#include <CAnnotatedMatrix.h>

Inheritance diagram for CArrayAnnotation:

Collaboration diagram for CArrayAnnotation:

Public Types
enum	Mode { OBJECTS, VECTOR, VECTOR_ON_THE_FLY, STRINGS, NUMBERS }

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

Public Member Functions
const CObjectInterface *	addElementReference (CCopasiAbstractArray::index_type index) const

const CObjectInterface *	addElementReference (C_INT32 u, C_INT32 v) const

const CObjectInterface *	addElementReference (C_INT32 u) const

void	appendElementReferences (std::set< const CCopasiObject * > &objects) const

CCopasiAbstractArray *	array ()

const CCopasiAbstractArray *	array () const

	CArrayAnnotation (const std::string &name, const CCopasiContainer pParent, CCopasiAbstractArray array, const bool &adopt)

bool	createAnnotationsCNFromCopasiVector (size_t d, const CCopasiContainer *v) const

void	createNumbers (size_t d) const

size_t	dimensionality () const

const std::vector < CRegisteredObjectName > &	getAnnotationsCN (size_t d) const

const std::vector< std::string > &	getAnnotationsString (size_t d, bool display=true) const

Mode	getDefaultMode () const

const std::string &	getDescription () const

const std::string &	getDimensionDescription (size_t d) const

Mode	getMode (size_t d) const

virtual const CObjectInterface *	getObject (const CCopasiObjectName &cn) const

virtual std::string	getObjectDisplayName (bool regular=true, bool richtext=false) const

bool	isEmpty ()

virtual void	print (std::ostream *ostream) const

void	printRecursively (std::ostream &ostream, size_t level, CCopasiAbstractArray::index_type &index, const std::vector< std::vector< std::string > > &display) const

void	reDimensionalize (size_t d)

void	resize ()

void	resizeOneDimension (size_t d)

void	setAnnotationCN (size_t d, size_t i, const std::string cn)

void	setAnnotationString (size_t d, size_t i, const std::string s)

void	setArray (CCopasiAbstractArray *a)

void	setCopasiVector (size_t d, const CCopasiContainer *v)

void	setDescription (const std::string &s)

void	setDimensionDescription (size_t d, const std::string &s)

void	setMode (size_t d, Mode m)

void	setMode (Mode m)

CCopasiAbstractArray::index_type	size () const

virtual	~CArrayAnnotation ()

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 objectMap &	getObjects () const

virtual std::string	getUnits () const

virtual const CCopasiObject *	getValueObject () 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 CCopasiObjectName	getCN () const

virtual const DataObjectSet &	getDirectDependencies (const DataObjectSet &context=DataObjectSet()) const

virtual const std::string &	getKey () const

CCopasiContainer *	getObjectAncestor (const std::string &type) const

CCopasiDataModel *	getObjectDataModel ()

const CCopasiDataModel *	getObjectDataModel () const

const std::string &	getObjectName () const

CCopasiContainer *	getObjectParent () const

const std::string &	getObjectType () const

virtual const CObjectInterface::ObjectSet &	getPrerequisites () const

virtual Refresh *	getRefresh () const

UpdateMethod *	getUpdateMethod () const

virtual void *	getValuePointer () 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
	CArrayAnnotation ()

	CArrayAnnotation (const CArrayAnnotation &)

CArrayAnnotation &	operator= (const CArrayAnnotation &)

Private Attributes
std::vector< std::vector < CRegisteredObjectName > >	mAnnotationsCN

std::vector< std::vector < std::string > >	mAnnotationsString

std::vector< const CCopasiContainer * >	mCopasiVectors

Mode	mDefaultMode

std::string	mDescription

bool	mDestructArray

std::vector< std::string >	mDimensionDescriptions

std::vector< Mode >	mModes

CCopasiAbstractArray *	mpArray

Friends
std::ostream &	operator<< (std::ostream &os, const CArrayAnnotation &o)

Additional Inherited Members
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 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 CCopasiContainer
template<class CType >
CCopasiObject *	addMatrixReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)

template<class CType >
CCopasiObject *	addObjectReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)

template<class CType >
CCopasiObject *	addVectorReference (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 CCopasiContainer
objectMap	mObjects

Static Protected Attributes inherited from CCopasiObject
static CRenameHandler *	smpRenameHandler = NULL

Detailed Description

This class contains the annotations to a n-dimensional array. Annotations can be provided for the array as such, for each of the dimensions, and for each of the indices (rows, columns, ...)

