103 const std::string & relativeTo)
107 os.imbue(std::locale::classic());
113 *
mpOstream <<
"<?xml version=\"1.0\" encoding=\"UTF-8\"?>"
116 *
mpOstream <<
"<!-- generated with COPASI "
118 <<
" (http://www.copasi.org) at "
123 *
mpOstream <<
"<?oxygen RNGSchema=\"http://www.copasi.org/static/schema/CopasiML.rng\" type=\"xml\"?>" << std::endl;
126 Attributes.
add(
"xmlns",
"http://www.copasi.org/static/schema");
158 if (!
saveGUI()) success =
false;
170 const std::string & relativeTo)
174 is.imbue(std::locale::classic());
189 #define BUFFER_SIZE 0xfffe
202 if (!Parser.
parse(pBuffer, -1, done))
436 Attributes.
add(
"key",
"");
437 Attributes.
add(
"name",
"");
438 Attributes.
add(
"simulationType",
"");
439 Attributes.
add(
"dimensionality",
"");
443 for (i = 0; i < imax; i++)
487 Attributes.
add(
"key",
"");
488 Attributes.
add(
"name",
"");
489 Attributes.
add(
"simulationType",
"");
490 Attributes.
add(
"compartment",
"");
492 for (i = 0; i < imax; i++)
537 Attributes.
add(
"key",
"");
538 Attributes.
add(
"name",
"");
539 Attributes.
add(
"simulationType",
"");
541 for (i = 0; i < imax; i++)
587 std::vector< const CCopasiObject * >
ObjectList;
591 Attributes.
add(
"key",
"");
592 Attributes.
add(
"name",
"");
593 Attributes.
add(
"reversible",
"");
594 Attributes.
add(
"fast",
"");
596 for (i = 0; i < imax; i++)
613 Attr.
add(
"metabolite",
"");
614 Attr.
add(
"stoichiometry",
"");
618 if ((jmax = pReactantList->
size()) > 0)
622 for (j = 0; j < jmax; j++)
624 Attr.
setValue(0, (*pReactantList)[j]->getMetaboliteKey());
625 Attr.
setValue(1, (*pReactantList)[j]->getMultiplicity());
637 if ((jmax = pReactantList->
size()) > 0)
641 for (j = 0; j < jmax; j++)
643 Attr.
setValue(0, (*pReactantList)[j]->getMetaboliteKey());
644 Attr.
setValue(1, (*pReactantList)[j]->getMultiplicity());
654 if ((jmax = pReactantList->
size()) > 0)
658 for (j = 0, jmax = pReactantList->
size(); j < jmax; j++)
660 Attr.
setValue(0, (*pReactantList)[j]->getMetaboliteKey());
661 Attr.
setValue(1, (*pReactantList)[j]->getMultiplicity());
673 if ((jmax = pParamList->
size()) > 0)
679 Attr.
add(
"name",
"");
680 Attr.
add(
"value",
"");
682 for (j = 0; j < jmax; j++)
703 const std::vector< std::vector<std::string> > & rMap =
706 for (j = 0; j < jmax; j++)
709 Attr.
add(
"functionParameter",
711 getFunction()->getVariables()[j]->getKey());
716 Attr.
add(
"reference",
"");
718 for (k = 0, kmax = rMap[j].size(); k < kmax; k++)
745 Attributes.
add(
"key",
"");
746 Attributes.
add(
"name",
"");
747 Attributes.
add(
"delayAssignment",
"");
748 Attributes.
add(
"fireAtInitialTime",
"");
749 Attributes.
add(
"persistentTrigger",
"");
751 for (i = 0; i < imax; i++)
790 if (Assignments.
size() > 0)
795 Attr.
add(
"targetKey",
"");
800 for (; it != end; ++it)
802 Attr.
setValue(0, (*it)->getTargetKey());
828 Attributes.
add(
"activeSet", pSet->
getKey());
833 Attributes.
add(
"key",
"");
834 Attributes.
add(
"name",
"");
848 for (; itSet != endSet; ++itSet)
857 for (i = 0; i < imax; i++)
868 itSet = pSet->
begin();
869 endSet = pSet->
end();
871 for (; itSet != endSet; ++itSet)
887 Attributes.
add(
"objectReference",
"");
888 std::pair< std::string, std::string > Variable;
893 for (; ppEntity != ppEntityEnd; ++ppEntity)
