From 784bc227537f369abbd16edb852a49bcd6d4b7dd Mon Sep 17 00:00:00 2001 From: "Habil, Ardalan (arhab001)" <ardalan.habil@uni-duesseldorf.de> Date: Wed, 7 Dec 2016 15:43:21 +0100 Subject: [PATCH] no need for validation var --- src/sybilSBML.h | 225 ++++++++++++++++++++++++------------------------ 1 file changed, 112 insertions(+), 113 deletions(-) diff --git a/src/sybilSBML.h b/src/sybilSBML.h index 7d0746f..9fac9ea 100644 --- a/src/sybilSBML.h +++ b/src/sybilSBML.h @@ -1,113 +1,112 @@ -/* sybilSBML.h - Link to libSBML for sybil. - - Copyright (C) 2010-2013 Gabriel Gelius-Dietrich, Dpt. for Bioinformatics, - Institute for Informatics, Heinrich-Heine-University, Duesseldorf, Germany. - All right reserved. - Email: geliudie@uni-duesseldorf.de - - This file is part of sybilSBML. - - SybilSBML is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - SybilSBML is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with sybilSBML. If not, see <http://www.gnu.org/licenses/>. -*/ - -#include "sbml.h" - -/* -------------------------------------------------------------------------- */ -/* help functions */ -/* -------------------------------------------------------------------------- */ - -/* check for pointer to sbml document */ -SEXP isSBMLdocptr(SEXP ptr); - -/* check for pointer to sbml model */ -SEXP isSBMLmodptr(SEXP ptr); - -/* check for NULL pointer */ -SEXP isNULLptr(SEXP ptr); - - -/* -------------------------------------------------------------------------- */ -/* API functions */ -/* -------------------------------------------------------------------------- */ - -/* get libsbml version number (dotted version) */ -SEXP getLibSBMLversion(); - -/* initialize sybilSBML */ -SEXP initSBML(void); - -/* remove sbml document pointer */ -SEXP delDocument(SEXP sbmldoc); - -/* remove model pointer */ -SEXP delModel(SEXP sbmlmodel); - -/* read SBML file */ -SEXP readSBMLfile(SEXP fname, SEXP ptrtype); - -/* get sbml document level */ -SEXP getSBMLlevel(SEXP sbmldoc); - -/* get sbml document version */ -SEXP getSBMLversion(SEXP sbmldoc); - -/* get sbml document FBC version */ -SEXP getSBMLFbcversion(SEXP sbmldoc); - -/* validate SBML document */ -SEXP validateDocument(SEXP sbmldoc); - -/* get SBML errors */ -SEXP getSBMLerrors(SEXP sbmldoc); - -/* get sbml model from sbml document */ -SEXP getSBMLmodel(SEXP sbmldoc, SEXP ptrtype); - -/* get model id */ -SEXP getSBMLmodId(SEXP sbmlmod); - -/* get model name */ -SEXP getSBMLmodName(SEXP sbmlmod); - -/* get model notes */ -SEXP getSBMLmodNotes(SEXP sbmlmod); - -/* get model annotation */ -SEXP getSBMLmodAnnotation(SEXP sbmlmod); - -/* get number of compartments */ -SEXP getSBMLnumCompart(SEXP sbmlmod); - -/* get number of species (metabolites) */ -SEXP getSBMLnumSpecies(SEXP sbmlmod); - -/* get number of reactions */ -SEXP getSBMLnumReactions(SEXP sbmlmod); - -/* get list of unit definitions */ -SEXP getSBMLunitDefinitionsList(SEXP sbmlmod); - -/* get list of compartments */ -SEXP getSBMLCompartList(SEXP sbmlmod); - -/* get list of species (metabolites) */ -SEXP getSBMLSpeciesList(SEXP sbmlmod); - -/* get list of reactions */ -SEXP getSBMLReactionsList(SEXP sbmlmod); - -/* export Modelorg to SBML*/ -SEXP exportSBML (SEXP version, SEXP level,SEXP FbcLevel, SEXP filename,SEXP sybil_max, SEXP mod_desc, SEXP mod_name, SEXP mod_compart, SEXP met_id, SEXP met_name, SEXP met_comp, SEXP met_form,SEXP met_charge, SEXP react_id, SEXP react_name, SEXP react_rev, SEXP lowbnd, SEXP uppbnd, SEXP obj_coef, SEXP subSys, SEXP gpr, SEXP SMatrix, SEXP mod_notes, SEXP mod_anno, SEXP com_notes , SEXP com_anno, SEXP met_notes, SEXP met_anno, SEXP met_bnd , SEXP react_notes, SEXP react_anno, SEXP ex_react,SEXP validation, 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 reactions */ +SEXP getSBMLReactionsList(SEXP sbmlmod); + +/* export Modelorg to SBML*/ +SEXP exportSBML (SEXP version, SEXP level,SEXP FbcLevel, SEXP filename,SEXP sybil_max, SEXP mod_desc, SEXP mod_name, SEXP mod_compart, SEXP met_id, SEXP met_name, SEXP met_comp, SEXP met_form,SEXP met_charge, SEXP react_id, SEXP react_name, SEXP react_rev, SEXP lowbnd, SEXP uppbnd, SEXP obj_coef, SEXP subSys, SEXP gpr, SEXP SMatrix, SEXP mod_notes, SEXP mod_anno, SEXP com_notes , SEXP com_anno, SEXP met_notes, SEXP met_anno, SEXP met_bnd , SEXP react_notes, SEXP react_anno, SEXP ex_react, SEXP allgenes); \ No newline at end of file -- GitLab