Added extra functionality to Point class( an iterator ) and PersistenceDiagram( dimension property and __len__ func ).
persistence-diagram.h:
Added a new read-only dimension member and member function to access it.
With a new constructor that that takes in an int type to initialize dimension.
persistence-diagram.cpp:
Added new bp::init constructor. Takes in an integer type to initialize the dimension. Exposed the dimension property. Exposed the size property via a __len__ method.
__init__.py:
Added an iterator for Point objects. This iterates over the coords and then the data( if present ).
/**
* Author: Dmitriy Morozov
* Department of Computer Science, Duke University, 2007
*/
#ifndef __AVIDA_POPULATION_DETAIL_H__
#define __AVIDA_POPULATION_DETAIL_H__
#include <string>
#include <vector>
/**
* Stores organism details stored in a single line of a population detail file in data/
* directory of Avida's output.
*/
class AvidaOrganismDetail
{
public:
typedef int IDType;
/// Distance between two genomes
typedef unsigned int DistanceType;
typedef unsigned int CountType;
AvidaOrganismDetail(std::string line);
DistanceType genome_distance(const AvidaOrganismDetail& other) const;
IDType id() const { return id_; }
float fitness() const { return fitness_; }
CountType length() const { return genome_length_; }
std::string genome() const { return genome_; }
private:
IDType id_, parent_id_;
int parent_distance_;
CountType num_organisms_alive_, num_organisms_ever_;
CountType genome_length_;
float merit_, gestation_time_;
float fitness_;
int update_born_, update_deactivated_, depth_phylogenetic_tree_;
std::string genome_;
};
/**
* Stores entire population details (all organisms in a given time step), i.e., stores
* an entire population detail file in data/ directory of Avida's ouptut.
*/
class AvidaPopulationDetail
{
public:
typedef std::vector<AvidaOrganismDetail> OrganismVector;
typedef OrganismVector::const_iterator OrganismIndex;
AvidaPopulationDetail(std::string filename);
const OrganismVector&
get_organisms() const { return organisms_; }
/// \name Rips
/// @{
typedef int IndexType;
typedef double DistanceType;
DistanceType operator()(IndexType a, IndexType b) const { return organisms_[a].genome_distance(organisms_[b]); }
size_t size() const { return organisms_.size(); }
IndexType begin() const { return 0; }
IndexType end() const { return size(); }
/// @}
private:
OrganismVector organisms_;
};
std::ostream& operator<<(std::ostream& out, AvidaPopulationDetail::OrganismIndex i)
{ return (out << (i->id())); }
#include "avida-population-detail.hpp"
#endif //__AVIDA_POPULATION_DETAIL_H__