Definition at line 44 of file CAnnotatedMatrix.h.

Member Enumeration Documentation

enum CArrayAnnotation::Mode

The annotation to an array can work in different modes. The mode for each dimension can be changed independently.

OBJECTS: The CNs for the rows, cols, ... of the array are given explicitly

VECTOR: A CCopasiVector is provided from which the CNs are generated at the time the vector is set

VECTOR_ON_THE_FLY: A CCopasiVector is provided, but the CNs are generated every time the annotations are retrieved (so that they are always up to date).

STRINGS: The annotations for the rows, cols, ... are given explicitly as strings.

NUMBERS: The rows, cols, ... of the array are only annotation with running numbers (starting with 0)-

Enumerator
OBJECTS
VECTOR
VECTOR_ON_THE_FLY
STRINGS
NUMBERS

Definition at line 66 of file CAnnotatedMatrix.h.

   {
     OBJECTS,
     VECTOR,
     VECTOR_ON_THE_FLY,
     STRINGS,
     NUMBERS
   };

Constructor & Destructor Documentation

CArrayAnnotation::CArrayAnnotation	(	const std::string &	name,
		const CCopasiContainer *	pParent,
		CCopasiAbstractArray *	array,
		const bool &	adopt
	)

Definition at line 36 of file CAnnotatedMatrix.cpp.

References mpArray, and resize().

     : CCopasiContainer(name, pParent, "Array" , CCopasiObject::Array),
     mpArray(array),
     mDestructArray(adopt),
     mDefaultMode(OBJECTS)
 {
   assert(mpArray);
 
   resize();
 
   //addObjectReference("Annotated Matrix", *this, CCopasiObject::ValueDbl);
 }

CArrayAnnotation::~CArrayAnnotation ( )

virtual

Definition at line 52 of file CAnnotatedMatrix.cpp.

References mDestructArray, mpArray, and pdelete.

 {
   if (mDestructArray)
     pdelete(mpArray);
 }

CArrayAnnotation::CArrayAnnotation ( )

private

CArrayAnnotation::CArrayAnnotation ( const CArrayAnnotation & )

private

Member Function Documentation

const CObjectInterface * CArrayAnnotation::addElementReference ( CCopasiAbstractArray::index_type index ) const

an object that will act as a reference to one element of an array will be created and inserted as a child of the array annotation. Basically most of the work will be done by getObject(). If the element already exists, the existing element will be returned.

Definition at line 251 of file CAnnotatedMatrix.cpp.

References getObject().

Referenced by addElementReference(), CCopasiSelectionDialog::chooseCellMatrix(), and CObjectLists::getListOfConstObjects().

 {
   //generate the index string
   std::string tmp;
   std::ostringstream indexString;
   size_t ii = 0;
 
   for (ii = 0; ii < index.size(); ++ii)
     {
       indexString << "[" << index[ii] << "]";
     }
 
   //handle zero-dimensional arrays
   if (index.size() == 0)
     indexString << "[.]";
 
   return this->getObject(indexString.str());
 }

const CObjectInterface * CArrayAnnotation::addElementReference	(	C_INT32	u,
		C_INT32	v
	)		const

a convenience function for 2-dimensional arrays.

Definition at line 270 of file CAnnotatedMatrix.cpp.

References addElementReference().

 {
   CCopasiAbstractArray::index_type index;
   index.push_back(u);
   index.push_back(v);
   return addElementReference(index);
 }

const CObjectInterface * CArrayAnnotation::addElementReference ( C_INT32 u ) const

a convenience function for 1-dimensional arrays.

Definition at line 278 of file CAnnotatedMatrix.cpp.

References addElementReference().

