/**
* Copy constructor.
*/
Curve::Curve(const Curve& source):SBase(source)
{
// copy the line segments
this->mCurveSegments=*source.getListOfCurveSegments();
connectToChild();
}
/*
* Constructor which sets the id, the coordinates and the dimensions to the
* given 3D values.
*/
BoundingBox::BoundingBox (LayoutPkgNamespaces* layoutns, const std::string id,
const Point* p,
const Dimensions* d)
: SBase (layoutns)
, mId (id)
, mPosition(layoutns)
, mDimensions(layoutns)
,mPositionExplicitlySet (true)
,mDimensionsExplicitlySet (true)
{
//
// set the element namespace of this object
//
setElementNamespace(layoutns->getURI());
if(p)
{
this->mPosition=*p;
}
mPosition.setElementName("position");
if(d)
{
this->mDimensions=*d;
}
connectToChild();
//
// load package extensions bound with this object (if any)
//
loadPlugins(layoutns);
}
LIBSBML_CPP_NAMESPACE_BEGIN
/** @cond doxygenLibsbmlInternal */
/*
* Creates a new RenderPoint object with the given SBML level
* and SBML version.
*
* @param level SBML level of the new object
* @param level SBML version of the new object
*/
RenderPoint::RenderPoint (unsigned int level, unsigned int version, unsigned int pkgVersion) :
SBase(level,version)
,mXOffset(RelAbsVector(0.0,0.0))
,mYOffset(RelAbsVector(0.0,0.0))
,mZOffset(RelAbsVector(0.0,0.0))
,mElementName("element")
{
if (!hasValidLevelVersionNamespaceCombination())
throw SBMLConstructorException();
RenderPkgNamespaces* renderns = new RenderPkgNamespaces(level, version, pkgVersion);
setSBMLNamespacesAndOwn(renderns);
connectToChild();
loadPlugins(renderns);
}
/*
* Creates a GeneralGlyph with the given @p id and set the id of the
* associated reaction to the second argument.
*/
GeneralGlyph::GeneralGlyph (LayoutPkgNamespaces* layoutns, const std::string& id,
const std::string& referenceId)
: GraphicalObject( layoutns, id )
,mReference ( referenceId )
,mReferenceGlyphs(layoutns)
,mSubGlyphs(layoutns)
,mCurve(layoutns)
, mCurveExplicitlySet (false)
{
mSubGlyphs.setElementName("listOfSubGlyphs");
//
// (NOTE) Developers don't have to invoke setElementNamespace function as follows (commentted line)
// in this constuctor because the function is properly invoked in the constructor of the
// base class (LineSegment).
//
// setElementNamespace(layoutns->getURI());
connectToChild();
//
// load package extensions bound with this object (if any)
//
loadPlugins(layoutns);
}
/*
* Creates a new RenderPoint object from the given XMLNode object.
* The XMLNode object has to contain a valid XML representation of a
* RenderPoint object as defined in the render extension specification.
* This method is normally called when render information is read from a file and
* should normally not have to be called explicitely.
*
* @param node the XMLNode object reference that describes the RenderPoint
* object to be instantiated.
*/
RenderPoint::RenderPoint(const XMLNode& node, unsigned int l2version) : SBase(2, l2version)
{
const XMLAttributes& attributes=node.getAttributes();
const XMLNode* child;
ExpectedAttributes ea;
addExpectedAttributes(ea);
this->readAttributes(attributes, ea);
unsigned int n=0,nMax = node.getNumChildren();
while(n<nMax)
{
child=&node.getChild(n);
const std::string& childName=child->getName();
if(childName=="annotation")
{
this->mAnnotation=new XMLNode(node);
}
else if(childName=="notes")
{
this->mNotes=new XMLNode(node);
}
else
{
//throw;
}
++n;
}
setSBMLNamespacesAndOwn(new RenderPkgNamespaces(2,l2version));
connectToChild();
}
/*
* Creates a CubicBezier and returns the pointer.
*/
CubicBezier::CubicBezier(LayoutPkgNamespaces* layoutns)
: LineSegment(layoutns)
,mBasePoint1(layoutns)
,mBasePoint2(layoutns)
, mBasePt1ExplicitlySet (false)
, mBasePt2ExplicitlySet (false)
{
this->mStartPoint.setElementName("start");
this->mEndPoint.setElementName("end");
this->mBasePoint1.setElementName("basePoint1");
this->mBasePoint2.setElementName("basePoint2");
connectToChild();
//
// (NOTE) Developers don't have to invoke setElementNamespace function as follows (commentted line)
// in this constuctor because the function is properly invoked in the constructor of the
// base class (LineSegment).
