COPASI API  4.16.103
test000067.cpp
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1 // Begin CVS Header
2 // $Source: /Volumes/Home/Users/shoops/cvs/copasi_dev/copasi/sbml/unittests/test000067.cpp,v $
3 // $Revision: 1.7 $
4 // $Name: $
5 // $Author: shoops $
6 // $Date: 2012/05/07 12:03:37 $
7 // End CVS Header
8 
9 // Copyright (C) 2012 - 2010 by Pedro Mendes, Virginia Tech Intellectual
10 // Properties, Inc., University of Heidelberg, and The University
11 // of Manchester.
12 // All rights reserved.
13 
14 // Copyright (C) 2008 by Pedro Mendes, Virginia Tech Intellectual
15 // Properties, Inc., EML Research, gGmbH, University of Heidelberg,
16 // and The University of Manchester.
17 // All rights reserved.
18 
19 #include "test000067.h"
20 
21 #include <sstream>
22 #include "utilities.hpp"
23 #include "copasi/CopasiDataModel/CCopasiDataModel.h"
24 #include "copasi/model/CModel.h"
25 #include "copasi/model/CModelValue.h"
26 #include "copasi/function/CFunctionDB.h"
27 
28 #include "sbml/SBMLDocument.h"
29 #include "sbml/Model.h"
30 #include "sbml/Rule.h"
31 #include "sbml/Species.h"
32 #include "sbml/Parameter.h"
33 #include "sbml/math/ASTNode.h"
34 
35 #include "test000059.h"
36 
37 #include "copasi/report/CCopasiRootContainer.h"
38 
39 CCopasiDataModel* test000067::pCOPASIDATAMODEL = NULL;
40 
41 void test000067::setUp()
42 {
43  // Create the root container.
44  CCopasiRootContainer::init(0, NULL, false);
45  // Create the global data model.
46  pCOPASIDATAMODEL = CCopasiRootContainer::addDatamodel();
47 }
48 
49 void test000067::tearDown()
50 {
51  CCopasiRootContainer::destroy();
52 }
53 
54 void test000067::test_bug1060()
55 {
56  CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
57  std::istringstream iss(test000067::MODEL_STRING1);
58  CPPUNIT_ASSERT(load_cps_model_from_stream(iss, *pDataModel) == true);
59  CPPUNIT_ASSERT(pDataModel->getModel() != NULL);
60  const SBMLDocument* pDocument = pDataModel->getCurrentSBMLDocument();
61  CPPUNIT_ASSERT(pDocument == NULL);
62  CPPUNIT_ASSERT(pDataModel->exportSBMLToString(NULL, 2, 3).empty() == false);
63  pDocument = pDataModel->getCurrentSBMLDocument();
64  const Model* pSBMLModel = pDocument->getModel();
65  CPPUNIT_ASSERT(pSBMLModel != NULL);
66  CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 3);
67  CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
68  CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 3);
69  CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 8);
70  CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
71  CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 0);
72  CPPUNIT_ASSERT(test000059::checkIfIdsUnique(pSBMLModel) == true);
73  // check if each reaction call the correct kinetic law
74  CFunctionDB* pFunDB = CCopasiRootContainer::getFunctionList();
75  CEvaluationTree* pModifiedMM = pFunDB->findFunction("Modified MM");
76  CPPUNIT_ASSERT(pModifiedMM != NULL);
77  CEvaluationTree* pModifiedCF = pFunDB->findFunction("modified constant flux");
78  CPPUNIT_ASSERT(pModifiedCF != NULL);
79  CEvaluationTree* pConstantFlux = pFunDB->findFunction("Constant flux (irreversible)");
80  CPPUNIT_ASSERT(pConstantFlux != NULL);
81  unsigned int i, iMax = pSBMLModel->getListOfReactions()->size();
82  const Reaction* pReaction = NULL;
83  const ASTNode* pRoot = NULL;
84  const std::map<CCopasiObject*, SBase*>& copasi2sbmlmap = pDataModel->getCopasi2SBMLMap();
85  std::map<CCopasiObject*, SBase*>::const_iterator mappos;
86 
87  for (i = 0; i < iMax; ++i)
88  {
89  pReaction = pSBMLModel->getReaction(i);
90  CPPUNIT_ASSERT(pReaction != NULL);
91  CPPUNIT_ASSERT(pReaction->getKineticLaw() != NULL);
92  pRoot = pReaction->getKineticLaw()->getMath();
93  CPPUNIT_ASSERT(pRoot != NULL);
94  CPPUNIT_ASSERT(pRoot->getType() == AST_TIMES);
95 
96  if (pRoot->getChild(0)->getType() == AST_NAME && pRoot->getChild(0)->getName() == pSBMLModel->getCompartment(0)->getId())
97  {
98  pRoot = pRoot->getChild(1);
99  }
100  else
101  {
102  pRoot = pRoot->getChild(0);
103  }
104 
105  if (pReaction->getName() == "y0Prod" || pReaction->getName() == "y1Prod" || pReaction->getName() == "xProdLin")
106  {
107  // uses modified constant flux
108  CPPUNIT_ASSERT(pRoot->getType() == AST_FUNCTION);
109  mappos = copasi2sbmlmap.find(pModifiedCF);
110  CPPUNIT_ASSERT(mappos != copasi2sbmlmap.end());
111  CPPUNIT_ASSERT(mappos->second != NULL);
112  CPPUNIT_ASSERT(pRoot->getName() == mappos->second->getId());
113  }
114  else if (pReaction->getName() == "xDegMM")
115  {
116  // uses modifed MM
117  CPPUNIT_ASSERT(pRoot->getType() == AST_FUNCTION);
118  mappos = copasi2sbmlmap.find(pModifiedMM);
119  CPPUNIT_ASSERT(mappos != copasi2sbmlmap.end());
120  CPPUNIT_ASSERT(mappos->second != NULL);
121  CPPUNIT_ASSERT(pRoot->getName() == mappos->second->getId());
122  }
123  else if (pReaction->getName() == "xProd")
124  {
125  // constant flux
126  CPPUNIT_ASSERT(pRoot->getType() == AST_FUNCTION);
127  mappos = copasi2sbmlmap.find(pConstantFlux);
128  CPPUNIT_ASSERT(mappos != copasi2sbmlmap.end());
129  CPPUNIT_ASSERT(mappos->second != NULL);
130  CPPUNIT_ASSERT(pRoot->getName() == mappos->second->getId());
131  }
132  else
133  {
134  // must be mass action
135  CPPUNIT_ASSERT(pRoot->getType() == AST_TIMES);
136  }
137  }
138 }
139 
140 const char* test000067::MODEL_STRING1 =
141 {
142  "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
143  "<!-- generated with COPASI 4.4 (Build 26) (http://www.copasi.org) at 2008-08-04 15:57:12 UTC -->\n"