 {
   CCopasiAbstractArray::index_type index;
   index.push_back(u);
   return addElementReference(index);
 }

void CArrayAnnotation::appendElementReferences ( std::set< const CCopasiObject * > & objects ) const

Appends all element references to the set of objects

Parameters

std::set< const CCopasiObject * > & objects

Definition at line 285 of file CAnnotatedMatrix.cpp.

References CCopasiContainer::mObjects.

Referenced by DataModelGUI::buildChangedObjects(), CModel::buildInitialRefreshSequence(), and CModel::buildInitialSequence().

 {
   objectMap::const_iterator it = mObjects.begin();
   objectMap::const_iterator end = mObjects.end();
 
   for (; it != end; ++it)
     if (dynamic_cast<const CArrayElementReference *>(it->second) != NULL)
       objects.insert(it->second);
 
   return;
 }

CCopasiAbstractArray* CArrayAnnotation::array ( )

inline

Definition at line 122 of file CAnnotatedMatrix.h.

References mpArray.

Referenced by CQArrayAnnotationsWidget::fillBarChart(), CQArrayAnnotationsWidget::fillTable0(), CQArrayAnnotationsWidget::fillTable1(), CQArrayAnnotationsWidget::fillTableN(), CArrayElementReference::getValuePointer(), operator<<(), and printRecursively().

123 {return mpArray;}

CArrayAnnotation::mpArray

CCopasiAbstractArray * mpArray

Definition: CAnnotatedMatrix.h:76

const CCopasiAbstractArray* CArrayAnnotation::array ( ) const

inline

Definition at line 125 of file CAnnotatedMatrix.h.

References mpArray.

126 {return mpArray;}

CArrayAnnotation::mpArray

CCopasiAbstractArray * mpArray

Definition: CAnnotatedMatrix.h:76

bool CArrayAnnotation::createAnnotationsCNFromCopasiVector	(	size_t	d,
		const CCopasiContainer *	v
	)		const

generate the list of CNs from the COPASI vector v. v needs to be a CCopasiVector (or derived from it)!

Definition at line 185 of file CAnnotatedMatrix.cpp.

References CCopasiAbstractArray::dimensionality(), CCopasiObject::isNameVector(), CCopasiObject::isVector(), mAnnotationsCN, mpArray, and CCopasiVector< T >::size().

Referenced by getAnnotationsCN(), getAnnotationsString(), and setCopasiVector().

 {
   if (!v) return false;
 
   if (!(v->isVector() || v->isNameVector())) return false;
 
   if (d >= mpArray->dimensionality()) return false;
 
   //now we know we have a vector. A CCopasiVector[N/S], hopefully, so that the following cast is valid:
   const CCopasiVector< CCopasiObject > * pVector =
     reinterpret_cast<const CCopasiVector< CCopasiObject > * >(v);
 
   mAnnotationsCN[d].resize(pVector->size());
   //if (pVector->size() < mAnnotations[d].size()) return false;
 
   size_t i;
 
   for (i = 0; i < mAnnotationsCN[d].size(); ++i)
     {
       if (!(*pVector)[i])
         return false;
       else
         mAnnotationsCN[d][i] = (*pVector)[i]->getCN();
     }
 
   return true;
 }

void CArrayAnnotation::createNumbers ( size_t d ) const

Definition at line 215 of file CAnnotatedMatrix.cpp.

Referenced by getAnnotationsString().

 {
   //TODO
 }

size_t CArrayAnnotation::dimensionality ( ) const

Definition at line 79 of file CAnnotatedMatrix.cpp.

References mModes.

Referenced by CCopasiSelectionDialog::chooseCellMatrix(), CQArrayAnnotationsWidget::fillTable(), CObjectLists::getListOfConstObjects(), CArrayElementReference::getValuePointer(), CQArrayAnnotationsWidget::initSelectionTable(), isEmpty(), operator<<(), printRecursively(), CQMatrixDialog::setArray(), and CQArrayAnnotationsWidget::setArrayAnnotation().

 {
   return mModes.size();
 }

const std::vector< CRegisteredObjectName > & CArrayAnnotation::getAnnotationsCN ( size_t d ) const

returns the vector of CNs that correspond to the rows, columns, ... of the array. This method must not be called if the mode for the dimension d is STRINGS or NUMBERS

Definition at line 117 of file CAnnotatedMatrix.cpp.

