[Avida-cvs] [avida-svn] r576 - in development/source: event main
brysonda@myxo.css.msu.edu
brysonda at myxo.css.msu.edu
Thu Apr 6 18:00:31 PDT 2006
Author: brysonda
Date: 2006-04-06 21:00:31 -0400 (Thu, 06 Apr 2006)
New Revision: 576
Modified:
development/source/event/cEventManager.cc
development/source/main/cStats.cc
development/source/main/cStats.h
Log:
Clean up stats file output events. Add separate event to trigger task_quality data printing (print_tasks_qual_data). This can still be triggered with tasksq.dat as well.
Modified: development/source/event/cEventManager.cc
===================================================================
--- development/source/event/cEventManager.cc 2006-04-05 18:41:28 UTC (rev 575)
+++ development/source/event/cEventManager.cc 2006-04-07 01:00:31 UTC (rev 576)
@@ -40,6 +40,7 @@
using namespace std;
+
class cEvent_exit : public cEvent {
public:
const cString GetName() const { return "exit"; }
@@ -220,10 +221,11 @@
}
};
+
///// print_data /////
/**
-* Output user-defined data from the cStats object...
+ * Output user-defined data from the cStats object...
*
* Parameters:
* filename (string)
@@ -231,506 +233,60 @@
* format
* A comma-seperated list of statistics to output.
**/
-
-
class cEvent_print_data : public cEvent {
private:
cString filename;
cString format;
public:
- const cString GetName() const { return "print_data"; }
+ const cString GetName() const { return "print_data"; }
const cString GetDescription() const { return "print_data <cString filename> <cString format>"; }
void Configure(cWorld* world, const cString& in_args)
{
- m_world = world;
- m_args = in_args;
- cString args(in_args);
+ m_world = world; m_args = in_args; cString args(in_args);
filename = args.PopWord();
format = args.PopWord();
}
- ///// print_data /////
- void Process(){
- m_world->GetStats().PrintDataFile(filename, format, ',');
- }
+ void Process() { m_world->GetStats().PrintDataFile(filename, format, ','); }
};
-///// print_average_data /////
-/**
-* Output various average quantities into datafile.
- *
- * Parameters:
- * filename (string) default: average.dat
- * The name of the data file.
- **/
+#define STATS_OUT_FILE(NAME, METHOD, DEFAULT) /* 1 */ \
+class cEvent_ ## NAME : public cEvent { /* 2 */ \
+private: /* 3 */ \
+ cString fname; /* 4 */ \
+public: /* 5 */ \
+ const cString GetName() const { return "NAME"; } /* 6 */ \
+ const cString GetDescription() const { return "NAME [cString fname=\"DEFAULT\"]"; } /* 7 */ \
+ void Configure(cWorld* world, const cString& in_args) /* 8 */ \
+ { /* 9 */ \
+ m_world = world; m_args = in_args; cString args(in_args); /* 10 */ \
+ if (args == "") fname="DEFAULT"; else fname=args.PopWord(); /* 11 */ \
+ } /* 12 */ \
+ void Process() { m_world->GetStats().METHOD(fname); } /* 13 */ \
+} /* 14 */ \
-class cEvent_print_average_data : public cEvent {
-private:
- cString fname;
-public:
- const cString GetName() const { return "print_average_data"; }
- const cString GetDescription() const { return "print_average_data [cString fname=\"average.dat\"]"; }
-
- void Configure(cWorld* world, const cString& in_args)
- {
- m_world = world;
- m_args = in_args;
- cString args(in_args);
- if (args == "") fname="average.dat"; else fname=args.PopWord();
- }
- ///// print_average_data /////
- void Process(){
- m_world->GetStats().PrintAverageData(fname);
- }
-};
+STATS_OUT_FILE(print_average_data, PrintAverageData, average.dat );
+STATS_OUT_FILE(print_error_data, PrintErrorData, error.dat );
+STATS_OUT_FILE(print_variance_data, PrintVarianceData, variance.dat );
+STATS_OUT_FILE(print_dominant_data, PrintDominantData, dominant.dat );
+STATS_OUT_FILE(print_stats_data, PrintStatsData, stats.dat );
+STATS_OUT_FILE(print_count_data, PrintCountData, count.dat );
+STATS_OUT_FILE(print_totals_data, PrintTotalsData, totals.dat );
+STATS_OUT_FILE(print_tasks_data, PrintTasksData, tasks.dat );
+STATS_OUT_FILE(print_tasks_exe_data, PrintTasksExeData, tasks_exe.dat );
+STATS_OUT_FILE(print_tasks_qual_data, PrintTasksQualData, tasks_quality.dat );
+STATS_OUT_FILE(print_resource_data, PrintResourceData, resource.dat );
+STATS_OUT_FILE(print_time_data, PrintTimeData, time.dat );
+STATS_OUT_FILE(print_mutation_data, PrintMutationData, mutation.dat );
+STATS_OUT_FILE(print_mutation_rate_data, PrintMutationRateData, mutation_rates.dat );
+STATS_OUT_FILE(print_divide_mut_data, PrintDivideMutData, divide_mut.dat );
+STATS_OUT_FILE(print_dom_parasite_data, PrintDominantParaData, parasite.dat );
+STATS_OUT_FILE(print_instruction_data, PrintInstructionData, instruction.dat );
+STATS_OUT_FILE(print_genotype_map, PrintGenotypeMap, genotype_map.m );
-///// print_error_data /////
-/**
-* Prints out various data related to statistical errors.
- *
- * Parameters:
- * filename (string) default: error.dat
- * The name of the data file.
- **/
-
-
-class cEvent_print_error_data : public cEvent {
-private:
- cString fname;
-public:
- const cString GetName() const { return "print_error_data"; }
- const cString GetDescription() const { return "print_error_data [cString fname=\"error.dat\"]"; }
-
- void Configure(cWorld* world, const cString& in_args)
- {
- m_world = world;
- m_args = in_args;
- cString args(in_args);
- if (args == "") fname="error.dat"; else fname=args.PopWord();
- }
- ///// print_error_data /////
- void Process(){
- m_world->GetStats().PrintErrorData(fname);
- }
-};
-
-///// print_variance_data /////
-
-/**
-* Prints out various variances.
- *
- * Parameters:
- * filename (string) default: variance.dat
- * The name of the data file.
