[Avida-SVN] r2420 - in development: documentation source/actions source/main source/utils/make_actions_html
baerb at myxo.css.msu.edu
baerb at myxo.css.msu.edu
Tue Mar 4 09:29:48 PST 2008
Author: baerb
Date: 2008-03-04 12:29:48 -0500 (Tue, 04 Mar 2008)
New Revision: 2420
Modified:
development/documentation/actions.html
development/source/actions/EnvironmentActions.cc
development/source/main/cEnvironment.cc
development/source/main/cPopulation.cc
development/source/main/cPopulation.h
development/source/utils/make_actions_html/actions_source_info
development/source/utils/make_actions_html/make_actions_html.pl
Log:
Create a new action called cActionChangeEnvironment that will allow lines
formatted like lines in the environment file to be uses as actions. Currently
these only effect resources and not reactions. Also there is no error checking.
This is definately a work in progress.
Continued improvments to actions.html creator. Sort now ignores underlines.
A number of deprecated actions were labled as such. A new actions.html
generated with these new changes.
Modified: development/documentation/actions.html
===================================================================
--- development/documentation/actions.html 2008-03-04 12:53:54 UTC (rev 2419)
+++ development/documentation/actions.html 2008-03-04 17:29:48 UTC (rev 2420)
@@ -9,7 +9,7 @@
<div class="revision">
Revised 2006-09-03 DMB
-<br>Generated Mon Feb 25 09:53:04 2008 by make_actions_html</div>
+<br>Generated Fri Feb 29 12:15:08 2008 by make_actions_html</div>
<p>
<a href="index.html">Return to the Index</a> |
@@ -59,77 +59,78 @@
<a href="#AnalyzeLandscape">AnalyzeLandscape</a><br>
<a href="#AnalyzePopulation">AnalyzePopulation</a><br>
<a href="#apocalypse">apocalypse</a><br>
+ <a href="#ChangeEnvironment">ChangeEnvironment</a><br>
<a href="#compete_demes">compete_demes</a><br>
+ <a href="#CompeteDemes">CompeteDemes</a><br>
<a href="#compete_organisms">compete_organisms</a><br>
- <a href="#CompeteDemes">CompeteDemes</a><br>
<a href="#CompeteOrganisms">CompeteOrganisms</a><br>
<a href="#connect_cells">connect_cells</a><br>
<a href="#ConnectCells">ConnectCells</a><br>
+ <a href="#CopyDeme">CopyDeme</a><br>
<a href="#copy_deme">copy_deme</a><br>
- <a href="#CopyDeme">CopyDeme</a><br>
<a href="#DelayedDemeEvent">DelayedDemeEvent</a><br>
<a href="#DeletionLandscape">DeletionLandscape</a><br>
<a href="#detail_parasite_pop">detail_parasite_pop</a><br>
<a href="#detail_pop">detail_pop</a><br>
<a href="#detail_sex_pop">detail_sex_pop</a><br>
+ <a href="#DisconnectCells">DisconnectCells</a><br>
<a href="#disconnect_cells">disconnect_cells</a><br>
- <a href="#DisconnectCells">DisconnectCells</a><br>
<a href="#DivideDemes">DivideDemes</a><br>
+ <a href="#DumpCellDataGrid">DumpCellDataGrid</a><br>
<a href="#dump_donor_grid">dump_donor_grid</a><br>
- <a href="#dump_fitness_grid">dump_fitness_grid</a><br>
- <a href="#dump_genotype_grid">dump_genotype_grid</a><br>
- <a href="#dump_historic_pop">dump_historic_pop</a><br>
- <a href="#dump_historic_sex_pop">dump_historic_sex_pop</a><br>
- <a href="#dump_lineage_grid">dump_lineage_grid</a><br>
- <a href="#dump_memory">dump_memory</a><br>
- <a href="#dump_phenotype_grid">dump_phenotype_grid</a><br>
- <a href="#dump_pop">dump_pop</a><br>
- <a href="#dump_receiver_grid">dump_receiver_grid</a><br>
- <a href="#dump_task_grid">dump_task_grid</a><br>
- <a href="#DumpCellDataGrid">DumpCellDataGrid</a><br>
<a href="#DumpDonorGrid">DumpDonorGrid</a><br>
<a href="#DumpEnergyGrid">DumpEnergyGrid</a><br>
<a href="#DumpExecutionRatioGrid">DumpExecutionRatioGrid</a><br>
+ <a href="#dump_fitness_grid">dump_fitness_grid</a><br>
<a href="#DumpFitnessGrid">DumpFitnessGrid</a><br>
+ <a href="#dump_genotype_grid">dump_genotype_grid</a><br>
<a href="#DumpGenotypeIDGrid">DumpGenotypeIDGrid</a><br>
+ <a href="#dump_historic_pop">dump_historic_pop</a><br>
+ <a href="#dump_historic_sex_pop">dump_historic_sex_pop</a><br>
<a href="#DumpLandscape">DumpLandscape</a><br>
+ <a href="#dump_lineage_grid">dump_lineage_grid</a><br>
<a href="#DumpLineageGrid">DumpLineageGrid</a><br>
+ <a href="#dump_memory">dump_memory</a><br>
<a href="#DumpMemory">DumpMemory</a><br>
+ <a href="#dump_phenotype_grid">dump_phenotype_grid</a><br>
<a href="#DumpPhenotypeIDGrid">DumpPhenotypeIDGrid</a><br>
+ <a href="#dump_pop">dump_pop</a><br>
<a href="#DumpPopulation">DumpPopulation</a><br>
+ <a href="#dump_receiver_grid">dump_receiver_grid</a><br>
<a href="#DumpReceiverGrid">DumpReceiverGrid</a><br>
<a href="#DumpSleepGrid">DumpSleepGrid</a><br>
+ <a href="#dump_task_grid">dump_task_grid</a><br>
<a href="#DumpTaskGrid">DumpTaskGrid</a><br>
<a href="#Echo">Echo</a><br>
<a href="#echo">echo</a><br>
<a href="#exit">exit</a><br>
<a href="#Exit">Exit</a><br>
- <a href="#exit_if_ave_lineage_label_larger">exit_if_ave_lineage_label_larger</a><br>
- <a href="#exit_if_ave_lineage_label_smaller">exit_if_ave_lineage_label_smaller</a><br>
<a href="#ExitAveGeneration">ExitAveGeneration</a><br>
<a href="#ExitAveLineageLabelGreater">ExitAveLineageLabelGreater</a><br>
<a href="#ExitAveLineageLabelLess">ExitAveLineageLabelLess</a><br>
<a href="#ExitElapsedTime">ExitElapsedTime</a><br>
+ <a href="#exit_if_ave_lineage_label_larger">exit_if_ave_lineage_label_larger</a><br>
+ <a href="#exit_if_ave_lineage_label_smaller">exit_if_ave_lineage_label_smaller</a><br>
<a href="#FullLandscape">FullLandscape</a><br>
<a href="#genetic_distance_pop_dump">genetic_distance_pop_dump</a><br>
<a href="#HillClimb">HillClimb</a><br>
<a href="#inject">inject</a><br>
<a href="#Inject">Inject</a><br>
<a href="#inject_all">inject_all</a><br>
+ <a href="#InjectAll">InjectAll</a><br>
<a href="#inject_all_random_repro">inject_all_random_repro</a><br>
- <a href="#inject_random">inject_random</a><br>
- <a href="#inject_range">inject_range</a><br>
- <a href="#inject_resource">inject_resource</a><br>
- <a href="#inject_scaled_resource">inject_scaled_resource</a><br>
- <a href="#inject_sequence">inject_sequence</a><br>
- <a href="#InjectAll">InjectAll</a><br>
<a href="#InjectDemes">InjectDemes</a><br>
<a href="#InjectParasite">InjectParasite</a><br>
<a href="#InjectParasitePair">InjectParasitePair</a><br>
+ <a href="#inject_random">inject_random</a><br>
<a href="#InjectRandom">InjectRandom</a><br>
<a href="#InjectRange">InjectRange</a><br>
+ <a href="#inject_range">inject_range</a><br>
<a href="#InjectResource">InjectResource</a><br>
+ <a href="#inject_resource">inject_resource</a><br>
+ <a href="#inject_scaled_resource">inject_scaled_resource</a><br>
<a href="#InjectScaledResource">InjectScaledResource</a><br>
+ <a href="#inject_sequence">inject_sequence</a><br>
<a href="#InjectSequence">InjectSequence</a><br>
<a href="#InjectSequenceWDivMutRate">InjectSequenceWDivMutRate</a><br>
<a href="#InsertionLandscape">InsertionLandscape</a><br>
@@ -137,19 +138,19 @@
<a href="#join_grid_row">join_grid_row</a><br>
<a href="#JoinGridCol">JoinGridCol</a><br>
<a href="#JoinGridRow">JoinGridRow</a><br>
- <a href="#kill_rectangle">kill_rectangle</a><br>
<a href="#KillProb">KillProb</a><br>
+ <a href="#KillRate">KillRate</a><br>
<td valign="top">
- <a href="#KillRate">KillRate</a><br>
<a href="#KillRectangle">KillRectangle</a><br>
+ <a href="#kill_rectangle">kill_rectangle</a><br>
+ <a href="#LoadClone">LoadClone</a><br>
<a href="#load_clone">load_clone</a><br>
<a href="#load_dump_file">load_dump_file</a><br>
- <a href="#LoadClone">LoadClone</a><br>
<a href="#LoadPopulation">LoadPopulation</a><br>
<a href="#ModMutProb">ModMutProb</a><br>
<a href="#MutationalNeighborhood">MutationalNeighborhood</a><br>
+ <a href="#NewTrial">NewTrial</a><br>
<a href="#new_trial">new_trial</a><br>
- <a href="#NewTrial">NewTrial</a><br>
<a href="#outflow_scaled_resource">outflow_scaled_resource</a><br>
<a href="#OutflowScaledResource">OutflowScaledResource</a><br>
<a href="#PairTestLandscape">PairTestLandscape</a><br>
@@ -157,49 +158,19 @@
<a href="#PredictNuLandscape">PredictNuLandscape</a><br>
<a href="#PredictWLandscape">PredictWLandscape</a><br>
