOf_get(spl, i); */
+ splel = Model_getSpecies(R_ExternalPtrAddr(sbmlmod), i);
+ /* id */
+ if (Species_isSetId(splel)) {
+ SET_STRING_ELT(metid, i, Rf_mkChar(Species_getId(splel)));
+ }
+ else {
+ SET_STRING_ELT(metid, i, Rf_mkChar("no_id"));
+ }
+ /* name */
+ if (Species_isSetName(splel)) {
+ SET_STRING_ELT(metname, i, Rf_mkChar(Species_getName(splel)));
+ }
+ else {
+ SET_STRING_ELT(metname, i, Rf_mkChar(""));
+ }
+ /* compartment */
+ if (Species_isSetCompartment(splel)) {
+ SET_STRING_ELT(metcomp, i, Rf_mkChar(Species_getCompartment(splel)));
+ }
+ else {
+ SET_STRING_ELT(metcomp, i, Rf_mkChar(""));
+ }
+ /* charge */
+ if (Species_isSetCharge(splel)) {
+ INTEGER(metcharge)[i] = Species_getCharge(splel);
+ }
+ else {
+ INTEGER(metcharge)[i] = 0;
+ }
+ /* boundary condition */
+ if (Species_isSetBoundaryCondition(splel)) {
+ LOGICAL(metbndcnd)[i] = Species_getBoundaryCondition(splel);
+ }
+ else {
+ LOGICAL(metbndcnd)[i] = 0;
+ }
+
+
+
+ /* notes */
+ if (SBase_isSetNotes((SBase_t *) splel)) {
+ SET_STRING_ELT(metnotes, i, Rf_mkChar(SBase_getNotesString((SBase_t *) splel)));
+ notescount=notescount+1;
+
+ }
+ else {
+ SET_STRING_ELT(metnotes, i, Rf_mkChar(""));
+ }
+
+ /* annotation */
+ if (SBase_isSetAnnotation((SBase_t *) splel)) {
+ //SET_STRING_ELT(metannot, i, Rf_mkChar(SBase_getAnnotationString((SBase_t *) splel)));
+ XMLNode_t* xml = SBase_getAnnotation((SBase_t *) splel);
+ annotcount=annotcount+1;
+ SET_STRING_ELT(metannot, i, Rf_mkChar(parseAnnotationTomorg(xml)));
+ }
+ else {
+ SET_STRING_ELT(metannot, i, Rf_mkChar(""));
+ }
+
+
+ /* FBC PLUGIN @ Ardalan */
+ SBasePlugin_t *SpeciesPlug = SBase_getPlugin((SBase_t *)(splel), "fbc");
+
+ /* FBCcharge */
+ if (FbcSpeciesPlugin_isSetCharge(SpeciesPlug)) {
+ INTEGER(metcharge)[i] = FbcSpeciesPlugin_getCharge(SpeciesPlug);
+ }
+
+ /* FBC chemicalFormula */
+ if (FbcSpeciesPlugin_isSetChemicalFormula(SpeciesPlug)) {
+ SET_STRING_ELT(metchemic, i, Rf_mkChar(FbcSpeciesPlugin_getChemicalFormula(SpeciesPlug)));
+ chcount=chcount+1;
+ }
+ else {
+ SET_STRING_ELT(metchemic, i, Rf_mkChar(""));
+ }
+
+
+ }
+
+ // NULL if empty
+ if (chcount==0) metchemic = R_NilValue;
+ if (notescount==0) metnotes = R_NilValue;
+ if (annotcount==0) metannot = R_NilValue;
+
+ PROTECT(out = Rf_allocVector(VECSXP, 8));
+ SET_VECTOR_ELT(out, 0, metid);
+ SET_VECTOR_ELT(out, 1, metname);
+ SET_VECTOR_ELT(out, 2, metcomp);
+ SET_VECTOR_ELT(out, 3, metcharge);
+ SET_VECTOR_ELT(out, 4, metchemic);
+ SET_VECTOR_ELT(out, 5, metbndcnd);
+ SET_VECTOR_ELT(out, 6, metannot);
+ SET_VECTOR_ELT(out, 7, metnotes);
+
+
+ PROTECT(listv = Rf_allocVector(STRSXP, 8));
+ SET_STRING_ELT(listv, 0, Rf_mkChar("id"));
+ SET_STRING_ELT(listv, 1, Rf_mkChar("name"));
+ SET_STRING_ELT(listv, 2, Rf_mkChar("compartment"));
+ SET_STRING_ELT(listv, 3, Rf_mkChar("charge"));
+ SET_STRING_ELT(listv, 4, Rf_mkChar("chemicalFormula"));
+ SET_STRING_ELT(listv, 5, Rf_mkChar("boundaryCondition"));
+ SET_STRING_ELT(listv, 6, Rf_mkChar("annotation"));
+ SET_STRING_ELT(listv, 7, Rf_mkChar("notes"));
+
+
+ Rf_setAttrib(out, R_NamesSymbol, listv);
+
+ /* make the list to be an instance of 'species_list' */
+ PROTECT(class = Rf_allocVector(STRSXP, 1));
+ SET_STRING_ELT(class, 0, Rf_mkChar("species_list"));
+ Rf_classgets(out, class);
+
+ UNPROTECT(11);
+ }
+ else {
+ out = R_NilValue;
+ }
+
+ return out;
+}
+
+
+/* -------------------------------------------------------------------------- */
+/* get list of reactions */
+SEXP getSBMLReactionsList(SEXP sbmlmod) {
+
+ SEXP out = R_NilValue;
+ SEXP class = R_NilValue;
+ SEXP listv = R_NilValue;
+ SEXP reactid = R_NilValue;
+ SEXP reactname = R_NilValue;
+ SEXP reactrev = R_NilValue;
+ SEXP reactnotes = R_NilValue;
+ SEXP reactannot = R_NilValue;
+ SEXP reactreact = R_NilValue;
+ SEXP reactprod = R_NilValue;
+ SEXP reactkl = R_NilValue;
+
+ SEXP parml = R_NilValue;
+ SEXP parmn = R_NilValue;
+ SEXP parmid = R_NilValue;
+ SEXP parmval = R_NilValue;
+ SEXP parmunit = R_NilValue;
+
+ SEXP fbclb = R_NilValue; //lowerbnd
+ SEXP fbcup = R_NilValue; //upperbnd
+ SEXP fbcgene = R_NilValue; //fbc gene Rules
+ SEXP fbcobj = R_NilValue; // fbc objective
+
+ unsigned int nre, i, j, nreactant, nproduct, nparm;
+
+ /* ListOf_t *rel; */
+ Reaction_t *relel;
+ KineticLaw_t *kl;
+ Parameter_t *parm;
+
+ checkModel(sbmlmod);
+
+ /* rel = Model_getListOfReactions(R_ExternalPtrAddr(sbmlmod)); */
+ nre = Model_getNumReactions(R_ExternalPtrAddr(sbmlmod));
+
+ if (nre > 0) {
+ PROTECT(reactid = Rf_allocVector(STRSXP, nre));
+ PROTECT(reactname = Rf_allocVector(STRSXP, nre));
+ PROTECT(reactrev = Rf_allocVector(LGLSXP, nre));
+ PROTECT(reactnotes = Rf_allocVector(STRSXP, nre));
+ PROTECT(reactannot = Rf_allocVector(STRSXP, nre));
+ PROTECT(reactreact = Rf_allocVector(VECSXP, nre));
+ PROTECT(reactprod = Rf_allocVector(VECSXP, nre));
+ PROTECT(reactkl = Rf_allocVector(VECSXP, nre));
+
+ PROTECT(fbclb = Rf_allocVector(REALSXP, nre));
+ PROTECT(fbcup = Rf_allocVector(REALSXP, nre));
+ PROTECT(fbcgene = Rf_allocVector(STRSXP , nre));
+ PROTECT(fbcobj = Rf_allocVector(REALSXP, nre));
+
+
+ int lbcount=0;
+ int upcount=0;
+ int genecount=0;
+ int objcount=0;
+ int annocount=0;
+ int notescount=0;
+
+ /* Help Var for Fbc Objective*/
+ double Objcoeff =0;
+ const char* Objreaction = NULL;
+ char* objActiv = NULL;
+ int fbcversion = 0;
+
+ /* FBC OBJECTIV @Ardalan*/
+ Objective_t * objective;
+ FluxObjective_t * fluxObjective;
+ SBasePlugin_t * modelPlug= NULL;
+
+ modelPlug = SBase_getPlugin((SBase_t *)(R_ExternalPtrAddr(sbmlmod)), "fbc");
+
+ // Read the Objectives when FBCPlugin for the model exists
+ if( modelPlug != NULL)
+ {
+
+ objActiv = FbcModelPlugin_getActiveObjectiveId(modelPlug);
+ int ob=0;
+ if(strcmp(objActiv,"") !=0)
+ {
+ for(ob; ob< FbcModelPlugin_getNumObjectives(modelPlug);ob++)
+ {
+ objective= FbcModelPlugin_getObjective(modelPlug,ob);
+ //printf("ObjectiveID: %s \n", Objective_getId(objective) );
+ if(strcmp(objActiv,Objective_getId(objective))==0)
+ { // TODO mehrer FLUXOBJECTIVE; MAXimierung Minimirung?
