Nemo  2.4.0
Simulate forward-in-time genetic evolution in a spatially explicit, individual-based stochastic simulator
param.h
Go to the documentation of this file.
1 
29 #ifndef PARAM_H
30 #define PARAM_H
31 
32 #include <iostream>
33 #include <fstream>
34 #include <string>
35 #include <string.h>
36 #include <assert.h>
37 #include <map>
38 #include <deque>
39 #include <list>
40 #include <vector>
41 #include "handler.h"
42 #include "tmatrix.h"
43 #include "types.h"
44 #include "output.h"
45 
46 using namespace std;
47 class SimComponent;
48 class ParamUpdaterBase;
52 class Param
53  {
55  string _name;
57  string _arg;
59  string _input_arg;
63  bool _isSet;
65  bool _isBounded;
70  double _bounds[2];
72  unsigned int _setAtGeneration;
77 
79  vector< string > _externalFile;
81 
83  map< unsigned int, string > _temporalArgs;
86 
88  vector< string > _multiArgs;
90 
91  public:
102  Param (string& Name, param_t Type, bool mandatory, bool bounded, double low_bnd, double up_bnd,
103  SimComponent* owner, ParamUpdaterBase* updater);
104 
106  Param (const Param& P);
107 
108  virtual ~Param ();
109 
111  void reset ();
112 
113  //accessors:
115  void setName (string value) {_name = value;}
117  void setArg (string value) {_arg = value; _input_arg = value;}
119  void setType (param_t value) {_type = value;}
121  void setIsSet (bool value) {_isSet = value;}
123  void setIsBounded (bool value) {_isBounded = value;}
125  void setIsRequired (bool value) {_isRequired = value;}
127  void setBounds (double low_bnd,double up_bnd) {_bounds[0]=low_bnd; _bounds[1]=up_bnd;}
129  void setOwner (SimComponent *owner) {_myOwner = owner;}
131  void setUpdater (ParamUpdaterBase* updater) {_myUpdater = updater;}
132 
133  void setAtGeneration (unsigned int generation) {_setAtGeneration = generation;}
134 
135 
136  string getName () {return _name;}
137  string getArg () {return _input_arg;}
138  param_t getType () {return _type;}
139  bool isSet () {return _isSet;}
140  bool isBounded () {return _isBounded;}
141  bool isRequired () {return _isRequired;}
142  bool isTemporal () {return _isTemporal;}
143  bool hasMultipleArgs () {return _hasMultipleArgs;}
144  bool hasExternalFile () {return _hasExternalFile;}
145  double getBound (unsigned int i) {return _bounds[i];}
146  SimComponent* getOwner () {return _myOwner;}
147  ParamUpdaterBase* getUpdater () {return _myUpdater;}
148 
149  deque< unsigned int > getUpdatingDates ();
150 
151  deque< string > getTemporalArgs();
152 
153  vector< string > getMultiArgs();
154 
155  vector< string > getExternalFiles() {return _externalFile;}
156 
160  bool set (string arg, string& errmsg);
161 
163  bool update (unsigned int generation);
164 
168  double getValue ();
169 
171  bool isMatrix ()
172  { return (_type == MAT || (_arg.size() != 0 ? _arg[0] == '{' : false) ); }
173 
178  void getMatrix (TMatrix* mat);
179 
180  void getVariableMatrix (vector< vector <double> >* mat);
181 
185  void parse_matrix (TMatrix* mat);
186  void parse_variable_matrix (vector< vector <double> >* mat);
187  bool parseArgument (string& arg);
188  bool parseTemporalArgument (const string& arg);
189  bool parseAgeSpecArgument (const string& arg);
190  bool parseSubParamArgument (const string& arg);
191  string checkArgumentForExpansion (string arg);
192  string getArgumentFromFile (string file);
193 
195  void show_up ();
196 
197  };
198 
199 
204 class ParamSet
205  {
207  string _name;
209  bool _isSet;
213  map<string, Param*> _params;
216 
217  public:
218 
219  ParamSet ( ) : _isSet(0), _isRequired(0), _myOwner(0) { }
220  ParamSet (const ParamSet& PS);
221  ~ParamSet ( );
223  void reset ( );
224 
226  void clear ( ) {_params.clear();}
