/*
* Creates a new RenderCubicBezier object from the given XMLNode object.
* The XMLNode object has to contain a valid XML representation of a
* RenderCubicBezier 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 RenderCubicBezier
* object to be instantiated.
*/
RenderCubicBezier::RenderCubicBezier(const XMLNode& node, unsigned int l2version)
:RenderPoint(node, 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 new SpeciesGlyph from the given XMLNode
*/
SpeciesGlyph::SpeciesGlyph(const XMLNode& node, unsigned int l2version)
: GraphicalObject(2, l2version)
,mSpecies("")
{
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=="boundingBox")
{
this->mBoundingBox=BoundingBox(*child);
}
else if(childName=="annotation")
{
this->mAnnotation=new XMLNode(*child);
}
else if(childName=="notes")
{
this->mNotes=new XMLNode(*child);
}
else
{
//throw;
}
++n;
}
}
/*
* Creates a new RenderCurve object from the given XMLNode object.
* The XMLNode object has to contain a valid XML representation of a
* RenderCurve 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 RenderCurve
* object to be instantiated.
*/
RenderCurve::RenderCurve(const XMLNode& node, unsigned int l2version)
: GraphicalPrimitive1D(node, l2version)
, mListOfElements(node, l2version)
{
const XMLAttributes& attributes=node.getAttributes();
ExpectedAttributes ea;
addExpectedAttributes(ea);
this->readAttributes(attributes, ea);
const XMLNode* child;
unsigned int n=0,nMax = node.getNumChildren();
while(n<nMax)
{
child=&node.getChild(n);
const std::string& childName=child->getName();
if(childName=="listOfElements")
{
this->mListOfElements=ListOfCurveElements(*child);
}
++n;
}
setSBMLNamespacesAndOwn(new RenderPkgNamespaces(2,l2version));
connectToChild();
}
/*
* Creates a new ListOfGlobalStyles object from the given XMLNode object.
* The XMLNode object has to contain a valid XML representation of a
* ListOfGlobalStyles 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 ListOfGlobalStyles
* object to be instantiated.
*/
ListOfGlobalStyles::ListOfGlobalStyles(const XMLNode& node)
{
const XMLAttributes& attributes=node.getAttributes();
const XMLNode* child;
ExpectedAttributes ea;
mURI = RenderExtension::getXmlnsL3V1V1();
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=="style")
{
GlobalStyle* style=new GlobalStyle(*child);
this->appendAndOwn(style);
}
else if(childName=="annotation")
{
this->mAnnotation=new XMLNode(*child);
}
else if(childName=="notes")
{
this->mNotes=new XMLNode(*child);
}
++n;
}
}
/*
* Creates a new SpeciesGlyph from the given XMLNode
*/
SpeciesGlyph::SpeciesGlyph(const XMLNode& node, unsigned int l2version)
: GraphicalObject(node, l2version)
,mSpecies("")
{
const XMLAttributes& attributes=node.getAttributes();
ExpectedAttributes ea;
addExpectedAttributes(ea);
this->readAttributes(attributes,ea);
}
/*
* 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();
}
/*
* 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();
}
/*
* 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 ReferenceGlyph from the given XMLNode
*/
ReferenceGlyph::ReferenceGlyph(const XMLNode& node, unsigned int l2version)
: GraphicalObject (node, l2version)
,mReference("")
,mGlyph ("")
,mRole ("")
, mCurve (2, l2version)
,mCurveExplicitlySet (false)
{
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=="curve")
{
// since the copy constructor of ListOf does not make deep copies
// of the objects, we have to add the individual curveSegments to the
// curve instead of just copying the whole curve.
Curve* pTmpCurve=new Curve(*child);
unsigned int i,iMax=pTmpCurve->getNumCurveSegments();
for(i=0;i<iMax;++i)
{
this->mCurve.addCurveSegment(pTmpCurve->getCurveSegment(i));
}
// we also have to copy mAnnotations, mNotes, mCVTerms and mHistory
if(pTmpCurve->isSetNotes()) this->mCurve.setNotes(new XMLNode(*pTmpCurve->getNotes()));
if(pTmpCurve->isSetAnnotation()) this->mCurve.setAnnotation(new XMLNode(*pTmpCurve->getAnnotation()));
if(pTmpCurve->getCVTerms()!=NULL)
{
iMax=pTmpCurve->getCVTerms()->getSize();
for(i=0;i<iMax;++i)
{
this->mCurve.getCVTerms()->add(static_cast<CVTerm*>(pTmpCurve->getCVTerms()->get(i))->clone());
}
}
delete pTmpCurve;
mCurveExplicitlySet = true;
}
++n;
}
connectToChild();
}
/**
* Creates a new LineSegment from the given XMLNode
*/
LineSegment::LineSegment(const XMLNode& node, unsigned int l2version)
: SBase (2, l2version)
, mStartPoint(2, l2version)
, mEndPoint (2, l2version)
{
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);
}
else if(childName=="end")
{
this->mEndPoint=Point(*child);
}
else if(childName=="annotation")
{
this->mAnnotation=new XMLNode(*child);
}
else if(childName=="notes")
{
this->mNotes=new XMLNode(*child);
}
else
{
//throw;
}
++n;
}
connectToChild();
setSBMLNamespacesAndOwn(new LayoutPkgNamespaces(2,l2version));
}
/*
* Parses the xml information in the given node and sets the attributes.
