From 3e988bb44f8069b122ccffa9d335c46201e19537 Mon Sep 17 00:00:00 2001
From: Mayo Roettger <mayo.roettger@uni-duesseldorf.de>
Date: Mon, 2 Mar 2020 15:47:09 +0100
Subject: [PATCH] changes to build without FBC and Groups plugins
---
DESCRIPTION | 6 +-
NAMESPACE | 4 +-
R/readSBMLmod.R | 177 +-
R/sbmlPtrClass.R | 2 +-
R/sybilSBML.R | 34 +
build/vignette.rds | Bin 217 -> 217 bytes
configure | 255 +-
configure.ac | 22 +-
inst/NEWS.Rd | 10 +
man/getSBMLReactionsList.Rd | 10 +-
man/getSBMLSpeciesList.Rd | 10 +-
man/isAvailableFbcPlugin.Rd | 27 +
man/isAvailableGroupsPlugin.Rd | 27 +
man/writeSBML.Rd | 8 +-
src/Makevars | 3 +
src/config.h | 82 +
src/config.h.in | 81 +
src/init.c | 140 +-
src/sbml.h | 3 +
src/sybilSBML.c | 4789 ++++++++++++++++----------------
src/sybilSBML.h | 236 +-
src/symbols.rds | Bin 0 -> 2023 bytes
22 files changed, 3241 insertions(+), 2685 deletions(-)
create mode 100644 man/isAvailableFbcPlugin.Rd
create mode 100644 man/isAvailableGroupsPlugin.Rd
create mode 100644 src/Makevars
create mode 100644 src/config.h
create mode 100644 src/config.h.in
create mode 100644 src/symbols.rds
diff --git a/DESCRIPTION b/DESCRIPTION
index 7b79b60..6798ad6 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: sybilSBML
Type: Package
Title: SBML Integration in Package 'Sybil'
-Version: 3.0.6
-Date: 2019-07-03
+Version: 3.0.7
+Date: 2019-08-02
Authors@R: c(person("Mayo", "Roettger", role = "cre", email = "mayo.roettger@hhu.de"),
person("Gabriel", "Gelius-Dietrich", role = c("aut", "ctb")),
person(c("C.", "Jonathan"), "Fritzemeier", role = "ctb", email = "clausjonathan.fritzemeier@uni-duesseldorf.de"),
@@ -17,7 +17,7 @@ License: GPL-3 | file LICENSE
LazyLoad: yes
Collate: generics.R sbmlPtrClass.R sbmlErrorClass.R sybilSBML.R
uglyHack.R readSBMLmod.R zzz.R
-Packaged: 2019-07-03 15:45:00 UTC; mayo
+Packaged: 2019-08-02 15:05:20 UTC; mayo
Author: Mayo Roettger [cre],
Gabriel Gelius-Dietrich [aut, ctb],
C. Jonathan Fritzemeier [ctb],
diff --git a/NAMESPACE b/NAMESPACE
index ef1a335..a6c8487 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -52,5 +52,7 @@ readSBMLmod,
writeSBML,
getSBMLFbcversion,
getSBMLmodNotes,
-getSBMLmodAnnotation
+getSBMLmodAnnotation,
+isAvailableFbcPlugin,
+isAvailableGroupsPlugin
)
diff --git a/R/readSBMLmod.R b/R/readSBMLmod.R
index c407a88..5575ee0 100644
--- a/R/readSBMLmod.R
+++ b/R/readSBMLmod.R
@@ -57,12 +57,13 @@ on.exit(expr = {
} )
#------------------------------------------------------------------------------#
-# open the model file
+# Does the model file exist?
if ( file.exists(filename) == FALSE ) {
stop("failed to open file ", sQuote(filename))
}
+# set description to filename, if not set
if (missing(description)) {
mdesc <- filename
}
@@ -96,6 +97,7 @@ entryforS <- function(X) {
CURR_MET <- character(n) # metabolites in X
t <- 0
+ # over all metabolite IDs:
for (i in seq(along = X[["species"]])) {
t <- t + 1
@@ -104,21 +106,23 @@ entryforS <- function(X) {
# The metabolite id's are removed from the metabolites list,
# but not from the reactions list.
- CURR_MET[t] <- X[["species"]][i]
+ CURR_MET[t] <- X[["species"]][i] # get current metabolite ID
+
if (isTRUE(mergeMet)) {
+ # find out, if the current metabolite is already in the list and remember matching position in CURR_MET vector:
met_indCURR <- match(CURR_MET[t], CURR_MET[-t])
}
else {
met_indCURR <- NA
}
- if (is.na(met_indCURR)) {
+ if (is.na(met_indCURR)) {# if we don't have to merge metabolite --> check this!####
sj[t] <- match(X[["species"]][i], met_id_tmp) # the row number
s_ji[t] <- X[["stoichiometry"]][i]
- remMet[t] <- ifelse(is.na(sj[t]), FALSE, TRUE)
+ remMet[t] <- ifelse(is.na(sj[t]), FALSE, TRUE) #
}
- else {
+ else {# we have to merge metabolite --> check this!####
remMet[t] <- FALSE
s_ji[met_indCURR] <- s_ji[met_indCURR] + X[["stoichiometry"]][i]
msg <- paste("reaction no.", i, dQuote(react_id_tmp[i]),
@@ -211,6 +215,8 @@ formatSBMLid <- function(idstr) {
#------------------------------------------------------------------------------#
# parse the notes field of the reactions
+# (notes is a character string)
+# extract gpr rules and subsystem from notes
#------------------------------------------------------------------------------#
parseNotesReact <- function(notes) {
@@ -226,35 +232,49 @@ parseNotesReact <- function(notes) {
#split <- "\n"
fields <- strsplit(notes, split, fixed = TRUE)
- # print(fields)
+ # print(fields)
+ # fields now contains a list in which each item is a vector with the strings separated by the <p> or <html:p> respectively
+ # we only have one element in the list here.
+
+ # extract the actual notes between the opening and closing tags:
start_tag <- paste("<", tag, ">", sep = "")
end_tag <- paste("</", tag, ">", sep = "")
regex <- paste("^(?:[\\t]*\\Q", start_tag, "\\E)?", "(.*)", "\\Q", end_tag, "\\E", "(?s).*$", sep = "")
-# regex <- paste("(.*)", end_tag, "(?s).*$", sep = "")
+ #regex <- paste("(.*)", end_tag, "(?s).*$", sep = "")
#print(regex)
fields_str <- sub(regex, "\\1", fields[[1]], perl = TRUE)
#print(fields_str)
+ # fields_str should now contain a vector of the actual notes without surrounding tags
- subSyst <- ""
- gpr <- ""
+
+ # extract gpr rule (genes and rules) and subsystem from notes:
+ subSyst <- ""# no sub system
+ gpr <- ""# no gene to protein to reaction interaction
gene_rule <- NA
for (j in 1:length(fields_str)) {
+ # Do we have a "GENE_ASSOCIATION" or "GENE ASSOCIATION" or GENEASSOCIATION?
if (grepl("GENE[_ ]?ASSOCIATION", fields_str[j])) {
#if (charmatch("GENE", fields_str[j], nomatch = -1) != -1) {
- gpr <- sub("GENE[_ ]?ASSOCIATION: *", "", fields_str[j])
- gene_rule <- sybil:::.parseBoolean(gpr)
+ gpr <- sub("GENE[_ ]?ASSOCIATION: *", "", fields_str[j])# delete the text, remaining gpr
+
+ # get the unique gene names and the rule with the x[gene number] codes:
+ gene_rule <- sybil:::.parseBoolean(gpr)# parse gene rule
#print(gene_rule)
-
+
}#Ardalan Habil
+ # Or do we have a "GPR_ASSOCIATION" or "GPR ASSOCIATION" or GPRASSOCIATION?
else if (grepl("GPR[_ ]?ASSOCIATION", fields_str[j])) {
gpr <- sub("GPR[_ ]?ASSOCIATION: *", "", fields_str[j])
+ # get the unique gene names and the rule with the x[gene number] codes:
gene_rule <- sybil:::.parseBoolean(gpr)
- }
-
+ }
+
+ # Do we have a "SUBSYSTEM"?
if (charmatch("SUBSYSTEM", fields_str[j], nomatch = -1) != -1) {
+ # remove SUBSYSTEM with trailing trailing spaces, then remove the S_ at the beginning, then exchange all _ by spaces:
subSyst <- sub("SUBSYSTEM: *", "", fields_str[j])
subSyst <- sub("^S_", "", subSyst, perl = TRUE)
subSyst <- gsub("[_]+", " ", subSyst)
@@ -267,7 +287,8 @@ parseNotesReact <- function(notes) {
if (!is.list(gene_rule)) {
gene_rule <- sybil:::.parseBoolean("")
}
-
+
+ # return sub system, genes, and rules:
return(list(sub_system = subSyst, genes = gene_rule$gene, rules = gene_rule$rule, gpr = gpr))
}
@@ -289,6 +310,16 @@ sbmldoc <- openSBMLfile(filename)
message("OK")
+# warning, if FBC plugin is missing:
+if (isAvailableFbcPlugin() == FALSE) {
+ warning("Missing FBC-plugin for libSBML. FBC constraints will be ignored.")
