[Avida-SVN] r1675 - in development/tests: . resources_9r resources_9r/config resources_9r/expected resources_9r/expected/data resources_9r/expected/data/archive
blwalker at myxo.css.msu.edu
blwalker at myxo.css.msu.edu
Wed Jun 13 09:22:25 PDT 2007
Author: blwalker
Date: 2007-06-13 12:22:25 -0400 (Wed, 13 Jun 2007)
New Revision: 1675
Added:
development/tests/resources_9r/
development/tests/resources_9r/config/
development/tests/resources_9r/config/9task.org
development/tests/resources_9r/config/avida.cfg
development/tests/resources_9r/config/environment.9resource
development/tests/resources_9r/config/events.cfg
development/tests/resources_9r/expected/
development/tests/resources_9r/expected/data/
development/tests/resources_9r/expected/data/archive/
development/tests/resources_9r/expected/data/archive/067-aaaaa.org
development/tests/resources_9r/expected/data/average.dat
development/tests/resources_9r/expected/data/count.dat
development/tests/resources_9r/expected/data/detail-100.pop
development/tests/resources_9r/expected/data/dominant.dat
development/tests/resources_9r/expected/data/historic-100.pop
development/tests/resources_9r/expected/data/resource.dat
development/tests/resources_9r/expected/data/stats.dat
development/tests/resources_9r/expected/data/tasks.dat
development/tests/resources_9r/expected/data/tasks_exe.dat
development/tests/resources_9r/expected/data/tasks_quality.dat
development/tests/resources_9r/expected/data/time.dat
development/tests/resources_9r/test_list
Log:
Adding test of 9resource environment, 100 updates, 9task organism
Added: development/tests/resources_9r/config/9task.org
===================================================================
--- development/tests/resources_9r/config/9task.org (rev 0)
+++ development/tests/resources_9r/config/9task.org 2007-06-13 16:22:25 UTC (rev 1675)
@@ -0,0 +1,101 @@
+# Sun Jun 10 22:58:09 2007
+# Filename........: creature.final
+# Update Output...: 100000
+# Is Viable.......: 1
+# Repro Cycle Size: 0
+# Depth to Viable.: 0
+# Update Created..: 99511
+# Genotype ID.....: 9002478
+# Parent Gen ID...: 8992690
+# Tree Depth......: 234
+# Parent Distance.: 1
+#
+# Generation: 0
+# Merit...........: 2248146944.000000
+# Gestation Time..: 220
+# Fitness.........: 10218849.745455
+# Errors..........: 1
+# Genome Size.....: 67
+# Copied Size.....: 67
+# Executed Size...: 67
+# Offspring.......: SELF
+#
+# Tasks Performed:
+# not 1 (1.000000)
+# nand 1 (1.000000)
+# and 1 (1.000000)
+# orn 1 (1.000000)
+# or 1 (1.000000)
+# andn 1 (1.000000)
+# nor 1 (1.000000)
+# xor 1 (1.000000)
+# equ 1 (1.000000)
+
+
+nop-A
+set-flow
+h-alloc
+set-flow
+nop-A
+mov-head
+nop-C
+h-divide
+h-search
+IO
+nop-C
+dec
+nand
+h-copy
+IO
+nop-C
+if-less
+nop-C
+swap
+swap-stk
+nand
+nop-C
+if-label
+pop
+nand
+nop-C
+IO
+nop-A
+push
+nop-C
+inc
+nop-B
+h-copy
+pop
+h-copy
+nand
+nop-C
+IO
+h-copy
+h-copy
+nand
+push
+IO
+IO
+nop-C
+h-copy
+h-copy
+h-copy
+h-copy
+inc
+h-copy
+if-label
+nop-C
+if-label
+mov-head
+nop-A
+h-copy
+swap-stk
+h-copy
+nop-A
+h-copy
+h-copy
+h-copy
+h-copy
+pop
+h-copy
+h-divide
Added: development/tests/resources_9r/config/avida.cfg
===================================================================
--- development/tests/resources_9r/config/avida.cfg (rev 0)
+++ development/tests/resources_9r/config/avida.cfg 2007-06-13 16:22:25 UTC (rev 1675)
@@ -0,0 +1,277 @@
+#############################################################################
+# This file includes all the basic run-time defines for Avida.
+# For more information, see doc/config.html
+#############################################################################
+
+VERSION_ID 2.7.0 # Do not change this value.
+
+### GENERAL_GROUP ###
+# General Settings
+ANALYZE_MODE 0 # 0 = Disabled
+ # 1 = Enabled
+ # 2 = Interactive
+VIEW_MODE 1 # Initial viewer screen
+CLONE_FILE - # Clone file to load
+VERBOSITY 1 # Control output verbosity
+
+### ARCH_GROUP ###
+# Architecture Variables
+WORLD_X 60 # Width of the Avida world
+WORLD_Y 60 # Height of the Avida world
+WORLD_GEOMETRY 2 # 1 = Bounded Grid
+ # 2 = Torus
+ # 3 = Clique
+RANDOM_SEED 0 # Random number seed (0 for based on time)
+HARDWARE_TYPE 0 # 0 = Original CPUs
+ # 1 = New SMT CPUs
+ # 2 = Transitional SMT
+ # 3 = Experimental CPU
+ # 4 = Gene Expression CPU
+
+### CONFIG_FILE_GROUP ###
+# Configuration Files
+DATA_DIR data # Directory in which config files are found
+INST_SET - # File containing instruction set
+EVENT_FILE events.cfg # File containing list of events during run
+ANALYZE_FILE analyze.cfg # File used for analysis mode
+ENVIRONMENT_FILE environment.9resource # File that describes the environment
+START_CREATURE 9task.org # Organism to seed the soup
+
+### DEME_GROUP ###
+# Demes and Germlines
+NUM_DEMES 1 # Number of independent groups in the population.
+DEMES_USE_GERMLINE 0 # Whether demes use a distinct germline; 0=off
+DEMES_HAVE_MERIT 0 # Whether demes have merit; 0=no
+GERMLINE_COPY_MUT 0.0075 # Prob. of copy mutations occuring during
+ # germline replication.
+GERMLINE_REPLACES_SOURCE 0 # Whether the source germline is updated
+ # on replication; 0=no.
+GERMLINE_RANDOM_PLACEMENT 0 # Whether the seed for a germline is placed
+ # randomly within the deme; 0=no.
+MAX_DEME_AGE 500 # The maximum age of a deme (in updates) to be
+ # used for age-based replication (default=500).
+
+### REPRODUCTION_GROUP ###
+# Birth and Death
+BIRTH_METHOD 0 # Which organism should be replaced on birth?
+ # 0 = Random organism in neighborhood
+ # 1 = Oldest in neighborhood
+ # 2 = Largest Age/Merit in neighborhood
+ # 3 = None (use only empty cells in neighborhood)
+ # 4 = Random from population (Mass Action)
+ # 5 = Oldest in entire population
+ # 6 = Random within deme
+ # 7 = Organism faced by parent
+ # 8 = Next grid cell (id+1)
+ # 9 = Largest energy used in entire population
+ # 10 = Largest energy used in neighborhood
+PREFER_EMPTY 1 # Give empty cells preference in offsping placement?
+ALLOW_PARENT 1 # Allow births to replace the parent organism?
+DEATH_METHOD 2 # 0 = Never die of old age.
+ # 1 = Die when inst executed = AGE_LIMIT (+deviation)
+ # 2 = Die when inst executed = length*AGE_LIMIT (+dev)
+AGE_LIMIT 20 # Modifies DEATH_METHOD
+AGE_DEVIATION 0 # Creates a distribution around AGE_LIMIT
+ALLOC_METHOD 0 # (Orignal CPU Only)
+ # 0 = Allocated space is set to default instruction.
+ # 1 = Set to section of dead genome (Necrophilia)
+ # 2 = Allocated space is set to random instruction.
+DIVIDE_METHOD 1 # 0 = Divide leaves state of mother untouched.
+ # 1 = Divide resets state of mother
+ # (after the divide, we have 2 children)
+ # 2 = Divide resets state of current thread only
+ # (does not touch possible parasite threads)
+INJECT_METHOD 0 # 0 = Leaves the parasite thread state untouched.
