[Avida-cvs] [avida-svn] r925 - development/documentation
brysonda at myxo.css.msu.edu
brysonda at myxo.css.msu.edu
Sun Sep 3 18:25:48 PDT 2006
Author: brysonda
Date: 2006-09-03 21:25:47 -0400 (Sun, 03 Sep 2006)
New Revision: 925
Modified:
development/documentation/actions.html
development/documentation/analyze.html
development/documentation/analyze_samples.html
development/documentation/code_c++_intro.html
development/documentation/code_death_birth.html
development/documentation/code_environment.html
development/documentation/main.css
Log:
Begin updating style --> semantic class usage.
Modified: development/documentation/actions.html
===================================================================
--- development/documentation/actions.html 2006-09-02 15:01:28 UTC (rev 924)
+++ development/documentation/actions.html 2006-09-04 01:25:47 UTC (rev 925)
@@ -5,8 +5,8 @@
</head>
<body>
-<div style="float: right">
-Revised 2006-08-28 DMB
+<div class="revision">
+Revised 2006-09-03 DMB
</div>
<p>
@@ -171,7 +171,7 @@
<!-------- Stats Out Files -------->
<li>
<strong><a name="PrintAverageData">PrintAverageData</a></strong>
- [<span style="color: #008800">string filename='average.dat'</span>]
+ [<span class="cmdarg">string filename='average.dat'</span>]
<p>
Print all of the population averages the specified file.
@@ -179,7 +179,7 @@
</li>
<li>
<strong><a name="PrintErrorData">PrintErrorData</a></strong>
- [<span style="color: #008800">string filename='error.dat'</span>]
+ [<span class="cmdarg">string filename='error.dat'</span>]
<p>
Print all of the standard errors of the average population statistics.
@@ -187,7 +187,7 @@
</li>
<li>
<strong><a name="PrintVarianceData">PrintVarianceData</a></strong>
- [<span style="color: #008800">string filename='variance.dat'</span>]
+ [<span class="cmdarg">string filename='variance.dat'</span>]
<p>
Print all of the variances of the average population statistics.
@@ -195,7 +195,7 @@
</li>
<li>
<strong><a name="PrintDominantData">PrintDominantData</a></strong>
- [<span style="color: #008800">string filename='dominant.dat'</span>]
+ [<span class="cmdarg">string filename='dominant.dat'</span>]
<p>
Print all of the statistics relating to the dominant genotype.
@@ -203,7 +203,7 @@
</li>
<li>
<strong><a name="PrintStatsData">PrintStatsData</a></strong>
- [<span style="color: #008800">string filename='stats.dat'</span>]
+ [<span class="cmdarg">string filename='stats.dat'</span>]
<p>
Print all of the miscellanous population statistics.
@@ -211,7 +211,7 @@
</li>
<li>
<strong><a name="PrintCountData">PrintCountData</a></strong>
- [<span style="color: #008800">string filename='count.dat'</span>]
+ [<span class="cmdarg">string filename='count.dat'</span>]
<p>
Print all of the statistics the keep track of counts (such as the number of organisms
@@ -220,7 +220,7 @@
</li>
<li>
<strong><a name="PrintTotalsData">PrintTotalsData</a></strong>
- [<span style="color: #008800">string filename='totals.dat'</span>]
+ [<span class="cmdarg">string filename='totals.dat'</span>]
<p>
Print various totals for the entire length of the run (for example, the total number of
@@ -229,7 +229,7 @@
</li>
<li>
<strong><a name="PrintTasksData">PrintTasksData</a></strong>
- [<span style="color: #008800">string filename='tasks.dat'</span>]
+ [<span class="cmdarg">string filename='tasks.dat'</span>]
<p>
Print the number of organisms that are able to perform each task. This uses the
@@ -238,7 +238,7 @@
</li>
<li>
<strong><a name="PrintTasksExeData">PrintTasksExeData</a></strong>
- [<span style="color: #008800">string filename='tasks_exe.dat'</span>]
+ [<span class="cmdarg">string filename='tasks_exe.dat'</span>]
<p>
Print number of times the particular task has been executed this update.
@@ -246,7 +246,7 @@
</li>
<li>
<strong><a name="PrintTasksQualData">PrintTasksQualData</a></strong>
- [<span style="color: #008800">string filename='tasks_quality.dat'</span>]
+ [<span class="cmdarg">string filename='tasks_quality.dat'</span>]
<p>
Print the total quality of each task. By default a successful task is valued
@@ -256,7 +256,7 @@
</li>
<li>
<strong><a name="PrintResourceData">PrintResourceData</a></strong>
- [<span style="color: #008800">string filename='resource.dat'</span>]
+ [<span class="cmdarg">string filename='resource.dat'</span>]
<p>
Print the current counts of each resource available to the population. This uses
@@ -267,7 +267,7 @@
</li>
<li>
<strong><a name="PrintTimeData">PrintTimeData</a></strong>
- [<span style="color: #008800">string filename='time.dat'</span>]
+ [<span class="cmdarg">string filename='time.dat'</span>]
<p>
Print all of the timing related statistics.
@@ -275,7 +275,7 @@
</li>
<li>
<strong><a name="PrintMutationRateData">PrintMutationRateData</a></strong>
- [<span style="color: #008800">string filename='mutation_rates.dat'</span>]
+ [<span class="cmdarg">string filename='mutation_rates.dat'</span>]
<p>
Output (regular and log) statistics about individual copy mutation rates
@@ -284,7 +284,7 @@
</li>
<li>
<strong><a name="PrintDivideMutData">PrintDivideMutData</a></strong>
- [<span style="color: #008800">string filename='divide_mut.dat'</span>]
+ [<span class="cmdarg">string filename='divide_mut.dat'</span>]
<p>
Output (regular and log) statistics about individual, per site, rates divide mutation
@@ -293,7 +293,7 @@
</li>
<li>
<strong><a name="PrintDominantParaData">PrintDominantParaData</a></strong>
- [<span style="color: #008800">string filename='parasite.dat'</span>]
+ [<span class="cmdarg">string filename='parasite.dat'</span>]
<p>
Print various quantites related to the dominant parasite.
@@ -301,7 +301,7 @@
</li>
<li>
<strong><a name="PrintInstructionData">PrintInstructionData</a></strong>
- [<span style="color: #008800">string filename='instruction.dat'</span>]
+ [<span class="cmdarg">string filename='instruction.dat'</span>]
<p>
Print the by-organisms counts of what instructions they _successfully_ executed
@@ -310,7 +310,7 @@
</li>
<li>
<strong><a name="PrintGenotypeMap">PrintGenotypeMap</a></strong>
- [<span style="color: #008800">string filename='genotype_map.m'</span>]
+ [<span class="cmdarg">string filename='genotype_map.m'</span>]
<p>
This event is used to output a map of the genotype IDs for the
@@ -321,7 +321,7 @@
<!-------- Population Out Files -------->
<li>
<strong><a name="PrintPhenotypeData">PrintPhenotypeData</a></strong>
- [<span style="color: #008800">string filename='phenotype_count.dat'</span>]
+ [<span class="cmdarg">string filename='phenotype_count.dat'</span>]
<p>
Print the number of phenotypes based on tasks executed this update. Executing
@@ -330,7 +330,7 @@
</li>
<li>
<strong><a name="PrintPhenotypeStatus">PrintPhenotypeStatus</a></strong>
- [<span style="color: #008800">string filename='phenotype_status.dat'</span>]
+ [<span class="cmdarg">string filename='phenotype_status.dat'</span>]
<p>
</p>
@@ -345,7 +345,7 @@
<!-------- Processed Data -------->
<li>
<strong><a name="PrintData">PrintData</a></strong>
- <<span style="color: #008800">string fname</span>> <<span style="color: #008800">string format</span>>
+ <<span class="cmdarg">string fname</span>> <<span class="cmdarg">string format</span>>
<p>
Append to the file specified (continuous output), the data given in the
@@ -359,7 +359,7 @@
</li>
<li>
<strong><a name="PrintInstructionAbundanceHistogram">PrintInstructionAbundanceHistogram</a></strong>
- [<span style="color: #008800">string filename='instruction_histogram.dat'</span>]
+ [<span class="cmdarg">string filename='instruction_histogram.dat'</span>]
<p>
Appends a line containing the bulk count (abundance) of each instruction
@@ -368,14 +368,14 @@
</li>
<li>
<strong><a name="PrintDepthHistogram">PrintDepthHistogram</a></strong>
- [<span style="color: #008800">string filename='depth_histogram.dat'</span>]
+ [<span class="cmdarg">string filename='depth_histogram.dat'</span>]
<p>
</p>
</li>
<li>
<strong><a name="Echo">Echo</a></strong>
- <<span style="color: #008800">string message</span>>
+ <<span class="cmdarg">string message</span>>
<p>
Print the supplied message to standard output.
@@ -383,7 +383,7 @@
</li>
<li>
<strong><a name="PrintGenotypeAbundanceHistogram">PrintGenotypeAbundanceHistogram</a></strong>
- [<span style="color: #008800">string fname='genotype_abundance_histogram.dat'</span>]
+ [<span class="cmdarg">string fname='genotype_abundance_histogram.dat'</span>]
<p>
Writes out a genotype abundance histogram.
@@ -391,7 +391,7 @@
</li>
<li>
<strong><a name="PrintSpeciesAbundanceHistogram">PrintSpeciesAbundanceHistogram</a></strong>
- [<span style="color: #008800">string fname='species_abundance_histogram.dat'</span>]
+ [<span class="cmdarg">string fname='species_abundance_histogram.dat'</span>]
<p>
Writes out a species abundance histogram.
@@ -399,21 +399,21 @@
</li>
<li>
<strong><a name="PrintLineageTotals">PrintLineageTotals</a></strong>
- [<span style="color: #008800">string fname='lineage_totals.dat'</span>] [<span style="color: #008800">int verbose=1</span>]
+ [<span class="cmdarg">string fname='lineage_totals.dat'</span>] [<span class="cmdarg">int verbose=1</span>]
<p>
</p>
</li>
<li>
<strong><a name="PrintLineageCounts">PrintLineageCounts</a></strong>
- [<span style="color: #008800">string fname='lineage_counts.dat'</span>] [<span style="color: #008800">int verbose=1</span>]
+ [<span class="cmdarg">string fname='lineage_counts.dat'</span>] [<span class="cmdarg">int verbose=1</span>]
<p>
</p>
</li>
<li>
<strong><a name="PrintDominantGenotype">PrintDominantGenotype</a></strong>
- [<span style="color: #008800">string fname=''</span>]
+ [<span class="cmdarg">string fname=''</span>]
<p>
Print the dominant organism's genome (and lots of information about it)
@@ -423,7 +423,7 @@
</li>
<li>
<strong><a name="PrintDominantParasiteGenotype">PrintDominantParasiteGenotype</a></strong>
- [<span style="color: #008800">string fname=''</span>]
+ [<span class="cmdarg">string fname=''</span>]
<p>
Print the dominant parasite's genome (and lots of information about it)
@@ -433,27 +433,27 @@
</li>
<li>
<strong><a name="PrintDetailedFitnessData">PrintDetailedFitnessData</a></strong>
- [<span style="color: #008800">int save_max_f_genotype=0</span>] [<span style="color: #008800">int print_fitness_histo=0</span>]
- [<span style="color: #008800">double hist_fmax=1</span>] [<span style="color: #008800">double hist_fstep=0.1</span>]
- [<span style="color: #008800">string datafn='fitness.dat'</span>]
- [<span style="color: #008800">string histofn='fitness_histos.dat'</span>]
- [<span style="color: #008800">string histotestfn='fitness_histos_testCPU.dat'</span>]
+ [<span class="cmdarg">int save_max_f_genotype=0</span>] [<span class="cmdarg">int print_fitness_histo=0</span>]
+ [<span class="cmdarg">double hist_fmax=1</span>] [<span class="cmdarg">double hist_fstep=0.1</span>]
+ [<span class="cmdarg">string datafn='fitness.dat'</span>]
+ [<span class="cmdarg">string histofn='fitness_histos.dat'</span>]
+ [<span class="cmdarg">string histotestfn='fitness_histos_testCPU.dat'</span>]
<p>
</p>
</li>
<li>
<strong><a name="PrintGeneticDistanceData">PrintGeneticDistanceData</a></strong>
- [<span style="color: #008800">string ref_creature_file='START_CREATURE'</span>]
- [<span style="color: #008800">string filename='genetic_distance.dat'</span>]
+ [<span class="cmdarg">string ref_creature_file='START_CREATURE'</span>]
+ [<span class="cmdarg">string filename='genetic_distance.dat'</span>]
<p>
</p>
</li>
<li>
<strong><a name="PrintPopulationDistanceData">PrintPopulationDistanceData</a></strong>
- [<span style="color: #008800">string creature='START_CREATURE'</span>] [<span style="color: #008800">string fname=''</span>]
- [<span style="color: #008800">int save_genotypes=0</span>]
+ [<span class="cmdarg">string creature='START_CREATURE'</span>] [<span class="cmdarg">string fname=''</span>]
+ [<span class="cmdarg">int save_genotypes=0</span>]
<p>
</p>
@@ -467,9 +467,9 @@
<li>
<strong><a name="PrintGenotypes">PrintGenotypes</a></strong>
- [<span style="color: #008800">string data_fields='all'</span>]
- [<span style="color: #008800">int print_historic=0</span>]
- [<span style="color: #008800">string filename='genotypes-<update>.dat'</span>]
+ [<span class="cmdarg">string data_fields='all'</span>]
+ [<span class="cmdarg">int print_historic=0</span>]
+ [<span class="cmdarg">string filename='genotypes-<update>.dat'</span>]
<p>
This command is used to print out information about all of the genotypes
@@ -477,7 +477,7 @@
back into the analyze mode of Avida with the <code>LOAD</code> command.
</p>
<p>
- The <span style="color: #008800">data_fields</span> parameter indicates what
+ The <span class="cmdarg">data_fields</span> parameter indicates what
columns should be included in the file, which must be comma seperated.
Options are:
<em>all, id, parent_id, parent2_id (for sex), parent_dist, num_cpus,
@@ -486,14 +486,14 @@
Use <em>all</em> (the default) if you want all of the fields included.
</p>
<p>
- The <span style="color: #008800">print_historic</span> parameter indicates how
+ The <span class="cmdarg">print_historic</span> parameter indicates how
many updates back in time should be included in this output. For example,
'200' would indicate that any ancestor of the current population that died
out in the last 200 updates should also be printed. A '-1' in this field
indicates that all ancestors should be printed.
</p>
<p>
- The <span style="color: #008800">filename</span> parameter simply indicates what
+ The <span class="cmdarg">filename</span> parameter simply indicates what
you want to call the file.
