Nemo
2.3.56
Simulate forward-in-time genetic evolution in a spatially explicit, individual-based stochastic simulator
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#include <ttrait.h>
Public Member Functions | |
virtual void | reset ()=0 |
Called at the end of a simulation to reset the Traits' prototypes (e.g. More... | |
virtual TTrait * | hatch ()=0 |
Creates the trait of which it is the prototype, called by IndFactory::makePrototype() . More... | |
virtual TraitPrototype * | clone ()=0 |
Returns a copy of itself. More... | |
virtual trait_t | get_type () const =0 |
Type accessor. More... | |
virtual void | set_index (int idx) |
Sets the traits index. More... | |
virtual int | get_index () |
Index getter. More... | |
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virtual void | store_data (BinaryStorageBuffer *saver)=0 |
Interface to store the component data (e.g. gene values) into a binary buffer. More... | |
virtual bool | retrieve_data (BinaryStorageBuffer *reader)=0 |
Interface to retrieve the same data from the binary buffer. More... | |
virtual | ~StorableComponent () |
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SimComponent () | |
virtual | ~SimComponent () |
virtual void | loadFileServices (FileServices *loader)=0 |
Loads the component's FileHandler onto the FileServices. More... | |
virtual void | loadStatServices (StatServices *loader)=0 |
Loads the component's StatHandler onto the StatServices. More... | |
virtual void | loadUpdaters (UpdaterServices *loader) |
Loads the parameters and component updater onto the updater manager. More... | |
virtual bool | setParameters ()=0 |
Default interface needed to initialize the component's variables from its input parameters value. More... | |
virtual void | set_paramset (ParamSet *paramset) |
Sets the ParamSet member. More... | |
virtual void | set_paramset (std::string name, bool required, SimComponent *owner) |
Sets a new ParamSet and name it. More... | |
virtual void | set_paramsetFromCopy (const ParamSet &PSet) |
Reset the set of parameters from a another set. More... | |
virtual ParamSet * | get_paramset () |
ParamSet accessor. More... | |
virtual void | add_parameter (Param *param) |
Interface to add a parameter to the set. More... | |
virtual void | add_parameter (std::string Name, param_t Type, bool isRequired, bool isBounded, double low_bnd, double up_bnd) |
Interface to add a parameter to the set. More... | |
virtual void | add_parameter (std::string Name, param_t Type, bool isRequired, bool isBounded, double low_bnd, double up_bnd, ParamUpdaterBase *updater) |
Interface to add a parameter and its updater to the set. More... | |
virtual Param * | get_parameter (std::string name) |
Param getter. More... | |
virtual double | get_parameter_value (std::string name) |
Param value getter. More... | |
virtual string | get_name () |
Returnd the name of the ParamSet, i.e. More... | |
virtual bool | has_parameter (std::string name) |
Param getter. More... | |
virtual bool | resetParameterFromSource (std::string param, SimComponent *cmpt)=0 |
Protected Attributes | |
int | _index |
The trait index in the Individual traits table. More... | |
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ParamSet * | _paramSet |
The parameters container. More... | |
TTrait setter.
Encapsulates the methods to set the traits parameters and to generate traits. Also stores the position of the trait in the individuals trait table. This class manages the file and stat handlers through its inheritance of the SimComponent interface.
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pure virtual |
Returns a copy of itself.
Note: calls the copy constructor and only copy the parameters state.
Implemented in TProtoBDMI, TProtoDeletMutations_bitstring, TProtoDispersal, TProtoNeutralGenes, TProtoQuanti, and TProtoWolbachia.
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inlinevirtual |
Index getter.
References _index.
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pure virtual |
Type accessor.
Implemented in TProtoBDMI, TProtoDeletMutations_bitstring, TProtoDispersal, TProtoNeutralGenes, TProtoQuanti, and TProtoWolbachia.
Referenced by TTProtoWithMap::registerGeneticMap(), TTProtoWithMap::reset(), TTProtoWithMap::setGeneticMapParameters(), and TTProtoWithMap::unregisterFromGeneticMap().
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pure virtual |
Creates the trait of which it is the prototype, called by IndFactory::makePrototype()
.
Implemented in TProtoBDMI, TProtoDeletMutations_bitstring, TProtoDispersal, TProtoNeutralGenes, TProtoQuanti, and TProtoWolbachia.
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pure virtual |
Called at the end of a simulation to reset the Traits' prototypes (e.g.
unregister genetic maps). Called by IndFactory::clearPrototype
.
Implemented in TProtoDeletMutations_bitstring, TProtoDispersal, TProtoNeutralGenes, TProtoQuanti, TTProtoWithMap, and TProtoWolbachia.
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inlinevirtual |
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protected |
The trait index in the Individual traits table.
Referenced by get_index(), and set_index().