diff --git a/DESCRIPTION b/DESCRIPTION
index d0982c35aec935ac92058c3e915c6c59d4dc034c..57f3938d67973197b589b77164f52b1b92f3d344 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: sybilSBML
Type: Package
Title: SBML Integration in Package 'Sybil'
-Version: 3.0.8
-Date: 2020-03-10
+Version: 3.1.0
+Date: 2020-03-23
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: 2020-03-10 09:00:00 UTC; mayo
+Packaged: 2020-03-23 12:00:00 UTC; mayo
Author: Mayo Roettger [cre],
Gabriel Gelius-Dietrich [aut, ctb],
C. Jonathan Fritzemeier [ctb],
diff --git a/configure b/configure
index c1eee2afb8b8e52383259ec7e164a4a8fe00fd82..6c660c64991c4b1c19d3d5ea69f266c6119a46fc 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 3.0.8.
+# Generated by GNU Autoconf 2.69 for sybilSBML 3.1.0.
#
# Report bugs to <mayo.roettger@hhu.de>.
#
@@ -580,8 +580,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='sybilSBML'
PACKAGE_TARNAME='sybilsbml'
-PACKAGE_VERSION='3.0.8'
-PACKAGE_STRING='sybilSBML 3.0.8'
+PACKAGE_VERSION='3.1.0'
+PACKAGE_STRING='sybilSBML 3.1.0'
PACKAGE_BUGREPORT='mayo.roettger@hhu.de'
PACKAGE_URL=''
@@ -623,6 +623,8 @@ ac_includes_default="\
ac_subst_vars='LTLIBOBJS
LIBOBJS
+HAVE_FBC_PLUGIN
+HAVE_GROUPS_PLUGIN
PKG_CPPFLAGS
PKG_LIBS
PKG_CFLAGS
@@ -1241,7 +1243,7 @@ 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 3.0.8 to adapt to many kinds of systems.
+\`configure' configures sybilSBML 3.1.0 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1303,7 +1305,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of sybilSBML 3.0.8:";;
+ short | recursive ) echo "Configuration of sybilSBML 3.1.0:";;
esac
cat <<\_ACEOF
@@ -1390,7 +1392,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-sybilSBML configure 3.0.8
+sybilSBML configure 3.1.0
generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1759,7 +1761,7 @@ 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 3.0.8, which was
+It was created by sybilSBML $as_me 3.1.0, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
@@ -2108,6 +2110,10 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
+ac_config_headers="$ac_config_headers src/config.h"
+
+
+
@@ -3050,11 +3056,6 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
-ac_config_headers="$ac_config_headers src/config.h"
-
-
-
-
ARGS_OK="FALSE"
if test -n "$PKG_CPPFLAGS" -a -n "$PKG_LIBS" ; then
@@ -3741,7 +3742,11 @@ done
-ac_config_files="$ac_config_files src/Makevars"
+
+
+
+ac_config_files="$ac_config_files src/Makevars.tmp:src/Makevars.in"
+
cat >confcache <<\_ACEOF
# This file is a shell script that caches the results of configure
@@ -4249,7 +4254,7 @@ cat >>$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 3.0.8, which was
+This file was extended by sybilSBML $as_me 3.1.0, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -4311,7 +4316,7 @@ _ACEOF
cat >>$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 3.0.8
+sybilSBML config.status 3.1.0
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
@@ -4433,7 +4438,7 @@ 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="$CONFIG_FILES src/Makevars" ;;
+ "src/Makevars.tmp") CONFIG_FILES="$CONFIG_FILES src/Makevars.tmp:src/Makevars.in" ;;
*) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5;;
esac
@@ -4979,6 +4984,24 @@ $as_echo "$as_me: $ac_file is unchanged" >&6;}
esac
+
+ case $ac_file$ac_mode in
+ "src/Makevars.tmp":F)
+ if test -f src/Makevars && cmp -s src/Makevars.tmp src/Makevars; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: creating src/Makevars" >&5
+$as_echo "$as_me: creating src/Makevars" >&6;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: src/Makevars is unchanged" >&5
+$as_echo "$as_me: src/Makevars is unchanged" >&6;}
+ rm src/Makevars.tmp
+ else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: creating src/Makevars" >&5
+$as_echo "$as_me: creating src/Makevars" >&6;}
+ mv src/Makevars.tmp src/Makevars
+ fi
+
+ ;;
+
+ esac
done # for ac_tag
