[Avida-SVN] r2597 - in development: . documentation source/actions source/targets/viewer-fltk source/utils/make_actions_html source/viewer-coreGUI tests/_task_optimize_lim_res/config tests/avida_GA_lim_res/config tests/avida_GA_sex/config tests/optimize_multivar_lim_res/config tests/string_match_embed3/config
baer at myxo.css.msu.edu
baer at myxo.css.msu.edu
Tue May 27 12:50:28 PDT 2008
Author: baer
Date: 2008-05-27 15:50:27 -0400 (Tue, 27 May 2008)
New Revision: 2597
Modified:
development/Avida.vcproj
development/documentation/actions.html
development/documentation/cpu_tour.html
development/source/actions/PopulationActions.cc
development/source/actions/PrintActions.cc
development/source/targets/viewer-fltk/cDriver_FLTKViewer.cc
development/source/utils/make_actions_html/actions_source_info
development/source/viewer-coreGUI/cGUIWidget.h
development/tests/_task_optimize_lim_res/config/events.cfg
development/tests/avida_GA_lim_res/config/events.cfg
development/tests/avida_GA_sex/config/events.cfg
development/tests/optimize_multivar_lim_res/config/events.cfg
development/tests/string_match_embed3/config/events.cfg
Log:
Fixed a few minor mistakes in the documentation.
Fixed a few typos in the actions routines.
Made modifications to allow the compiling of the FLTK Viewer.
Modifed the test files so they no longer have deprecated action
names (converted the names to the current version)
Modified: development/Avida.vcproj
===================================================================
--- development/Avida.vcproj 2008-05-26 07:58:18 UTC (rev 2596)
+++ development/Avida.vcproj 2008-05-27 19:50:27 UTC (rev 2597)
@@ -317,6 +317,10 @@
>
</File>
<File
+ RelativePath=".\source\tools\cConstBurstSchedule.h"
+ >
+ </File>
+ <File
RelativePath=".\source\tools\cConstSchedule.h"
>
</File>
@@ -1137,6 +1141,10 @@
>
</File>
<File
+ RelativePath=".\source\tools\cConstBurstSchedule.cc"
+ >
+ </File>
+ <File
RelativePath=".\source\tools\cConstSchedule.cc"
>
</File>
Modified: development/documentation/actions.html
===================================================================
--- development/documentation/actions.html 2008-05-26 07:58:18 UTC (rev 2596)
+++ development/documentation/actions.html 2008-05-27 19:50:27 UTC (rev 2597)
@@ -9,7 +9,7 @@
<div class="revision">
Revised 2006-09-03 DMB
-<br>Generated Thu Apr 3 16:13:04 2008 by make_actions_html</div>
+<br>Generated Tue May 27 15:04:24 2008 by make_actions_html</div>
<p>
<a href="index.html">Return to the Index</a> |
@@ -88,7 +88,6 @@
<a href="#dump_historic_pop">dump_historic_pop</a><br>
<a href="#dump_historic_sex_pop">dump_historic_sex_pop</a><br>
<a href="#DumpLandscape">DumpLandscape</a><br>
- <a href="#dump_lineage_grid">dump_lineage_grid</a><br>
<a href="#DumpLineageGrid">DumpLineageGrid</a><br>
<a href="#dump_memory">dump_memory</a><br>
<a href="#DumpMemory">DumpMemory</a><br>
@@ -119,6 +118,7 @@
<a href="#inject_all">inject_all</a><br>
<a href="#InjectAll">InjectAll</a><br>
<a href="#inject_all_random_repro">inject_all_random_repro</a><br>
+ <a href="#InjectAllRandomRepro">InjectAllRandomRepro</a><br>
<a href="#InjectDemes">InjectDemes</a><br>
<a href="#InjectParasite">InjectParasite</a><br>
<a href="#InjectParasitePair">InjectParasitePair</a><br>
@@ -142,9 +142,9 @@
<a href="#KillRate">KillRate</a><br>
<a href="#KillRectangle">KillRectangle</a><br>
<a href="#kill_rectangle">kill_rectangle</a><br>
- <td valign="top">
<a href="#LoadClone">LoadClone</a><br>
<a href="#load_clone">load_clone</a><br>
+ <td valign="top">
<a href="#load_dump_file">load_dump_file</a><br>
<a href="#LoadPopulation">LoadPopulation</a><br>
<a href="#ModMutProb">ModMutProb</a><br>
@@ -174,7 +174,10 @@
<a href="#PrintDemeAllStats">PrintDemeAllStats</a><br>
<a href="#PrintDemeAverageData">PrintDemeAverageData</a><br>