230  bool check_consistency ( );
232  void show_up ( );
234  void print (ofstream& FILE, bool commentOut = false);
236  int size ( ) {return _params.size();}
238  map<string, Param*>& getAllParams ( ) {return _params;}
241 
242  void add_param (Param* param) {_params[param->getName()] = param;}
251  void add_param (string Name, param_t Type, bool mandatory, bool isBounded,
252  double low_bnd, double up_bnd)
253  {add_param(Name, Type, mandatory, isBounded, low_bnd, up_bnd, 0);}
254 
255  void add_param (string Name, param_t Type, bool mandatory, bool isBounded,
256  double low_bnd, double up_bnd, ParamUpdaterBase* updater);
263  bool set_param (string Name, string Arg);
267  Param* find_param (string name);
271  Param* get_param (string name);
272 
276  bool has_param (string name);
277 
279  bool update_param (string Name, unsigned int generation);
281  void setName (string value) {_name = value;}
283  void setIsRequired (bool value) {_isRequired = value;}
285  void setOwner (SimComponent* owner) {_myOwner = owner;}
287  bool isSet () {return _isSet;}
289  string getName () {return _name;}
291  bool isRequired () {return _isRequired;}
293  bool isSet (string name) {return (get_param(name))->isSet();}
295  bool isMatrix (string name) {return (get_param(name))->isMatrix();}
297  bool isTemporal (string name) {return (get_param(name))->isTemporal();}
299  string getArg (string name) {return (get_param(name))->getArg();}
301  double getValue (string name) {return (get_param(name))->getValue();}
303  void getMatrix (string name, TMatrix* mat) {return (get_param(name))->getMatrix(mat);}
305  list<ParamUpdaterBase*> getUpdaters();
307  ParamSet& operator= (const ParamSet& PS);
308  };
309 
310 
311 //class ParamUpdaterBase
312 //
314 class ParamUpdaterBase : public Handler {
315 
316 protected:
318  list< Param* > _params;
319 
320 public:
321 
322  typedef list< Param* >::iterator PIT;
323 
324 public:
325 
327 
329  {
330  _params.assign(PU._params.begin(), PU._params.end());
331  }
332 
333  virtual ~ParamUpdaterBase() {}
334 
335  virtual void init () = 0;
336  virtual void update () {}
338  virtual bool update (unsigned int generation) = 0;
339 
340  virtual SimComponent* getComponent () = 0;
342  virtual void addParam (Param* param) {_params.push_back( param );}
344  virtual void reset ( ) {_params.clear();}
346  list< Param* > getParams ( ) {return _params;}
347 
348 };
349 
350 
351 //class ParamUpdater
352 //
362 template <class SC> class ParamUpdater : public virtual ParamUpdaterBase {
363 
364  bool (SC::*_myUpdaterFunction) (void);
366 
367 public:
368 
369  ParamUpdater(bool (SC::*updateFuncPtr) (void) ): _myComponent(0)
370  {
371  _myUpdaterFunction = updateFuncPtr;
372  }
373 
375  {
376  _params.assign(PU._params.begin(), PU._params.end());
377  _myUpdaterFunction = PU._myUpdaterFunction;
378  _myComponent = PU._myComponent;
379  }
380 
381  virtual ~ParamUpdater ()
382  {
383  for(PIT pit = _params.begin(); pit != _params.end(); pit++)
384  if((*pit)->getUpdater() == this) (*pit)->setUpdater(0);
385  }
386 
388  virtual void init ()
389  {
390  _myComponent = dynamic_cast<SC*> ( (*_params.begin())->getOwner() );
391 
392  for(PIT pit = ++_params.begin(); pit != _params.end(); pit++)
393  assert(_myComponent == (*pit)->getOwner());
394  }
396  virtual bool update (unsigned int generation)
397  {
398  return ((( dynamic_cast<SC*> (_myComponent))->*_myUpdaterFunction) ());
399  }
401  void setFuncPtr ( bool (SC::*updateFuncPtr) (void))
402  {
403  _myUpdaterFunction = updateFuncPtr;
404  }
406  virtual SC* getComponent () {return _myComponent;}
407 };
408 
409 #endif
Service handler (an observer).