144  "<COPASI xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:noNamespaceSchemaLocation=\"http://www.copasi.org/static/schema.xsd\" versionMajor=\"1\" versionMinor=\"0\" versionDevel=\"26\">\n"
145  " <ListOfFunctions>\n"
146  " <Function key=\"Function_6\" name=\"Constant flux (irreversible)\" type=\"PreDefined\" reversible=\"false\">\n"
147  " <Expression>\n"
148  " v\n"
149  " </Expression>\n"
150  " <ListOfParameterDescriptions>\n"
151  " <ParameterDescription key=\"FunctionParameter_49\" name=\"v\" order=\"0\" role=\"constant\"/>\n"
152  " </ListOfParameterDescriptions>\n"
153  " </Function>\n"
154  " <Function key=\"Function_13\" name=\"Mass action (irreversible)\" type=\"MassAction\" reversible=\"false\">\n"
155  " <Expression>\n"
156  " k1*PRODUCT&lt;substrate_i&gt;\n"
157  " </Expression>\n"
158  " <ListOfParameterDescriptions>\n"
159  " <ParameterDescription key=\"FunctionParameter_81\" name=\"k1\" order=\"0\" role=\"constant\"/>\n"
160  " <ParameterDescription key=\"FunctionParameter_79\" name=\"substrate\" order=\"1\" role=\"substrate\"/>\n"
161  " </ListOfParameterDescriptions>\n"
162  " </Function>\n"
163  " <Function key=\"Function_60\" name=\"Objective Function 1\" type=\"Expression\">\n"
164  " <Expression>\n"
165  " \n"
166  " </Expression>\n"
167  " </Function>\n"
168  " <Function key=\"Function_46\" name=\"Objective Function\" type=\"Expression\">\n"
169  " <Expression>\n"
170  " \n"
171  " </Expression>\n"
172  " </Function>\n"
173  " <Function key=\"Function_63\" name=\"modified constant flux\" type=\"UserDefined\" reversible=\"unspecified\">\n"
174  " <Expression>\n"
175  " k*M\n"
176  " </Expression>\n"
177  " <ListOfParameterDescriptions>\n"
178  " <ParameterDescription key=\"FunctionParameter_297\" name=\"k\" order=\"0\" role=\"constant\"/>\n"
179  " <ParameterDescription key=\"FunctionParameter_268\" name=\"M\" order=\"1\" role=\"modifier\"/>\n"
180  " </ListOfParameterDescriptions>\n"
181  " </Function>\n"
182  " <Function key=\"Function_52\" name=\"Modified MM\" type=\"UserDefined\" reversible=\"unspecified\">\n"
183  " <Expression>\n"
184  " a_k*y*(x/(x+k))\n"
185  " </Expression>\n"
186  " <ListOfParameterDescriptions>\n"
187  " <ParameterDescription key=\"FunctionParameter_272\" name=\"a_k\" order=\"0\" role=\"constant\"/>\n"
188  " <ParameterDescription key=\"FunctionParameter_250\" name=\"y\" order=\"1\" role=\"modifier\"/>\n"
189  " <ParameterDescription key=\"FunctionParameter_278\" name=\"x\" order=\"2\" role=\"substrate\"/>\n"
190  " <ParameterDescription key=\"FunctionParameter_264\" name=\"k\" order=\"3\" role=\"constant\"/>\n"
191  " </ListOfParameterDescriptions>\n"
192  " </Function>\n"
193  " <Function key=\"Function_67\" name=\"Objective Function 2\" type=\"Expression\">\n"
194  " <Expression>\n"
195  " \n"
196  " </Expression>\n"
197  " </Function>\n"
198  " </ListOfFunctions>\n"
199  " <Model key=\"Model_1\" name=\"New Model\" timeUnit=\"min\" volumeUnit=\"ml\" quantityUnit=\"mmol\" type=\"deterministic\">\n"
200  " <Comment>\n"
201  " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
202  " \n"
203  " </body>\n"
204  " </Comment>\n"
205  " <ListOfCompartments>\n"
206  " <Compartment key=\"Compartment_1\" name=\"compartment\" simulationType=\"fixed\">\n"
207  " </Compartment>\n"
208  " </ListOfCompartments>\n"
209  " <ListOfMetabolites>\n"
210  " <Metabolite key=\"Metabolite_5\" name=\"x\" simulationType=\"reactions\" compartment=\"Compartment_1\">\n"
211  " <InitialExpression>\n"
212  " 0.66\n"
213  " </InitialExpression>\n"
214  " </Metabolite>\n"
215  " <Metabolite key=\"Metabolite_4\" name=\"y0\" simulationType=\"reactions\" compartment=\"Compartment_1\">\n"
216  " </Metabolite>\n"
217  " <Metabolite key=\"Metabolite_3\" name=\"y1\" simulationType=\"reactions\" compartment=\"Compartment_1\">\n"
218  " <InitialExpression>\n"
219  " 0.92\n"
220  " </InitialExpression>\n"
221  " </Metabolite>\n"
222  " </ListOfMetabolites>\n"
223  " <ListOfReactions>\n"
224  " <Reaction key=\"Reaction_15\" name=\"y0Prod\" reversible=\"false\">\n"
225  " <ListOfProducts>\n"
226  " <Product metabolite=\"Metabolite_4\" stoichiometry=\"1\"/>\n"
227  " </ListOfProducts>\n"
228  " <ListOfModifiers>\n"
229  " <Modifier metabolite=\"Metabolite_5\" stoichiometry=\"1\"/>\n"
230  " </ListOfModifiers>\n"
231  " <ListOfConstants>\n"
232  " <Constant key=\"Parameter_290\" name=\"k\" value=\"0.1\"/>\n"
233  " </ListOfConstants>\n"
234  " <KineticLaw function=\"Function_63\">\n"
235  " <ListOfCallParameters>\n"
236  " <CallParameter functionParameter=\"FunctionParameter_297\">\n"
237  " <SourceParameter reference=\"Parameter_290\"/>\n"
238  " </CallParameter>\n"
239  " <CallParameter functionParameter=\"FunctionParameter_268\">\n"
240  " <SourceParameter reference=\"Metabolite_5\"/>\n"
241  " </CallParameter>\n"
242  " </ListOfCallParameters>\n"
243  " </KineticLaw>\n"
244  " </Reaction>\n"
245  " <Reaction key=\"Reaction_14\" name=\"y0toy1\" reversible=\"false\">\n"
246  " <ListOfSubstrates>\n"
247  " <Substrate metabolite=\"Metabolite_4\" stoichiometry=\"1\"/>\n"
248  " </ListOfSubstrates>\n"
249  " <ListOfProducts>\n"
250  " <Product metabolite=\"Metabolite_3\" stoichiometry=\"1\"/>\n"
251  " </ListOfProducts>\n"
252  " <ListOfConstants>\n"
253  " <Constant key=\"Parameter_203\" name=\"k1\" value=\"0.1\"/>\n"
254  " </ListOfConstants>\n"
255  " <KineticLaw function=\"Function_13\">\n"
256  " <ListOfCallParameters>\n"
257  " <CallParameter functionParameter=\"FunctionParameter_81\">\n"
258  " <SourceParameter reference=\"Parameter_203\"/>\n"
259  " </CallParameter>\n"
260  " <CallParameter functionParameter=\"FunctionParameter_79\">\n"
261  " <SourceParameter reference=\"Metabolite_4\"/>\n"
