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sybilSBML.c
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sybilSBML.c
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/* 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/>.
*/
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif /* HAVE_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);
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);