<a href="#print_average_data">print_average_data</a><br>
- <a href="#print_count_data">print_count_data</a><br>
- <a href="#print_data">print_data</a><br>
- <a href="#print_deme_stats">print_deme_stats</a><br>
- <a href="#print_depth_histogram">print_depth_histogram</a><br>
- <a href="#print_detailed_fitness_data">print_detailed_fitness_data</a><br>
- <a href="#print_divide_mut_data">print_divide_mut_data</a><br>
- <a href="#print_dom">print_dom</a><br>
- <a href="#print_dom_parasite">print_dom_parasite</a><br>
- <a href="#print_dominant_data">print_dominant_data</a><br>
- <a href="#print_donation_stats">print_donation_stats</a><br>
- <a href="#print_error_data">print_error_data</a><br>
- <a href="#print_genetic_distance_data">print_genetic_distance_data</a><br>
- <a href="#print_genotype_abundance_histogram">print_genotype_abundance_histogram</a><br>
- <a href="#print_genotype_map">print_genotype_map</a><br>
- <a href="#print_genotypes">print_genotypes</a><br>
- <a href="#print_instruction_abundance_histogram">print_instruction_abundance_histogram</a><br>
- <a href="#print_instruction_data">print_instruction_data</a><br>
- <a href="#print_lineage_counts">print_lineage_counts</a><br>
- <a href="#print_lineage_totals">print_lineage_totals</a><br>
- <a href="#print_market_data">print_market_data</a><br>
- <a href="#print_mutation_rate_data">print_mutation_rate_data</a><br>
- <a href="#print_number_phenotypes">print_number_phenotypes</a><br>
- <a href="#print_phenotype_status">print_phenotype_status</a><br>
- <a href="#print_resource_data">print_resource_data</a><br>
- <a href="#print_species_abundance_histogram">print_species_abundance_histogram</a><br>
- <a href="#print_stats_data">print_stats_data</a><br>
- <a href="#print_tasks_data">print_tasks_data</a><br>
- <a href="#print_tasks_exe_data">print_tasks_exe_data</a><br>
- <a href="#print_tasks_qual_data">print_tasks_qual_data</a><br>
- <a href="#print_time_data">print_time_data</a><br>
- <a href="#print_totals_data">print_totals_data</a><br>
- <a href="#print_tree_depths">print_tree_depths</a><br>
- <a href="#print_variance_data">print_variance_data</a><br>
- <a href="#print_viable_tasks_data">print_viable_tasks_data</a><br>
<a href="#PrintAverageData">PrintAverageData</a><br>
<a href="#PrintCCladeCounts">PrintCCladeCounts</a><br>
<a href="#PrintCCladeFitnessHistogram">PrintCCladeFitnessHistogram</a><br>
<a href="#PrintCCladeRelativeFitnessHistogram">PrintCCladeRelativeFitnessHistogram</a><br>
+ <a href="#PrintCellVisitsData">PrintCellVisitsData</a><br>
<a href="#PrintCompetitionData">PrintCompetitionData</a><br>
+ <a href="#print_count_data">print_count_data</a><br>
<a href="#PrintCountData">PrintCountData</a><br>
<a href="#PrintCurrentReactionData">PrintCurrentReactionData</a><br>
+ <a href="#print_data">print_data</a><br>
<a href="#PrintData">PrintData</a><br>
<a href="#PrintDebug">PrintDebug</a><br>
+ <a href="#print_deme_stats">print_deme_stats</a><br>
<a href="#PrintDemeAllStats">PrintDemeAllStats</a><br>
<a href="#PrintDemeAverageData">PrintDemeAverageData</a><br>
<a href="#PrintDemeDonorStats">PrintDemeDonorStats</a><br>
@@ -208,54 +179,85 @@
<a href="#PrintDemeSpacialEnergyStats">PrintDemeSpacialEnergyStats</a><br>
<a href="#PrintDemeSpacialSleepStats">PrintDemeSpacialSleepStats</a><br>
<a href="#PrintDemeStats">PrintDemeStats</a><br>
+ <a href="#print_depth_histogram">print_depth_histogram</a><br>
<a href="#PrintDepthHistogram">PrintDepthHistogram</a><br>
+ <a href="#print_detailed_fitness_data">print_detailed_fitness_data</a><br>
<a href="#PrintDetailedFitnessData">PrintDetailedFitnessData</a><br>
+ <a href="#print_divide_mut_data">print_divide_mut_data</a><br>
<a href="#PrintDivideMutData">PrintDivideMutData</a><br>
+ <a href="#print_dom">print_dom</a><br>
+ <a href="#print_dom_parasite">print_dom_parasite</a><br>
+ <a href="#print_dominant_data">print_dominant_data</a><br>
<a href="#PrintDominantData">PrintDominantData</a><br>
<a href="#PrintDominantGenotype">PrintDominantGenotype</a><br>
<a href="#PrintDominantParasiteGenotype">PrintDominantParasiteGenotype</a><br>
+ <a href="#print_donation_stats">print_donation_stats</a><br>
+ <a href="#print_error_data">print_error_data</a><br>
<a href="#PrintErrorData">PrintErrorData</a><br>
+ <a href="#print_genetic_distance_data">print_genetic_distance_data</a><br>
<a href="#PrintGeneticDistanceData">PrintGeneticDistanceData</a><br>
<a href="#PrintGenomicSiteEntropy">PrintGenomicSiteEntropy</a><br>
+ <a href="#print_genotype_abundance_histogram">print_genotype_abundance_histogram</a><br>
+ <a href="#print_genotype_map">print_genotype_map</a><br>
<a href="#PrintGenotypeAbundanceHistogram">PrintGenotypeAbundanceHistogram</a><br>
<a href="#PrintGenotypeMap">PrintGenotypeMap</a><br>
+ <a href="#print_genotypes">print_genotypes</a><br>
<a href="#PrintGenotypes">PrintGenotypes</a><br>
<a href="#PrintGermlineData">PrintGermlineData</a><br>
+ <a href="#print_instruction_abundance_histogram">print_instruction_abundance_histogram</a><br>
+ <a href="#print_instruction_data">print_instruction_data</a><br>
<a href="#PrintInstructionAbundanceHistogram">PrintInstructionAbundanceHistogram</a><br>
<a href="#PrintInstructionData">PrintInstructionData</a><br>
- <td valign="top">
+ <a href="#print_lineage_counts">print_lineage_counts</a><br>
+ <a href="#print_lineage_totals">print_lineage_totals</a><br>
<a href="#PrintLineageCounts">PrintLineageCounts</a><br>
<a href="#PrintLineageTotals">PrintLineageTotals</a><br>
<a href="#PrintLogFitnessHistogram">PrintLogFitnessHistogram</a><br>
+ <a href="#print_market_data">print_market_data</a><br>
<a href="#PrintMarketData">PrintMarketData</a><br>
+ <a href="#print_mutation_rate_data">print_mutation_rate_data</a><br>
<a href="#PrintMutationRateData">PrintMutationRateData</a><br>
+ <a href="#print_number_phenotypes">print_number_phenotypes</a><br>
<a href="#PrintParasiteData">PrintParasiteData</a><br>
+ <a href="#print_phenotype_status">print_phenotype_status</a><br>
<a href="#PrintPhenotypeData">PrintPhenotypeData</a><br>
<a href="#PrintPhenotypeStatus">PrintPhenotypeStatus</a><br>
<a href="#PrintPhenotypicPlasticity">PrintPhenotypicPlasticity</a><br>
<a href="#PrintPopulationDistanceData">PrintPopulationDistanceData</a><br>
<a href="#PrintReactionData">PrintReactionData</a><br>
+ <td valign="top">
<a href="#PrintReactionRewardData">PrintReactionRewardData</a><br>
<a href="#PrintRelativeFitnessHistogram">PrintRelativeFitnessHistogram</a><br>
+ <a href="#print_resource_data">print_resource_data</a><br>
<a href="#PrintResourceData">PrintResourceData</a><br>
<a href="#PrintSenseData">PrintSenseData</a><br>
<a href="#PrintSenseExeData">PrintSenseExeData</a><br>
<a href="#PrintSleepData">PrintSleepData</a><br>
+ <a href="#print_species_abundance_histogram">print_species_abundance_histogram</a><br>
<a href="#PrintSpeciesAbundanceHistogram">PrintSpeciesAbundanceHistogram</a><br>
+ <a href="#print_stats_data">print_stats_data</a><br>
<a href="#PrintStatsData">PrintStatsData</a><br>
+ <a href="#print_tasks_data">print_tasks_data</a><br>
+ <a href="#print_tasks_exe_data">print_tasks_exe_data</a><br>
+ <a href="#print_tasks_qual_data">print_tasks_qual_data</a><br>
<a href="#PrintTasksData">PrintTasksData</a><br>
<a href="#PrintTasksExeData">PrintTasksExeData</a><br>
<a href="#PrintTaskSnapshot">PrintTaskSnapshot</a><br>
<a href="#PrintTasksQualData">PrintTasksQualData</a><br>
+ <a href="#print_time_data">print_time_data</a><br>
<a href="#PrintTimeData">PrintTimeData</a><br>
+ <a href="#print_totals_data">print_totals_data</a><br>
<a href="#PrintTotalsData">PrintTotalsData</a><br>
+ <a href="#print_tree_depths">print_tree_depths</a><br>
<a href="#PrintTreeDepths">PrintTreeDepths</a><br>
+ <a href="#print_variance_data">print_variance_data</a><br>
<a href="#PrintVarianceData">PrintVarianceData</a><br>
+ <a href="#print_viable_tasks_data">print_viable_tasks_data</a><br>
<a href="#PrintViableTasksData">PrintViableTasksData</a><br>
<a href="#RandomLandscape">RandomLandscape</a><br>
