COPASI API  4.16.103
Public Member Functions | Private Member Functions | Private Attributes | List of all members
CPlotSpecification Class Reference

#include <CPlotSpecification.h>

Inheritance diagram for CPlotSpecification:
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Collaboration diagram for CPlotSpecification:
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Public Member Functions

virtual void cleanup ()
 
 CPlotSpecification (const std::string &name="NoName", const CCopasiContainer *pParent=NULL, const CPlotItem::Type &type=plot2d)
 
 CPlotSpecification (const CPlotSpecification &src, const CCopasiContainer *pParent=NULL)
 
bool createDefaultPlot (const CModel *model)
 
CPlotItemcreateItem (const std::string &name, CPlotItem::Type type)
 
const CCopasiVector< CPlotItem > & getItems () const
 
CCopasiVector< CPlotItem > & getItems ()
 
const bool & isActive () const
 
bool isLogX () const
 
bool isLogY () const
 
void setActive (const bool &active)
 
void setLogX (bool l)
 
void setLogY (bool l)
 
virtual ~CPlotSpecification ()
 
- Public Member Functions inherited from CPlotItem
void addChannel (const CPlotDataChannelSpec &channel)
 
void cleanup ()
 
 CPlotItem (const std::string &name="NoName", const CCopasiContainer *pParent=NULL, const Type &type=curve2d)
 
 CPlotItem (const CPlotItem &src, const CCopasiContainer *pParent=NULL)
 
const COutputInterface::ActivitygetActivity () const
 
std::vector
< CPlotDataChannelSpec > & 
getChannels ()
 
const std::vector
< CPlotDataChannelSpec > & 
getChannels () const
 
size_t getNumChannels () const
 
const std::string & getTitle () const
 
const CPlotItem::TypegetType () const
 
void setActivity (const COutputInterface::Activity &activity)
 
void setTitle (const std::string &title)
 
void setType (CPlotItem::Type type)
 
virtual ~CPlotItem ()
 
- Public Member Functions inherited from CCopasiParameterGroup
bool addGroup (const std::string &name)
 
bool addParameter (const CCopasiParameter &parameter)
 
bool addParameter (const std::string &name, const CCopasiParameter::Type type)
 
template<class CType >
bool addParameter (const std::string &name, const CCopasiParameter::Type type, const CType &value)
 
void addParameter (CCopasiParameter *pParameter)
 
CCopasiParameterGroupassertGroup (const std::string &name)
 
template<class CType >
CCopasiParameterassertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue)
 
index_iterator beginIndex () const
 
name_iterator beginName () const
 
 CCopasiParameterGroup (const CCopasiParameterGroup &src, const CCopasiContainer *pParent=NULL)
 
 CCopasiParameterGroup (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &objectType="ParameterGroup")
 
void clear ()
 
virtual bool elevateChildren ()
 
index_iterator endIndex () const
 
name_iterator endName () const
 
CCopasiParameterGroupgetGroup (const std::string &name)
 
const CCopasiParameterGroupgetGroup (const std::string &name) const
 
CCopasiParameterGroupgetGroup (const size_t &index)
 
const CCopasiParameterGroupgetGroup (const size_t &index) const
 
size_t getIndex (const std::string &name) const
 
std::string getKey (const std::string &name) const
 
std::string getKey (const size_t &index) const
 
virtual const std::string & getName (const size_t &index) const
 
virtual const CObjectInterfacegetObject (const CCopasiObjectName &cn) const
 
CCopasiParametergetParameter (const std::string &name)
 
const CCopasiParametergetParameter (const std::string &name) const
 
CCopasiParametergetParameter (const size_t &index)
 
const CCopasiParametergetParameter (const size_t &index) const
 
CCopasiParameter::Type getType (const std::string &name) const
 
CCopasiParameter::Type getType (const size_t &index) const
 
std::string getUniqueParameterName (const CCopasiParameter *pParameter) const
 
const CCopasiParameter::ValuegetValue (const std::string &name) const
 
const CCopasiParameter::ValuegetValue (const size_t &index) const
 
CCopasiParameter::ValuegetValue (const std::string &name)
 
