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/*****************************************************************************
* $CAMITK_LICENCE_BEGIN$
*
* CamiTK - Computer Assisted Medical Intervention ToolKit
* (c) 2001-2025 Univ. Grenoble Alpes, CNRS, Grenoble INP - UGA, TIMC, 38000 Grenoble, France
*
* 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 "AtomProperties.h"
// XSD / XercesC stuffs
#include <xercesc/util/XercesDefs.hpp>
#include <xercesc/dom/DOMAttr.hpp>
#include <xercesc/util/XMLString.hpp>
// pmlschema includes
#include <AtomProperties.hxx>
//----------------------- Class member init -----------------------
void AtomProperties::resetUniqueIndex() {
AtomProperties::maxUniqueIndex = 0;
}
// initializing the static class member
unsigned int AtomProperties::maxUniqueIndex = 0;
//----------------------- Constructors -----------------------
AtomProperties::AtomProperties(PhysicalModel* p) : StructureProperties(p, StructureProperties::ATOM) {
allocate();
setPosition(0.0, 0.0, 0.0);
index = maxUniqueIndex++;
}
AtomProperties::AtomProperties(PhysicalModel* p, physicalModel::AtomProperties xmlAtomProp) : StructureProperties(p, StructureProperties::ATOM) {
allocate();
// Begin the search by required atom's properties, such as index and its position (x,y,z)
setIndex(xmlAtomProp.index());
setPosition(xmlAtomProp.x(), xmlAtomProp.y(), xmlAtomProp.z());
// Search for any optional name given to the atom
if (xmlAtomProp.name().present()) {
setName(xmlAtomProp.name().get());
}
// Add the eventually unkown attributes
xmlToFields(xmlAtomProp.any_attribute());
}
AtomProperties::AtomProperties(PhysicalModel* p, const double pos[3]) : StructureProperties(p, StructureProperties::ATOM) {
allocate();
setPosition(pos);
index = maxUniqueIndex++;
}
AtomProperties::AtomProperties(PhysicalModel* p, const unsigned int ind) : StructureProperties(p, StructureProperties::ATOM) {
allocate();
setPosition(0.0, 0.0, 0.0);
index = ind;
if (ind >= maxUniqueIndex) {
maxUniqueIndex = ind + 1;
}
}
AtomProperties::AtomProperties(PhysicalModel* p, const unsigned int ind, const double pos[3]) : StructureProperties(p, StructureProperties::ATOM) {
allocate();
setPosition(pos);
index = ind;
if (ind >= maxUniqueIndex) {
maxUniqueIndex = ind + 1;
}
}
//----------------------- destructor -----------------------
AtomProperties::~AtomProperties() {
if (allocated) {
delete [] X;
}
}
//----------------------- allocate -----------------------
void AtomProperties::allocate() {
X = new double[3];
allocated = true;
}
//----------------------- setPositionPointer -----------------------
void AtomProperties::setPositionPointer(double* ptr, bool update) {
// store previous position if needed
double pos[3];
if (update) {
getPosition(pos);
}
// delete previous memory to avoid memory leaks, if needed
if (allocated) {
delete [] X;
allocated = false;
}
X = ptr;
// restore if needed
if (update) {
setPosition(pos);
}
}
// --------------- xmlPrint ---------------
void AtomProperties::xmlPrint(std::ostream& o) {
// beginning of the atom properties
o << "<atomProperties index=\"" << index << "\"";
o << " x=\"" << X[0] << "\" y=\"" << X[1] << "\" z=\"" << X[2] << "\"";
if (getName() != "") {
o << " name=\"" << getName().c_str() << "\"";
}
for (std::map<std::string, std::string>::iterator it = fields.begin(); it != fields.end() ; ++it) {
o << " " << (*it).first << "=\"" << (*it).second << "\"";
}
// end of the properties
o << "/>" << std::endl;
}
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