This structure stores one parameter, its definition and its string argument. More...

#include <param.h>

Collaboration diagram for Param:

Public Member Functions
	Param (string &Name, param_t Type, bool mandatory, bool bounded, double low_bnd, double up_bnd, SimComponent owner, ParamUpdaterBase updater)
	Constructor.
	Param (const Param &P)
	Copy cstor, provides shallow copy of the parameter definition, do not copy arguments.
virtual	~Param ()
void	reset ()
	Clears the _isSet flag and the argument string.
void	setName (string value)
	Sets the parameter's name.
void	setArg (string value)
	Sets the parameter's argument.
void	setType (param_t value)
	Sets the parameter's type (see types.h)
void	setIsSet (bool value)
	Sets the _isSet flag.
void	setIsBounded (bool value)
	Sets the _isBounded flag.
void	setBounds (double low_bnd, double up_bnd)
	Sets the bounds.
void	setOwner (SimComponent *owner)
	Sets the pointer to owner.
void	setUpdater (ParamUpdaterBase *updater)
	Sets the pointer to the updater object.
void	setAtGeneration (unsigned int generation)
string	getName ()
string	getArg ()
param_t	getType ()
bool	isSet ()
bool	isBounded ()
bool	isRequired ()
double	getBound (unsigned int i)
SimComponent *	getOwner ()
ParamUpdaterBase *	getUpdater ()
deque< unsigned int >	getUpdatingDates ()
deque< string >	getTemporalArgs ()
bool	set (string arg, string &errmsg)
	Sets the _isSet flag to true and _arg to arg if the arg is of the right type and whithin the bounds.
bool	update (unsigned int generation)
	Updates the parameter value at a given generation during the simulation.
double	getValue ()
	Returns the argument value according to its type.
bool	isMatrix ()
	Checks if the argument is of matrix type.
void	getMatrix (TMatrix *mat)
	Sets the matrix from the argument string if the parameter is set and of matrix type.
void	parse_matrix (TMatrix *mat)
	Parses the matrix from the argument string.
bool	parseArgument (string &arg)
bool	parseTemporalArgument (const string &arg)
bool	parseAgeSpecArgument (const string &arg)
bool	parseSubParamArgument (const string &arg)
void	show_up ()
	Print state to stdout.
Private Attributes
string	_name
	The name of the parameter as read in the init file.
string	_arg
	The argument string, set by the ParamsParser upon initialization.
param_t	_type
	The type of the argument, must one of DBL, INT, BOOL, STR or MAT (see types.h).
bool	_isSet
	Flag set once the parameter has recieved the right argument.
bool	_isBounded
	Flag telling if the parameter has a bounded argument value.
bool	_isRequired
	Flag telling if this parameter is mandatory.
double	_bounds [2]
	The argument value boundaries.
unsigned int	_setAtGeneration
	Generation at which the parameter has been set/updated.
SimComponent *	_myOwner
	Pointer to the component that declared this parameter.
ParamUpdaterBase *	_myUpdater
	Pointer to an ParamUpdater object.
map< string, Param * >	_subParams
map< unsigned int, string >	_temporalArgs
	The temporal arguments.
bool	_isTemporal

Detailed Description

This structure stores one parameter, its definition and its string argument.

Parameters are aggregated into a ParamSet.

Definition at line 52 of file param.h.

Constructor & Destructor Documentation

Param::Param	(	string &	Name,
		param_t	Type,
		bool	mandatory,
		bool	bounded,
		double	low_bnd,
		double	up_bnd,
		SimComponent *	owner,
		ParamUpdaterBase *	updater
	)

Constructor.

Parameters:

Name	the name of the parameter as read in the init file
Type	the type of the parameter argument (see types.h), used to convert the argument string into a value
mandatory	specifies whether this parameter is mandatory for the ParamSet owning it
bounded	specifies whether the values this parameter can take are bounded
low_bnd	the lower bound of the parameter value
up_bnd	the upper bound
owner	pointer to the SimComponents that owns this parameter
updater	the param updater object used to update the parameter's state during a simulation

Definition at line 41 of file param.cc.

References _bounds.

: _name(Name),_arg(""),_type(Type),_isSet(0),_isBounded(bounded),_isRequired(mandatory),_setAtGeneration(0),
_myOwner(owner), _myUpdater(updater)

{
  _bounds[0] = low_bnd;
  _bounds[1] = up_bnd;
}

Param::Param ( const Param & P )

Copy cstor, provides shallow copy of the parameter definition, do not copy arguments.

Definition at line 53 of file param.cc.

References _bounds.