References createAnnotationsCNFromCopasiVector(), mAnnotationsCN, mCopasiVectors, mModes, NUMBERS, STRINGS, and VECTOR_ON_THE_FLY.

 {
   assert(d < mModes.size());
   assert(mModes[d] != STRINGS);
   assert(mModes[d] != NUMBERS);
 
   if (mModes[d] == VECTOR_ON_THE_FLY)
     createAnnotationsCNFromCopasiVector(d, mCopasiVectors[d]);
 
   return mAnnotationsCN[d];
 }

const std::vector< std::string > & CArrayAnnotation::getAnnotationsString	(	size_t	d,
		bool	display = `true`
	)		const

This returns strings that annotate the rows, columns, ... of the array. If the mode is OBJECTS, VECTOR, or VECTOR_ON_THE_FLY the display argument determines if the object name or the object display name is used. Note that this method returns a reference. The content that the reference points to may be changes by later calls to the getAnnotationsCN() method with the same value for d. Specifically if you use this method to obtain a reference to the list of display names and then call the method again to get the plain object names, the first reference will after that also point to the plain object names.

Definition at line 129 of file CAnnotatedMatrix.cpp.

References createAnnotationsCNFromCopasiVector(), createNumbers(), CCopasiDataModel::getDataObject(), CCopasiObject::getObjectDataModel(), CCopasiObject::getObjectDisplayName(), CCopasiObject::getObjectName(), mAnnotationsCN, mAnnotationsString, mCopasiVectors, mModes, NUMBERS, OBJECTS, VECTOR, and VECTOR_ON_THE_FLY.

Referenced by CQArrayAnnotationsWidget::fillBarChart(), CQArrayAnnotationsWidget::fillTable1(), CQArrayAnnotationsWidget::fillTableN(), CQArrayAnnotationsWidget::initSelectionTable(), operator<<(), and CQMatrixDialog::setArray().

 {
   assert(d < mModes.size());
 
   //generate CNs (if necessary)
   if (mModes[d] == VECTOR_ON_THE_FLY)
     createAnnotationsCNFromCopasiVector(d, mCopasiVectors[d]);
 
   //generate DisplayNames
   if ((mModes[d] == VECTOR) || (mModes[d] == VECTOR_ON_THE_FLY) || (mModes[d] == OBJECTS))
     {
       size_t i, imax = mAnnotationsCN[d].size();
       mAnnotationsString[d].resize(imax);
       const CCopasiDataModel* pDataModel = getObjectDataModel();
       assert(pDataModel != NULL);
 
       for (i = 0; i < imax; ++i)
         {
           const CCopasiObject * obj = pDataModel->getDataObject(mAnnotationsCN[d][i]);
 
           if (obj)
             mAnnotationsString[d][i] =
               display ? obj->getObjectDisplayName() : obj->getObjectName();
           else
             mAnnotationsString[d][i] = "???";
         }
     }
 
   //generate Numbers
   if (mModes[d] == NUMBERS)
     createNumbers(d);
 
   // if the mode is STRINGS do nothing, mAnnotationsString is supposed to contain
   // the correct strings
 
   return mAnnotationsString[d];
 }

Mode CArrayAnnotation::getDefaultMode ( ) const

inline

Definition at line 143 of file CAnnotatedMatrix.h.

References mDefaultMode.

144 {return mDefaultMode;};

CArrayAnnotation::mDefaultMode

Mode mDefaultMode

Definition: CAnnotatedMatrix.h:94

const std::string & CArrayAnnotation::getDescription ( ) const

Definition at line 179 of file CAnnotatedMatrix.cpp.

References mDescription.

Referenced by operator<<().

180 {return mDescription;}

CArrayAnnotation::mDescription

std::string mDescription

Definition: CAnnotatedMatrix.h:96

const std::string & CArrayAnnotation::getDimensionDescription ( size_t d ) const

Definition at line 167 of file CAnnotatedMatrix.cpp.

References mDimensionDescriptions.