Definition: handler.h:35
Parameters container, implemented in each SimComponent.
Definition: param.h:205
map< string, Param * > _params
List of parameters indexed by name.
Definition: param.h:213
map< string, Param * > & getAllParams()
Returns the complete list of parameters.
Definition: param.h:238
SimComponent * _myOwner
Pointer to the component that declared this parameter.
Definition: param.h:215
void clear()
Empties the parameter containers (no delete).
Definition: param.h:226
void getMatrix(string name, TMatrix *mat)
Accessor to the parameters matrix.
Definition: param.h:303
string getArg(string name)
Accessor to the parameters argument string.
Definition: param.h:299
int size()
Returns the number of parameters contained.
Definition: param.h:236
double getValue(string name)
Accessor the parameters value.
Definition: param.h:301
ParamSet()
Definition: param.h:219
bool _isRequired
Flaf is true if component is required (mandatory) to run a simulation (e.g.
Definition: param.h:211
string getName()
Name accessor.
Definition: param.h:289
string _name
The name of the component.
Definition: param.h:207
bool isSet(string name)
Accessor to the parameters status flag.
Definition: param.h:293
void add_param(Param *param)
Adds the param argument to the list.
Definition: param.h:242
void setName(string value)
Sets the container's name.
Definition: param.h:281
bool isMatrix(string name)
Check if the parameter "name" is of matrix type.
Definition: param.h:295
void setOwner(SimComponent *owner)
Sets the pointer to the SimComponents that owns this set.
Definition: param.h:285
void setIsRequired(bool value)
Sets the _isRequired flag meaning this container is mandatory and must be set in order to run a simul...
Definition: param.h:283
bool _isSet
Flag is true if all mandatory parameters are correctly set from user's input file.
Definition: param.h:209
bool isSet()
Accessor to the status flag.
Definition: param.h:287
bool isRequired()
Accessor to the mandatory flag.
Definition: param.h:291
void add_param(string Name, param_t Type, bool mandatory, bool isBounded, double low_bnd, double up_bnd)
Adds a new param specified by arguments to the list.
Definition: param.h:251
bool isTemporal(string name)
Check if the parameter "name" has temporal arguments.
Definition: param.h:297
Base class of the ParamUpdater class used to handle the temporal parameter argument values.
Definition: param.h:314
virtual ~ParamUpdaterBase()
Definition: param.h:333
virtual void addParam(Param *param)
Adds a parameter to the stack.
Definition: param.h:342
list< Param * > getParams()
Returns the list of parameters.
Definition: param.h:346
list< Param * >::iterator PIT
Definition: param.h:322
virtual void reset()
Clears the parameters stack.
Definition: param.h:344
virtual SimComponent * getComponent()=0
virtual void update()
Definition: param.h:336
ParamUpdaterBase(const ParamUpdaterBase &PU)
Definition: param.h:328
ParamUpdaterBase()
Definition: param.h:326
virtual bool update(unsigned int generation)=0
Updating procedure.
list< Param * > _params
List of the parameters affected by this updater.
Definition: param.h:318
virtual void init()=0
Implementation of the ParamUpdaterBase interface.
Definition: param.h:362
bool(SC::* _myUpdaterFunction)(void)
Definition: param.h:364
virtual bool update(unsigned int generation)
Calls the SimComponent's updating function using its pointer.
Definition: param.h:396
virtual void init()
Sets the pointer to the SimComponent.
Definition: param.h:388
ParamUpdater(bool(SC::*updateFuncPtr)(void))
Definition: param.h:369
SC * _myComponent
Definition: param.h:365
virtual ~ParamUpdater()
Definition: param.h:381
virtual SC * getComponent()
Accessor to the SimComponent.