- **/
-
-
-class cEvent_print_variance_data : public cEvent {
-private:
- cString fname;
-public:
- const cString GetName() const { return "print_variance_data"; }
- const cString GetDescription() const { return "print_variance_data [cString fname=\"variance.dat\"]"; }
-
- void Configure(cWorld* world, const cString& in_args)
- {
- m_world = world;
- m_args = in_args;
- cString args(in_args);
- if (args == "") fname="variance.dat"; else fname=args.PopWord();
- }
- ///// print_variance_data /////
- void Process(){
- m_world->GetStats().PrintVarianceData(fname);
- }
-};
-
-///// print_dominant_data /////
-
-/**
-* Output various quantities related to the dominant organism.
- *
- * Parameters:
- * filename (string) default: dominant.dat
- * The name of the data file.
- **/
-
-
-class cEvent_print_dominant_data : public cEvent {
-private:
- cString fname;
-public:
- const cString GetName() const { return "print_dominant_data"; }
- const cString GetDescription() const { return "print_dominant_data [cString fname=\"dominant.dat\"]"; }
-
- void Configure(cWorld* world, const cString& in_args)
- {
- m_world = world;
- m_args = in_args;
- cString args(in_args);
- if (args == "") fname="dominant.dat"; else fname=args.PopWord();
- }
- ///// print_dominant_data /////
- void Process(){
- m_world->GetStats().PrintDominantData(fname);
- }
-};
-
-///// print_stats_data /////
-
-/**
-* Output various statistical quantities.
- *
- * Parameters:
- * filename (string) default: stats.dat
- * The name of the data file.
- **/
-
-
-class cEvent_print_stats_data : public cEvent {
-private:
- cString fname;
-public:
- const cString GetName() const { return "print_stats_data"; }
- const cString GetDescription() const { return "print_stats_data [cString fname=\"stats.dat\"]"; }
-
- void Configure(cWorld* world, const cString& in_args)
- {
- m_world = world;
- m_args = in_args;
- cString args(in_args);
- if (args == "") fname="stats.dat"; else fname=args.PopWord();
- }
- ///// print_stats_data /////
- void Process(){
- m_world->GetStats().PrintStatsData(fname);
- }
-};
-
-///// print_count_data /////
-
-/**
-* Output various counts, such as number of organisms etc.
- *
- * Parameters:
- * filename (string) default: count.dat
- * The name of the data file.
- **/
-
-
-class cEvent_print_count_data : public cEvent {
-private:
- cString fname;
-public:
- const cString GetName() const { return "print_count_data"; }
- const cString GetDescription() const { return "print_count_data [cString fname=\"count.dat\"]"; }
-
- void Configure(cWorld* world, const cString& in_args)
- {
- m_world = world;
- m_args = in_args;
- cString args(in_args);
- if (args == "") fname="count.dat"; else fname=args.PopWord();
- }
- ///// print_count_data /////
- void Process(){
- m_world->GetStats().PrintCountData(fname);
- }
-};
-
-///// print_totals_data /////
-
-/**
-* Various total numbers.
- *
- * Parameters:
- * filename (string) default: totals.dat
- * The name of the data file.
- **/
-
-
-class cEvent_print_totals_data : public cEvent {
-private:
- cString fname;
-public:
- const cString GetName() const { return "print_totals_data"; }
- const cString GetDescription() const { return "print_totals_data [cString fname=\"totals.dat\"]"; }
-
- void Configure(cWorld* world, const cString& in_args)
- {
- m_world = world;
- m_args = in_args;
- cString args(in_args);
- if (args == "") fname="totals.dat"; else fname=args.PopWord();
- }
- ///// print_totals_data /////
- void Process(){
- m_world->GetStats().PrintTotalsData(fname);
- }
-};
-
-///// print_tasks_data /////
-
-/**
-* Output the number of times the various tasks have been performed in the
- * last update.
- *
- * Parameters:
- * filename (string) default: tasks.dat
- * The name of the data file.
- **/
-
-
-class cEvent_print_tasks_data : public cEvent {
-private:
- cString fname;
-public:
- const cString GetName() const { return "print_tasks_data"; }
- const cString GetDescription() const { return "print_tasks_data [cString fname=\"tasks.dat\"]"; }
-
- void Configure(cWorld* world, const cString& in_args)
- {
- m_world = world;
- m_args = in_args;
- cString args(in_args);
- if (args == "") fname="tasks.dat"; else fname=args.PopWord();
- }
- ///// print_tasks_data /////
- void Process(){
- m_world->GetStats().PrintTasksData(fname);
- }
-};
-
-///// print_tasks_exe_data /////
-
-/**
-**/
-
-
-class cEvent_print_tasks_exe_data : public cEvent {
-private:
- cString fname;
-public:
- const cString GetName() const { return "print_tasks_exe_data"; }
- const cString GetDescription() const { return "print_tasks_exe_data [cString fname=\"tasks_exe.dat\"]"; }
-
- void Configure(cWorld* world, const cString& in_args)
- {
- m_world = world;
- m_args = in_args;
- cString args(in_args);
- if (args == "") fname="tasks_exe.dat"; else fname=args.PopWord();
- }
- ///// print_tasks_exe_data /////
- void Process(){
- m_world->GetStats().PrintTasksExeData(fname);
- }
-};
-
-///// print_resource_data /////
-
-/**
-**/
-
-
-class cEvent_print_resource_data : public cEvent {
-private:
- cString fname;
-public:
- const cString GetName() const { return "print_resource_data"; }
- const cString GetDescription() const { return "print_resource_data [cString fname=\"resource.dat\"]"; }
-
- void Configure(cWorld* world, const cString& in_args)
- {
- m_world = world;
- m_args = in_args;
- cString args(in_args);
- if (args == "") fname="resource.dat"; else fname=args.PopWord();
- }
- ///// print_resource_data /////
- void Process(){
- m_world->GetStats().PrintResourceData(fname);
- }
-};
-
-///// print_time_data /////
-
-/**
-* Output time related data, such as update, generation, etc.
- *
- * Parameters:
- * filename (string) default: time.dat
- * The name of the data file.