</p>
<p>
@@ -506,14 +506,14 @@
<li>
<strong><a name="TestDominant">TestDominant</a></strong>
- [<span style="color: #008800">string fname='dom-test.dat'</span>]
+ [<span class="cmdarg">string fname='dom-test.dat'</span>]
<p>
</p>
</li>
<li>
<strong><a name="PrintTaskSnapshot">PrintTaskSnapshot</a></strong>
- [<span style="color: #008800">string fname=''</span>]
+ [<span class="cmdarg">string fname=''</span>]
<p>
Run all organisms in the population through test cpus and print out the
@@ -522,14 +522,14 @@
</li>
<li>
<strong><a name="PrintViableTasksData">PrintViableTasksData</a></strong>
- [<span style="color: #008800">string fname='viable_tasks.dat'</span>]
+ [<span class="cmdarg">string fname='viable_tasks.dat'</span>]
<p>
</p>
</li>
<li>
<strong><a name="PrintTreeDepths">PrintTreeDepths</a></strong>
- [<span style="color: #008800">string fname=''</span>]
+ [<span class="cmdarg">string fname=''</span>]
<p>
Reconstruction of phylogenetic trees.
@@ -540,7 +540,7 @@
<!-------- Grid Information Dumps -------->
<li>
<strong><a name="DumpMemory">DumpMemory</a></strong>
- [<span style="color: #008800">string filename='memory_dump-<update>.dat'</span>]
+ [<span class="cmdarg">string filename='memory_dump-<update>.dat'</span>]
<p>
Dump memory summary information.
@@ -548,7 +548,7 @@
</li>
<li>
<strong><a name="DumpFitnessGrid">DumpFitnessGrid</a></strong>
- [<span style="color: #008800">string filename='grid_fitness.<update>.dat'</span>]
+ [<span class="cmdarg">string filename='grid_fitness.<update>.dat'</span>]
<p>
Print out the grid of organism fitness values.
@@ -556,7 +556,7 @@
</li>
<li>
<strong><a name="DumpGenotypeIDGrid">DumpGenotypeIDGrid</a></strong>
- [<span style="color: #008800">string filename='grid_genotype_id.<update>.dat'</span>]
+ [<span class="cmdarg">string filename='grid_genotype_id.<update>.dat'</span>]
<p>
Print out the grid of genotype IDs.
@@ -564,7 +564,7 @@
</li>
<li>
<strong><a name="DumpTaskGrid">DumpTaskGrid</a></strong>
- [<span style="color: #008800">string filename='grid_task.<update>.dat'</span>]
+ [<span class="cmdarg">string filename='grid_task.<update>.dat'</span>]
<p>
Print out the grid of takss that organisms do. For each organism, tasks are first
@@ -582,7 +582,7 @@
</li>
<li>
<strong><a name="DumpReceiverGrid">DumpRecieverGrid</a></strong>
- [<span style="color: #008800">string filename='grid_receiver.<update>.dat'</span>]
+ [<span class="cmdarg">string filename='grid_receiver.<update>.dat'</span>]
<p>
Print out the grid of organisms who received merit.
@@ -601,9 +601,9 @@
<ul>
<li>
<strong><a name="Inject">Inject</a></strong>
- [<span style="color: #008800">string fname='START_CREATURE'</span>] [<span style="color: #008800">int cell_id=0</span>]
- [<span style="color: #008800">double merit=-1</span>] [<span style="color: #008800">int lineage_label=0</span>]
- [<span style="color: #008800">double neutral_metric=0</span>]
+ [<span class="cmdarg">string fname='START_CREATURE'</span>] [<span class="cmdarg">int cell_id=0</span>]
+ [<span class="cmdarg">double merit=-1</span>] [<span class="cmdarg">int lineage_label=0</span>]
+ [<span class="cmdarg">double neutral_metric=0</span>]
<p>
Inject a single organisms into the population. Arguments must be
@@ -614,9 +614,9 @@
</li>
<li>
<strong><a name="InjectRandom">InjectRandom</a></strong>
- <<span style="color: #008800">int length</span>> [<span style="color: #008800">int cell_id=0</span>]
- [<span style="color: #008800">double merit=-1</span>] [<span style="color: #008800">int lineage_label=0</span>]
- [<span style="color: #008800">double neutral_metric=0</span>]
+ <<span class="cmdarg">int length</span>> [<span class="cmdarg">int cell_id=0</span>]
+ [<span class="cmdarg">double merit=-1</span>] [<span class="cmdarg">int lineage_label=0</span>]
+ [<span class="cmdarg">double neutral_metric=0</span>]
<p>
Injects a randomly generated genome of the supplied length into the population.
@@ -624,8 +624,8 @@
</li>
<li>
<strong><a name="InjectAll">InjectAll</a></strong>
- [<span style="color: #008800">string fname='START_CREATURE'</span>] [<span style="color: #008800">double merit=-1</span>]
- [<span style="color: #008800">int lineage_label=0] [<span style="color: #008800">double neutral_metric=0</span>]
+ [<span class="cmdarg">string fname='START_CREATURE'</span>] [<span class="cmdarg">double merit=-1</span>]
+ [<span class="cmdarg">int lineage_label=0] [<span class="cmdarg">double neutral_metric=0</span>]
<p>
Same as Inject, but no cell_id is specified and the organism is placed
@@ -634,9 +634,9 @@
</li>
<li>
<strong><a name="InjectRange">InjectRange</a></strong>
- [<span style="color: #008800">string fname='START_CREATURE'</span>] [<span style="color: #008800">int cell_start=0</span>]
- [<span style="color: #008800">int cell_end=-1</span>] [<span style="color: #008800">double merit=-1</span>]
- [<span style="color: #008800">int lineage_label=0</span>] [<span style="color: #008800">double neutral_metric=0</span>]
+ [<span class="cmdarg">string fname='START_CREATURE'</span>] [<span class="cmdarg">int cell_start=0</span>]
+ [<span class="cmdarg">int cell_end=-1</span>] [<span class="cmdarg">double merit=-1</span>]
+ [<span class="cmdarg">int lineage_label=0</span>] [<span class="cmdarg">double neutral_metric=0</span>]
<p>
Injects identical organisms into a range of cells of the population.
@@ -649,9 +649,9 @@
</li>
<li>
<strong><a name="InjectSequence">InjectSequence</a></strong>
- <<span style="color: #008800">string sequence</span>> [<span style="color: #008800">int cell_start=0</span>]
- [<span style="color: #008800">int cell_end=-1</span>] [<span style="color: #008800">double merit=-1</span>]
- [<span style="color: #008800">int lineage_label=0</span>] [<span style="color: #008800">double neutral_metric=0</span>]
+ <<span class="cmdarg">string sequence</span>> [<span class="cmdarg">int cell_start=0</span>]
+ [<span class="cmdarg">int cell_end=-1</span>] [<span class="cmdarg">double merit=-1</span>]
+ [<span class="cmdarg">int lineage_label=0</span>] [<span class="cmdarg">double neutral_metric=0</span>]
<p>
Injects identical organisms based on the supplied genome sequence into
@@ -666,8 +666,8 @@
<li>
<strong><a name="InjectParasite">InjectParasite</a></strong>
- <<span style="color: #008800">string filename</span>> <<span style="color: #008800">string label</span>>
- [<span style="color: #008800">int cell_start=0</span>] [<span style="color: #008800">int cell_end=-1</span>]
+ <<span class="cmdarg">string filename</span>> <<span class="cmdarg">string label</span>>
+ [<span class="cmdarg">int cell_start=0</span>] [<span class="cmdarg">int cell_end=-1</span>]
<p>
Attempt to inject a parasite genome into the supplied population cell
@@ -676,10 +676,10 @@
</li>
<li>
<strong><a name="InjectParasitePair">InjectParasitePair</a></strong>
- <<span style="color: #008800">string filename_genome</span>> <<span style="color: #008800">string filename_parasite</span>>
- <<span style="color: #008800">string label</span>> [<span style="color: #008800">int cell_start=0</span>]
- [<span style="color: #008800">int cell_end=-1</span>] [<span style="color: #008800">double merit=-1</span>]
- [<span style="color: #008800">int lineage_label=0</span>] [<span style="color: #008800">double neutral_metric=0</span>]
+ <<span class="cmdarg">string filename_genome</span>> <<span class="cmdarg">string filename_parasite</span>>
+ <<span class="cmdarg">string label</span>> [<span class="cmdarg">int cell_start=0</span>]
+ [<span class="cmdarg">int cell_end=-1</span>] [<span class="cmdarg">double merit=-1</span>]
+ [<span class="cmdarg">int lineage_label=0</span>] [<span class="cmdarg">double neutral_metric=0</span>]
<p>
Inject host parasite pairs into the population cell range specified.
@@ -688,7 +688,7 @@
<li>
<strong><a name="KillProb">KillProb</a></strong>
- [<span style="color: #008800">double probability=0.9</span>]
+ [<span class="cmdarg">double probability=0.9</span>]
<p>
Using the specified probability, test each organism to see if it is killed off.
@@ -696,7 +696,7 @@
</li>
<li>
<strong><a name="KillRate">KillRate</a></strong>
- [<span style="color: #008800">double probability=0.9</span>]
+ [<span class="cmdarg">double probability=0.9</span>]
<p>
Randomly removes a certain proportion of the population.
@@ -709,8 +709,8 @@
</li>
<li>
<strong><a name="KillRectangle">KillRectangle</a></strong>
- [<span style="color: #008800">int x1=0</span>] [<span style="color: #008800">int y1=0</span>]
- [<span style="color: #008800">int x2=0</span>] [<span style="color: #008800">int y2=0</span>]
+ [<span class="cmdarg">int x1=0</span>] [<span class="cmdarg">int y1=0</span>]
+ [<span class="cmdarg">int x2=0</span>] [<span class="cmdarg">int y2=0</span>]
<p>
Kill off all organisms in a rectangle defined by the points (x1, y1) and (x2, y2).
@@ -718,27 +718,27 @@
</li>
<li>
<strong><a name="SerialTransfer">SerialTransfer</a></strong>
- [<span style="color: #008800">int transfer_size=1</span>] [<span style="color: #008800">int ignore_deads=1</span>]
+ [<span class="cmdarg">int transfer_size=1</span>] [<span class="cmdarg">int ignore_deads=1</span>]
<p>
Similar to KillProb, but we specify the exact number of organisms to
- keep alive after the event. The <span style="color: #008800">ignore_deads</span>
+ keep alive after the event. The <span class="cmdarg">ignore_deads</span>
argument determines whether only living organisms are retainted.
</p>
</li>
<li>
<strong><a name="SetMutProb">SetMutProb</a></strong>
- [<span style="color: #008800">string mut_type='copy'</span>] [<span style="color: #008800">double prob=0.0</span>]
- [<span style="color: #008800">int start_cell=-1</span>] [<span style="color: #008800">int end_cell=-1</span>]
+ [<span class="cmdarg">string mut_type='copy'</span>] [<span class="cmdarg">double prob=0.0</span>]
+ [<span class="cmdarg">int start_cell=-1</span>] [<span class="cmdarg">int end_cell=-1</span>]
<p>
</p>
</li>
<li>
<strong><a name="ModMutProb">ModMutProb</a></strong>
- [<span style="color: #008800">string mut_type='copy'] [<span style="color: #008800">double prob=0.0</span>]
- [<span style="color: #008800">int start_cell=-1</span>] [<span style="color: #008800">int end_cell=-1</span>]
+ [<span class="cmdarg">string mut_type='copy'] [<span class="cmdarg">double prob=0.0</span>]
+ [<span class="cmdarg">int start_cell=-1</span>] [<span class="cmdarg">int end_cell=-1</span>]
<p>
</p>
@@ -753,7 +753,7 @@
<li>
<strong><a name="CompeteDemes">CompeteDemes</a></strong>
- [<span style="color: #008800">int type=1</span>]
+ [<span class="cmdarg">int type=1</span>]
<p>
</p>
@@ -766,7 +766,7 @@
</li>
<li>
<strong><a name="CopyDeme">CopyDeme</a></strong>
- <<span style="color: #008800">int src_id</span>> <<span style="color: #008800">int dest_id</span>>
+ <<span class="cmdarg">int src_id</span>> <<span class="cmdarg">int dest_id</span>>
<p>
</p>
@@ -774,8 +774,8 @@
<li>
<strong><a name="SeverGridCol">SeverGridCol</a></strong>
- [<span style="color: #008800">int col_id=-1</span>] [<span style="color: #008800">int min_row=0</span>]
- [<span style="color: #008800">int max_row=-1</span>]
+ [<span class="cmdarg">int col_id=-1</span>] [<span class="cmdarg">int min_row=0</span>]
+ [<span class="cmdarg">int max_row=-1</span>]
<p>
Remove the connections between cells along a column in an Avida grid.
@@ -783,8 +783,8 @@
</li>
<li>
<strong><a name="SeverGridRow">SeverGridRow</a></strong>
- [<span style="color: #008800">int row_id=-1</span>] [<span style="color: #008800">int min_col=0</span>]
- [<span style="color: #008800">int max_col=-1</span>]
+ [<span class="cmdarg">int row_id=-1</span>] [<span class="cmdarg">int min_col=0</span>]
+ [<span class="cmdarg">int max_col=-1</span>]
<p>
Remove the connections between cells along a row in an Avida grid.
@@ -792,8 +792,8 @@
</li>
<li>
<strong><a name="JoinGridCol">JoinGridCol</a></strong>
- [<span style="color: #008800">int col_id=-1</span>] [<span style="color: #008800">int min_row=0</span>]
- [<span style="color: #008800">int max_row=-1</span>]
+ [<span class="cmdarg">int col_id=-1</span>] [<span class="cmdarg">int min_row=0</span>]
+ [<span class="cmdarg">int max_row=-1</span>]
<p>
Add connections between cells along a column in an Avida grid.
@@ -801,8 +801,8 @@
</li>
<li>
<strong><a name="JoinGridRow">JoinGridRow</a></strong>
- [<span style="color: #008800">int row_id=-1</span>] [<span style="color: #008800">int min_col=0</span>]
- [<span style="color: #008800">int max_col=-1</span>]
+ [<span class="cmdarg">int row_id=-1</span>] [<span class="cmdarg">int min_col=0</span>]
+ [<span class="cmdarg">int max_col=-1</span>]
<p>
Add connections between cells along a row in an Avida grid.
@@ -811,8 +811,8 @@
<li>
<strong><a name="ConnectCells">ConnectCells</a></strong>
- <<span style="color: #008800">int cellA_x</span>> <<span style="color: #008800">int cellA_y</span>>
- <<span style="color: #008800">int cellB_x</span>> <<span style="color: #008800">int cellB_y</span>>
+ <<span class="cmdarg">int cellA_x</span>> <<span class="cmdarg">int cellA_y</span>>
+ <<span class="cmdarg">int cellB_x</span>> <<span class="cmdarg">int cellB_y</span>>
<p>
Connects a pair of specified cells.