+
+ // int fob=0;
+ // for(fob; ob<FbcModelPlugin_getNumObjectives(modelPlug);fob++ )
+ // {
+ fluxObjective= Objective_getFluxObjective(objective,0);
+ Objreaction= FluxObjective_getReaction(fluxObjective) ;
+ Objcoeff = FluxObjective_getCoefficient(fluxObjective);
+
+ //printf("ReactionObjectiveID: %s \n", Objreaction);
+ //printf("Coefficient: %f \n", Objcoeff);
+ // }
+ }
+
+ }
+
+ }
+
+
+ /* is FBC 1 */
+
+ if(strcmp("fbc",SBasePlugin_getPackageName(modelPlug) ) ==0)
+ fbcversion = SBasePlugin_getPackageVersion(modelPlug);
+ }
+
+
+ for (i = 0; i < nre; i++) {
+ /* relel = (Reaction_t *) ListOf_get(rel, i); */
+ relel = Model_getReaction(R_ExternalPtrAddr(sbmlmod), i);
+
+ nreactant = Reaction_getNumReactants(relel);
+ nproduct = Reaction_getNumProducts(relel);
+
+ /* id */
+ if (Reaction_isSetId(relel)) {
+ SET_STRING_ELT(reactid, i, Rf_mkChar(Reaction_getId(relel)));
+ }
+ else {
+ SET_STRING_ELT(reactid, i, Rf_mkChar("no_id"));
+ }
+ /* name */
+ if (Reaction_isSetName(relel)) {
+ SET_STRING_ELT(reactname, i, Rf_mkChar(Reaction_getName(relel)));
+ }
+ else {
+ SET_STRING_ELT(reactname, i, Rf_mkChar(""));
+ }
+ /* reversible */
+ if (Reaction_isSetReversible(relel)) {
+ LOGICAL(reactrev)[i] = Reaction_getReversible(relel);
+ }
+ else {
+ LOGICAL(reactrev)[i] = 0;
+ }
+ /* notes */
+ if (SBase_isSetNotes((SBase_t *) relel)) {
+ SET_STRING_ELT(reactnotes, i, Rf_mkChar(SBase_getNotesString((SBase_t *) relel)));
+ notescount=notescount+1;
+ }
+ else {
+ SET_STRING_ELT(reactnotes, i, Rf_mkChar(""));
+ }
+ /* annotation */
+ if (SBase_isSetAnnotation((SBase_t *) relel)) {
+ //SET_STRING_ELT(reactannot, i, Rf_mkChar(SBase_getAnnotationString((SBase_t *) relel)));
+ XMLNode_t* xml = SBase_getAnnotation((SBase_t *) relel);
+ SET_STRING_ELT(reactannot, i, Rf_mkChar(parseAnnotationTomorg(xml)));
+ annocount=annocount+1;
+ }
+ else {
+ SET_STRING_ELT(reactannot, i, Rf_mkChar(""));
+ }
+
+ /* FBC LEVEL 2 @Ardalan Habil*/
+
+ /* ReactionPLugin for FBC 2 */
+ SBasePlugin_t *reactionPlug = SBase_getPlugin((SBase_t *)(relel), "fbc");
+
+
+ /* LOWERFLUXBOUND */
+ if (FbcReactionPlugin_isSetLowerFluxBound(reactionPlug))
+ {
+ parm = Model_getParameterById(R_ExternalPtrAddr (sbmlmod) ,FbcReactionPlugin_getLowerFluxBound(reactionPlug));
+ //printf("LowerFLUXBOUND: %f \n", Parameter_getValue(parm));
+ REAL(fbclb)[i] = Parameter_getValue(parm);
+ lbcount=lbcount+1;
+ }
+ else{
+ REAL(fbclb)[i] = 0;
+ }
+
+ /* UPPERFLUXBOUND*/
+ if (FbcReactionPlugin_isSetUpperFluxBound(reactionPlug))
+ {
+ parm = Model_getParameterById(R_ExternalPtrAddr (sbmlmod) ,FbcReactionPlugin_getUpperFluxBound(reactionPlug));
+ //printf("UPPERFLUXBOUND: %f \n", Parameter_getValue(parm));
+ REAL(fbcup)[i] = Parameter_getValue(parm);
+ upcount=upcount+1;
+ }
+ else{
+ REAL(fbcup)[i] = 0;
+ }
+
+ /*FBC 1 read */
+ if (fbcversion==1)
+ {
+ /* Storing FBC1Bounds */
+ double fbc1lb=0;
+ double fbc1up=0;
+
+
+ int fluxb=0;
+ for(fluxb; fluxb< FbcModelPlugin_getNumFluxBounds(modelPlug);fluxb++)
+ {
+ FluxBound_t * currentFlux = FbcModelPlugin_getFluxBound(modelPlug,fluxb);
+
+ const char * currentFluxType ;
+ const char * currentFluxReaction;
+
+ if (FluxBound_isSetReaction(currentFlux)) currentFluxReaction = FluxBound_getReaction(currentFlux);
+ else continue;
+
+ if(strcmp(currentFluxReaction , Reaction_getId(relel) ) !=0) continue;
+
+
+ if (FluxBound_isSetOperation(currentFlux)) currentFluxType = FluxBound_getOperation(currentFlux);
+ else continue;
+
+
+ if(strcmp("greaterEqual" , currentFluxType ) ==0)
+ {
+ lbcount=lbcount+1;
+ if (FluxBound_isSetValue(currentFlux)) fbc1lb = FluxBound_getValue(currentFlux);
+ else continue;
+ }
+
+ else if(strcmp("lessEqual" , currentFluxType ) ==0)
+ {
+ upcount=upcount+1;
+ if (FluxBound_isSetValue(currentFlux)) fbc1up = FluxBound_getValue(currentFlux);
+ else continue;
+ }
+
+ else if(strcmp("equal" , currentFluxType ) ==0)
+ {
+ if (FluxBound_isSetValue(currentFlux))
+ {
+ lbcount=lbcount+1;
+ upcount=upcount+1;
+ fbc1lb = FluxBound_getValue(currentFlux);
+ fbc1up = FluxBound_getValue(currentFlux);
+ }
+ else continue;
+ }
+
+ }
+
+ /* FBC 1 save Bounds */
+ REAL(fbclb)[i] = fbc1lb;
+ REAL(fbcup)[i] = fbc1up;
+
+ }
+
+
+ /* FBC GENE */
+ if( FbcReactionPlugin_isSetGeneProductAssociation(reactionPlug) ) {