- **/
-
-
-class cEvent_print_time_data : public cEvent {
-private:
- cString fname;
-public:
- const cString GetName() const { return "print_time_data"; }
- const cString GetDescription() const { return "print_time_data [cString fname=\"time.dat\"]"; }
-
- void Configure(cWorld* world, const cString& in_args)
- {
- m_world = world;
- m_args = in_args;
- cString args(in_args);
- if (args == "") fname="time.dat"; else fname=args.PopWord();
- }
- ///// print_time_data /////
- void Process(){
- m_world->GetStats().PrintTimeData(fname);
- }
-};
-
-///// print_mutation_data /////
-
-/**
-**/
-
-
-class cEvent_print_mutation_data : public cEvent {
-private:
- cString fname;
-public:
- const cString GetName() const { return "print_mutation_data"; }
- const cString GetDescription() const { return "print_mutation_data [cString fname=\"mutation.dat\"]"; }
-
- void Configure(cWorld* world, const cString& in_args)
- {
- m_world = world;
- m_args = in_args;
- cString args(in_args);
- if (args == "") fname="mutation.dat"; else fname=args.PopWord();
- }
- ///// print_mutation_data /////
- void Process(){
- m_world->GetStats().PrintMutationData(fname);
- }
-};
-
-///// print_mutation_rate_data /////
-
-/**
-Output (regular and log) statistics about individual copy
- mutation rates (aver, stdev, skew, cur).
- Useful only when mutation rate is set per organism.
- **/
-
-
-class cEvent_print_mutation_rate_data : public cEvent {
-private:
- cString fname;
-public:
- const cString GetName() const { return "print_mutation_rate_data"; }
- const cString GetDescription() const { return "print_mutation_rate_data [cString fname=\"mutation_rates.dat\"]"; }
-
- void Configure(cWorld* world, const cString& in_args)
- {
- m_world = world;
- m_args = in_args;
- cString args(in_args);
- if (args == "") fname="mutation_rates.dat"; else fname=args.PopWord();
- }
- ///// print_mutation_rate_data /////
- void Process(){
- m_world->GetStats().PrintMutationRateData(fname);
- }
-};
-
-///// print_divide_mut_data /////
-
-/**
-Output (regular and log) statistics about individual, per site,
- rates divide mutation rates (aver, stdev, skew, cur).
- Use with multiple divide instuction set.
- **/
-
-
-class cEvent_print_divide_mut_data : public cEvent {
-private:
- cString fname;
-public:
- const cString GetName() const { return "print_divide_mut_data"; }
- const cString GetDescription() const { return "print_divide_mut_data [cString fname=\"divide_mut.dat\"]"; }
-
- void Configure(cWorld* world, const cString& in_args)
- {
- m_world = world;
- m_args = in_args;
- cString args(in_args);
- if (args == "") fname="divide_mut.dat"; else fname=args.PopWord();
- }
- ///// print_divide_mut_data /////
- void Process(){
- m_world->GetStats().PrintDivideMutData(fname);
- }
-};
-
-///// print_dom_parasite_data /////
-
-/**
-* Output various quantities related to the dominant parasite.
- *
- * Parameters:
- * filename (string) default: parasite.dat
- * The name of the data file.
- **/
-
-
-class cEvent_print_dom_parasite_data : public cEvent {
-private:
- cString fname;
-public:
- const cString GetName() const { return "print_dom_parasite_data"; }
- const cString GetDescription() const { return "print_dom_parasite_data [cString fname=\"parasite.dat\"]"; }
-
- void Configure(cWorld* world, const cString& in_args)
- {
- m_world = world;
- m_args = in_args;
- cString args(in_args);
- if (args == "") fname="parasite.dat"; else fname=args.PopWord();
- }
- ///// print_dom_parasite_data /////
- void Process(){
- m_world->GetStats().PrintDominantParaData(fname);
- }
-};
-
-///// print_instruction_data /////
-
-/**
-Sum of the by-organisms counts of what instructions they _successfully_
- execute beteween birth and divide. Prior to their first divide, organisms
- report values for their parents.
- **/
-
-
-class cEvent_print_instruction_data : public cEvent {
-private:
- cString fname;
-public:
- const cString GetName() const { return "print_instruction_data"; }
- const cString GetDescription() const { return "print_instruction_data [cString fname=\"instruction.dat\"]"; }
-
- void Configure(cWorld* world, const cString& in_args)
- {
- m_world = world;
- m_args = in_args;
- cString args(in_args);
- if (args == "") fname="instruction.dat"; else fname=args.PopWord();
- }
- ///// print_instruction_data /////
- void Process(){
- m_world->GetStats().PrintInstructionData(fname);
- }
-};
-
///// print_instruction_abundance_histogram /////
/**
@@ -1024,33 +580,6 @@
}
};
-///// print_genotype_map /////
-
-/**
-* write a matrix of genotype ID's to a file (matlab format)
- **/
-
-
-class cEvent_print_genotype_map : public cEvent {
-private:
- cString fname;
-public:
- const cString GetName() const { return "print_genotype_map"; }
- const cString GetDescription() const { return "print_genotype_map [cString fname=\"genotype_map.m\"]"; }
-
- void Configure(cWorld* world, const cString& in_args)
- {
- m_world = world;
- m_args = in_args;
- cString args(in_args);
- if (args == "") fname="genotype_map.m"; else fname=args.PopWord();
- }
- ///// print_genotype_map /////
- void Process(){
- m_world->GetStats().PrintGenotypeMap(fname);
- }
-};
-
///// print_number_phenotypes /////
/**
@@ -4008,117 +3537,120 @@
}
};
+#define REGISTER(EVENT_NAME) Register<cEvent_ ## EVENT_NAME>("EVENT_NAME")
+
cEventManager::cEventManager(cWorld* world) : m_world(world)
{
- Register<cEvent_exit>("exit");
- Register<cEvent_exit_if_generation_greater_than>("exit_if_generation_greater_than");
- Register<cEvent_exit_if_update_greater_than>("exit_if_update_greater_than");
- Register<cEvent_exit_if_ave_lineage_label_smaller>("exit_if_ave_lineage_label_smaller");