<a href="#rate_kill">rate_kill</a><br>
+ <a href="#ReplicateDemes">ReplicateDemes</a><br>
<a href="#replicate_demes">replicate_demes</a><br>
- <a href="#ReplicateDemes">ReplicateDemes</a><br>
<a href="#reset_demes">reset_demes</a><br>
<a href="#ResetDemes">ResetDemes</a><br>
<a href="#SampleLandscape">SampleLandscape</a><br>
@@ -266,12 +268,8 @@
<a href="#SaveParasitePopulation">SaveParasitePopulation</a><br>
<a href="#SavePopulation">SavePopulation</a><br>
<a href="#SaveSexPopulation">SaveSexPopulation</a><br>
+ <a href="#SerialTransfer">SerialTransfer</a><br>
<a href="#serial_transfer">serial_transfer</a><br>
- <a href="#SerialTransfer">SerialTransfer</a><br>
- <a href="#set_reaction_inst">set_reaction_inst</a><br>
- <a href="#set_reaction_value">set_reaction_value</a><br>
- <a href="#set_reaction_value_mult">set_reaction_value_mult</a><br>
- <a href="#set_resource">set_resource</a><br>
<a href="#SetCellResource">SetCellResource</a><br>
<a href="#SetEnvironmentInputs">SetEnvironmentInputs</a><br>
<a href="#SetEnvironmentRandomMask">SetEnvironmentRandomMask</a><br>
@@ -279,6 +277,9 @@
<a href="#SetNumInstBefore0Energy">SetNumInstBefore0Energy</a><br>
<a href="#SetOptimizeMinMax">SetOptimizeMinMax</a><br>
<a href="#SetPeriodicResource">SetPeriodicResource</a><br>
+ <a href="#set_reaction_inst">set_reaction_inst</a><br>
+ <a href="#set_reaction_value">set_reaction_value</a><br>
+ <a href="#set_reaction_value_mult">set_reaction_value_mult</a><br>
<a href="#SetReactionInst">SetReactionInst</a><br>
<a href="#SetReactionMaxTaskCount">SetReactionMaxTaskCount</a><br>
<a href="#SetReactionMinTaskCount">SetReactionMinTaskCount</a><br>
@@ -286,6 +287,7 @@
<a href="#SetReactionValue">SetReactionValue</a><br>
<a href="#SetReactionValueMult">SetReactionValueMult</a><br>
<a href="#SetResource">SetResource</a><br>
+ <a href="#set_resource">set_resource</a><br>
<a href="#SetResourceInflow">SetResourceInflow</a><br>
<a href="#SetResourceOutflow">SetResourceOutflow</a><br>
<a href="#SetTaskArgDouble">SetTaskArgDouble</a><br>
@@ -322,7 +324,8 @@
<i>No Arguments</i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
@@ -335,22 +338,6 @@
</p>
</li>
<li><p>
- <strong><a name="exit_if_ave_lineage_label_larger">exit_if_ave_lineage_label_larger</a></strong>
- <i><double threshold></i>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="exit_if_ave_lineage_label_smaller">exit_if_ave_lineage_label_smaller</a></strong>
- <i><double threshold></i>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
<strong><a name="ExitAveGeneration">ExitAveGeneration</a></strong>
<i><double generation></i>
</p>
@@ -387,6 +374,24 @@
</p>
</li>
<li><p>
+ <strong><a name="exit_if_ave_lineage_label_larger">exit_if_ave_lineage_label_larger</a></strong>
+ <i><double threshold></i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="exit_if_ave_lineage_label_smaller">exit_if_ave_lineage_label_smaller</a></strong>
+ <i><double threshold></i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
<strong><a name="StopFastForward">StopFastForward</a></strong>
<i>none</i>
</p>
@@ -404,6 +409,19 @@
</p>
<UL>
<li><p>
+ <strong><a name="ChangeEnvironment">ChangeEnvironment</a></strong>
+ <i><string env_string></i>
+ </p>
+ <p>
+ Action designed to read in and process a line formatted as if it were in the
+ <a href="environment.html">environment</a> file. This will change
+ environmental settings on the fly. <b>You should create all resources and
+ reactions in the environment file</b> and only use this file to change these
+ resources and reactions.
+
+ </p>
+</li>
+<li><p>
<strong><a name="DelayedDemeEvent">DelayedDemeEvent</a></strong>
<i><int x1> <int y1> <int x2> <int y2> <int delay> <int duraion></i>
</p>
@@ -412,29 +430,31 @@
</p>
</li>
<li><p>
- <strong><a name="inject_resource">inject_resource</a></strong>
+ <strong><a name="InjectResource">InjectResource</a></strong>
<i><string res_name> <double res_count></i>
</p>
<p>
-
+ Inject (add) a specified amount of a specified resource.
+ <span class="cmdarg">res_name</span> must already exist as
+ a resource in environment file.
+
</p>
</li>
<li><p>
- <strong><a name="inject_scaled_resource">inject_scaled_resource</a></strong>
+ <strong><a name="inject_resource">inject_resource</a></strong>
<i><string res_name> <double res_count></i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
- <strong><a name="InjectResource">InjectResource</a></strong>
+ <strong><a name="inject_scaled_resource">inject_scaled_resource</a></strong>
<i><string res_name> <double res_count></i>
</p>
<p>
- Inject (add) a specified amount of a specified resource.
- <span class="cmdarg">res_name</span> must already exist as
- a resource in environment file.
+ <font color="red">DEPRECATED</font>
</p>
</li>
@@ -451,7 +471,8 @@
<i><string res_name> <double res_percent></i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
@@ -463,38 +484,6 @@
</p>
</li>
<li><p>
- <strong><a name="set_reaction_inst">set_reaction_inst</a></strong>
- <i><string reaction_name> <string inst></i>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="set_reaction_value">set_reaction_value</a></strong>
- <i><string reaction_name> <double value></i>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="set_reaction_value_mult">set_reaction_value_mult</a></strong>
- <i><string reaction_name> <double value></i>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="set_resource">set_resource</a></strong>
- <i><string res_name> <double res_count></i>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
<strong><a name="SetCellResource">SetCellResource</a></strong>
<i><int cell_id> <string res_name> <double res_count></i>
</p>
@@ -546,6 +535,33 @@
</p>
</li>
<li><p>
+ <strong><a name="set_reaction_inst">set_reaction_inst</a></strong>
+ <i><string reaction_name> <string inst></i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="set_reaction_value">set_reaction_value</a></strong>
+ <i><string reaction_name> <double value></i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="set_reaction_value_mult">set_reaction_value_mult</a></strong>
+ <i><string reaction_name> <double value></i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
<strong><a name="SetReactionInst">SetReactionInst</a></strong>
<i><string reaction_name> <string inst></i>
</p>
@@ -626,6 +642,15 @@
</p>
</li>
<li><p>
+ <strong><a name="set_resource">set_resource</a></strong>
+ <i><string res_name> <double res_count></i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
<strong><a name="SetResourceInflow">SetResourceInflow</a></strong>
<i><string resource_name> <int inflow></i>
</p>
@@ -836,7 +861,8 @@
<i>[double probability=0.9]</i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
@@ -844,11 +870,12 @@
<i>[int type=1]</i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
- <strong><a name="compete_organisms">compete_organisms</a></strong>
+ <strong><a name="CompeteDemes">CompeteDemes</a></strong>
<i>[int type=1]</i>
</p>
<p>
@@ -856,11 +883,12 @@
</p>
</li>
<li><p>
- <strong><a name="CompeteDemes">CompeteDemes</a></strong>
+ <strong><a name="compete_organisms">compete_organisms</a></strong>
<i>[int type=1]</i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
@@ -889,7 +917,8 @@
<i><int cellA_x> <int cellA_y> <int cellB_x> <int cellB_y></i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
@@ -902,7 +931,7 @@
</p>
</li>
<li><p>
- <strong><a name="copy_deme">copy_deme</a></strong>
+ <strong><a name="CopyDeme">CopyDeme</a></strong>
<i><int src_id> <int dest_id></i>
</p>
<p>
@@ -910,27 +939,29 @@
</p>
</li>
<li><p>
- <strong><a name="CopyDeme">CopyDeme</a></strong>
+ <strong><a name="copy_deme">copy_deme</a></strong>
<i><int src_id> <int dest_id></i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
- <strong><a name="disconnect_cells">disconnect_cells</a></strong>
+ <strong><a name="DisconnectCells">DisconnectCells</a></strong>
<i><int cellA_x> <int cellA_y> <int cellB_x> <int cellB_y></i>
</p>
<p>
-
+ Disconnects a pair of specified cells.