Referenced by CQArrayAnnotationsWidget::initSelectionTable(), printRecursively(), CQMatrixDialog::setArray(), and CQArrayAnnotationsWidget::setArrayAnnotation().

 {
   assert(d < mDimensionDescriptions.size());
   return mDimensionDescriptions[d];
 }

Mode CArrayAnnotation::getMode ( size_t d ) const

inline

Definition at line 140 of file CAnnotatedMatrix.h.

References mModes.

141 {return mModes[d];};

CArrayAnnotation::mModes

std::vector< Mode > mModes

Definition: CAnnotatedMatrix.h:88

const CObjectInterface * CArrayAnnotation::getObject ( const CCopasiObjectName & cn ) const

virtual

Resolve a cn. Since this is an array, the CN can start with an index like "[2][3]". Since this is also a container, this is not necessarily the case.

Reimplemented from CCopasiContainer.

Definition at line 297 of file CAnnotatedMatrix.cpp.

References C_INT32, CCopasiObjectName::getElementName(), CCopasiContainer::getObject(), CCopasiObject::getObject(), CCopasiObjectName::getRemainder(), and CCopasiContainer::mObjects.

Referenced by addElementReference().

 {
   if (cn == "")
     {
       return this;
     }
 
   if (cn == "Property=DisplayName")
     {
       return CCopasiObject::getObject(cn);
     }
 
   //if there are no indices there could still be other children. This can be handled
   //by the container base class
   if (cn.getElementName(0, false) == "") //no indices
     return this->CCopasiContainer::getObject(cn);
 
   //so now we know we have indices. So we check if the array element reference
   //exists, if not we create it. Then getObject() of the element reference is called
   //with the remainder TODO
 
   /*
       //first get the array indices. At the moment only numerical indices...
       C_INT32 ii = 0;
       CCopasiArray::index_type index;
       while (cn.getElementName(ii, false) != "")
         {
           index.push_back(cn.getElementIndex(ii));
           ++ii;
         }
   */
 
   //first get the index string
   std::string tmp;
   std::string indexString;
   C_INT32 ii = 0;
 
   while ((tmp = cn.getElementName(ii, false)) != "")
     {
       indexString += "[" + tmp + "]";
       ++ii;
     }
 
   const CCopasiObject* pObject = NULL; //this will contain the element reference
 
   //if the reference object already exists, its name will be identical to the index
   std::pair< objectMap::const_iterator, objectMap::const_iterator > range =
     mObjects.equal_range(indexString);
 
   objectMap::const_iterator it = range.first;
 
   while (it != range.second && it->second->getObjectType() != "ElementReference") ++it;
 
   if (it == range.second) //not found
     {
       //create new element reference
       pObject = new CArrayElementReference(cn, this);
     }
   else
     {
       pObject = it->second;
     }
 
   if (pObject)
     return pObject->getObject(cn.getRemainder());
   else
     return NULL;
 
   /*
   if (index.size() != dimensionality())  //wrong number of indices for this array
     return NULL;
 
   size_t i;
   for (i = 0; i < dimensionality(); ++i)
     if (index[i] >= size()[i]) //out of range
       return NULL;
   */
 
   //TODO remove element children after resize
   //TODO check optimization expression widget...
 }

std::string CArrayAnnotation::getObjectDisplayName	(	bool	regular = `true`,
		bool	richtext = `false`
	)		const

virtual

generate a display name for the array annotation.

Reimplemented from CCopasiObject.

Definition at line 486 of file CAnnotatedMatrix.cpp.

References CCopasiObject::getObjectDisplayName(), CCopasiObject::getObjectName(), CCopasiObject::getObjectParent(), and CCopasiObject::getObjectType().

 {
   std::string part;
 
   if (getObjectParent() && getObjectParent()->getObjectType() != "Model")
     part = getObjectParent()->getObjectDisplayName(regular, richtext) + ".";
 
   return part + getObjectName() + "[[]]";
 }

bool CArrayAnnotation::isEmpty ( )

Check whether the size of array is greater than 0 for each dimension. Return true, if so. Otherwise, false.