* This method should never be called by the user. It is only used to read render
* information from annotations.
*
* @param node the XMLNode object reference that describes the ListOfGlobalRenderInformation
* object to be instantiated.
*/
void ListOfGlobalRenderInformation::parseXML(const XMLNode& node)
{
const XMLNode* child;
unsigned int n=0,nMax = node.getNumChildren();
const XMLAttributes& attributes=node.getAttributes();
ExpectedAttributes ea;
addExpectedAttributes(ea);
this->readAttributes(attributes, ea);
while(n<nMax)
{
child=&node.getChild(n);
const std::string& childName=child->getName();
if(childName=="renderInformation")
{
GlobalRenderInformation* pGRI=new GlobalRenderInformation(this->getLevel(),this->getVersion());
pGRI->parseXML(*child);
this->appendAndOwn(pGRI);
}
++n;
}
}
/*
* Parses the xml information in the given node and sets the attributes.
* This method should never be called by the user. It is only used to read render
* information from annotations.
*
* @param node the XMLNode object reference that describes the GlobalRenderInformation
* object to be instantiated.
*/
void GlobalRenderInformation::parseXML(const XMLNode& node)
{
this->RenderInformationBase::parseXML(node);
const XMLNode* child;
unsigned int n=0,nMax = node.getNumChildren();
const XMLAttributes& attributes=node.getAttributes();
ExpectedAttributes ea;
addExpectedAttributes(ea);
this->readAttributes(attributes, ea);
while(n<nMax)
{
child=&node.getChild(n);
const std::string& childName=child->getName();
if(childName=="listOfStyles")
{
this->mListOfStyles=ListOfGlobalStyles(*child);
this->mListOfStyles.setSBMLDocument(this->mSBML);
}
++n;
}
}
/*
* Creates a new Text object from the given XMLNode object.
* The XMLNode object has to contain a valid XML representation of a
* Text 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 Text
* object to be instantiated.
*/
Text::Text(const XMLNode& node, unsigned int l2version):GraphicalPrimitive1D(node, l2version)
{
const XMLAttributes& attributes=node.getAttributes();
ExpectedAttributes ea;
addExpectedAttributes(ea);
this->readAttributes(attributes,ea);
unsigned int i,iMax=node.getNumChildren();
for(i=0;i<iMax;++i)
{
if(node.getChild(i).isText())
{
mText=node.getChild(i).getCharacters();
break;
}
}
setSBMLNamespacesAndOwn(new RenderPkgNamespaces(2,l2version));
connectToChild();
}
/**
* Creates a new ReactionGlyph from the given XMLNode
*/
ReactionGlyph::ReactionGlyph(const XMLNode& node, unsigned int l2version)
: GraphicalObject(2,l2version)
,mReaction ("")
,mSpeciesReferenceGlyphs(2,l2version)
,mCurve(2,l2version)
{
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=="boundingBox")
{
this->mBoundingBox=BoundingBox(*child);
}
else if(childName=="annotation")
{
this->mAnnotation=new XMLNode(*child);
}
else if(childName=="notes")
{
this->mNotes=new XMLNode(*child);
}
else if(childName=="curve")
{
// since the copy constructor of ListOf does not make deep copies
// of the objects, we have to add the individual curveSegments to the
// curve instead of just copying the whole curve.