@@ -820,8 +820,8 @@
</li>
<li>
<strong><a name="DisconnectCells">DisconnectCells</a></strong>
- <<span style="color: #008800">int cellA_x</span>> <<span style="color: #008800">int cellA_y</span>>
- <<span style="color: #008800">int cellB_x</span>> <<span style="color: #008800">int cellB_y</span>>
+ <<span class="cmdarg">int cellA_x</span>> <<span class="cmdarg">int cellA_y</span>>
+ <<span class="cmdarg">int cellB_x</span>> <<span class="cmdarg">int cellB_y</span>>
<p>
Disconnects a pair of specified cells.
@@ -841,70 +841,70 @@
<ul>
<li>
<strong><a name="InjectResource">InjectResource</a></strong>
- <<span style="color: #008800">string res_name</span>> <<span style="color: #008800">double res_count</span>>
+ <<span class="cmdarg">string res_name</span>> <<span class="cmdarg">double res_count</span>>
<p>
Inject (add) a specified amount of a specified resource.
- <span style="color: #008800">res_name</span> must already exist as
+ <span class="cmdarg">res_name</span> must already exist as
a resource in environment file.
</p>
</li>
<li>
<strong><a name="InjectScaledResource">InjectScaledResource</a></strong>
- <<span style="color: #008800">string res_name</span>> <<span style="color: #008800">double res_count</span>>
+ <<span class="cmdarg">string res_name</span>> <<span class="cmdarg">double res_count</span>>
<p>
</p>
</li>
<li>
<strong><a name="OutflowScaledResource">OutflowScaledResource</a></strong>
- <<span style="color: #008800">string res_name</span>> <<span style="color: #008800">double res_percent</span>>
+ <<span class="cmdarg">string res_name</span>> <<span class="cmdarg">double res_percent</span>>
<p>
</p>
</li>
<li>
<strong><a name="SetResource">SetResource</a></strong>
- <<span style="color: #008800">string res_name</span>> <<span style="color: #008800">double res_count</span>>
+ <<span class="cmdarg">string res_name</span>> <<span class="cmdarg">double res_count</span>>
<p>
Set the resource amount to a specific level.
- <span style="color: #008800">res_name</span> must already exist as
+ <span class="cmdarg">res_name</span> must already exist as
a resource in environment file.
</p>
</li>
<li>
<strong><a name="SetReactionValue">SetReactionValue</a></strong>
- <<span style="color: #008800">string reaction_name</span>> <<span style="color: #008800">double value</span>>
+ <<span class="cmdarg">string reaction_name</span>> <<span class="cmdarg">double value</span>>
<p>
Set the reaction value to a specific level.
- <span style="color: #008800">reaction_name</span> must already
+ <span class="cmdarg">reaction_name</span> must already
exist in the environment file.
- <span style="color: #008800">value</span> can be negative.
+ <span class="cmdarg">value</span> can be negative.
</p>
</li>
<li>
<strong><a name="SetReactionValueMult">SetReactionValueMult</a></strong>
- <<span style="color: #008800">string reaction_name</span>> <<span style="color: #008800">double value</span>>
+ <<span class="cmdarg">string reaction_name</span>> <<span class="cmdarg">double value</span>>
<p>
- Multiply the reaction value by the <span style="color: #008800">value</span>.
- <span style="color: #008800">reaction_name</span> must already
+ Multiply the reaction value by the <span class="cmdarg">value</span>.
+ <span class="cmdarg">reaction_name</span> must already
exist in the environment file.
- <span style="color: #008800">value</span> can be negative.
+ <span class="cmdarg">value</span> can be negative.
</p>
</li>
<li>
<strong><a name="SetReactionInst">SetReactionInst</a></strong>
- <<span style="color: #008800">string reaction_name</span>> <<span style="color: #008800">string inst</span>>
+ <<span class="cmdarg">string reaction_name</span>> <<span class="cmdarg">string inst</span>>
<p>
Set the instruction triggered by this reaction.
- <span style="color: #008800">reaction_name</span> must already
+ <span class="cmdarg">reaction_name</span> must already
exist in the environment file.
- <span style="color: #008800">inst</span> must be in the instruction set.
+ <span class="cmdarg">inst</span> must be in the instruction set.
</p>
</li>
</ul>
@@ -919,7 +919,7 @@
<ul>
<li>
<strong><a name="SaveClone">SaveClone</a></strong>
- [<span style="color: #008800">string fname=''</span>]
+ [<span class="cmdarg">string fname=''</span>]
<p>
Save a clone of this organism to the file specified; if no filename is
@@ -933,7 +933,7 @@
</li>
<li>
<strong><a name="LoadClone">LoadClone</a></strong>
- <<span style="color: #008800">string fname</span>>
+ <<span class="cmdarg">string fname</span>>
<p>
</p>
@@ -941,7 +941,7 @@
<li>
<strong><a name="LoadPopulation">LoadPopulation</a></strong>
- <<span style="color: #008800">string fname</span>> [<span style="color: #008800">int update=-1</span>]
+ <<span class="cmdarg">string fname</span>> [<span class="cmdarg">int update=-1</span>]
<p>
Sets up a population based on a save file such as written out by
@@ -952,14 +952,14 @@
<li>
<strong><a name="DumpPopulation">DumpPopulation</a></strong>
- [<span style="color: #008800">string fname=''</span>]
+ [<span class="cmdarg">string fname=''</span>]
<p>
</p>
</li>
<li>
<strong><a name="SavePopulation">SavePopulation</a></strong>
- [<span style="color: #008800">string fname=''</span>]
+ [<span class="cmdarg">string fname=''</span>]
<p>
Save the genotypes and lots of statistics about the population to the
@@ -971,21 +971,21 @@
</li>
<li>
<strong><a name="SaveSexPopulation">SaveSexPopulation</a></strong>
- [<span style="color: #008800">string fname=''</span>]
+ [<span class="cmdarg">string fname=''</span>]
<p>
</p>
</li>
<li>
<strong><a name="SaveParasitePopulation">SaveParasitePopulation</a></strong>
- [<span style="color: #008800">string fname=''</span>]
+ [<span class="cmdarg">string fname=''</span>]
<p>
</p>
</li>
<li>
<strong><a name="SaveHistoricPopulation">SaveHistoricPopulation</a></strong>
- [<span style="color: #008800">int back_dist=-1</span>] [<span style="color: #008800">string fname=''</span>]
+ [<span class="cmdarg">int back_dist=-1</span>] [<span class="cmdarg">string fname=''</span>]
<p>
This action is used to output all of the ancestors of the currently
@@ -994,7 +994,7 @@
</li>
<li>
<strong><a name="SaveHistoricSexPopulation">SaveHistoricSexPopulation</a></strong>
- [<span style="color: #008800">string fname=''</span>]
+ [<span class="cmdarg">string fname=''</span>]
<p>
</p>
@@ -1025,9 +1025,9 @@
<ul>
<li>
<strong><a name="AnalyzeLandscape">AnalyzeLandscape</a></strong>
- [<span style="color: #008800">filename='land-analyze.dat'</span>] [<span style="color: #008800">int trials=1000</span>]
- [<span style="color: #008800">int min_found=0</span>] [<span style="color: #008800">int max_trials=0</span>]
- [<span style="color: #008800">int max_dist=10</span>]
+ [<span class="cmdarg">filename='land-analyze.dat'</span>] [<span class="cmdarg">int trials=1000</span>]
+ [<span class="cmdarg">int min_found=0</span>] [<span class="cmdarg">int max_trials=0</span>]
+ [<span class="cmdarg">int max_dist=10</span>]
<p>
</p>
@@ -1043,8 +1043,8 @@
</li>
<li>
<strong><a name="FullLandscape">FullLandscape</a></strong>
- [<span style="color: #008800">string filename='land-full.dat'</span>] [<span style="color: #008800">int distance=1</span>]
- [<span style="color: #008800">string entropy_file=''</span>] [<span style="color: #008800">string sitecount_file=''</span>]
+ [<span class="cmdarg">string filename='land-full.dat'</span>] [<span class="cmdarg">int distance=1</span>]
+ [<span class="cmdarg">string entropy_file=''</span>] [<span class="cmdarg">string sitecount_file=''</span>]
<p>
Do a landscape analysis of the dominant genotype or current batch of genotypes,
@@ -1055,52 +1055,52 @@
</li>
<li>
<strong><a name="DeletionLandscape">DeletionLandscape</a></strong>
- [<span style="color: #008800">string filename='land-del.dat'</span>] [<span style="color: #008800">int distance=1</span>]
- [<span style="color: #008800">string sitecount_file=''</span>]
+ [<span class="cmdarg">string filename='land-del.dat'</span>] [<span class="cmdarg">int distance=1</span>]
+ [<span class="cmdarg">string sitecount_file=''</span>]
<p>
</p>
</li>
<li>
<strong><a name="InsertionLandscape">InsertionLandscape</a></strong>
- [<span style="color: #008800">string filename='land-ins.dat'</span>] [<span style="color: #008800">int distance=1</span>]
- [<span style="color: #008800">string sitecount_file=''</span>]
+ [<span class="cmdarg">string filename='land-ins.dat'</span>] [<span class="cmdarg">int distance=1</span>]
+ [<span class="cmdarg">string sitecount_file=''</span>]
<p>
</p>
</li>
<li>
<strong><a name="PredictWLandscape">PredictWLandscape</a></strong>
- [<span style="color: #008800">string filename='land-predict.dat'</span>]
+ [<span class="cmdarg">string filename='land-predict.dat'</span>]
<p>
</p>
</li>
<li>
<strong><a name="PredictNuLandscape">PredictNuLandscape</a></strong>
- [<span style="color: #008800">string filename='land-predict.dat'</span>]
+ [<span class="cmdarg">string filename='land-predict.dat'</span>]
<p>
</p>
</li>
<li>
<strong><a name="RandomLandscape">RandomLandscape</a></strong>
- [<span style="color: #008800">string filename='land-random.dat'</span>] [<span style="color: #008800">int distance=1</span>]
- [<span style="color: #008800">int trials=0</span>]
+ [<span class="cmdarg">string filename='land-random.dat'</span>] [<span class="cmdarg">int distance=1</span>]
+ [<span class="cmdarg">int trials=0</span>]
<p>
</p>
</li>
<li>
<strong><a name="SampleLandscape">SampleLandscape</a></strong>
- [<span style="color: #008800">string filename='land-sample.dat'</span>] [<span style="color: #008800">int trials=0</span>]
+ [<span class="cmdarg">string filename='land-sample.dat'</span>] [<span class="cmdarg">int trials=0</span>]
<p>
</p>
</li>
<li>
<strong><a name="HillClimb">HillClimb</a></strong>
- [<span style="color: #008800">string filename='hillclimb.dat'</span>]
+ [<span class="cmdarg">string filename='hillclimb.dat'</span>]
<p>
Does a hill climb with the dominant genotype.
@@ -1108,21 +1108,21 @@
</li>
<li>
<strong><a name="HillClimbNeut">HillClimbNeut</a></strong>
- [<span style="color: #008800">string filename='hillclimb.dat'</span>]
+ [<span class="cmdarg">string filename='hillclimb.dat'</span>]
<p>
</p>
</li>
<li>
<strong><a name="HillClimbRand">HillClimbRand</a></strong>
- [<span style="color: #008800">string filename='hillclimb.dat'</span>]
+ [<span class="cmdarg">string filename='hillclimb.dat'</span>]
<p>
</p>
</li>
<li>
<strong><a name="PairTestLandscape">PairTestLandscape</a></strong>
- [<span style="color: #008800">string filename=''</span>] [<span style="color: #008800">int sample_size=0</span>]
+ [<span class="cmdarg">string filename=''</span>] [<span class="cmdarg">int sample_size=0</span>]
<p>
If sample_size = 0, pairtest the full landscape.
@@ -1148,20 +1148,20 @@
</li>
<li>
<strong><a name="ExitAveLineageLabelGreater">ExitAveLineageLabelGreater</a></strong>
- <<span style="color: #008800">double threshold</span>>
+ <<span class="cmdarg">double threshold</span>>
<p>
Halts the run if the current average lineage label is larger
- than <span style="color: #008800">threshold</span>.
+ than <span class="cmdarg">threshold</span>.
</p>
</li>
<li>
<strong><a name="ExitAveLineageLabelLess">ExitAveLineageLabelLess</a></strong>
- <<span style="color: #008800">double threshold</span>>
+ <<span class="cmdarg">double threshold</span>>
<p>
Halts the run if the current average lineage label is smaller
- than <span style="color: #008800">threshold</span>.
+ than <span class="cmdarg">threshold</span>.
</p>
</li>
</ul>
Modified: development/documentation/analyze.html
===================================================================
--- development/documentation/analyze.html 2006-09-02 15:01:28 UTC (rev 924)
+++ development/documentation/analyze.html 2006-09-04 01:25:47 UTC (rev 925)
@@ -5,8 +5,8 @@
</head>
<body>
-<div style="float: right">
-Revised 2006-08-28 DMB
+<div class="revision">
+Revised 2006-09-03 DMB
</div>
<p><a href="index.html">Return to the Index</a></p>
@@ -33,10 +33,10 @@
The rest of this file describes how individual commands work, as well
as some notes on other languages features, like how to use variables. As
a formatting guide, command arguments will be presented between brackets,
-such as [<span style="color: #0000AA">filename</span>]. If that argument is
+such as [<span class="cmdarg">filename</span>]. If that argument is
mandatory, it will be in blue. If it is optional, it will be in green, and
(if relevant) a default value will be listed, such as
-[<span style="color: #008800">filename='output.dat'</span>].
+[<span class="cmdargopt">filename='output.dat'</span>].
</p>
<p> </p>
@@ -55,20 +55,20 @@
There are currently four ways to load in genotypes:
</p>
<dl>
-<dt><strong>LOAD_ORGANISM [<font color="#0000AA">filename</font>]</strong></dt>
+<dt><strong>LOAD_ORGANISM [<span class="cmdarg">filename</span>]</strong></dt>
<dd>
Load in a normal single-organism file of the type that is output
from Avida. These consist of lots of organismal information inside
of comments, and then the full genome of the organism with one
instruction per line.
</dd>
-<dt><strong>LOAD [<font color="#0000AA">filename</font>]</strong></dt>
+<dt><strong>LOAD [<span class="cmdarg">filename</span>]</strong></dt>
<dd>
Load in a file that contains a list of genotypes, one-per-line with
additional informaiton about those genotypes. Avida now includes a header
on such files indicating the values containted in each column.