+
</p>
</li>
<li><p>
- <strong><a name="DisconnectCells">DisconnectCells</a></strong>
+ <strong><a name="disconnect_cells">disconnect_cells</a></strong>
<i><int cellA_x> <int cellA_y> <int cellB_x> <int cellB_y></i>
</p>
<p>
- Disconnects a pair of specified cells.
+ <font color="red">DEPRECATED</font>
</p>
</li>
@@ -947,7 +978,8 @@
<i>[string fname="START_CREATURE"] [int cell_id=0] [double merit=-1] [int lineage_label=0] [double neutral_metric=0]</i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
@@ -967,48 +999,26 @@
<i>[string fname="START_CREATURE"] [double merit=-1] [int lineage_label=0] [double neutral_metric=0]</i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
- <strong><a name="inject_all_random_repro">inject_all_random_repro</a></strong>
- <i><int length> [double merit=-1] [int lineage_label=0] [double neutral_metric=0]</i>
+ <strong><a name="InjectAll">InjectAll</a></strong>
+ <i>[string fname="START_CREATURE"] [double merit=-1] [int lineage_label=0] [double neutral_metric=0]</i>
</p>
<p>
-
+ Same as Inject, but no cell_id is specified and the organism is placed
+ into <em>all</em> cells in the population.
+
</p>
</li>
<li><p>
- <strong><a name="inject_random">inject_random</a></strong>
- <i><int length> [int cell_id=0] [double merit=-1] [int lineage_label=0] [double neutral_metric=0]</i>
+ <strong><a name="inject_all_random_repro">inject_all_random_repro</a></strong>
+ <i><int length> [double merit=-1] [int lineage_label=0] [double neutral_metric=0]</i>
</p>
<p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="inject_range">inject_range</a></strong>
- <i>[string fname="START_CREATURE"] [int cell_start=0] [int cell_end=-1] [double merit=-1] [int lineage_label=0] [double neutral_metric=0]</i>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="inject_sequence">inject_sequence</a></strong>
- <i>[string fname="START_CREATURE"] [int cell_id=0] [double merit=-1] [int lineage_label=0] [double neutral_metric=0]</i>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="InjectAll">InjectAll</a></strong>
- <i>[string fname="START_CREATURE"] [double merit=-1] [int lineage_label=0] [double neutral_metric=0]</i>
- </p>
- <p>
- Same as Inject, but no cell_id is specified and the organism is placed
- into <em>all</em> cells in the population.
+ <font color="red">DEPRECATED</font>
</p>
</li>
@@ -1040,6 +1050,15 @@
</p>
</li>
<li><p>
+ <strong><a name="inject_random">inject_random</a></strong>
+ <i><int length> [int cell_id=0] [double merit=-1] [int lineage_label=0] [double neutral_metric=0]</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
<strong><a name="InjectRandom">InjectRandom</a></strong>
<i><int length> [int cell_id=0] [double merit=-1] [int lineage_label=0] [double neutral_metric=0]</i>
</p>
@@ -1063,6 +1082,24 @@
</p>
</li>
<li><p>
+ <strong><a name="inject_range">inject_range</a></strong>
+ <i>[string fname="START_CREATURE"] [int cell_start=0] [int cell_end=-1] [double merit=-1] [int lineage_label=0] [double neutral_metric=0]</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="inject_sequence">inject_sequence</a></strong>
+ <i>[string fname="START_CREATURE"] [int cell_id=0] [double merit=-1] [int lineage_label=0] [double neutral_metric=0]</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
<strong><a name="InjectSequence">InjectSequence</a></strong>
<i><string sequence> [int cell_start=0] [int cell_end=-1] [double merit=-1] [int lineage_label=0] [double neutral_metric=0]</i>
</p>
@@ -1090,7 +1127,8 @@
<i>[int col_id=-1] [int min_row=0] [int max_row=-1]</i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
@@ -1098,7 +1136,8 @@
<i>[int row_id=-1] [int min_col=0] [int max_col=-1]</i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
@@ -1120,14 +1159,6 @@
</p>
</li>
<li><p>
- <strong><a name="kill_rectangle">kill_rectangle</a></strong>
- <i>[int x1=0] [int y1=0] [int x2=0] [int y2=0]</i>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
<strong><a name="KillProb">KillProb</a></strong>
<i>[double probability=0.9]</i>
</p>
@@ -1160,16 +1191,17 @@
</p>
</li>
<li><p>
- <strong><a name="ModMutProb">ModMutProb</a></strong>
- <i>[string mut_type="copy"] [double prob=0.0] [int start_cell=-1] [int end_cell=-1]</i>
+ <strong><a name="kill_rectangle">kill_rectangle</a></strong>
+ <i>[int x1=0] [int y1=0] [int x2=0] [int y2=0]</i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
- <strong><a name="new_trial">new_trial</a></strong>
- <i>[int type=1]</i>
+ <strong><a name="ModMutProb">ModMutProb</a></strong>
+ <i>[string mut_type="copy"] [double prob=0.0] [int start_cell=-1] [int end_cell=-1]</i>
</p>
<p>
@@ -1186,15 +1218,25 @@
</p>
</li>
<li><p>
+ <strong><a name="new_trial">new_trial</a></strong>
+ <i>[int type=1]</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
<strong><a name="rate_kill">rate_kill</a></strong>
<i><double probability></i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
- <strong><a name="replicate_demes">replicate_demes</a></strong>
+ <strong><a name="ReplicateDemes">ReplicateDemes</a></strong>
<i>[string trigger=full_deme]</i>
</p>
<p>
@@ -1202,11 +1244,12 @@
</p>
</li>
<li><p>
- <strong><a name="ReplicateDemes">ReplicateDemes</a></strong>
+ <strong><a name="replicate_demes">replicate_demes</a></strong>
<i>[string trigger=full_deme]</i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
@@ -1214,7 +1257,8 @@
<i>No Arguments</i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
@@ -1226,21 +1270,22 @@
</p>
</li>
<li><p>
- <strong><a name="serial_transfer">serial_transfer</a></strong>
+ <strong><a name="SerialTransfer">SerialTransfer</a></strong>
<i>[int transfer_size=1] [int ignore_deads=1]</i>
</p>
<p>
-
+ Similar to KillProb, but we specify the exact number of organisms to
+ keep alive after the event. The <span class="cmdarg">ignore_deads</span>
+ argument determines whether only living organisms are retainted.
+
</p>
</li>
<li><p>
- <strong><a name="SerialTransfer">SerialTransfer</a></strong>
+ <strong><a name="serial_transfer">serial_transfer</a></strong>
<i>[int transfer_size=1] [int ignore_deads=1]</i>
</p>
<p>
- Similar to KillProb, but we specify the exact number of organisms to
- keep alive after the event. The <span class="cmdarg">ignore_deads</span>
- argument determines whether only living organisms are retainted.
+ <font color="red">DEPRECATED</font>
</p>
</li>
@@ -1257,7 +1302,8 @@
<i>[int col_id=-1] [int min_row=0] [int max_row=-1]</i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
@@ -1265,7 +1311,8 @@
<i>[int row_id=-1] [int min_col=0] [int max_col=-1]</i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
@@ -1291,7 +1338,8 @@
<i><int cell_id1> <int cell_id2></i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
@@ -1323,7 +1371,8 @@
<i>No Arguments</i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
@@ -1347,7 +1396,7 @@
</p>
<UL>
<li><p>
- <strong><a name="dump_donor_grid">dump_donor_grid</a></strong>
+ <strong><a name="DumpCellDataGrid">DumpCellDataGrid</a></strong>
<i>[string fname=""]</i>
</p>
<p>
@@ -1355,7 +1404,7 @@
</p>
</li>
<li><p>
- <strong><a name="dump_fitness_grid">dump_fitness_grid</a></strong>
+ <strong><a name="dump_donor_grid">dump_donor_grid</a></strong>
<i>[string fname=""]</i>
</p>
<p>
@@ -1363,15 +1412,16 @@
</p>
</li>
<li><p>
- <strong><a name="dump_genotype_grid">dump_genotype_grid</a></strong>
+ <strong><a name="DumpDonorGrid">DumpDonorGrid</a></strong>
<i>[string fname=""]</i>
</p>
<p>
-
+ Print out the grid of organisms who donated their merit.
+
</p>
</li>
<li><p>
- <strong><a name="dump_lineage_grid">dump_lineage_grid</a></strong>
+ <strong><a name="DumpEnergyGrid">DumpEnergyGrid</a></strong>
<i>[string fname=""]</i>
</p>
<p>
@@ -1379,7 +1429,7 @@
</p>
</li>
<li><p>
- <strong><a name="dump_memory">dump_memory</a></strong>
+ <strong><a name="DumpExecutionRatioGrid">DumpExecutionRatioGrid</a></strong>
<i>[string fname=""]</i>
</p>
<p>
@@ -1387,7 +1437,7 @@
</p>
</li>
<li><p>
- <strong><a name="dump_phenotype_grid">dump_phenotype_grid</a></strong>
+ <strong><a name="dump_fitness_grid">dump_fitness_grid</a></strong>
<i>[string fname=""]</i>
</p>
<p>
@@ -1395,15 +1445,16 @@
</p>
</li>
<li><p>
- <strong><a name="dump_receiver_grid">dump_receiver_grid</a></strong>
+ <strong><a name="DumpFitnessGrid">DumpFitnessGrid</a></strong>
<i>[string fname=""]</i>
</p>
<p>
-
+ Print out the grid of organism fitness values.