Curve* pTmpCurve=new Curve(*child);
unsigned int i,iMax=pTmpCurve->getNumCurveSegments();
for(i=0;i<iMax;++i)
{
this->mCurve.addCurveSegment(pTmpCurve->getCurveSegment(i));
}
// we also have to copy mAnnotations, mNotes, mCVTerms and mHistory
if(pTmpCurve->isSetNotes()) this->mCurve.setNotes(new XMLNode(*pTmpCurve->getNotes()));
if(pTmpCurve->isSetAnnotation()) this->mCurve.setAnnotation(new XMLNode(*pTmpCurve->getAnnotation()));
if(pTmpCurve->getCVTerms()!=NULL)
{
iMax=pTmpCurve->getCVTerms()->getSize();
for(i=0;i<iMax;++i)
{
this->mCurve.getCVTerms()->add(static_cast<CVTerm*>(pTmpCurve->getCVTerms()->get(i))->clone());
}
}
delete pTmpCurve;
}
else if(childName=="listOfSpeciesReferenceGlyphs")
{
const XMLNode* innerChild;
unsigned int i=0,iMax=child->getNumChildren();
while(i<iMax)
{
innerChild=&child->getChild(i);
const std::string innerChildName=innerChild->getName();
if(innerChildName=="speciesReferenceGlyph")
{
this->mSpeciesReferenceGlyphs.appendAndOwn(new SpeciesReferenceGlyph(*innerChild));
}
else if(innerChildName=="annotation")
{
this->mSpeciesReferenceGlyphs.setAnnotation(new XMLNode(*innerChild));
}
else if(innerChildName=="notes")
{
this->mSpeciesReferenceGlyphs.setNotes(new XMLNode(*innerChild));
}
else
{
// throw
}
++i;
}
}
else
{
//throw;
}
++n;
}
connectToChild();
}
/*
* Creates a new ReactionGlyph from the given XMLNode
*/
Curve::Curve(const XMLNode& node, unsigned int l2version)
: SBase (2,l2version)
,mCurveSegments(2,l2version)
{
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=="annotation")
{
this->mAnnotation=new XMLNode(*child);
}
else if(childName=="notes")
{
this->mNotes=new XMLNode(*child);
}
else if(childName=="listOfCurveSegments")
{
const XMLNode* innerChild;
unsigned int i=0,iMax=child->getNumChildren();
while(i<iMax)
{
innerChild=&child->getChild(i);
const std::string innerChildName=innerChild->getName();
if(innerChildName=="curveSegment")
{
// get the type
const XMLAttributes& innerAttributes=innerChild->getAttributes();
int typeIndex=innerAttributes.getIndex("type");
if(typeIndex==-1 || innerAttributes.getURI(typeIndex)!="http://www.w3.org/2001/XMLSchema-instance")
{
// throw
++i;
continue;
}
if(innerAttributes.getValue(typeIndex)=="LineSegment")
{
this->mCurveSegments.appendAndOwn(new LineSegment(*innerChild));
}
else if(innerAttributes.getValue(typeIndex)=="CubicBezier")
{
this->mCurveSegments.appendAndOwn(new CubicBezier(*innerChild));
}
else
{
// throw
}
}
else if(innerChildName=="annotation")
{
this->mCurveSegments.setAnnotation(new XMLNode(*innerChild));
}
else if(innerChildName=="notes")
{
this->mCurveSegments.setNotes(new XMLNode(*innerChild));
}
else
{
// throw
}
++i;
}
}
else
{
//throw;
}
++n;
}
setSBMLNamespacesAndOwn(new LayoutPkgNamespaces(2,l2version));
connectToChild();
}
/** @cond doxygenLibsbmlInternal */
void GlobalRenderInformation::readAttributes (const XMLAttributes& attributes, const ExpectedAttributes& expectedAttributes)
{
ExpectedAttributes ea;
addExpectedAttributes(ea);
this->RenderInformationBase::readAttributes(attributes, ea);
}
/*
* Creates a new Style object from the given XMLNode object.
* The XMLNode object has to contain a valid XML representation of a
* Style 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 Style
* object to be instantiated.
*/
Style::Style(const XMLNode& node, unsigned int l2version) :
SBase(2,l2version),
mGroup(2,l2version)
{
mURI = RenderExtension::getXmlnsL3V1V1();
const XMLNode* child;
const XMLAttributes& attributes=node.getAttributes();
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=="g")
{
this->mGroup=RenderGroup(*child);
// set the unset values to the defaults
if(!this->mGroup.isSetStroke())
{
this->mGroup.setStroke("none");
}
if(!this->mGroup.isSetStrokeWidth())
{
this->mGroup.setStrokeWidth(0.0);
}
if(!this->mGroup.isSetDashArray())
{
this->mGroup.setDashArray(std::vector<unsigned int>());
}
if(!this->mGroup.isSetFillColor())
{
this->mGroup.setFillColor("none");
}
if(!this->mGroup.isSetFillRule())
{
this->mGroup.setFillRule(GraphicalPrimitive2D::NONZERO);
}
if(!this->mGroup.isSetFontFamily())
{
this->mGroup.setFontFamily("sans-serif");
}
if(!this->mGroup.isSetFontSize())
{
this->mGroup.setFontSize(0);
}
if(!this->mGroup.isSetFontWeight())
{
this->mGroup.setFontWeight(Text::WEIGHT_NORMAL);
}
if(!this->mGroup.isSetFontStyle())
{
this->mGroup.setFontStyle(Text::STYLE_NORMAL);
}
if(!this->mGroup.isSetStartHead())
{
this->mGroup.setStartHead("none");
}
if(!this->mGroup.isSetEndHead())
{
this->mGroup.setEndHead("none");
}
}
else if(childName=="annotation")
{
this->mAnnotation=new XMLNode(*child);
}
else if(childName=="notes")
{
this->mNotes=new XMLNode(*child);
}
++n;
}
setSBMLNamespacesAndOwn(new RenderPkgNamespaces(2,l2version));
connectToChild();
}
