Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

[detail level 12]

CBinaryDataLoader	A class to load a whole population from a binary data file
CBinaryDataSaver	A class to handle simulation data saving in binary format
CBinaryFileParser	Retrieves simulation parameters from a binary data file
CBinaryStorageBuffer	A class to store any kind of data in a char buffer before unloading it in a binary data file
►Cbitstring	Non-template and faster implementation of std::bitset
Creference
CComponentManager	Class to manage the simulation components and prototypes
CDataTable	A class to aggregate structured data in an array
CEventFileHandler	Template class for the LCEs StatHandler classes
CEventStatHandler	Template class for the LCEs StatHandler classes
CFHLogWriter	File Handler used to save the simulation parameters to a log file
CFHPedigreeReader	A class to read a pedigree from a file
CFileHandler	Interface to handle file input/output for any SimComponent
CFileParser	Text input parameter file parser
CFileServices	A class to manage the files associated with each components of the simulation
CGeneticMap	GeneticMap
CGenotyperFH	FileHandler to write joint genotype files for multiple mappable traits
CHandler	Service handler (an observer)
CIndFactory	Factory of Individual, stores the individual prototype and the trait prototypes, manages the individual garbage collector
CIndividual	This class contains traits along with other individual information (sex, pedigree, etc. )
CLCE_Aging	Removes all adults from the patches and randomly moves the offspring to the adults age class
CLCE_Breed	Implementation of the basic breeding and mating procedures, does not link to any trait
CLCE_Breed_base	Base class for the breeding (and mating) life cycle events
CLCE_Breed_Disperse	Performs breeding and migration in one, migration rates are backward rates
CLCE_Breed_Quanti	Implementation of the basic breeding and mating procedures, does not link to any trait
CLCE_Breed_Selection	Composite LCE implementing breeding and viability selection on a given trait type
CLCE_Breed_Selection_Disperse	Composite LCE performing breeding, migration and viability selection all in one
CLCE_Breed_Wolbachia	Breeding LCE when individuals carry the Wolbachia endosymbiotic parasite
CLCE_BreedAssortativeMating	Implementation of the basic breeding and mating procedures, does not link to any trait
CLCE_Cross	A class to perform crosses within patches, implements the NC1 mating design
CLCE_Disperse_base	The base class of the dispersal LCEs, all events move offspring to the post-dispersal patch containers
CLCE_Disperse_ConstDisp	Dispersal event with constant dispersal rates
CLCE_Disperse_EvolDisp	Dispersal event with an evolving dispersal rate given by the "disp" trait
CLCE_FileServicesNotifier	Event used to notify all file handlers to update their state through the FileServices::notify() interface
CLCE_Init_BDMI	Allelic frequency initialiser for the DBMI trait
CLCE_NtrlInit	Set patch-specifiec initial genotypes values
CLCE_ParamUpdaterNotifier	Calls the UpdaterServices to notify its components of a generation change
CLCE_Patch_Extinction	Randomly removes individuals from the patches according to the extinction rate parameter
CLCE_PhenotypeExpression
CLCE_QuantiInit	Set patch-specifiec initial genotypes values
CLCE_QuantiModifier	Set patch-specifiec initial genotypes values
CLCE_Regulation	Regulates the patches to their carrying capacity, acts on each age class separately
CLCE_Resize	A class to change the size of the population/patches during a simulation
CLCE_SeedDisp
CLCE_Selection_base	Base class performing (viability) selection on an arbitrary trait
CLCE_SelectionFH
CLCE_SelectionSH	StatHandler class for the LCE_Selection class
CLCE_StatFH	FileHandler of the LCE_StatServiceNotifier class, writes the recorded stats to txt files
CLCE_StatServiceNotifier	Initiates the StatServices' parameters (log time) when registering, calls StatServices::notify() when executing
CLifeCycleEvent	Base class of the Life Cycle Events, declares the LCE interface
CMacroCaller
CMetapop	Top class of the metapopulation structure, contains the patches
CMPFileHandler
CMPIenv	MPI environment setup
CMPImanager
CMPStatHandler	A StatHandler for the Metapop SimComponent
CParam	This structure stores one parameter, its definition and its string argument
CParamManager	Class to manage the sets of parameters of the simulation components
CParamSet	Parameters container, implemented in each SimComponent
CParamsParser	Provides interface to read input parameters from various sources and parses them
CParamUpdater	Implementation of the ParamUpdaterBase interface
CParamUpdaterBase	Base class of the ParamUpdater class used to handle the temporal parameter argument values
CPatch	Second class in the metapopulation design structure, between the Metapop and Individual classes
CRAND	Random number generation class, uses various types of random generators depending on the implementation
CService	Interface for the simulation services (files and stats)