+}
+
+# warning, if Groups plugin is missing:
+if (isAvailableGroupsPlugin() == FALSE) {
+ warning("Missing Groups-plugin for libSBML. Groups will be ignored.")
+}
+
# warning if new Version/Level/
SBMLlevel<- getSBMLlevel(sbmldoc)
SBMLversion<- getSBMLversion(sbmldoc)
@@ -298,6 +329,7 @@ if(SBMLlevel == 3 && SBMLversion > 1)
if (FBCversion > 2)
warning(paste("No support for Fbc Version ",FBCversion))
+
#------------------------------------------------------------------------------#
# check the model #
#------------------------------------------------------------------------------#
@@ -442,24 +474,24 @@ if (is.null(metabolitesList)) {
}
missingId(metabolitesList)
-metSpIds <- metabolitesList[["id"]]
+metSpIds <- metabolitesList[["id"]]# Metabolites IDs
#nummet <- getSBMLnumSpecies(sbmlmod)
if (isTRUE(bndCond)) {
- metSpBnd <- metabolitesList[["boundaryCondition"]]
- met_id_pos <- !metSpBnd
+ metSpBnd <- metabolitesList[["boundaryCondition"]]# TRUE for external, FALSE for internal metabolites
+ met_id_pos <- !metSpBnd# TRUE for internal metabolites
}
else {
# regular expression to identify external metabolites
extMetRegEx <- paste("_", extMetFlag, "$", sep = "")
- met_id_pos <- grep(extMetRegEx, metSpIds, invert = TRUE)
+ met_id_pos <- grep(extMetRegEx, metSpIds, invert = TRUE)# positions of internal metabolites
}
-met_id_tmp <- metSpIds[met_id_pos]
+met_id_tmp <- metSpIds[met_id_pos]# IDs of internal metabolites
# number of metabolites
-nummet <- length(met_id_tmp)
+nummet <- length(met_id_tmp)# No. internal metabolites
#------------------------------------------------------------------------------#
@@ -515,33 +547,35 @@ for (i in 1 : numreact) {
# Notes und Annotation can be null ( @Ardalan Habil)
if(!is.null( reactionsList[["notes"]]))
- if (nchar(notes) > 0) {
+ if (nchar(notes) > 0) {
- hasNotes <- TRUE
- notes_field <- parseNotesReact(notes)
- #print(notes_field)
- subSys[i] <- notes_field$sub_system # the reaction's sub system: glykolysis, TCA, ...
- genes[[i]] <- notes_field$genes # list of genes
- rules[i] <- notes_field$rules # rules
- gpr[i] <- notes_field$gpr # original gpr association
- #allGenes <- c(allGenes, genes[[i]])
+ hasNotes <- TRUE
+ notes_field <- parseNotesReact(notes)
+ #print(notes_field)
+ subSys[i] <- notes_field$sub_system # the reaction's sub system: glykolysis, TCA, ...
+ genes[[i]] <- notes_field$genes # list of genes
+ rules[i] <- notes_field$rules # rules
+ gpr[i] <- notes_field$gpr # original gpr association
+ #allGenes <- c(allGenes, genes[[i]])
- }
- else {
- if(!is.null( reactionsList[["annotation"]]))
- if (nchar(annot) > 0) {
- hasAnnot <- TRUE
- pn <- regexpr("Pathway Name: [^<]+", annot, perl = TRUE)
- subSys[i] <- substr(annot, (pn+14), pn + ((attr(pn, "match.length"))-1))
+ }
+ else {
+ if(!is.null( reactionsList[["annotation"]]))
+ if (nchar(annot) > 0) {
+ hasAnnot <- TRUE
+ pn <- regexpr("Pathway Name: [^<]+", annot, perl = TRUE)
+ subSys[i] <- substr(annot, (pn+14), pn + ((attr(pn, "match.length"))-1))
}
}
-
-
-
+
+
+
+ # get flux balance constraints, if fbcgprRules not null
fbcgene_rule <- NA
if ( !is.null(fbcgprRules))
{
+ # get the unique gene names and the rule with the x[gene number] codes:
fbcgene_rule<- sybil:::.parseBoolean(fbcgprRules[i])
genes[[i]] <- fbcgene_rule$gene # list of genes
@@ -549,12 +583,15 @@ for (i in 1 : numreact) {
gpr[i] <- fbcgprRules[i]
}
+
+
# Check here if reactants and products lists exist, same for the stoichiometry slot
# Entries for S -- the reactants
- S_tmp <- entryforS(reactionsList[["reactants"]][[i]])
+ S_tmp <- entryforS(reactionsList[["reactants"]][[i]])# todo: have to give i and met_id_tmp as argument, right now they are global (confusing)
#print(S_tmp)
if (is.list(S_tmp) == TRUE) {
+ # set stoichiometric matrix, values are set negative (reactants)
St[S_tmp$sj, i] <- (S_tmp$s_ji * -1)
#St[S_tmp$sj, S_tmp$si] <- (S_tmp$s_ji * -1)
}
@@ -638,10 +675,10 @@ for (i in 1 : numreact) {
}
}
#FBC Objective @Ardalan Habil
- if(!is.null(fbcObjectives))
- {
+ if(!is.null(fbcObjectives))
+ {
ocof[i]<-as.numeric(fbcObjectives[i])
- }
+ }
}
@@ -649,6 +686,8 @@ for (i in 1 : numreact) {
# get subsystem properties from the sbml groups plugin
subSysGroups <- getSBMLGroupsList(sbmlmod)
+
+
# ---------------------------------------------------------------------------- #
# search for unused metabolites and unused reactions
@@ -699,6 +738,7 @@ if ( any(SKIP_REACTION == FALSE) ) {
warning(msg, call. = FALSE)
}
+# if we do not want to remove, mark them as to skip
if (!isTRUE(remUnusedMetReact)) {
SKIP_METABOLITE[!SKIP_METABOLITE] <- TRUE
SKIP_REACTION[!SKIP_REACTION] <- TRUE
@@ -867,6 +907,7 @@ if (isTRUE(deadEndMet)) {
# ---------------------------------------------------------------------------- #
# S
+# only keep metabolites and reactions where SKIP mark is TRUE, remove the rest
St <- St[SKIP_METABOLITE, , drop = FALSE]
St <- St[ , SKIP_REACTION, drop = FALSE]
@@ -925,33 +966,36 @@ if (isTRUE(ignoreNoAn)) {
sybil::subSys(mod) <- Matrix::Matrix(FALSE, nrow = numreact, ncol = 1, sparse = TRUE)
}
else {
-
subSys <- subSys[SKIP_REACTION]
genes <- genes[SKIP_REACTION]
rules <- rules[SKIP_REACTION]
gpr <- gpr[SKIP_REACTION]
-
+
+ # if there were fbcgprRules or notes with gpr rules,
+ # create reaction x nGene matrix, with TRUE for respective genes for each reaction
if (isTRUE(hasNotes) || !is.null(fbcgprRules) ) {
message("GPR mapping ... ", appendLF = FALSE)
+ # Vector with all gene names != "":
#allGenes <- unique(allGenes)
#allGenesTMP <- unique(allGenes)
allGenesTMP <- unique(unlist(genes))
temp <- nchar(allGenesTMP)
allGenes <- allGenesTMP[which(temp != 0)]
-
rxnGeneMat <- Matrix::Matrix(FALSE,
nrow = numreact,
ncol = length(allGenes),
sparse = TRUE)
for (i in 1 : numreact) {
-
+ # if genes list element i has only 1 element and that element is not equal ""
if ( (length(genes[[i]] == 1)) && (genes[[i]] != "") ) {
- geneInd <- match(genes[[i]], allGenes)
+ geneInd <- match(genes[[i]], allGenes)# find gene in allGenes
+ # Mark which genes are used in reaction with TRUE
rxnGeneMat[i, geneInd] <- TRUE
+ # exchange x(j) with x[j] for each gene index:
for (j in 1 : length(geneInd)) {
pat <- paste("x(", j, ")", sep = "")
repl <- paste("x[", geneInd[j], "]", sep = "")
@@ -961,6 +1005,7 @@ else {
}
}
+ #
sybil::genes(mod) <- genes
sybil::gpr(mod) <- gpr
sybil::allGenes(mod) <- allGenes
@@ -979,13 +1024,15 @@ else {
message("OK")
}
- else {
+ else {# no notes and no fbcgprRules:
sybil::rxnGeneMat(mod) <- Matrix::Matrix(NA, nrow = 0, ncol = 0)
if (isTRUE(hasAnnot)) {
+ # then we extracted the subsystem from annotation, so set it:
#subSys(sbml) <- subSys
sybil::subSys(mod) <- sybil:::.prepareSubSysMatrix(subSys, numreact)
}
else {
+ # No subsystems:
sybil::subSys(mod) <- Matrix::Matrix(FALSE,
nrow = numreact,
ncol = 1,
@@ -1050,6 +1097,7 @@ if(newSybil)
#------------------------------------------------------------------------------#
if(!is.null(subSysGroups)){
+ # sub system groups for each reaction from subSysGroups:
subSysMat <- Matrix::Matrix(FALSE, nrow = numreact, ncol = length(subSysGroups), sparse = TRUE)
colnames(subSysMat) <- names(subSysGroups)
@@ -1072,6 +1120,7 @@ modanno<-getSBMLmodAnnotation(sbmlmod)
modnotes<-getSBMLmodNotes(sbmlmod)
if(newSybil)
{
+ # set model annotation and notes:
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
@@ -1082,6 +1131,7 @@ if(newSybil)
