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/*****************************************************************************
* $CAMITK_LICENCE_BEGIN$
*
* CamiTK - Computer Assisted Medical Intervention ToolKit
* (c) 2001-2016 Univ. Grenoble Alpes, CNRS, TIMC-IMAG UMR 5525 (GMCAO)
*
* Visit http://camitk.imag.fr for more information
*
* This file is part of CamiTK.
*
* CamiTK is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License version 3
* only, as published by the Free Software Foundation.
*
* CamiTK is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License version 3 for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* version 3 along with CamiTK. If not, see <http://www.gnu.org/licenses/>.
*
* $CAMITK_LICENCE_END$
****************************************************************************/
#include "Atom.h"
#include "StructuralComponent.h"
#include "PhysicalModel.h"
// pmlschema includes
#include <Atom.hxx>
//----------------------- Constructors -----------------------
Atom::Atom(PhysicalModel *p) {
properties = new AtomProperties(p);
}
Atom::Atom ( PhysicalModel * p, physicalModel::Atom node, unsigned int id) {
properties = new AtomProperties(p, node.atomProperties());
indexInAtoms = id;
}
Atom::Atom ( PhysicalModel *p, const double pos[3] ) {
properties = new AtomProperties ( p, pos );
}
Atom::Atom ( PhysicalModel *p, const unsigned int ind ) {
properties = new AtomProperties ( p, ind );
}
Atom::Atom ( PhysicalModel *p, const unsigned int ind, const double pos[3] ) {
properties = new AtomProperties ( p, ind, pos );
}
//----------------------- Destructor -----------------------
Atom::~Atom() {
delete ( AtomProperties * ) properties;
properties = NULL;
}
//----------------------- setIndex -----------------------
bool Atom::setIndex ( const unsigned int index ) {
// set the property
Structure::setIndex ( index );
// tell the physical model about the change (and return true if insertion was ok)
return properties->getPhysicalModel()->addGlobalIndexAtomPair ( std::GlobalIndexStructurePair ( index,this ) );
}
//----------------------- getIndexInAtoms -----------------------
unsigned int Atom::getIndexInAtoms() const {
return indexInAtoms;
}
// --------------- xmlPrint ---------------
void Atom::xmlPrint ( std::ostream &o, const StructuralComponent *sc ) {
// nothing is to be done in particular with sc, but it is here
// because of the Structure::xmlPrint method has to be overriden
// depending on the structure who do the calls, two cases:
if ( properties->getPhysicalModel() !=NULL && sc == properties->getPhysicalModel()->getAtoms() ) {
// - if it is the physical model atom list: the atom print its properties
// print the atom and its properties
o << "<atom>" << std::endl;
( ( AtomProperties * ) properties )->xmlPrint ( o );
o << "</atom>" << std::endl;
} else {
// - if it is any other structural component: the atom print its ref
o << "<atomRef index=\"" << getIndex() << "\"/>" << std::endl;
}
}
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