+
</p>
</li>
<li><p>
- <strong><a name="dump_task_grid">dump_task_grid</a></strong>
+ <strong><a name="dump_genotype_grid">dump_genotype_grid</a></strong>
<i>[string fname=""]</i>
</p>
<p>
@@ -1411,24 +1462,24 @@
</p>
</li>
<li><p>
- <strong><a name="DumpCellDataGrid">DumpCellDataGrid</a></strong>
+ <strong><a name="DumpGenotypeIDGrid">DumpGenotypeIDGrid</a></strong>
<i>[string fname=""]</i>
</p>
<p>
-
+ Print out the grid of genotype IDs.
+
</p>
</li>
<li><p>
- <strong><a name="DumpDonorGrid">DumpDonorGrid</a></strong>
+ <strong><a name="dump_lineage_grid">dump_lineage_grid</a></strong>
<i>[string fname=""]</i>
</p>
<p>
- Print out the grid of organisms who donated their merit.
-
+
</p>
</li>
<li><p>
- <strong><a name="DumpEnergyGrid">DumpEnergyGrid</a></strong>
+ <strong><a name="DumpLineageGrid">DumpLineageGrid</a></strong>
<i>[string fname=""]</i>
</p>
<p>
@@ -1436,7 +1487,7 @@
</p>
</li>
<li><p>
- <strong><a name="DumpExecutionRatioGrid">DumpExecutionRatioGrid</a></strong>
+ <strong><a name="dump_memory">dump_memory</a></strong>
<i>[string fname=""]</i>
</p>
<p>
@@ -1444,25 +1495,24 @@
</p>
</li>
<li><p>
- <strong><a name="DumpFitnessGrid">DumpFitnessGrid</a></strong>
+ <strong><a name="DumpMemory">DumpMemory</a></strong>
<i>[string fname=""]</i>
</p>
<p>
- Print out the grid of organism fitness values.
+ Dump memory summary information.
</p>
</li>
<li><p>
- <strong><a name="DumpGenotypeIDGrid">DumpGenotypeIDGrid</a></strong>
+ <strong><a name="dump_phenotype_grid">dump_phenotype_grid</a></strong>
<i>[string fname=""]</i>
</p>
<p>
- Print out the grid of genotype IDs.
-
+
</p>
</li>
<li><p>
- <strong><a name="DumpLineageGrid">DumpLineageGrid</a></strong>
+ <strong><a name="DumpPhenotypeIDGrid">DumpPhenotypeIDGrid</a></strong>
<i>[string fname=""]</i>
</p>
<p>
@@ -1470,16 +1520,15 @@
</p>
</li>
<li><p>
- <strong><a name="DumpMemory">DumpMemory</a></strong>
+ <strong><a name="dump_receiver_grid">dump_receiver_grid</a></strong>
<i>[string fname=""]</i>
</p>
<p>
- Dump memory summary information.
-
+
</p>
</li>
<li><p>
- <strong><a name="DumpPhenotypeIDGrid">DumpPhenotypeIDGrid</a></strong>
+ <strong><a name="DumpReceiverGrid">DumpReceiverGrid</a></strong>
<i>[string fname=""]</i>
</p>
<p>
@@ -1487,7 +1536,7 @@
</p>
</li>
<li><p>
- <strong><a name="DumpReceiverGrid">DumpReceiverGrid</a></strong>
+ <strong><a name="DumpSleepGrid">DumpSleepGrid</a></strong>
<i>[string fname=""]</i>
</p>
<p>
@@ -1495,7 +1544,7 @@
</p>
</li>
<li><p>
- <strong><a name="DumpSleepGrid">DumpSleepGrid</a></strong>
+ <strong><a name="dump_task_grid">dump_task_grid</a></strong>
<i>[string fname=""]</i>
</p>
<p>
@@ -1527,7 +1576,8 @@
<i><cString message></i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
@@ -1540,267 +1590,16 @@
</li>
<li><p>
<strong><a name="print_average_data">print_average_data</a></strong>
+ <i>[string fname="average.dat"]</i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
- <strong><a name="print_count_data">print_count_data</a></strong>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_data">print_data</a></strong>
- <i><cString fname> <cString format></i>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_deme_stats">print_deme_stats</a></strong>
- <i>No Arguments</i>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_depth_histogram">print_depth_histogram</a></strong>
- <i>[string fname="depth_histogram.dat"]</i>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_detailed_fitness_data">print_detailed_fitness_data</a></strong>
- <i>[int save_max_f_genotype=0] [int print_fitness_histo=0] [double hist_fmax=1] [double hist_fstep=0.1] [string datafn="fitness.dat"] [string histofn="fitness_histos.dat"] [string histotestfn="fitness_histos_testCPU.dat"]</i>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_divide_mut_data">print_divide_mut_data</a></strong>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_dom">print_dom</a></strong>
- <i>[string fname=""]</i>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_dom_parasite">print_dom_parasite</a></strong>
- <i>[string fname=""]</i>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_dominant_data">print_dominant_data</a></strong>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_donation_stats">print_donation_stats</a></strong>
- <i>No Arguments</i>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_error_data">print_error_data</a></strong>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_genetic_distance_data">print_genetic_distance_data</a></strong>
- <i>[string ref_creature_file="START_CREATURE"] [string fname="genetic_distance.dat"]</i>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_genotype_abundance_histogram">print_genotype_abundance_histogram</a></strong>
- <i>[string fname="genotype_abundance_histogram.dat"]</i>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_genotype_map">print_genotype_map</a></strong>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_genotypes">print_genotypes</a></strong>
- <i>[string data_fields="all"] [int historic=0] [string fname=""]</i>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_instruction_abundance_histogram">print_instruction_abundance_histogram</a></strong>
- <i>[string fname="instruction_histogram.dat"]</i>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_instruction_data">print_instruction_data</a></strong>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_lineage_counts">print_lineage_counts</a></strong>
- <i>[string fname="lineage_counts.dat"] [int verbose=1]</i>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_lineage_totals">print_lineage_totals</a></strong>
- <i>[string fname="lineage_totals.dat"] [int verbose=1]</i>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_market_data">print_market_data</a></strong>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_mutation_rate_data">print_mutation_rate_data</a></strong>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_number_phenotypes">print_number_phenotypes</a></strong>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_phenotype_status">print_phenotype_status</a></strong>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_resource_data">print_resource_data</a></strong>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_species_abundance_histogram">print_species_abundance_histogram</a></strong>
- <i>[string fname="species_abundance_histogram.dat"]</i>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_stats_data">print_stats_data</a></strong>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_tasks_data">print_tasks_data</a></strong>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_tasks_exe_data">print_tasks_exe_data</a></strong>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_tasks_qual_data">print_tasks_qual_data</a></strong>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_time_data">print_time_data</a></strong>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_totals_data">print_totals_data</a></strong>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_tree_depths">print_tree_depths</a></strong>
- <i>[string fname=""]</i>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_variance_data">print_variance_data</a></strong>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
- <strong><a name="print_viable_tasks_data">print_viable_tasks_data</a></strong>
- <i>[string fname="viable_tasks.dat"]</i>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
<strong><a name="PrintAverageData">PrintAverageData</a></strong>
+ <i>[string fname="average.dat"]</i>
</p>
<p>
[<span class="cmdarg">string filename='average.dat'</span>]
@@ -1856,7 +1655,16 @@
</p>
</li>
<li><p>
+ <strong><a name="PrintCellVisitsData">PrintCellVisitsData</a></strong>
+ <i>[string fname="visits.dat "]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintCompetitionData">PrintCompetitionData</a></strong>
+ <i>[string fname="competition.dat"]</i>
</p>
<p>
Print out CompeteOrganism statistics. Make the first call after the first set of trials has been completed to get a complete header.