#------------------------------------------------------------------------------#
# compartments Attr @Ardalan #
#------------------------------------------------------------------------------#
+# set comp_attr slot for model with 'annotation' and 'notes' from values in compartmentsList:
# 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)
@@ -1165,29 +1215,38 @@ 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}
+ {
+ sybil::met_attr(mod)[['chemicalFormula']]<-metformula
+ }
else{
if(length(metformulanote)==nummet)
- { if(max(nchar(metformulanote)) >0)
- sybil::met_attr(mod)[['chemicalFormula']]<-metformulanote
+ {
+ 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}
+ {
+ sybil::met_attr(mod)[['charge']]<-metcharge
+ }
else{
if( length(metchargenote)==nummet)
- { if(max(nchar(metchargenote)) >0)
- sybil::met_attr(mod)[['charge']]<-metchargenote
+ {
+ 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
+ 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
+ if( !is.null(metBnd) && length(metBnd)==nummet && !all(metBnd == FALSE) )
+ sybil::met_attr(mod)[['boundaryCondition']]<-metBnd
}
diff --git a/R/sbmlPtrClass.R b/R/sbmlPtrClass.R
index 81931e8..70e2b91 100644
--- a/R/sbmlPtrClass.R
+++ b/R/sbmlPtrClass.R
@@ -60,7 +60,7 @@ setMethod(f = "initialize",
)
-# contructor for pointers to sbml documents
+# constructor for pointers to sbml documents
sbmlDocPointer <- function(pointer) {
if (is(pointer, "sbml_doc_ptr")) {
diff --git a/R/sybilSBML.R b/R/sybilSBML.R
index 0b6dc6d..12c0a0a 100644
--- a/R/sybilSBML.R
+++ b/R/sybilSBML.R
@@ -346,6 +346,16 @@ writeSBML<- function(morg=NULL,level=2,version=4,fbcLevel=0,filename="export.xml
stop("morg has to be of class modelorg\n")
}
+ # warning, if FBC plugin is missing:
+ if (isAvailableFbcPlugin() == FALSE) {
+ warning("Missing FBC-plugin for libSBML. No SBML output will be written.")
+ }
+
+ # warning, if Groups plugin is missing:
+ if (isAvailableGroupsPlugin() == FALSE) {
+ warning("Missing Groups-plugin for libSBML. No SBML output will be written.")
+ }
+
###right
if(level==1)
{
@@ -643,3 +653,27 @@ writeSBML<- function(morg=NULL,level=2,version=4,fbcLevel=0,filename="export.xml
else message(paste("Could not write file ",filename,"\n",sep=""), appendLF = FALSE);
return (success)
}
+
+
+
+#------------------------------------------------------------------------------#
+
+isAvailableFbcPlugin <- function() {
+
+ avail <- .Call("isAvailableFbcPlugin", PACKAGE = "sybilSBML"
+ )
+
+ return(avail)
+}
+
+
+
+#------------------------------------------------------------------------------#
+
+isAvailableGroupsPlugin <- function() {
+
+ avail <- .Call("isAvailableGroupsPlugin", PACKAGE = "sybilSBML"
+ )
+
+ return(avail)
+}
diff --git a/build/vignette.rds b/build/vignette.rds
index 217b014b3aaa3d2181c33fc96a7045116045540b..1ff49c7676081ca7e745c1f7bfd0056761ffa96c 100644
GIT binary patch
delta 38
qcmcb~c#~07zMF#q44AtgBqbyyBqgM!rA-vw!{K<6@5gaQ1_l7q8w;WU
delta 38
qcmcb~c#~07zMF#q44AtgBqbyyBqgM!q)Zgu!?9iP0oQRx1_l7o(+fZV
diff --git a/configure b/configure
index a6d881c..331c6a4 100755
--- a/configure
+++ b/configure
@@ -1,6 +1,6 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for sybilSBML 3.0.6.
+# Generated by GNU Autoconf 2.69 for sybilSBML 3.0.7.
#
# Report bugs to <mayo.roettger@hhu.de>.
#
@@ -580,8 +580,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='sybilSBML'
PACKAGE_TARNAME='sybilsbml'
-PACKAGE_VERSION='3.0.6'
-PACKAGE_STRING='sybilSBML 3.0.6'
+PACKAGE_VERSION='3.0.7'
+PACKAGE_STRING='sybilSBML 3.0.7'
PACKAGE_BUGREPORT='mayo.roettger@hhu.de'
PACKAGE_URL=''
@@ -1241,7 +1241,7 @@ 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 3.0.6 to adapt to many kinds of systems.
+\`configure' configures sybilSBML 3.0.7 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1303,7 +1303,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of sybilSBML 3.0.6:";;
+ short | recursive ) echo "Configuration of sybilSBML 3.0.7:";;
esac
cat <<\_ACEOF
@@ -1390,7 +1390,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-sybilSBML configure 3.0.6
+sybilSBML configure 3.0.7
generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1759,7 +1759,7 @@ 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 3.0.6, which was
+It was created by sybilSBML $as_me 3.0.7, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
@@ -3050,6 +3050,8 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
+ac_config_headers="$ac_config_headers src/config.h"
+
@@ -3655,26 +3657,44 @@ else
fi
-ac_fn_c_check_header_compile "$LINENO" "sbml/packages/fbc/common/FbcExtensionTypes.h" "ac_cv_header_sbml_packages_fbc_common_FbcExtensionTypes_h" "#include <sbml/SBMLTypes.h>
+for ac_header in sbml/packages/fbc/common/FbcExtensionTypes.h
+do :
+ 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 :
+ cat >>confdefs.h <<_ACEOF
+#define HAVE_SBML_PACKAGES_FBC_COMMON_FBCEXTENSIONTYPES_H 1
+_ACEOF
else
- as_fn_error $? "Could not find specific FBC header of libSBML:
- make sure your libSBML version is >= 5.16 and including the FBC package." "$LINENO" 5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: Could not find specific FBC header of libSBML:
+ make sure your libSBML version is >= 5.18 and including the FBC package." >&5
+$as_echo "$as_me: WARNING: Could not find specific FBC header of libSBML:
+ make sure your libSBML version is >= 5.18 and including the FBC package." >&2;}
fi
+done
-ac_fn_c_check_header_compile "$LINENO" "sbml/packages/groups/common/GroupsExtensionTypes.h" "ac_cv_header_sbml_packages_groups_common_GroupsExtensionTypes_h" "#include <sbml/SBMLTypes.h>
+for ac_header in sbml/packages/groups/common/GroupsExtensionTypes.h
+do :
+ ac_fn_c_check_header_compile "$LINENO" "sbml/packages/groups/common/GroupsExtensionTypes.h" "ac_cv_header_sbml_packages_groups_common_GroupsExtensionTypes_h" "#include <sbml/SBMLTypes.h>
"
if test "x$ac_cv_header_sbml_packages_groups_common_GroupsExtensionTypes_h" = xyes; then :
+ cat >>confdefs.h <<_ACEOF
+#define HAVE_SBML_PACKAGES_GROUPS_COMMON_GROUPSEXTENSIONTYPES_H 1
+_ACEOF
+
+$as_echo "#define HAVE_GROUPS_PLUGIN 1" >>confdefs.h
else
- as_fn_error $? "Could not find specific groups package header of libSBML:
- make sure your libSBML version is >= 5.16 and including the groups package." "$LINENO" 5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: Could not find specific groups package header of libSBML:
+ make sure your libSBML version is >= 5.18 and including the groups package." >&5
+$as_echo "$as_me: WARNING: Could not find specific groups package header of libSBML:
+ make sure your libSBML version is >= 5.18 and including the groups package." >&2;}
fi
+done
#AC_CHECK_LIB([sbml], [SBMLExtensionRegistry_getRegisteredPackages], ,
@@ -3690,9 +3710,13 @@ if eval test \"x\$"$as_ac_var"\" = x"yes"; then :
#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1
_ACEOF
+$as_echo "#define HAVE_FBC_PLUGIN 1" >>confdefs.h
+
else
- as_fn_error $? "Could not find specific FBC function of libSBML:
- make sure your libSBML version is >= 5.16 and including the FBC package." "$LINENO" 5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: Could not find specific FBC function of libSBML:
+ make sure your libSBML version is >= 5.18 and including the FBC package." >&5
+$as_echo "$as_me: WARNING: Could not find specific FBC function of libSBML:
+ make sure your libSBML version is >= 5.18 and including the FBC package." >&2;}
