[Avida-SVN] r3137 - in development: documentation source/utils/make_actions_html
baerb at myxo.css.msu.edu
baerb at myxo.css.msu.edu
Wed Jan 28 12:33:34 PST 2009
Author: baerb
Date: 2009-01-28 15:33:34 -0500 (Wed, 28 Jan 2009)
New Revision: 3137
Modified:
development/documentation/actions.html
development/source/utils/make_actions_html/actions_source_info
Log:
Added documentation for a couple of Actions
Mainly wanted to triger an event on the buildbot system
Modified: development/documentation/actions.html
===================================================================
--- development/documentation/actions.html 2009-01-26 21:21:15 UTC (rev 3136)
+++ development/documentation/actions.html 2009-01-28 20:33:34 UTC (rev 3137)
@@ -9,7 +9,7 @@
<div class="revision">
Revised 2006-09-03 DMB
-<br>Generated Tue May 27 15:04:24 2008 by make_actions_html</div>
+<br>Generated Wed Jan 28 15:34:10 2009 by make_actions_html</div>
<p>
<a href="index.html">Return to the Index</a> |
@@ -59,17 +59,25 @@
<a href="#AnalyzeLandscape">AnalyzeLandscape</a><br>
<a href="#AnalyzePopulation">AnalyzePopulation</a><br>
<a href="#apocalypse">apocalypse</a><br>
+ <a href="#AssignRandomCellData">AssignRandomCellData</a><br>
<a href="#ChangeEnvironment">ChangeEnvironment</a><br>
<a href="#compete_demes">compete_demes</a><br>
<a href="#CompeteDemes">CompeteDemes</a><br>
+ <a href="#CompeteDemes_AttackKillAndEnergyConserve">CompeteDemes_AttackKillAndEnergyConserve</a><br>
+ <a href="#CompeteDemesByEnergyDistribution">CompeteDemesByEnergyDistribution</a><br>
+ <a href="#CompeteDemesByTaskCount">CompeteDemesByTaskCount</a><br>
+ <a href="#CompeteDemesByTaskCountAndEfficiency">CompeteDemesByTaskCountAndEfficiency</a><br>
<a href="#CompeteOrganisms">CompeteOrganisms</a><br>
<a href="#compete_organisms">compete_organisms</a><br>
<a href="#connect_cells">connect_cells</a><br>
<a href="#ConnectCells">ConnectCells</a><br>
<a href="#copy_deme">copy_deme</a><br>
<a href="#CopyDeme">CopyDeme</a><br>
+ <a href="#DecayPoints">DecayPoints</a><br>
<a href="#DelayedDemeEvent">DelayedDemeEvent</a><br>
+ <a href="#DelayedDemeEventsPerSlots">DelayedDemeEventsPerSlots</a><br>
<a href="#DeletionLandscape">DeletionLandscape</a><br>
+ <a href="#Desynchronization">Desynchronization</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>
@@ -110,6 +118,7 @@
<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="#Flash">Flash</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>
@@ -120,6 +129,8 @@
<a href="#inject_all_random_repro">inject_all_random_repro</a><br>
<a href="#InjectAllRandomRepro">InjectAllRandomRepro</a><br>
<a href="#InjectDemes">InjectDemes</a><br>
+ <a href="#InjectDemesFromNest">InjectDemesFromNest</a><br>
+ <a href="#InjectDemesRandom">InjectDemesRandom</a><br>
<a href="#InjectParasite">InjectParasite</a><br>
<a href="#InjectParasitePair">InjectParasitePair</a><br>
<a href="#InjectRandom">InjectRandom</a><br>
@@ -134,6 +145,7 @@
<a href="#InjectSequence">InjectSequence</a><br>
<a href="#InjectSequenceWDivMutRate">InjectSequenceWDivMutRate</a><br>
<a href="#InsertionLandscape">InsertionLandscape</a><br>
+ <a href="#IteratedConsensus">IteratedConsensus</a><br>
<a href="#join_grid_col">join_grid_col</a><br>
<a href="#join_grid_row">join_grid_row</a><br>
<a href="#JoinGridCol">JoinGridCol</a><br>
@@ -144,9 +156,9 @@
<a href="#kill_rectangle">kill_rectangle</a><br>
<a href="#LoadClone">LoadClone</a><br>