: _name(P._name),_arg(P._arg),_type(P._type),_isSet(P._isSet),_isBounded(P._isBounded),
_isRequired(P._isRequired),_setAtGeneration(P._setAtGeneration),_myOwner(P._myOwner),
_myUpdater(0)
{
  _bounds[0] = P._bounds[0];
  _bounds[1] = P._bounds[1];
}

Param::~Param ( ) [virtual]

Definition at line 64 of file param.cc.

References _myUpdater.

{
  if(_myUpdater) delete _myUpdater;
}

Member Function Documentation

string Param::getArg ( ) [inline]

Definition at line 125 of file param.h.

Referenced by LCE_Breed_base::setFecundity(), and BinaryDataSaver::setParameters().

{return _arg;}

double Param::getBound ( unsigned int i ) [inline]

Definition at line 130 of file param.h.

{return _bounds[i];}

void Param::getMatrix ( TMatrix * mat )

Sets the matrix from the argument string if the parameter is set and of matrix type.

Passes the param 'mat' to function Param::parse_matrix.

Parameters:

mat	a TMatrix ptr, mat dimensions and values will be reset to the values read in the init file.

Definition at line 257 of file param.cc.

References _isSet, _name, isMatrix(), parse_matrix(), and warning().

Referenced by LCE_Selection_base::set_sel_model().

{
  if( isMatrix() && _isSet ){
    
        parse_matrix(mat);

  } else
        warning("param \"%s\" is not a matrix!\n",_name.c_str());
}

string Param::getName ( ) [inline]

Definition at line 124 of file param.h.

Referenced by ParamSet::add_param().

{return _name;}

SimComponent* Param::getOwner ( ) [inline]

Definition at line 131 of file param.h.

{return _myOwner;}

deque< string > Param::getTemporalArgs ( )

Definition at line 93 of file param.cc.

References _temporalArgs.

{
  deque< string > args;
  
  for(map< unsigned int, string >::iterator tmp_it = _temporalArgs.begin();
      tmp_it != _temporalArgs.end(); tmp_it++)
    args.push_back( tmp_it->second );
  
  return args;
}

param_t Param::getType ( ) [inline]

Definition at line 126 of file param.h.

{return _type;}

ParamUpdaterBase* Param::getUpdater ( ) [inline]

Definition at line 132 of file param.h.

{return _myUpdater;}

deque< unsigned int > Param::getUpdatingDates ( )

Definition at line 80 of file param.cc.

References _temporalArgs.

{
  deque< unsigned int > dates;
  
  for(map< unsigned int, string >::iterator tmp_it = _temporalArgs.begin();
      tmp_it != _temporalArgs.end(); tmp_it++)
    dates.push_back( tmp_it->first );
  
  return dates;
}

double Param::getValue ( )

Returns the argument value according to its type.

Returns:: -1 if the parameter is not set or not of a the right type

Definition at line 247 of file param.cc.

References _arg, _isSet, _type, isMatrix(), and STR.

Referenced by TProtoNeutralGenes::loadFileServices(), and TProtoDeletMutations_bitstring::loadFileServices().

{
  if( !(isMatrix() || _type == STR) && _isSet)
        return atof(_arg.c_str());
  else
        return -1.0;
}

bool Param::isBounded ( ) [inline]

Definition at line 128 of file param.h.

{return _isBounded;}

bool Param::isMatrix ( ) [inline]

Checks if the argument is of matrix type.

Definition at line 151 of file param.h.

References MAT.

Referenced by getMatrix(), and getValue().

    {  return (_type == MAT || (_arg.size() != 0 ? _arg[0] == '{' : false) ); }

bool Param::isRequired ( ) [inline]

Definition at line 129 of file param.h.

{return _isRequired;}

bool Param::isSet ( ) [inline]

Definition at line 127 of file param.h.

Referenced by LCE_Resize::execute(), TProtoNeutralGenes::loadFileServices(), TProtoDeletMutations_bitstring::loadFileServices(), LCE_Selection_base::set_sel_model(), LCE_Breed_base::setFecundity(), LCE_Breed_base::setMatingSystem(), BinaryDataSaver::setParameters(), TProtoNeutralGenes::setParameters(), TProtoDeletMutations_bitstring::setParameters(), LCE_Breed_Wolbachia::setParameters(), LCE_Selection_base::setSelectionMatrix(), TProtoDeletMutations_bitstring::setSelectionParameters(), and LCE_Resize::updateParameters().

{return _isSet;}

void Param::parse_matrix ( TMatrix * mat )

Parses the matrix from the argument string.

Parameters:

mat	a TMatrix ptr, mat dimensions and values will be reset to the values read in the init file.

Definition at line 270 of file param.cc.

References _arg, _name, fatal(), TMatrix::reset(), and TMatrix::set().