CCopasiParameter::ValuegetValue (const size_t &index)
 
CCopasiParameterGroupoperator= (const CCopasiParameterGroup &rhs)
 
virtual void print (std::ostream *ostream) const
 
bool removeParameter (const std::string &name)
 
bool removeParameter (const size_t &index)
 
template<class CType >
bool setValue (const std::string &name, const CType &value)
 
template<class CType >
bool setValue (const size_t &index, const CType &value)
 
size_t size () const
 
bool swap (const size_t &iFrom, const size_t &iTo)
 
bool swap (index_iterator &from, index_iterator &to)
 
virtual ~CCopasiParameterGroup ()
 
- Public Member Functions inherited from CCopasiParameter
 CCopasiParameter (const CCopasiParameter &src, const CCopasiContainer *pParent=NULL)
 
 CCopasiParameter (const std::string &name, const Type &type, const void *pValue=NULL, const CCopasiContainer *pParent=NULL, const std::string &objectType="Parameter")
 
virtual CCopasiObjectName getCN () const
 
virtual const std::string & getKey () const
 
virtual std::string getObjectDisplayName (bool regular=true, bool richtext=false) const
 
const CCopasiParameter::TypegetType () const
 
const ValuegetValue () const
 
ValuegetValue ()
 
virtual voidgetValuePointer () const
 
CCopasiObjectgetValueReference () const
 
bool isValidValue (const C_FLOAT64 &value) const
 
bool isValidValue (const C_INT32 &value) const
 
bool isValidValue (const unsigned C_INT32 &value) const
 
bool isValidValue (const bool &value) const
 
bool isValidValue (const std::string &value) const
 
bool isValidValue (const CCopasiObjectName &value) const
 
bool isValidValue (const std::vector< CCopasiParameter * > &value) const
 
CCopasiParameteroperator= (const CCopasiParameter &rhs)
 
template<class CType >
bool setValue (const CType &value)
 
bool setValue (const std::vector< CCopasiParameter * > &value)
 
virtual ~CCopasiParameter ()
 
- Public Member Functions inherited from CCopasiContainer
virtual bool add (CCopasiObject *pObject, const bool &adopt=true)
 
 CCopasiContainer (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=CCopasiObject::Container)
 
 CCopasiContainer (const CCopasiContainer &src, const CCopasiContainer *pParent=NULL)
 
virtual std::string getChildObjectUnits (const CCopasiObject *pObject) const
 
virtual const objectMapgetObjects () const
 
virtual std::string getUnits () const
 
virtual const CCopasiObjectgetValueObject () const
 
virtual bool remove (CCopasiObject *pObject)
 
virtual ~CCopasiContainer ()
 
- Public Member Functions inherited from CCopasiObject
void addDirectDependency (const CCopasiObject *pObject)
 
 CCopasiObject (const CCopasiObject &src, const CCopasiContainer *pParent=NULL)
 
void clearDirectDependencies ()
 
void clearRefresh ()
 
bool dependsOn (DataObjectSet candidates, const DataObjectSet &context=DataObjectSet()) const
 
void getAllDependencies (DataObjectSet &dependencies, const DataObjectSet &context) const
 
virtual const DataObjectSetgetDirectDependencies (const DataObjectSet &context=DataObjectSet()) const
 