<a href="#load_clone">load_clone</a><br>
- <td valign="top">
<a href="#load_dump_file">load_dump_file</a><br>
<a href="#LoadPopulation">LoadPopulation</a><br>
+ <td valign="top">
<a href="#ModMutProb">ModMutProb</a><br>
<a href="#MutationalNeighborhood">MutationalNeighborhood</a><br>
<a href="#new_trial">new_trial</a><br>
@@ -155,6 +167,9 @@
<a href="#OutflowScaledResource">OutflowScaledResource</a><br>
<a href="#PairTestLandscape">PairTestLandscape</a><br>
<a href="#PrecalcLandscape">PrecalcLandscape</a><br>
+ <a href="#Pred_DemeEventMoveBetweenTargets">Pred_DemeEventMoveBetweenTargets</a><br>
+ <a href="#Pred_DemeEventMoveCenter">Pred_DemeEventMoveCenter</a><br>
+ <a href="#Pred_DemeEventNUniqueIndividualsMovedIntoTarget">Pred_DemeEventNUniqueIndividualsMovedIntoTarget</a><br>
<a href="#PredictNuLandscape">PredictNuLandscape</a><br>
<a href="#PredictWLandscape">PredictWLandscape</a><br>
<a href="#print_average_data">print_average_data</a><br>
@@ -162,19 +177,27 @@
<a href="#PrintCCladeCounts">PrintCCladeCounts</a><br>
<a href="#PrintCCladeFitnessHistogram">PrintCCladeFitnessHistogram</a><br>
<a href="#PrintCCladeRelativeFitnessHistogram">PrintCCladeRelativeFitnessHistogram</a><br>
+ <a href="#PrintCellData">PrintCellData</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="#PrintCurrentOpinions">PrintCurrentOpinions</a><br>
<a href="#PrintCurrentReactionData">PrintCurrentReactionData</a><br>
+ <a href="#PrintCurrentReactionRewardData">PrintCurrentReactionRewardData</a><br>
+ <a href="#PrintCurrentTaskCounts">PrintCurrentTaskCounts</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="#PrintDemeCompetitionData">PrintDemeCompetitionData</a><br>
+ <a href="#PrintDemeCurrentTaskExeData">PrintDemeCurrentTaskExeData</a><br>
<a href="#PrintDemeDonorStats">PrintDemeDonorStats</a><br>
+ <a href="#PrintDemeEnergySharingStats">PrintDemeEnergySharingStats</a><br>
<a href="#PrintDemeFoundersData">PrintDemeFoundersData</a><br>
+ <a href="#PrintDemeMigrationSuicidePoints">PrintDemeMigrationSuicidePoints</a><br>
<a href="#PrintDemeOrgReactionData">PrintDemeOrgReactionData</a><br>
<a href="#PrintDemeOrgTasksData">PrintDemeOrgTasksData</a><br>
<a href="#PrintDemeOrgTasksExeData">PrintDemeOrgTasksExeData</a><br>
@@ -184,12 +207,15 @@
<a href="#PrintDemeSpacialEnergyStats">PrintDemeSpacialEnergyStats</a><br>
<a href="#PrintDemeSpacialSleepStats">PrintDemeSpacialSleepStats</a><br>
<a href="#PrintDemeStats">PrintDemeStats</a><br>
+ <a href="#PrintDemesTotalAvgEnergy">PrintDemesTotalAvgEnergy</a><br>
<a href="#PrintDemeTasksData">PrintDemeTasksData</a><br>
<a href="#PrintDemeTasksExeData">PrintDemeTasksExeData</a><br>
+ <a href="#PrintDemeTestamentStats">PrintDemeTestamentStats</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="#PrintDetailedSynchronizationData">PrintDetailedSynchronizationData</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>
@@ -199,8 +225,11 @@
<a href="#PrintDominantGenotype">PrintDominantGenotype</a><br>
<a href="#PrintDominantParasiteGenotype">PrintDominantParasiteGenotype</a><br>
<a href="#print_donation_stats">print_donation_stats</a><br>
+ <a href="#PrintDynamicMaxMinData">PrintDynamicMaxMinData</a><br>
<a href="#print_error_data">print_error_data</a><br>
<a href="#PrintErrorData">PrintErrorData</a><br>
+ <a href="#PrintExtendedTimeData">PrintExtendedTimeData</a><br>
+ <a href="#PrintFlowRateTuples">PrintFlowRateTuples</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>
