#include <iostream>
#include <sstream>
#include <unistd.h>
#include <fstream>

#include <cometEventLoop.hxx>
#include "COMETGeomId.hxx"
#include "IGenericAlignmentLookup.hxx"
#include <TROOT.h>
#include <TGeoManager.h>
#include <TSystem.h>
#include <TFile.h>
#include <TMath.h>
#include <IGeomIdManager.hxx>
#include <IOADatabase.hxx>
#include <IApplyAlign.hxx>

#include <IGeomInfo.hxx>
#include <IGeomVisitor.hxx>
#include <IOARuntimeParameters.hxx>

int main(int argc, char *argv[])  
{
  std::cout << "WARNING!!! This application does nothing." << std::endl;
  /*
  if (argc != 2)
    std::cout<<"The command is ./RunApplyAlign.exe <input geometry file>"<<std::endl;
  else{
    bool applyTrackerSurvey = (bool)COMET::IOARuntimeParameters::Get().GetParameterI("oaApplyAlign.ApplyTrackerSurvey");
    bool applyFGDInternal = (bool)COMET::IOARuntimeParameters::Get().GetParameterI("oaApplyAlign.ApplyFGDIntAlign");
    bool applyMMSurvey = (bool)COMET::IOARuntimeParameters::Get().GetParameterI("oaApplyAlign.ApplyMMSurvey");

    std::string outputName;
    //COMET::IOADatabase::Get().SetGeometryFile(argv[1]);
          
    IApplyAlign* aligner = new IApplyAlign();
      
    if (aligner->AlignGeometry())
      {
  //Clark's code to strip geometry
  COMET::IOADatabase::Get().GeomId().BuildGeomIdMap();
  std::ostringstream geomName;
  if (applyTrackerSurvey)
    geomName << "tracker-survey-";
  if (applyFGDInternal)
    geomName << "FGD-internal-";
  if (applyMMSurvey)
    geomName << "MM-survey-";
  geomName << "aligned-geom"; 
  geomName << std::hex << std::nouppercase << std::setfill('0');
  for (int i = 0; i<5; ++i) 
    {
      geomName << "-";
      //geomName << std::setw(8) << COMET::IOADatabase::Get().GeomId().GetHash(i);
    }
  geomName  << ".root";

  if (outputName != "") outputName += "_";
  outputName += geomName.str();
  std::cout<<"Output geometry file name:"<<std::endl;
  std::cout << outputName << std::endl;
    
  TFile outputFile(outputName.c_str(),"RECREATE");
  if (!outputFile.IsOpen()) 
    std::cerr << "Cannot open output file" << std::endl;
  
  gGeoManager->Write();
  outputFile.Close();
      }
    else
      std::cout<<"No output geometry generated due to overlaps"<<std::endl;
  }
  */
}