+ # 1 = Resets the calling thread state on inject
+GENERATION_INC_METHOD 1 # 0 = Only the generation of the child is
+ # increased on divide.
+ # 1 = Both the generation of the mother and child are
+ # increased on divide (good with DIVIDE_METHOD 1).
+
+### RECOMBINATION_GROUP ###
+# Sexual Recombination and Modularity
+RECOMBINATION_PROB 1.0 # probability of recombination in div-sex
+MAX_BIRTH_WAIT_TIME -1 # Updates incipiant orgs can wait for crossover
+MODULE_NUM 0 # number of modules in the genome
+CONT_REC_REGS 1 # are (modular) recombination regions continuous
+CORESPOND_REC_REGS 1 # are (modular) recombination regions swapped randomly
+ # or with corresponding positions?
+TWO_FOLD_COST_SEX 0 # 1 = only one recombined offspring is born.
+ # 2 = both offspring are born
+SAME_LENGTH_SEX 0 # 0 = recombine with any genome
+ # 1 = only recombine w/ same length
+
+### DIVIDE_GROUP ###
+# Divide Restrictions
+CHILD_SIZE_RANGE 2.0 # Maximal differential between child and parent sizes.
+MIN_COPIED_LINES 0.5 # Code fraction which must be copied before divide.
+MIN_EXE_LINES 0.5 # Code fraction which must be executed before divide.
+REQUIRE_ALLOCATE 1 # (Original CPU Only) Require allocate before divide?
+REQUIRED_TASK -1 # Task ID required for successful divide.
+IMMUNITY_TASK -1 # Task providing immunity from the required task.
+REQUIRED_REACTION -1 # Reaction ID required for successful divide.
+REQUIRED_BONUS 0 # The bonus that an organism must accumulate to divide.
+
+### MUTATION_GROUP ###
+# Mutations
+POINT_MUT_PROB 0.0 # Mutation rate (per-location per update)
+COPY_MUT_PROB 0.0075 # Mutation rate (per copy)
+INS_MUT_PROB 0.0 # Insertion rate (per site, applied on divide)
+DEL_MUT_PROB 0.0 # Deletion rate (per site, applied on divide)
+DIV_MUT_PROB 0.0 # Mutation rate (per site, applied on divide)
+DIVIDE_MUT_PROB 0.0 # Mutation rate (per divide)
+DIVIDE_INS_PROB 0.05 # Insertion rate (per divide)
+DIVIDE_DEL_PROB 0.05 # Deletion rate (per divide)
+PARENT_MUT_PROB 0.0 # Per-site, in parent, on divide
+SPECIAL_MUT_LINE -1 # If this is >= 0, ONLY this line is mutated
+INJECT_INS_PROB 0.0 # Insertion rate (per site, applied on inject)
+INJECT_DEL_PROB 0.0 # Deletion rate (per site, applied on inject)
+INJECT_MUT_PROB 0.0 # Mutation rate (per site, applied on inject)
+META_COPY_MUT 0.0 # Prob. of copy mutation rate changing (per gen)
+META_STD_DEV 0.0 # Standard deviation of meta mutation size.
+MUT_RATE_SOURCE 1 # 1 = Mutation rates determined by environment.
+ # 2 = Mutation rates inherited from parent.
+
+### REVERSION_GROUP ###
+# Mutation Reversion
+# These slow down avida a lot, and should be set to 0.0 normally.
+REVERT_FATAL 0.0 # Should any mutations be reverted on birth?
+REVERT_DETRIMENTAL 0.0 # 0.0 to 1.0; Probability of reversion.
+REVERT_NEUTRAL 0.0 #
+REVERT_BENEFICIAL 0.0 #
+STERILIZE_FATAL 0.0 # Should any mutations clear (kill) the organism?
+STERILIZE_DETRIMENTAL 0.0 #
+STERILIZE_NEUTRAL 0.0 #
+STERILIZE_BENEFICIAL 0.0 #
+FAIL_IMPLICIT 0 # Should copies that failed *not* due to mutations
+ # be eliminated?
+NEUTRAL_MAX 0.0 # The percent benifical change from parent fitness
+ # to be considered neutral.
+NEUTRAL_MIN 0.0 # The percent deleterious change from parent fitness
+ # to be considered neutral.
+
+### TIME_GROUP ###
+# Time Slicing
+AVE_TIME_SLICE 30 # Ave number of insts per org per update
+SLICING_METHOD 1 # 0 = CONSTANT: all organisms get default...
+ # 1 = PROBABILISTIC: Run _prob_ proportional to merit.
+ # 2 = INTEGRATED: Perfectly integrated deterministic.
+BASE_MERIT_METHOD 4 # 0 = Constant (merit independent of size)
+ # 1 = Merit proportional to copied size
+ # 2 = Merit prop. to executed size
+ # 3 = Merit prop. to full size
+ # 4 = Merit prop. to min of executed or copied size
+ # 5 = Merit prop. to sqrt of the minimum size
+ # 6 = Merit prop. to num times MERIT_BONUS_INST is in genome.
+BASE_CONST_MERIT 100 # Base merit when BASE_MERIT_METHOD set to 0
+DEFAULT_BONUS 1.0 # Initial bonus before any tasks
+MERIT_DEFAULT_BONUS 0 # Scale the merit of an offspring by the default bonus
+ # rather than the accumulated bonus of the parent?
+MERIT_BONUS_INST 0 # in BASE_MERIT_METHOD 6, this sets which instruction counts
+ # (-1 = none, 0 = First in INST_SET.)
+MERIT_BONUS_EFFECT 0 # in BASE_MERIT_METHOD 6, this sets how much merit is earned
+ # per instruction (-1 = penalty, 0 = no effect.)
+FITNESS_VALLEY 0 # in BASE_MERIT_METHOD 6, this creates valleys from
+ # FITNESS_VALLEY_START to FITNESS_VALLEY_STOP
+ # (0 = off, 1 = on)
+FITNESS_VALLEY_START 0 # if FITNESS_VALLEY = 1, orgs with num_key_instructions
+ # from FITNESS_VALLEY_START to FITNESS_VALLEY_STOP
+ # get fitness 1 (lowest)
+FITNESS_VALLEY_STOP 0 # if FITNESS_VALLEY = 1, orgs with num_key_instructions
+ # from FITNESS_VALLEY_START to FITNESS_VALLEY_STOP
+ # get fitness 1 (lowest)
+MAX_CPU_THREADS 1 # Number of Threads a CPU can spawn
+THREAD_SLICING_METHOD 0 # Formula for and organism's thread slicing
+ # (num_threads-1) * THREAD_SLICING_METHOD + 1
+ # 0 = One thread executed per time slice.
+ # 1 = All threads executed each time slice.
+MAX_LABEL_EXE_SIZE 1 # Max nops marked as executed when labels are used
+MERIT_GIVEN 0.0 # Fraction of merit donated with 'donate' command
+MERIT_RECEIVED 0.0 # Multiplier of merit given with 'donate' command
+MAX_DONATE_KIN_DIST -1 # Limit on distance of relation for donate; -1=no max
+MAX_DONATE_EDIT_DIST -1 # Limit on genetic (edit) distance for donate; -1=no max
+MIN_GB_DONATE_THRESHOLD -1 # threshold green beard donates only to orgs above this
+ # donation attempt threshold; -1=no thresh
+DONATE_THRESH_QUANTA 10 # The size of steps between quanta donate thresholds
+MAX_DONATES 1000000 # Limit on number of donates organisms are allowed.
+
+### PROMOTER_GROUP ###
+# Promoters
+PROMOTERS_ENABLED 0 # Use the promoter/terminator execution scheme.
+ # Certain instructions must also be included.
+PROMOTER_PROCESSIVITY 1.0 # Chance of not terminating after each cpu cycle.
+PROMOTER_PROCESSIVITY_INST 1.0 # Chance of not terminating after each instruction.
+PROMOTER_BG_STRENGTH 0 # Probability of positions that are not promoter
+ # instructions initiating execution (promoters are 1).
+REGULATION_STRENGTH 1 # Strength added or subtracted to a promoter by regulation.