CCopasiContainergetObjectAncestor (const std::string &type) const
 
CCopasiDataModelgetObjectDataModel ()
 
const CCopasiDataModelgetObjectDataModel () const
 
const std::string & getObjectName () const
 
CCopasiContainergetObjectParent () const
 
const std::string & getObjectType () const
 
virtual const
CObjectInterface::ObjectSet
getPrerequisites () const
 
virtual RefreshgetRefresh () const
 
UpdateMethodgetUpdateMethod () const
 
bool hasCircularDependencies (DataObjectSet &candidates, DataObjectSet &verified, const DataObjectSet &context) const
 
bool hasUpdateMethod () const
 
bool isArray () const
 
bool isContainer () const
 
bool isDataModel () const
 
bool isMatrix () const
 
bool isNameVector () const
 
bool isNonUniqueName () const
 
virtual bool isPrerequisiteForContext (const CObjectInterface *pObject, const CMath::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const
 
bool isReference () const
 
bool isRoot () const
 
bool isSeparator () const
 
bool isStaticString () const
 
bool isValueBool () const
 
bool isValueDbl () const
 
bool isValueInt () const
 
bool isValueInt64 () const
 
bool isValueString () const
 
bool isVector () const
 
virtual bool mustBeDeleted (const DataObjectSet &deletedObjects) const
 
void removeDirectDependency (const CCopasiObject *pObject)
 
void setDirectDependencies (const DataObjectSet &directDependencies)
 
bool setObjectName (const std::string &name)
 
virtual bool setObjectParent (const CCopasiContainer *pParent)
 
void setObjectValue (const C_FLOAT64 &value)
 
void setObjectValue (const C_INT32 &value)
 
void setObjectValue (const bool &value)
 
template<class CType >
void setRefresh (CType *pType, void(CType::*method)(void))
 
template<class CType >
void setUpdateMethod (CType *pType, void(CType::*method)(const C_FLOAT64 &))
 
template<class CType >
void setUpdateMethod (CType *pType, void(CType::*method)(const C_INT32 &))
 
template<class CType >
void setUpdateMethod (CType *pType, void(CType::*method)(const bool &))
 
virtual ~CCopasiObject ()
 
- Public Member Functions inherited from CObjectInterface
 CObjectInterface ()
 
virtual ~CObjectInterface ()
 

Private Member Functions

void initObjects ()
 

Private Attributes

CCopasiVector< CPlotItemitems
 
bool mActive
 

Additional Inherited Members

- Public Types inherited from CPlotItem
enum  Type {
  unset = 0, curve2d, histoItem1d, bandedGraph,
  surface, plot2d, simWiz
}
 
- Public Types inherited from CCopasiParameterGroup
typedef parameterGroup::iterator index_iterator
 
typedef
CCopasiContainer::objectMap::iterator 
name_iterator
 
typedef std::vector
< CCopasiParameter * > 
parameterGroup
 
- Public Types inherited from CCopasiParameter
enum  Type {
  DOUBLE = 0, UDOUBLE, INT, UINT,
  BOOL, GROUP, STRING, CN,
  KEY, FILE, EXPRESSION, INVALID
}
 
- Public Types inherited from CCopasiContainer
typedef std::multimap
< std::string, CCopasiObject * > 
objectMap
 
- Public Types inherited from CCopasiObject
typedef std::set< const
CCopasiObject * > 
DataObjectSet
 
typedef std::vector< Refresh * > DataUpdateSequence
 
- Public Types inherited from CObjectInterface
typedef std::set< const
CObjectInterface * > 
ObjectSet
 
typedef std::vector
< CObjectInterface * > 
UpdateSequence
 
- Static Public Member Functions inherited from CCopasiObject
static std::vector< Refresh * > buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet())
 
static void setRenameHandler (CRenameHandler *rh)
 
- Static Public Attributes inherited from CPlotItem
static const std::string RecordingActivityName []
 
static const std::string TypeName []
 
static const char * XMLRecordingActivity []
 
static const char * XMLType []
 
- Static Public Attributes inherited from CCopasiParameter
static const std::string TypeName []
 
static const char * XMLType []
 
- Static Public Attributes inherited from CCopasiContainer
static const std::vector
< CCopasiContainer * > 
EmptyList
 