CSimBuilder	Provides methods to build the user's selected set of life cycle events and traits from the parameters
CSimComponent	Interface to all basic components of a simulation (traits, life cycle events, pop, etc. )
CSIMenv	Global class exposing the current SimRunner throughout the code
CSimRunner	Performs the setup of the Metapop and SimComponents and runs the simulation
CStatHandler	A class to compute and store the summary statistics associated with a SimComponent
CStatHandlerBase	Base class of the StatHandler class, implements the Handler interface
CStatRecBase	Base class for the StatRecorder's, declares the interface to record stat values
CStatRecorder	Stores the pointers to the StatHandler's stat functions
CStatServices	The Service class used to manage the StatHandler objects
CStorableComponent	Provides an interface to binary data saving and uploading
CStreamParser	Read parameters from a text buffer
CTMatrix	A class to handle matrix in params, coerces matrix into a vector of same total size
CTProtoBDMI
CTProtoDeletMutations_bitstring	Prototype class of the bitstring-deleterious mutations trait class
CTProtoDispersal	Prototype of the evolving dispersal trait, defines the sex-specific trait type
CTProtoNeutralGenes	Prototype class for the TTNeutralGenes trait class
CTProtoQuanti	TProtoQuanti
CTProtoWolbachia	Prototype of the Wolbachia trait
CTraitFileHandler	Template class for the trait's FileHandler
CTraitPrototype	TTrait setter
CTraitStatHandler	Template class for the trait's StatHandler
Ctstring	A global class to handle string conversions and operations
CTT_BDMI
CTTBDMI_FH	FileHandler for the DBMI trait
CTTBDMI_SH	StatHandler for the DBMI trait
CTTDeletMutations_bitstring	Bitstring implementation of TTDeletMutations with recombination
CTTDeletMutBitstrFH	The FileHandler associated with the TTDeletMutations_bitstring trait
CTTDeletMutBitstrSH	The StatHandler for TTDeletMutations_bitstring
CTTDispersal	Evolving dispersal trait, codes for female (_type = FDISP) or male (_type = MDISP) sex-specific dispersal rates
CTTDispersalSH	The StatHandler for the evolving dispersal traits
CTTNeutralGenes	Abstract base class for neutral gene traits
CTTNeutralGenes_bitstring	TTNeutralGenes_bitstring : diallelic neutral loci encoded as bitstrings
CTTNeutralGenes_byte	Byte-encoded neutral gene trait (unsigned char per allele)
CTTNeutralGenesFH	A file handler to save the neutral markers genotypes in the FSTAT format (extended)
CTTNeutralGenesSH	The stat handler for neutral markers
CTTNOhtaStats	TTNOhtaStats
CTTProtoWithMap	TTProtoWithMap
CTTQFreqExtractor	TTQFreqExtractor
CTTQOhtaStats	TTQOhtaStats
CTTQuanti	TTQuanti
CTTQuanti_continuous	TTQuanti_continuous
CTTQuanti_continuous_full_pleio	TTQuanti_continuous_full_pleio : universal pleiotropy
CTTQuanti_continuous_full_pleio_epistasis	TTQuanti_continuous_full_pleio : universal pleiotropy
CTTQuanti_continuous_no_pleio	TTQuanti_continuous_no_pleio : multiple non-pleiotropic traits
CTTQuanti_continuous_no_pleio_epistasis	TTQuanti_continuous_no_pleio : multiple non-pleiotropic traits with epistasis
CTTQuanti_continuous_single	TTQuanti_continuous_single : simple implementation for a single quantitative trait with continuous allele values
CTTQuanti_continuous_var_pleio	TTQuanti_continuous_var_pleio : variable pleiotropy
CTTQuanti_diallelic	TTQuanti_diallelic
CTTQuanti_diallelic_bitstring	TTQuanti_diallelic_bitstring
CTTQuanti_diallelic_bitstring_full_pleio	TTQuanti_diallelic_bitstring_full_pleio : pleiotropic di-allelic loci, max PD = 2
CTTQuanti_diallelic_bitstring_full_pleio_epistasis	TTQuanti_diallelic_bitstring_full_pleio_epistasis : pleiotropic di-allelic bitstring with epistasis
CTTQuanti_diallelic_bitstring_no_pleio	TTQuanti_diallelic_bitstring_no_pleio : single or multiple non-pleiotropic traits, di-allelic
CTTQuanti_diallelic_bitstring_no_pleio_epistasis	TTQuanti_diallelic_bitstring_no_pleio_epistasis : non-pleiotropic di-allelic bitstring with epistasis
CTTQuanti_diallelic_bitstring_var_pleio	TTQuanti_diallelic_bitstring_var_pleio : variable pleiotropic di-allelic loci, max PD = 2
CTTQuanti_diallelic_full_pleio	TTQuanti_diallelic_full_pleio : pleiotropic di-allelic loci, max PD = 2
CTTQuanti_diallelic_full_pleio_epistasis	TTQuanti_diallelic_full_pleio : pleiotropic di-allelic loci, max PD = 2
CTTQuanti_diallelic_no_pleio	TTQuanti_diallelic_no_pleio : single or multiple non-pleiotropic traits, di-allelic
CTTQuanti_diallelic_no_pleio_epistasis	TTQuanti_diallelic_no_pleio_epistasis : single or multiple non-pleiotropic traits, di-allelic
CTTQuanti_diallelic_var_pleio	TTQuanti_diallelic_var_pleio : variable pleiotropic di-allelic loci, max PD = 2
CTTQuantiFH	TTQuantiFH
CTTQuantiSH	TTQuantiSH
CTTrait	Interface for all trait types, declares all basic trait operations
CTTraitWithMap	TTraitWithMap
CTTWolbachia	Trait used to study the dynamics of spread of Wolbachia, an endosymbiotic parasite causing cytoplasmic incompatibility
CTTWolbachiaFH	FileHandler of the Wolbachia trait
CTTWolbachiaSH	StatHandler of the Wolbachia trait
CUpdaterServices	Class to update the simulation components' state during a simulation