+ GeneProductAssociation_t* gpa = FbcReactionPlugin_getGeneProductAssociation(reactionPlug);
+ FbcAssociation_t* asso= (FbcAssociation_t*) GeneProductAssociation_getAssociation(gpa);
+ SET_STRING_ELT(fbcgene, i, Rf_mkChar(FbcAssociation_toInfix(asso)));
+ //printf("Gene: %s \n", FbcAssociation_toInfix(asso));
+ genecount=genecount+1;
+ }
+ else {
+ SET_STRING_ELT(fbcgene, i, Rf_mkChar(""));
+ }
+
+ /* FBC OBJECTIVES*/
+ if (Objreaction != NULL && strcmp(Objreaction , Reaction_getId(relel) )==0)
+ {
+
+ REAL(fbcobj)[i] = Objcoeff;
+ objcount=objcount+1;
+ }
+ else{
+ REAL(fbcobj)[i] = 0;
+ }
+
+
+ /* reactants */
+ SET_VECTOR_ELT(reactreact, i, getSpeciesReference(relel, nreactant, 0));
+
+ /* products */
+ SET_VECTOR_ELT(reactprod, i, getSpeciesReference(relel, nproduct, 1));
+
+ /* kineticLaw */
+ if (Reaction_isSetKineticLaw(relel)) {
+ kl = Reaction_getKineticLaw(relel);
+ nparm = KineticLaw_getNumParameters(kl);
+
+ if (nparm > 0) {
+ PROTECT(parmid = Rf_allocVector(STRSXP, nparm));
+ PROTECT(parmval = Rf_allocVector(REALSXP, nparm));
+ PROTECT(parmunit = Rf_allocVector(STRSXP, nparm));
+
+ for (j = 0; j < nparm; j++) {
+ parm = KineticLaw_getParameter(kl, j);
+
+ /* id */
+ if (Parameter_isSetId(parm)) {
+ SET_STRING_ELT(parmid, j, Rf_mkChar(Parameter_getId(parm)));
+ }
+ else {
+ SET_STRING_ELT(parmid, j, Rf_mkChar("no_id"));
+ }
+ /* value */
+ if (Parameter_isSetValue(parm)) {
+ REAL(parmval)[j] = Parameter_getValue(parm);
+ }
+ else {
+ REAL(parmval)[j] = 0;
+ }
+ /* units */
+ if (Parameter_isSetUnits(parm)) {
+ SET_STRING_ELT(parmunit, j, Rf_mkChar(Parameter_getUnits(parm)));
+ }
+ else {
+ SET_STRING_ELT(parmunit, j, Rf_mkChar(""));
+ }
+ }
+
+ PROTECT(parml = Rf_allocVector(VECSXP, 3));
+ SET_VECTOR_ELT(parml, 0, parmid);
+ SET_VECTOR_ELT(parml, 1, parmval);
+ SET_VECTOR_ELT(parml, 2, parmunit);
+
+ PROTECT(parmn = Rf_allocVector(STRSXP, 3));
+ SET_STRING_ELT(parmn, 0, Rf_mkChar("id"));
+ SET_STRING_ELT(parmn, 1, Rf_mkChar("value"));
+ SET_STRING_ELT(parmn, 2, Rf_mkChar("units"));
+ Rf_setAttrib(parml, R_NamesSymbol, parmn);
+
+ UNPROTECT(5);
+ }
+ else {
+ parml = R_NilValue;
+ }
+ SET_VECTOR_ELT(reactkl, i, parml);
+ }
+ else {
+ SET_VECTOR_ELT(reactkl, i, R_NilValue);
+ }
+
+
+ }
+
+ // NULL if empty
+ if(lbcount==0) fbclb = R_NilValue;
+ if(upcount==0) fbcup = R_NilValue;
+ if(genecount==0) fbcgene = R_NilValue;
+ if(objcount==0) fbcobj = R_NilValue;
+ if(annocount==0) reactannot= R_NilValue;
+ if(notescount==0) reactnotes= R_NilValue;
+
+
+ PROTECT(out = Rf_allocVector(VECSXP, 12));
+ SET_VECTOR_ELT(out, 0, reactid);
+ SET_VECTOR_ELT(out, 1, reactname);
+ SET_VECTOR_ELT(out, 2, reactrev);
+ SET_VECTOR_ELT(out, 3, reactnotes);
+ SET_VECTOR_ELT(out, 4, reactannot);
+ SET_VECTOR_ELT(out, 5, reactreact);
+ SET_VECTOR_ELT(out, 6, reactprod);
+ SET_VECTOR_ELT(out, 7, reactkl);
+ SET_VECTOR_ELT(out, 8, fbclb);
+ SET_VECTOR_ELT(out, 9, fbcup);
+ SET_VECTOR_ELT(out, 10, fbcgene);
+ SET_VECTOR_ELT(out, 11, fbcobj);
+
+
+ PROTECT(listv = Rf_allocVector(STRSXP, 12));
+ SET_STRING_ELT(listv, 0, Rf_mkChar("id"));
+ SET_STRING_ELT(listv, 1, Rf_mkChar("name"));
+ SET_STRING_ELT(listv, 2, Rf_mkChar("reversible"));
+ SET_STRING_ELT(listv, 3, Rf_mkChar("notes"));
+ SET_STRING_ELT(listv, 4, Rf_mkChar("annotation"));
+ SET_STRING_ELT(listv, 5, Rf_mkChar("reactants"));
+ SET_STRING_ELT(listv, 6, Rf_mkChar("products"));
+ SET_STRING_ELT(listv, 7, Rf_mkChar("kinetic_law"));
+ SET_STRING_ELT(listv, 8, Rf_mkChar("fbc_lowbnd"));
+ SET_STRING_ELT(listv, 9, Rf_mkChar("fbc_uppbnd"));
+ SET_STRING_ELT(listv, 10, Rf_mkChar("fbc_gprRules"));
+ SET_STRING_ELT(listv, 11, Rf_mkChar("fbc_Objectives"));
+
+ Rf_setAttrib(out, R_NamesSymbol, listv);
+
+ /* make the list to be an instance of 'reactions_list' */
+ PROTECT(class = Rf_allocVector(STRSXP, 1));
+ SET_STRING_ELT(class, 0, Rf_mkChar("reactions_list"));
+ Rf_classgets(out, class);
+
+ UNPROTECT(15);
+ }
+ else {
+ out = R_NilValue;
+ }
+
+ return out;
+}
+
+/* -------------------------------------------------------------------------- */
+/* export SBML*/
+
+void ParseModtoAnno (SBase_t* comp , char* Mannocopy)
+
+{
+
+ char delimiter[] = ";";
+ char *ptr;
+ ptr = strtok(Mannocopy, delimiter);
+ char* quali;
+ CVTerm_t *cv;
+ int first=0;
+
+ while(ptr != NULL) {
+
+ if(strncmp("bqbiol", ptr, strlen("bqbiol")) == 0)