@@ -224,6 +253,7 @@
<a href="#PrintLogFitnessHistogram">PrintLogFitnessHistogram</a><br>
<a href="#print_market_data">print_market_data</a><br>
<a href="#PrintMarketData">PrintMarketData</a><br>
+ <a href="#PrintMessageData">PrintMessageData</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>
@@ -231,14 +261,16 @@
<a href="#PrintPerDemeGenPerFounderData">PrintPerDemeGenPerFounderData</a><br>
<a href="#PrintPerDemeReactionData">PrintPerDemeReactionData</a><br>
<a href="#PrintPerDemeTasksData">PrintPerDemeTasksData</a><br>
+ <td valign="top">
<a href="#PrintPerDemeTasksExeData">PrintPerDemeTasksExeData</a><br>
<a href="#print_phenotype_status">print_phenotype_status</a><br>
<a href="#PrintPhenotypeData">PrintPhenotypeData</a><br>
<a href="#PrintPhenotypeStatus">PrintPhenotypeStatus</a><br>
- <td valign="top">
<a href="#PrintPhenotypicPlasticity">PrintPhenotypicPlasticity</a><br>
<a href="#PrintPopulationDistanceData">PrintPopulationDistanceData</a><br>
+ <a href="#PrintPredicatedMessages">PrintPredicatedMessages</a><br>
<a href="#PrintReactionData">PrintReactionData</a><br>
+ <a href="#PrintReactionExeData">PrintReactionExeData</a><br>
<a href="#PrintReactionRewardData">PrintReactionRewardData</a><br>
<a href="#PrintRelativeFitnessHistogram">PrintRelativeFitnessHistogram</a><br>
<a href="#print_resource_data">print_resource_data</a><br>
@@ -250,6 +282,7 @@
<a href="#PrintSpeciesAbundanceHistogram">PrintSpeciesAbundanceHistogram</a><br>
<a href="#print_stats_data">print_stats_data</a><br>
<a href="#PrintStatsData">PrintStatsData</a><br>
+ <a href="#PrintSynchronizationData">PrintSynchronizationData</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>
@@ -285,6 +318,7 @@
<a href="#SerialTransfer">SerialTransfer</a><br>
<a href="#serial_transfer">serial_transfer</a><br>
<a href="#SetCellResource">SetCellResource</a><br>
+ <a href="#SetConfig">SetConfig</a><br>
<a href="#SetEnvironmentInputs">SetEnvironmentInputs</a><br>
<a href="#SetEnvironmentRandomMask">SetEnvironmentRandomMask</a><br>
<a href="#SetMigrationRate">SetMigrationRate</a><br>
@@ -305,6 +339,9 @@
<a href="#set_resource">set_resource</a><br>
<a href="#SetResourceInflow">SetResourceInflow</a><br>
<a href="#SetResourceOutflow">SetResourceOutflow</a><br>
+ <a href="#SetSeasonalResource">SetSeasonalResource</a><br>
+ <a href="#SetSeasonalResource10Kyears_1To_1">SetSeasonalResource10Kyears_1To_1</a><br>
+ <a href="#SetSeasonalResource1Kyears_1To_1">SetSeasonalResource1Kyears_1To_1</a><br>
<a href="#SetTaskArgDouble">SetTaskArgDouble</a><br>
<a href="#SetTaskArgInt">SetTaskArgInt</a><br>
<a href="#SetTaskArgString">SetTaskArgString</a><br>
@@ -316,11 +353,13 @@
<a href="#StopFastForward">StopFastForward</a><br>
<a href="#swap_cells">swap_cells</a><br>
<a href="#SwapCells">SwapCells</a><br>
+ <a href="#Synchronization">Synchronization</a><br>
<a href="#task_snapshot">task_snapshot</a><br>
<a href="#test_dom">test_dom</a><br>
<a href="#TestDominant">TestDominant</a><br>
<a href="#ToggleFitnessValley">ToggleFitnessValley</a><br>
<a href="#ToggleRewardInstruction">ToggleRewardInstruction</a><br>
+ <a href="#TrackAllMessages">TrackAllMessages</a><br>
<a href="#VERBOSE">VERBOSE</a><br>
<a href="#zero_muts">zero_muts</a><br>
<a href="#ZeroMuts">ZeroMuts</a><br>
@@ -438,13 +477,21 @@
</li>
<li><p>
<strong><a name="DelayedDemeEvent">DelayedDemeEvent</a></strong>