- Register<cEvent_exit_if_ave_lineage_label_larger>("exit_if_ave_lineage_label_larger");
- Register<cEvent_echo>("echo");
- Register<cEvent_print_data>("print_data");
- Register<cEvent_print_average_data>("print_average_data");
- Register<cEvent_print_error_data>("print_error_data");
- Register<cEvent_print_variance_data>("print_variance_data");
- Register<cEvent_print_dominant_data>("print_dominant_data");
- Register<cEvent_print_stats_data>("print_stats_data");
- Register<cEvent_print_count_data>("print_count_data");
- Register<cEvent_print_totals_data>("print_totals_data");
- Register<cEvent_print_tasks_data>("print_tasks_data");
- Register<cEvent_print_tasks_exe_data>("print_tasks_exe_data");
- Register<cEvent_print_resource_data>("print_resource_data");
- Register<cEvent_print_time_data>("print_time_data");
- Register<cEvent_print_mutation_data>("print_mutation_data");
- Register<cEvent_print_mutation_rate_data>("print_mutation_rate_data");
- Register<cEvent_print_divide_mut_data>("print_divide_mut_data");
- Register<cEvent_print_dom_parasite_data>("print_dom_parasite_data");
- Register<cEvent_print_instruction_data>("print_instruction_data");
- Register<cEvent_print_instruction_abundance_histogram>("print_instruction_abundance_histogram");
- Register<cEvent_print_depth_histogram>("print_depth_histogram");
- Register<cEvent_print_genotype_abundance_histogram>("print_genotype_abundance_histogram");
- Register<cEvent_print_species_abundance_histogram>("print_species_abundance_histogram");
- Register<cEvent_print_lineage_totals>("print_lineage_totals");
- Register<cEvent_print_lineage_counts>("print_lineage_counts");
- Register<cEvent_print_dom>("print_dom");
- Register<cEvent_parasite_debug>("parasite_debug");
- Register<cEvent_print_dom_parasite>("print_dom_parasite");
- Register<cEvent_print_genotype_map>("print_genotype_map");
- Register<cEvent_print_number_phenotypes>("print_number_phenotypes");
- Register<cEvent_print_phenotype_status>("print_phenotype_status");
- Register<cEvent_save_population>("save_population");
- Register<cEvent_load_population>("load_population");
- Register<cEvent_save_clone>("save_clone");
- Register<cEvent_load_clone>("load_clone");
- Register<cEvent_load_dump_file>("load_dump_file");
- Register<cEvent_dump_pop>("dump_pop");
- Register<cEvent_print_genotypes>("print_genotypes");
- Register<cEvent_detail_pop>("detail_pop");
- Register<cEvent_detail_sex_pop>("detail_sex_pop");
- Register<cEvent_detail_parasite_pop>("detail_parasite_pop");
- Register<cEvent_dump_historic_pop>("dump_historic_pop");
- Register<cEvent_dump_historic_sex_pop>("dump_historic_sex_pop");
- Register<cEvent_dump_memory>("dump_memory");
- Register<cEvent_inject>("inject");
- Register<cEvent_inject_all>("inject_all");
- Register<cEvent_inject_range>("inject_range");
- Register<cEvent_inject_sequence>("inject_sequence");
- Register<cEvent_inject_random>("inject_random");
- Register<cEvent_inject_range_parasite>("inject_range_parasite");
- Register<cEvent_inject_range_pair>("inject_range_pair");
- Register<cEvent_zero_muts>("zero_muts");
- Register<cEvent_mod_copy_mut>("mod_copy_mut");
- Register<cEvent_mod_div_mut>("mod_div_mut");
- Register<cEvent_set_copy_mut>("set_copy_mut");
- Register<cEvent_mod_point_mut>("mod_point_mut");
- Register<cEvent_set_point_mut>("set_point_mut");
- Register<cEvent_calc_landscape>("calc_landscape");
- Register<cEvent_predict_w_landscape>("predict_w_landscape");
- Register<cEvent_predict_nu_landscape>("predict_nu_landscape");
- Register<cEvent_sample_landscape>("sample_landscape");
- Register<cEvent_random_landscape>("random_landscape");
- Register<cEvent_analyze_landscape>("analyze_landscape");
- Register<cEvent_pairtest_landscape>("pairtest_landscape");
- Register<cEvent_test_dom>("test_dom");
- Register<cEvent_analyze_population>("analyze_population");
- Register<cEvent_print_detailed_fitness_data>("print_detailed_fitness_data");
- Register<cEvent_print_genetic_distance_data>("print_genetic_distance_data");
- Register<cEvent_genetic_distance_pop_dump>("genetic_distance_pop_dump");
- Register<cEvent_task_snapshot>("task_snapshot");
- Register<cEvent_print_viable_tasks_data>("print_viable_tasks_data");
- Register<cEvent_apocalypse>("apocalypse");
- Register<cEvent_kill_rectangle>("kill_rectangle");
- Register<cEvent_rate_kill>("rate_kill");
- Register<cEvent_serial_transfer>("serial_transfer");
- Register<cEvent_hillclimb>("hillclimb");
- Register<cEvent_hillclimb_neut>("hillclimb_neut");
- Register<cEvent_hillclimb_rand>("hillclimb_rand");
- Register<cEvent_compete_demes>("compete_demes");
- Register<cEvent_reset_demes>("reset_demes");
- Register<cEvent_print_deme_stats>("print_deme_stats");
- Register<cEvent_copy_deme>("copy_deme");
- Register<cEvent_calc_consensus>("calc_consensus");
- Register<cEvent_test_size_change_robustness>("test_size_change_robustness");
- Register<cEvent_test_threads>("test_threads");
- Register<cEvent_print_threads>("print_threads");
- Register<cEvent_dump_fitness_grid>("dump_fitness_grid");
- Register<cEvent_dump_genotype_grid>("dump_genotype_grid");
- Register<cEvent_dump_task_grid>("dump_task_grid");
- Register<cEvent_dump_donor_grid>("dump_donor_grid");
- Register<cEvent_dump_receiver_grid>("dump_receiver_grid");
- Register<cEvent_print_tree_depths>("print_tree_depths");
- Register<cEvent_sever_grid_col>("sever_grid_col");
- Register<cEvent_sever_grid_row>("sever_grid_row");
- Register<cEvent_join_grid_col>("join_grid_col");
- Register<cEvent_join_grid_row>("join_grid_row");