@@ -1864,7 +1672,17 @@
</p>
</li>
<li><p>
+ <strong><a name="print_count_data">print_count_data</a></strong>
+ <i>[string fname="count.dat"]</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintCountData">PrintCountData</a></strong>
+ <i>[string fname="count.dat"]</i>
</p>
<p>
Print all of the statistics the keep track of counts (such as the number of organisms
@@ -1874,12 +1692,22 @@
</li>
<li><p>
<strong><a name="PrintCurrentReactionData">PrintCurrentReactionData</a></strong>
+ <i>[string fname="cur_reactions.dat"]</i>
</p>
<p>
</p>
</li>
<li><p>
+ <strong><a name="print_data">print_data</a></strong>
+ <i><cString fname> <cString format></i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintData">PrintData</a></strong>
<i><cString fname> <cString format></i>
</p>
@@ -1903,6 +1731,15 @@
</p>
</li>
<li><p>
+ <strong><a name="print_deme_stats">print_deme_stats</a></strong>
+ <i>No Arguments</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintDemeAllStats">PrintDemeAllStats</a></strong>
<i>No Arguments</i>
</p>
@@ -1912,6 +1749,7 @@
</li>
<li><p>
<strong><a name="PrintDemeAverageData">PrintDemeAverageData</a></strong>
+ <i>[string fname="deme_average.dat"]</i>
</p>
<p>
@@ -1927,6 +1765,7 @@
</li>
<li><p>
<strong><a name="PrintDemeReplicationData">PrintDemeReplicationData</a></strong>
+ <i>[string fname="deme_repl.dat"]</i>
</p>
<p>
@@ -1965,6 +1804,15 @@
</p>
</li>
<li><p>
+ <strong><a name="print_depth_histogram">print_depth_histogram</a></strong>
+ <i>[string fname="depth_histogram.dat"]</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintDepthHistogram">PrintDepthHistogram</a></strong>
<i>[string fname="depth_histogram.dat"]</i>
</p>
@@ -1973,6 +1821,14 @@
</p>
</li>
<li><p>
+ <strong><a name="print_detailed_fitness_data">print_detailed_fitness_data</a></strong>
+ <i>[int save_max_f_genotype=0] [int print_fitness_histo=0] [double hist_fmax=1] [double hist_fstep=0.1] [string datafn="fitness.dat"] [string histofn="fitness_histos.dat"] [string histotestfn="fitness_histos_testCPU.dat"]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintDetailedFitnessData">PrintDetailedFitnessData</a></strong>
<i>[int save_max_f_genotype=0] [int print_fitness_histo=0] [double hist_fmax=1] [double hist_fstep=0.1] [string datafn="fitness.dat"] [string histofn="fitness_histos.dat"] [string histotestfn="fitness_histos_testCPU.dat"]</i>
</p>
@@ -1981,7 +1837,17 @@
</p>
</li>
<li><p>
+ <strong><a name="print_divide_mut_data">print_divide_mut_data</a></strong>
+ <i>[string fname="divide_mut.dat"]</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintDivideMutData">PrintDivideMutData</a></strong>
+ <i>[string fname="divide_mut.dat"]</i>
</p>
<p>
Output (regular and log) statistics about individual, per site, rates divide mutation
@@ -1990,7 +1856,33 @@
</p>
</li>
<li><p>
+ <strong><a name="print_dom">print_dom</a></strong>
+ <i>[string fname=""]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="print_dom_parasite">print_dom_parasite</a></strong>
+ <i>[string fname=""]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="print_dominant_data">print_dominant_data</a></strong>
+ <i>[string fname="dominant.dat"]</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintDominantData">PrintDominantData</a></strong>
+ <i>[string fname="dominant.dat"]</i>
</p>
<p>
Print all of the statistics relating to the dominant genotype.
@@ -2020,7 +1912,26 @@
</p>
</li>
<li><p>
+ <strong><a name="print_donation_stats">print_donation_stats</a></strong>
+ <i>No Arguments</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="print_error_data">print_error_data</a></strong>
+ <i>[string fname="error.dat"]</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintErrorData">PrintErrorData</a></strong>
+ <i>[string fname="error.dat"]</i>
</p>
<p>
Print all of the standard errors of the average population statistics.
@@ -2028,6 +1939,14 @@
</p>
</li>
<li><p>
+ <strong><a name="print_genetic_distance_data">print_genetic_distance_data</a></strong>
+ <i>[string ref_creature_file="START_CREATURE"] [string fname="genetic_distance.dat"]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintGeneticDistanceData">PrintGeneticDistanceData</a></strong>
<i>[string ref_creature_file="START_CREATURE"] [string fname="genetic_distance.dat"]</i>
</p>
@@ -2051,6 +1970,24 @@
</p>
</li>
<li><p>
+ <strong><a name="print_genotype_abundance_histogram">print_genotype_abundance_histogram</a></strong>
+ <i>[string fname="genotype_abundance_histogram.dat"]</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="print_genotype_map">print_genotype_map</a></strong>
+ <i>[string fname="genotype_map.m"]</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintGenotypeAbundanceHistogram">PrintGenotypeAbundanceHistogram</a></strong>
<i>[string fname="genotype_abundance_histogram.dat"]</i>
</p>
@@ -2061,6 +1998,7 @@
</li>
<li><p>
<strong><a name="PrintGenotypeMap">PrintGenotypeMap</a></strong>
+ <i>[string fname="genotype_map.m"]</i>
</p>
<p>
This event is used to output a map of the genotype IDs for the
@@ -2069,6 +2007,14 @@
</p>
</li>
<li><p>
+ <strong><a name="print_genotypes">print_genotypes</a></strong>
+ <i>[string data_fields="all"] [int historic=0] [string fname=""]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintGenotypes">PrintGenotypes</a></strong>
<i>[string data_fields="all"] [int historic=0] [string fname=""]</i>
</p>
@@ -2107,12 +2053,31 @@
</li>
<li><p>
<strong><a name="PrintGermlineData">PrintGermlineData</a></strong>
+ <i>[string fname="germline.dat"]</i>
</p>
<p>
</p>
</li>
<li><p>
+ <strong><a name="print_instruction_abundance_histogram">print_instruction_abundance_histogram</a></strong>
+ <i>[string fname="instruction_histogram.dat"]</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="print_instruction_data">print_instruction_data</a></strong>
+ <i>[string fname="instruction.dat"]</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintInstructionAbundanceHistogram">PrintInstructionAbundanceHistogram</a></strong>
<i>[string fname="instruction_histogram.dat"]</i>
</p>
@@ -2124,6 +2089,7 @@
</li>
<li><p>
<strong><a name="PrintInstructionData">PrintInstructionData</a></strong>
+ <i>[string fname="instruction.dat"]</i>
</p>
<p>
Print the by-organisms counts of what instructions they _successfully_ executed
@@ -2132,6 +2098,23 @@
</p>
</li>
<li><p>
+ <strong><a name="print_lineage_counts">print_lineage_counts</a></strong>
+ <i>[string fname="lineage_counts.dat"] [int verbose=1]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="print_lineage_totals">print_lineage_totals</a></strong>
+ <i>[string fname="lineage_totals.dat"] [int verbose=1]</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintLineageCounts">PrintLineageCounts</a></strong>
<i>[string fname="lineage_counts.dat"] [int verbose=1]</i>
</p>
@@ -2165,14 +2148,34 @@
</p>
</li>
<li><p>
+ <strong><a name="print_market_data">print_market_data</a></strong>
+ <i>[string fname="market.dat"]</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintMarketData">PrintMarketData</a></strong>
+ <i>[string fname="market.dat"]</i>
</p>
<p>
</p>
</li>
<li><p>
+ <strong><a name="print_mutation_rate_data">print_mutation_rate_data</a></strong>
+ <i>[string fname="mutation_rates.dat"]</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintMutationRateData">PrintMutationRateData</a></strong>
+ <i>[string fname="mutation_rates.dat"]</i>
</p>
<p>
Output (regular and log) statistics about individual copy mutation rates
@@ -2181,14 +2184,34 @@
</p>
</li>
<li><p>
+ <strong><a name="print_number_phenotypes">print_number_phenotypes</a></strong>
+ <i>[string fname="phenotype_count.dat"]</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintParasiteData">PrintParasiteData</a></strong>
+ <i>[string fname="parasite.dat"]</i>
</p>
<p>
</p>
</li>
<li><p>
+ <strong><a name="print_phenotype_status">print_phenotype_status</a></strong>
+ <i>[string fname="phenotype_status.dat"]</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintPhenotypeData">PrintPhenotypeData</a></strong>
+ <i>[string fname="phenotype_count.dat"]</i>
</p>
<p>
[<span class="cmdarg">string filename='phenotype_count.dat'</span>]
@@ -2199,6 +2222,7 @@
</li>
<li><p>
<strong><a name="PrintPhenotypeStatus">PrintPhenotypeStatus</a></strong>
+ <i>[string fname="phenotype_status.dat"]</i>
</p>
<p>
@@ -2229,6 +2253,7 @@
</li>
<li><p>
<strong><a name="PrintReactionData">PrintReactionData</a></strong>
+ <i>[string fname="reactions.dat"]</i>
</p>
<p>
@@ -2236,6 +2261,7 @@
</li>
<li><p>
<strong><a name="PrintReactionRewardData">PrintReactionRewardData</a></strong>
+ <i>[string fname="reaction_reward.dat"]</i>
</p>
<p>
@@ -2259,7 +2285,17 @@
</p>
</li>
<li><p>
+ <strong><a name="print_resource_data">print_resource_data</a></strong>
+ <i>[string fname="resource.dat"]</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintResourceData">PrintResourceData</a></strong>
+ <i>[string fname="resource.dat"]</i>
</p>
<p>
Print the current counts of each resource available to the population. This uses
@@ -2271,6 +2307,7 @@
</li>
<li><p>
<strong><a name="PrintSenseData">PrintSenseData</a></strong>
+ <i>[string fname="sense.dat"]</i>
</p>
<p>
@@ -2278,6 +2315,7 @@
</li>
<li><p>
<strong><a name="PrintSenseExeData">PrintSenseExeData</a></strong>
+ <i>[string fname="sense_exe.dat"]</i>
</p>
<p>
@@ -2285,12 +2323,22 @@
</li>
<li><p>
<strong><a name="PrintSleepData">PrintSleepData</a></strong>
+ <i>[string fname="sleep.dat"]</i>
</p>
<p>
</p>
</li>
<li><p>
+ <strong><a name="print_species_abundance_histogram">print_species_abundance_histogram</a></strong>
+ <i>[string fname="species_abundance_histogram.dat"]</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintSpeciesAbundanceHistogram">PrintSpeciesAbundanceHistogram</a></strong>
<i>[string fname="species_abundance_histogram.dat"]</i>
</p>
@@ -2300,7 +2348,17 @@
</p>
</li>
<li><p>
+ <strong><a name="print_stats_data">print_stats_data</a></strong>
+ <i>[string fname="stats.dat"]</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintStatsData">PrintStatsData</a></strong>
+ <i>[string fname="stats.dat"]</i>
</p>
<p>
Print all of the miscellanous population statistics.