- <i><int x1> <int y1> <int x2> <int y2> <int delay> <int duraion></i>
+ <i><int x1> <int y1> <int x2> <int y2> <int delay> <int duraion> <bool static_position> <int total_events></i>
</p>
<p>
</p>
</li>
<li><p>
+ <strong><a name="DelayedDemeEventsPerSlots">DelayedDemeEventsPerSlots</a></strong>
+ <i><int x1> <int y1> <int x2> <int y2> <int delay> <int duraion> <bool static_position> <int total_slots_per_deme> <int total_events_per_slot_max> <int total_events_per_slot_min> <int tolal_event_flow_levels></i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="InjectResource">InjectResource</a></strong>
<i><string res_name> <double res_count></i>
</p>
@@ -507,6 +554,14 @@
</p>
</li>
<li><p>
+ <strong><a name="SetConfig">SetConfig</a></strong>
+ <i><string config_var> <string value></i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="SetEnvironmentInputs">SetEnvironmentInputs</a></strong>
<i><int input_1> <int input_2> <int input_3> </i>
</p>
@@ -688,6 +743,27 @@
</p>
</li>
<li><p>
+ <strong><a name="SetSeasonalResource">SetSeasonalResource</a></strong>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="SetSeasonalResource10Kyears_1To_1">SetSeasonalResource10Kyears_1To_1</a></strong>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="SetSeasonalResource1Kyears_1To_1">SetSeasonalResource1Kyears_1To_1</a></strong>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="SetTaskArgDouble">SetTaskArgDouble</a></strong>
<i><int task> <int arg> <double value></i>
</p>
@@ -881,6 +957,14 @@
</p>
</li>
<li><p>
+ <strong><a name="AssignRandomCellData">AssignRandomCellData</a></strong>
+ <i>No Arguments</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="compete_demes">compete_demes</a></strong>
<i>[int type=1]</i>
</p>
@@ -898,6 +982,44 @@
</p>
</li>
<li><p>
+ <strong><a name="CompeteDemes_AttackKillAndEnergyConserve">CompeteDemes_AttackKillAndEnergyConserve</a></strong>
+ <i>No Arguments</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="CompeteDemesByEnergyDistribution">CompeteDemesByEnergyDistribution</a></strong>
+ <i>Competes demes according to the distribution of energy among the organisms</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="CompeteDemesByTaskCount">CompeteDemesByTaskCount</a></strong>
+ <i>Competes demes according to the number of times a given task has been completed within that deme</i>
+ </p>
+ <p>
+ Competes demes based on the total number of times that a
+ task has been completed by an organism in the deme since the
+ was initialized. This action takes one integer parameter representing
+ number of the task that is to be used for competition. If no parameter
+ supplied, the class uses the first task defined in the environment file
+ compete the demes.
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="CompeteDemesByTaskCountAndEfficiency">CompeteDemesByTaskCountAndEfficiency</a></strong>
+ <i>Competes demes according to the number of times a given task has been completed within that deme and the efficiency with which it was done</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="CompeteOrganisms">CompeteOrganisms</a></strong>
<i>[int type=0] [int parents_survive=0] [double scaled_time=1.0] [int dynamic_scaling=0]</i>
</p>
@@ -963,6 +1085,22 @@
</p>
</li>
<li><p>
+ <strong><a name="DecayPoints">DecayPoints</a></strong>
+ </p>
+ <p>
+ Decays the number of points a deme has accumulated by
+ a percentage that is set in the configuration file.