895 Attributes.
setValue(0, (*ppEntity)->getKey());
903 Attributes.
add(
"type",
"initialState");
908 for (; ppEntity != ppEntityEnd; ++ppEntity)
910 *
mpOstream << (
DBL)(*ppEntity)->getInitialValue() <<
" ";
946 Attributes.
add(
"name",
"");
948 for (; it != end; ++it)
979 Attributes.
add(
"cn", pModelParameter->
getCN());
999 Attributes.
add(
"cn", pModelParameter->
getCN());
1007 for (; it != end; ++it)
1020 bool success =
true;
1026 if (!imax)
return success;
1033 for (i = 0; i < imax; i++)
1035 pFunction = (*mpFunctionList)[i];
1038 Attributes.
add(
"key", pFunction->
getKey());
1047 Attributes.
add(
"reversible",
"unspecified");
1051 Attributes.
add(
"reversible",
"false");
1055 Attributes.
add(
"reversible",
"true");
1079 Attributes.
add(
"key",
"");
1080 Attributes.
add(
"name",
"");
1081 Attributes.
add(
"order",
"");
1082 Attributes.
add(
"role",
"");
1084 for (j = 0; j < jmax; j++)
1109 bool success =
true;
1120 if (!imax)
return success;
1126 for (i = 0; i < imax; i++)
1140 for (j = 0; j < jmax; j++)
1152 for (k = 0; k < kmax; k++)
1156 Attributes.
add(
"cn", pDataChannelSpec);
1160 Attributes.
add(
"min", pDataChannelSpec.
min);
1165 Attributes.
add(
"max", pDataChannelSpec.
max);
1186 bool success =
true;
1192 if (!imax)
return success;
1199 for (i = 0; i < imax; i++)
1201 pTask = (*mpTaskList)[i];
1207 Attributes.
add(
"scheduled", pTask->
isScheduled() ?
"true" :
"false");
1220 std::string Target = tReport.
getTarget();
1226 Attributes.
add(
"target", Target);
1227 Attributes.
add(
"append", tReport.
append());
1244 Attributes.
add(
"name", tMethod->CCopasiParameter::getObjectName());
1260 const std::vector <CRegisteredObjectName> & section)
1263 Attributes.
add(
"NoName",
"");
1265 size_t j, jmax = section.size();
1271 for (j = 0; j < jmax; j++)
1273 if (section[j].getObjectType() ==
"html")
1277 Attributes.
set(0,
"xmlns",
"http://www.w3.org/1999/xhtml");
1279 saveData(section[j].getObjectName());
1286 Attributes.
set(0,
"cn", section[j]);
1299 bool success =
true;
1305 if (!imax)
return success;
1312 for (i = 0; i < imax; i++)
1314 pReport = (*mpReportList)[i];
1317 Attributes.
add(
"key", pReport->
getKey());
1332 Attributes.
add(
"printTitle", pReport->
getTitle());
1335 const std::vector <CRegisteredObjectName> & Table = * pReport->
getTableAddr();
1336 size_t j, jmax = Table.size();
1339 Attributes.
add(
"cn",
"");
1341 for (j = 0; j < jmax; j++)
1368 Attributes.
add(
"x", p.
getX());
1369 Attributes.
add(
"y", p.
getY());
1400 for (i = 0; i < imax; ++i)
1407 Attributes.
add(
"xsi:type",
"CubicBezier");
1409 Attributes.
add(
"xsi:type",
"LineSegment");
1433 bool success =
true;
1439 if (!imax)
return success;
1443 Attributes.
add(
"xmlns:xsi",
"http://www.w3.org/2001/XMLSchema-instance");
1446 for (i = 0; i < imax; i++)
1448 pLayout = (*mpLayoutList)[i];
1451 Attributes.
add(
"key", pLayout->
getKey());
1469 for (j = 0; j < jmax; ++j)
1494 Attributes.
add(
"metabolite",
"");
1497 if (cg->
getObjectRole().find_first_not_of(
" \t\r\n") != std::string::npos)
1519 for (j = 0; j < jmax; ++j)
1544 Attributes.
add(
"metabolite",
"");
1547 if (cg->
getObjectRole().find_first_not_of(
" \t\r\n") != std::string::npos)
1569 for (j = 0; j < jmax; ++j)
1593 if (cg->
getObjectRole().find_first_not_of(
" \t\r\n") != std::string::npos)
1609 for (k = 0; k < kmax; ++k)
1619 if (mrg->
getObjectRole().find_first_not_of(
" \t\r\n") != std::string::npos)
1649 for (j = 0; j < jmax; ++j)
1656 if (cg->
isTextSet() ||
id.find_first_not_of(
" \t\r\n") != std::string::npos)
