23 #include "utilities.hpp"
35 throw std::runtime_error(
"Received SIGABRT signal.");
48 pNewAct =
new struct sigaction();
50 pOldAct =
new struct sigaction();
55 std::cerr <<
"Setting the signal handler failed." << std::endl;
69 int x = sigaction(SIGABRT,
pOldAct, NULL);
73 std::cerr <<
"Resetting the signal handler failed." << std::endl;
94 CPPUNIT_ASSERT_MESSAGE(
"The first export to Level 2 Version 1 failed.",
false);
103 CPPUNIT_ASSERT_MESSAGE(
"The second export to Level 3 Version 1 failed.",
false);
122 CPPUNIT_ASSERT_MESSAGE(
"The first export to Level 3 Version 1 failed.",
false);
131 CPPUNIT_ASSERT_MESSAGE(
"The second export to Level 2 Version 1 failed.",
false);
138 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
139 "<!-- generated with COPASI 4.7.34 (Debug) (http://www.copasi.org) at 2011-09-08 08:14:18 UTC -->\n"
140 "<?oxygen RNGSchema=\"http://www.copasi.org/static/schema/CopasiML.rng\" type=\"xml\"?>\n"
141 "<COPASI xmlns=\"http://www.copasi.org/static/schema\" versionMajor=\"1\" versionMinor=\"0\" versionDevel=\"34\">\n"
142 " <ListOfFunctions>\n"
143 " <Function key=\"Function_6\" name=\"Constant flux (irreversible)\" type=\"PreDefined\" reversible=\"false\">\n"
147 " <ListOfParameterDescriptions>\n"
148 " <ParameterDescription key=\"FunctionParameter_49\" name=\"v\" order=\"0\" role=\"constant\"/>\n"
149 " </ListOfParameterDescriptions>\n"
151 " <Function key=\"Function_13\" name=\"Mass action (irreversible)\" type=\"MassAction\" reversible=\"false\">\n"
153 " k1*PRODUCT<substrate_i>\n"
155 " <ListOfParameterDescriptions>\n"
156 " <ParameterDescription key=\"FunctionParameter_81\" name=\"k1\" order=\"0\" role=\"constant\"/>\n"
157 " <ParameterDescription key=\"FunctionParameter_79\" name=\"substrate\" order=\"1\" role=\"substrate\"/>\n"
158 " </ListOfParameterDescriptions>\n"
160 " </ListOfFunctions>\n"
161 " <Model key=\"Model_0\" name=\"New Model\" simulationType=\"time\" timeUnit=\"s\" volumeUnit=\"µl\" areaUnit=\"m²\" lengthUnit=\"m\" quantityUnit=\"nmol\" type=\"deterministic\" avogadroConstant=\"6.02214179e+23\">\n"
162 " <ListOfCompartments>\n"
163 " <Compartment key=\"Compartment_0\" name=\"cell\" simulationType=\"fixed\" dimensionality=\"3\">\n"
165 " </ListOfCompartments>\n"
166 " <ListOfMetabolites>\n"
167 " <Metabolite key=\"Metabolite_0\" name=\"glucose\" simulationType=\"fixed\" compartment=\"Compartment_0\">\n"
169 " <Metabolite key=\"Metabolite_1\" name=\"glucose-6-phosphate\" simulationType=\"reactions\" compartment=\"Compartment_0\">\n"
171 " <Metabolite key=\"Metabolite_2\" name=\"ATP\" simulationType=\"fixed\" compartment=\"Compartment_0\">\n"
173 " <Metabolite key=\"Metabolite_3\" name=\"ADP\" simulationType=\"reactions\" compartment=\"Compartment_0\">\n"
175 " </ListOfMetabolites>\n"
176 " <ListOfModelValues>\n"
177 " <ModelValue key=\"ModelValue_0\" name=\"rateConstant\" simulationType=\"assignment\">\n"
182 " </ListOfModelValues>\n"