</dd>
-<dt><strong>LOAD_SEQUENCE [<font color="#0000AA">sequence</font>]</strong></dt>
+<dt><strong>LOAD_SEQUENCE [<span class="cmdarg">sequence</span>]</strong></dt>
<dd>
Load in a user-provided sequence as the genotype. Avida has a
symbol associated with each instruction; this command is simply
@@ -76,9 +76,9 @@
into a proper genotype.
</dd>
<dt><strong>
- LOAD_MULTI_DETAIL [<font color="#0000AA">start-UD</font>]
- [<font color="#0000AA">step-UD</font>] [<font color="#0000AA">stop-UD</font>]
- [<font color="#008800">dir='./'</font>] [<font color="#008800">start batch=0</font>]
+ LOAD_MULTI_DETAIL [<span class="cmdarg">start-UD</span>]
+ [<span class="cmdarg">step-UD</span>] [<span class="cmdarg">stop-UD</span>]
+ [<span class="cmdargopt">dir='./'</span>] [<span class="cmdargopt">start batch=0</span>]
</strong></dt>
<dd>
Allows the user to load in multiple detail files at once, one per
@@ -109,23 +109,23 @@
</p>
<dl>
-<dt><strong>SET_BATCH [<font color="#0000AA">id</font>]</strong></dt>
+<dt><strong>SET_BATCH [<span class="cmdarg">id</span>]</strong></dt>
<dd>
Set the batch that is currently active; the initial active batch
at the start of a program is 0.
</dd>
-<dt><strong>NAME_BATCH [<font color="#0000AA">name</font>]</strong></dt>
+<dt><strong>NAME_BATCH [<span class="cmdarg">name</span>]</strong></dt>
<dd>
Attach a name to the current batch. Some of the printing methods
will print data from multiple batches, and we want the data from each
batch to be attached to a meaningful identifier.
</dd>
-<dt><strong>PURGE_BATCH [<font color="#008800">id=current</font>]</strong></dt>
+<dt><strong>PURGE_BATCH [<span class="cmdargopt">id=current</span>]</strong></dt>
<dd>
Remove all genotypes in the specified batch (if no argument is given,
the current batch is purged.
</dd>
-<dt><strong>DUPLICATE [<font color="#0000AA">id1</font>] [<font color="#008800">id2=current</font>]</strong></dt>
+<dt><strong>DUPLICATE [<span class="cmdarg">id1</span>] [<span class="cmdargopt">id2=current</span>]</strong></dt>
<dd>
Copy the genotypes from batch id1 into id2. By default,
copy id1 into the current batch. Note that duplicate is
@@ -160,13 +160,13 @@
recommended if you're in interactive mode.
<br />Levels: SILENT, NORMAL, ON, DETAILS
</dd>
-<dt><strong>SYSTEM [<font color="#0000AA">command</font>]</strong></dt>
+<dt><strong>SYSTEM [<span class="cmdarg">command</span>]</strong></dt>
<dd>
Run the command listed on the command line. This is particularly
useful if you need to unzip files before you can use them, or if
you want to delete files no longer in use.
</dd>
-<dt><strong>INCLUDE [<font color="#0000AA">filename</font>]</strong></dt>
+<dt><strong>INCLUDE [<span class="cmdarg">filename</span>]</strong></dt>
<dd>
Include another file into this one and run its contents immediately.
This is useful if you have some pre-written routines that you want
@@ -181,8 +181,8 @@
processing done before interactive mode starts. You can type <kbd>quit</kbd>
at any point to continue with the normal processing of the file.
</dd>
-<dt><strong>DEBUG [<font color="#0000AA">message</font>]</strong></dt>
-<dt><strong>ECHO [<font color="#0000AA">message</font>]</strong></dt>
+<dt><strong>DEBUG [<span class="cmdarg">message</span>]</strong></dt>
+<dt><strong>ECHO [<span class="cmdarg">message</span>]</strong></dt>
<dd>
These are both <em>echo</em> commands that will print a message (the
arguments given) onto the screen. If there are any variables (see
@@ -203,7 +203,7 @@
</p>
<dl>
-<dt><strong>RECALCULATE [<font color="#008800">use_resources=0</font>]</strong></dt>
+<dt><strong>RECALCULATE [<span class="cmdargopt">use_resources=0</span>]</strong></dt>
<dd>
Run all of the genotypes in the current batch through a test CPU
and record the measurements taken (fitness, gestation time, etc.).
@@ -212,7 +212,7 @@
test cpu will use resources when it runs. For more information
on resources, see the <a href="#USING_RESOURCES">summary</a> below.
</dd>
-<dt><strong>FIND_GENOTYPE [<font color="#008800">type='num_cpus' ...</font>]</strong></dt>
+<dt><strong>FIND_GENOTYPE [<span class="cmdargopt">type='num_cpus' ...</span>]</strong></dt>
<dd>
Remove all genotypes but the one selected. Type indicates which
genotype to choose. Options available for type are <em>num_cpus</em> (to
@@ -224,7 +224,7 @@
this command, in which case all those genotypes in that list will be
preserved and the remainder deleted.
</dd>
-<dt><strong>FIND_ORGANISM [<font color="#008800">random</font>]</strong></dt>
+<dt><strong>FIND_ORGANISM [<span class="cmdargopt">random</span>]</strong></dt>
<dd>
Picks out a random organism from the population and removes all
others. It is different from FIND_GENOTYPE because it takes into
@@ -232,7 +232,7 @@
more than one organisms, list the word 'random' multiple times. This
is essentially sampling without replacement from the population.
</dd>
-<dt><strong>FIND_LINEAGE [<font color="#008800">type="num_cpus"</font>]</strong></dt>
+<dt><strong>FIND_LINEAGE [<span class="cmdargopt">type="num_cpus"</span>]</strong></dt>
<dd>
Delete everything except the lineage from the chosen genotype back
to the most distant ancestor available. This command will only
@@ -240,8 +240,8 @@
genotypes. Type is the same as the FIND_GENOTYPE command.
</dd>
<dt><strong>
- FIND_SEX_LINEAGE [<font color="#008800">type="num_cpus"</font>]
- [<font color="#008800">parent_method="rec_region_size"</font>]
+ FIND_SEX_LINEAGE [<span class="cmdargopt">type="num_cpus"</span>]
+ [<span class="cmdargopt">parent_method="rec_region_size"</span>]
</strong></dt>
<dd>
Delete everything except the lineage from the chosen genotype back
@@ -263,7 +263,7 @@
must first be run on the batch in order for the alignment to be
possible.
</dd>
-<dt><strong>SAMPLE_ORGANISMS [<font color="#0000AA">fraction</font>] [<font color="#008800">test_viable=0</font>]</strong></dt>
+<dt><strong>SAMPLE_ORGANISMS [<span class="cmdarg">fraction</span>] [<span class="cmdargopt">test_viable=0</span>]</strong></dt>
<dd>
Keep only fraction of organisms in the current batch. This
is done per organism, <em>not</em> per genotype. Thus, genotypes of high
@@ -271,12 +271,12 @@
of abundance 1 will either stay or be removed entirely. If test_viable is
set to 1, sample only from the viable organisms.
</dd>
-<dt><strong>SAMPLE_GENOTYPES [<font color="#0000AA">fraction</font>] [<font color="#008800">test_viable=0</font>]</strong></dt>
+<dt><strong>SAMPLE_GENOTYPES [<span class="cmdarg">fraction</span>] [<span class="cmdargopt">test_viable=0</span>]</strong></dt>
<dd>
Keep only fraction of genotypes in the current batch. If test_viable is
set to 1, sample only from the viable genotypes.
</dd>
-<dt><strong>RENAME [<font color="#008800">start_id=0</font>]</strong></dt>
+<dt><strong>RENAME [<span class="cmdargopt">start_id=0</span>]</strong></dt>
<dd>
Change the id numbers of all the genotypes to start at a given value.
Often in long runs we will be dealing with ID's in the millions. In
@@ -295,14 +295,14 @@
</p>
<dl>
-<dt><strong>PRINT [<font color="#008800">dir='archive/'</font>] [<font color="#008800">filename</font>]</strong></dt>
+<dt><strong>PRINT [<span class="cmdargopt">dir='archive/'</span>] [<span class="cmdargopt">filename</span>]</strong></dt>
<dd>
Print the genotypes from the current batch as individual files (one
genotype per file) in the directory given. If no filename is specified,
the files will be named by the genotype name, with a <kbd>.gen</kbd> appended to
them. Specifying the filename is useful when printing a single genotype.
</dd>
-<dt><strong>TRACE [<font color="#008800">dir='archive/'</font>] [ <font color="#008800">use_resources=0</font>]</strong></dt>
+<dt><strong>TRACE [<span class="cmdargopt">dir='archive/'</span>] [ <span class="cmdargopt">use_resources=0</span>]</strong></dt>
<dd>
Trace all of the genotypes and print a listing of their execution.
This will show step-by-step the status of all of the CPU components
@@ -312,14 +312,14 @@
resources when it runs. For more information on resources, see the
<a href="#USING_RESOURCES">summary</a> below.
</dd>
-<dt><strong>PRINT_TASKS [<font color="#008800">file='tasks.dat'</font>]</strong></dt>
+<dt><strong>PRINT_TASKS [<span class="cmdargopt">file='tasks.dat'</span>]</strong></dt>
<dd>
This will print out the tasks doable by each genotype, one per line
in the output file specified. Note that this information must either
have been loaded in, or a RECALCULATE must have been run to collect
it.
</dd>
-<dt><strong>DETAIL [<font color="#008800">file='detail.dat'</font>] [<font color="#008800">format ...</font>]</strong></dt>
+<dt><strong>DETAIL [<span class="cmdargopt">file='detail.dat'</span>] [<span class="cmdargopt">format ...</span>]</strong></dt>
<dd>
Print out all of the stats for each genotype, one per line. The
format indicates the layout of columns in the file. If the filename
@@ -328,31 +328,31 @@
<a href="#OUTPUT_FORMATS">Output Formats</a> below.
</dd>
<dt><strong>
- DETAIL_TIMELINE [<font color="#008800">file='detail_timeline.dat'</font>]
- [<font color="#008800">time_step=100</font>]
- [<font color="#008800">max_time=100000</font>]
+ DETAIL_TIMELINE [<span class="cmdargopt">file='detail_timeline.dat'</span>]
+ [<span class="cmdargopt">time_step=100</span>]
+ [<span class="cmdargopt">max_time=100000</span>]
</strong></dt>
<dd>
Details a time-sequence of dump files.
</dd>
<dt><strong>
- DETAIL_BATCHES [<font color="#008800">file='detail_baches.dat'</font>]
- [<font color="#008800">format ...</font>]
+ DETAIL_BATCHES [<span class="cmdargopt">file='detail_baches.dat'</span>]
+ [<span class="cmdargopt">format ...</span>]
</strong></dt>
<dd>
Details all batches.
</dd>
<dt><strong>
- DETAIL_INDEX [<font color="#0000AA">file</font>]
- [<font color="#0000AA">min_batch</font>] [<font color="#0000AA">max_batch</font>]
- [<font color="#008800">format ...</font>]
+ DETAIL_INDEX [<span class="cmdarg">file</span>]
+ [<span class="cmdarg">min_batch</span>] [<span class="cmdarg">max_batch</span>]
+ [<span class="cmdargopt">format ...</span>]
</strong></dt>
<dd>
Detail all the batches between min_batch and max_batch.
</dd>
<dt><strong>
- DETAIL_AVERAGE [<font color="#008800">file="detail.dat"</font>]
- [<font color="#008800">format ...</font>]
+ DETAIL_AVERAGE [<span class="cmdargopt">file="detail.dat"</span>]
+ [<span class="cmdargopt">format ...</span>]
</strong></dt>
<dd>
Detail the current batch, but print out the average for each argument, as opposed to the
@@ -373,8 +373,8 @@
<dl>
<dt><strong>
- ANALYZE_EPISTASIS [<font color="#008800">file='epistasis.dat'</font>]
- [<font color="#008800">num_test=(all)</font>]
+ ANALYZE_EPISTASIS [<span class="cmdargopt">file='epistasis.dat'</span>]
+ [<span class="cmdargopt">num_test=(all)</span>]
</strong></dt>
<dd>
For each genotype in the current batch, test possible
@@ -384,8 +384,8 @@
number to be tested.
</dd>
<dt><strong>
- MAP_TASKS [<font color="#008800">dir="phenotype/"</font>]
- [<font color="#008800">flags ...</font>] [<font color="#008800">format ...</font>]
+ MAP_TASKS [<span class="cmdargopt">dir="phenotype/"</span>]
+ [<span class="cmdargopt">flags ...</span>] [<span class="cmdargopt">format ...</span>]
</strong></dt>
<dd>
Construct a genotype-phenotype array for each genotype in the
@@ -396,8 +396,8 @@
consecutive genotypes in a lineage.
</dd>
<dt><strong>
- MAP_MUTATIONS [<font color="#008800">dir="mutations/"</font>]
- [<font color="#008800">flags ...</font>]
+ MAP_MUTATIONS [<span class="cmdargopt">dir="mutations/"</span>]
+ [<span class="cmdargopt">flags ...</span>]
</strong></dt>
<dd>
Construct a genome-mutation array for each genotype in the
@@ -408,8 +408,8 @@
If the 'html' flag is used, the charts will be output in HTML format.
</dd>
<dt><strong>
- MAP_DEPTH [<font color="#008800">filename='depth_map.dat'</font>]
- [<font color="#008800">min_batch=0</font>] [<font color="#008800">max_batch=cur_batch-1</font>]
+ MAP_DEPTH [<span class="cmdargopt">filename='depth_map.dat'</span>]
+ [<span class="cmdargopt">min_batch=0</span>] [<span class="cmdargopt">max_batch=cur_batch-1</span>]
</strong></dt>
<dd>
This will create a depth map (like those we use for phylogeny
@@ -418,9 +418,9 @@
a LOAD_MULTI_DETAIL.
</dd>
<dt><strong>
- AVERAGE_MODULATITY [<font color="#008800">file='modularity.dat'</font>]
- [<font color="#008800">task.0 task.1 task.2 task.3 task.4 task.5
- task.6 task.7 task.8</font>]
+ AVERAGE_MODULATITY [<span class="cmdargopt">file='modularity.dat'</span>]
+ [<span class="cmdargopt">task.0 task.1 task.2 task.3 task.4 task.5
+ task.6 task.7 task.8</span>]
</strong></dt>
<dd>
Calculate several modularity measuers, such as how many tasks is an
@@ -431,16 +431,16 @@
output format and works with only 1 and 2 input tasks.
</dd>
<dt><strong>
- HAMMING [<font color="#008800">file="hamming.dat"</font>]
- [<font color="#008800">b1=current</font>] [<font color="#008800">b2=b1</font>]
+ HAMMING [<span class="cmdargopt">file="hamming.dat"</span>]
+ [<span class="cmdargopt">b1=current</span>] [<span class="cmdargopt">b2=b1</span>]
</strong></dt>
<dd>
Calculate the hamming distance between batches b1 and b2. If only
one batch is given, calculations are on all pairs within that batch.