262  " </CallParameter>\n"
263  " </ListOfCallParameters>\n"
264  " </KineticLaw>\n"
265  " </Reaction>\n"
266  " <Reaction key=\"Reaction_12\" name=\"y1Deg\" reversible=\"false\">\n"
267  " <ListOfSubstrates>\n"
268  " <Substrate metabolite=\"Metabolite_3\" stoichiometry=\"1\"/>\n"
269  " </ListOfSubstrates>\n"
270  " <ListOfConstants>\n"
271  " <Constant key=\"Parameter_102\" name=\"k1\" value=\"0.1\"/>\n"
272  " </ListOfConstants>\n"
273  " <KineticLaw function=\"Function_13\">\n"
274  " <ListOfCallParameters>\n"
275  " <CallParameter functionParameter=\"FunctionParameter_81\">\n"
276  " <SourceParameter reference=\"Parameter_102\"/>\n"
277  " </CallParameter>\n"
278  " <CallParameter functionParameter=\"FunctionParameter_79\">\n"
279  " <SourceParameter reference=\"Metabolite_3\"/>\n"
280  " </CallParameter>\n"
281  " </ListOfCallParameters>\n"
282  " </KineticLaw>\n"
283  " </Reaction>\n"
284  " <Reaction key=\"Reaction_11\" name=\"y0Deg\" reversible=\"false\">\n"
285  " <ListOfSubstrates>\n"
286  " <Substrate metabolite=\"Metabolite_4\" stoichiometry=\"1\"/>\n"
287  " </ListOfSubstrates>\n"
288  " <ListOfConstants>\n"
289  " <Constant key=\"Parameter_282\" name=\"k1\" value=\"0.1\"/>\n"
290  " </ListOfConstants>\n"
291  " <KineticLaw function=\"Function_13\">\n"
292  " <ListOfCallParameters>\n"
293  " <CallParameter functionParameter=\"FunctionParameter_81\">\n"
294  " <SourceParameter reference=\"Parameter_282\"/>\n"
295  " </CallParameter>\n"
296  " <CallParameter functionParameter=\"FunctionParameter_79\">\n"
297  " <SourceParameter reference=\"Metabolite_4\"/>\n"
298  " </CallParameter>\n"
299  " </ListOfCallParameters>\n"
300  " </KineticLaw>\n"
301  " </Reaction>\n"
302  " <Reaction key=\"Reaction_8\" name=\"xDegMM\" reversible=\"false\">\n"
303  " <ListOfSubstrates>\n"
304  " <Substrate metabolite=\"Metabolite_5\" stoichiometry=\"1\"/>\n"
305  " </ListOfSubstrates>\n"
306  " <ListOfModifiers>\n"
307  " <Modifier metabolite=\"Metabolite_3\" stoichiometry=\"1\"/>\n"
308  " </ListOfModifiers>\n"
309  " <ListOfConstants>\n"
310  " <Constant key=\"Parameter_412\" name=\"a_k\" value=\"0.1\"/>\n"
311  " <Constant key=\"Parameter_139\" name=\"k\" value=\"0.1\"/>\n"
312  " </ListOfConstants>\n"
313  " <KineticLaw function=\"Function_52\">\n"
314  " <ListOfCallParameters>\n"
315  " <CallParameter functionParameter=\"FunctionParameter_272\">\n"
316  " <SourceParameter reference=\"Parameter_412\"/>\n"
317  " </CallParameter>\n"
318  " <CallParameter functionParameter=\"FunctionParameter_250\">\n"
319  " <SourceParameter reference=\"Metabolite_3\"/>\n"
320  " </CallParameter>\n"
321  " <CallParameter functionParameter=\"FunctionParameter_278\">\n"
322  " <SourceParameter reference=\"Metabolite_5\"/>\n"
323  " </CallParameter>\n"
324  " <CallParameter functionParameter=\"FunctionParameter_264\">\n"
325  " <SourceParameter reference=\"Parameter_139\"/>\n"
326  " </CallParameter>\n"
327  " </ListOfCallParameters>\n"
328  " </KineticLaw>\n"
329  " </Reaction>\n"
330  " <Reaction key=\"Reaction_7\" name=\"y1Prod\" reversible=\"false\">\n"
331  " <ListOfProducts>\n"
332  " <Product metabolite=\"Metabolite_3\" stoichiometry=\"1\"/>\n"
333  " </ListOfProducts>\n"
334  " <ListOfModifiers>\n"
335  " <Modifier metabolite=\"Metabolite_4\" stoichiometry=\"1\"/>\n"
336  " </ListOfModifiers>\n"
337  " <ListOfConstants>\n"
338  " <Constant key=\"Parameter_275\" name=\"k\" value=\"0.1\"/>\n"
339  " </ListOfConstants>\n"
340  " <KineticLaw function=\"Function_63\">\n"
341  " <ListOfCallParameters>\n"
342  " <CallParameter functionParameter=\"FunctionParameter_297\">\n"
343  " <SourceParameter reference=\"Parameter_275\"/>\n"
344  " </CallParameter>\n"
345  " <CallParameter functionParameter=\"FunctionParameter_268\">\n"
346  " <SourceParameter reference=\"Metabolite_4\"/>\n"
347  " </CallParameter>\n"
348  " </ListOfCallParameters>\n"
349  " </KineticLaw>\n"
350  " </Reaction>\n"
351  " <Reaction key=\"Reaction_1\" name=\"xProd\" reversible=\"false\">\n"
352  " <ListOfProducts>\n"
353  " <Product metabolite=\"Metabolite_5\" stoichiometry=\"1\"/>\n"
354  " </ListOfProducts>\n"
355  " <ListOfModifiers>\n"
356  " <Modifier metabolite=\"Metabolite_3\" stoichiometry=\"1\"/>\n"
357  " </ListOfModifiers>\n"
358  " <ListOfConstants>\n"
359  " <Constant key=\"Parameter_339\" name=\"v\" value=\"0.1\"/>\n"
360  " </ListOfConstants>\n"
361  " <KineticLaw function=\"Function_6\">\n"
362  " <ListOfCallParameters>\n"
363  " <CallParameter functionParameter=\"FunctionParameter_49\">\n"
364  " <SourceParameter reference=\"Parameter_339\"/>\n"
365  " </CallParameter>\n"
366  " </ListOfCallParameters>\n"
367  " </KineticLaw>\n"
368  " </Reaction>\n"
369  " <Reaction key=\"Reaction_0\" name=\"xProdLin\" reversible=\"false\">\n"
370  " <ListOfProducts>\n"
371  " <Product metabolite=\"Metabolite_5\" stoichiometry=\"1\"/>\n"
372  " </ListOfProducts>\n"
373  " <ListOfModifiers>\n"
374  " <Modifier metabolite=\"Metabolite_5\" stoichiometry=\"1\"/>\n"
375  " </ListOfModifiers>\n"
376  " <ListOfConstants>\n"
377  " <Constant key=\"Parameter_306\" name=\"k\" value=\"0.1\"/>\n"
378  " </ListOfConstants>\n"
379  " <KineticLaw function=\"Function_63\">\n"
380  " <ListOfCallParameters>\n"
381  " <CallParameter functionParameter=\"FunctionParameter_297\">\n"
382  " <SourceParameter reference=\"Parameter_306\"/>\n"
383  " </CallParameter>\n"
384  " <CallParameter functionParameter=\"FunctionParameter_268\">\n"
385  " <SourceParameter reference=\"Metabolite_5\"/>\n"
386  " </CallParameter>\n"
387  " </ListOfCallParameters>\n"