+REGULATION_DECAY_FRAC 0.1 # Fraction of regulation that decays away.
+ # Max regulation = 2^(REGULATION_STRENGTH/REGULATION_DECAY_FRAC)
+
+### GENEOLOGY_GROUP ###
+# Geneology
+TRACK_MAIN_LINEAGE 1 # Keep all ancestors of the active population?
+ # 0=no, 1=yes, 2=yes,w/sexual population
+THRESHOLD 3 # Number of organisms in a genotype needed for it
+ # to be considered viable.
+GENOTYPE_PRINT 0 # 0/1 (off/on) Print out all threshold genotypes?
+GENOTYPE_PRINT_DOM 0 # Print out a genotype if it stays dominant for
+ # this many updates. (0 = off)
+SPECIES_THRESHOLD 2 # max failure count for organisms to be same species
+SPECIES_RECORDING 0 # 1 = full, 2 = limited search (parent only)
+SPECIES_PRINT 0 # 0/1 (off/on) Print out all species?
+TEST_CPU_TIME_MOD 20 # Time allocated in test CPUs (multiple of length)
+
+### LOG_GROUP ###
+# Log Files
+LOG_CREATURES 0 # 0/1 (off/on) toggle to print file.
+LOG_GENOTYPES 0 # 0 = off, 1 = print ALL, 2 = print threshold ONLY.
+LOG_THRESHOLD 0 # 0/1 (off/on) toggle to print file.
+LOG_SPECIES 0 # 0/1 (off/on) toggle to print file.
+
+### LINEAGE_GROUP ###
+# Lineage
+# NOTE: This should probably be called "Clade"
+# This one can slow down avida a lot. It is used to get an idea of how
+# often an advantageous mutation arises, and where it goes afterwards.
+# Lineage creation options are. Works only when LOG_LINEAGES is set to 1.
+# 0 = manual creation (on inject, use successive integers as lineage labels).
+# 1 = when a child's (potential) fitness is higher than that of its parent.
+# 2 = when a child's (potential) fitness is higher than max in population.
+# 3 = when a child's (potential) fitness is higher than max in dom. lineage
+# *and* the child is in the dominant lineage, or (2)
+# 4 = when a child's (potential) fitness is higher than max in dom. lineage
+# (and that of its own lineage)
+# 5 = same as child's (potential) fitness is higher than that of the
+# currently dominant organism, and also than that of any organism
+# currently in the same lineage.
+# 6 = when a child's (potential) fitness is higher than any organism
+# currently in the same lineage.
+# 7 = when a child's (potential) fitness is higher than that of any
+# organism in its line of descent
+LOG_LINEAGES 0 #
+LINEAGE_CREATION_METHOD 0 #
+
+### ORGANISM_NETWORK_GROUP ###
+# Organism Network Communication
+NET_ENABLED 0 # Enable Network Communication Support
+NET_DROP_PROB 0.0 # Message drop rate
+NET_MUT_PROB 0.0 # Message corruption probability
+NET_MUT_TYPE 0 # Type of message corruption. 0 = Random Single Bit, 1 = Always Flip Last
+NET_STYLE 0 # Communication Style. 0 = Random Next, 1 = Receiver Facing
+
+### BUY_SELL_GROUP ###
+# Buying and Selling Parameters
+SAVE_RECEIVED 0 # Enable storage of all inputs bought from other orgs
+BUY_PRICE 0 # price offered by organisms attempting to buy
+SELL_PRICE 0 # price offered by organisms attempting to sell
+
+### ANALYZE_GROUP ###
+# Analysis Settings
+MT_CONCURRENCY 1 # Number of concurrent analyze threads
+ANALYZE_OPTION_1 # String variable accessible from analysis scripts
+ANALYZE_OPTION_2 # String variable accessible from analysis scripts
+
+### SECOND_PASS_GROUP ###
+# Tracking metrics known after the running experiment previously
+TRACK_CCLADES 0 # Enable tracking of coalescence clades
+TRACK_CCLADES_IDS coalescence.ids # File storing coalescence IDs
Added: development/tests/resources_9r/config/environment.9resource
===================================================================
--- development/tests/resources_9r/config/environment.9resource (rev 0)
+++ development/tests/resources_9r/config/environment.9resource 2007-06-13 16:22:25 UTC (rev 1675)
@@ -0,0 +1,33 @@
+##############################################################################
+#
+# This is the setup file for the task/resource system. From here, you can
+# setup the available resources (including their inflow and outflow rates) as
+# well as the reactions that the organisms can trigger by performing tasks.
+#
+# This environmental setup is that of a chemostat with 9 resources, each
+# with a unique task corresponding to them. All resources have a set inflow
+# of 100, and outflow rate of 0.01, setting their an equilibrium level at
+# 10,000. Given a maximum population size of 3600 and neighborhood size of
+# 9, the fraction of the resource absorbable in each reaction is simply
+# 9/3600 or 0.0025.
+#
+# For information on how to use this file, see: doc/environment.html
+# For other sample environments, see: source/support/config/
+#
+##############################################################################
+
+RESOURCE resNOT:inflow=100:outflow=0.01 resNAND:inflow=100:outflow=0.01
+RESOURCE resAND:inflow=100:outflow=0.01 resORN:inflow=100:outflow=0.01
+RESOURCE resOR:inflow=100:outflow=0.01 resANDN:inflow=100:outflow=0.01
+RESOURCE resNOR:inflow=100:outflow=0.01 resXOR:inflow=100:outflow=0.01
+RESOURCE resEQU:inflow=100:outflow=0.01
+
+REACTION NOT not process:resource=resNOT:value=1.0:frac=0.0025:max=25
+REACTION NAND nand process:resource=resNAND:value=1.0:frac=0.0025:max=25
+REACTION AND and process:resource=resAND:value=2.0:frac=0.0025:max=25
+REACTION ORN orn process:resource=resORN:value=2.0:frac=0.0025:max=25
+REACTION OR or process:resource=resOR:value=4.0:frac=0.0025:max=25
+REACTION ANDN andn process:resource=resANDN:value=4.0:frac=0.0025:max=25
+REACTION NOR nor process:resource=resNOR:value=8.0:frac=0.0025:max=25
+REACTION XOR xor process:resource=resXOR:value=8.0:frac=0.0025:max=25
+REACTION EQU equ process:resource=resEQU:value=16.0:frac=0.0025:max=25
Added: development/tests/resources_9r/config/events.cfg
===================================================================
--- development/tests/resources_9r/config/events.cfg (rev 0)
+++ development/tests/resources_9r/config/events.cfg 2007-06-13 16:22:25 UTC (rev 1675)
@@ -0,0 +1,16 @@
+# Print all of the standard data files...
+u 0:10:end PrintAverageData # Save info about they average genotypes
+u 0:10:end PrintDominantData # Save info about most abundant genotypes
+u 0:10:end PrintStatsData # Collect satistics about entire pop.
+u 0:10:end PrintCountData # Count organisms, genotypes, species, etc.
+u 0:10:end PrintTasksData # Save organisms counts for each task.
+u 0:10:end PrintTimeData # Track time conversion (generations, etc.)
+u 0:10:end PrintResourceData # Track resource abundance.
+u 0:10:end PrintDominantGenotype # Save the most abundant genotypes
+u 0:10:end PrintTasksExeData # Num. times tasks have been executed.
+u 0:10:end PrintTasksQualData # Task quality information
+
+# Setup the exit time and full population data collection.
+u 100 SavePopulation # Save current state of population.
+u 100 SaveHistoricPopulation # Save ancestors of current population.