//
// setElementNamespace(layoutns->getURI());
//
// load package extensions bound with this object (if any)
//
loadPlugins(layoutns);
}
/**
* Copy constructor.
*/
ReactionGlyph::ReactionGlyph(const ReactionGlyph& source):GraphicalObject(source)
{
this->mReaction=source.getReactionId();
this->mCurve=*source.getCurve();
this->mSpeciesReferenceGlyphs=*source.getListOfSpeciesReferenceGlyphs();
connectToChild();
}
/*
* Copy constructor.
*/
CubicBezier::CubicBezier(const CubicBezier& orig):LineSegment(orig)
{
this->mBasePoint1=orig.mBasePoint1;
this->mBasePoint2=orig.mBasePoint2;
this->mBasePt1ExplicitlySet=orig.mBasePt1ExplicitlySet;
this->mBasePt2ExplicitlySet=orig.mBasePt2ExplicitlySet;
connectToChild();
}
LIBSBML_CPP_NAMESPACE_BEGIN
CompSBasePlugin::CompSBasePlugin (const std::string &uri, const std::string &prefix, CompPkgNamespaces *compns)
: SBasePlugin(uri,prefix, compns)
, mListOfReplacedElements(NULL)
, mReplacedBy(NULL)
{
connectToChild();
}
/*
* Copy constructor.
*/
BoundingBox::BoundingBox(const BoundingBox& orig):SBase(orig)
{
this->mId = orig.mId;
this->mPosition=orig.mPosition;
this->mDimensions=orig.mDimensions;
this->mPositionExplicitlySet = orig.mPositionExplicitlySet;
this->mDimensionsExplicitlySet = orig.mDimensionsExplicitlySet;
connectToChild();
}
/**
* Copy constructor.
*/
SpeciesReferenceGlyph::SpeciesReferenceGlyph(const SpeciesReferenceGlyph& source) :
GraphicalObject(source)
{
this->mSpeciesReference=source.getSpeciesReferenceId();
this->mSpeciesGlyph=source.getSpeciesGlyphId();
this->mRole=source.getRole();
this->mCurve=*source.getCurve();
connectToChild();
}
/*
* Copy constructor.
*/
GeneralGlyph::GeneralGlyph(const GeneralGlyph& source):GraphicalObject(source)
{
this->mReference=source.getReferenceId();
this->mCurve=*source.getCurve();
this->mReferenceGlyphs=*source.getListOfReferenceGlyphs();
this->mSubGlyphs=*source.getListOfSubGlyphs();
this->mCurveExplicitlySet = source.mCurveExplicitlySet;
connectToChild();
}
/*
* Creates a new CubicBezier from the given XMLNode
*/
CubicBezier::CubicBezier(const XMLNode& node, unsigned int l2version)
: LineSegment(2, l2version)
,mBasePoint1(2, l2version)
,mBasePoint2(2, l2version)
, mBasePt1ExplicitlySet (false)
, mBasePt2ExplicitlySet (false)
{
const XMLAttributes& attributes=node.getAttributes();
const XMLNode* child;
//ExpectedAttributes ea(getElementName());
ExpectedAttributes ea;
addExpectedAttributes(ea);
this->readAttributes(attributes,ea);
unsigned int n=0,nMax = node.getNumChildren();
while(n<nMax)
{
child=&node.getChild(n);
const std::string& childName=child->getName();
if(childName=="start")
{
this->mStartPoint=Point(*child);
this->mStartExplicitlySet = true;
}
else if(childName=="end")
{
this->mEndPoint=Point(*child);
this->mEndExplicitlySet = true;
}
else if(childName=="basePoint1")
{
this->mBasePoint1=Point(*child);
this->mBasePt1ExplicitlySet = true;
}
else if(childName=="basePoint2")
{
this->mBasePoint2=Point(*child);
this->mBasePt2ExplicitlySet = true;
}
else if(childName=="annotation")
{
this->mAnnotation=new XMLNode(*child);
}
else if(childName=="notes")
{
this->mNotes=new XMLNode(*child);
}
else
{
//throw;
}
++n;
}
connectToChild();
}
/*
* Copy constructor.
*/
ReferenceGlyph::ReferenceGlyph(const ReferenceGlyph& source) :
GraphicalObject(source)
{
this->mReference=source.mReference;
this->mGlyph=source.mGlyph;
this->mRole=source.mRole;
this->mCurve=*source.getCurve();
this->mCurveExplicitlySet = source.mCurveExplicitlySet;
connectToChild();
}
/*
* Default Constructor set position and dimensions to (0.0,0.0,0.0) and the
* id to an empty string.