<a href="#PrintDemeDonorStats">PrintDemeDonorStats</a><br>
- <a href="#PrintDemeFounders">PrintDemeFounders</a><br>
+ <a href="#PrintDemeFoundersData">PrintDemeFoundersData</a><br>
+ <a href="#PrintDemeOrgReactionData">PrintDemeOrgReactionData</a><br>
+ <a href="#PrintDemeOrgTasksData">PrintDemeOrgTasksData</a><br>
+ <a href="#PrintDemeOrgTasksExeData">PrintDemeOrgTasksExeData</a><br>
<a href="#PrintDemeReactionData">PrintDemeReactionData</a><br>
<a href="#PrintDemeReplicationData">PrintDemeReplicationData</a><br>
<a href="#PrintDemeResourceStats">PrintDemeResourceStats</a><br>
@@ -223,13 +226,17 @@
<a href="#PrintMutationRateData">PrintMutationRateData</a><br>
<a href="#print_number_phenotypes">print_number_phenotypes</a><br>
<a href="#PrintParasiteData">PrintParasiteData</a><br>
+ <a href="#PrintPerDemeGenPerFounderData">PrintPerDemeGenPerFounderData</a><br>
+ <a href="#PrintPerDemeReactionData">PrintPerDemeReactionData</a><br>
+ <a href="#PrintPerDemeTasksData">PrintPerDemeTasksData</a><br>
+ <a href="#PrintPerDemeTasksExeData">PrintPerDemeTasksExeData</a><br>
<a href="#print_phenotype_status">print_phenotype_status</a><br>
<a href="#PrintPhenotypeData">PrintPhenotypeData</a><br>
<a href="#PrintPhenotypeStatus">PrintPhenotypeStatus</a><br>
+ <td valign="top">
<a href="#PrintPhenotypicPlasticity">PrintPhenotypicPlasticity</a><br>
<a href="#PrintPopulationDistanceData">PrintPopulationDistanceData</a><br>
<a href="#PrintReactionData">PrintReactionData</a><br>
- <td valign="top">
<a href="#PrintReactionRewardData">PrintReactionRewardData</a><br>
<a href="#PrintRelativeFitnessHistogram">PrintRelativeFitnessHistogram</a><br>
<a href="#print_resource_data">print_resource_data</a><br>
@@ -1029,6 +1036,14 @@
</p>
</li>
<li><p>
+ <strong><a name="InjectAllRandomRepro">InjectAllRandomRepro</a></strong>
+ <i><int length> [double merit=-1] [int lineage_label=0] [double neutral_metric=0]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="InjectDemes">InjectDemes</a></strong>
<i>[string fname="START_CREATURE"] [double merit=-1] [int lineage_label=0] [double neutral_metric=0]</i>
</p>
@@ -1098,7 +1113,7 @@
</li>
<li><p>
<strong><a name="inject_sequence">inject_sequence</a></strong>
- <i>[string fname="START_CREATURE"] [int cell_id=0] [double merit=-1] [int lineage_label=0] [double neutral_metric=0]</i>
+ <i><string sequence> [int cell_start=0] [int cell_end=-1] [double merit=-1] [int lineage_label=0] [double neutral_metric=0]</i>
</p>
<p>
<font color="red">DEPRECATED</font>
@@ -1485,19 +1500,12 @@
</p>
</li>
<li><p>
- <strong><a name="dump_lineage_grid">dump_lineage_grid</a></strong>
- <i>[string fname=""]</i>
- </p>
- <p>
-
- </p>
-</li>
-<li><p>
<strong><a name="DumpLineageGrid">DumpLineageGrid</a></strong>
- <i>[string fname=""]</i>
+ <i>[string fname="grid_linage.update.dat"]</i>
</p>
<p>
-
+ Print out the grid of lineage labels (set when ancestor was injected with action like InjectSequence)
+
</p>
</li>
<li><p>
@@ -1778,7 +1786,7 @@
</p>
</li>
<li><p>
- <strong><a name="PrintDemeFounders">PrintDemeFounders</a></strong>
+ <strong><a name="PrintDemeFoundersData">PrintDemeFoundersData</a></strong>
<i>[string fname="deme_founders.dat"]</i>
</p>
<p>
@@ -1786,6 +1794,30 @@
</p>
</li>
<li><p>
+ <strong><a name="PrintDemeOrgReactionData">PrintDemeOrgReactionData</a></strong>
+ <i>[string fname="deme_org_reactions.dat"]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="PrintDemeOrgTasksData">PrintDemeOrgTasksData</a></strong>
+ <i>[string fname="deme_org_tasks.dat"]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="PrintDemeOrgTasksExeData">PrintDemeOrgTasksExeData</a></strong>
+ <i>[string fname="deme_org_tasks_exe.dat"]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="PrintDemeReactionData">PrintDemeReactionData</a></strong>
<i>[string fname="deme_reactions.dat"]</i>
