/* File containing description of types, typedefs, and structures used in the program. 06/17/94 AW Created. */ /* To monitor the progress of the program, define DEBUG. This prints a message each time the program enters and leaves a subroutine. */ #define DEBUG 0 #undef DEBUG #define ERROR 0 #define OK 1 /***** output files *****/ #define NUM_OUTPUT_FILES 4 #define PR_PARAMS 1 #ifdef PR_PARAMS #define PARAMS_FILE 0 #define PARAMS_EXT "params" #define PARAMS_HEADER TRUE #endif #define PR_RANDOM 1 #ifdef PR_RANDOM #define RANDOM_FILE 1 #define RANDOM_EXT "random" #define RANDOM_HEADER FALSE #endif #define PR_STATS 1 #ifdef PR_STATS #define STATS_FILE 2 #define STATS_EXT "stats" #define STATS_HEADER TRUE #endif #define PR_GENEOLOGY 1 #ifdef PR_GENEOLOGY #define GENE_FILE 3 #define GENE_EXT "geneology" #define GENE_HEADER FALSE #endif /***** constants *****/ #define NUM_METABOLITES 10 /***** typedefs *****/ /* All of our types begin with a capital letter */ typedef enum {FALSE, TRUE} Boolean; /* FALSE=0, TRUE=1 */ typedef unsigned int Metabolite; typedef int Genetype; typedef Genetype *Chromosome; /*An array of Genetypes.*/ typedef int Gut; /*An array of # of metabolites.*/ typedef enum {BREAKDOWN, CREATION} Reaction_class; /***** structures *****/ /* the Reaction structure stores an efficient representation of one */ /* reaction in a critter's metabolism. The entire metabolism of a */ /* critter will be a linked list of these Reaction structures. I'm */ /* leaving the details of this to James ***/ struct reaction_struct { struct reaction_struct *next_reaction; /*the next reaction in the */ /*linked list.*/ Reaction_class reaction_type; /*creation or breakdown*/ int first_reactant; int second_reactant; }; typedef struct reaction_struct Reaction; /* An interaction_list structure stores the number of parasitisms from members of the species para_species on members of the species host_species. Each structure is a member of two separate linked lists. One is a list of the current host species of para_species, and is accessed by following the next_host pointer. The other is a list of species which are currently parasites on host_species; this is accessed by following the next_para pointer. */ struct interaction_list { /* The following two pointers specify the host and parasite species. No memory is allocated for these when the node is created. They just point to the appropriate species_list structs, defined below. */ struct species_list *host_species; struct species_list *para_species; int num_interactions; /* How many critters from para_species are parasites on critters from host_species */ struct interaction_list *next_host; /* next host of para_species */ struct interaction_list *prev_host; /* prev host of para_species */ struct interaction_list *next_para; /* next para of host_species */ struct interaction_list *prev_para; /* prev para of host_species */ } ; typedef struct interaction_list Interaction_node; /* The species_list structure stores the metabolism of a gvien species (which is how the species is identified), a list of the species which are currently parasitizing it (para_species), and a list of the species which it is currently a parasite on (host_species). The set of current species is represented by a linked list these structures. */ struct species_list { Reaction *species; /* A species is identified by it's metabolism. */ int num_critters; /* number of critters alive in this species. */ struct species_list *next_species; struct species_list *prev_species; Interaction_node *host_species; /* list of hosting species */ Interaction_node *para_species; /* list of parasitizing species */ } ; typedef struct species_list Species_list; /* the Critter structure stores all info on a single agent */ struct critter_struct { /* Critter ID info */ int id_num; /* id number specific to critter */ int parent_id; /* the id_num of the parent, 0 = orig gen */ struct critter_struct *p_next; /* ptr to next critter in population */ struct critter_struct *p_prev; /* ptr to previous critter in */ /* the population. */ /* genetic material */ Chromosome hide; Chromosome seek; Chromosome metabolism; int hide_len; /* length of the above chromosomes */ int seek_len; int meta_len; /* metabolism stuff */ Reaction *fast_metabolism; /*A more efficient representation of the */ /*matabolism as an array of numbers, rather */ /*than bits. (goes here)*/ Reaction *next_reaction; /*This points to the next reaction in the */ /*metabolism that the critter will execute.*/ Species_list *species; /* Pointer into the species list. */ Gut gut[NUM_METABOLITES]; /* list of stored metabolites */ int amt_food; /* how many metabolites are currently in gut */ /* how do we add and delete metabolites? Probably don't want linked list */ /* instead of a list of metabolites, could have a list of how many of each metabolite there are -- but then we would have to specify all possible metabolites before the run starts. */ struct critter_struct *mouth; /* if parasite, hosts stomach; ow, NULL */ struct critter_struct *prev_metabolizer; struct critter_struct *next_metabolizer; /*These set up a doubly */ /*linked list of critters */ /*for iterating the */ /*metabolisms.*/ /* Critter's current state */ int energy; /* energy level of parasite */ int age; /* age in timesteps */ int para_age; /* # timesteps critter has been a parasite */ int num_offspring; /* # of offspring sired */ int num_times_host; /* # times critter has hosted parasites */ int num_times_para; /* # times critter has been a parasite */ int num_curr_para; /* # parasites currently being hosted */ }; typedef struct critter_struct Critter; /* the Population structure stores info on the population and a pointer to the linked list of Critters in the population. It now also stores the population's environment. */ typedef struct { int current_size; /* # Critters in population */ Gut environment[NUM_METABOLITES]; /* An array of resouceses (Metabolites) in the */ /* environment.*/ Critter *metabolizer; /* pointer to the next critter to metabolize.*/ Critter *critters; /* pointer to population of individuals, */ /* which will be a doubly linked list. */ int num_species; /* number of species in current population. */ Species_list *species_list; /* a list of all current species. */ } Population; /* the Context structure stores parameter information and current global run variables for the program */ typedef struct { /* general run information */ int run_num; /* id num for current run */ int rerun; /* -1 = don't rerun, >0 = run num */ long seed; /* random seed, necessary for reruns */ char output_path[100]; /* where output files should be printed */ int time_step; /* current timestep */ int critter_num; /* id num of last critter */ /* limits and standard values for run */ int max_steps; /* max # timesteps to execute */ double mutation_prob; /* mutation rate */ } Context; /* the Output_file structure holds name, pointer, and other information on all output files that the user chooses to have printed out. The user chooses the files by defining or undefining PR_constants in this file. Those files that are not to be printed will still have a structure in the output_file array, but the pointer and name will be undefined. */ typedef struct { Boolean active; /* t=file will be printed, f=ignore file */ Boolean header; /* t=print header, f=don't print header */ char filename[100]; /* file name max length = 100 chars */ FILE *fp; /* pointer to file */ } Output_file; /* the Stats structure collects statistical and other data from each run for printout into files if desired */ typedef struct { int num_critters; int num_hosts; int num_parasites; int num_species; double avg_num_para_per_host; double avg_num_offspring; double avg_age; double avg_energy; double avg_size; /* length of genome */ } Stats; /***** global variables *****/ Context *the_context; Population *the_population; Stats *stats; Output_file *output_file;