- Register<cEvent_connect_cells>("connect_cells");
- Register<cEvent_disconnect_cells>("disconnect_cells");
- Register<cEvent_inject_resource>("inject_resource");
- Register<cEvent_set_resource>("set_resource");
- Register<cEvent_inject_scaled_resource>("inject_scaled_resource");
- Register<cEvent_outflow_scaled_resource>("outflow_scaled_resource");
- Register<cEvent_set_reaction_value>("set_reaction_value");
- Register<cEvent_set_reaction_value_mult>("set_reaction_value_mult");
- Register<cEvent_set_reaction_inst>("set_reaction_inst");
+ REGISTER(exit);
+ REGISTER(exit_if_generation_greater_than);
+ REGISTER(exit_if_update_greater_than);
+ REGISTER(exit_if_ave_lineage_label_smaller);
+ REGISTER(exit_if_ave_lineage_label_larger);
+ REGISTER(echo);
+ REGISTER(print_data);
+ REGISTER(print_average_data);
+ REGISTER(print_error_data);
+ REGISTER(print_variance_data);
+ REGISTER(print_dominant_data);
+ REGISTER(print_stats_data);
+ REGISTER(print_count_data);
+ REGISTER(print_totals_data);
+ REGISTER(print_tasks_data);
+ REGISTER(print_tasks_exe_data);
+ REGISTER(print_tasks_qual_data);
+ REGISTER(print_resource_data);
+ REGISTER(print_time_data);
+ REGISTER(print_mutation_data);
+ REGISTER(print_mutation_rate_data);
+ REGISTER(print_divide_mut_data);
+ REGISTER(print_dom_parasite_data);
+ REGISTER(print_instruction_data);
+ REGISTER(print_instruction_abundance_histogram);
+ REGISTER(print_depth_histogram);
+ REGISTER(print_genotype_abundance_histogram);
+ REGISTER(print_species_abundance_histogram);
+ REGISTER(print_lineage_totals);
+ REGISTER(print_lineage_counts);
+ REGISTER(print_dom);
+ REGISTER(parasite_debug);
+ REGISTER(print_dom_parasite);
+ REGISTER(print_genotype_map);
+ REGISTER(print_number_phenotypes);
+ REGISTER(print_phenotype_status);
+ REGISTER(save_population);
+ REGISTER(load_population);
+ REGISTER(save_clone);
+ REGISTER(load_clone);
+ REGISTER(load_dump_file);
+ REGISTER(dump_pop);
+ REGISTER(print_genotypes);
+ REGISTER(detail_pop);
+ REGISTER(detail_sex_pop);
+ REGISTER(detail_parasite_pop);
+ REGISTER(dump_historic_pop);
+ REGISTER(dump_historic_sex_pop);
+ REGISTER(dump_memory);
+ REGISTER(inject);
+ REGISTER(inject_all);
+ REGISTER(inject_range);
+ REGISTER(inject_sequence);
+ REGISTER(inject_random);
+ REGISTER(inject_range_parasite);
+ REGISTER(inject_range_pair);
+ REGISTER(zero_muts);
+ REGISTER(mod_copy_mut);
+ REGISTER(mod_div_mut);
+ REGISTER(set_copy_mut);
+ REGISTER(mod_point_mut);
+ REGISTER(set_point_mut);
+ REGISTER(calc_landscape);
+ REGISTER(predict_w_landscape);
+ REGISTER(predict_nu_landscape);
+ REGISTER(sample_landscape);
+ REGISTER(random_landscape);
+ REGISTER(analyze_landscape);
+ REGISTER(pairtest_landscape);
+ REGISTER(test_dom);
+ REGISTER(analyze_population);
+ REGISTER(print_detailed_fitness_data);
+ REGISTER(print_genetic_distance_data);
+ REGISTER(genetic_distance_pop_dump);
+ REGISTER(task_snapshot);
+ REGISTER(print_viable_tasks_data);
+ REGISTER(apocalypse);
+ REGISTER(kill_rectangle);
+ REGISTER(rate_kill);
+ REGISTER(serial_transfer);
+ REGISTER(hillclimb);
+ REGISTER(hillclimb_neut);
+ REGISTER(hillclimb_rand);
+ REGISTER(compete_demes);
+ REGISTER(reset_demes);
+ REGISTER(print_deme_stats);
+ REGISTER(copy_deme);
+ REGISTER(calc_consensus);
+ REGISTER(test_size_change_robustness);
+ REGISTER(test_threads);
+ REGISTER(print_threads);
+ REGISTER(dump_fitness_grid);
+ REGISTER(dump_genotype_grid);
+ REGISTER(dump_task_grid);
+ REGISTER(dump_donor_grid);
+ REGISTER(dump_receiver_grid);
+ REGISTER(print_tree_depths);
+ REGISTER(sever_grid_col);
+ REGISTER(sever_grid_row);
+ REGISTER(join_grid_col);
+ REGISTER(join_grid_row);
+ REGISTER(connect_cells);
+ REGISTER(disconnect_cells);
+ REGISTER(inject_resource);
+ REGISTER(set_resource);
+ REGISTER(inject_scaled_resource);
+ REGISTER(outflow_scaled_resource);
+ REGISTER(set_reaction_value);
+ REGISTER(set_reaction_value_mult);
+ REGISTER(set_reaction_inst);
}
cEvent* cEventManager::ConstructEvent(const cString name, const cString & args)
Modified: development/source/main/cStats.cc
===================================================================
--- development/source/main/cStats.cc 2006-04-05 18:41:28 UTC (rev 575)
+++ development/source/main/cStats.cc 2006-04-07 01:00:31 UTC (rev 576)
@@ -383,36 +383,32 @@
max_fitness = 0.0;
}
-void cStats::RemoveLineage(int id_num, int parent_id, int update_born,
- double generation_born,
- int total_CPUs, int total_genotypes, double fitness,
- double lineage_stat1, double lineage_stat2 )
+void cStats::RemoveLineage(int id_num, int parent_id, int update_born, double generation_born, int total_CPUs,
+ int total_genotypes, double fitness, double lineage_stat1, double lineage_stat2 )
{
num_lineages--;
if (m_world->GetConfig().LOG_LINEAGES.Get()) {
cDataFile& lineage_log = m_world->GetDataFile("lineage.log");
- lineage_log.WriteComment("(1) lineage id (2) parent lineage id (3) initial fitness (4) total number of creatures (5) total number of genotypes (6) update born (7) update extinct (8) generation born (9) generation extinct (10) lineage stat1 (11) lineage stat2 [10, 11 depend on lineage creation method chosen]");
- lineage_log.Endl();
+ lineage_log.WriteComment("Columns 10, 11 depend on lineage creation method chosen.");
- lineage_log.GetOFStream()
- << id_num << " " // 1
- << parent_id << " " // 2
- << fitness << " " // 3
- << total_CPUs << " " // 4
- << total_genotypes << " " // 5
- << update_born << " " // 6
- << cStats::GetUpdate() << " " // 7
- << generation_born << " " // 8
- << SumGeneration().Average() << " " // 9
- << lineage_stat1 << " " // 10
- << lineage_stat2 << " " << endl;