*/
BoundingBox::BoundingBox(unsigned int level, unsigned int version, unsigned int pkgVersion)
: SBase(level,version)
,mPosition(level,version,pkgVersion)
,mDimensions(level,version,pkgVersion)
,mPositionExplicitlySet (false)
,mDimensionsExplicitlySet (false)
{
mPosition.setElementName("position");
setSBMLNamespacesAndOwn(new LayoutPkgNamespaces(level,version,pkgVersion));
connectToChild();
}
/**
* Assignment operator.
*/
LineSegment& LineSegment::operator=(const LineSegment& orig)
{
if(&orig!=this)
{
this->SBase::operator=(orig);
this->mStartPoint=orig.mStartPoint;
this->mEndPoint=orig.mEndPoint;
connectToChild();
}
return *this;
}
/*
* Creates a new Transformation2D object with the given SBMLNamespaces.
*
* @param sbmlns The SBML namespace for the object.
*/
Transformation2D::Transformation2D (RenderPkgNamespaces* renderns):
Transformation(renderns)
{
this->updateMatrix2D();
// set the element namespace of this object
setElementNamespace(renderns->getURI());
// connect child elements to this element.
connectToChild();
// load package extensions bound with this object (if any)
loadPlugins(renderns);
}
/*
* Creates a new Transformation2D object from the given XMLNode object.
* The XMLNode object has to contain a valid XML representation of a
* Transformation2D object as defined in the render extension specification.
* This method is normally called when render information is read from a file and
* should normally not have to be called explicitely.
*
* @param node the XMLNode object reference that describes the Transformation2D
* object to be instantiated.
*/
Transformation2D::Transformation2D(const XMLNode& node, unsigned int l2version)
:Transformation(node, l2version)
{
ExpectedAttributes ea;
addExpectedAttributes(ea);
this->readAttributes(node.getAttributes(), ea);
setSBMLNamespacesAndOwn(new RenderPkgNamespaces(2,l2version));
connectToChild();
}
LIBSBML_CPP_NAMESPACE_BEGIN
/**
* Creates a curve with the given SBML level, version and package version and
* an empty list of segments.
*/
Curve::Curve (unsigned int level, unsigned int version, unsigned int pkgVersion)
: SBase (level,version)
,mCurveSegments(level,version,pkgVersion)
{
setSBMLNamespacesAndOwn(new LayoutPkgNamespaces(level,version,pkgVersion));
connectToChild();
}
/**
* Assignment operator.
*/
ReactionGlyph& ReactionGlyph::operator=(const ReactionGlyph& source)
{
if(&source!=this)
{
GraphicalObject::operator=(source);
this->mReaction=source.getReactionId();
this->mCurve=*source.getCurve();
this->mSpeciesReferenceGlyphs=*source.getListOfSpeciesReferenceGlyphs();
connectToChild();
}
return *this;
}
/*
* Assignment operator.
*/
Curve& Curve::operator=(const Curve& source)
{
if(&source!=this)
{
this->SBase::operator=(source);
// copy the line segments
this->mCurveSegments=*source.getListOfCurveSegments();
connectToChild();
}
return *this;
}
/*
* Assignment operator.
*/
CubicBezier& CubicBezier::operator=(const CubicBezier& orig)
{
if(&orig!=this)
{
LineSegment::operator=(orig);
this->mBasePoint1=orig.mBasePoint1;
this->mBasePoint2=orig.mBasePoint2;
this->mBasePt1ExplicitlySet=orig.mBasePt1ExplicitlySet;
this->mBasePt2ExplicitlySet=orig.mBasePt2ExplicitlySet;
connectToChild();
}
return *this;
}
/*
* Creates a new GlobalRenderInformation object with the given SBMLNamespaces.
*
* @param sbmlns The SBML namespace for the object.
*/
GlobalRenderInformation::GlobalRenderInformation (RenderPkgNamespaces* renderns):
RenderInformationBase(renderns), mListOfStyles(renderns)
{
if (!hasValidLevelVersionNamespaceCombination())
throw SBMLConstructorException();
// set the element namespace of this object
setElementNamespace(renderns->getURI());
// connect child elements to this element.
connectToChild();
// load package extensions bound with this object (if any)
loadPlugins(renderns);
}
/*
* Creates a new RenderCubicBezier object with the given SBMLNamespaces.
*
* @param sbmlns The SBML namespace for the object.
*/
RenderCubicBezier::RenderCubicBezier (RenderPkgNamespaces* renderns):
RenderPoint(renderns)
{
if (!hasValidLevelVersionNamespaceCombination())
throw SBMLConstructorException();
// set the element namespace of this object
setElementNamespace(renderns->getURI());
// connect child elements to this element.
connectToChild();
// load package extensions bound with this object (if any)
loadPlugins(renderns);
}
/*
* Creates a new Style object with the given SBMLNamespaces.