Referenced by getMatrix().

{
  std::vector< std::vector<double>* > tmpMat;
  std::istringstream IN;
  
  IN.str(_arg);
  
  unsigned int cols = 0;
  double elmnt;
  char c;

  
  int rows = -1, pos = -1;
  //we count the number of rows
  do {
    pos = _arg.find("{", pos + 1);
    //message("pos %i, arg %s\n",pos,_arg.c_str());
    rows++;
  }while(pos != (int)string::npos);
  //decrement by 1, the first doesn't count for a row
  rows--;
  
  for(int i = 0; i < rows; i++)
    tmpMat.push_back( new vector<double>);
  
  //remove the first enclosing bracket
  IN>>c;
  //then read the rows
  for(unsigned int i = 0; i < tmpMat.size(); i++) {
    
    cols = 0;
    
    //read a row enclosed by {...}:
    while(IN) {
      
      //first character:
      IN>>c;
          
          if(c == '{' || c == ',' || c == ';') {
                //read a row element:
                IN>>elmnt;
                cols++;
                tmpMat[i]->push_back(elmnt);
                
          } else if(c == '}')
                //go to next row
                break;
                
        }
  }
  //check for matrix coherence:
  for(unsigned int i = 0; i < tmpMat.size(); i++) {
        if(tmpMat[i]->size() != cols)
          fatal("%s: not same number of elements in all rows of matrix! (%i, cols %i)\n",_name.c_str(),tmpMat[i]->size(),cols);
        cols = tmpMat[i]->size();
  }
  
  //copy to input TMatrix:
  mat->reset(rows, cols);
  for(int i = 0; i < rows; ++i)
        for(unsigned int j = 0; j < cols; ++j)
          mat->set(i,j,(*tmpMat[i])[j]);
}

bool Param::parseAgeSpecArgument ( const string & arg )

Definition at line 233 of file param.cc.

Referenced by parseArgument().

{
  return true;
}

bool Param::parseArgument ( string & arg )

Definition at line 155 of file param.cc.

References _isTemporal, _myUpdater, _name, _temporalArgs, error(), parseAgeSpecArgument(), parseSubParamArgument(), parseTemporalArgument(), tstring::removeEnclosingChar(), tstring::splitExcludeEnclosedDelimiters(), and warning().

Referenced by set().

{
  arg = tstring::removeEnclosingChar(arg, '(', ')');
  
  vector< string > args = tstring::splitExcludeEnclosedDelimiters(arg);
  
  _temporalArgs.clear();
//  _ageSpecArgs.clear();
//  _subParams.clear();
  
//  cout<< "Param::parseArgument:" << endl;
  
  for(unsigned int i = 0; i < args.size(); ++i) {
    //cout << args[i] << endl;
    if(args[i][0] == '@') {
      if(args[i][1] == 'g') if(!parseTemporalArgument(args[i])) return false;
      else if(args[i][1] == 'a') if(!parseAgeSpecArgument(args[i])) return false;
      else {
        error("parameter \"%s\"'s argument string \"%s\" has unrecognized specifier.\n", _name.c_str(), args[i].c_str());
        return false;
      }
    } else
      parseSubParamArgument(args[i]);
  }

  
  if(_temporalArgs.size() != 0) {
    
    //cout << "temporal arg values:\n";
    //    for(map< unsigned int , string >::iterator iter = _temporalArgs.begin();
    //        iter != _temporalArgs.end();
    //        iter++)
    //        cout << iter->first <<" "<< iter->second << endl;
    
    if(_myUpdater != 0) {
      
      if(_temporalArgs.find(0) != _temporalArgs.end()) {
        _isTemporal = true;
        //set the value for the first generation
        arg = _temporalArgs.find(0)->second;
      }
      else {
        error("first generation argument value for temporal parameter \"%s\" is missing; no \"@g0\".\n", _name.c_str());
        return false;
      }
      
    } else {
      warning("trying to pass a temporal argument to a non temporal parameter (\"%s\").\n", _name.c_str());
      _isTemporal = false;
      _temporalArgs.clear();
    }
    
  } else _isTemporal = false;
  
  
  return true;
}

bool Param::parseSubParamArgument ( const string & arg )

Definition at line 240 of file param.cc.

Referenced by parseArgument().

{
  return true;
}

bool Param::parseTemporalArgument ( const string & arg )

Definition at line 215 of file param.cc.

References _name, _temporalArgs, error(), tstring::removeFirstCharOf(), tstring::split(), and tstring::str2uint().

Referenced by parseArgument().