fi
done
@@ -3809,43 +3833,7 @@ test "x$prefix" = xNONE && prefix=$ac_default_prefix
# Let make expand exec_prefix.
test "x$exec_prefix" = xNONE && exec_prefix='${prefix}'
-# Transform confdefs.h into DEFS.
-# Protect against shell expansion while executing Makefile rules.
-# Protect against Makefile macro expansion.
-#
-# If the first sed substitution is executed (which looks for macros that
-# take arguments), then branch to the quote section. Otherwise,
-# look for a macro that doesn't take arguments.
-ac_script='
-:mline
-/\\$/{
- N
- s,\\\n,,
- b mline
-}
-t clear
-:clear
-s/^[ ]*#[ ]*define[ ][ ]*\([^ (][^ (]*([^)]*)\)[ ]*\(.*\)/-D\1=\2/g
-t quote
-s/^[ ]*#[ ]*define[ ][ ]*\([^ ][^ ]*\)[ ]*\(.*\)/-D\1=\2/g
-t quote
-b any
-:quote
-s/[ `~#$^&*(){}\\|;'\''"<>?]/\\&/g
-s/\[/\\&/g
-s/\]/\\&/g
-s/\$/$$/g
-H
-:any
-${
- g
- s/^\n//
- s/\n/ /g
- p
-}
-'
-DEFS=`sed -n "$ac_script" confdefs.h`
-
+DEFS=-DHAVE_CONFIG_H
ac_libobjs=
ac_ltlibobjs=
@@ -4261,7 +4249,7 @@ 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 3.0.6, which was
+This file was extended by sybilSBML $as_me 3.0.7, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -4279,11 +4267,15 @@ case $ac_config_files in *"
"*) set x $ac_config_files; shift; ac_config_files=$*;;
esac
+case $ac_config_headers in *"
+"*) set x $ac_config_headers; shift; ac_config_headers=$*;;
+esac
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
# Files that config.status was made for.
config_files="$ac_config_files"
+config_headers="$ac_config_headers"
_ACEOF
@@ -4304,17 +4296,22 @@ Usage: $0 [OPTION]... [TAG]...
--recheck update $as_me by reconfiguring in the same conditions
--file=FILE[:TEMPLATE]
instantiate the configuration file FILE
+ --header=FILE[:TEMPLATE]
+ instantiate the configuration header FILE
Configuration files:
$config_files
+Configuration headers:
+$config_headers
+
Report bugs to <mayo.roettger@hhu.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 3.0.6
+sybilSBML config.status 3.0.7
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
@@ -4368,7 +4365,18 @@ do
esac
as_fn_append CONFIG_FILES " '$ac_optarg'"
ac_need_defaults=false;;
- --he | --h | --help | --hel | -h )
+ --header | --heade | --head | --hea )
+ $ac_shift
+ case $ac_optarg in
+ *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ esac
+ as_fn_append CONFIG_HEADERS " '$ac_optarg'"
+ ac_need_defaults=false;;
+ --he | --h)
+ # Conflict between --help and --header
+ as_fn_error $? "ambiguous option: \`$1'
+Try \`$0 --help' for more information.";;
+ --help | --hel | -h )
$as_echo "$ac_cs_usage"; exit ;;
-q | -quiet | --quiet | --quie | --qui | --qu | --q \
| -silent | --silent | --silen | --sile | --sil | --si | --s)
@@ -4424,6 +4432,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
for ac_config_target in $ac_config_targets
do
case $ac_config_target in
+ "src/config.h") CONFIG_HEADERS="$CONFIG_HEADERS src/config.h" ;;
"src/Makevars") CONFIG_FILES="$CONFIG_FILES src/Makevars" ;;
*) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5;;
@@ -4437,6 +4446,7 @@ done
# bizarre bug on SunOS 4.1.3.
if $ac_need_defaults; then
test "${CONFIG_FILES+set}" = set || CONFIG_FILES=$config_files
+ test "${CONFIG_HEADERS+set}" = set || CONFIG_HEADERS=$config_headers
fi
# Have a temporary directory for convenience. Make it in the build tree
@@ -4624,8 +4634,116 @@ fi
cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
fi # test -n "$CONFIG_FILES"
+# Set up the scripts for CONFIG_HEADERS section.
+# No need to generate them if there are no CONFIG_HEADERS.
+# This happens for instance with `./config.status Makefile'.
+if test -n "$CONFIG_HEADERS"; then
+cat >"$ac_tmp/defines.awk" <<\_ACAWK ||
+BEGIN {
+_ACEOF
+
+# Transform confdefs.h into an awk script `defines.awk', embedded as
+# here-document in config.status, that substitutes the proper values into
+# config.h.in to produce config.h.
+
+# Create a delimiter string that does not exist in confdefs.h, to ease
+# handling of long lines.
+ac_delim='%!_!# '
+for ac_last_try in false false :; do
+ ac_tt=`sed -n "/$ac_delim/p" confdefs.h`
+ if test -z "$ac_tt"; then
+ break
+ elif $ac_last_try; then
+ as_fn_error $? "could not make $CONFIG_HEADERS" "$LINENO" 5
+ else
+ ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
+ fi
+done
+
+# For the awk script, D is an array of macro values keyed by name,
+# likewise P contains macro parameters if any. Preserve backslash
+# newline sequences.
+
+ac_word_re=[_$as_cr_Letters][_$as_cr_alnum]*
+sed -n '
+s/.\{148\}/&'"$ac_delim"'/g
+t rset
+:rset
+s/^[ ]*#[ ]*define[ ][ ]*/ /
+t def
+d
+:def
+s/\\$//
+t bsnl
+s/["\\]/\\&/g
+s/^ \('"$ac_word_re"'\)\(([^()]*)\)[ ]*\(.*\)/P["\1"]="\2"\
+D["\1"]=" \3"/p
+s/^ \('"$ac_word_re"'\)[ ]*\(.*\)/D["\1"]=" \2"/p
+d
+:bsnl
+s/["\\]/\\&/g
+s/^ \('"$ac_word_re"'\)\(([^()]*)\)[ ]*\(.*\)/P["\1"]="\2"\
+D["\1"]=" \3\\\\\\n"\\/p
+t cont
+s/^ \('"$ac_word_re"'\)[ ]*\(.*\)/D["\1"]=" \2\\\\\\n"\\/p
+t cont
+d
+:cont
+n
+s/.\{148\}/&'"$ac_delim"'/g
+t clear
+:clear
+s/\\$//
+t bsnlc
+s/["\\]/\\&/g; s/^/"/; s/$/"/p
+d
+:bsnlc
+s/["\\]/\\&/g; s/^/"/; s/$/\\\\\\n"\\/p
+b cont
+' <confdefs.h | sed '
+s/'"$ac_delim"'/"\\\
+"/g' >>$CONFIG_STATUS || ac_write_fail=1
+
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ for (key in D) D_is_set[key] = 1
+ FS = ""
+}
+/^[\t ]*#[\t ]*(define|undef)[\t ]+$ac_word_re([\t (]|\$)/ {
+ line = \$ 0
+ split(line, arg, " ")
+ if (arg[1] == "#") {
+ defundef = arg[2]
+ mac1 = arg[3]
+ } else {
+ defundef = substr(arg[1], 2)
+ mac1 = arg[2]
+ }
+ split(mac1, mac2, "(") #)
+ macro = mac2[1]
+ prefix = substr(line, 1, index(line, defundef) - 1)
+ if (D_is_set[macro]) {
+ # Preserve the white space surrounding the "#".