</dd>
<dt><strong>
- LEVENSTEIN [<font color="#008800">file='lev.dat'</font>]
- [<font color="#008800">batch1</font>] [<font color="#008800">b2=b1</font>]
+ LEVENSTEIN [<span class="cmdargopt">file='lev.dat'</span>]
+ [<span class="cmdargopt">batch1</span>] [<span class="cmdargopt">b2=b1</span>]
</strong></dt>
<dd>
Calculate the levenstein distance (edit distance) between batches b1
@@ -449,9 +449,9 @@
move from one sequence to the other.
</dd>
<dt><strong>
- SPECIES [<font color="#008800">file='species.dat'</font>]
- [<font color="#0000AA">batch1</font>] [<font color="#0000AA">batch2</font>]
- [<font color="#0000AA">num_recombinants</font>]
+ SPECIES [<span class="cmdargopt">file='species.dat'</span>]
+ [<span class="cmdarg">batch1</span>] [<span class="cmdarg">batch2</span>]
+ [<span class="cmdarg">num_recombinants</span>]
</strong></dt>
<dd>
Calculates the percentage of non-viable recombinants between all
@@ -463,8 +463,8 @@
</dd>
<dt><strong>
RECOMBINE
- [<font color="#0000AA">batch1</font>] [<font color="#0000AA">batch2</font>]
- [<font color="#0000AA">batch3</font>] [<font color="#0000AA">num_recombinants</font>]
+ [<span class="cmdarg">batch1</span>] [<span class="cmdarg">batch2</span>]
+ [<span class="cmdarg">batch3</span>] [<span class="cmdarg">num_recombinants</span>]
</strong></dt>
<dd>
Similar to Species command, but instead of calculating things on the spot,
@@ -513,7 +513,7 @@
This command first prints the whether or not the test cpu is using
resources. Then it will print the concentration for each resource.
</dd>
-<dt><strong>LOAD_RESOURCES [<font color="#008800">file_name="resource.dat"</font>]</strong></dt>
+<dt><strong>LOAD_RESOURCES [<span class="cmdargopt">file_name="resource.dat"</span>]</strong></dt>
<dd>
This command loads a time oriented list of resource concentrations.
The command takes a file name containing this type of data, and
@@ -658,13 +658,13 @@
</p>
<dl>
-<dt><strong>SET [<font color="#0000AA">variable</font>] [<font color="#0000AA">value</font>]</strong></dt>
+<dt><strong>SET [<span class="cmdarg">variable</span>] [<span class="cmdarg">value</span>]</strong></dt>
<dd>
Sets the variable to the value...
</dd>
<dt><strong>
- FOREACH [<font color="#0000AA">variable</font>] [<font color="#0000AA">value</font>]
- [<font color="#008800">value ...</font>]
+ FOREACH [<span class="cmdarg">variable</span>] [<span class="cmdarg">value</span>]
+ [<span class="cmdargopt">value ...</span>]
</strong></dt>
<dd>
Set the variable to each of the values listed, and run the code that
@@ -672,8 +672,8 @@
those values.
</dd>
<dt><strong>
- FORRANGE [<font color="#0000AA">variable</font>] [<font color="#0000AA">min_value</font>]
- [<font color="#0000AA">max_value</font>] [<font color="#008800">step_value=1</font>]
+ FORRANGE [<span class="cmdarg">variable</span>] [<span class="cmdarg">min_value</span>]
+ [<span class="cmdarg">max_value</span>] [<span class="cmdargopt">step_value=1</span>]
</strong></dt>
<dd>
Set the variable to each of the values between min and max (at steps
@@ -694,7 +694,7 @@
</p>
<dl>
-<dt><strong>FUNCTION [<font color="#0000AA">name</font>]</strong></dt>
+<dt><strong>FUNCTION [<span class="cmdarg">name</span>]</strong></dt>
<dd>
This will create a function of the given name, including in it all
of the commands up until an END is found. These commands will be
Modified: development/documentation/analyze_samples.html
===================================================================
--- development/documentation/analyze_samples.html 2006-09-02 15:01:28 UTC (rev 924)
+++ development/documentation/analyze_samples.html 2006-09-04 01:25:47 UTC (rev 925)
@@ -5,8 +5,8 @@
</head>
<body>
-<div style="float: right">
-Revised 2006-08-29 DMB
+<div class="revision">
+Revised 2006-09-03 DMB
</div>
<p><a href="index.html">Return to the Index</a></p>
Modified: development/documentation/code_c++_intro.html
===================================================================
--- development/documentation/code_c++_intro.html 2006-09-02 15:01:28 UTC (rev 924)
+++ development/documentation/code_c++_intro.html 2006-09-04 01:25:47 UTC (rev 925)
@@ -5,8 +5,8 @@
</head>
<body>
-<div style="float: right">
-Revised 2006-08-29 DMB
+<div class="revision">
+Revised 2006-09-03 DMB
</div>
<p><a href="index.html">Return to the Index</a></p>
@@ -44,45 +44,45 @@
<table width="90%">
<tr>
<td width="50%">
- <span style="color: #886600"><strong>Comments</strong> are in BROWN</span>
- <br /><span style="color: #008800">Names of <strong>methods</strong> are in GREEN</span>
+ <span class="comment"><strong>Comments</strong> are in BROWN</span>
+ <br /><span class="method">Names of <strong>methods</strong> are in GREEN</span>
</td>
<td width="50%">
- <span style="color: #880000">Names of <strong>classes</strong> are in RED</span>
- <br /><span style="color: #0000AA">Names of <strong>objects</strong> are in BLUE</span>
+ <span class="class">Names of <strong>classes</strong> are in RED</span>
+ <br /><span class="object">Names of <strong>objects</strong> are in BLUE</span>
</td>
</tr>
</table>
</div>
<pre>
-class <span style="color: #880000">cOrganism</span>
+class <span class="class">cOrganism</span>
{
-private: <span style="color: #886600">// Data in this class cannot be directly accessed from outside.</span>
- const <span style="color: #880000">cGenome</span> <span style="color: #0000AA">m_genome</span>; <span style="color: #886600">// The initial genome that this organism was born with.</span>
- <span style="color: #880000">cPhenotype</span> <span style="color: #0000AA">m_phenotype</span>; <span style="color: #886600">// Maintains the status of this organism's phenotypic traits.</span>
+private: <span class="comment">// Data in this class cannot be directly accessed from outside.</span>
+ const <span class="class">cGenome</span> <span class="object">m_genome</span>; <span class="comment">// The initial genome that this organism was born with.</span>
+ <span class="class">cPhenotype</span> <span class="object">m_phenotype</span>; <span class="comment">// Maintains the status of this organism's phenotypic traits.</span>
- <span style="color: #880000">cOrgInterface</span>* <span style="color: #0000AA">m_interface</span>; <span style="color: #886600">// Interface back to the population.</span>
+ <span class="class">cOrgInterface</span>* <span class="object">m_interface</span>; <span class="comment">// Interface back to the population.</span>
- <span style="color: #880000">cGenotype</span>* <span style="color: #0000AA">m_genotype;</span> <span style="color: #886600">// A pointer to the genotype that this organism belongs to.</span>
- <span style="color: #880000">cHardwareBase</span>* <span style="color: #0000AA">m_hardware;</span> <span style="color: #886600">// The virtual machinery that this organism's genome is run on.</span>
+ <span class="class">cGenotype</span>* <span class="object">m_genotype;</span> <span class="comment">// A pointer to the genotype that this organism belongs to.</span>
+ <span class="class">cHardwareBase</span>* <span class="object">m_hardware;</span> <span class="comment">// The virtual machinery that this organism's genome is run on.</span>
-public: <span style="color: #886600"> // The methods are accessible to other classes.</span>
- <span style="color: #008800">cOrganism</span>(<span style="color: #880000">cWorld</span>* <span style="color: #0000AA">world</span>, <span style="color: #880000">cAvidaContext</span>& <span style="color: #0000AA">ctx</span>, const <span style="color: #880000">cGenome</span>& <span style="color: #0000AA">in_genome</span>);
- <span style="color: #008800">~cOrganism</span>();
+public: <span class="comment"> // The methods are accessible to other classes.</span>
+ <span class="method">cOrganism</span>(<span class="class">cWorld</span>* <span class="object">world</span>, <span class="class">cAvidaContext</span>& <span class="object">ctx</span>, const <span class="class">cGenome</span>& <span class="object">in_genome</span>);
+ <span class="method">~cOrganism</span>();
- <span style="color: #886600">// This batch of methods involve interaction with the population to resolve.</span>
- <span style="color: #880000">cOrganism</span>* <span style="color: #008800">GetNeighbor</span>() { return <span style="color: #0000AA">m_interface</span>-><span style="color: #008800">GetNeighbor</span>(); }
- int <span style="color: #008800">GetNeighborhoodSize</span>() { return <span style="color: #0000AA">m_interface</span>-><span style="color: #008800">GetNumNeighbors</span>(); }
- void <span style="color: #008800">Rotate</span>(int direction) { <span style="color: #0000AA">m_interface</span>-><span style="color: #008800">Rotate</span>(direction); }
- int <span style="color: #008800">GetInput</span>() { return <span style="color: #0000AA">m_interface</span>-><span style="color: #008800">GetInput</span>(); }
- void <span style="color: #008800">Die</span>() { <span style="color: #0000AA">m_interface</span>-><span style="color: #008800">Die</span>(); }
+ <span class="comment">// This batch of methods involve interaction with the population to resolve.</span>
+ <span class="class">cOrganism</span>* <span class="method">GetNeighbor</span>() { return <span class="object">m_interface</span>-><span class="method">GetNeighbor</span>(); }
+ int <span class="method">GetNeighborhoodSize</span>() { return <span class="object">m_interface</span>-><span class="method">GetNumNeighbors</span>(); }
+ void <span class="method">Rotate</span>(int direction) { <span class="object">m_interface</span>-><span class="method">Rotate</span>(direction); }
+ int <span class="method">GetInput</span>() { return <span class="object">m_interface</span>-><span class="method">GetInput</span>(); }
+ void <span class="method">Die</span>() { <span class="object">m_interface</span>-><span class="method">Die</span>(); }
- <span style="color: #886600">// Accessors -- these are used to gain access to private data.</span>
- const <span style="color: #880000">cGenome</span>& <span style="color: #008800">GetGenome()</span> const { return <span style="color: #0000AA">m_genome</span>; }
- <span style="color: #880000">cHardwareBase</span>& <span style="color: #008800">GetHardware()</span> { return *<span style="color: #0000AA">m_hardware</span>; }
- <span style="color: #880000">cPhenotype</span>& <span style="color: #008800">GetPhenotype()</span> { return <span style="color: #0000AA">m_phenotype</span>; }
- <span style="color: #880000">cGenotype</span>* <span style="color: #008800">GetGenotype()</span> { return <span style="color: #0000AA">m_genotype</span>; }
+ <span class="comment">// Accessors -- these are used to gain access to private data.</span>
+ const <span class="class">cGenome</span>& <span class="method">GetGenome()</span> const { return <span class="object">m_genome</span>; }
+ <span class="class">cHardwareBase</span>& <span class="method">GetHardware()</span> { return *<span class="object">m_hardware</span>; }
+ <span class="class">cPhenotype</span>& <span class="method">GetPhenotype()</span> { return <span class="object">m_phenotype</span>; }
+ <span class="class">cGenotype</span>* <span class="method">GetGenotype()</span> { return <span class="object">m_genotype</span>; }
};
</pre>
@@ -132,20 +132,20 @@
</p>
<dl>
-<dt><span style="color: #0000AA">an_example_variable</span></dt>
+<dt><span class="object">an_example_variable</span></dt>
<dd>
Variable names (including object names) are always all in lowercase
letters, with individual words separated by underscores. Variables are
either user-defined classes, numbers (integers, boolean values, floating
point numbers, etc.) or characters (single symbols)</dd>
</dd>
-<dt><span style="color: #008800">ExampleMethod</span></dt>
+<dt><span class="method">ExampleMethod</span></dt>
<dd>
Method names always have the first letter of each word capitalized, with the
remainder of the word in lowercase. The one exception to this is Constructors
and Destructors, which must have the same name as the class (see below).
</dd>
-<dt><span style="color: #880000">cExampleClass</span></dt>
+<dt><span class="class">cExampleClass</span></dt>
<dd>
Classes use a similar format to methods, but always begin with a single,
lowercase 'c'. Some other specialized types also used this format, but with a
@@ -176,7 +176,7 @@
<p>
The section labeled <code>private</code> above lists those data that are unique
to each organism; these are objects and pointers that exist <em>inside</em> of
-an organism object. First, <span style="color: #0000AA">m_genome</span> keeps
+an organism object. First, <span class="object">m_genome</span> keeps
the initial state of the organism. Since we never want this genome to change
over the organism's life, we place a <code>const</code> directive in front of
it. The <code>const</code> command exists so that C++ knows to warn the
@@ -184,14 +184,14 @@
is not supposed to be altered.
</p>
<p>
-The internal <span style="color: #0000AA">m_phenotype</span> object is used to
+The internal <span class="object">m_phenotype</span> object is used to
record the behaviors and abilities that the organism demonstrates during its
life. This class has variables to track everything from the tasks performed to
the gestation time of the organism and the number of offspring it has ever
-produced. The <span style="color: #0000AA">m_interface</span> allows an
+produced. The <span class="object">m_interface</span> allows an
organism to communicate with the environment (either the
-<span style="color: #880000">cPopulation</span> or the
-<span style="color: #880000">cTestCPU</span>) that it is part of. This is used,
+<span class="class">cPopulation</span> or the
+<span class="class">cTestCPU</span>) that it is part of. This is used,
for example, when an organism is ready to finish replicating and needs its
offspring to be placed into the population. If an organism is being run on a
test CPU rather than in a proper population object, then this interface will
@@ -203,15 +203,15 @@
represents ("points to") a location in the physical memory of the computer. A
pointer can be identified by the asterisk ('*') that follows the type name. The
code "<code>cGenotype* genotype</code>" indicates that the variable
-<span style="color: #0000AA">genotype</span> points to a location in memory
-where an object of class <span style="color: #880000">cGenotype</span> is
+<span class="object">genotype</span> points to a location in memory
+where an object of class <span class="class">cGenotype</span> is
stored. In this case, all of the organisms that are of a single genotype all
point to the <em>same</em> cGenotype object so that the genotypic information
is accessible to all organisms that may need to make use of it.
</p>
<p>
-The final data element is <span style="color: #0000AA">m_hardware</span>, a
-pointer to an object of type <span style="color: #880000">cHardwareBase</span>.