{
  vector< string > args = tstring::split(arg, ' ', true);
  
  if(args.size() != 2) {
    error("Param::parseTemporalArgument:: missing argument value in \"%s %s\".\n", _name.c_str(), arg.c_str());
    return false;
  }
  
  unsigned int gen = tstring::str2uint(tstring::removeFirstCharOf(tstring::removeFirstCharOf(args[0], '@'), 'g'));
  
  _temporalArgs[gen] = args[1];

  return true;
}

void Param::reset ( )

Clears the _isSet flag and the argument string.

Definition at line 71 of file param.cc.

References _arg, _isSet, and _setAtGeneration.

{
  _arg = "";
  _isSet = 0;
  _setAtGeneration = 0;
}

bool Param::set	(	string	arg,
		string &	errmsg
	)

Sets the _isSet flag to true and _arg to arg if the arg is of the right type and whithin the bounds.

Called at simulation setup (i.e. generation 0). For parameter update during the simulation, check the Param::update member function.

!a matrix may also be specified!! in that case, we don't check values here

Definition at line 106 of file param.cc.

References _arg, _bounds, _isBounded, _isSet, _type, BOOL, DBL, INT, tstring::isanumber(), MAT, parseArgument(), tstring::str2dble(), and tstring::str2int().

{  
  //cout << "Param::set ("<<arg<<")\n";
  if( arg[0] == '(' ) 
    if( !parseArgument( arg ) ) {
      errmsg = "could not parse the argument string";
      return false;
    }
  //integer or decimal: 
  if(_type == INT || _type == DBL) {
        if(arg[0] != '{') {
          
          if(!tstring::isanumber(arg)) {
        errmsg = "argument is not a number";
        return false;
          }
      
          double val = tstring::str2dble(arg);
          
          if(_isBounded && (val < _bounds[0] || val > _bounds[1]) ){
        errmsg = "argument is out of bounds";
        return false;
          }
        }
        
  //boolean:
  } else if(_type == BOOL) {
        
        if( !tstring::isanumber(arg) ){
      errmsg = "argument is not a boolean";
      return false;
    }
        
  } else if(_type == MAT) {
        if(arg[0] != '{'){
      errmsg = "argument is not a matrix";
      return false;
    }
  }
  // else if(_type == P || _type == S): no conditions to check
  
  _isSet = (_type == BOOL && tstring::str2int(arg) == 0 ? false : true);
  _arg = arg;
  return true;  
}

void Param::setArg ( string value ) [inline]

Sets the parameter's argument.

Definition at line 107 of file param.h.

{_arg = value;}

void Param::setAtGeneration ( unsigned int generation ) [inline]

Definition at line 121 of file param.h.

{_setAtGeneration = generation;}

void Param::setBounds	(	double	low_bnd,
		double	up_bnd
	)		`[inline]`

Sets the bounds.

Definition at line 115 of file param.h.

{_bounds[0]=low_bnd; _bounds[1]=up_bnd;}

void Param::setIsBounded ( bool value ) [inline]

Sets the _isBounded flag.

Definition at line 113 of file param.h.

{_isBounded = value;}

void Param::setIsSet ( bool value ) [inline]

Sets the _isSet flag.

Definition at line 111 of file param.h.

{_isSet = value;}

void Param::setName ( string value ) [inline]

Sets the parameter's name.

Definition at line 105 of file param.h.

{_name = value;}

void Param::setOwner ( SimComponent * owner ) [inline]

Sets the pointer to owner.

Definition at line 117 of file param.h.

{_myOwner = owner;}

void Param::setType ( param_t value ) [inline]

Sets the parameter's type (see types.h)

Definition at line 109 of file param.h.

{_type = value;}

void Param::setUpdater ( ParamUpdaterBase * updater ) [inline]

Sets the pointer to the updater object.

Definition at line 119 of file param.h.

{_myUpdater = updater;}

void Param::show_up ( )

Print state to stdout.

Definition at line 352 of file param.cc.

References _arg, _isSet, _name, _setAtGeneration, and message().

{
  message("%s = %s",_name.c_str(),_arg.c_str());
  if(_isSet)
    message(" (set at gen %i)\n",_setAtGeneration);
  else
    message(" (not set)\n");
}

bool Param::update ( unsigned int generation )

Updates the parameter value at a given generation during the simulation.

Definition at line 336 of file param.cc.

References _name, _temporalArgs, and error().

{
  string error_msg;
  if(_temporalArgs.find( generation ) != _temporalArgs.end()) {
    if( !set( _temporalArgs[generation], error_msg ) ){
      error("could not set \"%s\": %s", _name.c_str(), error_msg.c_str());
      return false;
    } else
      return true;
  } else
    error("parameters \"%s\" does not have an argument value for generation %i.\n", _name.c_str(), generation);
  return false; 
}