- Protected Types inherited from CCopasiObject
enum  Flag {
  Container = 0x1, Vector = 0x2, Matrix = 0x4, NameVector = 0x8,
  Reference = 0x10, ValueBool = 0x20, ValueInt = 0x40, ValueInt64 = 0x80,
  ValueDbl = 0x100, NonUniqueName = 0x200, StaticString = 0x400, ValueString = 0x800,
  Separator = 0x1000, ModelEntity = 0x2000, Array = 0x4000, DataModel = 0x8000,
  Root = 0x10000, Gui = 0x20000
}
 
- Protected Member Functions inherited from CCopasiParameterGroup
 CCopasiParameterGroup ()
 
- Protected Member Functions inherited from CCopasiContainer
template<class CType >
CCopasiObjectaddMatrixReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
 
template<class CType >
CCopasiObjectaddObjectReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
 
template<class CType >
CCopasiObjectaddVectorReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
 
void initObjects ()
 
- Protected Member Functions inherited from CCopasiObject
 CCopasiObject ()
 
 CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0)
 
- Protected Attributes inherited from CCopasiParameter
std::string mKey
 
CCopasiObjectmpValueReference
 
size_t mSize
 
Value mValue
 
- Protected Attributes inherited from CCopasiContainer
objectMap mObjects
 
- Static Protected Attributes inherited from CCopasiObject
static CRenameHandlersmpRenameHandler = NULL
 

Detailed Description

Definition at line 27 of file CPlotSpecification.h.

Constructor & Destructor Documentation

CPlotSpecification::CPlotSpecification ( const std::string &  name = "NoName",
const CCopasiContainer pParent = NULL,
const CPlotItem::Type type = plot2d 
)

Definition at line 28 of file CPlotSpecification.cpp.

References initObjects().

30  :
31  CPlotItem(name, pParent, type),
32  items("Curves", this),
33  mActive(true)
34 {initObjects();}
CPlotItem(const std::string &name="NoName", const CCopasiContainer *pParent=NULL, const Type &type=curve2d)
Definition: CPlotItem.cpp:75
CCopasiVector< CPlotItem > items
CPlotSpecification::CPlotSpecification ( const CPlotSpecification src,
const CCopasiContainer pParent = NULL 
)

Definition at line 36 of file CPlotSpecification.cpp.

References initObjects().

37  :
38  CPlotItem(src, pParent),
39  items(src.getItems(), this),
40  mActive(src.mActive)
41 {initObjects();}
CPlotItem(const std::string &name="NoName", const CCopasiContainer *pParent=NULL, const Type &type=curve2d)
Definition: CPlotItem.cpp:75
CCopasiVector< CPlotItem > items
const CCopasiVector< CPlotItem > & getItems() const
CPlotSpecification::~CPlotSpecification ( )
virtual

Destructor

Definition at line 43 of file CPlotSpecification.cpp.

43 {}

Member Function Documentation

void CPlotSpecification::cleanup ( )
virtual

Definition at line 45 of file CPlotSpecification.cpp.

References CPlotItem::cleanup(), CCopasiVector< T >::cleanup(), and items.

Referenced by CQPlotSubwidget::saveToPlotSpec().

46 {
47  items.cleanup();
48  this->CPlotItem::cleanup();
49 }
CCopasiVector< CPlotItem > items
virtual void cleanup()
void cleanup()
Definition: CPlotItem.cpp:150
bool CPlotSpecification::createDefaultPlot ( const CModel model)

Definition at line 99 of file CPlotSpecification.cpp.

References CPlotItem::addChannel(), createItem(), CPlotItem::curve2d, CCopasiObject::getCN(), CModel::getMetabolites(), CCopasiObject::getObjectDisplayName(), CModelEntity::getValueReference(), mActive, and CCopasiVector< T >::size().