Definition at line 467 of file CAnnotatedMatrix.cpp.

References dimensionality(), and size().

Referenced by CQSimpleSelectionTree::populateTree().

 {
   // either the dimension itself ...
   size_t dim = dimensionality();
 
   if (dim == 0) return false;
 
   // ... or the size of each dimension should be greater than zero.
   size_t idx = 0;
 
   for (idx = 0; idx < dim; idx++)
     {
       if (!size()[idx])
         return true;
     }
 
   return false;
 }

CArrayAnnotation& CArrayAnnotation::operator= ( const CArrayAnnotation & )

private

void CArrayAnnotation::print ( std::ostream * ostream ) const

virtual

This is the output method for any object. The default implementation provided with CCopasiObject uses the ostream operator<< of the object to print the object.To override this default behavior one needs to reimplement the virtual print function.

Parameters

std::ostream * ostream

Reimplemented from CCopasiObject.

Definition at line 379 of file CAnnotatedMatrix.cpp.

380 {*ostream << *this;}

void CArrayAnnotation::printRecursively	(	std::ostream &	ostream,
		size_t	level,
		CCopasiAbstractArray::index_type &	index,
		const std::vector< std::vector< std::string > > &	display
	)		const

Definition at line 384 of file CAnnotatedMatrix.cpp.

References array(), dimensionality(), getDimensionDescription(), size(), and SPC.

Referenced by operator<<().

 {
   size_t indent = 2 * (dimensionality() - 1 - level);
 
   if (level == 0) //only vector
     {
       ostream << SPC(indent) << "Rows: " << getDimensionDescription(level) << "\n";
 
       size_t imax = size()[0];
 
       for (index[0] = 0; index[0] < imax; ++index[0])
         ostream << SPC(indent) << display[0][index[0]] << "\t" << (*array())[index] << "\n";
     }
   else if (level == 1) //matrix
     {
       ostream << SPC(indent) << "Rows:    " << getDimensionDescription(level - 1) << "\n";
       ostream << SPC(indent) << "Columns: " << getDimensionDescription(level) << "\n";
 
       size_t imax = size()[0];
       size_t jmax = size()[1];
       ostream << SPC(indent);
 
       for (index[1] = 0; index[1] < jmax; ++index[1])
         ostream << "\t" << display[1][index[1]];
 
       ostream << "\n";
 
       for (index[0] = 0; index[0] < imax; ++index[0])
         {
           ostream << SPC(indent) << display[0][index[0]];
 
           for (index[1] = 0; index[1] < jmax; ++index[1])
             ostream << "\t" << (*array())[index];
 
           ostream << "\n";
         }
     }
   else //dimensionality > 2
     {
       size_t i, imax = size()[level];
 
       for (i = 0; i < imax; ++i)
         {
           ostream << SPC(indent) << getDimensionDescription(level) << ": " << display[level][i] << "\n";
           index[level] = i;
           printRecursively(ostream, level - 1, index, display);
         }
     }
 }

void CArrayAnnotation::reDimensionalize ( size_t d )

resize the internal vectors according to the dimensionality of the array

Definition at line 221 of file CAnnotatedMatrix.cpp.

References mAnnotationsCN, mAnnotationsString, mCopasiVectors, mDefaultMode, mDimensionDescriptions, and mModes.

Referenced by resize().

 {
   mAnnotationsCN.resize(d);
   mAnnotationsString.resize(d);
   mDimensionDescriptions.resize(d);
   mCopasiVectors.resize(d);
   mModes.resize(d, mDefaultMode);
 }

void CArrayAnnotation::resize ( )

adjust the dimensionality and size to that of the array

Definition at line 240 of file CAnnotatedMatrix.cpp.

References CCopasiAbstractArray::dimensionality(), mpArray, reDimensionalize(), and resizeOneDimension().

Referenced by CArrayAnnotation(), CFitProblem::initialize(), CSensMethod::initialize(), CSteadyStateTask::initialize(), CCSPMethod::predifineAnnotation(), CMCAMethod::resizeAllMatrices(), CLNAMethod::resizeAllMatrices(), CILDMModifiedMethod::setAnnotationM(), CILDMMethod::setAnnotationM(), CCSPMethod::setAnnotationM(), CCSPMethod::start(), CSteadyStateTask::updateMatrices(), and CModel::updateMatrixAnnotations().