+The final data element is <span class="object">m_hardware</span>, a
+pointer to an object of type <span class="class">cHardwareBase</span>.
This variable is a pointer for a different reason than the genotype. Where a
single genotype is shared by many different organisms, each organism does
possess its own hardware. However, Avida supports more than one type of
@@ -230,7 +230,7 @@
Class descriptions (with limited exceptions) must contain two specific
methods called the <strong>constructor</strong> and the
<strong>destructor</strong>. The constructor always has the same name as the
-class (it's called <span style="color: #008800">cOrganism</span>(...) in this
+class (it's called <span class="method">cOrganism</span>(...) in this
case), and is executed in order to create a new object of that class. The
arguments for the constructor must include all of the information required to
build on object of the desired class. For an organism, we need the world
@@ -247,7 +247,7 @@
such as freeing allocated memory (see the section on memory management
below). The name of a destructor is always the same as the class name,
but with a tilde ('~') in front of it. Thus, the cOrganism's destructor
-is called <span style="color: #008800">~cOrganism</span>(). A destructor can
+is called <span class="method">~cOrganism</span>(). A destructor can
never take any arguments, and there must be only one of them in a class
definition.
</p>
@@ -256,19 +256,19 @@
to perform some behavior, which in all of these cases involves it interacting
with the population. For example, if you need to know at whom an organism
is facing, you can call the method
-<span style="color: #008800">GetNeighbor</span>()
+<span class="method">GetNeighbor</span>()
on it, and a pointer to the neighbor currently faced will be returned.
Likewise, if you need to kill an organism, you can call the method
-<span style="color: #008800">Die</span>() on it, and it will be terminated.
+<span class="method">Die</span>() on it, and it will be terminated.
Since each of these require interaction on the population level, the population
itself takes care of the bulk of the functionality.
</p>
<p>
The 'Accessors' are methods that provide access to otherwise private
-data. For example, the method <span style="color: #008800">GetGenome</span>()
+data. For example, the method <span class="method">GetGenome</span>()
will literally pass the genome of the organism to the object that calls it. In
particular, the hardware object associated with an organism will often call
-<span style="color: #008800">GetPhenotype</span>() in order to get the current
+<span class="method">GetPhenotype</span>() in order to get the current
state of the organism's phenotype and update it with something new the organism
has done. Several things to take note of here. In the first three accessors,
the name of the class being returned is followed by an ampersand ('&').
@@ -304,9 +304,9 @@
the three methods below:
</p>
<pre>
- <span style="color: #880000">cGenome</span> <span style="color: #008800">GetGenomeValue</span>();
- <span style="color: #880000">cGenome</span>* <span style="color: #008800">GetGenomePointer</span>();
- <span style="color: #880000">cGenome</span>& <span style="color: #008800">GetGenomeReference</span>();
+ <span class="class">cGenome</span> <span class="method">GetGenomeValue</span>();
+ <span class="class">cGenome</span>* <span class="method">GetGenomePointer</span>();
+ <span class="class">cGenome</span>& <span class="method">GetGenomeReference</span>();
</pre>
<p>
These three cases are all very different. In the first case
@@ -341,7 +341,7 @@
you could type:
</p>
<pre>
- <span style="color: #880000">cGenome</span>* <span style="color: #0000AA">created_genome</span> = new <span style="color: #008800">cGenome</span>(100);
+ <span class="class">cGenome</span>* <span class="object">created_genome</span> = new <span class="method">cGenome</span>(100);
</pre>
<p>
The variable created_genome is defined as a pointer to a memory location
@@ -358,7 +358,7 @@
it, we type:
</p>
<pre>
- delete <span style="color: #0000AA">created_genome</span>;
+ delete <span class="object">created_genome</span>;
</pre>
<p>
And the memory pointed to by the created_genome
@@ -388,14 +388,14 @@
</p>
<p>
For example, in the Avida scheduler, we use a class called
-<span style="color: #880000">cSchedule</span> to determine which organism's
+<span class="class">cSchedule</span> to determine which organism's
virtual CPU executes the next instruction. Well, this cSchedule object is not
all that clever. In fact, all that it does is run through the list of
organisms that need to go, lets them each execute a single instruction, and
then does it all over again. But sometimes we need to make some organisms
execute instructions at a faster rate than others. For that reason, there are
several derived classes, including
-<span style="color: #880000">cIntegratedSchedule</span>, which takes in a merit
+<span class="class">cIntegratedSchedule</span>, which takes in a merit
value for each organism, and assigns CPU cycles proportional to that merit.
Since this new class uses cSchedule as its base class, it can be dynamically
plugged in during run time, after looking at what the user chooses in the
@@ -410,9 +410,9 @@
<strong>interface class</strong> or <strong>protocol</strong>) and is used
simply as a method contract for derived classes. An example in Avida where this
is used is the organism interface with the environemnt. The class
-<span style="color: #880000">cOrgInterface</span> is an abstract base class,
-with <span style="color: #880000">cPopulationInterface</span> and
-<span style="color: #880000">cTestCPUInterface</span> as derived classes. This
+<span class="class">cOrgInterface</span> is an abstract base class,
+with <span class="class">cPopulationInterface</span> and
+<span class="class">cTestCPUInterface</span> as derived classes. This
organization allows for organism objects to interact with both the population
and the test environment, without having to write separate code for each.
</p>
Modified: development/documentation/code_death_birth.html
===================================================================
--- development/documentation/code_death_birth.html 2006-09-02 15:01:28 UTC (rev 924)
+++ development/documentation/code_death_birth.html 2006-09-04 01:25:47 UTC (rev 925)
@@ -5,8 +5,8 @@
</head>
<body>
-<div style="float: right">
-Revised 2006-08-30 DMB
+<div class="revision">
+Revised 2006-09-03 DMB
</div>
<p><a href="index.html">Return to the Index</a></p>
@@ -36,32 +36,32 @@
</p>
<pre>
-void <span style="color: #880000">cPopulation</span>::<span style="color: #008800">KillOrganism</span>(<span style="color: #880000">cPopulationCell</span>& <span style="color: #000088">in_cell</span>)
+void <span class="class">cPopulation</span>::<span class="method">KillOrganism</span>(<span class="class">cPopulationCell</span>& <span class="object">in_cell</span>)
{
- <span style="color: #886600">// do we actually have something to kill?</span>
- if (<span style="color: #000088">in_cell</span>.<span style="color: #008800">IsOccupied</span>() == false) return;
+ <span class="comment">// do we actually have something to kill?</span>
+ if (<span class="object">in_cell</span>.<span class="method">IsOccupied</span>() == false) return;
- <span style="color: #886600">// Statistics...</span>
- <span style="color: #880000">cOrganism</span>* <span style="color: #000088">organism</span> = <span style="color: #000088">in_cell</span>.<span style="color: #008800">GetOrganism</span>();
- <span style="color: #880000">cGenotype</span>* <span style="color: #000088">genotype</span> = <span style="color: #000088">organism</span>-><span style="color: #008800">GetGenotype</span>();
- <span style="color: #000088">m_world</span>-><span style="color: #008800">GetStats</span>().<span style="color: #008800">RecordDeath</span>();
+ <span class="comment">// Statistics...</span>
+ <span class="class">cOrganism</span>* <span class="object">organism</span> = <span class="object">in_cell</span>.<span class="method">GetOrganism</span>();
+ <span class="class">cGenotype</span>* <span class="object">genotype</span> = <span class="object">organism</span>-><span class="method">GetGenotype</span>();
+ <span class="object">m_world</span>-><span class="method">GetStats</span>().<span class="method">RecordDeath</span>();
- <span style="color: #886600">// Do the lineage handling</span>
- if (<span style="color: #000088">m_world</span>-><span style="color: #008800">GetConfig</span>().<span style="color: #000088">LOG_LINEAGES</span>.<span style="color: #008800">Get</span>()) { <span style="color: #000088">m_world</span>-><span style="color: #008800">GetClassificationManager</span>().<span style="color: #008800">RemoveLineageOrganism</span>(<span style="color: #000088">organism</span>); }
+ <span class="comment">// Do the lineage handling</span>
+ if (<span class="object">m_world</span>-><span class="method">GetConfig</span>().<span class="object">LOG_LINEAGES</span>.<span class="method">Get</span>()) { <span class="object">m_world</span>-><span class="method">GetClassificationManager</span>().<span class="method">RemoveLineageOrganism</span>(<span class="object">organism</span>); }
- <span style="color: #000088">num_organisms</span>--;
- <span style="color: #000088">genotype</span>-><span style="color: #008800">RemoveOrganism</span>();
+ <span class="object">num_organisms</span>--;
+ <span class="object">genotype</span>-><span class="method">RemoveOrganism</span>();
- <span style="color: #886600">// And clear it!</span>
- <span style="color: #000088">in_cell</span>.<span style="color: #008800">RemoveOrganism</span>();
- if (!<span style="color: #000088">organism</span>-><span style="color: #008800">GetIsRunning</span>()) delete <span style="color: #000088">organism</span>;
- else <span style="color: #000088">organism</span>-><span style="color: #008800">GetPhenotype</span>().<span style="color: #008800">SetToDelete</span>();
+ <span class="comment">// And clear it!</span>
+ <span class="object">in_cell</span>.<span class="method">RemoveOrganism</span>();
+ if (!<span class="object">organism</span>-><span class="method">GetIsRunning</span>()) delete <span class="object">organism</span>;
+ else <span class="object">organism</span>-><span class="method">GetPhenotype</span>().<span class="method">SetToDelete</span>();
- <span style="color: #886600">// Alert the scheduler that this cell has a 0 merit.</span>
- <span style="color: #000088">schedule</span>-><span style="color: #008800">Adjust</span>(<span style="color: #000088">in_cell</span>.<span style="color: #008800">GetID</span>(), <span style="color: #880000">cMerit</span>(0));
+ <span class="comment">// Alert the scheduler that this cell has a 0 merit.</span>
+ <span class="object">schedule</span>-><span class="method">Adjust</span>(<span class="object">in_cell</span>.<span class="method">GetID</span>(), <span class="class">cMerit</span>(0));
- <span style="color: #886600">// Update the archive (note: genotype adjustment may be defered)</span>
- <span style="color: #000088">m_world</span>-><span style="color: #008800">GetClassificationManager</span>().<span style="color: #008800">AdjustGenotype</span>(*<span style="color: #000088">genotype</span>);
+ <span class="comment">// Update the archive (note: genotype adjustment may be defered)</span>
+ <span class="object">m_world</span>-><span class="method">GetClassificationManager</span>().<span class="method">AdjustGenotype</span>(*<span class="object">genotype</span>);
}
</pre>
@@ -74,7 +74,7 @@
</p>
<p>
Once the statistics are finished, the cell itself is cleared with the
-<span style="color: #880000">cPopulationCell</span>::<span style="color: #008800">RemoveOrganism</span>()
+<span class="class">cPopulationCell</span>::<span class="method">RemoveOrganism</span>()
method (in which the pointer to the organism it once contained is set to NULL).
At this point if the organism is not the currently running CPU it will be
deleted. Otherwise, a flag is set that marks the organism for deletion after
@@ -91,62 +91,62 @@
If an organism is going to be placed into a specific cell of the population,
the method ActivateOrganism can be called on the population, telling it the
location in memory of the organism to be placed and the cell to place it in.
-This method will call the <span style="color: #008800">KillOrganism</span>() method
+This method will call the <span class="method">KillOrganism</span>() method
to make sure the cell is unoccupied. This method is called from the
-<span style="color: #008800">Inject</span>() method as well as
-<span style="color: #008800">ActivateOffspring</span>(), described below.
+<span class="method">Inject</span>() method as well as
+<span class="method">ActivateOffspring</span>(), described below.