+ {
+ if (first != 0){ SBase_addCVTerm((SBase_t*)comp, cv);CVTerm_free(cv);}
+ //CVTerm_free(cv);
+ quali = strcpy(&ptr[0],&ptr[7]);
+ cv = CVTerm_createWithQualifierType(BIOLOGICAL_QUALIFIER);
+ CVTerm_setBiologicalQualifierTypeByString( cv, (const char*) quali);
+ first=1;
+ }
+ else if(strncmp("bqmodel", ptr, strlen("bqmodel")) == 0)
+ {
+ if (first != 0) { SBase_addCVTerm((SBase_t*)comp, cv);CVTerm_free(cv);}
+ //CVTerm_free(cv);
+ quali = strcpy(&ptr[0],&ptr[8]);
+ cv = CVTerm_createWithQualifierType(MODEL_QUALIFIER);
+ CVTerm_setModelQualifierTypeByString( cv, (const char*) quali);
+ }
+ else
+ {
+ CVTerm_addResource(cv,ptr );
+ }
+
+ // naechsten Abschnitt erstellen
+ ptr = strtok(NULL, delimiter);
+ }
+ SBase_addCVTerm((SBase_t*)comp, cv);
+
+}
+
+
+
+SEXP exportSBML (SEXP version, SEXP level,SEXP FbcLevel, SEXP filename,SEXP sybil_max, SEXP mod_desc, SEXP mod_name, SEXP mod_compart, SEXP met_id, SEXP met_name, SEXP met_comp, SEXP met_form,SEXP met_charge, SEXP react_id, SEXP react_name, SEXP react_rev, SEXP lowbnd, SEXP uppbnd, SEXP obj_coef, SEXP subSys, SEXP gpr, SEXP SMatrix, SEXP mod_notes, SEXP mod_anno, SEXP com_notes , SEXP com_anno, SEXP met_notes, SEXP met_anno, SEXP met_bnd , SEXP react_notes, SEXP react_anno, SEXP ex_react,SEXP allgenes)
+{
+ //Varaibles from R
+ const char* fname = CHAR(STRING_ELT(filename, 0));
+ const char* model_desc = CHAR(STRING_ELT(mod_desc, 0));
+ const char* model_name = CHAR(STRING_ELT(mod_name, 0));
+
+ int SBMLlevel = INTEGER(level)[0];
+ int SBMLversion = INTEGER(version)[0];
+ int SBMLfbcversion = INTEGER(FbcLevel)[0];
+ double sybilmax = REAL(sybil_max)[0];
+ double sybilmin = sybilmax*(-1);
+
+ // variable FBC
+ XMLNamespaces_t * fbc;
+ SBMLNamespaces_t * sbmlns;
+ FluxBound_t * fluxBound;
+ Objective_t * objective;
+ FluxObjective_t * fluxObjective;
+ SBMLDocumentPlugin_t * docPlug;
+ SBasePlugin_t * modelPlug;
+ SBasePlugin_t *reactionPlug;
+ SBasePlugin_t *SpeciesPlug ;
+
+ FbcAssociation_t* asso;
+
+
+ // Variable inital
+
+ SBMLDocument_t* sbmlDoc;
+ Model_t* model;
+ XMLNamespaces_t* xmlns;
+
+ UnitDefinition_t* unitdef;
+ Unit_t* unit;
+
+ Species_t *sp;
+ Reaction_t* reaction;
+ SpeciesReference_t* spr;
+ Compartment_t* comp;
+ KineticLaw_t* kl;
+ Parameter_t* para;
+
+ // ASTNode_t* flux;
+ ASTNode_t* astMath;
+ //ASTNode_t* ast;
+ //char* mathXMLString;
+
+ /*---------------------------------------------------------------------------
+ *
+ * Creates an SBMLDocument object
+ *
+ *---------------------------------------------------------------------------*/
+
+ if (SBMLlevel == 1 || SBMLlevel == 2)
+ {
+ sbmlDoc = SBMLDocument_createWithLevelAndVersion(SBMLlevel,SBMLversion);
+ xmlns = (XMLNamespaces_t*) SBMLDocument_getNamespaces(sbmlDoc);
+ XMLNamespaces_add(xmlns, "http://www.w3.org/1999/xhtml", "html");
+ }
+ else if(SBMLlevel == 3)
+ {
+ if(SBMLfbcversion == 0)
+ {
+ sbmlDoc = SBMLDocument_createWithLevelAndVersion(3,1);
+ xmlns = (XMLNamespaces_t*) SBMLDocument_getNamespaces(sbmlDoc);
+ XMLNamespaces_add(xmlns, "http://www.w3.org/1999/xhtml", "html");
+
+ } else {
+
+ /* FBC LEVEL */
+ /* get fbc registry entry */
+ SBMLExtension_t *sbmlext = SBMLExtensionRegistry_getExtension("fbc");
+
+ /* create the sbml namespaces object with fbc */
+ fbc = XMLNamespaces_create();
+ XMLNamespaces_add(fbc, SBMLExtension_getURI(sbmlext, 3, 1, SBMLfbcversion), "fbc");
+
+ sbmlns = SBMLNamespaces_create(3, 1);
+ SBMLNamespaces_addNamespaces(sbmlns, fbc);
+
+
+ /* create the document */
+ sbmlDoc = SBMLDocument_createWithSBMLNamespaces(sbmlns);
+
+ /* XHTML for notes*/
+ xmlns = (XMLNamespaces_t*) SBMLDocument_getNamespaces(sbmlDoc);
+ XMLNamespaces_add(xmlns, "http://www.w3.org/1999/xhtml", "html");
+
+ /* set the fbc reqd attribute to false */
+ docPlug = (SBMLDocumentPlugin_t*)(SBase_getPlugin((SBase_t*)(sbmlDoc), "fbc"));
+ SBMLDocumentPlugin_setRequired(docPlug, 0);
+
+ }
+
+ }
+
+
+ /*---------------------------------------------------------------------------
+ *
+ * Creates a Model object inside the SBMLDocument object.
+ *
+ *---------------------------------------------------------------------------*/
+
+ model = SBMLDocument_createModel(sbmlDoc);
+ Model_setId(model,model_name);
+
+ // Get a SBasePlugin_t object plugged in the model object.
