servicenotifiers.h

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#include "types.h"
#include "lifecycleevent.h"
#include "fileservices.h"
#include "statservices.h"
#include "updaterservices.h"
#include "filehandler.h"
#include "stathandler.h"
#include <map>
 
//LCE_ParamUpdaterNotifier
//
class LCE_ParamUpdaterNotifier : public LifeCycleEvent {
 
private:
  UpdaterServices* _manager;
 
public:
 
  LCE_ParamUpdaterNotifier () : LifeCycleEvent("param_updater",""), _manager(0) { }
  virtual ~LCE_ParamUpdaterNotifier() {}
 
  void setManager (UpdaterServices* mng) {_manager = mng;}
  virtual void execute ();
  virtual bool setParameters () {return true;}
 
  virtual LifeCycleEvent* clone ( ) {return new LCE_ParamUpdaterNotifier();}
 
  //SimComponent overrides:
  virtual void  loadFileServices ( FileServices* loader ) {}
  virtual void  loadStatServices ( StatServices* loader ) {}
  virtual void  loadUpdaters ( UpdaterServices* loader) {_manager = loader;}
  virtual bool resetParameterFromSource (std::string param, SimComponent* cmpt) {return false;}
  virtual age_t removeAgeClass ( ) {return 0;}
  virtual age_t addAgeClass ( ) {return 0;}
  virtual age_t requiredAgeClass () {return 0;}
};
 
// LCE_FileServicesNotifier
//
// forward decl
class GenotyperFH;
class LCE_FileServicesNotifier: public LifeCycleEvent
{
 
  FileServices* _service;
  TMatrix       _sample_patch;
  unsigned int  _sample_patch_num;
  TMatrix       _sample_size;
  TMatrix       _sample_age;
 
  vector< GenotyperFH* >  _genotypers;
 
public:
  LCE_FileServicesNotifier(); //: LifeCycleEvent("save_files",""), _service(0) { }
  virtual ~LCE_FileServicesNotifier( );
 
  virtual void execute ();
  virtual bool setParameters ();
 
  bool         setSamplingParameters  ();
  bool         setGenotyperParameters ();
 
  virtual LifeCycleEvent* clone ( ) {return new LCE_FileServicesNotifier();}
 
  //SimComponent implementation
  virtual void  loadFileServices ( FileServices* loader );
  virtual void  loadStatServices ( StatServices* loader ) {}
  virtual bool  resetParameterFromSource (std::string param, SimComponent* cmpt) {return false;}
  virtual age_t removeAgeClass ( ) {return 0;}
  virtual age_t addAgeClass ( ) {return 0;}
  virtual age_t requiredAgeClass () {return 0;}
};
 
// ----------------------------------------------------------------------------------------
 
// GenotyperFH
 
// ----------------------------------------------------------------------------------------
class GenotyperFH : public EventFileHandler < LCE_FileServicesNotifier > {
 
  vector< trait_t >       _traits; // which traits are selected
  vector< unsigned int >  _trait_index;
  string                  _format;
  string                  _logtime;
  bool                    _is_diallelic;
  bool                    _trim_loci;
  double                  _trim_maf;
 
public:
  GenotyperFH(LCE_FileServicesNotifier* event) : EventFileHandler(event, "") , _is_diallelic(0), _trim_loci(0), _trim_maf(0) {}
 
  virtual ~GenotyperFH() {}
 
  virtual void FHwrite();
  virtual void FHread (string& filename) {}
 
  void setTraits           (vector< trait_t >& traits);
 
  void setTraitIndex       (vector< unsigned int>& indices);
 
  void setFormat           (string format) {_format = format;}
 
  void setLogtime          (string logtime) {_logtime = logtime;}
 
  void set_isDiallelic     (bool test) {_is_diallelic = test;}
 
  void set_trimFixedLoci   (bool test, double maf) {_trim_loci = test; _trim_maf = maf;}
 
  void prepare_data_table  (map< unsigned int, vector<unsigned int> >& trait_locus, vector<string>& col_names);
  void print_genotypes     (ofstream& FH, map< unsigned int, vector<unsigned int> >& table);
  void print_snp_genotypes (ofstream& FH, map< unsigned int, vector<unsigned int> >& table);
  void print_snp_id        (ofstream& FH, map< unsigned int, vector<unsigned int> >& table);
  void print_PLINK         (string file, map< unsigned int, vector<unsigned int> >& table);
  void print_map_positions (ofstream& FH, vector< unsigned int >& positions, vector<string>& col_names);
};
 
// ----------------------------------------------------------------------------------------
 
// LCE_StatFH
//
class LCE_StatFH : public FileHandler {
 
  StatServices* _statService;
 
public:
 
  LCE_StatFH () 
: FileHandler(".txt"), _statService(0)
{
    FileHandler::set(false,false,0,0,0,"");
    set_isMasterExec(true);
}
 
  ~LCE_StatFH() { };
 
  virtual vector< string > ifExist();
 
  void set_statService(StatServices* srv) {_statService = srv;}
 
  virtual void FHwrite();
  virtual void FHread (string& filename) {}
 
  void PrintStat_byGen ( );
};
 
 
// LCE_StatServiceNotifier
//
class LCE_StatServiceNotifier: public LifeCycleEvent
{
 
  StatServices* _service;
 
  unsigned int _occurrence;
 
  string _arg, _dir;
 
  LCE_StatFH _fileHandler;
 
public:
 
  LCE_StatServiceNotifier ( );
 
  virtual ~LCE_StatServiceNotifier ( ) { }
 
  FileHandler& getFH() {return _fileHandler;}
  bool setOccurence ();
  bool dummyUpdate  (){return true;}
 
  virtual bool setParameters ();
  virtual void  execute ();
 
  virtual LCE_StatServiceNotifier* clone ( ) {return new LCE_StatServiceNotifier();}
 
  //SimComponent overrides:
  virtual void loadFileServices ( FileServices* loader ) {loader->attach(&_fileHandler);}
  virtual void loadStatServices ( StatServices* loader );
  virtual bool resetParameterFromSource (std::string param, SimComponent* cmpt) {return false;}
  virtual age_t removeAgeClass ( ) {return 0;}
  virtual age_t addAgeClass ( ) {return 0;}
  virtual age_t requiredAgeClass () {return 0;}
 
};