lod.cpp

/* lod_tracking.cpp
 *
 * This file is part of EALib.
 *
 * Copyright 2014 David B. Knoester.
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
#include <ea/evolutionary_algorithm.h>
#include <ea/generational_models/steady_state.h>
#include <ea/genome_types/bitstring.h>
#include <ea/fitness_functions/all_ones.h>
#include <ea/cmdline_interface.h>
#include <ea/datafiles/fitness.h>
#include <ea/line_of_descent.h>
using namespace ealib;


/*! Evolutionary algorithm definition.  EAs are assembled by providing a series of
 components (representation, selection type, mutation operator, etc.) as template
 parameters.
 
 In this case, we're modifying the individual to include LOD-specific traits,
 which are used by lod_event to track the individual's parent(s).
 */
typedef evolutionary_algorithm
< direct<bitstring>
, all_ones
, mutation::operators::per_site<mutation::site::bit>
, recombination::asexual
, generational_models::steady_state< >
, ancestors::random_bitstring
, dont_stop
, fill_population
, default_lifecycle
, lod_with_fitness_trait
> ea_type;


/*! Define the EA's command-line interface.  Ealib provides an integrated command-line
 and configuration file parser.  This class specializes that parser for this EA.
 */
template <typename EA>
class cli : public cmdline_interface<EA> {
public:
    //! Define the options that can be parsed.
    virtual void gather_options() {
        add_option<REPRESENTATION_SIZE>(this);
        add_option<POPULATION_SIZE>(this);
        add_option<STEADY_STATE_LAMBDA>(this);
        add_option<MUTATION_PER_SITE_P>(this);
        add_option<TOURNAMENT_SELECTION_N>(this);
        add_option<TOURNAMENT_SELECTION_K>(this);
        add_option<RUN_UPDATES>(this);
        add_option<RUN_EPOCHS>(this);
        add_option<RNG_SEED>(this);
        add_option<RECORDING_PERIOD>(this);
    }
    
    //! Define events (e.g., datafiles) here.
    virtual void gather_events(EA& ea) {
        add_event<datafiles::fitness_dat>(ea);
        add_event<lod_event>(ea);
        add_event<datafiles::mrca_lineage>(ea);
    };
};


// This macro connects the cli defined above to the main() function provided by ealib.
LIBEA_CMDLINE_INSTANCE(ea_type, cli);