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="Desynchronization">Desynchronization</a></strong>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="DisconnectCells">DisconnectCells</a></strong>
<i><int cellA_x> <int cellA_y> <int cellB_x> <int cellB_y></i>
</p>
@@ -989,6 +1127,13 @@
</p>
</li>
<li><p>
+ <strong><a name="Flash">Flash</a></strong>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="inject">inject</a></strong>
<i>[string fname="START_CREATURE"] [int cell_id=0] [double merit=-1] [int lineage_label=0] [double neutral_metric=0]</i>
</p>
@@ -1054,6 +1199,22 @@
</p>
</li>
<li><p>
+ <strong><a name="InjectDemesFromNest">InjectDemesFromNest</a></strong>
+ <i>[int num_orgs=1] [int nest_cellid=0] [double merit=-1] [int lineage_label=0] [double neutral_metric=0]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="InjectDemesRandom">InjectDemesRandom</a></strong>
+ <i>[int num_orgs=1] [double merit=-1] [int lineage_label=0] [double neutral_metric=0]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="InjectParasite">InjectParasite</a></strong>
<i><string filename> <string label> [int cell_start=0] [int cell_end=-1]</i>
</p>
@@ -1146,6 +1307,14 @@
</p>
</li>
<li><p>
+ <strong><a name="IteratedConsensus">IteratedConsensus</a></strong>
+ <i>[int compete_period=100 [int replace_number=0]]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="join_grid_col">join_grid_col</a></strong>
<i>[int col_id=-1] [int min_row=0] [int max_row=-1]</i>
</p>
@@ -1226,7 +1395,6 @@
<strong><a name="ModMutProb">ModMutProb</a></strong>
<i>[string mut_type="COPY_MUT"] [double prob=0.0] [int start_cell=-1] [int end_cell=-1]</i>
</p>
- For a list of values for mut_type, see <a href="#SetMutProb">SetMutProb<a/>.
<p>
</p>
@@ -1251,6 +1419,30 @@
</p>
</li>
<li><p>
+ <strong><a name="Pred_DemeEventMoveBetweenTargets">Pred_DemeEventMoveBetweenTargets</a></strong>
+ <i>[int times=1]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="Pred_DemeEventMoveCenter">Pred_DemeEventMoveCenter</a></strong>
+ <i>[int times=1]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="Pred_DemeEventNUniqueIndividualsMovedIntoTarget">Pred_DemeEventNUniqueIndividualsMovedIntoTarget</a></strong>
+ <i>[int numorgs=1]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="rate_kill">rate_kill</a></strong>
<i><double probability></i>
</p>
@@ -1325,13 +1517,6 @@
<strong><a name="SetMutProb">SetMutProb</a></strong>
<i>[string mut_type="COPY_MUT"] [double prob=0.0] [int start_cell=-1] [int end_cell=-1]</i>
</p>
- Values for mut_type are POINT, COPY_MUT, COPY_INS, COPY_DEL, COPY_UNIFORM,
- COPY_SLIP, DIV_MUT, DIV_INS, DIV_DEL, DIV_UNIFORM, DIV_SLIP, DIVIDE_MUT,
- DIVIDE_INS, DIVIDE_DEL, DIVIDE_UNIFORM, DIVIDE_SLIP, PARENT, INJECT_MUT,
- INJECT_INS, and INJECT_DEL. These correspond to their counterparts in avida.cfg.
- <br>
- <br>
- To turn off all mutations, use <a href="#ZeroMuts">ZeroMuts</a>.
<p>
</p>
@@ -1390,6 +1575,13 @@
</p>
</li>
<li><p>
+ <strong><a name="Synchronization">Synchronization</a></strong>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="ToggleFitnessValley">ToggleFitnessValley</a></strong>
<i>No Arguments</i>
</p>
@@ -1406,6 +1598,13 @@
</p>
</li>
<li><p>
+ <strong><a name="TrackAllMessages">TrackAllMessages</a></strong>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="zero_muts">zero_muts</a></strong>
<i>No Arguments</i>
</p>
@@ -1419,9 +1618,7 @@
<i>No Arguments</i>
</p>
<p>
- This event will set all mutation rates to zero. That is, it will set all
- cell mutation rates to zero, so that new organisms born will have zero mutation
- rates. Current organsims will not be affected, and may still mutate.
+ This event will set all mutation rates to zero.