diff --git a/configure.ac b/configure.ac
index da793207fa181a33719c5d9fe87272dca88b8919..f589d1c3777aa261e1a8fe517190a5c3f63bb88a 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,4 +1,10 @@
-AC_INIT([sybilSBML], [3.0.8], [mayo.roettger@hhu.de])
+AC_INIT([sybilSBML], [3.1.0], [mayo.roettger@hhu.de])
+
+dnl # --------------------------------------------------------------------
+dnl # template config.h.in
+dnl # --------------------------------------------------------------------
+AC_CONFIG_HEADERS([src/config.h])
+
dnl # --------------------------------------------------------------------
dnl # global (environment) variables
@@ -28,13 +34,6 @@ AC_PROG_CC
AC_PROG_CPP
-dnl # --------------------------------------------------------------------
-dnl # template config.h.in
-dnl # --------------------------------------------------------------------
-
-AC_CONFIG_HEADERS([src/config.h])
-
-
dnl # --------------------------------------------------------------------
dnl # test for global variables
dnl # --------------------------------------------------------------------
@@ -280,6 +279,21 @@ dnl # --------------------------------------------------------------------
AC_SUBST(PKG_CFLAGS)
AC_SUBST(PKG_LIBS)
AC_SUBST(PKG_CPPFLAGS)
-AC_OUTPUT(src/Makevars)
+AC_SUBST(HAVE_GROUPS_PLUGIN)
+AC_SUBST(HAVE_FBC_PLUGIN)
+
+AC_CONFIG_FILES([src/Makevars.tmp:src/Makevars.in], [
+ if test -f src/Makevars && cmp -s src/Makevars.tmp src/Makevars; then
+ AC_MSG_NOTICE([creating src/Makevars])
+ AC_MSG_NOTICE([src/Makevars is unchanged])
+ rm src/Makevars.tmp
+ else
+ AC_MSG_NOTICE([creating src/Makevars])
+ mv src/Makevars.tmp src/Makevars
+ fi
+ ]
+)
+
+AC_OUTPUT
exit 0
diff --git a/inst/INSTALL b/inst/INSTALL
index 6611c9dc5c669ec9c889cd0c9e540709aa45d404..be0fd7c5d5e062a6d3083938f15e4cb2d5fe0b5a 100644
--- a/inst/INSTALL
+++ b/inst/INSTALL
@@ -80,4 +80,7 @@ all: $(SHLIB)
with the environment variable LIB_SBML being the installation directory
of libSBML.
+If you want to build the package with libSBML FBC and Groups plugins functionality,
+please exchange the the first row in the Makevars.win file in src/ into
+PKG_CPPFLAGS= -D_R_=1 -DUSE_R=1 -DHAVE_FBC_PLUGIN=1 -DHAVE_GROUPS_PLUGIN=1 -I"$(LIB_SBML)/include"
diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
index bf802cd533a26157a145f683858b87dcbf1c8634..eeeea6a5d96713d02f4b3ac83587710a3cbf0ec5 100644
--- a/inst/NEWS.Rd
+++ b/inst/NEWS.Rd
@@ -6,7 +6,7 @@
\newcommand{\CRANpkg}{\href{https://cran.r-project.org/package=#1}{\pkg{#1}}}
% ---------------------------------------------------------------------------- %
-\section{Changes in version 3.0.4 - 3.0.8 2020-03-10}{
+\section{Changes in version 3.0.4 - 3.1.0 2020-03-23}{
\itemize{
\item Maintainer change.
\item Changes to be able to build package without libSBML FBC and Groups
diff --git a/src/Makevars b/src/Makevars
deleted file mode 100644
index fa653da3c5f9c10258f6cb3b5227e8ec99fed2fa..0000000000000000000000000000000000000000
--- a/src/Makevars
+++ /dev/null
@@ -1,3 +0,0 @@
-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
\ No newline at end of file
diff --git a/src/Makevars.in b/src/Makevars.in
index f03b4d39e17631bd443edc49d5d1275b76391553..76cd4de1e0c2a43fa3b651a87d314b5b936e89f4 100644
--- a/src/Makevars.in
+++ b/src/Makevars.in
@@ -1,3 +1,3 @@
PKG_CFLAGS=@PKG_CFLAGS@
-PKG_CPPFLAGS=@PKG_CPPFLAGS@
+PKG_CPPFLAGS=@DEFS@ @PKG_CPPFLAGS@
PKG_LIBS=@PKG_LIBS@
diff --git a/src/config.h b/src/config.h
deleted file mode 100644
index 60423413a273333855cd80ab44d6eeff29f80032..0000000000000000000000000000000000000000
--- a/src/config.h
+++ /dev/null
@@ -1,82 +0,0 @@
-/* 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/sybilSBML.c b/src/sybilSBML.c
index a76ff8ce9583d690b933fbffb970526e7ad70286..1011b2b5ee830251e2591dccb922118e66922e7d 100644
--- a/src/sybilSBML.c
+++ b/src/sybilSBML.c
@@ -21,7 +21,9 @@ 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/>.