+ print prefix "define", macro P[macro] D[macro]
+ next
+ } else {
+ # Replace #undef with comments. This is necessary, for example,
+ # in the case of _POSIX_SOURCE, which is predefined and required
+ # on some systems where configure will not decide to define it.
+ if (defundef == "undef") {
+ print "/*", prefix defundef, macro, "*/"
+ next
+ }
+ }
+}
+{ print }
+_ACAWK
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+ as_fn_error $? "could not setup config headers machinery" "$LINENO" 5
+fi # test -n "$CONFIG_HEADERS"
+
-eval set X " :F $CONFIG_FILES "
+eval set X " :F $CONFIG_FILES :H $CONFIG_HEADERS "
shift
for ac_tag
do
@@ -4833,7 +4951,30 @@ which seems to be undefined. Please make sure it is defined" >&2;}
esac \
|| as_fn_error $? "could not create $ac_file" "$LINENO" 5
;;
-
+ :H)
+ #
+ # CONFIG_HEADER
+ #
+ if test x"$ac_file" != x-; then
+ {
+ $as_echo "/* $configure_input */" \
+ && eval '$AWK -f "$ac_tmp/defines.awk"' "$ac_file_inputs"
+ } >"$ac_tmp/config.h" \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+ if diff "$ac_file" "$ac_tmp/config.h" >/dev/null 2>&1; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: $ac_file is unchanged" >&5
+$as_echo "$as_me: $ac_file is unchanged" >&6;}
+ else
+ rm -f "$ac_file"
+ mv "$ac_tmp/config.h" "$ac_file" \
+ || as_fn_error $? "could not create $ac_file" "$LINENO" 5
+ fi
+ else
+ $as_echo "/* $configure_input */" \
+ && eval '$AWK -f "$ac_tmp/defines.awk"' "$ac_file_inputs" \
+ || as_fn_error $? "could not create -" "$LINENO" 5
+ fi
+ ;;
esac
diff --git a/configure.ac b/configure.ac
index da399d0..b063948 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,4 +1,4 @@
-AC_INIT([sybilSBML], [3.0.6], [mayo.roettger@hhu.de])
+AC_INIT([sybilSBML], [3.0.7], [mayo.roettger@hhu.de])
dnl # --------------------------------------------------------------------
dnl # global (environment) variables
@@ -32,7 +32,7 @@ dnl # --------------------------------------------------------------------
dnl # template config.h.in
dnl # --------------------------------------------------------------------
-dnl # AC_CONFIG_HEADERS([src/config.h])
+AC_CONFIG_HEADERS([src/config.h])
dnl # --------------------------------------------------------------------
@@ -239,23 +239,23 @@ 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 >= 5.16 and including the FBC package.]),
+AC_CHECK_HEADERS([sbml/packages/fbc/common/FbcExtensionTypes.h], ,
+ AC_MSG_WARN([Could not find specific FBC header of libSBML:
+ make sure your libSBML version is >= 5.18 and including the FBC package.]),
[#include <sbml/SBMLTypes.h>])
-AC_CHECK_HEADER([sbml/packages/groups/common/GroupsExtensionTypes.h], ,
- AC_MSG_ERROR([Could not find specific groups package header of libSBML:
- make sure your libSBML version is >= 5.16 and including the groups package.]),
+AC_CHECK_HEADERS([sbml/packages/groups/common/GroupsExtensionTypes.h], AC_DEFINE([HAVE_GROUPS_PLUGIN], [1], [define if Groups plugin is available]),
+ AC_MSG_WARN([Could not find specific groups package header of libSBML:
+ make sure your libSBML version is >= 5.18 and including the groups package.]),
[#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 >= 5.16.]))
-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 >= 5.16 and including the FBC package.]))
+AC_CHECK_FUNCS([SBase_getPlugin SBMLExtensionRegistry_getRegisteredPackages GeneProductAssociation_setAssociation FbcReactionPlugin_getLowerFluxBound], AC_DEFINE([HAVE_FBC_PLUGIN], [1], [define if FBC plugin is available]),
+ AC_MSG_WARN([Could not find specific FBC function of libSBML:
+ make sure your libSBML version is >= 5.18 and including the FBC package.]))
#AC_SEARCH_LIBS([SBase_getPlugin], [sbml], ,
# AC_MSG_ERROR([Could not find specific FBC function of libSBML:
diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
index 4aa76fe..06c5ee4 100644
--- a/inst/NEWS.Rd
+++ b/inst/NEWS.Rd
@@ -6,6 +6,16 @@
\newcommand{\CRANpkg}{\href{https://cran.r-project.org/package=#1}{\pkg{#1}}}
% ---------------------------------------------------------------------------- %
+\section{Changes in version 3.0.4 - 3.0.7 2019-08-02}{
+ \itemize{
+ \item Maintainer change.
+ \item Changes to be able to build package without libSBML FBC and Groups
+ plugins. In that case, FBC-constraints and groups in the SBML model will
+ be ignored. Added functions \code{isAvailableFBCPlugin} and
+ \code{isAvailableGroupsPlugin}.
+ }
+}
+% ---------------------------------------------------------------------------- %
\section{Changes in version 3.0.3 2018-01-02}{
\itemize{
\item Added support for the groups plugin of SBML. Now the \code{subSys}
diff --git a/man/getSBMLReactionsList.Rd b/man/getSBMLReactionsList.Rd
index 268e9bf..9461121 100644
--- a/man/getSBMLReactionsList.Rd
+++ b/man/getSBMLReactionsList.Rd
@@ -6,7 +6,15 @@
}
\description{
- Retrieve list of reactions included in a SBML model
+ Retrieve list of reactions included in a SBML model.
+
+ If sybilSBML was built with a libSBML version, that was not including the FBC plugin,
+ FBC constraints are ignored. Please make sure that you build sybilSBML with the
+ libSBML version containing the FBC plugin (check out installation details).
+
+ If sybilSBML was built with a libSBML version, that was not including the Groups plugin,
+ Groups are ignored. Please make sure that you build sybilSBML with the
+ libSBML version containing the Groups plugin (check out installation details).
}
\usage{
getSBMLReactionsList(sbmlm)
diff --git a/man/getSBMLSpeciesList.Rd b/man/getSBMLSpeciesList.Rd
index d9781a1..e12b983 100644
--- a/man/getSBMLSpeciesList.Rd
+++ b/man/getSBMLSpeciesList.Rd
@@ -6,7 +6,15 @@
}
\description{
- Retrieve list of species included in a SBML model
+ Retrieve list of species included in a SBML model.
+
+ If sybilSBML was built with a libSBML version, that was not including the FBC plugin,
+ FBC constraints are ignored. Please make sure that you build sybilSBML with the
+ libSBML version containing the FBC plugin (check out installation details).
+
+ If sybilSBML was built with a libSBML version, that was not including the Groups plugin,
+ Groups are ignored. Please make sure that you build sybilSBML with the
+ libSBML version containing the Groups plugin (check out installation details).
}
\usage{
diff --git a/man/isAvailableFbcPlugin.Rd b/man/isAvailableFbcPlugin.Rd
new file mode 100644
index 0000000..c9c843a
--- /dev/null
+++ b/man/isAvailableFbcPlugin.Rd
@@ -0,0 +1,27 @@
+\name{isAvailableFbcPlugin}
+\alias{isAvailableFbcPlugin}
+
+\title{
+ Check for libSBML FBC plugin
+}
+
+\description{
+ Check, if sybilSBML was built with libSBML containing the FBC plugin.
+}
+
+\usage{
+ isAvailableFbcPlugin()
+}
+
+\value{
+ A single boolean value for the availability of the FBC plugin.