1672 Attributes.
add(
"originOfText",
id);
1677 Attributes.
add(
"text",
"unset");
1690 if (cg->
getObjectRole().find_first_not_of(
" \t\r\n") != std::string::npos)
1713 for (j = 0; j < jmax; ++j)
1739 if (cg->
getObjectRole().find_first_not_of(
" \t\r\n") != std::string::npos)
1781 bool success =
true;
1783 if (!
haveGUI())
return success;
1794 Attributes.
add(
"key",
"");
1795 Attributes.
add(
"associatedEntityKey",
"");
1796 Attributes.
add(
"objectCN",
"");
1797 Attributes.
add(
"objectType",
"");
1798 Attributes.
add(
"objectValue",
"");
1799 Attributes.
add(
"minValue",
"");
1800 Attributes.
add(
"maxValue",
"");
1801 Attributes.
add(
"tickNumber",
"");
1802 Attributes.
add(
"tickFactor",
"");
1803 Attributes.
add(
"scaling",
"");
1807 for (i = 0; i < imax; i++)
1849 Attributes.
add(
"file", SBMLFile);
1853 Attributes.
add(
"SBMLid",
"");
1854 Attributes.
add(
"COPASIkey",
"");
1856 std::map<std::string, std::string>::const_iterator it =
mSBMLReference.begin();
1857 std::map<std::string, std::string>::const_iterator end =
mSBMLReference.end();
1859 for (; it != end; ++it)
1862 Attributes.
setValue(1, it->second);
1874 bool success =
true;
1896 if (pTask == NULL)
return;
1913 if (pTask == NULL)
return;
1926 size_t i, iMax = list.
size();
1928 for (i = 0; i < iMax; ++i)
1942 size_t i, iMax = list.
size();
1944 for (i = 0; i < iMax; ++i)
1970 for (i = 0; i < iMax; ++i)
1999 for (i = 0; i < iMax; ++i)
2013 attributes.
add(
"key", renderInfo.
getKey());
2015 std::string s = renderInfo.
getName();
2016 const char* ws =
" \t\n\r";
2018 if (s.find_first_not_of(ws) != std::string::npos)
2020 attributes.
add(
"name", s);
2026 if (s.find_first_not_of(ws) != std::string::npos)
2029 attributes.
add(
"backgroundColor", s);
2035 if (s.find_first_not_of(ws) != std::string::npos)
2038 attributes.
add(
"referenceRenderInformation", s);
2053 for (i = 0; i < iMax; ++i)
2068 for (i = 0; i < iMax; ++i)
2072 if (dynamic_cast<const CLRadialGradient*>(pGradient))
2076 else if (dynamic_cast<const CLLinearGradient*>(pGradient))
2091 for (i = 0; i < iMax; ++i)
2106 attributes.
add(
"id", color.
getId());
2169 attributes.
add(
"id", gradient.
getId());
2174 attributes.
add(
"spreadMethod",
"repeat");
2178 attributes.
add(
"spreadMethod",
"reflect");
2183 attributes.
add(
"spreadMethod",
"pad");
2197 for (i = 0; i < iMax; ++i)
2219 attributes.
add(
"id", lineEnding.
getId());
2225 assert(lineEnding.
getGroup() != NULL);
2297 saveTextAttributes<CLGroup>(group, attributes);
2298 saveArrowHeadAttributes<CLGroup>(group, attributes);
2300 size_t i, iMax = group.getNumElements();
2304 for (i = 0; i < iMax; ++i)
2356 std::ostringstream os;
2358 attributes.
add(
"stroke-width", os.str());
2364 std::ostringstream os;
2368 for (i = 1; i < iMax; ++i)
2373 attributes.
add(
"stroke-dasharray", os.str());
2397 attributes.
add(
"fill-rule",
"evenodd");
2402 attributes.
add(
"fill-rule",
"nonzero");
2412 template<
typename TEXTELEMENT>
2416 if (text.isSetFontSize())
2418 attributes.
add(
"font-size", text.getFontSize().toString());
2422 if (text.isSetFontFamily())
2424 attributes.
add(
"font-family", text.getFontFamily());
2428 if (text.isSetFontWeight())
2430 switch (text.getFontWeight())
2433 attributes.