+ if(SBMLfbcversion == 2)
+ {
+ modelPlug = SBase_getPlugin((SBase_t *)(model), "fbc");
+
+ // set the fbc strict attribute
+ FbcModelPlugin_setStrict(modelPlug, 1);
+ }
+
+ // Model NOTERS
+ if (!Rf_isNull(mod_notes))
+ {
+ char *Modnotes = (char*) CHAR(STRING_ELT(mod_notes, 0));
+ if ((Modnotes != NULL) && (Modnotes[0] != '\0'))
+ {
+ //printf("Canno: %s", Cnotes);
+ SBase_setNotesString((SBase_t*) model , Modnotes);
+ }
+ }
+
+ /*Annotation*/
+ if (!Rf_isNull(mod_anno) )
+ { char *Manno = (char*) CHAR(STRING_ELT(mod_anno, 0));
+ if((Manno != NULL) && (Manno[0] != '\0' ))
+ {
+ SBase_setMetaId((SBase_t*)model,model_name);
+ char Mannocopy[strlen(Manno)+1];
+ strcpy(Mannocopy,Manno);
+ // PARSING
+ ParseModtoAnno((SBase_t*)model, Mannocopy);
+
+ }
+ }
+
+ /*---------------------------------------------------------------------------
+ *
+ * Creates UnitDefinition objects inside the Model object.
+ *
+ *---------------------------------------------------------------------------*/
+ /*
+ unitdef = Model_createUnitDefinition(model);
+ UnitDefinition_setId(unitdef,"litre_per_mole_per_second");
+
+ // Creates an Unit inside the UnitDefinition object ("litre_per_mole_per_second")
+
+ unit = UnitDefinition_createUnit(unitdef);
+ Unit_setKind(unit,UNIT_KIND_MOLE);
+ Unit_setExponent(unit,-1);
+
+ // Creates an Unit inside the UnitDefinition object ("litre_per_mole_per_second")
+
+ unit = UnitDefinition_createUnit(unitdef);
+ Unit_setKind(unit,UNIT_KIND_LITRE);
+ Unit_setExponent(unit,1);
+
+ // Creates an Unit inside the UnitDefinition object ("litre_per_mole_per_second")
+
+ unit = UnitDefinition_createUnit(unitdef);
+ Unit_setKind(unit,UNIT_KIND_SECOND);
+ Unit_setExponent(unit,-1);
+
+ */
+
+ /*---------------------------------------------------------------------------
+ *
+ * Creates a Compartment object inside the Model object.
+ *
+ *---------------------------------------------------------------------------*/
+
+ const char *sName;
+ int i;
+ int hasBoundary=0;
+ for (i=0; i<LENGTH(mod_compart); i++)
+ {
+ sName = CHAR(STRING_ELT(mod_compart, i));
+ comp = Model_createCompartment(model);
+ Compartment_setId(comp,sName);
+ Compartment_setConstant(comp,1);
+ if( strcmp(sName,"BOUNDARY")==0 || strcmp(sName,"Boundary")==0 || strcmp(sName,"boundary")==0)hasBoundary=1;
+ if (!Rf_isNull(com_notes) && Rf_length(com_notes) > 1)
+ {
+ char *Cnotes = (char*) CHAR(STRING_ELT(com_notes, i));
+ if ((Cnotes != NULL) && (Cnotes[0] != '\0'))
+ {
+ //printf("Canno: %s", Cnotes);
+ SBase_setNotesString((SBase_t*)comp, Cnotes);
+ }
+ }
+
+
+ if (!Rf_isNull(com_anno) && Rf_length(com_anno) > 1 )
+ { char *Manno = (char*) CHAR(STRING_ELT(com_anno, i));
+ if((Manno != NULL) && (Manno[0] != '\0' ))
+ {
+ SBase_setMetaId((SBase_t*)comp, CHAR(STRING_ELT(mod_compart, i)));
+ char Mannocopy[strlen(Manno)+1];
+ strcpy(Mannocopy,Manno);
+ ParseModtoAnno((SBase_t*) comp,Mannocopy);
+
+ }
+ }
+
+ }
+
+
+ /* Boundary Compartment */
+ if(hasBoundary==0 && Rf_isNull(met_bnd) && Rf_length(met_bnd) <= 1 && !Rf_isNull(ex_react))
+ {
+ comp = Model_createCompartment(model);
+ Compartment_setId(comp,"BOUNDARY");
+ Compartment_setConstant(comp,1);
+ hasBoundary=1;
+ }
+ /*---------------------------------------------------------------------------
+ *
+ * Creates Species objects inside the Model object.
+ *
+ *---------------------------------------------------------------------------*/
+ for (i=0; i<LENGTH(met_name); i++)
+ {
+
+
+ sp = Model_createSpecies(model);
+ Species_setId(sp,CHAR(STRING_ELT(met_id, i)));
+ Species_setName(sp,CHAR(STRING_ELT(met_name, i)));
+ Species_setCompartment(sp,CHAR(STRING_ELT(met_comp, i)));
+ Species_setHasOnlySubstanceUnits(sp, 0);
+ Species_setConstant(sp, 0);
+
+ //Bondary Condition
+ if (!Rf_isNull(met_bnd) && Rf_length(met_bnd) > 1) Species_setBoundaryCondition(sp, LOGICAL(met_bnd)[i]);
+ else Species_setBoundaryCondition(sp, 0);
+
+
+ int hasNotes=0;
+ const char* metnote="";
+ if (!Rf_isNull(met_form) && Rf_length(met_form) > 1)
+ {
+ if (SBMLfbcversion >0)
+ {
+ SpeciesPlug = SBase_getPlugin((SBase_t *)(sp), "fbc");
+ FbcSpeciesPlugin_setChemicalFormula(SpeciesPlug, CHAR(STRING_ELT(met_form, i)));
+ }
+
+ else{
+ metnote = append_strings(metnote,"<html:p>FORMULA: ","");
+ metnote =append_strings(metnote,CHAR(STRING_ELT(met_form, i)),"");
+ metnote =append_strings(metnote," </html:p>","");
+ hasNotes=1;
+ }
+ }
+
+ if (!Rf_isNull(met_charge) && Rf_length(met_charge) > 1)
+ {
+ if (SBMLfbcversion >0)
+ {
+ SpeciesPlug = SBase_getPlugin((SBase_t *)(sp), "fbc");
+ FbcSpeciesPlugin_setCharge(SpeciesPlug, INTEGER(met_charge)[i]);
+ }
+ else
+ {
+ metnote = append_strings(metnote,"<html:p>CHARGE: ","");
+ char chint[256];
+ sprintf(chint, "%d", INTEGER(met_charge)[i]);
+ metnote =append_strings(metnote,chint,"");
+ metnote =append_strings(metnote," </html:p>","");
+ hasNotes=1;
+ }
+ }
+
+
+ if (!Rf_isNull(met_notes) && Rf_length(met_notes) > 1)
+ {
+ char *Mnotes = (char*) CHAR(STRING_ELT(met_notes, i));
+ if ((Mnotes != NULL) && (Mnotes[0] != '\0'))
+ {
+ SBase_setNotesString((SBase_t*)sp, Mnotes);
+ hasNotes=0;
+ }
+
+ }
+
+
+ if(hasNotes !=0 )SBase_setNotesString((SBase_t*)sp, metnote);
+
+ if (!Rf_isNull(met_anno) && Rf_length(met_anno) > 1 )
+ { char *Manno = (char*) CHAR(STRING_ELT(met_anno, i));
+
+ if((Manno != NULL) && (Manno[0] != '\0' ))
+ {
+
+ SBase_setMetaId((SBase_t*)sp, CHAR(STRING_ELT(met_id, i)));
+
+ // COPY STRING
+ char *Manno = (char*) CHAR(STRING_ELT(met_anno, i));
+ char Mannocopy[strlen(Manno)+1];
+ strcpy(Mannocopy,Manno);
+ // PARSING
+ ParseModtoAnno((SBase_t*)sp, Mannocopy);
+
+ }
+ }
+
+
+
+ }
+ /*---------------------------------------------------------------------------
+ *
+ * Creates Reaction objects inside the Model object.