+}
+
+\author{
+ Mayo Roettger <mayo.roettger@hhu.de>
+
+ Maintainer: Mayo Roettger <mayo.roettger@hhu.de>
+}
+
+
+\keyword{ IO }
diff --git a/man/isAvailableGroupsPlugin.Rd b/man/isAvailableGroupsPlugin.Rd
new file mode 100644
index 0000000..22ec90f
--- /dev/null
+++ b/man/isAvailableGroupsPlugin.Rd
@@ -0,0 +1,27 @@
+\name{isAvailableGroupsPlugin}
+\alias{isAvailableGroupsPlugin}
+
+\title{
+ Check for libSBML Groups plugin
+}
+
+\description{
+ Check, if sybilSBML was built with libSBML containing the Groups plugin.
+}
+
+\usage{
+ isAvailableFbcPlugin()
+}
+
+\value{
+ A single boolean value for the availability of the Groups plugin.
+}
+
+\author{
+ Mayo Roettger <mayo.roettger@hhu.de>
+
+ Maintainer: Mayo Roettger <mayo.roettger@hhu.de>
+}
+
+
+\keyword{ IO }
diff --git a/man/writeSBML.Rd b/man/writeSBML.Rd
index caef946..268d20f 100644
--- a/man/writeSBML.Rd
+++ b/man/writeSBML.Rd
@@ -61,11 +61,15 @@
\details{
The library \code{libSBML} is used to export a \code{\link[sybil]{modelorg}}
to a SBML file.
-
+
+ If sybilSBML was built with a libSBML version, that was not including the FBC plugin
+ and the Groups plugin, the function is not writing an output file and returns FALSE.
+ Please make sure that you build sybilSBML with the libSBML version containing the
+ FBC and Group plugins (check out installation details).
}
\value{
- A single boolean value for a successful export .
+ A single boolean value for a successful export.
}
\references{
diff --git a/src/Makevars b/src/Makevars
new file mode 100644
index 0000000..5838658
--- /dev/null
+++ b/src/Makevars
@@ -0,0 +1,3 @@
+PKG_CFLAGS=
+PKG_CPPFLAGS=-I/usr/include -I/usr/local/include -I/usr/include/sbml -I/usr/local/include/sbml
+PKG_LIBS= -L/usr/local/lib -L/usr/lib -L/usr/lib64 -lsbml
diff --git a/src/config.h b/src/config.h
new file mode 100644
index 0000000..6042341
--- /dev/null
+++ b/src/config.h
@@ -0,0 +1,82 @@
+/* src/config.h. Generated from config.h.in by configure. */
+/* src/config.h.in. Generated from configure.ac by autoheader. */
+
+/* Define to 1 if you have the `FbcReactionPlugin_getLowerFluxBound' function.
+ */
+#define HAVE_FBCREACTIONPLUGIN_GETLOWERFLUXBOUND 1
+
+/* define if FBC plugin is available */
+#define HAVE_FBC_PLUGIN 1
+
+/* Define to 1 if you have the `GeneProductAssociation_setAssociation'
+ function. */
+#define HAVE_GENEPRODUCTASSOCIATION_SETASSOCIATION 1
+
+/* define if Groups plugin is available */
+#define HAVE_GROUPS_PLUGIN 1
+
+/* Define to 1 if you have the <inttypes.h> header file. */
+#define HAVE_INTTYPES_H 1
+
+/* Define to 1 if you have the `sbml' library (-lsbml). */
+#define HAVE_LIBSBML 1
+
+/* Define to 1 if you have the <memory.h> header file. */
+#define HAVE_MEMORY_H 1
+
+/* Define to 1 if you have the `SBase_getPlugin' function. */
+#define HAVE_SBASE_GETPLUGIN 1
+
+/* Define to 1 if you have the `SBMLExtensionRegistry_getRegisteredPackages'
+ function. */
+#define HAVE_SBMLEXTENSIONREGISTRY_GETREGISTEREDPACKAGES 1
+
+/* Define to 1 if you have the <sbml/packages/fbc/common/FbcExtensionTypes.h>
+ header file. */
+#define HAVE_SBML_PACKAGES_FBC_COMMON_FBCEXTENSIONTYPES_H 1
+
+/* Define to 1 if you have the
+ <sbml/packages/groups/common/GroupsExtensionTypes.h> header file. */
+#define HAVE_SBML_PACKAGES_GROUPS_COMMON_GROUPSEXTENSIONTYPES_H 1
+
+/* Define to 1 if you have the <stdint.h> header file. */
+#define HAVE_STDINT_H 1
+
+/* Define to 1 if you have the <stdlib.h> header file. */
+#define HAVE_STDLIB_H 1
+
+/* Define to 1 if you have the <strings.h> header file. */
+#define HAVE_STRINGS_H 1
+
+/* Define to 1 if you have the <string.h> header file. */
+#define HAVE_STRING_H 1
+
+/* Define to 1 if you have the <sys/stat.h> header file. */
+#define HAVE_SYS_STAT_H 1
+
+/* Define to 1 if you have the <sys/types.h> header file. */
+#define HAVE_SYS_TYPES_H 1
+
+/* Define to 1 if you have the <unistd.h> header file. */
+#define HAVE_UNISTD_H 1
+
+/* Define to the address where bug reports for this package should be sent. */
+#define PACKAGE_BUGREPORT "mayo.roettger@hhu.de"
+
+/* Define to the full name of this package. */
+#define PACKAGE_NAME "sybilSBML"
+
+/* Define to the full name and version of this package. */
+#define PACKAGE_STRING "sybilSBML 3.0.6"
+
+/* Define to the one symbol short name of this package. */
+#define PACKAGE_TARNAME "sybilsbml"
+
+/* Define to the home page for this package. */
+#define PACKAGE_URL ""
+
+/* Define to the version of this package. */
+#define PACKAGE_VERSION "3.0.6"
+
+/* Define to 1 if you have the ANSI C header files. */
+#define STDC_HEADERS 1
diff --git a/src/config.h.in b/src/config.h.in
new file mode 100644
index 0000000..099e987
--- /dev/null
+++ b/src/config.h.in
@@ -0,0 +1,81 @@
+/* src/config.h.in. Generated from configure.ac by autoheader. */
+
+/* Define to 1 if you have the `FbcReactionPlugin_getLowerFluxBound' function.