183 " <ListOfReactions>\n"
184 " <Reaction key=\"Reaction_0\" name=\"hexokinase\" reversible=\"false\">\n"
185 " <ListOfSubstrates>\n"
186 " <Substrate metabolite=\"Metabolite_0\" stoichiometry=\"1\"/>\n"
187 " <Substrate metabolite=\"Metabolite_2\" stoichiometry=\"1\"/>\n"
188 " </ListOfSubstrates>\n"
189 " <ListOfProducts>\n"
190 " <Product metabolite=\"Metabolite_1\" stoichiometry=\"1\"/>\n"
191 " <Product metabolite=\"Metabolite_3\" stoichiometry=\"1\"/>\n"
192 " </ListOfProducts>\n"
193 " <ListOfConstants>\n"
194 " <Constant key=\"Parameter_93\" name=\"v\" value=\"0.5\"/>\n"
195 " </ListOfConstants>\n"
196 " <KineticLaw function=\"Function_6\">\n"
197 " <ListOfCallParameters>\n"
198 " <CallParameter functionParameter=\"FunctionParameter_49\">\n"
199 " <SourceParameter reference=\"Parameter_93\"/>\n"
200 " </CallParameter>\n"
201 " </ListOfCallParameters>\n"
204 " <Reaction key=\"Reaction_1\" name=\"hexokinase-backwards\" reversible=\"false\">\n"
205 " <ListOfSubstrates>\n"
206 " <Substrate metabolite=\"Metabolite_1\" stoichiometry=\"1\"/>\n"
207 " <Substrate metabolite=\"Metabolite_3\" stoichiometry=\"1\"/>\n"
208 " </ListOfSubstrates>\n"
209 " <ListOfProducts>\n"
210 " <Product metabolite=\"Metabolite_0\" stoichiometry=\"1\"/>\n"
211 " <Product metabolite=\"Metabolite_2\" stoichiometry=\"1\"/>\n"
212 " </ListOfProducts>\n"
213 " <ListOfConstants>\n"
214 " <Constant key=\"Parameter_94\" name=\"k1\" value=\"1\"/>\n"
215 " </ListOfConstants>\n"
216 " <KineticLaw function=\"Function_13\">\n"
217 " <ListOfCallParameters>\n"
218 " <CallParameter functionParameter=\"FunctionParameter_81\">\n"
219 " <SourceParameter reference=\"ModelValue_0\"/>\n"
220 " </CallParameter>\n"
221 " <CallParameter functionParameter=\"FunctionParameter_79\">\n"
222 " <SourceParameter reference=\"Metabolite_1\"/>\n"
223 " <SourceParameter reference=\"Metabolite_3\"/>\n"
224 " </CallParameter>\n"
225 " </ListOfCallParameters>\n"
228 " </ListOfReactions>\n"
230 " <StateTemplateVariable objectReference=\"Model_0\"/>\n"
231 " <StateTemplateVariable objectReference=\"Metabolite_1\"/>\n"
232 " <StateTemplateVariable objectReference=\"Metabolite_3\"/>\n"
233 " <StateTemplateVariable objectReference=\"ModelValue_0\"/>\n"
234 " <StateTemplateVariable objectReference=\"Metabolite_0\"/>\n"
235 " <StateTemplateVariable objectReference=\"Metabolite_2\"/>\n"
236 " <StateTemplateVariable objectReference=\"Compartment_0\"/>\n"
237 " </StateTemplate>\n"
238 " <InitialState type=\"initialState\">\n"
239 " 0 0 0 2.25 3.011070895e+16 3.011070895e+16 5 \n"
static const char * CPS_STRING
std::string exportSBMLToString(CProcessReport *pExportHandler, int sbmlLevel, int sbmlVersion)
struct sigaction * pNewAct
bool load_cps_model_from_stream(std::istream &is, CCopasiDataModel &dataModel)
static CCopasiDataModel * addDatamodel()
CCopasiDataModel * pDataModel
static void init(int argc, char *argv[], const bool &withGui=false)
struct sigaction * pOldAct