+ *
+ *---------------------------------------------------------------------------*/
+
+ /* LISTOFGENES
+ *
+ */
+ if(SBMLfbcversion == 2 && Rf_length(gpr) > 1)
+ {
+ if (!Rf_isNull(gpr) && Rf_length(gpr) > 1)
+ {
+ modelPlug = SBase_getPlugin((SBase_t *)(model), "fbc");
+ //GeneProduct_t* gene;
+ char* genid = malloc( 100 );
+
+ for (i=0; i<LENGTH(allgenes); i++)
+ {
+ GeneProduct_t* gene = GeneProduct_create(3,1,2);
+ sprintf(genid,"G_%s", CHAR(STRING_ELT(allgenes, i)));
+ GeneProduct_setId(gene ,genid);
+ GeneProduct_setLabel(gene ,CHAR(STRING_ELT(allgenes, i)));
+ FbcModelPlugin_addGeneProduct(modelPlug,gene);
+ }
+ free(genid);
+ }
+ /*
+ ListOfParemters
+ */
+
+ // create the Parameters
+
+ para = Model_createParameter(model);
+ Parameter_setId(para, "default_lb");
+ Parameter_setConstant(para, 1);
+ Parameter_setValue(para, sybilmin);
+ SBase_setSBOTerm((SBase_t *)para,626);
+
+ para = Model_createParameter(model);
+ Parameter_setId(para, "default_ub");
+ Parameter_setConstant(para, 1);
+ Parameter_setValue(para, sybilmax);
+ SBase_setSBOTerm((SBase_t *)para,626);
+
+ para = Model_createParameter(model);
+ Parameter_setId(para, "default_0");
+ Parameter_setConstant(para, 1);
+ Parameter_setValue(para, 0);
+ SBase_setSBOTerm((SBase_t *)para,626);
+
+ }
+
+
+ // LOOP FOR REACTION
+ for (i=0; i<LENGTH(react_name); i++)
+ {
+ reaction = Model_createReaction(model);
+
+ Reaction_setId(reaction, CHAR(STRING_ELT(react_id, i)));
+ Reaction_setName(reaction, CHAR(STRING_ELT(react_name, i)));
+ Reaction_setReversible(reaction,LOGICAL(react_rev)[i]);
+ Reaction_setFast(reaction, 0);
+
+ if(SBMLfbcversion == 2)
+ {
+ // FBCv2
+ reactionPlug = SBase_getPlugin((SBase_t *)(reaction), "fbc");
+ GeneProductAssociation_t* gpa = GeneProductAssociation_create(3,1,2);
+
+ // FbcAnd_t * und= FbcAnd_create(3,1,2);
+ asso= FbcAssociation_parseFbcInfixAssociation(CHAR(STRING_ELT(gpr, i)),modelPlug);
+ GeneProductAssociation_setAssociation(gpa,asso);
+ FbcReactionPlugin_setGeneProductAssociation(reactionPlug,gpa);
+ }
+
+
+
+ const char* notesString = "";
+
+
+
+ if (!Rf_isNull(react_notes) && Rf_length(react_notes) > 1)
+ {
+ char *Rnotes = (char*) CHAR(STRING_ELT(react_notes, i));
+ if ((Rnotes != NULL) && (Rnotes[0] != '\0'))
+ {
+ //printf("Reaction Nores:%s ",Rnotes);
+ SBase_setNotesString((SBase_t*)reaction, Rnotes);
+ }
+
+ }
+ else
+ {
+ if(SBMLfbcversion == 0)
+ {
+ if (!Rf_isNull(gpr) && Rf_length(gpr) > 1)
+ {
+ notesString = append_strings(notesString,"<html:p>GENE_ASSOCIATION: ","");
+ notesString =append_strings(notesString,CHAR(STRING_ELT(gpr, i)),"");
+ notesString =append_strings(notesString," </html:p>","");
+ }
+ if (!Rf_isNull(subSys) && Rf_length(subSys) > 1)
+ {
+ notesString = append_strings(notesString,"<html:p>SUBSYSTEM: ","");
+ notesString =append_strings(notesString,CHAR(STRING_ELT(subSys, i)),"");
+ notesString =append_strings(notesString," </html:p>","");
+ }
+
+ SBase_setNotesString((SBase_t*)reaction, notesString);
+ }
+ }
+
+ const double *lower_bnd = REAL(lowbnd);
+ const double *upper_bnd = REAL(uppbnd);
+
+ // KineticLaw
+ if(SBMLfbcversion == 0)
+ {
+ kl = Reaction_createKineticLaw(reaction);
+
+ astMath = ASTNode_createWithType(AST_NAME);
+ ASTNode_setName(astMath, "FLUX_VALUE");
+
+ KineticLaw_setMath( kl, astMath);
+
+
+ para = KineticLaw_createParameter( kl );
+ Parameter_setId(para, "LOWER_BOUND");
+ Parameter_setValue( para, lower_bnd[i]);
+ //Parameter_setUnits( para, "litre_per_mole_per_second");
+
+ para = KineticLaw_createParameter( kl );
+ Parameter_setId(para, "UPPER_BOUND");
+ Parameter_setValue( para, upper_bnd[i]);
+ //Parameter_setUnits( para, "litre_per_mole_per_second");
+
+ para = KineticLaw_createParameter( kl );
+ Parameter_setId(para, "OBJECTIVE_COEFFICIENT");
+ Parameter_setValue( para, INTEGER(obj_coef)[i]);
+
+ para = KineticLaw_createParameter( kl );
+ Parameter_setId(para, "FLUX_VALUE");
+ Parameter_setValue( para, 0);
+ }
+
+
+ int isexchange=0;
+ int k;
+ if (Rf_isNull(met_bnd) && Rf_length(met_bnd) <= 1 && !Rf_isNull(ex_react))
+ for (k=0; k<LENGTH(ex_react); k++)
+ if( i+1 == INTEGER(ex_react)[k])
+ isexchange=1;
+
+ int j=0;
+ for (j=0; j<LENGTH(met_id); j++)
+ {
+
+ int hash = LENGTH(met_id) * i + j;
+ if (REAL(SMatrix)[hash] != 0.00 )
+ {
+
+ if(REAL(SMatrix)[hash] < 0.00)
+ {
+ spr = Reaction_createReactant(reaction);
+ SpeciesReference_setConstant(spr, 1);
+ SpeciesReference_setSpecies(spr,CHAR(STRING_ELT(met_id, j)));
+ SpeciesReference_setStoichiometry(spr, fabs(REAL(SMatrix)[hash]));
+
+ //is Exchange Reaction
+ if(isexchange==1 && !Rf_isNull(ex_react))
+ {
+ /* Create boundary Species */
+ sp = Model_createSpecies(model);
+
+ Species_setId(sp, append_strings(CHAR(STRING_ELT(met_id, j)),"BOUNDARY","_") );
+ Species_setName(sp,append_strings(CHAR(STRING_ELT(met_name, j)),"BOUNDARY"," ") );
+
+ Species_setCompartment(sp,"BOUNDARY");
+ Species_setHasOnlySubstanceUnits(sp, 0);
+ Species_setBoundaryCondition(sp, 1);
+ Species_setConstant(sp, 1);
+
+ /* Add boundary Species as Product */
+ spr = Reaction_createProduct(reaction);
+ SpeciesReference_setSpecies(spr,append_strings(CHAR(STRING_ELT(met_id, j)),"BOUNDARY","_") );
+ SpeciesReference_setStoichiometry(spr,1);
+
+ SpeciesReference_setConstant(spr, 1);
+ }
+
+
+ }else{
+ spr = Reaction_createProduct(reaction);
+ SpeciesReference_setConstant(spr, 1);
+ SpeciesReference_setSpecies(spr,CHAR(STRING_ELT(met_id, j)));
+ SpeciesReference_setStoichiometry(spr, fabs(REAL(SMatrix)[hash]));
+ }
+
+ }
+ }
+
+
+
+ /*Annotation*/
+ if (!Rf_isNull(react_anno) && Rf_length(react_anno) > 1 )
+ { char *Manno = (char*) CHAR(STRING_ELT(react_anno, i));
+ if((Manno != NULL) && (Manno[0] != '\0' ))
+ {
+ SBase_setMetaId((SBase_t*)reaction, CHAR(STRING_ELT(react_id, i)));
+ char Mannocopy[strlen(Manno)+1];
+ strcpy(Mannocopy,Manno);
+ // PARSING
+ ParseModtoAnno((SBase_t*)reaction, Mannocopy);
+
+ }
+ }
+
+
+
+ /* FBC LEVEL 2 */
+ if(SBMLfbcversion == 2)
+ {
+ // Get a SBasePlugin_t object plugged in the reaction object.