 {
   assert(mpArray);
   reDimensionalize(mpArray->dimensionality());
 
   size_t i, imax = mpArray->dimensionality();
 
   for (i = 0; i < imax; ++i)
     resizeOneDimension(i);
 }

void CArrayAnnotation::resizeOneDimension ( size_t d )

Definition at line 231 of file CAnnotatedMatrix.cpp.

References mAnnotationsCN, mAnnotationsString, mModes, mpArray, CCopasiAbstractArray::size(), and VECTOR.

Referenced by resize(), setAnnotationCN(), setAnnotationString(), and setMode().

 {
   if (mModes[d] != VECTOR)
     {
       mAnnotationsCN[d].resize(mpArray->size()[d]);
       mAnnotationsString[d].resize(mpArray->size()[d]);
     }
 }

void CArrayAnnotation::setAnnotationCN	(	size_t	d,
		size_t	i,
		const std::string	cn
	)

Definition at line 95 of file CAnnotatedMatrix.cpp.

References mAnnotationsCN, mModes, OBJECTS, resizeOneDimension(), and size().

Referenced by CSensMethod::initialize(), CSteadyStateTask::initialize(), CSteadyStateTask::updateMatrices(), and CModel::updateMatrixAnnotations().

 {
   assert(d < mAnnotationsCN.size());
   assert(mModes[d] == OBJECTS);
 
   resizeOneDimension(d);
   assert(i < mAnnotationsCN[d].size());
 
   mAnnotationsCN[d][i] = cn;
 }

void CArrayAnnotation::setAnnotationString	(	size_t	d,
		size_t	i,
		const std::string	s
	)

Definition at line 106 of file CAnnotatedMatrix.cpp.

References mAnnotationsString, mModes, resizeOneDimension(), size(), and STRINGS.

Referenced by CFitProblem::initialize(), CILDMModifiedMethod::setAnnotationM(), CILDMMethod::setAnnotationM(), and CCSPMethod::setAnnotationM().

 {
   assert(d < mAnnotationsString.size());
   assert(mModes[d] == STRINGS);
 
   resizeOneDimension(d);
   assert(i < mAnnotationsString[d].size());
 
   mAnnotationsString[d][i] = s;
 }

void CArrayAnnotation::setArray ( CCopasiAbstractArray * a )

let the ArrayAnnotation point to a different array. If you use this method without updating the annotations afterwards it is your responsibility to make sure the new array fits the existing annotation (in dimensionality and, if not in VECTOR_ON_THE_FLY mode, in size).

Definition at line 58 of file CAnnotatedMatrix.cpp.

References mpArray.

 {
   mpArray = a;
 }

void CArrayAnnotation::setCopasiVector	(	size_t	d,
		const CCopasiContainer *	v
	)

Associates a dimension d of the array with a CCopasiVector of CCopasiObjects. If the mode of the dimension d is VECTOR than the CNs of the objects in the vector are generated and stored immediately. If the mode is VECTOR_ON_THE_FLY the CNs are generated when getAnnotationsCN() or getAnnotationsString() is called.

Definition at line 84 of file CAnnotatedMatrix.cpp.

References createAnnotationsCNFromCopasiVector(), mCopasiVectors, mModes, VECTOR, and VECTOR_ON_THE_FLY.

Referenced by CModel::initObjects(), CCSPMethod::predifineAnnotation(), CMCAMethod::resizeAllMatrices(), CLNAMethod::resizeAllMatrices(), CILDMModifiedMethod::setAnnotationM(), CILDMMethod::setAnnotationM(), CCSPMethod::setAnnotationM(), and CCSPMethod::start().

 {
   assert(d < mCopasiVectors.size());
   assert((mModes[d] == VECTOR) || (mModes[d] == VECTOR_ON_THE_FLY));
 
   mCopasiVectors[d] = v;
 
   if (mModes[d] == VECTOR)
     createAnnotationsCNFromCopasiVector(d, mCopasiVectors[d]);
 }

void CArrayAnnotation::setDescription ( const std::string & s )

Definition at line 182 of file CAnnotatedMatrix.cpp.