add(
"font-weight",
"bold");
2442 if (text.isSetFontStyle())
2444 switch (text.getFontStyle())
2447 attributes.
add(
"font-style",
"italic");
2456 if (text.isSetTextAnchor())
2458 switch (text.getTextAnchor())
2461 attributes.
add(
"text-anchor",
"middle");
2465 attributes.
add(
"text-anchor",
"end");
2469 attributes.
add(
"text-anchor",
"start");
2478 if (text.isSetVTextAnchor())
2480 switch (text.getVTextAnchor())
2483 attributes.
add(
"vtext-anchor",
"middle");
2487 attributes.
add(
"vtext-anchor",
"bottom");
2491 attributes.
add(
"vtext-anchor",
"top");
2504 template<
typename HEADELEMENT>
2508 if (element.isSetStartHead())
2510 attributes.
add(
"startHead", element.getStartHead());
2514 if (element.isSetEndHead())
2516 attributes.
add(
"endHead", element.getEndHead());
2526 if (dynamic_cast<const CLGraphicalPrimitive1D*>(&transformation))
2528 if (dynamic_cast<const CLRenderCurve*>(&transformation))
2532 else if (dynamic_cast<const CLGraphicalPrimitive2D*>(&transformation))
2534 if (dynamic_cast<const CLRectangle*>(&transformation))
2538 else if (dynamic_cast<const CLEllipse*>(&transformation))
2542 else if (dynamic_cast<const CLPolygon*>(&transformation))
2546 else if (dynamic_cast<const CLGroup*>(&transformation))
2556 else if (dynamic_cast<const CLText*>(&transformation))
2566 else if (dynamic_cast<const CLImage*>(&transformation))
2681 saveTextAttributes<CLText>(text, attributes);
2709 saveArrowHeadAttributes<CLRenderCurve>(curve, attributes);
2721 size_t i, iMax = curveElements.size();
2723 for (i = 0; i < iMax; ++i)
const CLRelAbsVector & getRadius() const
size_t getNumTypes() const
CCopasiVectorN< CFunction > * getFunctionList() const
CCopasiVector< CSlider > * getSliderList()
const C_FLOAT64 & getAvogadro() const
const CLRelAbsVector & basePoint1_X() const
std::string getInitialExpression() const
const CLRelAbsVector & getCenterY() const
const CCopasiVectorN< CEventAssignment > & getAssignments() const
const CLRelAbsVector & getYPoint1() const
void saveColorDefinition(const CLColorDefinition &color)
static const char * ModelTypeNames[]
void saveBoundingBox(const CLBoundingBox &bb)
const CCopasiVector< CLTextGlyph > & getListOfTextGlyphs() const
void saveDimensions(const CLDimensions &d)
const C_FLOAT64 & getWidth() const
const CModelParameterSet & getModelParameterSet() const
const CLRelAbsVector & getCenterX() const
void save1DAttributes(const CLGraphicalPrimitive1D &primitive, CXMLAttributeList &attributes)
bool isSetDashArray() const
const bool & getDelayAssignment() const
virtual const std::string & getName(const size_t &index) const
const char * convertScaleToScaleName(Scale scale)
static CFunction * getUndefinedFunction()
const CLRelAbsVector & getZPoint1() const
const CLRelAbsVector & basePoint2_Y() const
CCopasiVectorN< CEvent > & getEvents()
const CLRelAbsVector & getHeight() const
void saveGradientElements(const CLGradientBase &gradient)
CCopasiProblem * getProblem()
const bool & confirmOverwrite() const
bool set(const size_t &index, const std::string &name, const CType &value)
const CompareResult & getCompareResult() const
bool saveElement(const std::string &name, CXMLAttributeList &attributeList)
const CLBoundingBox & getBoundingBox() const
const std::string & getSBMLId() const
const CCopasiVector< CMetab > & getMetabolites() const
void saveCurveElements(const std::vector< CLRenderPoint * > &curveElements)
const std::string & getObjectName() const
bool startSaveElement(const std::string &name)
void saveLocalStyle(const CLLocalStyle &style)
static bool isRelativePath(const std::string &path)
void saveTransformation2D(const CLTransformation2D &transformation)
const CCopasiVectorN< CModelValue > & getModelValues() const
CCopasiVectorN< CCopasiTask > * getTaskList() const
const CCopasiVector< CLLocalRenderInformation > & getListOfLocalRenderInformationObjects() const
unsigned C_INT32 getDimensionality() const
CReportDefinitionVector * mpReportList
virtual size_t size() const
virtual std::string getText() const
const CLRelAbsVector & getZ() const
const CLRelAbsVector & z() const
const CLRelAbsVector & getY() const
bool setModel(CModel *pModel)
const bool & isUpdateModel() const
bool saveParameterGroup(const std::vector< CCopasiParameter * > &group)
virtual const std::string & getKey() const