Definition: param.h:406
void setFuncPtr(bool(SC::*updateFuncPtr)(void))
Sets the pointer to the updating function.
Definition: param.h:401
ParamUpdater(const ParamUpdater< SC > &PU)
Definition: param.h:374
This structure stores one parameter, its definition and its string argument.
Definition: param.h:53
bool hasMultipleArgs()
Definition: param.h:143
bool _hasMultipleArgs
Definition: param.h:89
unsigned int _setAtGeneration
Generation at which the parameter has been set/updated.
Definition: param.h:72
void setArg(string value)
Sets the parameter's argument.
Definition: param.h:117
bool _isSet
Flag set once the parameter has recieved the right argument.
Definition: param.h:63
param_t getType()
Definition: param.h:138
bool isMatrix()
Checks if the argument is of matrix type.
Definition: param.h:171
vector< string > getExternalFiles()
Definition: param.h:155
bool isRequired()
Definition: param.h:141
param_t _type
The type of the argument, must one of DBL, INT, BOOL, STR or MAT (see types.h).
Definition: param.h:61
bool _isRequired
Flag telling if this parameter is mandatory.
Definition: param.h:68
bool isTemporal()
Definition: param.h:142
string getName()
Definition: param.h:136
map< unsigned int, string > _temporalArgs
The temporal arguments.
Definition: param.h:83
bool isBounded()
Definition: param.h:140
SimComponent * _myOwner
Pointer to the component that declared this parameter.
Definition: param.h:74
vector< string > _externalFile
External argument file.
Definition: param.h:79
bool _isBounded
Flag telling if the parameter has a bounded argument value.
Definition: param.h:65
void setBounds(double low_bnd, double up_bnd)
Sets the bounds.
Definition: param.h:127
vector< string > _multiArgs
Multiple arguments.
Definition: param.h:88
double getBound(unsigned int i)
Definition: param.h:145
string _arg
The argument string, set by the ParamsParser upon initialization.
Definition: param.h:57
string getArg()
Definition: param.h:137
void setType(param_t value)
Sets the parameter's type (see types.h)
Definition: param.h:119
ParamUpdaterBase * _myUpdater
Pointer to an ParamUpdater object.
Definition: param.h:76
bool _hasExternalFile
Definition: param.h:80
void setName(string value)
Sets the parameter's name.
Definition: param.h:115
ParamUpdaterBase * getUpdater()
Definition: param.h:147
void setUpdater(ParamUpdaterBase *updater)
Sets the pointer to the updater object.
Definition: param.h:131
string _name
The name of the parameter as read in the init file.
Definition: param.h:55
bool hasExternalFile()
Definition: param.h:144
bool isSet()
Definition: param.h:139
void setIsSet(bool value)
Sets the _isSet flag.
Definition: param.h:121
void setIsBounded(bool value)
Sets the _isBounded flag.
Definition: param.h:123
bool _isTemporal
Flag telling if this parameter has temporal arguments.
Definition: param.h:85
void setAtGeneration(unsigned int generation)
Definition: param.h:133
void setIsRequired(bool value)
Sets the isRequired flag.
Definition: param.h:125
SimComponent * getOwner()
Definition: param.h:146
string _input_arg
The input argument string, kept untouched as a backup for logging.
Definition: param.h:59
void setOwner(SimComponent *owner)
Sets the pointer to owner.
Definition: param.h:129
Interface to all basic components of a simulation (traits, life cycle events, pop,...
Definition: simcomponent.h:44
A class to handle matrix in params, coerces matrix into a vector of same total size.
Definition: tmatrix.h:49
Nemo2.
Nemo2.
Nemo2.
Nemo2.
param_t
Param's types.
Definition: types.h:76
@ MAT
Definition: types.h:77

Generated for Nemo v2.4.0 by  doxygen 1.9.1 -- Nemo is hosted on  Download Nemo

Locations of visitors to this page
Catalogued on GSR