+u 100 exit # exit
Added: development/tests/resources_9r/expected/data/archive/067-aaaaa.org
===================================================================
--- development/tests/resources_9r/expected/data/archive/067-aaaaa.org (rev 0)
+++ development/tests/resources_9r/expected/data/archive/067-aaaaa.org 2007-06-13 16:22:25 UTC (rev 1675)
@@ -0,0 +1,101 @@
+# Wed Jun 13 12:20:25 2007
+# Filename........: archive/067-aaaaa.org
+# Update Output...: 100
+# Is Viable.......: 1
+# Repro Cycle Size: 0
+# Depth to Viable.: 0
+# Update Created..: -1
+# Genotype ID.....: 1
+# Parent Gen ID...: -1
+# Tree Depth......: 0
+# Parent Distance.: -1
+#
+# Generation: 0
+# Merit...........: 67.000000
+# Gestation Time..: 220
+# Fitness.........: 0.304545
+# Errors..........: 1
+# Genome Size.....: 67
+# Copied Size.....: 67
+# Executed Size...: 67
+# Offspring.......: SELF
+#
+# Tasks Performed:
+# not 2 (2.000000)
+# nand 3 (3.000000)
+# and 1 (1.000000)
+# orn 2 (2.000000)
+# or 2 (2.000000)
+# andn 1 (1.000000)
+# nor 2 (2.000000)
+# xor 1 (1.000000)
+# equ 1 (1.000000)
+
+
+nop-A
+set-flow
+h-alloc
+set-flow
+nop-A
+mov-head
+nop-C
+h-divide
+h-search
+IO
+nop-C
+dec
+nand
+h-copy
+IO
+nop-C
+if-less
+nop-C
+swap
+swap-stk
+nand
+nop-C
+if-label
+pop
+nand
+nop-C
+IO
+nop-A
+push
+nop-C
+inc
+nop-B
+h-copy
+pop
+h-copy
+nand
+nop-C
+IO
+h-copy
+h-copy
+nand
+push
+IO
+IO
+nop-C
+h-copy
+h-copy
+h-copy
+h-copy
+inc
+h-copy
+if-label
+nop-C
+if-label
+mov-head
+nop-A
+h-copy
+swap-stk
+h-copy
+nop-A
+h-copy
+h-copy
+h-copy
+h-copy
+pop
+h-copy
+h-divide
Added: development/tests/resources_9r/expected/data/average.dat
===================================================================
--- development/tests/resources_9r/expected/data/average.dat (rev 0)
+++ development/tests/resources_9r/expected/data/average.dat 2007-06-13 16:22:25 UTC (rev 1675)
@@ -0,0 +1,30 @@
+# Avida Average Data
+# Wed Jun 13 12:20:25 2007
+# 1: Update
+# 2: Merit
+# 3: Gestation Time
+# 4: Fitness
+# 5: Repro Rate?
+# 6: Size
+# 7: Copied Size
+# 8: Executed Size
+# 9: Abundance
+# 10: Proportion of organisms that gave birth in this update
+# 11: Proportion of Breed True Organisms
+# 12: Genotype Depth
+# 13: Generation
+# 14: Neutral Metric
+# 15: Lineage Label
+# 16: True Replication Rate (based on births/update, time-averaged)
+
+0 67.000000 220.000000 0.000000 0.000000 67.000000 67.000000 67.000000 1.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000
+10 4685.4 220 21.2973 0 67 67 67 1 0 0 0.5 1 -0.374898 0 0
+20 12208 249.5 49.6528 0 67.25 67 67 1.33333 0 0 0.75 2 -1.05753 0 0
+30 22077.5 237.7 95.074 0 68.3 68.2 67 1.42857 0.2 0 0.9 3.5 -2.94021 0 0
+40 27582.9 231.8 120.32 0 68.6667 68.6 67 1.66667 0.0666667 0 0.866667 4.53333 -3.27186 0 0
+50 25178.9 223.667 113.51 0 67.6389 67.6389 66.8889 1.63636 0.0277778 0.0277778 1.13889 6.61111 -3.61746 0 0
+60 26122 219.582 117.775 0 67.4 66.3273 64.7091 1.57143 0.0545455 0.0181818 1.16364 8.16364 -4.10834 0 0
+70 28390.9 238.447 117.798 0 66.6842 65.9474 65.2763 1.58333 0.0789474 0.0526316 1.28947 9.73684 -4.9693 0 0
+80 24015.2 225.374 107.735 0 66.3434 65.7172 65.9091 1.7069 0.10101 0.0505051 1.28283 11.4141 -4.95699 0 0
+90 24623.2 237.548 104.71 0 67.037 66.7185 66.2667 1.75325 0.118519 0.0814815 1.32593 13.2889 -4.97173 0 0
+100 21989.5 232.219 91.8791 0 67.7751 66.8402 65.7988 1.76042 0.0828402 0.0295858 1.36686 14.8817 -5.25401 0 0
Added: development/tests/resources_9r/expected/data/count.dat
===================================================================
--- development/tests/resources_9r/expected/data/count.dat (rev 0)
+++ development/tests/resources_9r/expected/data/count.dat 2007-06-13 16:22:25 UTC (rev 1675)
@@ -0,0 +1,30 @@
+# Avida count data
+# Wed Jun 13 12:20:25 2007
+# 1: update
+# 2: number of insts executed this update
+# 3: number of organisms
+# 4: number of different genotypes
+# 5: number of different threshold genotypes
+# 6: number of different species
+# 7: number of different threshold species
+# 8: number of different lineages
+# 9: number of births in this update
+# 10: number of deaths in this update
+# 11: number of breed true
+# 12: number of breed true organisms?
+# 13: number of no-birth organisms
+# 14: number of single-threaded organisms
+# 15: number of multi-threaded organisms
+# 16: number of modified organisms
+
+0 30 1 1 1 0 0 0 1 0 1 1 1 1 0 0
+10 60 2 2 1 0 0 0 0 0 0 1 1 2 0 0
+20 120 4 3 1 0 0 0 0 0 0 2 2 4 0 0
+30 240 10 7 1 0 0 0 2 0 0 4 6 10 0 0
+40 450 15 9 2 0 0 0 1 1 0 7 9 15 0 0
+50 1050 36 22 2 0 0 0 1 0 1 15 20 36 0 0
+60 1590 55 35 2 0 0 0 3 1 1 23 31 55 0 0
+70 2190 76 48 2 0 0 0 6 3 4 31 46 76 0 0
+80 2820 99 58 4 0 0 0 10 5 5 43 59 99 0 0
+90 3810 135 77 6 0 0 0 16 8 11 63 79 135 0 0
+100 4950 169 96 9 0 0 0 14 10 5 80 95 169 0 0
Added: development/tests/resources_9r/expected/data/detail-100.pop
===================================================================
--- development/tests/resources_9r/expected/data/detail-100.pop (rev 0)
+++ development/tests/resources_9r/expected/data/detail-100.pop 2007-06-13 16:22:25 UTC (rev 1675)
@@ -0,0 +1,113 @@
+#filetype genotype_data
+#format id parent_id parent_dist num_cpus total_cpus length merit gest_time fitness update_born update_dead depth sequence
+
+# 1: ID
+# 2: parent ID
+# 3: parent distance
+# 4: number of orgranisms currently alive
+# 5: total number of organisms that ever existed
+# 6: length of genome
+# 7: merit
+# 8: gestation time
+# 9: fitness
+# 10: update born
+# 11: update deactivated
+# 12: depth in phylogentic tree
+# 13: genome of organism
+
+1 -1 -1 37 108 67 33169.8 220 150.772 -1 -1 0 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgqqcttttltycyvathtattttfts
+5 1 1 19 41 67 32925.6 220 149.662 22 -1 1 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgqqcttttltycyvfthtattttfts
+64 5 1 4 4 67 7550.73 217 34.796 69 -1 2 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcpttpgqqcttttltycyvfthtattttfts
+11 1 1 4 6 67 6495.2 215 30.2102 41 -1 1 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttqgqqcttttltycyvathtattttfts
+77 1 1 3 3 67 9036.56 220 41.0753 74 -1 1 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttppqqcttttltycyvathtattttfts
+136 5 1 3 3 67 5481.88 220 24.9176 89 -1 2 azrzavcsuqcmptqcecfhpcyfpcqagclbtftpcqttpgqqcttttltycyvfthtattttfts
+78 66 1 2 3 67 22184.3 226 98.1605 74 -1 3 azrzavcsuqcmptqrecihpcyipcqagclbtftpcqttpgqqcttttltycyvfthtattttfts
+54 5 1 2 2 67 2814.26 226 12.4525 64 -1 2 azrzavcsuqcmptqcecihpcyfpcqarclbtftpcqttpgqqcttttltycyvfthtattttfts
+113 1 1 2 2 67 8960.93 211 42.4689 83 -1 1 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgaqcttttltycyvathtattttfts
+129 1 1 2 2 67 3260.17 226 14.4255 87 -1 1 azrzavcsuqcmptqcecihpcyfpcqahclbtftpcqttpgqqcttttltycyvathtattttfts
+137 5 1 2 2 67 28440.5 220 129.275 89 -1 2 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgqqcttttltycyvftltattttfts
+35 8 2 2 2 67 6952.07 220 31.6003 55 -1 2 azrzavcsuqcmptqcecphpcyfpcqagclbtftpcqttpfqqcttttltycyvathtattttfts
+143 1 1 2 2 67 7184.39 219 32.8055 91 -1 1 azrzavcsuqcmptqcecihpcyfpcqaiclbtftpcqttpgqqcttttltycyvathtattttfts
+173 1 1 2 2 66 33790.2 220 153.592 97 -1 1 azrzavcsuqcmptqcecipcyfpcqagclbtftpcqttpgqqcttttltycyvathtattttfts
+116 76 1 2 5 66 29872.2 219 136.403 84 -1 2 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgqqcttttltycyvathtattttfs
+134 30 12 1 2 79 26632.9 287 92.7975 89 -1 2 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgqqctdttltycyvathtattttftsazrzavcsuqrm
+165 1 1 1 2 67 34028.5 220 154.675 96 -1 1 aprzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgqqcttttltycyvathtattttfts
+44 1 1 1 2 67 6562.06 220 29.8276 59 -1 1 azrzavcsuqcmptqcecohpcyfpcqagclbtftpcqttpgqqcttttltycyvathtattttfts
+21 5 1 1 1 67 4702.92 130 36.1763 48 -1 2 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpsqqcttttltycyvfthtattttfts
+26 17 2 1 1 66 29842.2 220 135.646 49 -1 3 azzavcsuqlmptqcecihpcyfpcqagclbtftpcqttpgqqcttttptycyvfthtattttfts
+30 1 1 1 1 67 32312.8 287 112.588 53 -1 1 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgqqctdttltycyvathtattttfts
+45 34 1 1 1 67 1009.44 287 3.51721 60 -1 2 azrzavcsuqcmptqcecihpcyfpcqagclctflpcqttpgqqcttttltycyvathtattttfts
+56 43 1 1 1 67 34260.4 220 155.729 64 -1 3 wzrzavcsugcmptqcecihpcyfpcqagclbtftpcqttpgqqcttttltycyvfthtattttfts
+67 51 1 1 1 67 8664.08 226 38.3366 69 -1 2 azrzavcsuqcmptqcecihpcyppcqagelbtftpcqttpgqqcttttltycyvathtattttfts
+71 35 1 1 1 67 13285.4 220 60.3883 70 -1 3 azuzavcsuqcmptqcecphpcyfpcqagclbtftpcqttpfqqcttttltycyvathtattttfts
+75 1 1 1 1 67 13564.1 222 61.0998 73 -1 1 azrzavcsuqcmptqqecihpcyfpcqagclbtftpcqttpgqqcttttltycyvathtattttfts
+76 1 1 1 1 67 31054.1 219 141.799 74 -1 1 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgqqcttttltycyvathtattttfss
+79 61 1 1 1 67 33012.4 220 150.056 74 -1 3 azruavcsuqcmptqcecihpcyfgcqagclbtftpcqttigqqcttttltycyvathtattttfts
+81 5 1 1 1 67 163472 1032 158.403 75 -1 2 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgqqcttttltyayvfthtattttfts
+86 1 1 1 1 67 8065.46 217 37.168 76 -1 1 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcrttpgqqcttttltycyvathtattttfts
+88 45 24 1 1 67 31323.9 220 142.382 77 -1 3 ptqcecihpcyfpcqagclctflpcqttpgqqcttttltycyvathtattttftsazrzavcsuqcm
+90 75 1 1 1 67 35022.6 220 159.193 78 -1 2 azrzavcsuqcmptqqecihpcyfpcqagclbtftpcqttpgqqcttttltycyvathtattttftv
+91 1 1 1 1 67 35323 220 160.559 78 -1 1 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgqqctzttltycyvathtattttfts
+92 1 1 1 1 67 33809.5 220 153.679 78 -1 1 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgqqcttttltycyvathtatpttfts
+93 1 2 1 1 68 35335.8 220 160.617 78 -1 1 azrzdvcsuqcmptqcecihpcyfpcqagclbtftpcqttpgqqctltttltycyvathtattttfts
+100 5 3 1 1 67 16368.4 287 57.0328 80 -1 2 azrzavcsuqcmptqcecihgcyfpcqagclbtftpcqdtggqqcttttltycyvfthtattttfts
+104 60 2 1 1 79 63 255 0.247059 82 -1 3 azrzavcsuqcmptqcecihocyfpcqagclbkftpcqttpgqqctdttltycyvathtattttftsazrzavesuqcm
+106 51 2 1 1 67 12138.3 287 42.2938 82 -1 2 azrzavcsuqcmptqcecihpcyppcqagcpbtftpcqttpgqqctdttltycyvathtattttfts
+110 67 1 1 1 67 33595.5 220 152.707 83 -1 3 azrzavcsuqcmptqcecihpcyppcqagelbtftpcqttpgqqcttttltycyvavhtattttfts
+115 95 4 1 1 67 35342.8 220 160.649 84 -1 2 azrzaecskqcmptqcecihpcyfpcqagclbtftpcqttpgqmcttttltycyvathtaqtltfts
+117 5 3 1 1 67 35721.1 220 162.368 84 -1 2 azrzavcsuccmptqcecihpcyfpcqagclbtftpcqttpgqqcmtttltycyvfthtfttttfts
+119 5 1 1 1 67 29844.5 221.5 134.815 85 -1 2 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgqqcttttltycyvfthmattttfts
+122 1 1 1 1 68 35118.9 220 159.631 85 -1 1 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgqeqcttttltycyvathtattttfts
+125 101 25 1 1 66 35345.4 220 160.661 86 -1 2 ptqcecihpcyfcqagclbtftpcqltpgqqcttttltycyvathtattttftsazrzavcsuqcm
+128 104 32 1 1 79 34041 287 118.61 87 -1 4 tftsazrzavesuqcmazrzavcsuqcmptqcecihocyfpcqagclbkftpcqttpgqqctdttltycyvathtattt
+130 1 1 1 1 67 34933.5 220 158.789 88 -1 1 azrzancsuqcmptqcecihpcyfpcqagclbtftpcqttpgqqcttttltycyvathtattttfts
+133 1 1 1 1 67 1097.83 142 7.73119 88 -1 1 azrzavcsuqcsptqcecihpcyfpcqagclbtftpcqttpgqqcttttltycyvathtattttfts
+135 5 1 1 1 67 24604.4 220 111.838 89 -1 2 dzrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgqqcttttltycyvfthtattttfts
+139 119 2 1 1 67 35520.7 220 161.458 90 -1 3 sazrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgqqcttttltycyvfthmattttft
+140 75 3 1 1 66 14346.3 222 64.6228 90 -1 2 azrzavcsuqcmpnqqecihpcyfpcqagcltftpcqttpgqqcttttltyxyvathtattttfts
+141 121 5 1 1 67 345.438 142 2.43266 90 -1 2 sazrzavcsuqcmptqcecihpcyfpyqagclbtftxcqttpgqqsttttltycyvathtatttbft