const CLRelAbsVector & getRadiusY() const
bool saveData(const std::string &data)
CListOfLayouts * getLayoutList() const
const CLRelAbsVector & getWidth() const
const std::vector< CLLineSegment > & getCurveSegments() const
double getStrokeWidth() const
const CCopasiTask::Type & getTaskType() const
void saveRenderPoint(const CLRenderPoint &point)
std::string getTimeUnitName() const
const CCopasiReportSeparator & getSeparator() const
const std::string & getSliderObjectCN() const
const std::string & getObjectRole() const
bool setFunctionList(CCopasiVectorN< CFunction > *pFunctionList)
const std::string & getAssociatedEntityKey() const
virtual const std::string & getKey() const
const std::string & getId() const
const std::string & getKey() const
static const char * TypeNames[]
const CLRelAbsVector & basePoint2_Z() const
const bool & isScheduled() const
std::vector< CPlotDataChannelSpec > & getChannels()
std::vector< CFunction * > getUsedFunctions(const CModel *pModel) const
bool saveXhtml(const std::string &xhtml)
size_t getNumChannels() const
const CEvaluationTree::Type & getType() const
static std::string fileName(const std::string &path)
const std::string & getTarget() const
const std::set< std::string > & getKeyList() const
CCopasiVectorN< CFunction > * mpFunctionList
std::string getExpression() const
CLGradientStop * getGradientStop(size_t i)
std::string getTriggerExpression() const
bool isSetStrokeWidth() const
const CLRelAbsVector & basePoint2_X() const
void saveGradientAttributes(const CLGradientBase &gradient, CXMLAttributeList &attributes)
CSlider::Type getSliderType() const
const CLRelAbsVector & getXPoint2() const
virtual size_t getIndex(const std::string &name) const
const bool & isActive() const
SCopasiXMLGUI * getGUI() const
const CCopasiMethod::SubType & getSubType() const
COutputDefinitionVector * getPlotList() const
void saveListOfGlobalRenderInformation(const CCopasiVector< CLGlobalRenderInformation > &list)
void saveTextAttributes(const TEXTELEMENT &text, CXMLAttributeList &attributes)
const std::string & getComment() const
bool haveFunctionList() const
const std::string & getStroke() const
const CCopasiObjectName & getCN() const
const CLPoint & getBase1() const
void saveLinearGradient(const CLLinearGradient &gradient)
const size_t & size() const
const std::string & getKey() const
const std::string & getMiriamAnnotation() const
static const std::string RoleNameXML[]
const unsigned C_INT32 & getPrecision() const
void saveListOfLocalRenderInformation(const CCopasiVector< CLLocalRenderInformation > &list)
const std::string & getImageReference() const
const CCopasiVector< CLCompartmentGlyph > & getListOfCompartmentGlyphs() const
size_t getNumGradientStops() const
void saveStyleAttributes(const CLStyle &style, CXMLAttributeList &attributes)
const CLRelAbsVector & getX() const
virtual const std::string & getKey() const
const CLRelAbsVector & getRX() const
std::string getKey(const std::string &name) const
static const char * TypeName[]
size_t getNumKeys() const
void setModelObjectKey(const std::string &k)
const CLDimensions & getDimensions() const
const CLRelAbsVector & getY() const
bool skip(const size_t &index)
const CLRelAbsVector & getCY() const
const CLRelAbsVector & getRadiusX() const
const std::string & getSBMLId() const
const CLRelAbsVector & getCenterZ() const
static const char * XMLType[]
const std::string & getStaticString() const
void saveImageElement(const CLImage &image)
bool havePlotList() const
bool setValue(const size_t &index, const CType &value)
void saveRectangleElement(const CLRectangle &rectangle)
const CCopasiVector< CChemEqElement > & getProducts() const
bool saveAnnotation(const CAnnotation *pAnnotation)
const std::string & getStopColor() const
const bool & getPersistentTrigger() const
const bool & append() const
void saveGlobalStyle(const CLGlobalStyle &style)
const CFunction * getFunction() const
const CLRelAbsVector & y() const
const CLPoint & getBase2() const
bool haveTaskList() const
const CLRelAbsVector & getOffset() const
bool setDatamodel(CCopasiDataModel *pDataModel)
const CLPoint & getEnd() const
const CFunctionParameters & getFunctionParameters() const
const std::set< std::string > & getRoleList() const
CCopasiDataModel * mpDataModel
static const char * XMLType[]