Here is the ActivateOrganism method:
<pre>
-void <span style="color: #880000">cPopulation</span>::<span style="color: #008800">ActivateOrganism</span>(<span style="color: #880000">cAvidaContext</span>& <span style="color: #000088">ctx</span>, <span style="color: #880000">cOrganism</span>* <span style="color: #000088">in_organism</span>, <span style="color: #880000">cPopulationCell</span>& <span style="color: #000088">target_cell</span>)
+void <span class="class">cPopulation</span>::<span class="method">ActivateOrganism</span>(<span class="class">cAvidaContext</span>& <span class="object">ctx</span>, <span class="class">cOrganism</span>* <span class="object">in_organism</span>, <span class="class">cPopulationCell</span>& <span class="object">target_cell</span>)
{
- <span style="color: #000088">in_organism</span>-><span style="color: #008800">SetOrgInterface</span>(new <span style="color: #880000">cPopulationInterface</span>(<span style="color: #000088">m_world</span>));
+ <span class="object">in_organism</span>-><span class="method">SetOrgInterface</span>(new <span class="class">cPopulationInterface</span>(<span class="object">m_world</span>));
- <span style="color: #886600">// If the organism does not have a genotype, give it one! No parent</span>
- <span style="color: #886600">// information is provided so we must set parents to NULL.</span>
- if (<span style="color: #000088">in_organism</span>-><span style="color: #008800">GetGenotype</span>() == NULL) {
- <span style="color: #880000">cGenotype</span>* <span style="color: #000088">new_genotype</span> = <span style="color: #000088">m_world</span>-><span style="color: #008800">GetClassificationManager</span>().<span style="color: #008800">GetGenotype</span>(<span style="color: #000088">in_organism</span>-><span style="color: #008800">GetGenome</span>(), NULL, NULL);
- <span style="color: #000088">in_organism</span>-><span style="color: #008800">SetGenotype</span>(<span style="color: #000088">new_genotype</span>);
+ <span class="comment">// If the organism does not have a genotype, give it one! No parent</span>
+ <span class="comment">// information is provided so we must set parents to NULL.</span>
+ if (<span class="object">in_organism</span>-><span class="method">GetGenotype</span>() == NULL) {
+ <span class="class">cGenotype</span>* <span class="object">new_genotype</span> = <span class="object">m_world</span>-><span class="method">GetClassificationManager</span>().<span class="method">GetGenotype</span>(<span class="object">in_organism</span>-><span class="method">GetGenome</span>(), NULL, NULL);
+ <span class="object">in_organism</span>-><span class="method">SetGenotype</span>(<span class="object">new_genotype</span>);
}
- <span style="color: #880000">cGenotype</span>* <span style="color: #000088">in_genotype</span> = <span style="color: #000088">in_organism</span>-><span style="color: #008800">GetGenotype</span>();
+ <span class="class">cGenotype</span>* <span class="object">in_genotype</span> = <span class="object">in_organism</span>-><span class="method">GetGenotype</span>();
- <span style="color: #886600">// Save the old genotype from this cell...</span>
- <span style="color: #880000">cGenotype</span>* <span style="color: #000088">old_genotype</span> = NULL;
- if (<span style="color: #000088">target_cell</span>.<span style="color: #008800">IsOccupied</span>()) {
- <span style="color: #000088">old_genotype</span> = <span style="color: #000088">target_cell</span>.<span style="color: #008800">GetOrganism</span>()-><span style="color: #008800">GetGenotype</span>();
+ <span class="comment">// Save the old genotype from this cell...</span>
+ <span class="class">cGenotype</span>* <span class="object">old_genotype</span> = NULL;
+ if (<span class="object">target_cell</span>.<span class="method">IsOccupied</span>()) {
+ <span class="object">old_genotype</span> = <span class="object">target_cell</span>.<span class="method">GetOrganism</span>()-><span class="method">GetGenotype</span>();
- <span style="color: #886600">// Sometimes a new organism will kill off the last member of its genotype</span>
- <span style="color: #886600">// in the population. Normally this would remove the genotype, so we</span>
- <span style="color: #886600">// want to defer adjusting that genotype until the new one is placed.</span>
- <span style="color: #000088">old_genotype</span>-><span style="color: #008800">IncDeferAdjust</span>();
+ <span class="comment">// Sometimes a new organism will kill off the last member of its genotype</span>
+ <span class="comment">// in the population. Normally this would remove the genotype, so we</span>
+ <span class="comment">// want to defer adjusting that genotype until the new one is placed.</span>
+ <span class="object">old_genotype</span>-><span class="method">IncDeferAdjust</span>();
}
- <span style="color: #886600">// Update the contents of the target cell.</span>
- <span style="color: #008800">KillOrganism</span>(<span style="color: #000088">target_cell</span>);
- <span style="color: #000088">target_cell</span>.<span style="color: #008800">InsertOrganism</span>(*<span style="color: #000088">in_organism</span>);
+ <span class="comment">// Update the contents of the target cell.</span>
+ <span class="method">KillOrganism</span>(<span class="object">target_cell</span>);
+ <span class="object">target_cell</span>.<span class="method">InsertOrganism</span>(*<span class="object">in_organism</span>);
- <span style="color: #886600">// Update the archive...</span>
- <span style="color: #000088">in_genotype</span>-><span style="color: #008800">AddOrganism</span>();
+ <span class="comment">// Update the archive...</span>
+ <span class="object">in_genotype</span>-><span class="method">AddOrganism</span>();
- if (<span style="color: #000088">old_genotype</span> != NULL) {
- <span style="color: #000088">old_genotype</span>-><span style="color: #008800">DecDeferAdjust</span>();
- <span style="color: #000088">m_world</span>-><span style="color: #008800">GetClassificationManager</span>().<span style="color: #008800">AdjustGenotype</span>(*<span style="color: #000088">old_genotype</span>);
+ if (<span class="object">old_genotype</span> != NULL) {
+ <span class="object">old_genotype</span>-><span class="method">DecDeferAdjust</span>();
+ <span class="object">m_world</span>-><span class="method">GetClassificationManager</span>().<span class="method">AdjustGenotype</span>(*<span class="object">old_genotype</span>);
}
- <span style="color: #000088">m_world</span>-><span style="color: #008800">GetClassificationManager</span>().<span style="color: #008800">AdjustGenotype</span>(*<span style="color: #000088">in_genotype</span>);
+ <span class="object">m_world</span>-><span class="method">GetClassificationManager</span>().<span class="method">AdjustGenotype</span>(*<span class="object">in_genotype</span>);
- <span style="color: #886600">// Initialize the time-slice for this new organism.</span>
- <span style="color: #000088">schedule</span>-><span style="color: #008800">Adjust</span>(<span style="color: #000088">target_cell</span>.<span style="color: #008800">GetID</span>(), <span style="color: #000088">in_organism</span>-><span style="color: #008800">GetPhenotype</span>().<span style="color: #008800">GetMerit</span>());
+ <span class="comment">// Initialize the time-slice for this new organism.</span>
+ <span class="object">schedule</span>-><span class="method">Adjust</span>(<span class="object">target_cell</span>.<span class="method">GetID</span>(), <span class="object">in_organism</span>-><span class="method">GetPhenotype</span>().<span class="method">GetMerit</span>());
- <span style="color: #886600">// Special handling for certain birth methods.</span>
- if (<span style="color: #000088">m_world</span>-><span style="color: #008800">GetConfig</span>().<span style="color: #000088">BIRTH_METHOD</span>.<span style="color: #008800">Get</span>() == POSITION_CHILD_FULL_SOUP_ELDEST) {
- <span style="color: #000088">reaper_queue</span>.<span style="color: #008800">Push</span>(&<span style="color: #000088">target_cell</span>);
+ <span class="comment">// Special handling for certain birth methods.</span>
+ if (<span class="object">m_world</span>-><span class="method">GetConfig</span>().<span class="object">BIRTH_METHOD</span>.<span class="method">Get</span>() == POSITION_CHILD_FULL_SOUP_ELDEST) {
+ <span class="object">reaper_queue</span>.<span class="method">Push</span>(&<span class="object">target_cell</span>);
}
- <span style="color: #000088">num_organisms</span>++;
+ <span class="object">num_organisms</span>++;
- <span style="color: #886600">// Statistics...</span>
- <span style="color: #000088">m_world</span>-><span style="color: #008800">GetStats</span>().<span style="color: #008800">RecordBirth</span>(<span style="color: #000088">target_cell</span>.<span style="color: #008800">GetID</span>(), <span style="color: #000088">in_genotype</span>-><span style="color: #008800">GetID</span>(),
- <span style="color: #000088">in_organism</span>-><span style="color: #008800">GetPhenotype</span>().<span style="color: #008800">ParentTrue</span>());
+ <span class="comment">// Statistics...</span>
+ <span class="object">m_world</span>-><span class="method">GetStats</span>().<span class="method">RecordBirth</span>(<span class="object">target_cell</span>.<span class="method">GetID</span>(), <span class="object">in_genotype</span>-><span class="method">GetID</span>(),
+ <span class="object">in_organism</span>-><span class="method">GetPhenotype</span>().<span class="method">ParentTrue</span>());
}
</pre>
@@ -165,7 +165,7 @@
Before we erase the organism currently in this cell, we want to keep track of
what genotype it was part of for use in updating the archive later. We then
kill the organism in the cell (as described above) and insert the new one.
-The <span style="color: #880000">cPopulationCell</span>::<span style="color: #008800">InsertOrganism</span>()
+The <span class="class">cPopulationCell</span>::<span class="method">InsertOrganism</span>()
method will setup the organism based on the environmental conditions of this
cell (mutation rate, tasks rewarded, etc), and store the organism for future
use.
@@ -196,7 +196,7 @@
When an organism gives birth, we must collect some relevent statistics,
which can best be accomplished in the population object. Then we must
place the offspring into its own cell in the population. This is all done
-with the <span style="color: #880000">cPopulation</span>::<span style="color: #008800">ActivateOffspring</span>
+with the <span class="class">cPopulation</span>::<span class="method">ActivateOffspring</span>
method. This method takes as arguments the parent organism and child genome
that we're working with. It is called by the divide command via the
population interface. As this method is quite long, refer to it in the source
@@ -204,17 +204,17 @@
</p>
<p>
The first step in activing an offspring involves performing some book keeping
-on the parent's phenotype via the <span style="color: #008800">DivideReset</span>()
+on the parent's phenotype via the <span class="method">DivideReset</span>()
method. After this, the child genome is submitted to the birth chamber. The
birth chamber is responsible for handling the details of reproduction, such as
genome recombination in sexual populations. The
-<span style="color: #008800">SubmitOffspring</span>() method will add organism objects
-to the <span style="color: #000088">child_array</span> for each offspring produced.
+<span class="method">SubmitOffspring</span>() method will add organism objects
+to the <span class="object">child_array</span> for each offspring produced.
</p>
<p>
The next section of code is in charge of finding where in the population each
child organism should be placed. The cell of the parent is looked up, and then
-the <span style="color: #008800">PositionChild</span>() method is called to determine
+the <span class="method">PositionChild</span>() method is called to determine
the child's cell.
</p>
<p>
@@ -242,9 +242,9 @@
test CPU to get its initial merit, and activate it! You should be able to
go line-by-line through the code to see how exactly this happens for
yourself. See
-<span style="color: #880000">cPopulation</span>::<span style="color: #008800">InjectGenome</span>,
+<span class="class">cPopulation</span>::<span class="method">InjectGenome</span>,
and more importantly
-<span style="color: #880000">cPopulation</span>::<span style="color: #008800">InjectGenotype</span>
+<span class="class">cPopulation</span>::<span class="method">InjectGenotype</span>
in <kbd>cPopulation.cc</kbd>.
</p>
Modified: development/documentation/code_environment.html
===================================================================
--- development/documentation/code_environment.html 2006-09-02 15:01:28 UTC (rev 924)
+++ development/documentation/code_environment.html 2006-09-04 01:25:47 UTC (rev 925)
@@ -5,8 +5,8 @@
</head>
<body>
-<div style="float: right">
-Revised 2006-08-30 DMB
+<div class="revision">
+Revised 2006-09-03 DMB
</div>
<p><a href="index.html">Return to the Index</a></p>
@@ -30,28 +30,28 @@
describes a single task that can be used to trigger reactions.
</p>
<pre>
-typedef <span style="color: #880000">double</span> (<span style="color: #880000">cTaskLib</span>::*<span style="color: #000088">tTaskTest</span>)(<span style="color: #880000">cTaskContext</span>*) const;
+typedef <span class="class">double</span> (<span class="class">cTaskLib</span>::*<span class="object">tTaskTest</span>)(<span class="class">cTaskContext</span>*) const;
-class <span style="color: #880000">cTaskEntry</span> {
+class <span class="class">cTaskEntry</span> {
private:
- <span style="color: #880000">cString</span> <span style="color: #000088">m_name</span>; <span style="color: #886600">// Short keyword for task</span>
- <span style="color: #880000">cString</span> <span style="color: #000088">m_desc</span>; <span style="color: #886600">// For more human-understandable output...</span>
- <span style="color: #880000">int</span> <span style="color: #000088">m_id</span>;
- <span style="color: #880000">tTaskTest</span> <span style="color: #000088">m_test_fun</span>;
- <span style="color: #880000">cString</span> <span style="color: #000088">m_info</span>; <span style="color: #886600">// extra info (like the string or whatever to match)</span>
+ <span class="class">cString</span> <span class="object">m_name</span>; <span class="comment">// Short keyword for task</span>
+ <span class="class">cString</span> <span class="object">m_desc</span>; <span class="comment">// For more human-understandable output...</span>
+ <span class="class">int</span> <span class="object">m_id</span>;
+ <span class="class">tTaskTest</span> <span class="object">m_test_fun</span>;
+ <span class="class">cString</span> <span class="object">m_info</span>; <span class="comment">// extra info (like the string or whatever to match)</span>
public:
- <span style="color: #008800">cTaskEntry</span>(const <span style="color: #880000">cString</span>& <span style="color: #000088">name</span>, const <span style="color: #880000">cString</span>& <span style="color: #000088">desc</span>, int <span style="color: #000088">in_id</span>, <span style="color: #880000">tTaskTest</span> <span style="color: #000088">test_fun</span>, const <span style="color: #880000">cString</span>& <span style="color: #000088">info</span>);
+ <span class="method">cTaskEntry</span>(const <span class="class">cString</span>& <span class="object">name</span>, const <span class="class">cString</span>& <span class="object">desc</span>, int <span class="object">in_id</span>, <span class="class">tTaskTest</span> <span class="object">test_fun</span>, const <span class="class">cString</span>& <span class="object">info</span>);
: m_name(name), m_desc(desc), m_id(in_id), m_test_fun(test_fun), m_info(info)
{
}
- ~<span style="color: #008800">cTaskEntry</span>() { ; }
+ ~<span class="method">cTaskEntry</span>() { ; }
- const <span style="color: #880000">cString</span>& <span style="color: #008800">GetName</span>() const { return <span style="color: #000088">m_name</span>; }
- const <span style="color: #880000">cString</span>& <span style="color: #008800">GetDesc</span>() const { return <span style="color: #000088">m_desc</span>; }
- const int <span style="color: #008800">GetID</span>() const { return <span style="color: #000088">m_id</span>; }
- const <span style="color: #880000">tTaskTest</span> <span style="color: #008800">GetTestFun</span>() const { return <span style="color: #000088">m_test_fun</span>; }
- const <span style="color: #880000">cString</span>& <span style="color: #008800">GetInfo</span>() const { return <span style="color: #000088">m_info</span>; }
+ const <span class="class">cString</span>& <span class="method">GetName</span>() const { return <span class="object">m_name</span>; }
+ const <span class="class">cString</span>& <span class="method">GetDesc</span>() const { return <span class="object">m_desc</span>; }
+ const int <span class="method">GetID</span>() const { return <span class="object">m_id</span>; }
+ const <span class="class">tTaskTest</span> <span class="method">GetTestFun</span>() const { return <span class="object">m_test_fun</span>; }
+ const <span class="class">cString</span>& <span class="method">GetInfo</span>() const { return <span class="object">m_info</span>; }
};
</pre>
@@ -75,28 +75,28 @@
</p>
<pre>
-class <span style="color: #880000">cTaskLib</span> {
+class <span class="class">cTaskLib</span> {
private:
- <span style="color: #880000">tArray</span><<span style="color: #880000">cTaskEntry</span>*> <span style="color: #000088">task_array</span>;
+ <span class="class">tArray</span><<span class="class">cTaskEntry</span>*> <span class="object">task_array</span>;
public:
- int <span style="color: #008800">GetSize</span>() const { return <span style="color: #000088">task_array</span>.<span style="color: #008800">GetSize</span>(); }
+ int <span class="method">GetSize</span>() const { return <span class="object">task_array</span>.<span class="method">GetSize</span>(); }
- <span style="color: #880000">cTaskEntry</span>* <span style="color: #008800">AddTask</span>(const <span style="color: #880000">cString</span>& <span style="color: #000088">name</span>, const <span style="color: #880000">cString</span>& <span style="color: #000088">info</span>);
- const <span style="color: #880000">cTaskEntry</span>& <span style="color: #008800">GetTask</span>(<span style="color: #880000">int</span> <span style="color: #000088">id</span>) const;
+ <span class="class">cTaskEntry</span>* <span class="method">AddTask</span>(const <span class="class">cString</span>& <span class="object">name</span>, const <span class="class">cString</span>& <span class="object">info</span>);
+ const <span class="class">cTaskEntry</span>& <span class="method">GetTask</span>(<span class="class">int</span> <span class="object">id</span>) const;
- void <span style="color: #008800">SetupTests</span>(<span style="color: #880000">cTaskContext</span>& <span style="color: #000088">ctx</span>) const;
- inline double <span style="color: #008800">TestOutput</span>(const <span style="color: #880000">cTaskEntry</span>& <span style="color: #000088">task</span>, <span style="color: #880000">cTaskContext</span>* ctx) const;
+ void <span class="method">SetupTests</span>(<span class="class">cTaskContext</span>& <span class="object">ctx</span>) const;
+ inline double <span class="method">TestOutput</span>(const <span class="class">cTaskEntry</span>& <span class="object">task</span>, <span class="class">cTaskContext</span>* ctx) const;
private:
- double <span style="color: #008800">Task_Echo</span>(<span style="color: #880000">cTaskContext</span>* <span style="color: #000088">ctx</span>) const;
- double <span style="color: #008800">Task_Add</span>(<span style="color: #880000">cTaskContext</span>* <span style="color: #000088">ctx</span>) const;
- double <span style="color: #008800">Task_Sub</span>(<span style="color: #880000">cTaskContext</span>* <span style="color: #000088">ctx</span>) const;
+ double <span class="method">Task_Echo</span>(<span class="class">cTaskContext</span>* <span class="object">ctx</span>) const;
+ double <span class="method">Task_Add</span>(<span class="class">cTaskContext</span>* <span class="object">ctx</span>) const;
+ double <span class="method">Task_Sub</span>(<span class="class">cTaskContext</span>* <span class="object">ctx</span>) const;
- double <span style="color: #008800">Task_Not</span>(<span style="color: #880000">cTaskContext</span>* <span style="color: #000088">ctx</span>) const;
- double <span style="color: #008800">Task_Nand</span>(<span style="color: #880000">cTaskContext</span>* <span style="color: #000088">ctx</span>) const;
- double <span style="color: #008800">Task_And</span>(<span style="color: #880000">cTaskContext</span>* <span style="color: #000088">ctx</span>) const;
- <span style="color: #886600">// ... And a whole bunch more ...</span>
+ double <span class="method">Task_Not</span>(<span class="class">cTaskContext</span>* <span class="object">ctx</span>) const;
+ double <span class="method">Task_Nand</span>(<span class="class">cTaskContext</span>* <span class="object">ctx</span>) const;
+ double <span class="method">Task_And</span>(<span class="class">cTaskContext</span>* <span class="object">ctx</span>) const;
+ <span class="comment">// ... And a whole bunch more ...</span>
};
</pre>
@@ -106,9 +106,9 @@
rewarded (or otherwise acted upon) tasks in an environment.