388  " </KineticLaw>\n"
389  " </Reaction>\n"
390  " </ListOfReactions>\n"
391  " <StateTemplate>\n"
392  " <StateTemplateVariable objectReference=\"Model_1\"/>\n"
393  " <StateTemplateVariable objectReference=\"Metabolite_5\"/>\n"
394  " <StateTemplateVariable objectReference=\"Metabolite_4\"/>\n"
395  " <StateTemplateVariable objectReference=\"Metabolite_3\"/>\n"
396  " <StateTemplateVariable objectReference=\"Compartment_1\"/>\n"
397  " </StateTemplate>\n"
398  " <InitialState type=\"initialState\">\n"
399  " 0 3.974613390000001e+20 1.2044283e+20 5.540370180000001e+20 1\n"
400  " </InitialState>\n"
401  " </Model>\n"
402  " <ListOfTasks>\n"
403  " <Task key=\"Task_15\" name=\"Steady-State\" type=\"steadyState\" scheduled=\"false\" updateModel=\"false\">\n"
404  " <Report reference=\"Report_13\" target=\"\" append=\"1\"/>\n"
405  " <Problem>\n"
406  " <Parameter name=\"JacobianRequested\" type=\"bool\" value=\"1\"/>\n"
407  " <Parameter name=\"StabilityAnalysisRequested\" type=\"bool\" value=\"1\"/>\n"
408  " </Problem>\n"
409  " <Method name=\"Enhanced Newton\" type=\"EnhancedNewton\">\n"
410  " <Parameter name=\"Resolution\" type=\"unsignedFloat\" value=\"1e-09\"/>\n"
411  " <Parameter name=\"Derivation Factor\" type=\"unsignedFloat\" value=\"0.001\"/>\n"
412  " <Parameter name=\"Use Newton\" type=\"bool\" value=\"1\"/>\n"
413  " <Parameter name=\"Use Integration\" type=\"bool\" value=\"1\"/>\n"
414  " <Parameter name=\"Use Back Integration\" type=\"bool\" value=\"1\"/>\n"
415  " <Parameter name=\"Accept Negative Concentrations\" type=\"bool\" value=\"0\"/>\n"
416  " <Parameter name=\"Iteration Limit\" type=\"unsignedInteger\" value=\"50\"/>\n"
417  " </Method>\n"
418  " </Task>\n"
419  " <Task key=\"Task_7\" name=\"Time-Course\" type=\"timeCourse\" scheduled=\"false\" updateModel=\"false\">\n"
420  " <Problem>\n"
421  " <Parameter name=\"StepNumber\" type=\"unsignedInteger\" value=\"3500\"/>\n"
422  " <Parameter name=\"StepSize\" type=\"float\" value=\"0.01\"/>\n"
423  " <Parameter name=\"Duration\" type=\"float\" value=\"35\"/>\n"
424  " <Parameter name=\"TimeSeriesRequested\" type=\"bool\" value=\"1\"/>\n"
425  " <Parameter name=\"OutputStartTime\" type=\"float\" value=\"0\"/>\n"
426  " </Problem>\n"
427  " <Method name=\"Deterministic (LSODA)\" type=\"Deterministic(LSODA)\">\n"
428  " <Parameter name=\"Integrate Reduced Model\" type=\"bool\" value=\"0\"/>\n"
429  " <Parameter name=\"Relative Tolerance\" type=\"unsignedFloat\" value=\"1e-06\"/>\n"
430  " <Parameter name=\"Absolute Tolerance\" type=\"unsignedFloat\" value=\"1e-12\"/>\n"
431  " <Parameter name=\"Adams Max Order\" type=\"unsignedInteger\" value=\"12\"/>\n"
432  " <Parameter name=\"BDF Max Order\" type=\"unsignedInteger\" value=\"5\"/>\n"
433  " <Parameter name=\"Max Internal Steps\" type=\"unsignedInteger\" value=\"10000\"/>\n"
434  " </Method>\n"
435  " </Task>\n"
436  " <Task key=\"Task_13\" name=\"Scan\" type=\"scan\" scheduled=\"false\" updateModel=\"false\">\n"
437  " <Problem>\n"
438  " <Parameter name=\"Subtask\" type=\"unsignedInteger\" value=\"1\"/>\n"
439  " <ParameterGroup name=\"ScanItems\">\n"
440  " </ParameterGroup>\n"
441  " <Parameter name=\"Output in subtask\" type=\"bool\" value=\"1\"/>\n"
442  " <Parameter name=\"Adjust initial conditions\" type=\"bool\" value=\"0\"/>\n"
443  " </Problem>\n"
444  " <Method name=\"Scan Framework\" type=\"ScanFramework\">\n"
445  " </Method>\n"
446  " </Task>\n"
447  " <Task key=\"Task_8\" name=\"Elementary Flux Modes\" type=\"fluxMode\" scheduled=\"false\" updateModel=\"false\">\n"
448  " <Report reference=\"Report_12\" target=\"\" append=\"1\"/>\n"
449  " <Problem>\n"
450  " </Problem>\n"
451  " <Method name=\"EFM Algorithm\" type=\"EFMAlgorithm\">\n"
452  " </Method>\n"
453  " </Task>\n"
454  " <Task key=\"Task_11\" name=\"Optimization\" type=\"optimization\" scheduled=\"false\" updateModel=\"false\">\n"
455  " <Report reference=\"Report_11\" target=\"\" append=\"1\"/>\n"
456  " <Problem>\n"
457  " <Parameter name=\"Steady-State\" type=\"key\" value=\"\"/>\n"
458  " <Parameter name=\"Time-Course\" type=\"key\" value=\"Task_7\"/>\n"
459  " <Parameter name=\"ObjectiveFunction\" type=\"key\" value=\"Function_67\"/>\n"
460  " <Parameter name=\"Maximize\" type=\"bool\" value=\"0\"/>\n"
461  " <ParameterGroup name=\"OptimizationItemList\">\n"
462  " </ParameterGroup>\n"
463  " <ParameterGroup name=\"OptimizationConstraintList\">\n"
464  " </ParameterGroup>\n"
465  " </Problem>\n"
466  " <Method name=\"Random Search\" type=\"RandomSearch\">\n"
467  " <Parameter name=\"Number of Iterations\" type=\"unsignedInteger\" value=\"100000\"/>\n"
468  " <Parameter name=\"Random Number Generator\" type=\"unsignedInteger\" value=\"1\"/>\n"
469  " <Parameter name=\"Seed\" type=\"unsignedInteger\" value=\"0\"/>\n"
470  " </Method>\n"
471  " </Task>\n"
472  " <Task key=\"Task_20\" name=\"Parameter Estimation\" type=\"parameterFitting\" scheduled=\"true\" updateModel=\"true\">\n"
473  " <Report reference=\"Report_10\" target=\"\" append=\"1\"/>\n"
474  " <Problem>\n"
475  " <Parameter name=\"Steady-State\" type=\"key\" value=\"Task_15\"/>\n"
476  " <Parameter name=\"Time-Course\" type=\"key\" value=\"Task_7\"/>\n"
477  " <ParameterGroup name=\"OptimizationItemList\">\n"
478  " <ParameterGroup name=\"FitItem\">\n"
479  " <Parameter name=\"ObjectCN\" type=\"cn\" value=\"CN=Root,Model=New Model,Vector=Reactions[y0Prod],ParameterGroup=Parameters,Parameter=k,Reference=Value\"/>\n"
480  " <Parameter name=\"LowerBound\" type=\"cn\" value=\"0.001\"/>\n"
481  " <Parameter name=\"UpperBound\" type=\"cn\" value=\"100\"/>\n"