</p>
@@ -2247,6 +2279,38 @@
</p>
</li>
<li><p>
+ <strong><a name="PrintPerDemeGenPerFounderData">PrintPerDemeGenPerFounderData</a></strong>
+ <i>[string fname="deme_gen_between_founders.dat"]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="PrintPerDemeReactionData">PrintPerDemeReactionData</a></strong>
+ <i>[string fname="per_deme_reactions.dat"]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="PrintPerDemeTasksData">PrintPerDemeTasksData</a></strong>
+ <i>[string fname="per_deme_tasks.dat"]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
+ <strong><a name="PrintPerDemeTasksExeData">PrintPerDemeTasksExeData</a></strong>
+ <i>[string fname="per_deme_tasks_exe.dat"]</i>
+ </p>
+ <p>
+
+ </p>
+</li>
+<li><p>
<strong><a name="print_phenotype_status">print_phenotype_status</a></strong>
<i>[string fname="phenotype_status.dat"]</i>
</p>
Modified: development/documentation/cpu_tour.html
===================================================================
--- development/documentation/cpu_tour.html 2008-05-26 07:58:18 UTC (rev 2596)
+++ development/documentation/cpu_tour.html 2008-05-27 19:50:27 UTC (rev 2597)
@@ -1,6 +1,6 @@
<html>
<head>
- <title>Avida : A Guided Tour of an Ancestor and its Gardware</title>
+ <title>Avida : A Guided Tour of an Ancestor and its Hardware</title>
<link rel="stylesheet" type="text/css" href="main.css" />
</head>
<body>
@@ -44,7 +44,7 @@
stacks, but for practical purposes we currently limit the maximum stack
depth to ten.</li>
<li>An <strong style="color: #CCCC00">input buffer</strong> and an
- <strong style="color: #CCCC00">output buffer</strong>that the organism
+ <strong style="color: #CCCC00">output buffer</strong> that the organism
uses to receive information, and return the processed results.</li>
<li>A <strong style="color: #8888FF">Read-Head</strong>, a
<strong style="color: #8888FF">Write-Head</strong>, and a
@@ -139,7 +139,7 @@
the first complementary template (<code>nop-B</code>) and moves the Flow-Head
there. Templates may be composed of more than a single <code>nop</code>
instruction. A series of nops is typically abbreviated to the associated
-lecodeer and separated by colons. This the sequence "<code>nop-A nop-A nop-C</code>"
+letter and separated by colons. This the sequence "<code>nop-A nop-A nop-C</code>"
would be displayed as "<code>A:A:C</code>".
</p>
<p>
@@ -147,7 +147,7 @@
default, we have three: <code>nop-A</code>'s complement is <code>nop-B</code>,
<code>nop-B</code>'s is <code>nop-C</code>, and <code>nop-C</code>'s is <code>nop-A</code>.
Likewise, some instructions talk about the complement of a register or head
--- the same pacodeern is used in those cases. So if an instruction tests if
+-- the same pattern is used in those cases. So if an instruction tests if
<code>?BX?</code> is equal to its complement, it will test if
<code>BX == CX</code> by default, but if it is followed by a
<code>nop-C</code> it will test if <code>CX == AX</code>.
@@ -287,7 +287,7 @@
(which we placed at the beginning of the offspring). With any copy command
there is a user-specified chance of a copy mutation. If one occurs, the
Write-Head will place a random instruction rather than the one that it
-gathered from the Read-Head. After the copy occurs (for becodeer or worse),
+gathered from the Read-Head. After the copy occurs (for better or worse),
both the Read-Head and the Write-Head are advanced to the next instruction
in the genome. It is for this reason that a common mutation we see happening
will place a long string of h-copy instruction one after another.
@@ -307,7 +307,7 @@
beginning of the copy loop.
</p>
<p>
-This process will continue until all of the lines of code have been copies,
+This process will continue until all of the lines of code have been copied,
and an offspring is born.