+
+ reactionPlug = SBase_getPlugin((SBase_t *)(reaction), "fbc");
+
+ const char* para_lb;
+ const char* para_ub;
+
+ //default Parameter or new one
+ if (lower_bnd[i]<= sybilmin)
+ {
+ para_lb="default_lb";
+ }
+ else if (lower_bnd[i] == 0)
+ {
+ para_lb="default_0";
+ }
+ else
+ { //creacte Lower_bound Paramater
+ para = Model_createParameter(model);
+ Parameter_setId(para, append_strings(CHAR(STRING_ELT(react_id, i)),"lower_bound","_"));
+ Parameter_setConstant(para, 1);
+ Parameter_setValue(para, lower_bnd[i]);
+ SBase_setSBOTerm((SBase_t *)para,625);
+
+ para_lb=append_strings(CHAR(STRING_ELT(react_id, i)),"lower_bound","_");
+
+ }
+
+ if (upper_bnd[i] >= sybilmax)
+ {
+ para_ub="default_ub";
+ }
+
+ else if (upper_bnd[i] == 0)
+ {
+ para_ub="default_0";
+ }
+
+ else
+ {
+ //creacte upper_bound Paramater
+ para = Model_createParameter(model);
+ Parameter_setId(para, append_strings(CHAR(STRING_ELT(react_id, i)),"upper_bound","_"));
+ Parameter_setConstant(para, 1);
+ Parameter_setValue(para, upper_bnd[i]);
+ SBase_setSBOTerm((SBase_t *)para,625);
+
+ para_ub=append_strings(CHAR(STRING_ELT(react_id, i)),"upper_bound","_");
+ }
+
+ // set the flux bounds for this reaction
+ FbcReactionPlugin_setLowerFluxBound(reactionPlug, para_lb);
+ FbcReactionPlugin_setUpperFluxBound(reactionPlug, para_ub);
+
+ // OBJECTIVES
+ if (INTEGER(obj_coef)[i]!=0)
+ {
+ objective = Objective_create(3, 1, 2);
+ Objective_setId(objective, "obj");
+ Objective_setType(objective, "maximize");
+
+ fluxObjective = Objective_createFluxObjective(objective);
+ FluxObjective_setReaction(fluxObjective, CHAR(STRING_ELT(react_id, i)));
+ FluxObjective_setCoefficient(fluxObjective, INTEGER(obj_coef)[i]);
+
+ FbcModelPlugin_addObjective(modelPlug, objective);
+
+ // mark obj1 as active objective
+ FbcModelPlugin_setActiveObjectiveId(modelPlug, "obj");
+
+ }
+ }
+
+
+ }// ENDE REACTION
+ if(SBMLfbcversion == 1)
+ {
+
+ // FBC LEVEL 1
+
+ // Get a SBasePlugin_t object plugged in the model object.
+
+ modelPlug = SBase_getPlugin((SBase_t *)(model), "fbc");
+ int ObjCounter = 0;
+ for (i=0; i<LENGTH(react_name); i++)
+ {
+
+ const double *lower_bnd = REAL(lowbnd);
+ const double *upper_bnd = REAL(uppbnd);
+
+ char buf[20];
+ // FBC1 FLUXBOUNDS
+ sprintf(buf, "LOWER_BOUND%d", i);
+ if (INTEGER(obj_coef)[i] != 1)
+ {
+ fluxBound = FluxBound_create(3, 1, 1);
+ FluxBound_setId(fluxBound, buf);
+ FluxBound_setReaction(fluxBound, CHAR(STRING_ELT(react_id, i)));
+ FluxBound_setOperation(fluxBound, "greaterEqual");
+ FluxBound_setValue(fluxBound, lower_bnd[i]);
+ FbcModelPlugin_addFluxBound(modelPlug, fluxBound);
+
+ //printf("Upper: %s\n", buf);
+ sprintf(buf, "UPPER_BOUND%d", i);
+ fluxBound = FluxBound_create(3, 1, 1);
+ FluxBound_setId(fluxBound, buf);
+ FluxBound_setReaction(fluxBound, CHAR(STRING_ELT(react_id, i)));
+ FluxBound_setOperation(fluxBound, "lessEqual");
+ FluxBound_setValue(fluxBound, upper_bnd[i]);
+
+ FbcModelPlugin_addFluxBound(modelPlug, fluxBound);
+ }
+
+ if (INTEGER(obj_coef)[i] == 1 && ObjCounter == 0)
+ {
+ sprintf(buf, "OBJ%d", i);
+ objective = Objective_create(3, 1, 1);
+ Objective_setId(objective, buf);
+ Objective_setType(objective, "maximize");
+
+ fluxObjective = Objective_createFluxObjective(objective);
+ FluxObjective_setReaction(fluxObjective, CHAR(STRING_ELT(react_id, i)));
+ FluxObjective_setCoefficient(fluxObjective, 1);
+
+ FbcModelPlugin_addObjective(modelPlug, objective);
+ FbcModelPlugin_setActiveObjectiveId(modelPlug, buf);
+ ObjCounter = ObjCounter +1;
+ }
+
+
+
+ }
+ }
+
+ // write SBML file
+ int result = writeSBML(sbmlDoc, fname);
+ SEXP out = R_NilValue;
+ if (result)out = Rf_ScalarLogical(1);
+ else out = Rf_ScalarLogical(0);
+
+ return out;
+}
+
+
+
+
+/* -------------------------------------------------------------------------- */
\ No newline at end of file
diff --git a/src/sybilSBML.h b/src/sybilSBML.h
index 03345246ae9388cac9daf15eb52cb152151da0ca..9fac9ea3f09297661487956e0deca29afa6a2976 100644
--- a/src/sybilSBML.h
+++ b/src/sybilSBML.h
@@ -1,100 +1,112 @@
-/* sybilSBML.h
- Link to libSBML for sybil.