+142 114 24 1 1 67 35249.6 220 160.225 90 -1 2 ptqcecihpcyfpcqagclbtftpcqttpgqqctnttltycyvathtattttftsazrzavcsuqcm
+146 133 55 1 1 67 34877.7 220 158.535 92 -1 2 pgqqcttttltycyvathtattttftsazrzavcsuqcsptqcecihpcyfpcqagclbtvtpcqtt
+148 1 1 1 1 68 34384.2 220 156.292 93 -1 1 azrzavcsuqcmptqcecihpcyfpcqhagclbtftpcqttpgqqcttttltycyvathtattttfts
+149 1 1 1 1 67 6329.59 220 28.7708 93 -1 1 azrzavcsuqcmptqcecihecyfpcqagclbtftpcqttpgqqcttttltycyvathtattttfts
+47 1 1 1 3 67 20807 220 94.5774 62 -1 1 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttigqqcttttltycyvathtattttfts
+150 141 59 1 1 67 35153.3 220 159.788 94 -1 3 txcqttpgqqsttttltycyvathtatttbftsazrzavcsuqcmptqcecihpcyfpyqagclbtf
+151 78 1 1 1 67 24536.2 226 108.567 94 -1 4 azrzavcsuqcmptqrecihpcyipcqagclbtftpcqhtpgqqcttttltycyvfthtattttfts
+152 55 1 1 1 67 3977.2 217 18.3281 95 -1 3 azrzavcmuqcmptqcecihpcyfpcqagclbtftpcqttpgqmcttttltycyvfthtattttfts
+154 135 1 1 1 67 35474 220 161.245 95 -1 3 dzrzavcsuqcmptqcecihpcyfpcqamclbtftpcqttpgqqcttttltycyvfthtattttfts
+155 5 1 1 1 67 34300.6 220 155.912 95 -1 2 azrzavcsuqcmptqcecihpcyfpcqagclbxftpcqttpgqqcttttltycyvfthtattttfts
+156 5 1 1 1 67 34225.1 220 155.569 95 -1 2 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgqqcttetltycyvfthtattttfts
+157 76 2 1 1 67 33320.8 219 152.15 95 -1 2 azrzavcsuqcmptqcecihpcyfpcqagclbrtftpcqttpgqqcttttltycyvathtattttfs
+12 5 1 1 2 67 2843.45 226 12.5816 42 -1 2 azrzavcsuqcmptqcecihpcyfpcqaaclbtftpcqttpgqqcttttltycyvfthtattttfts
+159 5 1 1 1 66 33907.2 220 154.123 95 -1 2 azrzavcsuqmptqcecihpcyfpcqagclbtftpcqttpgqqcttttltycyvfthtattttfts
+160 5 2 1 1 66 33833.5 220 153.789 95 -1 2 azgzavcsucmptqcecihpcyfpcqagclbtftpcqttpgqqcttttltycyvfthtattttfts
+161 119 54 1 1 120 31019.1 219 141.64 95 -1 3 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgqqcttttltycyvfthmattttftaaaaaaaaaaaaaaaamaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
+163 5 1 1 1 67 33765.6 220 153.48 96 -1 2 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpnqqcttttltycyvfthtattttfts
+164 77 1 1 1 67 9187.96 220 41.7635 96 -1 2 azrzavcsuqcmptqcecihpcyfpcqagclbtftpaqttppqqcttttltycyvathtattttfts
+166 30 14 1 1 79 33383 287 116.317 96 -1 2 azrzavcsuqcmptqcecispcyfpcqagclblftpcqttpgqqctdttltycyvathtattttftsazrzavcsuqcm
+60 30 12 1 3 79 30353.4 287 105.761 67 -1 2 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgqqctdttltycyvathtattttftsazrzavesuqcm
+167 60 1 1 1 79 32249.8 287 112.369 96 -1 3 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgqqctdttlmycyvathtattttftsazrzavesuqcm
+168 5 2 1 1 68 33618.8 220 152.813 96 -1 2 azrzavcsuqchptqcecihpcyfpcqagclbtftpvcqttpgqqcttttltycyvfthtattttfts
+169 1 1 1 1 68 33857.9 220 153.9 96 -1 1 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgqqcttttltycyvkathtattttfts
+170 60 2 1 1 79 31122.4 287 108.44 96 -1 3 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgkqctdtfltycyvathtattttftsazrzavesuqcm
+172 12 3 1 1 67 3178.71 226 14.0651 97 -1 3 afzrzavcsuqcmptqcecihpcyfpcqaclbtftpcqttjgqqcttttltycyvfthtattttfts
+144 1 1 1 2 67 36755.4 215 170.955 91 -1 1 azrzavcsuqcmptqcecibpcyfpcqagclbtftpcqttpgqqcttttltycyvathtattttfts
+174 81 58 1 1 67 35870.9 220 163.049 97 -1 3 ttpgqqcttttltyayvfthtatttoftsgzrzavcsuqcmptqcecihpcyfpcqagclbtftpcq
+68 53 1 1 2 67 7869.36 220 35.7698 69 -1 3 azrzavcsuqcmptqcecihpcyfpcqagcmbtftpcqttjgqqcttttltycyvfthtattttfts
+175 1 1 1 1 66 33618.4 220 152.811 98 -1 1 azrzavcsuqcmptqecihpcyfpcqagclbtftpcqttpgqqcttttltycyvathtattttfts
+176 11 1 1 1 66 6823.72 215 31.7382 98 -1 2 azrzavcsuqcmptqcecihpcyfpcqaclbtftpcqttqgqqcttttltycyvathtattttfts
+177 149 1 1 1 67 34327.9 220 156.036 98 -1 2 azrzavcsuqcmptqcecijecyfpcqagclbtftpcqttpgqqcttttltycyvathtattttfts
+178 1 3 1 1 67 33584.6 220 152.657 98 -1 1 azrzavcsuqcpptqcezihpcyfpcqagclbtftpcqttpguqcttttltycyvathtattttfts
+179 1 1 1 1 67 33549.4 220 152.497 98 -1 1 azrzavcsuqcmptqcecihpcyficqagclbtftpcqttpgqqcttttltycyvathtattttfts
+180 162 57 1 1 67 34161.2 220 155.278 99 -1 2 qttpgqqcttttltacyvathtattttftsazrzavcsuqcmptqcecihpcyfpcqagclbtftpc
+181 1 2 1 1 67 33444.5 220 152.02 99 -1 1 azrzavcsuqcaptqceciapcyfpcqagclbtftpcqttpgqqcttttltycyvathtattttfts
+182 106 25 1 1 67 14170 220 64.4092 99 -1 3 ptqcecihpcyppcqwgcpbtftpcqttpgqqctdttltycyvathtattttftsazrzavcsuqcm
+183 1 2 1 1 67 33341.3 220 151.551 99 -1 1 azrzavcsuqcmptqcecihpcyfpcqagwlbtftpcqttpgqqcttttldycyvathtattttfts
+109 47 1 1 2 67 7982.2 220 36.2827 83 -1 2 azrzavcsuqcmptqcecihpcyfpcqagclbtftdcqttigqqcttttltycyvathtattttfts
+185 137 6 1 1 66 29808.4 220 135.493 100 -1 3 azrmavcsuqcmptqcecihpcyfpcqawcbtftpbqttpgqqyttttltycyvftltatsttfts
+186 1 1 1 1 67 33273.9 220 151.245 100 -1 1 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgqqcttttltycyvathtattttfti
+187 5 1 1 1 67 33467.2 220 152.124 100 -1 2 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgqqcttttlsycyvfthtattttfts
+188 5 1 1 1 67 33372.9 220 151.695 100 -1 2 azrzavcsuqcmptqcecihpgyfpcqagclbtftpcqttpgqqcttttltycyvfthtattttfts
+189 144 1 1 1 68 37829.9 215 175.953 100 -1 2 azrzapvcsuqcmptqcecibpcyfpcqagclbtftpcqttpgqqcttttltycyvathtattttfts
+190 1 1 1 1 67 33204.7 220 150.93 100 -1 1 azrzavcsuqcmptqcecihpcyfpcqagclitftpcqttpgqqcttttltycyvathtattttfts
+55 5 1 1 3 67 3299.34 217 15.2043 64 -1 2 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgqmcttttltycyvfthtattttfts
Added: development/tests/resources_9r/expected/data/dominant.dat
===================================================================
--- development/tests/resources_9r/expected/data/dominant.dat (rev 0)
+++ development/tests/resources_9r/expected/data/dominant.dat 2007-06-13 16:22:25 UTC (rev 1675)
@@ -0,0 +1,30 @@
+# Avida Dominant Data
+# Wed Jun 13 12:20:25 2007
+# 1: Update
+# 2: Average Merit of the Dominant Genotype
+# 3: Average Gestation Time of the Dominant Genotype
+# 4: Average Fitness of the Dominant Genotype
+# 5: Repro Rate?