References mDescription.

Referenced by CILDMModifiedMethod::createAnnotationsM(), CILDMMethod::createAnnotationsM(), CCSPMethod::createAnnotationsM(), CLNAMethod::initObjects(), CMCAMethod::initObjects(), CSensProblem::initObjects(), CSteadyStateTask::initObjects(), and CModel::initObjects().

183 {mDescription = s;}

CArrayAnnotation::mDescription

std::string mDescription

Definition: CAnnotatedMatrix.h:96

void CArrayAnnotation::setDimensionDescription	(	size_t	d,
		const std::string &	s
	)

Definition at line 173 of file CAnnotatedMatrix.cpp.

References mDimensionDescriptions.

Referenced by CILDMModifiedMethod::createAnnotationsM(), CILDMMethod::createAnnotationsM(), CCSPMethod::createAnnotationsM(), CSensMethod::initialize(), CLNAMethod::initObjects(), CMCAMethod::initObjects(), CSteadyStateTask::initObjects(), and CModel::initObjects().

 {
   assert(d < mDimensionDescriptions.size());
   mDimensionDescriptions[d] = s;
 }

void CArrayAnnotation::setMode	(	size_t	d,
		Mode	m
	)

set the mode for the dimension d

Definition at line 63 of file CAnnotatedMatrix.cpp.

References mModes, and resizeOneDimension().

Referenced by CILDMModifiedMethod::createAnnotationsM(), CILDMMethod::createAnnotationsM(), CCSPMethod::createAnnotationsM(), CLNAMethod::initObjects(), CMCAMethod::initObjects(), CSensProblem::initObjects(), CSteadyStateTask::initObjects(), CModel::initObjects(), and setMode().

 {
   mModes[d] = m;
   resizeOneDimension(d);
 }

void CArrayAnnotation::setMode ( Mode m )

set the mode for all dimensions, this also sets the default mode that is used when resizing the ArrayAnnotion to a larger dimensionality

Definition at line 69 of file CAnnotatedMatrix.cpp.

References mDefaultMode, mModes, and setMode().

 {
   mDefaultMode = m;
 
   size_t i;
 
   for (i = 0; i < mModes.size(); ++i)
     setMode(i, m);
 }

CCopasiAbstractArray::index_type CArrayAnnotation::size ( ) const

inline

Definition at line 148 of file CAnnotatedMatrix.h.

References mpArray, and CCopasiAbstractArray::size().

Referenced by CCopasiSelectionDialog::chooseCellMatrix(), CQArrayAnnotationsWidget::fillBarChart(), CQArrayAnnotationsWidget::fillTable1(), CQArrayAnnotationsWidget::fillTableN(), CObjectLists::getListOfConstObjects(), CArrayElementReference::getValuePointer(), isEmpty(), printRecursively(), setAnnotationCN(), setAnnotationString(), and CQMatrixDialog::setArray().

149 {return mpArray->size();}

CCopasiAbstractArray::size

virtual const index_type & size() const =0

CArrayAnnotation::mpArray

CCopasiAbstractArray * mpArray

Definition: CAnnotatedMatrix.h:76

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	os,
		const CArrayAnnotation &	o
	)

friend

Definition at line 438 of file CAnnotatedMatrix.cpp.

 {
   if (!o.array()) return os;
 
   //cache the display names
   std::vector<std::vector<std::string> > displaynames;
   size_t i;
 
   for (i = 0; i < o.dimensionality(); ++i)
     displaynames.push_back(o.getAnnotationsString(i));
 
   os << o.getObjectName() << std::endl;
   os << o.getDescription() << std::endl;
 
   CCopasiAbstractArray::index_type arraysize = o.array()->size();
 
   if (o.dimensionality() == 0)
     {
       //only one scalar value
       os << (*o.array())[arraysize] << std::endl;
     }
   else
     {
       o.printRecursively(os, o.dimensionality() - 1, arraysize, displaynames);
     }
 
   return os;
 }