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//
// This example is provided by the Geant4-DNA collaboration
// Any report or published results obtained using the Geant4-DNA software 
// and the DNA geometry given in the Geom_DNA example 
// shall cite the following Geant4-DNA collaboration publications:
// [1] NIM B 298 (2013) 47-54
// [2] Med. Phys. 37 (2010) 4692-4708
// The Geant4-DNA web site is available at http://geant4-dna.org
//

#include "G4VPhysicalVolume.hh"
#include "G4ThreeVector.hh"
#include "G4Box.hh"
#include "ChromosomeParameterisation.hh"
#include <fstream>
#include "G4SystemOfUnits.hh"

using namespace std;

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....

ChromosomeParameterisation::ChromosomeParameterisation(const char* filename)
{
  ifstream f(filename, ios::in);
  if (!f)
    return;

  fPositions.reserve(100);
  fRotations.reserve(100);

  while (!f.eof())
  {
    double x, y, z, rot;
    f >> x >> y >> z >> rot;
    fPositions.push_back(new G4ThreeVector(x * nanometer, y * nanometer, z * nanometer));
    fRotations.push_back(new G4RotationMatrix(0, 0, rot * degree));
  }
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....

ChromosomeParameterisation::~ChromosomeParameterisation()
{
  unsigned int i;
  for (i = 0; i < fPositions.size(); i++)
    delete fPositions[i];
  for (i = 0; i < fRotations.size(); i++)
    delete fRotations[i];
}
   
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....

void ChromosomeParameterisation::ComputeDimensions(
    G4Tubs& /*rosette*/, const G4int /*copyNo*/, const G4VPhysicalVolume* /*physVol*/) const
{
  
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....

void ChromosomeParameterisation::ComputeTransformation(
    const G4int copyNo, G4VPhysicalVolume* physVol) const
{
  // see passive vs active method to specify
  // this transformation
  physVol->SetTranslation(*fPositions[copyNo]);
  physVol->SetRotation(fRotations[copyNo]);
}