+# 6: Size of Dominant Genotype
+# 7: Copied Size of Dominant Genotype
+# 8: Executed Size of Dominant Genotype
+# 9: Abundance of Dominant Genotype
+# 10: Number of Births
+# 11: Number of Dominant Breed True?
+# 12: Dominant Gene Depth
+# 13: Dominant Breed In
+# 14: Max Fitness?
+# 15: Genotype ID of Dominant Genotype
+# 16: Name of the Dominant Genotype
+
+0 0.000000 0.000000 0.000000 0.000000 67 0.000000 0.000000 1 0 0 0 0 0.000000 1 067-aaaaa
+10 4685.4 220 21.2973 0.00454545 67 67 67 1 0 0 0 0 21.2973 1 067-aaaaa
+20 8477 220 38.5318 0.00454545 67 67 67 2 0 0 0 0 55.7663 1 067-aaaaa
+30 17196.5 220 78.166 0.00454545 67 67 67 3 1 0 0 0 113.197 1 067-aaaaa
+40 21139.3 220 96.0879 0.00454545 67 67 67 5 0 0 0 0 135.324 1 067-aaaaa
+50 28956.7 220 131.621 0.00454545 67 67 67 10 1 1 0 0 165.235 1 067-aaaaa
+60 33012.4 220 150.056 0.00454545 67 67 67 13 1 1 0 0 173.852 1 067-aaaaa
+70 34831.9 220 158.327 0.00454545 67 67 67 19 4 4 0 0 173.485 1 067-aaaaa
+80 35337.4 220 160.625 0.00454545 67 67 67 23 6 3 0 0 173.485 1 067-aaaaa
+90 34709.7 220 157.771 0.00454545 67 67 67 29 4 4 0 0 173.485 1 067-aaaaa
+100 33169.8 220 150.772 0.00454545 67 67 67 37 4 1 0 0 165.958 1 067-aaaaa
Added: development/tests/resources_9r/expected/data/historic-100.pop
===================================================================
--- development/tests/resources_9r/expected/data/historic-100.pop (rev 0)
+++ development/tests/resources_9r/expected/data/historic-100.pop 2007-06-13 16:22:25 UTC (rev 1675)
@@ -0,0 +1,30 @@
+#filetype genotype_data
+#format id parent_id parent_dist num_cpus total_cpus length merit gest_time fitness update_born update_dead depth sequence
+
+# 1: ID
+# 2: parent ID
+# 3: parent distance
+# 4: number of orgranisms currently alive
+# 5: total number of organisms that ever existed
+# 6: length of genome
+# 7: merit
+# 8: gestation time
+# 9: fitness
+# 10: update born
+# 11: update deactivated
+# 12: depth in phylogentic tree
+# 13: genome of organism
+
+162 1 1 0 1 67 4267.22 123 34.6928 96 100 1 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgqqcttttltacyvathtattttfts
+114 1 1 0 1 67 6871.98 287 23.9442 83 96 1 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgqqctnttltycyvathtattttfts
+101 1 1 0 1 67 10054.1 287 35.0317 80 96 1 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqltpgqqcttttltycyvathtattttfts
+121 1 1 0 1 67 30593.9 220 139.063 85 94 1 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgqqcttttltycyvathtatttbfts
+95 1 1 0 1 67 3263.42 217 15.0388 79 89 1 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttpgqmcttttltycyvathtattttfts
+51 1 1 0 1 67 13484.1 220 61.2914 63 89 1 azrzavcsuqcmptqcecihpcyppcqagclbtftpcqttpgqqcttttltycyvathtattttfts
+43 5 1 0 1 67 1552.9 216 7.18936 59 84 2 azrzavcsugcmptqcecihpcyfpcqagclbtftpcqttpgqqcttttltycyvfthtattttfts
+66 5 1 0 1 67 16147.3 220 73.3966 69 80 2 azrzavcsuqcmptqcecihpcyipcqagclbtftpcqttpgqqcttttltycyvfthtattttfts
+61 47 1 0 1 67 21094.6 220 95.8845 67 75 2 azrzavcsuqcmptqcecihpcyfgcqagclbtftpcqttigqqcttttltycyvathtattttfts
+34 1 1 0 1 67 15313.1 220 69.6049 55 69 1 azrzavcsuqcmptqcecihpcyfpcqagclctftpcqttpgqqcttttltycyvathtattttfts
+53 5 1 0 1 67 8250.52 220 37.5024 63 69 2 azrzavcsuqcmptqcecihpcyfpcqagclbtftpcqttjgqqcttttltycyvfthtattttfts
+8 1 1 0 2 67 13830.5 220 62.866 35 63 1 azrzavcsuqcmptqcecghpcyfpcqagclbtftpcqttpgqqcttttltycyvathtattttfts
+17 5 1 0 1 67 9999.38 227 44.0501 44 52 2 azrzavcsuqlmptqcecihpcyfpcqagclbtftpcqttpgqqcttttltycyvfthtattttfts
Added: development/tests/resources_9r/expected/data/resource.dat
===================================================================
--- development/tests/resources_9r/expected/data/resource.dat (rev 0)
+++ development/tests/resources_9r/expected/data/resource.dat 2007-06-13 16:22:25 UTC (rev 1675)
@@ -0,0 +1,26 @@
+# Avida resource data
+# Wed Jun 13 12:20:25 2007
+# First column gives the current update, all further columns give the quantity
+# of the particular resource at that update.
+# 1: Update
+# 2: resNOT
+# 3: resNAND
+# 4: resAND
+# 5: resORN
+# 6: resOR
+# 7: resANDN
+# 8: resNOR
+# 9: resXOR
+# 10: resEQU
+
+0 99.489312 99.489312 99.489312 99.489312 99.290539 99.489312 99.489312 99.489312 99.489312
+10 1034.53 1034.34 1038.56 1034.52 1036.03 1035.66 1035.83 1039.88 1039.83
+20 1861.76 1854.66 1877.72 1861.76 1865.11 1880.1 1864.69 1885.12 1884.93
+30 2576.52 2495.09 2611.83 2567.61 2581.84 2631.47 2581.01 2623.45 2622.89
+40 2981.25 2902.05 3201.13 2967.51 3133.72 3198.86 3139.89 3265.36 3280.97
+50 3121.08 2937.7 3592.27 3161.57 3365.15 3654.91 3369.62 3761.39 3759.96
+60 2908.88 2653.94 3759.94 2922.85 3306.54 3849.04 3336.94 4033.76 4041.35
+70 2634.89 2264.19 3770 2608.77 3069.99 3962.85 3137.78 4141.29 4145.65
+80 2197.65 1697.2 3446.6 2146.91 2635.24 3785.76 2747.81 4111.76 4122.92
+90 1768.54 1176.64 3031.68 1781.58 2126.84 3448.42 2226.79 3857.92 3881.33
+100 1270.06 750.326 2434.01 1208.49 1593.83 2813.31 1732.15 3421.07 3435.6
Added: development/tests/resources_9r/expected/data/stats.dat
===================================================================
--- development/tests/resources_9r/expected/data/stats.dat (rev 0)
+++ development/tests/resources_9r/expected/data/stats.dat 2007-06-13 16:22:25 UTC (rev 1675)
@@ -0,0 +1,26 @@
+# Generic Statistics Data
+# Wed Jun 13 12:20:25 2007
+# 1: update
+# 2: average inferiority (energy)
+# 3: ave probability of any mutations in genome
+# 4: probability of any mutations in dom genome
+# 5: log(average fidelity)
+# 6: log(dominant fidelity)
+# 7: change in number of genotypes
+# 8: genotypic entropy
+# 9: species entropy
+# 10: depth of most reacent coalescence
+# 11: Total number of resamplings this generation
+# 12: Total number of organisms that failed to resample this generation
+
+0 0.000000 0.444291 0.444291 0.587510 0.587510 1 0.000000 0.000000 0 0 0
+10 0 0.444291 0.444291 0.58751 0.58751 0 0.693147 0 0 0 0
+20 -0.253571 0.445295 0.444291 0.58932 0.58751 0 1.03972 0 0 0 0
+30 -0.195821 0.449495 0.444291 0.596919 0.58751 2 1.83437 0 0 0 0