*
* @param sbmlns The SBML namespace for the object.
*/
Style::Style (RenderPkgNamespaces* renderns):
SBase(renderns)
,mId("")
,mGroup(renderns)
{
// set the element namespace of this object
setElementNamespace(renderns->getURI());
// connect child elements to this element.
connectToChild();
// load package extensions bound with this object (if any)
loadPlugins(renderns);
}
/*
* Constructor which creates a GlobalStyle with the given @p id
* and all lists empty.
*
* @param id the new id for the GlobalStyle.
*
* This constructor is deprecated. The new libsbml API only has
* constructors which take the SBML level and version or one that takes
* an SBMLNamespaces object.
*/
GlobalStyle::GlobalStyle(RenderPkgNamespaces* renderns, const std::string& id):Style(renderns,id)
{
#ifdef DEPRECATION_WARNINGS
std::cerr << "Warning. GlobalStyle::GlobalStyle(const std::string& id) is deprecated." << std::endl;
#endif // DEPRECATION_WARNINGS
// set the element namespace of this object
setElementNamespace(renderns->getURI());
// connect child elements to this element.
connectToChild();
// load package extensions bound with this object (if any)
loadPlugins(renderns);
}
/*
* Creates a new BoundingBox from the given XMLNode
*/
BoundingBox::BoundingBox(const XMLNode& node, unsigned int l2version)
: SBase(2,l2version)
, mId("")
, mPosition(2,l2version)
, mDimensions(2,l2version)
,mPositionExplicitlySet (false)
,mDimensionsExplicitlySet (false)
{
mPosition.setElementName("position");
const XMLAttributes& attributes=node.getAttributes();
const XMLNode* child;
//ExpectedAttributes ea(getElementName());
ExpectedAttributes ea;
addExpectedAttributes(ea);
this->readAttributes(attributes,ea);
unsigned int n=0,nMax = node.getNumChildren();
while(n<nMax)
{
child=&node.getChild(n);
const std::string& childName=child->getName();
if(childName=="position")
{
this->mPosition=Point(*child);
this->mPositionExplicitlySet = true;
}
else if(childName=="dimensions")
{
this->mDimensions=Dimensions(*child);
this->mDimensionsExplicitlySet = true;
}
else if(childName=="annotation")
{
this->mAnnotation=new XMLNode(*child);
}
else if(childName=="notes")
{
this->mNotes=new XMLNode(*child);
}
else
{
//throw;
}
++n;
}
setSBMLNamespacesAndOwn(new LayoutPkgNamespaces(2,l2version));
connectToChild();
}
/*
* Creates a new ReactionGlyph. The list of species reference glyph is
* empty and the id of the associated reaction is set to the empty string.
*/
ReactionGlyph::ReactionGlyph(unsigned int level, unsigned int version, unsigned int pkgVersion)
: GraphicalObject (level,version,pkgVersion)
,mReaction("")
,mSpeciesReferenceGlyphs(level,version,pkgVersion)
,mCurve(level,version,pkgVersion)
,mCurveExplicitlySet (false)
{
connectToChild();
//
// (NOTE) Developers don't have to invoke setSBMLNamespacesAndOwn function as follows (commentted line)
// in this constuctor because the function is properly invoked in the constructor of the
// base class (GraphicalObject).
//
//setSBMLNamespacesAndOwn(new LayoutPkgNamespaces(level,version,pkgVersion));
}
/*
* Assignment operator.
*/
GeneralGlyph& GeneralGlyph::operator=(const GeneralGlyph& source)
{
if(&source!=this)
{
GraphicalObject::operator=(source);
this->mReference=source.mReference;
this->mCurve=*source.getCurve();
this->mReferenceGlyphs=*source.getListOfReferenceGlyphs();
this->mSubGlyphs=*source.getListOfSubGlyphs();
this->mCurveExplicitlySet = source.mCurveExplicitlySet;
connectToChild();
}
return *this;
}
/*
* Constructor with id and values for the matrix.
*/
Transformation2D::Transformation2D(RenderPkgNamespaces* renderns, const double matrix[6]):Transformation(renderns)
{
#ifdef DEPRECATION_WARNINGS
std::cerr << "Warning. Transformation2D::Transformation2D(const double matrix[6]) is deprecated." << std::endl;
#endif // DEPRECATION_WARNINGS
this->setMatrix2D(matrix);
// set the element namespace of this object
setElementNamespace(renderns->getURI());
// connect child elements to this element.
connectToChild();
// load package extensions bound with this object (if any)
loadPlugins(renderns);
}