482  " <Parameter name=\"StartValue\" type=\"float\" value=\"0.1\"/>\n"
483  " <ParameterGroup name=\"Affected Experiments\">\n"
484  " </ParameterGroup>\n"
485  " </ParameterGroup>\n"
486  " <ParameterGroup name=\"FitItem\">\n"
487  " <Parameter name=\"ObjectCN\" type=\"cn\" value=\"CN=Root,Model=New Model,Vector=Reactions[y0toy1],ParameterGroup=Parameters,Parameter=k1,Reference=Value\"/>\n"
488  " <Parameter name=\"LowerBound\" type=\"cn\" value=\"0.001\"/>\n"
489  " <Parameter name=\"UpperBound\" type=\"cn\" value=\"100\"/>\n"
490  " <Parameter name=\"StartValue\" type=\"float\" value=\"0.1\"/>\n"
491  " <ParameterGroup name=\"Affected Experiments\">\n"
492  " </ParameterGroup>\n"
493  " </ParameterGroup>\n"
494  " <ParameterGroup name=\"FitItem\">\n"
495  " <Parameter name=\"ObjectCN\" type=\"cn\" value=\"CN=Root,Model=New Model,Vector=Reactions[y1Deg],ParameterGroup=Parameters,Parameter=k1,Reference=Value\"/>\n"
496  " <Parameter name=\"LowerBound\" type=\"cn\" value=\"0.001\"/>\n"
497  " <Parameter name=\"UpperBound\" type=\"cn\" value=\"100\"/>\n"
498  " <Parameter name=\"StartValue\" type=\"float\" value=\"0.1\"/>\n"
499  " <ParameterGroup name=\"Affected Experiments\">\n"
500  " </ParameterGroup>\n"
501  " </ParameterGroup>\n"
502  " <ParameterGroup name=\"FitItem\">\n"
503  " <Parameter name=\"ObjectCN\" type=\"cn\" value=\"CN=Root,Model=New Model,Vector=Reactions[y0Deg],ParameterGroup=Parameters,Parameter=k1,Reference=Value\"/>\n"
504  " <Parameter name=\"LowerBound\" type=\"cn\" value=\"0.001\"/>\n"
505  " <Parameter name=\"UpperBound\" type=\"cn\" value=\"100\"/>\n"
506  " <Parameter name=\"StartValue\" type=\"float\" value=\"0.1\"/>\n"
507  " <ParameterGroup name=\"Affected Experiments\">\n"
508  " </ParameterGroup>\n"
509  " </ParameterGroup>\n"
510  " <ParameterGroup name=\"FitItem\">\n"
511  " <Parameter name=\"ObjectCN\" type=\"cn\" value=\"CN=Root,Model=New Model,Vector=Reactions[xDegMM],ParameterGroup=Parameters,Parameter=a_k,Reference=Value\"/>\n"
512  " <Parameter name=\"LowerBound\" type=\"cn\" value=\"0.001\"/>\n"
513  " <Parameter name=\"UpperBound\" type=\"cn\" value=\"100\"/>\n"
514  " <Parameter name=\"StartValue\" type=\"float\" value=\"0.1\"/>\n"
515  " <ParameterGroup name=\"Affected Experiments\">\n"
516  " </ParameterGroup>\n"
517  " </ParameterGroup>\n"
518  " <ParameterGroup name=\"FitItem\">\n"
519  " <Parameter name=\"ObjectCN\" type=\"cn\" value=\"CN=Root,Model=New Model,Vector=Reactions[xDegMM],ParameterGroup=Parameters,Parameter=k,Reference=Value\"/>\n"
520  " <Parameter name=\"LowerBound\" type=\"cn\" value=\"0.001\"/>\n"
521  " <Parameter name=\"UpperBound\" type=\"cn\" value=\"100\"/>\n"
522  " <Parameter name=\"StartValue\" type=\"float\" value=\"0.1\"/>\n"
523  " <ParameterGroup name=\"Affected Experiments\">\n"
524  " </ParameterGroup>\n"
525  " </ParameterGroup>\n"
526  " <ParameterGroup name=\"FitItem\">\n"
527  " <Parameter name=\"ObjectCN\" type=\"cn\" value=\"CN=Root,Model=New Model,Vector=Reactions[y1Prod],ParameterGroup=Parameters,Parameter=k,Reference=Value\"/>\n"
528  " <Parameter name=\"LowerBound\" type=\"cn\" value=\"0.001\"/>\n"
529  " <Parameter name=\"UpperBound\" type=\"cn\" value=\"100\"/>\n"
530  " <Parameter name=\"StartValue\" type=\"float\" value=\"0.1\"/>\n"
531  " <ParameterGroup name=\"Affected Experiments\">\n"
532  " </ParameterGroup>\n"
533  " </ParameterGroup>\n"
534  " <ParameterGroup name=\"FitItem\">\n"
535  " <Parameter name=\"ObjectCN\" type=\"cn\" value=\"CN=Root,Model=New Model,Vector=Reactions[xProd],ParameterGroup=Parameters,Parameter=k,Reference=Value\"/>\n"
536  " <Parameter name=\"LowerBound\" type=\"cn\" value=\"0.001\"/>\n"
537  " <Parameter name=\"UpperBound\" type=\"cn\" value=\"100\"/>\n"
538  " <Parameter name=\"StartValue\" type=\"float\" value=\"0.1\"/>\n"
539  " <ParameterGroup name=\"Affected Experiments\">\n"
540  " </ParameterGroup>\n"
541  " </ParameterGroup>\n"
542  " <ParameterGroup name=\"FitItem\">\n"
543  " <Parameter name=\"ObjectCN\" type=\"cn\" value=\"CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[y0],Reference=InitialConcentration\"/>\n"
544  " <Parameter name=\"LowerBound\" type=\"cn\" value=\"0.01\"/>\n"
545  " <Parameter name=\"UpperBound\" type=\"cn\" value=\"1\"/>\n"
546  " <Parameter name=\"StartValue\" type=\"float\" value=\"0.2\"/>\n"
547  " <ParameterGroup name=\"Affected Experiments\">\n"
548  " </ParameterGroup>\n"
549  " </ParameterGroup>\n"
550  " </ParameterGroup>\n"
551  " <ParameterGroup name=\"OptimizationConstraintList\">\n"
552  " </ParameterGroup>\n"
553  " <ParameterGroup name=\"Experiment Set\">\n"
554  " <ParameterGroup name=\"Experiment\">\n"
555  " <Parameter name=\"Key\" type=\"key\" value=\"Experiment_2\"/>\n"
556  " <Parameter name=\"File Name\" type=\"file\" value=\"Geva-ZatorskyCutoff.txt\"/>\n"
557  " <Parameter name=\"First Row\" type=\"unsignedInteger\" value=\"1\"/>\n"
558  " <Parameter name=\"Last Row\" type=\"unsignedInteger\" value=\"93\"/>\n"
559  " <Parameter name=\"Experiment Type\" type=\"unsignedInteger\" value=\"1\"/>\n"
560  " <Parameter name=\"Separator\" type=\"string\" value=\"&#x09;\"/>\n"
561  " <Parameter name=\"Weight Method\" type=\"unsignedInteger\" value=\"2\"/>\n"
562  " <Parameter name=\"Data is Row Oriented\" type=\"bool\" value=\"1\"/>\n"
563  " <Parameter name=\"Row containing Names\" type=\"unsignedInteger\" value=\"1\"/>\n"
564  " <Parameter name=\"Number of Columns\" type=\"unsignedInteger\" value=\"3\"/>\n"
565  " <ParameterGroup name=\"Object Map\">\n"
566  " <ParameterGroup name=\"0\">\n"