*/
+#ifdef HAVE_CONFIG_H
#include "config.h"
+#endif /* HAVE_CONFIG_H */
#include "sybilSBML.h"
@@ -397,7 +399,7 @@ SEXP getSBMLFbcversion(SEXP sbmldoc) {
unsigned int version;
checkDocument(sbmldoc);
- //hierher
+
SBasePlugin_t * modelPlug= NULL;
modelPlug = SBase_getPlugin((SBase_t *)(R_ExternalPtrAddr(sbmldoc)), "fbc");
if( modelPlug != NULL)
@@ -1284,17 +1286,17 @@ SEXP getSBMLReactionsList(SEXP sbmlmod) {
int objcount=0;
int annocount=0;
int notescount=0;
+
+#ifdef HAVE_FBC_PLUGIN
/* 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;
@@ -2156,147 +2158,148 @@ SEXP exportSBML (SEXP version, SEXP level, SEXP FbcLevel, SEXP filename, SEXP sy
if( i+1 == INTEGER(ex_react)[k])
isexchange=1;
- int j=0;
- for (j=0; j<LENGTH(met_id); j++)
+ int j=0;
+ for (j=0; j<LENGTH(met_id); j++)
+ {
+
+ int hash = LENGTH(met_id) * i + j;
+ if (REAL(SMatrix)[hash] != 0.00 )
{
- 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]));
- if(REAL(SMatrix)[hash] < 0.00)
+ //is Exchange Reaction
+ if(isexchange==1 && !Rf_isNull(ex_react))
{
- spr = Reaction_createReactant(reaction);
- SpeciesReference_setConstant(spr, 1);
- SpeciesReference_setSpecies(spr,CHAR(STRING_ELT(met_id, j)));
- SpeciesReference_setStoichiometry(spr, fabs(REAL(SMatrix)[hash]));
+ /* Create boundary Species */
+ sp = Model_createSpecies(model);
- //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);
- }
+ 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);
- }else{
+ /* 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);
- SpeciesReference_setSpecies(spr,CHAR(STRING_ELT(met_id, j)));
- SpeciesReference_setStoichiometry(spr, fabs(REAL(SMatrix)[hash]));
}
+
+
+ }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);
-
- }
+ /*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;
- /* FBC LEVEL 2 */
- if(SBMLfbcversion == 2)
- {
- // Get a SBasePlugin_t object plugged in the reaction object.
-
- reactionPlug = SBase_getPlugin((SBase_t *)(reaction), "fbc");
+ //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);
- const char* para_lb;
- const char* para_ub;
+ para_lb=append_strings(CHAR(STRING_ELT(react_id, i)),"lower_bound","_");
- //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);
- if (upper_bnd[i] >= sybilmax)
- {
- para_ub="default_ub";
- }
+ 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");
- else if (upper_bnd[i] == 0)
- {
- para_ub="default_0";
- }
+ fluxObjective = Objective_createFluxObjective(objective);
+ FluxObjective_setReaction(fluxObjective, CHAR(STRING_ELT(react_id, i)));
+ FluxObjective_setCoefficient(fluxObjective, INTEGER(obj_coef)[i]);
- 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","_");
- }
+ FbcModelPlugin_addObjective(modelPlug, objective);
- // set the flux bounds for this reaction
- FbcReactionPlugin_setLowerFluxBound(reactionPlug, para_lb);
- FbcReactionPlugin_setUpperFluxBound(reactionPlug, para_ub);
+ // mark obj1 as active objective
+ FbcModelPlugin_setActiveObjectiveId(modelPlug, "obj");
- // 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