/**
* Creates a new CubicBezier and adds it to the end of the list. A
* reference to the new CubicBezier object is returned.
*/
CubicBezier* Curve::createCubicBezier ()
{
CubicBezier* cb = NULL;
try
{
cb = new CubicBezier(getSBMLNamespaces());
}
catch (...)
{
/* here we do not create a default object as the level/version must
* match the parent object
*
* so do nothing
*/
}
/* if the ListOf is empty it doesnt know its parent */
if (mCurveSegments.size() == 0)
{
mCurveSegments.setSBMLDocument(this->getSBMLDocument());
mCurveSegments.setParentSBMLObject(this);
}
if(cb != NULL)
{
this->mCurveSegments.appendAndOwn(cb);
}
return cb;
}
/**
* Creates a new LineSegment and adds it to the end of the list. A
* reference to the new LineSegment object is returned.
*/
LineSegment*
Curve::createLineSegment ()
{
LineSegment* ls = NULL;
try
{
ls = new LineSegment(getSBMLNamespaces());
}
catch (...)
{
/* here we do not create a default object as the level/version must
* match the parent object
*
* so do nothing
*/
}
/* if the ListOf is empty it doesnt know its parent */
if (mCurveSegments.size() == 0)
{
mCurveSegments.setSBMLDocument(this->getSBMLDocument());
mCurveSegments.setParentSBMLObject(this);
}
if(ls != NULL)
{
this->mCurveSegments.appendAndOwn(ls);
}
return ls;
}
/**
* Creates a new CubicBezier and adds it to the end of the list. A
* reference to the new CubicBezier object is returned.
*/
CubicBezier* Curve::createCubicBezier ()
{
LAYOUT_CREATE_NS(layoutns,getSBMLNamespaces());
CubicBezier* cb = new CubicBezier(layoutns);
this->mCurveSegments.appendAndOwn(cb);
return cb;
}
/** @cond doxygenLibsbmlInternal */
SBase*
CompSBasePlugin::createObject(XMLInputStream& stream)
{
SBase* object = 0;
const std::string& name = stream.peek().getName();
const XMLNamespaces& xmlns = stream.peek().getNamespaces();
const std::string& prefix = stream.peek().getPrefix();
const std::string& targetPrefix = (xmlns.hasURI(mURI)) ? xmlns.getPrefix(mURI) : mPrefix;
if (prefix == targetPrefix)
{
if ( name == "listOfReplacedElements" )
{
if (mListOfReplacedElements != NULL)
{
getErrorLog()->logPackageError("comp", CompOneListOfReplacedElements,
getPackageVersion(), getLevel(), getVersion());
}
createListOfReplacedElements();
object = mListOfReplacedElements;
if (targetPrefix.empty())
{
//
// (NOTE)
//
// A top-level element (listOfReplacedElements) of the comp extension is located
// in a default namespace, and thus xmlns=".." attribute must be added to
// the element.
// This is done by invoking SBMLDocument::enableDefaultNS() function with
// the two arguments (the URI of this package and true value).
//
mListOfReplacedElements->getSBMLDocument()->enableDefaultNS(mURI,true);
}
}
if ( name == "replacedBy" ) {
if (mReplacedBy != NULL)
{
if (mSBML != NULL && getErrorLog() != NULL)
{
getErrorLog()->logPackageError("comp", CompOneReplacedByElement,
getPackageVersion(), getLevel(), getVersion());
}
}
delete mReplacedBy;
COMP_CREATE_NS(compns, getSBMLNamespaces());
mReplacedBy = new ReplacedBy(compns);
object = mReplacedBy;
object->connectToParent(getParentSBMLObject());
delete compns;
}
}
return object;
}
/*
* Creates a new SpeciesReferenceGlyph object, adds it to the end of the
* list of species reference objects and returns a reference to the newly
* created object.
*/
SpeciesReferenceGlyph*
ReactionGlyph::createSpeciesReferenceGlyph ()
{
LAYOUT_CREATE_NS(layoutns,getSBMLNamespaces());
SpeciesReferenceGlyph* srg = new SpeciesReferenceGlyph(layoutns);
this->mSpeciesReferenceGlyphs.appendAndOwn(srg);
return srg;
}
/**
* Creates a new LineSegment and adds it to the end of the list. A
* reference to the new LineSegment object is returned.
*/
LineSegment*
Curve::createLineSegment ()
{
LAYOUT_CREATE_NS(layoutns,getSBMLNamespaces());
LineSegment* ls = new LineSegment(layoutns);
this->mCurveSegments.appendAndOwn(ls);
return ls;
}
/*
* Creates a new ReferenceGlyph object, adds it to the end of the
* list of reference objects and returns a reference to the newly
* created object.