+ lineage_log.Write(id_num, "lineage id");
+ lineage_log.Write(parent_id, "parent lineage id");
+ lineage_log.Write(fitness, "initial fitness");
+ lineage_log.Write(total_CPUs, "total number of creatures");
+ lineage_log.Write(total_genotypes, "total number of genotypes");
+ lineage_log.Write(update_born, "update born");
+ lineage_log.Write(cStats::GetUpdate(), "update extinct");
+ lineage_log.Write(generation_born, "generation born");
+ lineage_log.Write(SumGeneration().Average(), "generation extinct");
+ lineage_log.Write(lineage_stat1, "lineage stat1");
+ lineage_log.Write(lineage_stat2, "lineage stat2");
+ lineage_log.Endl();
}
}
-void cStats::PrintDataFile(const cString & filename, const cString & format,
- char sep)
+void cStats::PrintDataFile(const cString& filename, const cString& format, char sep)
{
cDataFile & data_file = m_world->GetDataFile(filename);
data_manager.PrintRow(data_file, format, sep);
@@ -426,23 +422,23 @@
df.WriteComment( "Avida average data" );
df.WriteTimeStamp();
- df.Write(GetUpdate(), "update" );
- df.Write(sum_merit.Average(), "average merit" );
- df.Write(sum_gestation.Average(), "average gestation time" );
- df.Write(sum_fitness.Average(), "average fitness" );
- df.Write(sum_repro_rate.Average(), "repro rate?" );
- df.Write(sum_size.Average(), "average size" );
- df.Write(sum_copy_size.Average(), "average copied size" );
- df.Write(sum_exe_size.Average(), "average executed size" );
- df.Write(sum_abundance.Average(), "average abundance?" );
- df.Write((double)num_births/num_creatures,
- "proportion of organisms that gave birth in this update" );
- df.Write((double)num_breed_true/num_creatures,
- "proportion of breed true organisms" );
- df.Write(sum_genotype_depth.Average(), "average genotype depth" );
- df.Write(sum_generation.Average(), "average generation" );
- df.Write(sum_neutral_metric.Average(), "average neutral metric" );
- df.Write(sum_lineage_label.Average(), "average lineage label" );
+ df.Write(GetUpdate(), "update");
+ df.Write(sum_merit.Average(), "average merit");
+ df.Write(sum_gestation.Average(), "average gestation time");
+ df.Write(sum_fitness.Average(), "average fitness");
+ df.Write(sum_repro_rate.Average(), "repro rate?");
+ df.Write(sum_size.Average(), "average size");
+ df.Write(sum_copy_size.Average(), "average copied size");
+ df.Write(sum_exe_size.Average(), "average executed size");
+ df.Write(sum_abundance.Average(), "average abundance?");
+ df.Write(static_cast<double>(num_births / num_creatures),
+ "proportion of organisms that gave birth in this update");
+ df.Write(static_cast<double>(num_breed_true / num_creatures),
+ "proportion of breed true organisms");
+ df.Write(sum_genotype_depth.Average(), "average genotype depth");
+ df.Write(sum_generation.Average(), "average generation");
+ df.Write(sum_neutral_metric.Average(), "average neutral metric");
+ df.Write(sum_lineage_label.Average(), "average lineage label");
df.Write(rave_true_replication_rate.Average(),
"true replication rate (based on births/update, time-averaged)");
df.Endl();
@@ -496,7 +492,7 @@
void cStats::PrintDominantData(const cString & filename)
{
- cDataFile & df = m_world->GetDataFile(filename);
+ cDataFile& df = m_world->GetDataFile(filename);
df.WriteComment( "Avida dominant data" );
df.WriteTimeStamp();
@@ -603,7 +599,7 @@
}
-void cStats::PrintTasksData(const cString & filename)
+void cStats::PrintTasksData(const cString& filename)
{
cString file = filename;
@@ -611,21 +607,11 @@
if (filename == "tasksq.dat")
{
file = "tasks.dat";
- cDataFile & df2 = m_world->GetDataFile("taskquality.dat");
- df2.WriteComment( "First column gives the current update, rest give average and max task quality" );
- df2.Write( GetUpdate(), "Update");
- for(int i = 0; i < task_last_count.GetSize(); i++) {
- double qual=0;
- if (task_last_count[i] > 0)
- qual = task_last_quality[i]/(double)task_last_count[i];
- df2.Write( qual, task_names[i] );
- df2.Write( task_last_max_quality[i], "Max" );
- }
- df2.Endl();
+ PrintTasksQualData("taskquality.dat");
}
// print tasks.dat
- cDataFile & df = m_world->GetDataFile(file);
+ cDataFile& df = m_world->GetDataFile(file);
df.WriteComment( "Avida tasks data" );
df.WriteTimeStamp();
df.WriteComment( "First column gives the current update, next columns give the number" );
@@ -636,17 +622,14 @@
df.Write( task_last_count[i], task_names[i] );
}
df.Endl();
-
- //cDataFile & df = m_world->GetDataFile(filename);
-
}
-void cStats::PrintTasksExeData(const cString & filename)
+void cStats::PrintTasksExeData(const cString& filename)
{
- cDataFile & df = m_world->GetDataFile(filename);
+ cDataFile& df = m_world->GetDataFile(filename);
- df.WriteComment( "Avida tasks data" );
+ df.WriteComment( "Avida tasks execution data" );
df.WriteTimeStamp();
df.WriteComment( "First column gives the current update, all further columns give the number" );
df.WriteComment( "of times the particular task has been executed this update." );
@@ -659,12 +642,29 @@
df.Endl();
}
+void cStats::PrintTasksQualData(const cString& filename)
+{
+ cDataFile& df = m_world->GetDataFile(filename);
+ df.WriteComment( "Avida tasks quality data" );
+ df.WriteTimeStamp();
+ df.WriteComment( "First column gives the current update, rest give average and max task quality" );
+ df.Write( GetUpdate(), "Update");
+ for(int i = 0; i < task_last_count.GetSize(); i++) {
+ double qual = 0.0;
+ if (task_last_count[i] > 0)
+ qual = task_last_quality[i] / static_cast<double>(task_last_count[i]);
+ df.Write(qual, task_names[i] + " Average");
+ df.Write(task_last_max_quality[i], task_names[i] + " Max");
+ }
+ df.Endl();
+}
+