@@ -2308,7 +2366,35 @@
</p>
</li>
<li><p>
+ <strong><a name="print_tasks_data">print_tasks_data</a></strong>
+ <i>[string fname="tasks.dat"]</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="print_tasks_exe_data">print_tasks_exe_data</a></strong>
+ <i>[string fname="tasks_exe.dat"]</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="print_tasks_qual_data">print_tasks_qual_data</a></strong>
+ <i>[string fname="tasks_quality.dat"]</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintTasksData">PrintTasksData</a></strong>
+ <i>[string fname="tasks.dat"]</i>
</p>
<p>
Print the number of organisms that are able to perform each task. This uses the
@@ -2318,6 +2404,7 @@
</li>
<li><p>
<strong><a name="PrintTasksExeData">PrintTasksExeData</a></strong>
+ <i>[string fname="tasks_exe.dat"]</i>
</p>
<p>
Print number of times the particular task has been executed this update.
@@ -2336,6 +2423,7 @@
</li>
<li><p>
<strong><a name="PrintTasksQualData">PrintTasksQualData</a></strong>
+ <i>[string fname="tasks_quality.dat"]</i>
</p>
<p>
Print the total quality of each task. By default a successful task is valued
@@ -2345,7 +2433,17 @@
</p>
</li>
<li><p>
+ <strong><a name="print_time_data">print_time_data</a></strong>
+ <i>[string fname="time.dat"]</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintTimeData">PrintTimeData</a></strong>
+ <i>[string fname="time.dat"]</i>
</p>
<p>
Print all of the timing related statistics.
@@ -2353,7 +2451,17 @@
</p>
</li>
<li><p>
+ <strong><a name="print_totals_data">print_totals_data</a></strong>
+ <i>[string fname="totals.dat"]</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintTotalsData">PrintTotalsData</a></strong>
+ <i>[string fname="totals.dat"]</i>
</p>
<p>
Print various totals for the entire length of the run (for example, the total number of
@@ -2362,6 +2470,14 @@
</p>
</li>
<li><p>
+ <strong><a name="print_tree_depths">print_tree_depths</a></strong>
+ <i>[string fname=""]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintTreeDepths">PrintTreeDepths</a></strong>
<i>[string fname=""]</i>
</p>
@@ -2371,7 +2487,17 @@
</p>
</li>
<li><p>
+ <strong><a name="print_variance_data">print_variance_data</a></strong>
+ <i>[string fname="variance.dat"]</i>
+ </p>
+ <p>
+ <font color="red">DEPRECATED</font>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintVarianceData">PrintVarianceData</a></strong>
+ <i>[string fname="variance.dat"]</i>
</p>
<p>
Print all of the variances of the average population statistics.
@@ -2379,6 +2505,14 @@
</p>
</li>
<li><p>
+ <strong><a name="print_viable_tasks_data">print_viable_tasks_data</a></strong>
+ <i>[string fname="viable_tasks.dat"]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintViableTasksData">PrintViableTasksData</a></strong>
<i>[string fname="viable_tasks.dat"]</i>
</p>
@@ -2444,7 +2578,8 @@
<i>[string fname=""]</i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
@@ -2452,7 +2587,8 @@
<i>[string fname=""]</i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
@@ -2460,7 +2596,8 @@
<i>[string fname=""]</i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
@@ -2468,7 +2605,8 @@
<i>[int back_dist=-1] [string fname=""]</i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
@@ -2476,7 +2614,8 @@
<i>[string fname=""]</i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
@@ -2484,7 +2623,8 @@
<i>[string fname=""]</i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
@@ -2496,7 +2636,7 @@
</p>
</li>
<li><p>
- <strong><a name="load_clone">load_clone</a></strong>
+ <strong><a name="LoadClone">LoadClone</a></strong>
<i><cString fname></i>
</p>
<p>
@@ -2504,19 +2644,21 @@
</p>
</li>
<li><p>
- <strong><a name="load_dump_file">load_dump_file</a></strong>
- <i><cString fname> [int update=-1]</i>
+ <strong><a name="load_clone">load_clone</a></strong>
+ <i><cString fname></i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
- <strong><a name="LoadClone">LoadClone</a></strong>
- <i><cString fname></i>
+ <strong><a name="load_dump_file">load_dump_file</a></strong>
+ <i><cString fname> [int update=-1]</i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
@@ -2535,7 +2677,8 @@
<i>[string fname=""]</i>
</p>
<p>
-
+ <font color="red">DEPRECATED</font>
+
</p>
</li>
<li><p>
Modified: development/source/actions/EnvironmentActions.cc
===================================================================
--- development/source/actions/EnvironmentActions.cc 2008-03-04 12:53:54 UTC (rev 2419)
+++ development/source/actions/EnvironmentActions.cc 2008-03-04 17:29:48 UTC (rev 2420)
@@ -17,8 +17,8 @@
* 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, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+ * along with this program; if not, write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*
*/
@@ -127,6 +127,7 @@
}
};
+/* Change the amount of a particular global resource */
class cActionSetResource : public cAction
{
@@ -173,6 +174,8 @@
}
};
+/* Change the amount of a particular resource in a particular cells */
+
class cActionSetCellResource : public cAction
{
private:
@@ -217,6 +220,29 @@
};
+/* Change Environment settings */
+
+class cActionChangeEnvironment : public cAction
+{
+private:
+ cString env_string;
+
+public:
+ cActionChangeEnvironment(cWorld* world, const cString& args) : cAction(world, args), env_string("")
+ {
+ cString largs(args);
+ if (largs.GetSize()) env_string = largs;
+ }
+
+ static const cString GetDescription() { return "Arguments: <string env_string>"; }
+
+ void Process(cAvidaContext& ctx)
+ {
+ m_world->GetEnvironment().LoadLine(env_string);
+ m_world->GetPopulation().UpdateResourceCount(m_world->GetVerbosity());
+ }
+};
+
// Set the values associated with a specified reaction. If the name of the
// reaction used is "ALL" then all reactions will be changed. If the name is
// "RANDOM:3" then random reactions will be set to the specified value. The
@@ -739,7 +765,8 @@
action_lib->Register<cActionOutflowScaledResource>("OutflowScaledResource");
action_lib->Register<cActionSetResource>("SetResource");
action_lib->Register<cZeroResources>("ZeroResources");
- action_lib->Register<cActionSetCellResource>("SetCellResource");
+ action_lib->Register<cActionSetCellResource>("SetCellResource");
+ action_lib->Register<cActionChangeEnvironment>("ChangeEnvironment");
action_lib->Register<cActionSetReactionValue>("SetReactionValue");
action_lib->Register<cActionSetReactionValueMult>("SetReactionValueMult");
Modified: development/source/main/cEnvironment.cc
===================================================================
--- development/source/main/cEnvironment.cc 2008-03-04 12:53:54 UTC (rev 2419)
+++ development/source/main/cEnvironment.cc 2008-03-04 17:29:48 UTC (rev 2420)
@@ -557,8 +557,8 @@
// Make sure this reaction hasn't already been loaded with a different
// definition.
if (new_reaction->GetTask() != NULL) {
- cerr << "Error: Re-defining reaction '" << name << "'." << endl;
- return false;
+ cerr << "Warning: Re-defining reaction '" << name << "'." << endl;
+ // return false;
}
// Finish loading in this reaction.