567  " <Parameter name=\"Role\" type=\"unsignedInteger\" value=\"3\"/>\n"
568  " </ParameterGroup>\n"
569  " <ParameterGroup name=\"1\">\n"
570  " <Parameter name=\"Role\" type=\"unsignedInteger\" value=\"2\"/>\n"
571  " <Parameter name=\"Object CN\" type=\"cn\" value=\"CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[x],Reference=Concentration\"/>\n"
572  " </ParameterGroup>\n"
573  " <ParameterGroup name=\"2\">\n"
574  " <Parameter name=\"Role\" type=\"unsignedInteger\" value=\"2\"/>\n"
575  " <Parameter name=\"Object CN\" type=\"cn\" value=\"CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[y1],Reference=Concentration\"/>\n"
576  " </ParameterGroup>\n"
577  " </ParameterGroup>\n"
578  " </ParameterGroup>\n"
579  " </ParameterGroup>\n"
580  " </Problem>\n"
581  " <Method name=\"Evolutionary Programming\" type=\"EvolutionaryProgram\">\n"
582  " <Parameter name=\"Number of Generations\" type=\"unsignedInteger\" value=\"2000\"/>\n"
583  " <Parameter name=\"Population Size\" type=\"unsignedInteger\" value=\"100\"/>\n"
584  " <Parameter name=\"Random Number Generator\" type=\"unsignedInteger\" value=\"1\"/>\n"
585  " <Parameter name=\"Seed\" type=\"unsignedInteger\" value=\"0\"/>\n"
586  " </Method>\n"
587  " </Task>\n"
588  " <Task key=\"Task_19\" name=\"Metabolic Control Analysis\" type=\"metabolicControlAnalysis\" scheduled=\"false\" updateModel=\"false\">\n"
589  " <Report reference=\"Report_9\" target=\"\" append=\"1\"/>\n"
590  " <Problem>\n"
591  " <Parameter name=\"Steady-State\" type=\"key\" value=\"Task_15\"/>\n"
592  " </Problem>\n"
593  " <Method name=\"MCA Method (Reder)\" type=\"MCAMethod(Reder)\">\n"
594  " <Parameter name=\"Modulation Factor\" type=\"unsignedFloat\" value=\"1e-09\"/>\n"
595  " </Method>\n"
596  " </Task>\n"
597  " <Task key=\"Task_18\" name=\"Lyapunov Exponents\" type=\"lyapunovExponents\" scheduled=\"false\" updateModel=\"false\">\n"
598  " <Report reference=\"Report_8\" target=\"\" append=\"1\"/>\n"
599  " <Problem>\n"
600  " <Parameter name=\"ExponentNumber\" type=\"unsignedInteger\" value=\"3\"/>\n"
601  " <Parameter name=\"DivergenceRequested\" type=\"bool\" value=\"1\"/>\n"
602  " <Parameter name=\"TransientTime\" type=\"float\" value=\"0\"/>\n"
603  " </Problem>\n"
604  " <Method name=\"Wolf Method\" type=\"WolfMethod\">\n"
605  " <Parameter name=\"Orthonormalization Interval\" type=\"unsignedFloat\" value=\"1\"/>\n"
606  " <Parameter name=\"Overall time\" type=\"unsignedFloat\" value=\"1000\"/>\n"
607  " <Parameter name=\"Relative Tolerance\" type=\"unsignedFloat\" value=\"1e-06\"/>\n"
608  " <Parameter name=\"Use Default Absolute Tolerance\" type=\"bool\" value=\"1\"/>\n"
609  " <Parameter name=\"Absolute Tolerance\" type=\"unsignedFloat\" value=\"1e-12\"/>\n"
610  " <Parameter name=\"Adams Max Order\" type=\"unsignedInteger\" value=\"12\"/>\n"
611  " <Parameter name=\"BDF Max Order\" type=\"unsignedInteger\" value=\"5\"/>\n"
612  " <Parameter name=\"Max Internal Steps\" type=\"unsignedInteger\" value=\"10000\"/>\n"
613  " </Method>\n"
614  " </Task>\n"
615  " <Task key=\"Task_17\" name=\"Sensitivities\" type=\"sensitivities\" scheduled=\"false\" updateModel=\"false\">\n"
616  " <Report reference=\"Report_7\" target=\"\" append=\"1\"/>\n"
617  " <Problem>\n"
618  " <Parameter name=\"SubtaskType\" type=\"unsignedInteger\" value=\"1\"/>\n"
619  " <ParameterGroup name=\"TargetFunctions\">\n"
620  " <Parameter name=\"SingleObject\" type=\"cn\" value=\"\"/>\n"
621  " <Parameter name=\"ObjectListType\" type=\"unsignedInteger\" value=\"7\"/>\n"
622  " </ParameterGroup>\n"
623  " <ParameterGroup name=\"ListOfVariables\">\n"
624  " <ParameterGroup name=\"Variables\">\n"
625  " <Parameter name=\"SingleObject\" type=\"cn\" value=\"\"/>\n"
626  " <Parameter name=\"ObjectListType\" type=\"unsignedInteger\" value=\"41\"/>\n"
627  " </ParameterGroup>\n"
628  " </ParameterGroup>\n"
629  " </Problem>\n"
630  " <Method name=\"Sensitivities Method\" type=\"SensitivitiesMethod\">\n"
631  " <Parameter name=\"Delta factor\" type=\"unsignedFloat\" value=\"1e-06\"/>\n"
632  " <Parameter name=\"Delta minimum\" type=\"unsignedFloat\" value=\"1e-12\"/>\n"
633  " </Method>\n"
634  " </Task>\n"
635  " <Task key=\"Task_10\" name=\"Moieties\" type=\"moieties\" scheduled=\"false\" updateModel=\"false\">\n"
636  " <Problem>\n"
637  " </Problem>\n"
638  " <Method name=\"Householder Reduction\" type=\"Householder\">\n"
639  " </Method>\n"
640  " </Task>\n"
641  " </ListOfTasks>\n"
642  " <ListOfReports>\n"
643  " <Report key=\"Report_13\" name=\"Steady-State\" taskType=\"steadyState\" separator=\"&#x09;\" precision=\"6\">\n"
644  " <Comment>\n"
645  " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
646  " Automatically generated report.\n"
647  " </body>\n"
648  " </Comment>\n"
649  " <Footer>\n"
650  " <Object cn=\"CN=Root,Vector=TaskList[Steady-State]\"/>\n"
651  " </Footer>\n"
652  " </Report>\n"
653  " <Report key=\"Report_12\" name=\"Elementary Flux Modes\" taskType=\"fluxMode\" separator=\"&#x09;\" precision=\"6\">\n"
654  " <Comment>\n"
655  " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
656  " Automatically generated report.\n"
657  " </body>\n"
658  " </Comment>\n"
659  " <Footer>\n"
660  " <Object cn=\"CN=Root,Vector=TaskList[Elementary Flux Modes],Object=Result\"/>\n"
661  " </Footer>\n"
662  " </Report>\n"
663  " <Report key=\"Report_11\" name=\"Optimization\" taskType=\"optimization\" separator=\"&#x09;\" precision=\"6\">\n"
664  " <Comment>\n"
665  " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
666  " Automatically generated report.\n"
667  " </body>\n"
668  " </Comment>\n"
669  " <Header>\n"