void cStats::PrintReactionData(const cString & filename)
{
- cDataFile & df = m_world->GetDataFile(filename);
+ cDataFile& df = m_world->GetDataFile(filename);
- df.WriteComment( "Avida tasks data" );
+ df.WriteComment( "Avida reaction data" );
df.WriteTimeStamp();
df.WriteComment( "First column gives the current update, all further columns give the number" );
df.WriteComment( "of currently living organisms each reaction has affected." );
@@ -808,7 +808,7 @@
void cStats::PrintDivideMutData(const cString & filename)
{
- cDataFile & df = m_world->GetDataFile(filename);
+ cDataFile& df = m_world->GetDataFile(filename);
df.WriteComment( "Avida divide mutation rate data" );
df.WriteTimeStamp();
@@ -826,23 +826,22 @@
df.Write( sum_log_div_mut_rate.Skw(), "Skew in log(divide mutation rate)" );
df.Write( sum_log_div_mut_rate.Kur(), "Kurtosis in log(divide mutation rate)" );
df.Endl();
-
}
void cStats::PrintInstructionData(const cString & filename)
{
- cDataFile & df = m_world->GetDataFile(filename);
+ cDataFile& df = m_world->GetDataFile(filename);
df.WriteComment( "Avida instruction execution data" );
df.WriteTimeStamp();
#ifdef INSTRUCTION_COUNT
- df.Write( GetUpdate(), "Update" );
+ df.Write( GetUpdate(), "Update" );
for( int i=0; i < sum_exe_inst_array.GetSize(); i++ ){
df.Write( (int) sum_exe_inst_array[i].Sum(), inst_names[i] );
}
#else // INSTRUCTION_COUNT undefined
- cerr<<"Warning: Instruction Counts not compiled in"<<endl;
+ cerr << "Warning: Instruction Counts not compiled in" << endl;
#endif // ifdef INSTRUCTION_COUNT
df.Endl();
Modified: development/source/main/cStats.h
===================================================================
--- development/source/main/cStats.h 2006-04-05 18:41:28 UTC (rev 575)
+++ development/source/main/cStats.h 2006-04-07 01:00:31 UTC (rev 576)
@@ -237,26 +237,16 @@
void SetupPrintDatabase();
void ProcessUpdate();
+ inline void SetCurrentUpdate(int new_update) { current_update = new_update; sub_update = 0; }
+ inline void IncCurrentUpdate() { current_update++; sub_update = 0; }
+ inline void IncSubUpdate() { sub_update++; }
- // GLOBAL STATS
- inline void SetCurrentUpdate(int new_update) {
- current_update = new_update;
- sub_update = 0;
- }
-
- inline void IncCurrentUpdate() {
- current_update++;
- sub_update = 0;
- }
-
- void IncSubUpdate() { sub_update++; }
-
// Accessors...
int GetUpdate() const { return current_update; }
int GetSubUpdate() const { return sub_update; }
double GetGeneration() const { return SumGeneration().Average(); }
- cGenotype * GetDomGenotype() const { return dom_genotype; }
+ cGenotype* GetDomGenotype() const { return dom_genotype; }
double GetDomMerit() const { return dom_merit; }
double GetDomGestation() const { return dom_gestation; }
double GetDomReproRate() const { return dom_repro_rate; }
@@ -337,61 +327,61 @@
void SetEntropy(double in_entropy) { entropy = in_entropy; }
void SetSpeciesEntropy(double in_ent) { species_entropy = in_ent; }
- cDoubleSum & SumFitness() { return sum_fitness; }
- cDoubleSum & SumGestation() { return sum_gestation; }
- cDoubleSum & SumMerit() { return sum_merit; }
- cDoubleSum & SumReproRate() { return sum_repro_rate; }
+ cDoubleSum& SumFitness() { return sum_fitness; }
+ cDoubleSum& SumGestation() { return sum_gestation; }
+ cDoubleSum& SumMerit() { return sum_merit; }
+ cDoubleSum& SumReproRate() { return sum_repro_rate; }
- cDoubleSum & SumCreatureAge() { return sum_creature_age; }
- cDoubleSum & SumGenotypeAge() { return sum_genotype_age; }
- cDoubleSum & SumGeneration() { return sum_generation; }
- cDoubleSum & SumAbundance() { return sum_abundance; }
- cDoubleSum & SumGenotypeDepth() { return sum_genotype_depth; }
- cDoubleSum & SumThresholdAge() { return sum_threshold_age; }
- cDoubleSum & SumSpeciesAge() { return sum_species_age; }
+ cDoubleSum& SumCreatureAge() { return sum_creature_age; }
+ cDoubleSum& SumGenotypeAge() { return sum_genotype_age; }
+ cDoubleSum& SumGeneration() { return sum_generation; }
+ cDoubleSum& SumAbundance() { return sum_abundance; }
+ cDoubleSum& SumGenotypeDepth() { return sum_genotype_depth; }
+ cDoubleSum& SumThresholdAge() { return sum_threshold_age; }
+ cDoubleSum& SumSpeciesAge() { return sum_species_age; }
- cDoubleSum & SumNeutralMetric() { return sum_neutral_metric; }
- cDoubleSum & SumLineageLabel() { return sum_lineage_label; }
- cDoubleSum & SumCopyMutRate() { return sum_copy_mut_rate; }
- cDoubleSum & SumLogCopyMutRate() { return sum_log_copy_mut_rate; }
- cDoubleSum & SumDivMutRate() { return sum_div_mut_rate; }
- cDoubleSum & SumLogDivMutRate() { return sum_log_div_mut_rate; }
+ cDoubleSum& SumNeutralMetric() { return sum_neutral_metric; }
+ cDoubleSum& SumLineageLabel() { return sum_lineage_label; }
+ cDoubleSum& SumCopyMutRate() { return sum_copy_mut_rate; }
+ cDoubleSum& SumLogCopyMutRate() { return sum_log_copy_mut_rate; }
+ cDoubleSum& SumDivMutRate() { return sum_div_mut_rate; }
+ cDoubleSum& SumLogDivMutRate() { return sum_log_div_mut_rate; }
- cDoubleSum & SumSize() { return sum_size; }
- cDoubleSum & SumCopySize() { return sum_copy_size; }
- cDoubleSum & SumExeSize() { return sum_exe_size; }
- cDoubleSum & SumMemSize() { return sum_mem_size; }
+ cDoubleSum& SumSize() { return sum_size; }
+ cDoubleSum& SumCopySize() { return sum_copy_size; }
+ cDoubleSum& SumExeSize() { return sum_exe_size; }
+ cDoubleSum& SumMemSize() { return sum_mem_size; }
#ifdef INSTRUCTION_COUNT
void ZeroInst();
#endif
- tArray<cIntSum> & SumExeInst() { return sum_exe_inst_array; }
+ tArray<cIntSum>& SumExeInst() { return sum_exe_inst_array; }
// And constant versions of the above...