Modified: development/source/main/cPopulation.cc
===================================================================
--- development/source/main/cPopulation.cc 2008-03-04 12:53:54 UTC (rev 2419)
+++ development/source/main/cPopulation.cc 2008-03-04 17:29:48 UTC (rev 2420)
@@ -3853,3 +3853,55 @@
NewTrial();
}
+
+/* This routine is designed to change values in the resource count in the
+ middle of a run. This is designed to work with cActionChangeEnvironment
+ routine BDB 22-Feb-2008 */
+
+void cPopulation::UpdateResourceCount(const int Verbosity) {
+ const cResourceLib & resource_lib = environment.GetResourceLib();
+ int global_res_index = -1;
+ int deme_res_index = -1;
+ int num_deme_res = 0;
+
+ //setting size of global and deme-level resources
+ for(int i = 0; i < resource_lib.GetSize(); i++) {
+ cResource * res = resource_lib.GetResource(i);
+ if(res->GetDemeResource())
+ num_deme_res++;
+ }
+
+ for(int i = 0; i < GetNumDemes(); i++) {
+ cResourceCount tmp_deme_res_count(num_deme_res);
+ GetDeme(i).SetDemeResourceCount(tmp_deme_res_count);
+ }
+
+ for (int i = 0; i < resource_lib.GetSize(); i++) {
+ cResource * res = resource_lib.GetResource(i);
+ if (!res->GetDemeResource()) {
+ global_res_index++;
+ const double decay = 1.0 - res->GetOutflow();
+ resource_count.Setup(global_res_index, res->GetName(), res->GetInitial(),
+ res->GetInflow(), decay,
+ res->GetGeometry(), res->GetXDiffuse(),
+ res->GetXGravity(), res->GetYDiffuse(),
+ res->GetYGravity(), res->GetInflowX1(),
+ res->GetInflowX2(), res->GetInflowY1(),
+ res->GetInflowY2(), res->GetOutflowX1(),
+ res->GetOutflowX2(), res->GetOutflowY1(),
+ res->GetOutflowY2(), res->GetCellListPtr(),
+ Verbosity);
+ m_world->GetStats().SetResourceName(global_res_index, res->GetName());
+ } else if(res->GetDemeResource()) {
+ deme_res_index++;
+ for(int j = 0; j < GetNumDemes(); j++) {
+ GetDeme(j).SetupDemeRes(deme_res_index, res, Verbosity);
+ // could add deme resources to global resource stats here
+ }
+ } else {
+ cerr<< "ERROR: Resource \"" << res->GetName() <<"\"is not a global or deme resource. Exit";
+ exit(1);
+ }
+ }
+
+}
Modified: development/source/main/cPopulation.h
===================================================================
--- development/source/main/cPopulation.h 2008-03-04 12:53:54 UTC (rev 2419)
+++ development/source/main/cPopulation.h 2008-03-04 17:29:48 UTC (rev 2420)
@@ -294,6 +294,9 @@
// Trials and genetic algorithm @JEB
void NewTrial();
void CompeteOrganisms(int competition_type, int parents_survive);
+
+ // Let users change environmental variables durning the run @BDB 22-Feb-2008
+ void UpdateResourceCount(const int Verbosity);
};
Modified: development/source/utils/make_actions_html/actions_source_info
===================================================================
--- development/source/utils/make_actions_html/actions_source_info 2008-03-04 12:53:54 UTC (rev 2419)
+++ development/source/utils/make_actions_html/actions_source_info 2008-03-04 17:29:48 UTC (rev 2420)
@@ -392,6 +392,154 @@
<span class="cmdarg">inst</span> must be in the instruction set.
=== Action ZeroResources ===
Set all resurce levels to zero.
+=== Action ChangeEnvironment ===
+ Action designed to read in and process a line formatted as if it were in the
+ <a href="environment.html">environment</a> file. This will change
+ environmental settings on the fly. <b>You should create all resources and
+ reactions in the environment file</b> and only use this file to change these
+ resources and reactions.
+=== Action inject_resource ===
+ <font color="red">DEPRECATED</font>
+=== Action inject_scaled_resource ===
+ <font color="red">DEPRECATED</font>
+=== Action outflow_scaled_resource ===
+ <font color="red">DEPRECATED</font>
+=== Action set_resource ===
+ <font color="red">DEPRECATED</font>
+=== Action set_reaction_value ===
+ <font color="red">DEPRECATED</font>
+=== Action set_reaction_value_mult ===
+ <font color="red">DEPRECATED</font>
+=== Action set_reaction_inst ===
+ <font color="red">DEPRECATED</font>
+=== Action exit ===
+ <font color="red">DEPRECATED</font>
+=== Action exit_if_ave_lineage_label_larger ===
+ <font color="red">DEPRECATED</font>
+=== Action exit_if_ave_lineage_label_smaller ===
+ <font color="red">DEPRECATED</font>
+=== Action inject ===
+ <font color="red">DEPRECATED</font>
+=== Action inject_random ===
+ <font color="red">DEPRECATED</font>
+=== Action inject_all_random_repro ===
+ <font color="red">DEPRECATED</font>
+=== Action inject_all ===
+ <font color="red">DEPRECATED</font>
+=== Action inject_range ===
+ <font color="red">DEPRECATED</font>
+=== Action inject_sequence ===
+ <font color="red">DEPRECATED</font>
+=== Action apocalypse ===
+ <font color="red">DEPRECATED</font>
+=== Action rate_kill ===
+ <font color="red">DEPRECATED</font>
+=== Action kill_rectangle ===
+ <font color="red">DEPRECATED</font>
+=== Action serial_transfer ===
+ <font color="red">DEPRECATED</font>
+=== Action zero_muts ===
+ <font color="red">DEPRECATED</font>
+=== Action compete_demes ===
+ <font color="red">DEPRECATED</font>
+=== Action replicate_demes ===
+ <font color="red">DEPRECATED</font>
+=== Action reset_demes ===
+ <font color="red">DEPRECATED</font>
+=== Action copy_deme ===
+ <font color="red">DEPRECATED</font>
+=== Action new_trial ===
+ <font color="red">DEPRECATED</font>
+=== Action compete_organisms ===
+ <font color="red">DEPRECATED</font>
+=== Action sever_grid_col ===
+ <font color="red">DEPRECATED</font>
+=== Action sever_grid_row ===
+ <font color="red">DEPRECATED</font>
+=== Action join_grid_col ===
+ <font color="red">DEPRECATED</font>
+=== Action join_grid_row ===
+ <font color="red">DEPRECATED</font>
+=== Action connect_cells ===
+ <font color="red">DEPRECATED</font>
+=== Action disconnect_cells ===
+ <font color="red">DEPRECATED</font>
+=== Action swap_cells ===
+ <font color="red">DEPRECATED</font>
+=== Action print_average_data ===
+ <font color="red">DEPRECATED</font>
+=== Action print_error_data ===
+ <font color="red">DEPRECATED</font>
+=== Action print_variance_data ===
+ <font color="red">DEPRECATED</font>
+=== Action print_dominant_data ===
+ <font color="red">DEPRECATED</font>
+=== Action print_stats_data ===
+ <font color="red">DEPRECATED</font>
+=== Action print_count_data ===
+ <font color="red">DEPRECATED</font>
+=== Action print_totals_data ===
+ <font color="red">DEPRECATED</font>
+=== Action print_tasks_data ===
+ <font color="red">DEPRECATED</font>
+=== Action print_tasks_exe_data ===
+ <font color="red">DEPRECATED</font>
+=== Action print_tasks_qual_data ===
+ <font color="red">DEPRECATED</font>
+=== Action print_resource_data ===
+ <font color="red">DEPRECATED</font>
+=== Action print_time_data ===
+ <font color="red">DEPRECATED</font>
+=== Action print_mutation_rate_data ===
+ <font color="red">DEPRECATED</font>
+=== Action print_divide_mut_data ===
+ <font color="red">DEPRECATED</font>
+=== Action print_instruction_data ===
+ <font color="red">DEPRECATED</font>
+=== Action print_genotype_map ===
+ <font color="red">DEPRECATED</font>
+=== Action print_market_data ===
+ <font color="red">DEPRECATED</font>
+=== Action print_number_phenotypes ===
+ <font color="red">DEPRECATED</font>
+=== Action print_phenotype_status ===
+ <font color="red">DEPRECATED</font>
+=== Action print_donation_stats ===
+ <font color="red">DEPRECATED</font>
+=== Action print_deme_stats ===
+ <font color="red">DEPRECATED</font>
+=== Action print_data ===
+ <font color="red">DEPRECATED</font>
+=== Action print_instruction_abundance_histogram ===
+ <font color="red">DEPRECATED</font>
+=== Action print_depth_histogram ===
+ <font color="red">DEPRECATED</font>
+=== Action echo ===
+ <font color="red">DEPRECATED</font>
+=== Action print_genotype_abundance_histogram ===
+ <font color="red">DEPRECATED</font>
+=== Action print_species_abundance_histogram ===
+ <font color="red">DEPRECATED</font>
+=== Action print_lineage_totals ===
+ <font color="red">DEPRECATED</font>
+=== Action save_clone ===
+ <font color="red">DEPRECATED</font>
+=== Action load_clone ===
+ <font color="red">DEPRECATED</font>
+=== Action load_dump_file ===
+ <font color="red">DEPRECATED</font>
+=== Action dump_pop ===
+ <font color="red">DEPRECATED</font>
+=== Action detail_pop ===
+ <font color="red">DEPRECATED</font>
+=== Action detail_sex_pop ===
+ <font color="red">DEPRECATED</font>
+=== Action detail_parasite_pop ===
+ <font color="red">DEPRECATED</font>
+=== Action dump_historic_pop ===
+ <font color="red">DEPRECATED</font>
+=== Action dump_historic_sex_pop ===
+ <font color="red">DEPRECATED</font>
=== head ===
<html>
<!-- This HTML was generated by the make_actions_html routine please modify --->
Modified: development/source/utils/make_actions_html/make_actions_html.pl
===================================================================
--- development/source/utils/make_actions_html/make_actions_html.pl 2008-03-04 12:53:54 UTC (rev 2419)
+++ development/source/utils/make_actions_html/make_actions_html.pl 2008-03-04 17:29:48 UTC (rev 2420)
@@ -1,4 +1,16 @@
#!/usr/bin/perl
+
+#########################################################################
+#
+# Script to create the ../../../documentation/actions.html file based on
+# routines in the *Action.cc files in the ../../actions/ and information
+# in the actions_source_info file in the current directory
+#
+# Created by B.D.Baer 20-February-2007
+# Copyright 2008 Michigan State University. All rights reserved.
+#
+#########################################################################
+
use strict;
use Time::Local;
@@ -209,8 +221,10 @@
close (TEMPLATE);
}
-# Create sort that ignores case
+# Create sort that ignores case and underscores
sub sort_ic {
- lc($a) cmp lc($b);
+ my $c = $a; my $d = $b;
+ $c =~ s/_//; $d =~ s/_//;
+ lc($c) cmp lc($d);
}
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