A class to read a pedigree from a file. More...

#include <LCEmisc.h>

Inheritance diagram for FHPedigreeReader:

Collaboration diagram for FHPedigreeReader:

Public Member Functions
	FHPedigreeReader (LCE_Cross *event)

virtual	~FHPedigreeReader ()

virtual void	FHwrite ()

virtual void	FHread (string &filename)

vector< unsigned long * > &	getPedigree ()

Public Member Functions inherited from EventFileHandler< LCE_Cross >
	EventFileHandler (LCE_Cross event, const char ext)

virtual	~EventFileHandler ()

virtual void	FHwrite ()=0

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_Cross *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	FHwrite ()=0
	Default behavior of the class, called by Handler::update(). More...

virtual void	FHread (string &filename)=0
	Default input function. More...

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 void	init ()=0
	Inits state. More...

virtual void	update ()=0
	Updates the handler state. More...

virtual	~Handler ()

Private Attributes
vector< unsigned long * >	_pedigree

Additional Inherited Members
Protected Attributes inherited from EventFileHandler< LCE_Cross >
LCE_Cross *	_FHLinkedEvent

Protected Attributes inherited from FileHandler
Metapop *	_pop
	Pointer to the current metapop, set during initialization within the init function. More...

Detailed Description

A class to read a pedigree from a file.

Constructor & Destructor Documentation

◆ FHPedigreeReader()

FHPedigreeReader::FHPedigreeReader ( LCE_Cross * event )

                                                  :
                EventFileHandler< LCE_Cross > (event, ".ped")
{
 
}

◆ ~FHPedigreeReader()

virtual FHPedigreeReader::~FHPedigreeReader ( )

inlinevirtual

206{}

Member Function Documentation

◆ FHread()

void FHPedigreeReader::FHread ( string & filename )

virtual

Implements FileHandler.

{
        ifstream FILE(filename.c_str(),ios::in);
 
        if(!FILE) fatal("could not open pedigree input file \"%s\"\n",filename.c_str());
 
        string ID, sire, dam;
 
        unsigned int line = 0;
 
        unsigned long * record = 0;
 
        _pedigree.clear();
 
        message("\n++++ reading pedigree file: %s\n",filename.c_str());
 
        while(FILE){
 
                line++;
 
                FILE >> ID >> sire >> dam;
 
                if(!FILE || FILE.eof()) break;
 
                record = new unsigned long [3];
 
                if(tstring::isanumber(ID)) record[0] = tstring::str2ulong(ID);
                else if(tstring::isNA(ID)) record[0] = 0;
                else {
                        error("%s: ID on line %i is not a number\n",filename.c_str(),line);
                        delete [] record; record = 0;
                        continue;
                }
 
                if(tstring::isanumber(sire)) record[1] = tstring::str2ulong(sire);
                else if(tstring::isNA(sire)) record[1] = 0;
                else {
                        error("%s: 'sire' on line %i is not a number\n",filename.c_str(),line);
                        delete [] record; record = 0;
                        continue;
                }
 
                if(tstring::isanumber(dam)) record[2] = tstring::str2ulong(dam);
                else if(tstring::isNA(dam)) record[2] = 0;
                else {
                        error("%s: 'dam' on line %i is not a number\n",filename.c_str(),line);
                        delete [] record; record = 0;
                        continue;
                }
//              cout<<line<<": "<<ID<<" "<<sire<<" "<<dam<<endl;
 
                _pedigree.push_back(record);
        }
 
        if(FILE) FILE.close();
 
        message("++++ pedigree has %i valid records\n", _pedigree.size());
}