- const cDoubleSum & SumFitness() const { return sum_fitness; }
- const cDoubleSum & SumGestation() const { return sum_gestation; }
- const cDoubleSum & SumMerit() const { return sum_merit; }
- const cDoubleSum & SumReproRate() const { return sum_repro_rate; }
+ const cDoubleSum& SumFitness() const { return sum_fitness; }
+ const cDoubleSum& SumGestation() const { return sum_gestation; }
+ const cDoubleSum& SumMerit() const { return sum_merit; }
+ const cDoubleSum& SumReproRate() const { return sum_repro_rate; }
- const cDoubleSum & SumCreatureAge() const { return sum_creature_age; }
- const cDoubleSum & SumGenotypeAge() const { return sum_genotype_age; }
- const cDoubleSum & SumGeneration() const { return sum_generation; }
- const cDoubleSum & SumAbundance() const { return sum_abundance; }
- const cDoubleSum & SumGenotypeDepth() const { return sum_genotype_depth; }
- const cDoubleSum & SumThresholdAge() const { return sum_threshold_age; }
- const cDoubleSum & SumSpeciesAge() const { return sum_species_age; }
+ const cDoubleSum& SumCreatureAge() const { return sum_creature_age; }
+ const cDoubleSum& SumGenotypeAge() const { return sum_genotype_age; }
+ const cDoubleSum& SumGeneration() const { return sum_generation; }
+ const cDoubleSum& SumAbundance() const { return sum_abundance; }
+ const cDoubleSum& SumGenotypeDepth() const { return sum_genotype_depth; }
+ const cDoubleSum& SumThresholdAge() const { return sum_threshold_age; }
+ const cDoubleSum& SumSpeciesAge() const { return sum_species_age; }
- const cDoubleSum & SumNeutralMetric() const { return sum_neutral_metric; }
- const cDoubleSum & SumLineageLabel() const { return sum_lineage_label; }
- const cDoubleSum & SumCopyMutRate() const { return sum_copy_mut_rate; }
- const cDoubleSum & SumLogCopyMutRate() const{ return sum_log_copy_mut_rate; }
- const cDoubleSum & SumDivMutRate() const { return sum_div_mut_rate; }
- const cDoubleSum & SumLogDivMutRate() const{ return sum_log_div_mut_rate; }
+ const cDoubleSum& SumNeutralMetric() const { return sum_neutral_metric; }
+ const cDoubleSum& SumLineageLabel() const { return sum_lineage_label; }
+ const cDoubleSum& SumCopyMutRate() const { return sum_copy_mut_rate; }
+ const cDoubleSum& SumLogCopyMutRate() const{ return sum_log_copy_mut_rate; }
+ const cDoubleSum& SumDivMutRate() const { return sum_div_mut_rate; }
+ const cDoubleSum& SumLogDivMutRate() const{ return sum_log_div_mut_rate; }
- const cDoubleSum & SumSize() const { return sum_size; }
- const cDoubleSum & SumCopySize() const { return sum_copy_size; }
- const cDoubleSum & SumExeSize() const { return sum_exe_size; }
- const cDoubleSum & SumMemSize() const { return sum_mem_size; }
+ const cDoubleSum& SumSize() const { return sum_size; }
+ const cDoubleSum& SumCopySize() const { return sum_copy_size; }
+ const cDoubleSum& SumExeSize() const { return sum_exe_size; }
+ const cDoubleSum& SumMemSize() const { return sum_mem_size; }
void CalcEnergy();
void CalcFidelity();
@@ -535,29 +525,29 @@
double GetMaxViableFitness() const { return max_viable_fitness; }
// User-defined datafile...
- void PrintDataFile(const cString & filename, const cString & format,
- char sep=' ');
+ void PrintDataFile(const cString& filename, const cString& format, char sep=' ');
// Public calls to output data files (for events)
- void PrintAverageData(const cString & filename);
- void PrintErrorData(const cString & filename);
- void PrintVarianceData(const cString & filename);
- void PrintDominantData(const cString & filename);
- void PrintDominantParaData(const cString & filename);
- void PrintStatsData(const cString & filename);
- void PrintCountData(const cString & filename);
- void PrintTotalsData(const cString & filename);
- void PrintTasksData(const cString & filename);
- void PrintTasksExeData(const cString & filename);
- void PrintReactionData(const cString & filename);
- void PrintResourceData(const cString & filename);
- void PrintSpatialResData(const cString & filename, int i);
- void PrintTimeData(const cString & filename);
- void PrintMutationData(const cString & filename);
- void PrintDivideMutData(const cString & filename);
- void PrintMutationRateData(const cString & filename);
- void PrintInstructionData(const cString & filename);
- void PrintGenotypeMap(const cString & filename);
+ void PrintAverageData(const cString& filename);
+ void PrintErrorData(const cString& filename);
+ void PrintVarianceData(const cString& filename);
+ void PrintDominantData(const cString& filename);
+ void PrintDominantParaData(const cString& filename);
+ void PrintStatsData(const cString& filename);
+ void PrintCountData(const cString& filename);
+ void PrintTotalsData(const cString& filename);
+ void PrintTasksData(const cString& filename);
+ void PrintTasksExeData(const cString& filename);
+ void PrintTasksQualData(const cString& filename);
+ void PrintReactionData(const cString& filename);
+ void PrintResourceData(const cString& filename);
+ void PrintSpatialResData(const cString& filename, int i);
+ void PrintTimeData(const cString& filename);
+ void PrintMutationData(const cString& filename);
+ void PrintDivideMutData(const cString& filename);
+ void PrintMutationRateData(const cString& filename);
+ void PrintInstructionData(const cString& filename);
+ void PrintGenotypeMap(const cString& filename);
};
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