*/
ReferenceGlyph*
GeneralGlyph::createReferenceGlyph ()
{
LAYOUT_CREATE_NS(layoutns,getSBMLNamespaces());
ReferenceGlyph* srg = new ReferenceGlyph(layoutns);
this->mReferenceGlyphs.appendAndOwn(srg);
delete layoutns;
return srg;
}
void
CompSBasePlugin::createListOfReplacedElements()
{
if (mListOfReplacedElements==NULL) {
COMP_CREATE_NS(compns, getSBMLNamespaces());
mListOfReplacedElements = new ListOfReplacedElements(compns);
mListOfReplacedElements->connectToParent(getParentSBMLObject());
delete compns;
}
}
/*
* Creates a ReplacedElement object, adds it to the end of the replacedElement
* objects list and returns a reference to the newly created object.
*/
ReplacedElement*
CompSBasePlugin::createReplacedElement ()
{
createListOfReplacedElements();
COMP_CREATE_NS(compns, getSBMLNamespaces());
ReplacedElement* m = new ReplacedElement(compns);
mListOfReplacedElements->appendAndOwn(m);
delete compns;
return m;
}
ReplacedBy*
CompSBasePlugin::createReplacedBy()
{
if (mReplacedBy!=NULL) {
delete mReplacedBy;
}
COMP_CREATE_NS(compns, getSBMLNamespaces());
mReplacedBy = new ReplacedBy(compns);
mReplacedBy->connectToParent(getParentSBMLObject());
delete compns;
return mReplacedBy;
}
void
Model::dealWithModelUnits()
{
UnitRefsFilter filter;
List * elements = getAllElements(&filter);
unsigned int n = 0;
unsigned int num = elements->getSize();
if (isSetVolumeUnits())
{
std::string volume = getVolumeUnits();
// if in an L3 model a user used volume as an id of a UnitDefinition
// but they declared the volume units of teh model to be something
// else then the UD with id volume is nothing to do with the
// L2 interpretation of volume
// so replace that UD and all references to it
if (volume != "volume")
{
UnitDefinition * existingUD = removeUnitDefinition("volume");
if (existingUD != NULL)
{
std::string newSubsName = "volumeFromOriginal";
existingUD->setId(newSubsName);
SBase* obj;
for (n = 0; n < num; n++)
{
obj = (SBase*)(elements->get(n));
obj->renameUnitSIdRefs("volume", newSubsName);
}
addUnitDefinition(existingUD);
}
}
UnitDefinition * ud = getUnitDefinition(volume) != NULL ?
getUnitDefinition(volume)->clone() : NULL;
if (ud != NULL)
{
ud->setId("volume");
}
else
{
Unit *u = new Unit(getSBMLNamespaces());
u->initDefaults();
u->setKind(UnitKind_forName(volume.c_str()));
ud = new UnitDefinition(getSBMLNamespaces());
ud->setId("volume");
ud->addUnit(u);
}
addUnitDefinition(ud);
}
if (isSetAreaUnits())
{
std::string area = getAreaUnits();
// if in an L3 model a user used area as an id of a UnitDefinition
// but they declared the area units of teh model to be something
// else then the UD with id area is nothing to do with the
// L2 interpretation of area
// so replace that UD and all references to it
if (area != "area")
{
UnitDefinition * existingUD = removeUnitDefinition("area");
if (existingUD != NULL)
{
std::string newSubsName = "areaFromOriginal";
existingUD->setId(newSubsName);
SBase* obj;
for (n = 0; n < num; n++)
{
obj = (SBase*)(elements->get(n));
obj->renameUnitSIdRefs("area", newSubsName);
}
addUnitDefinition(existingUD);
}
}
UnitDefinition * ud = getUnitDefinition(area) != NULL ?
getUnitDefinition(area)->clone() : NULL;
if (ud != NULL)
{
ud->setId("area");
}
else
{
Unit *u = new Unit(getSBMLNamespaces());
u->initDefaults();
u->setKind(UnitKind_forName(area.c_str()));
ud = new UnitDefinition(getSBMLNamespaces());
ud->setId("area");
ud->addUnit(u);
}
addUnitDefinition(ud);
}
if (isSetLengthUnits())
{
std::string length = getLengthUnits();
// if in an L3 model a user used length as an id of a UnitDefinition
// but they declared the length units of teh model to be something
// else then the UD with id length is nothing to do with the
// L2 interpretation of length
// so replace that UD and all references to it
if (length != "length")
{
UnitDefinition * existingUD = removeUnitDefinition("length");
if (existingUD != NULL)
{
std::string newSubsName = "lengthFromOriginal";
existingUD->setId(newSubsName);
SBase* obj;
for (n = 0; n < num; n++)
{
obj = (SBase*)(elements->get(n));
obj->renameUnitSIdRefs("length", newSubsName);
}
addUnitDefinition(existingUD);
}
}
UnitDefinition * ud = getUnitDefinition(length) != NULL ?