+40 -0.224894 0.450954 0.444291 0.599573 0.58751 0 1.95185 0 0 0 0
+50 0.148035 0.446855 0.444291 0.592134 0.58751 0 2.73684 0 0 0 0
+60 0.242234 0.445897 0.444291 0.590405 0.58751 1 3.15394 0 0 0 0
+70 0.295687 0.443019 0.444291 0.585225 0.58751 2 3.36197 0 0 0 0
+80 0.399397 0.441644 0.444291 0.582758 0.58751 2 3.51131 0 0 0 0
+90 0.409955 0.44444 0.444291 0.587778 0.58751 5 3.66725 0 0 0 0
+100 0.495294 0.4474 0.444291 0.593121 0.58751 5 3.82986 0 0 0 0
Added: development/tests/resources_9r/expected/data/tasks.dat
===================================================================
--- development/tests/resources_9r/expected/data/tasks.dat (rev 0)
+++ development/tests/resources_9r/expected/data/tasks.dat 2007-06-13 16:22:25 UTC (rev 1675)
@@ -0,0 +1,26 @@
+# Avida tasks data
+# Wed Jun 13 12:20:25 2007
+# First column gives the current update, next columns give the number
+# of organisms that have the particular task as a component of their merit
+# 1: Update
+# 2: Not
+# 3: Nand
+# 4: And
+# 5: OrNot
+# 6: Or
+# 7: AndNot
+# 8: Nor
+# 9: Xor
+# 10: Equals
+
+0 0 0 0 0 0 0 0 0 0
+10 2 2 2 2 2 2 2 2 2
+20 4 4 4 4 4 4 4 4 4
+30 10 10 10 10 10 10 10 10 10
+40 15 15 15 15 15 15 15 15 15
+50 34 27 27 27 31 23 31 23 23
+60 50 43 41 44 48 38 46 37 35
+70 66 60 59 58 67 49 64 50 49
+80 85 74 72 73 84 62 82 57 57
+90 115 108 104 106 114 94 113 83 83
+100 145 136 129 133 141 114 136 105 105
Added: development/tests/resources_9r/expected/data/tasks_exe.dat
===================================================================
--- development/tests/resources_9r/expected/data/tasks_exe.dat (rev 0)
+++ development/tests/resources_9r/expected/data/tasks_exe.dat 2007-06-13 16:22:25 UTC (rev 1675)
@@ -0,0 +1,26 @@
+# Avida tasks execution data
+# Wed Jun 13 12:20:25 2007
+# First column gives the current update, all further columns give the number
+# of times the particular task has been executed this update.
+# 1: Update
+# 2: Not
+# 3: Nand
+# 4: And
+# 5: OrNot
+# 6: Or
+# 7: AndNot
+# 8: Nor
+# 9: Xor
+# 10: Equals
+
+0 0 0 0 0 0 0 0 0 0
+10 4 6 2 4 4 2 4 2 2
+20 10 16 6 10 6 4 6 4 4
+30 23 36 13 23 17 10 17 10 10
+40 33 51 18 33 27 15 27 15 15
+50 91 85 28 61 53 23 53 23 23
+60 118 134 45 99 81 40 77 37 35
+70 172 206 76 137 116 50 112 60 59
+80 197 230 85 162 142 72 138 57 57
+90 278 358 137 279 209 129 206 87 87
+100 367 451 161 346 255 143 237 119 119
Added: development/tests/resources_9r/expected/data/tasks_quality.dat
===================================================================
--- development/tests/resources_9r/expected/data/tasks_quality.dat (rev 0)
+++ development/tests/resources_9r/expected/data/tasks_quality.dat 2007-06-13 16:22:25 UTC (rev 1675)
@@ -0,0 +1,34 @@
+# Avida tasks quality data
+# Wed Jun 13 12:20:25 2007
+# First column gives the current update, rest give average and max task quality
+# 1: Update
+# 2: Not Average
+# 3: Not Max
+# 4: Nand Average
+# 5: Nand Max
+# 6: And Average
+# 7: And Max
+# 8: OrNot Average
+# 9: OrNot Max
+# 10: Or Average
+# 11: Or Max
+# 12: AndNot Average
+# 13: AndNot Max
+# 14: Nor Average
+# 15: Nor Max
+# 16: Xor Average
+# 17: Xor Max
+# 18: Equals Average
+# 19: Equals Max
+
+0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
+10 2 2 3 3 1 1 2 2 2 2 1 1 2 2 1 1 1 1
+20 2.5 3 4 5 1.5 2 2.5 3 1.5 2 1 1 1.5 2 1 1 1 1
+30 2.3 3 3.6 5 1.3 2 2.3 3 1.7 2 1 1 1.7 2 1 1 1 1
+40 2.2 3 3.4 5 1.2 2 2.2 3 1.8 2 1 1 1.8 2 1 1 1 1
+50 2.67647 10 3.14815 6 1.03704 2 2.25926 5 1.70968 2 1 1 1.70968 2 1 1 1 1
+60 2.36 10 3.11628 6 1.09756 2 2.25 5 1.6875 2 1.05263 2 1.67391 2 1 1 1 1
+70 2.60606 10 3.43333 16 1.28814 5 2.36207 10 1.73134 3 1.02041 2 1.75 3 1.2 6 1.20408 6
+80 2.31765 10 3.10811 10 1.18056 5 2.21918 6 1.69048 3 1.16129 6 1.68293 3 1 1 1 1
+90 2.41739 11 3.31481 9 1.31731 5 2.63208 11 1.83333 6 1.37234 6 1.82301 6 1.04819 3 1.04819 3
+100 2.53103 14 3.31618 17 1.24806 5 2.6015 14 1.80851 4 1.25439 6 1.74265 4 1.13333 7 1.13333 7
Added: development/tests/resources_9r/expected/data/time.dat
===================================================================
--- development/tests/resources_9r/expected/data/time.dat (rev 0)
+++ development/tests/resources_9r/expected/data/time.dat 2007-06-13 16:22:25 UTC (rev 1675)
@@ -0,0 +1,18 @@
+# Avida time data
+# Wed Jun 13 12:20:25 2007
+# 1: update
+# 2: avida time
+# 3: average generation
+# 4: num_executed?
+
+0 0.000000 0.000000 30
+10 0.105118 1 60
+20 0.106657 2 120
+30 0.10729 3.5 240
+40 0.10771 4.53333 450
+50 0.108091 6.61111 1050
+60 0.108492 8.16364 1590
+70 0.108865 9.73684 2190
+80 0.109253 11.4141 2820
+90 0.109671 13.2889 3810
+100 0.110109 14.8817 4950
Added: development/tests/resources_9r/test_list
===================================================================
--- development/tests/resources_9r/test_list (rev 0)
+++ development/tests/resources_9r/test_list 2007-06-13 16:22:25 UTC (rev 1675)
@@ -0,0 +1,35 @@
+;--- Begin Test Configuration File (test_list) ---
+[main]
+args = -s 100 ; Command line arguments to pass to the application
+app = %(app)s ; Application path to test
+nonzeroexit = disallow ; Exit code handling (disallow, allow, or require)
+ ; disallow - treat non-zero exit codes as failures
+ ; allow - all exit codes are acceptable
+ ; require - treat zero exit codes as failures, useful
+ ; for creating tests for app error checking
+createdby = blw ; Who created the test
+email = blwalker at egr.msu.edu ; Email address for the test's creator
+
+[consistency]
+enabled = yes ; Is this test a consistency test?
+long = no ; Is this test a long test?
+
+[performance]
+enabled = no ; Is this test a performance test?
+long = no ; Is this test a long test?
+
+; The following variables can be used in constructing setting values by calling
+; them with %(variable_name)s. For example see 'app' above.
+;
+; app
+; builddir
+; cpus
+; mode
+; perf_repeat
+; perf_user_margin
+; perf_wall_margin
+; svn
+; svnmetadir
+; svnversion
+; testdir
+;--- End Test Configuration File ---
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