const CLRelAbsVector & getHeight() const
virtual const std::string & getKey() const
size_t getNumRoles() const
void saveGradientStop(const CLGradientStop &stop)
const std::set< std::string > & getTypeList() const
void saveTransformationAttributes(const CLTransformation2D &transformation, CXMLAttributeList &attributes)
const C_FLOAT64 & getX() const
const TriLogic & isReversible() const
const std::string & getNotes() const
std::vector< CRegisteredObjectName > * getTableAddr()
virtual const std::string & getKey() const
CReportDefinitionVector * getReportList() const
const CLRelAbsVector & getFocalPointY() const
const CLPoint & getPosition() const
std::vector< CRegisteredObjectName > * getFooterAddr()
bool setTaskList(CCopasiVectorN< CCopasiTask > *pTaskList)
COutputDefinitionVector * mpPlotList
const CLGroup * getGroup() const
void saveGroupElement(const CLGroup &group)
std::string getInitialExpression() const
const std::string & getSBMLFileName() const
const CPlotItem::Type & getType() const
int getCurrentColumnNumber()
const C_FLOAT64 & getSliderValue() const
const CCopasiVector< CLMetabGlyph > & getListOfMetaboliteGlyphs() const
void setDatamodel(CCopasiDataModel *pDataModel)
std::string getLengthUnitName() const
const CLGroup * getGroup() const
const CLRelAbsVector & getZPoint2() const
std::map< std::string, std::string > mSBMLReference
bool setPlotList(COutputDefinitionVector *pPlotList)
void save2DAttributes(const CLGraphicalPrimitive2D &primitive, CXMLAttributeList &attributes)
void saveLineEnding(const CLLineEnding &lineEnding)
const CCopasiVectorN< CModelParameterSet > & getModelParameterSets() const
void saveArrowHeadAttributes(const HEADELEMENT &element, CXMLAttributeList &attributes)
void saveRenderInformationAttributes(const CLRenderInformationBase &renderInfo, CXMLAttributeList &attributes)
const std::string & getId() const
virtual const double & getValue(const Framework &framework) const
bool isSetFillRule() const
const CCopasiVector< CChemEqElement > & getSubstrates() const
virtual const std::string & getKey() const
const std::string & getKey() const
bool isReversible() const
bool setLayoutList(const CListOfLayouts &reportList)
static CFunctionDB * getFunctionList()
static const char * XMLStatus[]
std::string getDelayExpression() const
bool haveLayoutList() const
const CLRelAbsVector & getWidth() const
const CCopasiVector< CLGeneralGlyph > & getListOfGeneralGlyphs() const
const CLRelAbsVector & getCZ() const
virtual const std::string & getKey() const
const std::string & getKey() const
CReportDefinitionVector * getReportList() const
void saveCurve(const CLCurve &c)
const C_FLOAT64 & getMaxValue() const
void saveLocalRenderInformation(const CLLocalRenderInformation &renderInfo)
const bool & isFast() const
std::string getAreaUnitName() const
const CModelEntity::Status & getSimulationType() const
CCopasiVectorNS< CCompartment > & getCompartments()
void savePolygonElement(const CLPolygon &polygon)
const CLRelAbsVector & getRY() const
void saveEllipseElement(const CLEllipse &ellipse)
CLBoundingBox * getBoundingBox()
const std::string & getModelObjectKey() const
const C_FLOAT64 & getY() const
CCopasiMethod * getMethod()
CModel * getModel() const
bool setGUI(SCopasiXMLGUI *pGUI)
const std::string & getSBMLId() const
std::string getQuantityUnitName() const
const C_FLOAT64 & getHeight() const
bool setReportList(CReportDefinitionVector *pReportList)
const CCopasiVector< CPlotItem > & getItems() const
const std::string & getFillColor() const
void saveStyleElements(const CLStyle &style)
const CCopasiVector< CChemEqElement > & getModifiers() const
const CCopasiParameterGroup & getParameters() const
std::vector< CModelParameter * >::const_iterator const_iterator
void setText(const std::string &t)
void savePosition(const CLPoint &p, const std::string &tag="Position")
const CStateTemplate & getStateTemplate() const
bool endSaveElement(const std::string &name)
virtual const std::string & getKey() const
CListOfLayouts * mpLayoutList
std::vector< CLRenderPoint * > * getListOfElements()
std::vector< CRegisteredObjectName > * getBodyAddr()
std::string UTCTimeStamp()
std::string toString() const
const ModelType & getModelType() const
COutputDefinitionVector * getPlotList() const
The class for handling a chemical kinetic function.