670  " <Object cn=\"CN=Root,Vector=TaskList[Optimization],Object=Description\"/>\n"
671  " <Object cn=\"String=\\[Function Evaluations\\]\"/>\n"
672  " <Object cn=\"Separator=&#x09;\"/>\n"
673  " <Object cn=\"String=\\[Best Value\\]\"/>\n"
674  " <Object cn=\"Separator=&#x09;\"/>\n"
675  " <Object cn=\"String=\\[Best Parameters\\]\"/>\n"
676  " </Header>\n"
677  " <Body>\n"
678  " <Object cn=\"CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Function Evaluations\"/>\n"
679  " <Object cn=\"Separator=&#x09;\"/>\n"
680  " <Object cn=\"CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Best Value\"/>\n"
681  " <Object cn=\"Separator=&#x09;\"/>\n"
682  " <Object cn=\"CN=Root,Vector=TaskList[Optimization],Problem=Optimization,Reference=Best Parameters\"/>\n"
683  " </Body>\n"
684  " <Footer>\n"
685  " <Object cn=\"String=&#x0a;\"/>\n"
686  " <Object cn=\"CN=Root,Vector=TaskList[Optimization],Object=Result\"/>\n"
687  " </Footer>\n"
688  " </Report>\n"
689  " <Report key=\"Report_10\" name=\"Parameter Estimation\" taskType=\"parameterFitting\" separator=\"&#x09;\" precision=\"6\">\n"
690  " <Comment>\n"
691  " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
692  " Automatically generated report.\n"
693  " </body>\n"
694  " </Comment>\n"
695  " <Header>\n"
696  " <Object cn=\"CN=Root,Vector=TaskList[Parameter Estimation],Object=Description\"/>\n"
697  " <Object cn=\"String=\\[Function Evaluations\\]\"/>\n"
698  " <Object cn=\"Separator=&#x09;\"/>\n"
699  " <Object cn=\"String=\\[Best Value\\]\"/>\n"
700  " <Object cn=\"Separator=&#x09;\"/>\n"
701  " <Object cn=\"String=\\[Best Parameters\\]\"/>\n"
702  " </Header>\n"
703  " <Body>\n"
704  " <Object cn=\"CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,Reference=Function Evaluations\"/>\n"
705  " <Object cn=\"Separator=&#x09;\"/>\n"
706  " <Object cn=\"CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,Reference=Best Value\"/>\n"
707  " <Object cn=\"Separator=&#x09;\"/>\n"
708  " <Object cn=\"CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,Reference=Best Parameters\"/>\n"
709  " </Body>\n"
710  " <Footer>\n"
711  " <Object cn=\"String=&#x0a;\"/>\n"
712  " <Object cn=\"CN=Root,Vector=TaskList[Parameter Estimation],Object=Result\"/>\n"
713  " </Footer>\n"
714  " </Report>\n"
715  " <Report key=\"Report_9\" name=\"Metabolic Control Analysis\" taskType=\"metabolicControlAnalysis\" separator=\"&#x09;\" precision=\"6\">\n"
716  " <Comment>\n"
717  " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
718  " Automatically generated report.\n"
719  " </body>\n"
720  " </Comment>\n"
721  " <Header>\n"
722  " <Object cn=\"CN=Root,Vector=TaskList[Metabolic Control Analysis],Object=Description\"/>\n"
723  " </Header>\n"
724  " <Footer>\n"
725  " <Object cn=\"String=&#x0a;\"/>\n"
726  " <Object cn=\"CN=Root,Vector=TaskList[Metabolic Control Analysis],Object=Result\"/>\n"
727  " </Footer>\n"
728  " </Report>\n"
729  " <Report key=\"Report_8\" name=\"Lyapunov Exponents\" taskType=\"lyapunovExponents\" separator=\"&#x09;\" precision=\"6\">\n"
730  " <Comment>\n"
731  " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
732  " Automatically generated report.\n"
733  " </body>\n"
734  " </Comment>\n"
735  " <Header>\n"
736  " <Object cn=\"CN=Root,Vector=TaskList[Lyapunov Exponents],Object=Description\"/>\n"
737  " </Header>\n"
738  " <Footer>\n"
739  " <Object cn=\"String=&#x0a;\"/>\n"
740  " <Object cn=\"CN=Root,Vector=TaskList[Lyapunov Exponents],Object=Result\"/>\n"
741  " </Footer>\n"
742  " </Report>\n"
743  " <Report key=\"Report_7\" name=\"Sensitivities\" taskType=\"sensitivities\" separator=\"&#x09;\" precision=\"6\">\n"
744  " <Comment>\n"
745  " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
746  " Automatically generated report.\n"
747  " </body>\n"
748  " </Comment>\n"
749  " <Header>\n"
750  " <Object cn=\"CN=Root,Vector=TaskList[Sensitivities],Object=Description\"/>\n"
751  " </Header>\n"
752  " <Footer>\n"
753  " <Object cn=\"String=&#x0a;\"/>\n"
754  " <Object cn=\"CN=Root,Vector=TaskList[Sensitivities],Object=Result\"/>\n"
755  " </Footer>\n"
756  " </Report>\n"
757  " </ListOfReports>\n"
758  " <ListOfPlots>\n"
759  " <PlotSpecification name=\"Concentrations, Volumes, and Global Quantity Values\" type=\"Plot2D\" active=\"1\">\n"
760  " <Parameter name=\"log X\" type=\"bool\" value=\"0\"/>\n"
761  " <Parameter name=\"log Y\" type=\"bool\" value=\"0\"/>\n"
762  " <ListOfPlotItems>\n"
763  " <PlotItem name=\"[x]\" type=\"Curve2D\">\n"
764  " <Parameter name=\"Line type\" type=\"unsignedInteger\" value=\"0\"/>\n"
765  " <Parameter name=\"Recording Activity\" type=\"string\" value=\"during\"/>\n"
766  " <ListOfChannels>\n"
767  " <ChannelSpec cn=\"CN=Root,Model=New Model,Reference=Time\"/>\n"
768  " <ChannelSpec cn=\"CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[x],Reference=Concentration\"/>\n"
769  " </ListOfChannels>\n"
770  " </PlotItem>\n"
771  " <PlotItem name=\"[y0]\" type=\"Curve2D\">\n"
772  " <Parameter name=\"Line type\" type=\"unsignedInteger\" value=\"0\"/>\n"
773  " <Parameter name=\"Recording Activity\" type=\"string\" value=\"during\"/>\n"
774  " <ListOfChannels>\n"
775  " <ChannelSpec cn=\"CN=Root,Model=New Model,Reference=Time\"/>\n"
776  " <ChannelSpec cn=\"CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[y0],Reference=Concentration\"/>\n"
777  " </ListOfChannels>\n"
778  " </PlotItem>\n"
779  " <PlotItem name=\"[y]\" type=\"Curve2D\">\n"
780  " <Parameter name=\"Line type\" type=\"unsignedInteger\" value=\"0\"/>\n"
781  " <Parameter name=\"Recording Activity\" type=\"string\" value=\"during\"/>\n"