-
- Copyright (C) 2010-2013 Gabriel Gelius-Dietrich, Dpt. for Bioinformatics,
- Institute for Informatics, Heinrich-Heine-University, Duesseldorf, Germany.
- All right reserved.
- Email: geliudie@uni-duesseldorf.de
-
- This file is part of sybilSBML.
-
- SybilSBML 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.
-
- SybilSBML 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 sybilSBML. If not, see <http://www.gnu.org/licenses/>.
-*/
-
-#include "sbml.h"
-
-/* -------------------------------------------------------------------------- */
-/* help functions */
-/* -------------------------------------------------------------------------- */
-
-/* check for pointer to sbml document */
-SEXP isSBMLdocptr(SEXP ptr);
-
-/* check for pointer to sbml model */
-SEXP isSBMLmodptr(SEXP ptr);
-
-/* check for NULL pointer */
-SEXP isNULLptr(SEXP ptr);
-
-
-/* -------------------------------------------------------------------------- */
-/* API functions */
-/* -------------------------------------------------------------------------- */
-
-/* get libsbml version number (dotted version) */
-SEXP getLibSBMLversion();
-
-/* initialize sybilSBML */
-SEXP initSBML(void);
-
-/* remove sbml document pointer */
-SEXP delDocument(SEXP sbmldoc);
-
-/* remove model pointer */
-SEXP delModel(SEXP sbmlmodel);
-
-/* read SBML file */
-SEXP readSBMLfile(SEXP fname, SEXP ptrtype);
-
-/* get sbml document level */
-SEXP getSBMLlevel(SEXP sbmldoc);
-
-/* get sbml document version */
-SEXP getSBMLversion(SEXP sbmldoc);
-
-/* validate SBML document */
-SEXP validateDocument(SEXP sbmldoc);
-
-/* get SBML errors */
-SEXP getSBMLerrors(SEXP sbmldoc);
-
-/* get sbml model from sbml document */
-SEXP getSBMLmodel(SEXP sbmldoc, SEXP ptrtype);
-
-/* get model id */
-SEXP getSBMLmodId(SEXP sbmlmod);
-
-/* get model name */
-SEXP getSBMLmodName(SEXP sbmlmod);
-
-/* get number of compartments */
-SEXP getSBMLnumCompart(SEXP sbmlmod);
-
-/* get number of species (metabolites) */
-SEXP getSBMLnumSpecies(SEXP sbmlmod);
-
-/* get number of reactions */
-SEXP getSBMLnumReactions(SEXP sbmlmod);
-
-/* get list of unit definitions */
-SEXP getSBMLunitDefinitionsList(SEXP sbmlmod);
-
-/* get list of compartments */
-SEXP getSBMLCompartList(SEXP sbmlmod);
-
-/* get list of species (metabolites) */
-SEXP getSBMLSpeciesList(SEXP sbmlmod);
-
-/* get list of reactions */
-SEXP getSBMLReactionsList(SEXP sbmlmod);
+/* sybilSBML.h
+ Link to libSBML for sybil.
+
+ Copyright (C) 2010-2013 Gabriel Gelius-Dietrich, Dpt. for Bioinformatics,
+ Institute for Informatics, Heinrich-Heine-University, Duesseldorf, Germany.
+ All right reserved.
+ Email: geliudie@uni-duesseldorf.de
+
+ This file is part of sybilSBML.
+
+ SybilSBML 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.
+
+ SybilSBML 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 sybilSBML. If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#include "sbml.h"
+
+/* -------------------------------------------------------------------------- */
+/* help functions */
+/* -------------------------------------------------------------------------- */
+
+/* check for pointer to sbml document */
+SEXP isSBMLdocptr(SEXP ptr);
+
+/* check for pointer to sbml model */
+SEXP isSBMLmodptr(SEXP ptr);
+
+/* check for NULL pointer */
+SEXP isNULLptr(SEXP ptr);
+
+
+/* -------------------------------------------------------------------------- */
+/* API functions */
+/* -------------------------------------------------------------------------- */
+
+/* get libsbml version number (dotted version) */
+SEXP getLibSBMLversion();
+
+/* initialize sybilSBML */
+SEXP initSBML(void);
+
+/* remove sbml document pointer */
+SEXP delDocument(SEXP sbmldoc);
+
+/* remove model pointer */
+SEXP delModel(SEXP sbmlmodel);
+
+/* read SBML file */
+SEXP readSBMLfile(SEXP fname, SEXP ptrtype);
+
+/* get sbml document level */
+SEXP getSBMLlevel(SEXP sbmldoc);
+
+/* get sbml document version */
+SEXP getSBMLversion(SEXP sbmldoc);
+
+/* get sbml document FBC version */
+SEXP getSBMLFbcversion(SEXP sbmldoc);
+
+/* validate SBML document */
+SEXP validateDocument(SEXP sbmldoc);
+
+/* get SBML errors */
+SEXP getSBMLerrors(SEXP sbmldoc);
+
+/* get sbml model from sbml document */
+SEXP getSBMLmodel(SEXP sbmldoc, SEXP ptrtype);
+
+/* get model id */
+SEXP getSBMLmodId(SEXP sbmlmod);
+
+/* get model name */
+SEXP getSBMLmodName(SEXP sbmlmod);
+
+/* get model notes */
+SEXP getSBMLmodNotes(SEXP sbmlmod);
+
+/* get model annotation */
+SEXP getSBMLmodAnnotation(SEXP sbmlmod);
+
+/* get number of compartments */
+SEXP getSBMLnumCompart(SEXP sbmlmod);
+
+/* get number of species (metabolites) */
+SEXP getSBMLnumSpecies(SEXP sbmlmod);
+
+/* get number of reactions */
+SEXP getSBMLnumReactions(SEXP sbmlmod);
+
+/* get list of unit definitions */
+SEXP getSBMLunitDefinitionsList(SEXP sbmlmod);
+
+/* get list of compartments */
+SEXP getSBMLCompartList(SEXP sbmlmod);
+
+/* get list of species (metabolites) */
+SEXP getSBMLSpeciesList(SEXP sbmlmod);
+
+/* get list of reactions */
+SEXP getSBMLReactionsList(SEXP sbmlmod);
+
+/* export Modelorg to SBML*/
+SEXP exportSBML (SEXP version, SEXP level,SEXP FbcLevel, SEXP filename,SEXP sybil_max, SEXP mod_desc, SEXP mod_name, SEXP mod_compart, SEXP met_id, SEXP met_name, SEXP met_comp, SEXP met_form,SEXP met_charge, SEXP react_id, SEXP react_name, SEXP react_rev, SEXP lowbnd, SEXP uppbnd, SEXP obj_coef, SEXP subSys, SEXP gpr, SEXP SMatrix, SEXP mod_notes, SEXP mod_anno, SEXP com_notes , SEXP com_anno, SEXP met_notes, SEXP met_anno, SEXP met_bnd , SEXP react_notes, SEXP react_anno, SEXP ex_react, SEXP allgenes);
\ No newline at end of file