</p>
</li>
@@ -1689,6 +1886,13 @@
</p>
</li>
<li><p>
+ <strong><a name="PrintCellData">PrintCellData</a></strong>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintCellVisitsData">PrintCellVisitsData</a></strong>
<i>[string fname="visits.dat "]</i>
</p>
@@ -1725,6 +1929,13 @@
</p>
</li>
<li><p>
+ <strong><a name="PrintCurrentOpinions">PrintCurrentOpinions</a></strong>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintCurrentReactionData">PrintCurrentReactionData</a></strong>
<i>[string fname="cur_reactions.dat"]</i>
</p>
@@ -1733,6 +1944,22 @@
</p>
</li>
<li><p>
+ <strong><a name="PrintCurrentReactionRewardData">PrintCurrentReactionRewardData</a></strong>
+ <i>[string fname="cur_reaction_reward.dat"]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="PrintCurrentTaskCounts">PrintCurrentTaskCounts</a></strong>
+ <i>[string fname="curr_task_counts.dat"]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="print_data">print_data</a></strong>
<i><cString fname> <cString format></i>
</p>
@@ -1790,6 +2017,22 @@
</p>
</li>
<li><p>
+ <strong><a name="PrintDemeCompetitionData">PrintDemeCompetitionData</a></strong>
+ <i>[string fname="deme_compete.dat"]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="PrintDemeCurrentTaskExeData">PrintDemeCurrentTaskExeData</a></strong>
+ <i>[string fname=" deme_cur_task_exe.dat "]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintDemeDonorStats">PrintDemeDonorStats</a></strong>
<i>No Arguments</i>
</p>
@@ -1798,6 +2041,14 @@
</p>
</li>
<li><p>
+ <strong><a name="PrintDemeEnergySharingStats">PrintDemeEnergySharingStats</a></strong>
+ <i>No Arguments</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintDemeFoundersData">PrintDemeFoundersData</a></strong>
<i>[string fname="deme_founders.dat"]</i>
</p>
@@ -1806,6 +2057,14 @@
</p>
</li>
<li><p>
+ <strong><a name="PrintDemeMigrationSuicidePoints">PrintDemeMigrationSuicidePoints</a></strong>
+ <i>[string fname=" deme_mig_suicide_points.dat "]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintDemeOrgReactionData">PrintDemeOrgReactionData</a></strong>
<i>[string fname="deme_org_reactions.dat"]</i>
</p>
@@ -1878,6 +2137,14 @@
</p>
</li>
<li><p>
+ <strong><a name="PrintDemesTotalAvgEnergy">PrintDemesTotalAvgEnergy</a></strong>
+ <i>No Arguments</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintDemeTasksData">PrintDemeTasksData</a></strong>
<i>[string fname="deme_tasks.dat"]</i>
</p>
@@ -1894,6 +2161,14 @@
</p>
</li>
<li><p>
+ <strong><a name="PrintDemeTestamentStats">PrintDemeTestamentStats</a></strong>
+ <i>[string fname="deme_testament.dat"]</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>
@@ -1927,6 +2202,14 @@
</p>
</li>
<li><p>
+ <strong><a name="PrintDetailedSynchronizationData">PrintDetailedSynchronizationData</a></strong>
+ <i>[string fname="sync-detail.dat"]</i>
+ </p>
+ <p>
+
+ </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>
@@ -2011,6 +2294,14 @@
</p>
</li>
<li><p>
+ <strong><a name="PrintDynamicMaxMinData">PrintDynamicMaxMinData</a></strong>
+ <i>[string fname=" maxmin.dat "]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="print_error_data">print_error_data</a></strong>
<i>[string fname="error.dat"]</i>
</p>
@@ -2029,6 +2320,21 @@
</p>
</li>
<li><p>
+ <strong><a name="PrintExtendedTimeData">PrintExtendedTimeData</a></strong>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="PrintFlowRateTuples">PrintFlowRateTuples</a></strong>
+ <i>[string fname="flow_rate_tuples.dat"]</i>
+ </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>
@@ -2188,25 +2494,20 @@
</p>
</li>
<li><p>
- <strong><a name="PrintInternalTasksData">PrintInternalTasksData</a></strong>
- <i>[string fname="in_tasks.dat"]</i>
- </p>
- <p>
- Print the number of organisms that have performed each task using internal resources.