+ */
+#undef HAVE_FBCREACTIONPLUGIN_GETLOWERFLUXBOUND
+
+/* define if FBC plugin is available */
+#undef HAVE_FBC_PLUGIN
+
+/* Define to 1 if you have the `GeneProductAssociation_setAssociation'
+ function. */
+#undef HAVE_GENEPRODUCTASSOCIATION_SETASSOCIATION
+
+/* define if Groups plugin is available */
+#undef HAVE_GROUPS_PLUGIN
+
+/* Define to 1 if you have the <inttypes.h> header file. */
+#undef HAVE_INTTYPES_H
+
+/* Define to 1 if you have the `sbml' library (-lsbml). */
+#undef HAVE_LIBSBML
+
+/* Define to 1 if you have the <memory.h> header file. */
+#undef HAVE_MEMORY_H
+
+/* Define to 1 if you have the `SBase_getPlugin' function. */
+#undef HAVE_SBASE_GETPLUGIN
+
+/* Define to 1 if you have the `SBMLExtensionRegistry_getRegisteredPackages'
+ function. */
+#undef HAVE_SBMLEXTENSIONREGISTRY_GETREGISTEREDPACKAGES
+
+/* Define to 1 if you have the <sbml/packages/fbc/common/FbcExtensionTypes.h>
+ header file. */
+#undef HAVE_SBML_PACKAGES_FBC_COMMON_FBCEXTENSIONTYPES_H
+
+/* Define to 1 if you have the
+ <sbml/packages/groups/common/GroupsExtensionTypes.h> header file. */
+#undef HAVE_SBML_PACKAGES_GROUPS_COMMON_GROUPSEXTENSIONTYPES_H
+
+/* Define to 1 if you have the <stdint.h> header file. */
+#undef HAVE_STDINT_H
+
+/* Define to 1 if you have the <stdlib.h> header file. */
+#undef HAVE_STDLIB_H
+
+/* Define to 1 if you have the <strings.h> header file. */
+#undef HAVE_STRINGS_H
+
+/* Define to 1 if you have the <string.h> header file. */
+#undef HAVE_STRING_H
+
+/* Define to 1 if you have the <sys/stat.h> header file. */
+#undef HAVE_SYS_STAT_H
+
+/* Define to 1 if you have the <sys/types.h> header file. */
+#undef HAVE_SYS_TYPES_H
+
+/* Define to 1 if you have the <unistd.h> header file. */
+#undef HAVE_UNISTD_H
+
+/* Define to the address where bug reports for this package should be sent. */
+#undef PACKAGE_BUGREPORT
+
+/* Define to the full name of this package. */
+#undef PACKAGE_NAME
+
+/* Define to the full name and version of this package. */
+#undef PACKAGE_STRING
+
+/* Define to the one symbol short name of this package. */
+#undef PACKAGE_TARNAME
+
+/* Define to the home page for this package. */
+#undef PACKAGE_URL
+
+/* Define to the version of this package. */
+#undef PACKAGE_VERSION
+
+/* Define to 1 if you have the ANSI C header files. */
+#undef STDC_HEADERS
diff --git a/src/init.c b/src/init.c
index ef92c06..89e831f 100644
--- a/src/init.c
+++ b/src/init.c
@@ -1,69 +1,71 @@
-/* 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},
- {"getSBMLGroupsList", (DL_FUNC) &getSBMLGroupsList, 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, 34},
- {"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);
-}
+/* 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},
+ {"getSBMLGroupsList", (DL_FUNC) &getSBMLGroupsList, 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, 34},
+ {"getSBMLFbcversion", (DL_FUNC) &getSBMLFbcversion, 1},
+ {"isAvailableFbcPlugin", (DL_FUNC) &isAvailableFbcPlugin, 0},
+ {"isAvailableGroupsPlugin", (DL_FUNC) &isAvailableGroupsPlugin, 0},
+ {NULL, NULL, 0}
+};
+
+
+/* -------------------------------------------------------------------------- */
+
+void R_init_sybilSBML(DllInfo *info) {
+ R_registerRoutines(info, NULL, callMethods, NULL, NULL);
+ R_useDynamicSymbols(info, FALSE);
+}
diff --git a/src/sbml.h b/src/sbml.h
index 4d3b9c9..d745e56 100644
--- a/src/sbml.h
+++ b/src/sbml.h
@@ -39,6 +39,9 @@
#include <R.h>
#include <Rinternals.h>
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif /* HAVE_CONFIG_H */
/* -------------------------------------------------------------------------- */
/* NULL */
diff --git a/src/sybilSBML.c b/src/sybilSBML.c
index 61b3d17..32e1b94 100644
--- a/src/sybilSBML.c
+++ b/src/sybilSBML.c
@@ -1,2365 +1,2424 @@
-/* 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>
-
-/*groups plugin*/
-#include <sbml/packages/groups/common/GroupsExtensionTypes.h>
-#include <sbml/packages/groups/extension/GroupsSBMLDocumentPlugin.h>
-#include <sbml/packages/groups/extension/GroupsExtension.h>
-#include <sbml/packages/groups/extension/GroupsModelPlugin.h>
-
-#include <sbml/packages/groups/sbml/Group.h>
-#include <sbml/packages/groups/sbml/ListOfGroups.h>
-#include <sbml/packages/groups/sbml/ListOfMembers.h>
-#include <sbml/packages/groups/sbml/Member.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;
-}
-
-
-SEXP getSBMLGroupsList(SEXP sbmlmod) {
- GroupsModelPlugin_t * modelPlug = NULL;
- modelPlug = (GroupsModelPlugin_t *) SBase_getPlugin((SBase_t *)(R_ExternalPtrAddr(sbmlmod)), "groups");
-
- if(modelPlug != NULL){
- int n = GroupsModelPlugin_getNumGroups(modelPlug);
- SEXP rgroups = PROTECT(Rf_allocVector(VECSXP, n));
- SEXP groupnames = PROTECT(Rf_allocVector(STRSXP, n));
- for(int i=0; i<n; i++){
- Group_t* group = GroupsModelPlugin_getGroup(modelPlug, i);
- if(Group_isSetName(group) == 1){ // skip group if no name is set
- SET_STRING_ELT(groupnames, i, Rf_mkChar(Group_getName(group)));
-
- int m = Group_getNumMembers(group);
- SEXP rmembers = PROTECT(Rf_allocVector(STRSXP, m));
- for(int j=0; j < m; j++){
- Member_t * member = Group_getMember(group, j);
- char * memref = Member_getIdRef(member);
- SET_STRING_ELT(rmembers, j, Rf_mkChar(memref));
- }
- SET_VECTOR_ELT(rgroups, i, rmembers);
- UNPROTECT(1);
- }else{
- SET_VECTOR_ELT(rgroups, i, R_NilValue);
- }
- }
- Rf_namesgets(rgroups, groupnames);
- UNPROTECT(2);
- return rgroups;
- }else{
- return R_NilValue;
- }
- return R_NilValue;
-}
-
-/* -------------------------------------------------------------------------- */
-/* 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 subSysGroups, 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];
- int SBMLgroupsversion = 1;
- 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 */
- XMLNamespaces_t * fbc = XMLNamespaces_create();
- XMLNamespaces_add(fbc, SBMLExtension_getURI(sbmlext, 3, 1, SBMLfbcversion), "fbc");
-
- sbmlns = SBMLNamespaces_create(3, 1);
- SBMLNamespaces_addNamespaces(sbmlns, fbc);
-
- /* add groups extention */
- SBMLExtension_t *sbmlgext = SBMLExtensionRegistry_getExtension("groups");
- XMLNamespaces_t * groups = XMLNamespaces_create();
- XMLNamespaces_add(groups, SBMLExtension_getURI(sbmlgext, SBMLlevel, SBMLversion, SBMLgroupsversion), "groups");
- SBMLNamespaces_addNamespaces(sbmlns, groups);
-
- /* 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[21]; // changed from 20 to 21 to avoid buffer overflow
- // 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;
- }
-
-
-
- }
- }
-
- /* add subsystem as groups if fbc is >= 2 */
- if(SBMLfbcversion >= 2){
- if(!Rf_isNull(subSysGroups)){
- GroupsModelPlugin_t* groupsPlug = NULL;
- groupsPlug = (GroupsModelPlugin_t*) SBase_getPlugin((SBase_t *)(model), "groups");
-
- for(int i=0; i < Rf_length(subSysGroups); i++){
- Group_t* newGroup = GroupsModelPlugin_createGroup(groupsPlug);
-
- Group_setKindAsString(newGroup, "partonomy");
- Group_setName(newGroup, CHAR(STRING_ELT(Rf_getAttrib(subSysGroups, R_NamesSymbol), i)));
- SBase_setSBOTerm((SBase_t *) newGroup, 0000633);
-
- for(int j=0; j < Rf_length(VECTOR_ELT(subSysGroups, i)); j++){
- Member_t* newMember = Member_create(SBMLlevel, SBMLversion, SBMLgroupsversion);
- Member_setIdRef(newMember, CHAR(STRING_ELT(VECTOR_ELT(subSysGroups, i), j)));
- Group_addMember(newGroup, newMember);
- }
- //GroupsModelPlugin_addGroup(groupsPlug, newGroup);
- }
- }
- }
-
- // 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;
-}
-
-
-
-
-/* -------------------------------------------------------------------------- */
+/* 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 "config.h"
+
+#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>
+
+#ifdef HAVE_FBC_PLUGIN
+/* 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>
+#endif
+
+#ifdef HAVE_GROUPS_PLUGIN