CCopasiVectorNS< CReaction > & getReactions()
UnsupportedAnnotation & getUnsupportedAnnotations()
void setGUI(SCopasiXMLGUI *pGUI)
void setFunctionList(CCopasiVectorN< CFunction > *pFunctionList)
CCopasiVectorN< CCopasiTask > * mpTaskList
const CLRelAbsVector & basePoint1_Z() const
const CLRelAbsVector & getFocalPointX() const
std::string createValueString() const
const CCopasiVector< CLMetabReferenceGlyph > & getListOfMetabReferenceGlyphs() const
static std::string createStringFromSet(const std::set< std::string > &set)
bool getIsEnabledRotationalMapping() const
const CLRelAbsVector & getCX() const
void saveRenderInformationDefinitionElements(const CLRenderInformationBase &renderInfo)
const CLRelAbsVector & x() const
const CCopasiParameter::Value & getValue(const std::string &name) const
int getCurrentLineNumber() const
const CLRelAbsVector & basePoint1_Y() const
bool parse(const char *pszBuffer, int nLength=-1, bool fIsFinal=true)
const std::string & getSBMLId() const
static const char * XMLType[]
SPREADMETHOD getSpreadMethod() const
static const char * XMLSubType[]
const bool & getFireAtInitialTime() const
const Type & getType() const
virtual bool load(std::istream &is, const std::string &pwd)
C_INT32 getVersionDevel() const
FILL_RULE getFillRule() const
unsigned C_INT32 getTickNumber() const
const CModelEntity::Status & getStatus() const
std::string getVolumeUnitName() const
const CLRelAbsVector & getX() const
const std::string & getId() const
CReportDefinition * getReportDefinition()
const std::vector< std::vector< std::string > > & getParameterMappings() const
const XML_LChar * getErrorString()
static bool makePathRelative(std::string &absolutePath, const std::string &relativeTo)
bool hasValidModelReference() const
const std::string & getVersion() const
bool saveReportSection(const std::string &name, const std::vector< CRegisteredObjectName > §ion)
CCopasiVectorN< CCopasiTask > * getTaskList() const
void saveRadialGradient(const CLRadialGradient &gradient)
bool haveReportList() const
std::vector< CRegisteredObjectName > * getHeaderAddr()
const CLCurve & getCurve() const
const CLRelAbsVector & getYPoint2() const
const C_FLOAT64 & getMinValue() const
size_t getNumCurveSegments() const
void saveRenderTextElement(const CLText &text)
void saveGlobalRenderInformation(const CLGlobalRenderInformation &renderInfo)
const CChemEq & getChemEq() const
virtual const std::string & getKey() const
unsigned C_INT32 getTickFactor() const
virtual bool save(std::ostream &os, const std::string &relativeTo)
const CCopasiVector< CLReactionGlyph > & getListOfReactionGlyphs() const
bool saveModelParameter(const CModelParameter *pModelParameter)
const CLRelAbsVector & getXPoint1() const
const std::string & getInfix() const
const std::string & getGraphicalObjectKey() const
void setLayoutList(CListOfLayouts *pLayoutList)
CFunctionParameters & getVariables()
bool add(const std::string &name, const CType &value)
const std::vector< unsigned int > & getDashArray() const
CModelEntity ** getEntities()
const CLRelAbsVector & getZ() const
CListOfLayouts * getLayoutList() const
const CLDimensions & getDimensions() const
const CLPoint & getStart() const
CModel * getModel() const
const CCopasiVector< CLGlobalRenderInformation > & getListOfGlobalRenderInformationObjects() const
void saveRenderCurveElement(const CLRenderCurve &curve)
const CLRelAbsVector & getFocalPointZ() const
static const CVersion VERSION