getUnitDefinition(length)->clone() : NULL;
if (ud != NULL)
{
ud->setId("length");
}
else
{
Unit *u = new Unit(getSBMLNamespaces());
u->initDefaults();
u->setKind(UnitKind_forName(length.c_str()));
ud = new UnitDefinition(getSBMLNamespaces());
ud->setId("length");
ud->addUnit(u);
}
addUnitDefinition(ud);
}
if (isSetSubstanceUnits())
{
std::string substance = getSubstanceUnits();
// if in an L3 model a user used substance as an id of a UnitDefinition
// but they declared the substance units of teh model to be something
// else then the UD with id substance is nothing to do with the
// L2 interpretation of substance
// so replace that UD and all references to it
if (substance != "substance")
{
UnitDefinition * existingUD = removeUnitDefinition("substance");
if (existingUD != NULL)
{
std::string newSubsName = "substanceFromOriginal";
existingUD->setId(newSubsName);
SBase* obj;
for (n = 0; n < num; n++)
{
obj = (SBase*)(elements->get(n));
obj->renameUnitSIdRefs("substance", newSubsName);
}
addUnitDefinition(existingUD);
}
}
UnitDefinition * ud = getUnitDefinition(substance) != NULL ?
getUnitDefinition(substance)->clone() : NULL;
if (ud != NULL)
{
ud->setId("substance");
}
else
{
Unit *u = new Unit(getSBMLNamespaces());
u->initDefaults();
u->setKind(UnitKind_forName(substance.c_str()));
ud = new UnitDefinition(getSBMLNamespaces());
ud->setId("substance");
ud->addUnit(u);
}
addUnitDefinition(ud);
}
if (isSetTimeUnits())
{
std::string time = getTimeUnits();
// if in an L3 model a user used time as an id of a UnitDefinition
// but they declared the time units of teh model to be something
// else then the UD with id time is nothing to do with the
// L2 interpretation of time
// so replace that UD and all references to it
if (time != "time")
{
UnitDefinition * existingUD = removeUnitDefinition("time");
if (existingUD != NULL)
{
std::string newSubsName = "timeFromOriginal";
existingUD->setId(newSubsName);
SBase* obj;
for (n = 0; n < num; n++)
{
obj = (SBase*)(elements->get(n));
obj->renameUnitSIdRefs("time", newSubsName);
}
addUnitDefinition(existingUD);
}
}
UnitDefinition * ud = getUnitDefinition(time) != NULL ?
getUnitDefinition(time)->clone() : NULL;
if (ud != NULL)
{
ud->setId("time");
}
else
{
ud = new UnitDefinition(getSBMLNamespaces());
ud->setId("time");
Unit *u = ud->createUnit();
u->initDefaults();
u->setKind(UnitKind_forName(time.c_str()));
}
addUnitDefinition(ud);
}
}
void
Model::dealWithModelUnits()
{
if (isSetVolumeUnits())
{
std::string volume = getVolumeUnits();
UnitDefinition * ud = removeUnitDefinition(volume);
if (ud != NULL)
{
ud->setId("volume");
}
else
{
Unit *u = new Unit(getSBMLNamespaces());
u->initDefaults();
u->setKind(UnitKind_forName(volume.c_str()));
ud = new UnitDefinition(getSBMLNamespaces());
ud->setId("volume");
ud->addUnit(u);
}
addUnitDefinition(ud);
}
if (isSetAreaUnits())
{
std::string area = getAreaUnits();
UnitDefinition * ud = removeUnitDefinition(area);
if (ud != NULL)
{
ud->setId("area");
}
else
{
Unit *u = new Unit(getSBMLNamespaces());
u->initDefaults();
u->setKind(UnitKind_forName(area.c_str()));
ud = new UnitDefinition(getSBMLNamespaces());
ud->setId("area");
ud->addUnit(u);
}
addUnitDefinition(ud);
}
if (isSetLengthUnits())
{
std::string length = getLengthUnits();
UnitDefinition * ud = removeUnitDefinition(length);
if (ud != NULL)
{
ud->setId("length");
}
else
{
Unit *u = new Unit(getSBMLNamespaces());
u->initDefaults();
u->setKind(UnitKind_forName(length.c_str()));
ud = new UnitDefinition(getSBMLNamespaces());
ud->setId("length");
ud->addUnit(u);
}
addUnitDefinition(ud);
}
if (isSetSubstanceUnits())
{
std::string substance = getSubstanceUnits();
UnitDefinition * ud = removeUnitDefinition(substance);
if (ud != NULL)
{
ud->setId("substance");
}
else
{
Unit *u = new Unit(getSBMLNamespaces());
u->initDefaults();
u->setKind(UnitKind_forName(substance.c_str()));
ud = new UnitDefinition(getSBMLNamespaces());
ud->setId("substance");
ud->addUnit(u);
}
addUnitDefinition(ud);
}
if (isSetTimeUnits())
{
std::string time = getTimeUnits();
UnitDefinition * ud = removeUnitDefinition(time);
if (ud != NULL)
{
ud->setId("time");
}
else
{
ud = new UnitDefinition(getSBMLNamespaces());
ud->setId("time");
Unit *u = ud->createUnit();
u->initDefaults();
u->setKind(UnitKind_forName(time.c_str()));
}
addUnitDefinition(ud);
}
}