</p>
<p>
-The <span style="color: #008800">TestOutput</span>() method can only be run with
-as <span style="color: #880000">cTaskContext</span> object that has been initialized
-with the <span style="color: #008800">SetupTests</span> method. It will test the
+The <span class="method">TestOutput</span>() method can only be run with
+as <span class="class">cTaskContext</span> object that has been initialized
+with the <span class="method">SetupTests</span> method. It will test the
specific task passed in and return the 0.0 - 1.0 quality measure of how well
that task was done with the most recent output.
</p>
@@ -117,12 +117,12 @@
Below is a sample task-tester implementation:
<pre>
-double <span style="color: #880000">cTaskLib</span>::<span style="color: #008800">Task_Add</span>(<span style="color: #880000">cTaskContext</span>* <span style="color: #000088">ctx</span>) const
+double <span class="class">cTaskLib</span>::<span class="method">Task_Add</span>(<span class="class">cTaskContext</span>* <span class="object">ctx</span>) const
{
- const int <span style="color: #000088">test_output</span> = <span style="color: #000088">ctx</span>-><span style="color: #000088">output_buffer</span>[0];
- for (<span style="color: #880000">int</span> <span style="color: #000088">i</span> = 0; <span style="color: #000088">i</span> < <span style="color: #000088">ctx</span>-><span style="color: #000088">input_buffer</span>.<span style="color: #008800">GetNumStored</span>(); <span style="color: #000088">i</span>++) {
- for (<span style="color: #880000">int</span> <span style="color: #000088">j</span> = 0; <span style="color: #000088">j</span> < <span style="color: #000088">i</span>; <span style="color: #000088">j</span>++) {
- if (<span style="color: #000088">test_output</span> == <span style="color: #000088">ctx</span>-><span style="color: #000088">input_buffer</span>[<span style="color: #000088">i</span>] + <span style="color: #000088">ctx</span>-><span style="color: #000088">input_buffer</span>[<span style="color: #000088">j</span>]) return 1.0;
+ const int <span class="object">test_output</span> = <span class="object">ctx</span>-><span class="object">output_buffer</span>[0];
+ for (<span class="class">int</span> <span class="object">i</span> = 0; <span class="object">i</span> < <span class="object">ctx</span>-><span class="object">input_buffer</span>.<span class="method">GetNumStored</span>(); <span class="object">i</span>++) {
+ for (<span class="class">int</span> <span class="object">j</span> = 0; <span class="object">j</span> < <span class="object">i</span>; <span class="object">j</span>++) {
+ if (<span class="object">test_output</span> == <span class="object">ctx</span>-><span class="object">input_buffer</span>[<span class="object">i</span>] + <span class="object">ctx</span>-><span class="object">input_buffer</span>[<span class="object">j</span>]) return 1.0;
}
}
return 0.0;
@@ -137,19 +137,19 @@
</p>
<p>
-The <span style="color: #008800">SetupTests</span> method performs some
+The <span class="method">SetupTests</span> method performs some
precomptution for all of the logic tasks, creating the value
-<span style="color: #000088">logic_id</span> within the task context. The
-<span style="color: #000088">logic_id</span> has 256 possible values, each of which
+<span class="object">logic_id</span> within the task context. The
+<span class="object">logic_id</span> has 256 possible values, each of which
can only be associated with a single logic task. These tests look more like:
</p>
<pre>
-double <span style="color: #880000">cTaskLib</span>::<span style="color: #008800">Task_AndNot</span>(<span style="color: #880000">cTaskContext</span>* <span style="color: #000088">ctx</span>) const
+double <span class="class">cTaskLib</span>::<span class="method">Task_AndNot</span>(<span class="class">cTaskContext</span>* <span class="object">ctx</span>) const
{
- const int <span style="color: #000088">logic_id</span> = <span style="color: #000088">ctx</span>-><span style="color: #000088">logic_id</span>;
- if (<span style="color: #000088">logic_id</span> == 10 || <span style="color: #000088">logic_id</span> == 12 || <span style="color: #000088">logic_id</span> == 34 ||
- <span style="color: #000088">logic_id</span> == 48 || <span style="color: #000088">logic_id</span> == 68 || <span style="color: #000088">logic_id</span> == 80) return 1.0;
+ const int <span class="object">logic_id</span> = <span class="object">ctx</span>-><span class="object">logic_id</span>;
+ if (<span class="object">logic_id</span> == 10 || <span class="object">logic_id</span> == 12 || <span class="object">logic_id</span> == 34 ||
+ <span class="object">logic_id</span> == 48 || <span class="object">logic_id</span> == 68 || <span class="object">logic_id</span> == 80) return 1.0;
return 0.0;
}
</pre>
@@ -180,43 +180,43 @@
<p>
Resources are a little more complicated than task entries to manage
-and understand. An object of type <span style="color: #880000">cResource</span>
+and understand. An object of type <span class="class">cResource</span>
contains 18 pieces of data, and the associated accessors. Like all of the
other individual units we have discussed, resources have a unique
-<span style="color: #000088">name</span> and numerical
-<span style="color: #000088">id</span>. For all resource we store the quantities
-associated with their <span style="color: #000088">inflow</span>,
-<span style="color: #000088">outflow</span>, and
-<span style="color: #000088">initial</span> count (each stored as a
-double) as well as the <span style="color: #000088">geometry</span> of that resource.
+<span class="object">name</span> and numerical
+<span class="object">id</span>. For all resource we store the quantities
+associated with their <span class="object">inflow</span>,
+<span class="object">outflow</span>, and
+<span class="object">initial</span> count (each stored as a
+double) as well as the <span class="object">geometry</span> of that resource.
<p>
For spatial resources we need to be able to describe how a resource
exists in space so we store data for:
<ul>
<li>
- <span style="color: #000088">inflowX1</span>,
- <span style="color: #000088">inflowX2</span>,
- <span style="color: #000088">inflowY1</span>, and
- <span style="color: #000088">inflowY2</span> to describe a rectangle where
+ <span class="object">inflowX1</span>,
+ <span class="object">inflowX2</span>,
+ <span class="object">inflowY1</span>, and
+ <span class="object">inflowY2</span> to describe a rectangle where
resources flow in.
</li>
<li>
- <span style="color: #000088">outflowX1</span>,
- <span style="color: #000088">outflowX2</span>,
- <span style="color: #000088">outflowY1</span>, and
- <span style="color: #000088">outfowY2</span> for a rectangle where resources
+ <span class="object">outflowX1</span>,
+ <span class="object">outflowX2</span>,
+ <span class="object">outflowY1</span>, and
+ <span class="object">outfowY2</span> for a rectangle where resources
flow out.
</li>
<li>
- <span style="color: #000088">xdiffuse</span> and
- <span style="color: #000088">ydiffuse</span> describe how fast resources will
+ <span class="object">xdiffuse</span> and
+ <span class="object">ydiffuse</span> describe how fast resources will
flow from cells of higher amounts of that resource to cells with
lower amounts of that resource.
</li>
<li>
- <span style="color: #000088">xgravity</span> and
- <span style="color: #000088">ygravity</span> describe the preferential flow of
+ <span class="object">xgravity</span> and
+ <span class="object">ygravity</span> describe the preferential flow of
resource in a given direction.
</li>
</ul>
@@ -239,46 +239,46 @@
</p>
<pre>
-class <span style="color: #880000">cEnvironment</span> {
+class <span class="class">cEnvironment</span> {
private:
- <span style="color: #886600">// Keep libraries of resources, reactions, and tasks.</span>
- <span style="color: #880000">cResourceLib</span> <span style="color: #000088">resource_lib</span>;
- <span style="color: #880000">cReactionLib</span> <span style="color: #000088">reaction_lib</span>;
- <span style="color: #880000">cTaskLib</span> <span style="color: #000088">task_lib</span>;
- <span style="color: #880000">cInstLib</span> <span style="color: #000088">inst_lib</span>;
- <span style="color: #880000">cMutationRates</span> <span style="color: #000088">mut_rates</span>;
+ <span class="comment">// Keep libraries of resources, reactions, and tasks.</span>
+ <span class="class">cResourceLib</span> <span class="object">resource_lib</span>;
+ <span class="class">cReactionLib</span> <span class="object">reaction_lib</span>;
+ <span class="class">cTaskLib</span> <span class="object">task_lib</span>;
+ <span class="class">cInstLib</span> <span class="object">inst_lib</span>;
+ <span class="class">cMutationRates</span> <span class="object">mut_rates</span>;
public:
- <span style="color: #880000">bool</span> <span style="color: #008800">Load</span>(const <span style="color: #880000">cString</span>& <span style="color: #000088">filename</span>);
+ <span class="class">bool</span> <span class="method">Load</span>(const <span class="class">cString</span>& <span class="object">filename</span>);
- <span style="color: #886600">// Interaction with the organisms</span>
- <span style="color: #880000">bool</span> <span style="color: #008800">TestOutput</span>(<span style="color: #880000">cAvidaContext</span>& <span style="color: #000088">ctx</span>, <span style="color: #880000">cReactionResult</span>& <span style="color: #000088">result</span>, <span style="color: #880000">cTaskContext</span>& <span style="color: #000088">taskctx</span>,
- const <span style="color: #880000">tBuffer</span><int>& <span style="color: #000088">send_buf</span>, const <span style="color: #880000">tBuffer</span><int>& <span style="color: #000088">receive_buf</span>,
- const <span style="color: #880000">tArray</span><int>& <span style="color: #000088">task_count</span>, const <span style="color: #880000">tArray</span><int>& <span style="color: #000088">reaction_count</span>,
- const <span style="color: #880000">tArray</span><double>& <span style="color: #000088">resource_count</span>) const;
+ <span class="comment">// Interaction with the organisms</span>
+ <span class="class">bool</span> <span class="method">TestOutput</span>(<span class="class">cAvidaContext</span>& <span class="object">ctx</span>, <span class="class">cReactionResult</span>& <span class="object">result</span>, <span class="class">cTaskContext</span>& <span class="object">taskctx</span>,
+ const <span class="class">tBuffer</span><int>& <span class="object">send_buf</span>, const <span class="class">tBuffer</span><int>& <span class="object">receive_buf</span>,
+ const <span class="class">tArray</span><int>& <span class="object">task_count</span>, const <span class="class">tArray</span><int>& <span class="object">reaction_count</span>,
+ const <span class="class">tArray</span><double>& <span class="object">resource_count</span>) const;
};
</pre>
<p>
The private data members include all of the libraries needed to specify
the environment, plus its mutation rates. The
-<span style="color: #008800">Load</span>() method takes a filename
+<span class="method">Load</span>() method takes a filename
(<kbd>environment.cfg</kbd> by default) and will fill out all of the libraries
in this environment. The most important feature of this class is the
-<span style="color: #008800">TestOutput</span>() method, which takes in all sorts
+<span class="method">TestOutput</span>() method, which takes in all sorts
of information about the current state of the organism that has just done
an output and fills out an object of type
-<span style="color: #880000">cReactionResult</span> with information about what
+<span class="class">cReactionResult</span> with information about what
happened. It also directly returns a bool that will indicate if there have
been any changes at all. The specific information it uses to determine
the results are the inputs the organism has taken in and the outputs it has
produced -- both needed to determine what tasks have been done, and therefore
what reactions may have been triggered. This information is encapsulated in
-the task context <span style="color: #000088">taskctx</span>. The organism's
-previous <span style="color: #000088">task_count</span> and
-<span style="color: #000088">resource_count</span> are also needed to determine
+the task context <span class="object">taskctx</span>. The organism's
+previous <span class="object">task_count</span> and
+<span class="object">resource_count</span> are also needed to determine
if the reactions requisites have been met. And finally the
-<span style="color: #000088">resource_count</span> available to the organisms is
+<span class="object">resource_count</span> available to the organisms is
needed to determine how much of each resource can be used in the reactions.
</p>
Modified: development/documentation/main.css
===================================================================
--- development/documentation/main.css 2006-09-02 15:01:28 UTC (rev 924)
+++ development/documentation/main.css 2006-09-04 01:25:47 UTC (rev 925)
@@ -1,3 +1,28 @@
pre {
margin-left: 10px;
}
+
+div.revision {
+ float: right;
+}
+
+.cmdarg {
+ color: #0000AA;
+}
+
+.cmdargopt {
+ color: #008800;
+}
+
+.comment {
+ color: #886600;
+}
+.method {
+ color: #008800;
+}
+.class {
+ color: #880000;
+}
+.object {
+ color: #0000AA;
+}
More information about the Avida-cvs
mailing list