</p>
Modified: development/source/actions/PopulationActions.cc
===================================================================
--- development/source/actions/PopulationActions.cc 2008-05-26 07:58:18 UTC (rev 2596)
+++ development/source/actions/PopulationActions.cc 2008-05-27 19:50:27 UTC (rev 2597)
@@ -330,7 +330,7 @@
void Process(cAvidaContext& ctx)
{
if (m_cell_start < 0 || m_cell_end > m_world->GetPopulation().GetSize() || m_cell_start >= m_cell_end) {
- m_world->GetDriver().NotifyWarning("InjectRange has invalid range!");
+ m_world->GetDriver().NotifyWarning("InjectSequence has invalid range!");
} else {
cGenome genome(m_sequence);
for (int i = m_cell_start; i < m_cell_end; i++) {
@@ -391,7 +391,7 @@
void Process(cAvidaContext& ctx)
{
if (m_cell_start < 0 || m_cell_end > m_world->GetPopulation().GetSize() || m_cell_start >= m_cell_end) {
- m_world->GetDriver().NotifyWarning("InjectRange has invalid range!");
+ m_world->GetDriver().NotifyWarning("InjectSequenceWithDivMutRate has invalid range!");
} else {
cGenome genome(m_sequence);
for (int i = m_cell_start; i < m_cell_end; i++) {
@@ -1650,6 +1650,7 @@
{
action_lib->Register<cActionInject>("Inject");
action_lib->Register<cActionInjectRandom>("InjectRandom");
+ action_lib->Register<cActionInjectAllRandomRepro>("InjectAllRandomRepro");
action_lib->Register<cActionInjectAll>("InjectAll");
action_lib->Register<cActionInjectRange>("InjectRange");
action_lib->Register<cActionInjectSequence>("InjectSequence");
@@ -1695,7 +1696,7 @@
action_lib->Register<cActionInjectAllRandomRepro>("inject_all_random_repro");
action_lib->Register<cActionInjectAll>("inject_all");
action_lib->Register<cActionInjectRange>("inject_range");
- action_lib->Register<cActionInject>("inject_sequence");
+ action_lib->Register<cActionInjectSequence>("inject_sequence");
action_lib->Register<cActionKillProb>("apocalypse");
action_lib->Register<cActionKillRate>("rate_kill");
Modified: development/source/actions/PrintActions.cc
===================================================================
--- development/source/actions/PrintActions.cc 2008-05-26 07:58:18 UTC (rev 2596)
+++ development/source/actions/PrintActions.cc 2008-05-27 19:50:27 UTC (rev 2597)
@@ -2338,7 +2338,7 @@
cString largs(args);
if (largs.GetSize()) m_filename = largs.PopWord();
}
- static const cString GetDescription() { return "Arguments: [string fname='']"; }
+ static const cString GetDescription() { return "Arguments: [string fname='grid_linage.update.dat']"; }
void Process(cAvidaContext& ctx)
{
cString filename(m_filename);
@@ -2804,7 +2804,6 @@
action_lib->Register<cActionDumpFitnessGrid>("dump_fitness_grid");
action_lib->Register<cActionDumpGenotypeIDGrid>("dump_genotype_grid");
action_lib->Register<cActionDumpPhenotypeIDGrid>("dump_phenotype_grid");
- action_lib->Register<cActionDumpLineageGrid>("dump_lineage_grid");
action_lib->Register<cActionDumpTaskGrid>("dump_task_grid");
action_lib->Register<cActionDumpDonorGrid>("dump_donor_grid");
action_lib->Register<cActionDumpReceiverGrid>("dump_receiver_grid");
Modified: development/source/targets/viewer-fltk/cDriver_FLTKViewer.cc
===================================================================
--- development/source/targets/viewer-fltk/cDriver_FLTKViewer.cc 2008-05-26 07:58:18 UTC (rev 2596)
+++ development/source/targets/viewer-fltk/cDriver_FLTKViewer.cc 2008-05-27 19:50:27 UTC (rev 2597)
@@ -47,6 +47,9 @@
#include <cstdlib>
#include <FL/Fl.H>
+
+#include <signal.h>
+
// #include <FL/Fl_JPEG_Image.H>
using namespace std;
Modified: development/source/utils/make_actions_html/actions_source_info
===================================================================
--- development/source/utils/make_actions_html/actions_source_info 2008-05-26 07:58:18 UTC (rev 2596)
+++ development/source/utils/make_actions_html/actions_source_info 2008-05-27 19:50:27 UTC (rev 2597)
@@ -196,6 +196,8 @@
Dump memory summary information.