782  " <ListOfChannels>\n"
783  " <ChannelSpec cn=\"CN=Root,Model=New Model,Reference=Time\"/>\n"
784  " <ChannelSpec cn=\"CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[y1],Reference=Concentration\"/>\n"
785  " </ListOfChannels>\n"
786  " </PlotItem>\n"
787  " </ListOfPlotItems>\n"
788  " </PlotSpecification>\n"
789  " <PlotSpecification name=\"Experiment\" type=\"Plot2D\" active=\"1\">\n"
790  " <Parameter name=\"log X\" type=\"bool\" value=\"0\"/>\n"
791  " <Parameter name=\"log Y\" type=\"bool\" value=\"0\"/>\n"
792  " <ListOfPlotItems>\n"
793  " <PlotItem name=\"[x](Measured Value)\" type=\"Curve2D\">\n"
794  " <Parameter name=\"Line type\" type=\"unsignedInteger\" value=\"2\"/>\n"
795  " <Parameter name=\"Recording Activity\" type=\"string\" value=\"after\"/>\n"
796  " <ListOfChannels>\n"
797  " <ChannelSpec cn=\"CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Experiment,Vector=Fitted Points[0],Reference=Independent Value\"/>\n"
798  " <ChannelSpec cn=\"CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Experiment,Vector=Fitted Points[0],Reference=Measured Value\"/>\n"
799  " </ListOfChannels>\n"
800  " </PlotItem>\n"
801  " <PlotItem name=\"[x](Fitted Value)\" type=\"Curve2D\">\n"
802  " <Parameter name=\"Line type\" type=\"unsignedInteger\" value=\"0\"/>\n"
803  " <Parameter name=\"Recording Activity\" type=\"string\" value=\"after\"/>\n"
804  " <ListOfChannels>\n"
805  " <ChannelSpec cn=\"CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Experiment,Vector=Fitted Points[0],Reference=Independent Value\"/>\n"
806  " <ChannelSpec cn=\"CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Experiment,Vector=Fitted Points[0],Reference=Fitted Value\"/>\n"
807  " </ListOfChannels>\n"
808  " </PlotItem>\n"
809  " <PlotItem name=\"[y](Measured Value)\" type=\"Curve2D\">\n"
810  " <Parameter name=\"Line type\" type=\"unsignedInteger\" value=\"2\"/>\n"
811  " <Parameter name=\"Recording Activity\" type=\"string\" value=\"after\"/>\n"
812  " <ListOfChannels>\n"
813  " <ChannelSpec cn=\"CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Experiment,Vector=Fitted Points[0],Reference=Independent Value\"/>\n"
814  " <ChannelSpec cn=\"CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Experiment,Vector=Fitted Points[1],Reference=Measured Value\"/>\n"
815  " </ListOfChannels>\n"
816  " </PlotItem>\n"
817  " <PlotItem name=\"[y](Fitted Value)\" type=\"Curve2D\">\n"
818  " <Parameter name=\"Line type\" type=\"unsignedInteger\" value=\"0\"/>\n"
819  " <Parameter name=\"Recording Activity\" type=\"string\" value=\"after\"/>\n"
820  " <ListOfChannels>\n"
821  " <ChannelSpec cn=\"CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Experiment,Vector=Fitted Points[0],Reference=Independent Value\"/>\n"
822  " <ChannelSpec cn=\"CN=Root,Vector=TaskList[Parameter Estimation],Problem=Parameter Estimation,ParameterGroup=Experiment Set,ParameterGroup=Experiment,Vector=Fitted Points[1],Reference=Fitted Value\"/>\n"
823  " </ListOfChannels>\n"
824  " </PlotItem>\n"
825  " </ListOfPlotItems>\n"
826  " </PlotSpecification>\n"
827  " </ListOfPlots>\n"
828  " <GUI>\n"
829  " </GUI>\n"
830  " <SBMLReference file=\"MasterModel.xml\">\n"
831  " <SBMLMap SBMLid=\"compartment_1\" COPASIkey=\"Compartment_1\"/>\n"
832  " <SBMLMap SBMLid=\"function_1\" COPASIkey=\"Function_52\"/>\n"
833  " <SBMLMap SBMLid=\"function_2\" COPASIkey=\"Function_63\"/>\n"
834  " <SBMLMap SBMLid=\"reaction_3\" COPASIkey=\"Reaction_15\"/>\n"
835  " <SBMLMap SBMLid=\"reaction_4\" COPASIkey=\"Reaction_14\"/>\n"
836  " <SBMLMap SBMLid=\"reaction_5\" COPASIkey=\"Reaction_12\"/>\n"
837  " <SBMLMap SBMLid=\"reaction_8\" COPASIkey=\"Reaction_11\"/>\n"
838  " <SBMLMap SBMLid=\"species_1\" COPASIkey=\"Metabolite_5\"/>\n"
839  " <SBMLMap SBMLid=\"species_2\" COPASIkey=\"Metabolite_4\"/>\n"
840  " <SBMLMap SBMLid=\"species_3\" COPASIkey=\"Metabolite_3\"/>\n"
841  " </SBMLReference>\n"
842  "</COPASI>\n"
843 };
test000067::tearDown
void tearDown()
Definition: test000067.cpp:49
CCopasiDataModel::getCurrentSBMLDocument
SBMLDocument * getCurrentSBMLDocument()
Definition: CCopasiDataModel.cpp:1835
CModelValue.h
Header file of class CModelEntity and CModelValue.
test000067::setUp
void setUp()
Definition: test000067.cpp:41
CCopasiDataModel::exportSBMLToString
std::string exportSBMLToString(CProcessReport *pExportHandler, int sbmlLevel, int sbmlVersion)
Definition: CCopasiDataModel.cpp:709
test000059::checkIfIdsUnique
static bool checkIfIdsUnique(const Model *pSBMLModel)
Definition: test000059.cpp:44
test000067::test_bug1060
void test_bug1060()
Definition: test000067.cpp:54
test000067::MODEL_STRING1
static const char * MODEL_STRING1
Definition: test000067.h:36
load_cps_model_from_stream
bool load_cps_model_from_stream(std::istream &is, CCopasiDataModel &dataModel)
Definition: utilities.cpp:21
CCopasiRootContainer::getFunctionList
static CFunctionDB * getFunctionList()
Definition: CCopasiRootContainer.cpp:137
CCopasiRootContainer::addDatamodel
static CCopasiDataModel * addDatamodel()
Definition: CCopasiRootContainer.cpp:149
test000067::pCOPASIDATAMODEL
static CCopasiDataModel * pCOPASIDATAMODEL
Definition: test000067.h:37
CCopasiRootContainer::init
static void init(int argc, char *argv[], const bool &withGui=false)
Definition: CCopasiRootContainer.cpp:78
CCopasiDataModel::getCopasi2SBMLMap
std::map< CCopasiObject *, SBase * > & getCopasi2SBMLMap()
Definition: CCopasiDataModel.cpp:1854
CFunctionDB::findFunction
CFunction * findFunction(const std::string &functionName)
Definition: CFunctionDB.cpp:325
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