- </p>
- <p>
- Note that tasks performed using internal resources are also counted as tasks performed (by <a href="#PrintTasksData">PrintTasksData</a>), so that if you wish to know the number of tasks performed <i>not</i> using internal resources you must do some subtraction:
- <br><br>
- (number from PrintTasksData) - (number from PrintInternalTasksData) = number of organisms who have performed this task <i>not</i> using internal resources
- </p>
+ <strong><a name="PrintInternalTasksData">PrintInternalTasksData</a></strong>
+ <i>[string fname="in_tasks.dat"]</i>
+ </p>
+ <p>
+
+ </p>
</li>
<li><p>
- <strong><a name="PrintInternalTasksQualData">PrintInternalTasksQualData</a></strong>
- <i>[string fname="in_tasks_quality.dat"]</i>
- </p>
- <p>
- Print the total quality of each task when performed using internal resources. (See <a href="#PrintTasksQualData">PrintTasksQualData</a> for more about task quality.)
- </p>
+ <strong><a name="PrintInternalTasksQualData">PrintInternalTasksQualData</a></strong>
+ <i>[string fname="in_tasks_quality.dat"]</i>
+ </p>
+ <p>
+
+ </p>
</li>
<li><p>
<strong><a name="print_lineage_counts">print_lineage_counts</a></strong>
@@ -2276,6 +2577,14 @@
</p>
</li>
<li><p>
+ <strong><a name="PrintMessageData">PrintMessageData</a></strong>
+ <i>[string fname="message.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>
@@ -2395,6 +2704,13 @@
</p>
</li>
<li><p>
+ <strong><a name="PrintPredicatedMessages">PrintPredicatedMessages</a></strong>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintReactionData">PrintReactionData</a></strong>
<i>[string fname="reactions.dat"]</i>
</p>
@@ -2403,6 +2719,14 @@
</p>
</li>
<li><p>
+ <strong><a name="PrintReactionExeData">PrintReactionExeData</a></strong>
+ <i>[string fname="reactions_exe.dat"]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintReactionRewardData">PrintReactionRewardData</a></strong>
<i>[string fname="reaction_reward.dat"]</i>
</p>
@@ -2509,6 +2833,13 @@
</p>
</li>
<li><p>
+ <strong><a name="PrintSynchronizationData">PrintSynchronizationData</a></strong>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="print_tasks_data">print_tasks_data</a></strong>
<i>[string fname="tasks.dat"]</i>
</p>
Modified: development/source/utils/make_actions_html/actions_source_info
===================================================================
--- development/source/utils/make_actions_html/actions_source_info 2009-01-26 21:21:15 UTC (rev 3136)
+++ development/source/utils/make_actions_html/actions_source_info 2009-01-28 20:33:34 UTC (rev 3137)
@@ -400,6 +400,34 @@
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 cAssignRandomCellData ===
+ Assign a random identifier to the data for each cell and save those IDs for
+ later use, respecting deme boundaries.
+=== Action CompeteDemesByTaskCount ===
+ Competes demes based on the total number of times that a
+ task has been completed by an organism in the deme since the
+ was initialized. This action takes one integer parameter representing
+ number of the task that is to be used for competition. If no parameter
+ supplied, the class uses the first task defined in the environment file
+ compete the demes.
+=== Action DecayPoints ===
+ Decays the number of points a deme has accumulated by
+ a percentage that is set in the configuration file.
+=== InjectDemesRandom ===
+ Injects one or more organisms into all demes in a randomly-chosen cell.
+ <P>* Note: This gets the genotype from the germline, so germline use is required</P>
+ <p>* Note: one organism is inserted each time this is called, and it will
+ stop when the given number of organisms has been injected.</p>
+
+ <p>Parameters:
+ <ul>
+ <li>number of orgs (int): number of organisms to inject into each deme - default 1
+ <li>merit (double): The initial merit of the organism. If set to -1, this is ignored - default -1
+ <li>lineage label (integer): An integer that marks all descendants of this organism - default 0
+ <li>neutral metric (double): A double value that randomly drifts over time - default 0
+ </ul>
+ </p>
+
=== Action inject_resource ===
<font color="red">DEPRECATED</font>
=== Action inject_scaled_resource ===
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