+/*groups plugin*/
+#include <sbml/packages/groups/common/GroupsExtensionTypes.h>
+#include <sbml/packages/groups/extension/GroupsSBMLDocumentPlugin.h>
+#include <sbml/packages/groups/extension/GroupsExtension.h>
+#include <sbml/packages/groups/extension/GroupsModelPlugin.h>
+
+#include <sbml/packages/groups/sbml/Group.h>
+#include <sbml/packages/groups/sbml/ListOfGroups.h>
+#include <sbml/packages/groups/sbml/ListOfMembers.h>
+#include <sbml/packages/groups/sbml/Member.h>
+#endif
+
+
+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;
+
+#ifdef HAVE_FBC_PLUGIN
+ 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);
+#else
+ out = Rf_ScalarInteger(0);
+#endif
+ 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 chargecount = 0;
+ 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(""));
+ }
+
+
+#ifdef HAVE_FBC_PLUGIN
+ /* FBC PLUGIN @ Ardalan */
+ SBasePlugin_t *SpeciesPlug = SBase_getPlugin((SBase_t *)(splel), "fbc");
+
+ /* get charge and chemical formula from FBC plugin: */
+ if (SpeciesPlug != NULL) {
+ /* FBCcharge */
+ if (FbcSpeciesPlugin_isSetCharge(SpeciesPlug)) {
+ INTEGER(metcharge)[i] = FbcSpeciesPlugin_getCharge(SpeciesPlug);
+ chargecount = chargecount + 1;
+ }
+
+ /* 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(""));
+ }
+ }
+#endif
+ }
+
+ // NULL if empty
+ if (chargecount == 0) metcharge = R_NilValue;
+ 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;
+}
+
+
+SEXP getSBMLGroupsList(SEXP sbmlmod) {
+#ifdef HAVE_GROUPS_PLUGIN
+ GroupsModelPlugin_t * modelPlug = NULL;
+ modelPlug = (GroupsModelPlugin_t *) SBase_getPlugin((SBase_t *)(R_ExternalPtrAddr(sbmlmod)), "groups");
+
+ if(modelPlug != NULL){
+ int n = GroupsModelPlugin_getNumGroups(modelPlug);
+ SEXP rgroups = PROTECT(Rf_allocVector(VECSXP, n));
+ SEXP groupnames = PROTECT(Rf_allocVector(STRSXP, n));
+ for(int i=0; i<n; i++){
+ Group_t* group = GroupsModelPlugin_getGroup(modelPlug, i);
+ if(Group_isSetName(group) == 1){ // skip group if no name is set
+ SET_STRING_ELT(groupnames, i, Rf_mkChar(Group_getName(group)));
+
+ int m = Group_getNumMembers(group);
+ SEXP rmembers = PROTECT(Rf_allocVector(STRSXP, m));
+ for(int j=0; j < m; j++){
+ Member_t * member = Group_getMember(group, j);
+ char * memref = Member_getIdRef(member);
+ SET_STRING_ELT(rmembers, j, Rf_mkChar(memref));
+ }
+ SET_VECTOR_ELT(rgroups, i, rmembers);
+ UNPROTECT(1);
+ }else{
+ SET_VECTOR_ELT(rgroups, i, R_NilValue);
+ }
+ }
+ Rf_namesgets(rgroups, groupnames);
+ UNPROTECT(2);
+ return rgroups;
+ }else{
+ return R_NilValue;
+ }
+#endif
+ return R_NilValue;
+}
+
+/* -------------------------------------------------------------------------- */
+/* 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)); */
+ /* get number of ractions: */
+ 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;
+
+
+ SBasePlugin_t * modelPlug= NULL;
+
+ #ifdef HAVE_FBC_PLUGIN
+ /* FBC OBJECTIV @Ardalan*/
+ Objective_t * objective = NULL;
+ FluxObjective_t * fluxObjective = NULL;
+ modelPlug = SBase_getPlugin((SBase_t *)(R_ExternalPtrAddr(sbmlmod)), "fbc");
+
+ // Read the Objectives when FBCPlugin for the model exists
+ // (Save only active objective)
+ if( modelPlug != NULL)
+ {
+
+ objActiv = FbcModelPlugin_getActiveObjectiveId(modelPlug);
+ if(strcmp(objActiv,"") !=0)
+ {
+ for(int ob = 0; 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);
+ }
+#endif
+
+
+ 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(""));
+ }
+
+
+#ifdef HAVE_FBC_PLUGIN
+ /* FBC LEVEL 2 @Ardalan Habil*/
+
+ /* ReactionPLugin for FBC 2 */
+ SBasePlugin_t *reactionPlug = SBase_getPlugin((SBase_t *)(relel), "fbc");
+
+ if (reactionPlug != NULL) {
+ /* 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;
+
+ for(int fluxb = 0; 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;
+ }
+ } else {
+ REAL(fbclb)[i] = 0;
+ REAL(fbcup)[i] = 0;
+ SET_STRING_ELT(fbcgene, i, Rf_mkChar(""));
+ REAL(fbcobj)[i] = 0;
+ }
+#else
+ REAL(fbclb)[i] = 0;
+ REAL(fbcup)[i] = 0;
+ SET_STRING_ELT(fbcgene, i, Rf_mkChar(""));
+ REAL(fbcobj)[i] = 0;
+#endif
+
+
+ /* 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 subSysGroups, 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)
+{
+#if defined(HAVE_FBC_PLUGIN) && defined(HAVE_GROUPS_PLUGIN)
+ //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];
+ int SBMLgroupsversion = 1;
+ 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 */
+ XMLNamespaces_t * fbc = XMLNamespaces_create();
+ XMLNamespaces_add(fbc, SBMLExtension_getURI(sbmlext, 3, 1, SBMLfbcversion), "fbc");
+
+ sbmlns = SBMLNamespaces_create(3, 1);
+ SBMLNamespaces_addNamespaces(sbmlns, fbc);
+
+ /* add groups extention */
+ SBMLExtension_t *sbmlgext = SBMLExtensionRegistry_getExtension("groups");
+ XMLNamespaces_t * groups = XMLNamespaces_create();
+ XMLNamespaces_add(groups, SBMLExtension_getURI(sbmlgext, SBMLlevel, SBMLversion, SBMLgroupsversion), "groups");
+ SBMLNamespaces_addNamespaces(sbmlns, groups);
+
+ /* 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[21]; // changed from 20 to 21 to avoid buffer overflow
+ // 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;
+ }
+
+
+
+ }
+ }
+
+ /* add subsystem as groups if fbc is >= 2 */
+ if(SBMLfbcversion >= 2){
+ if(!Rf_isNull(subSysGroups)){
+ GroupsModelPlugin_t* groupsPlug = NULL;
+ groupsPlug = (GroupsModelPlugin_t*) SBase_getPlugin((SBase_t *)(model), "groups");
+
+ for(int i=0; i < Rf_length(subSysGroups); i++){
+ Group_t* newGroup = GroupsModelPlugin_createGroup(groupsPlug);
+
+ Group_setKindAsString(newGroup, "partonomy");
+ Group_setName(newGroup, CHAR(STRING_ELT(Rf_getAttrib(subSysGroups, R_NamesSymbol), i)));
+ SBase_setSBOTerm((SBase_t *) newGroup, 0000633);
+
+ for(int j=0; j < Rf_length(VECTOR_ELT(subSysGroups, i)); j++){
+ Member_t* newMember = Member_create(SBMLlevel, SBMLversion, SBMLgroupsversion);
+ Member_setIdRef(newMember, CHAR(STRING_ELT(VECTOR_ELT(subSysGroups, i), j)));
+ Group_addMember(newGroup, newMember);
+ }
+ //GroupsModelPlugin_addGroup(groupsPlug, newGroup);
+ }
+ }
+ }
+
+ // write SBML file
+ int result = writeSBML(sbmlDoc, fname);
+ SEXP out = R_NilValue;
+ if (result)out = Rf_ScalarLogical(1);
+ else out = Rf_ScalarLogical(0);
+#else
+ SEXP out = Rf_ScalarLogical(0);/* no success */
+#endif
+
+ return out;
+}
+
+
+/* -------------------------------------------------------------------------- */
+/* check, if FBC-Plugin is available */
+SEXP isAvailableFbcPlugin() {
+ SEXP out = R_NilValue;
+#ifdef HAVE_FBC_PLUGIN
+ out = Rf_ScalarLogical(1);
+#else
+ out = Rf_ScalarLogical(0);
+#endif
+ return out;
+}
+
+
+/* -------------------------------------------------------------------------- */
+/* check, if Groups-Plugin is available */
+SEXP isAvailableGroupsPlugin() {
+ SEXP out = R_NilValue;
+#ifdef HAVE_GROUPS_PLUGIN
+ out = Rf_ScalarLogical(1);
+#else
+ out = Rf_ScalarLogical(0);
+#endif
+ return out;
+}
+
+
+/* -------------------------------------------------------------------------- */
diff --git a/src/sybilSBML.h b/src/sybilSBML.h
index 6393177..3f7526a 100644
--- a/src/sybilSBML.h
+++ b/src/sybilSBML.h
@@ -1,115 +1,121 @@
-/* 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 groups */
-SEXP getSBMLGroupsList(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 subSysGroups, 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);
+/* 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 groups */
+SEXP getSBMLGroupsList(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 subSysGroups, 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);
+
+/* check, if FBC-Plugin is available */
+SEXP isAvailableFbcPlugin();
+
+/* check, if Groups-Plugin is available */
+SEXP isAvailableGroupsPlugin();
diff --git a/src/symbols.rds b/src/symbols.rds
new file mode 100644
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--
GitLab