GenotyperFH Class Reference

#include <servicenotifiers.h>

Inheritance diagram for GenotyperFH:

Collaboration diagram for GenotyperFH:

Public Member Functions
	GenotyperFH (LCE_FileServicesNotifier *event)
virtual	~GenotyperFH ()
virtual void	FHwrite ()
virtual void	FHread (string &filename)
void	setTraits (vector< trait_t > &traits)
void	setFormat (string format)
void	setLogtime (string logtime)
Public Member Functions inherited from EventFileHandler< LCE_FileServicesNotifier >
	EventFileHandler (LCE_FileServicesNotifier *event, const char *ext)
virtual	~EventFileHandler ()
virtual void	FHread (string &filename)=0
virtual void	set (bool rpl_per, bool gen_per, int rpl_occ, int gen_occ, int rank, string path, LCE_FileServicesNotifier *event)
Public Member Functions inherited from FileHandler
	FileHandler (const char *ext)
virtual	~FileHandler ()
virtual void	init ()
	Called by notifier during simulation setup, performs file checking. More...
virtual vector< string >	ifExist ()
	Checks if any file associated with the current file name already exists on disk. More...
virtual void	set (bool rpl_per, bool gen_per, int rpl_occ, int gen_occ, int rank, string path)
	Sets the hanlder parameters. More...
virtual void	set_multi (bool rpl_per, bool gen_per, int rpl_occ, TMatrix *Occ, string path)
virtual void	update ()
	Updates the inner replicate and generation counters and calls FHwrite if needed by the the periodicity of the file. More...
Metapop *	get_pop_ptr ()
	Returns the pointer to the current metapop through the FileServices interface. More...
void	set_pop_ptr (Metapop *pop_ptr)
FileServices *	get_service ()
	Returns pointer to the FileServices. More...
void	set_service (FileServices *srv)
std::string &	get_path ()
void	set_path ()
std::string &	get_extension ()
void	set_extension (const char *ext)
std::string &	get_filename ()
	Builds and returns the current file name depending on the periodicity of the file. More...
bool	get_isInputHandler ()
void	set_isInputHandler (bool val)
bool	get_isReplicatePeriodic ()
void	set_isReplicatePeriodic (bool val)
unsigned int	get_ReplicateOccurrence ()
void	set_ReplicateOccurrence (unsigned int val)
bool	get_isGenerationPeriodic ()
void	set_isGenerationPeriodic (bool val)
unsigned int	get_GenerationOccurrence ()
void	set_GenerationOccurrence (unsigned int val)
unsigned int	get_ExecRank ()
	unused yet... More...
void	set_ExecRank (int val)
TMatrix *	get_OccMatrix ()
void	set_OccMatrix (TMatrix *occ)
bool	get_isMasterExec ()
void	set_isMasterExec (bool is)
Public Member Functions inherited from Handler
virtual	~Handler ()

Private Attributes
vector< trait_t >	_traits
vector< unsigned int >	_map_index
multimap< unsigned int, TraitPrototype * >	_locposition_map
unsigned int	_ntrait
string	_format
string	_logtime

Additional Inherited Members
Protected Attributes inherited from EventFileHandler< LCE_FileServicesNotifier >
LCE_FileServicesNotifier *	_FHLinkedEvent
Protected Attributes inherited from FileHandler
Metapop *	_pop
	Pointer to the current metapop, set during initialization within the init function. More...

Constructor & Destructor Documentation

GenotyperFH()

GenotyperFH::GenotyperFH ( LCE_FileServicesNotifier *  event )

inline

                                               :
    EventFileHandler(event, ""), _ntrait(0) {}

~GenotyperFH()

virtual GenotyperFH::~GenotyperFH ( )

inlinevirtual

{}

Member Function Documentation

FHread()

virtual void GenotyperFH::FHread ( string &  filename )

inlinevirtual

Implements FileHandler.

{}

FHwrite()

void GenotyperFH::FHwrite ( )

virtual

Implements EventFileHandler< LCE_FileServicesNotifier >.

{
 
}

setFormat()

void GenotyperFH::setFormat ( string  format )

inline

{_format = format;}

References _format.

setLogtime()

void GenotyperFH::setLogtime ( string  logtime )

inline

{_logtime = logtime;}

References _logtime.

setTraits()

void GenotyperFH::setTraits

(

vector< trait_t > &

traits

)

{
  _traits.assign(traits.begin(), traits.end());
 
  unsigned int nlocus;
  unsigned int* pos_table;
  int index;
 
  for(unsigned int i = 0; i < _traits.size(); ++i)
  {
    //get the trait's index
//    index = _pop->getTraitIndex(traits[i]);
//    _map_index.push_back(index);
    //nlocus =
    //get the loci positions
 
    //add to the locus-trait map
 
  }
 
  // build locus-pos-trat mapping
 
 
}

References _traits.

Referenced by LCE_FileServicesNotifier::loadFileServices().

Member Data Documentation

_format

string GenotyperFH::_format

private

Referenced by setFormat().

_locposition_map

multimap< unsigned int, TraitPrototype* > GenotyperFH::_locposition_map

private

_logtime

string GenotyperFH::_logtime

private

Referenced by setLogtime().

_map_index

vector< unsigned int> GenotyperFH::_map_index

private

_ntrait

unsigned int GenotyperFH::_ntrait

private

_traits

vector< trait_t > GenotyperFH::_traits

private

Referenced by setTraits().

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The documentation for this class was generated from the following files:

• servicenotifiers.h
• servicenotifiers.cc