=== Action DumpFitnessGrid ===
Print out the grid of organism fitness values.
+=== Action DumpLineageGrid ===
+ Print out the grid of lineage labels (set when ancestor was injected with action like InjectSequence)
=== Action DumpGenotypeIDGrid ===
Print out the grid of genotype IDs.
=== Action DumpTaskGrid ===
Modified: development/source/viewer-coreGUI/cGUIWidget.h
===================================================================
--- development/source/viewer-coreGUI/cGUIWidget.h 2008-05-26 07:58:18 UTC (rev 2596)
+++ development/source/viewer-coreGUI/cGUIWidget.h 2008-05-27 19:50:27 UTC (rev 2597)
@@ -28,6 +28,7 @@
#define cGUIWidget_h
#include "cString.h"
+#include "cGUIEvent.h"
class cGUIContainer;
class cGUIEvent;
Modified: development/tests/_task_optimize_lim_res/config/events.cfg
===================================================================
--- development/tests/_task_optimize_lim_res/config/events.cfg 2008-05-26 07:58:18 UTC (rev 2596)
+++ development/tests/_task_optimize_lim_res/config/events.cfg 2008-05-27 19:50:27 UTC (rev 2597)
@@ -13,8 +13,8 @@
#
##############################################################################
-u 0 inject_all START_CREATURE
-u 80 zero_muts
+u 0 InjectAll START_CREATURE
+u 80 ZeroMuts
# Print all of the standard data files...
# Print all of the standard data files...
Modified: development/tests/avida_GA_lim_res/config/events.cfg
===================================================================
--- development/tests/avida_GA_lim_res/config/events.cfg 2008-05-26 07:58:18 UTC (rev 2596)
+++ development/tests/avida_GA_lim_res/config/events.cfg 2008-05-27 19:50:27 UTC (rev 2597)
@@ -13,7 +13,7 @@
#
##############################################################################
-i inject_all_random_repro 40
+i InjectAllRandomRepro 40
# Print all of the standard data files...
# Print all of the standard data files...
Modified: development/tests/avida_GA_sex/config/events.cfg
===================================================================
--- development/tests/avida_GA_sex/config/events.cfg 2008-05-26 07:58:18 UTC (rev 2596)
+++ development/tests/avida_GA_sex/config/events.cfg 2008-05-27 19:50:27 UTC (rev 2597)
@@ -13,7 +13,7 @@
#
##############################################################################
-i inject_all_random_repro 40 100 0 0 1
+i InjectAllRandomRepro 40 100 0 0 1
# Print all of the standard data files...
u 0:100:end PrintAverageData # Save info about they average genotypes
Modified: development/tests/optimize_multivar_lim_res/config/events.cfg
===================================================================
--- development/tests/optimize_multivar_lim_res/config/events.cfg 2008-05-26 07:58:18 UTC (rev 2596)
+++ development/tests/optimize_multivar_lim_res/config/events.cfg 2008-05-27 19:50:27 UTC (rev 2597)
@@ -13,7 +13,7 @@
#
##############################################################################
-i inject_all_random_repro 93
+i InjectAllRandomRepro 93
# Print all of the standard data files...
u 0:10:end PrintAverageData # Save info about they average genotypes
Modified: development/tests/string_match_embed3/config/events.cfg
===================================================================
--- development/tests/string_match_embed3/config/events.cfg 2008-05-26 07:58:18 UTC (rev 2596)
+++ development/tests/string_match_embed3/config/events.cfg 2008-05-27 19:50:27 UTC (rev 2597)
@@ -14,7 +14,7 @@
# For other sample event configurations, see: source/support/config/
#
##############################################################################
-u 0 inject_all START_CREATURE
+u 0 InjectAll START_CREATURE
# Print all of the standard data files...
# Print all of the standard data files...
u 0:10:end PrintAverageData # Save info about they average genotypes
@@ -29,7 +29,7 @@
u 0:10:end PrintTasksQualData # Task quality information
# Setup the exit time and full population data collection.
-u 100:100 detail_pop # Save current state of population.
-u 100:100 dump_historic_pop # Save ancestors of current population.
+u 100:100 SavePopulation # Save current state of population.
+u 100:100 SaveHistoricPopulation # Save ancestors of current population.
u 100 exit # exit
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