100 {
101  mActive = true;
102 
103  //TODO cleanup before?
104  //title = "Default Data Plot 2D";
105 
106  CPlotItem * plItem;
107  std::string itemTitle;
108  CPlotDataChannelSpec name2;
109  const CCopasiObject * tmp;
110 
111  CPlotDataChannelSpec name1 = model->getValueReference()->getCN();
112 
113  size_t i, imax = model->getMetabolites().size();
114 
115  for (i = 0; i < imax; ++i)
116  {
117  tmp = model->getMetabolites()[i]->getConcentrationReference();
118  name2 = tmp->getCN();
119  itemTitle = tmp->getObjectDisplayName();
120 
121  plItem = this->createItem(itemTitle, CPlotItem::curve2d);
122  plItem->addChannel(name1);
123  plItem->addChannel(name2);
124  }
125 
126  return true; //TODO: really check;
127 }
virtual std::string getObjectDisplayName(bool regular=true, bool richtext=false) const
virtual CCopasiObjectName getCN() const
const CCopasiVector< CMetab > & getMetabolites() const
Definition: CModel.cpp:1051
virtual size_t size() const
void addChannel(const CPlotDataChannelSpec &channel)
Definition: CPlotItem.cpp:223
CPlotItem * createItem(const std::string &name, CPlotItem::Type type)
CCopasiObject * getValueReference() const
CPlotItem * CPlotSpecification::createItem ( const std::string &  name,
CPlotItem::Type  type 
)

Definition at line 86 of file CPlotSpecification.cpp.

References CCopasiVector< T >::add(), CPlotItem::CPlotItem(), and items.

Referenced by COutputAssistant::createDefaultOutput(), createDefaultPlot(), COutputAssistant::createPlot(), SEDMLImporter::readListOfPlotsFromSedMLOutput(), and CCopasiXMLParser::PlotItemElement::start().

87 {
88  CPlotItem * itm = new CPlotItem(name, NULL, type);
89 
90  if (!items.add(itm, true))
91  {
92  delete itm;
93  return NULL;
94  }
95 
96  return itm;
97 }
CPlotItem(const std::string &name="NoName", const CCopasiContainer *pParent=NULL, const Type &type=curve2d)
Definition: CPlotItem.cpp:75
CCopasiVector< CPlotItem > items
virtual bool add(const CType &src)
const CCopasiVector<CPlotItem>& CPlotSpecification::getItems ( ) const
inline
CCopasiVector<CPlotItem>& CPlotSpecification::getItems ( )
inline

Definition at line 56 of file CPlotSpecification.h.

References items.

56 {return items;};
CCopasiVector< CPlotItem > items
void CPlotSpecification::initObjects ( )
private

Initialize the contained CCopasiObjects

Definition at line 51 of file CPlotSpecification.cpp.

Referenced by CPlotSpecification().

52 {
53  // CCopasiContainer::addObjectReference("Active", mActive, CCopasiObject::ValueBool);
54 }
const bool & CPlotSpecification::isActive ( ) const
bool CPlotSpecification::isLogX ( ) const
bool CPlotSpecification::isLogY ( ) const
void CPlotSpecification::setActive ( const bool &  active)
void CPlotSpecification::setLogX ( bool  l)

Definition at line 74 of file CPlotSpecification.cpp.

References CCopasiParameterGroup::setValue().

Referenced by COutputAssistant::createPlot(), SEDMLImporter::readListOfPlotsFromSedMLOutput(), and CQPlotSubwidget::saveToPlotSpec().

75 {
76  setValue("log X", l);
77 }
bool setValue(const std::string &name, const CType &value)
void CPlotSpecification::setLogY ( bool  l)

Member Data Documentation

CCopasiVector<CPlotItem> CPlotSpecification::items
private

Definition at line 31 of file CPlotSpecification.h.

Referenced by cleanup(), createItem(), and getItems().

bool CPlotSpecification::mActive
private

Definition at line 32 of file CPlotSpecification.h.

Referenced by createDefaultPlot(), isActive(), and setActive().


The documentation for this class was generated from the following files: