[Avida-SVN] r1647 - in branches/collect: Avida.xcodeproj source/classification source/main tests/default_classic_500u tests/demes_germline tests/demes_germline/expected tests/demes_germline/expected/data tests/demes_germline/expected/data/archive
blwalker at myxo.css.msu.edu
blwalker at myxo.css.msu.edu
Tue Jun 5 19:10:09 PDT 2007
Author: blwalker
Date: 2007-06-05 22:10:08 -0400 (Tue, 05 Jun 2007)
New Revision: 1647
Added:
branches/collect/tests/demes_germline/expected/
branches/collect/tests/demes_germline/expected/data/
branches/collect/tests/demes_germline/expected/data/archive/
branches/collect/tests/demes_germline/expected/data/archive/100-aaaaa.org
branches/collect/tests/demes_germline/expected/data/average.dat
branches/collect/tests/demes_germline/expected/data/count.dat
branches/collect/tests/demes_germline/expected/data/detail-100.pop
branches/collect/tests/demes_germline/expected/data/dominant.dat
branches/collect/tests/demes_germline/expected/data/historic-100.pop
branches/collect/tests/demes_germline/expected/data/resource.dat
branches/collect/tests/demes_germline/expected/data/stats.dat
branches/collect/tests/demes_germline/expected/data/tasks.dat
branches/collect/tests/demes_germline/expected/data/tasks_exe.dat
branches/collect/tests/demes_germline/expected/data/tasks_quality.dat
branches/collect/tests/demes_germline/expected/data/time.dat
Removed:
branches/collect/tests/default_classic_500u/expected/
Modified:
branches/collect/Avida.xcodeproj/project.pbxproj
branches/collect/source/classification/cGenotype.cc
branches/collect/source/classification/cGenotypeControl.cc
branches/collect/source/classification/cGenotype_BirthData.cc
branches/collect/source/classification/cGenotype_BirthData.h
branches/collect/source/main/cPopulation.cc
Log:
Porting r1643:1646 (Dave's coalescence workaround) from development.
Modified: branches/collect/Avida.xcodeproj/project.pbxproj
===================================================================
--- branches/collect/Avida.xcodeproj/project.pbxproj 2007-06-06 01:51:15 UTC (rev 1646)
+++ branches/collect/Avida.xcodeproj/project.pbxproj 2007-06-06 02:10:08 UTC (rev 1647)
@@ -198,23 +198,6 @@
};
/* End PBXBuildRule section */
-/* Begin PBXBuildStyle section */
- B56E89620C144AFE00B99261 /* Development */ = {
- isa = PBXBuildStyle;
- buildSettings = {
- COPY_PHASE_STRIP = NO;
- };
- name = Development;
- };
- B56E89630C144AFE00B99261 /* Deployment */ = {
- isa = PBXBuildStyle;
- buildSettings = {
- COPY_PHASE_STRIP = YES;
- };
- name = Deployment;
- };
-/* End PBXBuildStyle section */
-
/* Begin PBXContainerItemProxy section */
7023ECA60C0A436000362B9C /* PBXContainerItemProxy */ = {
isa = PBXContainerItemProxy;
@@ -1690,12 +1673,6 @@
DCC30C4D0762532C008F7A48 /* Project object */ = {
isa = PBXProject;
buildConfigurationList = 702442D70859E0B00059BD9B /* Build configuration list for PBXProject "Avida" */;
- buildSettings = {
- };
- buildStyles = (
- B56E89620C144AFE00B99261 /* Development */,
- B56E89630C144AFE00B99261 /* Deployment */,
- );
hasScannedForEncodings = 0;
mainGroup = DCC30C490762532C008F7A48;
productRefGroup = DCC3164E07626CF3008F7A48 /* Products */;
Modified: branches/collect/source/classification/cGenotype.cc
===================================================================
--- branches/collect/source/classification/cGenotype.cc 2007-06-06 01:51:15 UTC (rev 1646)
+++ branches/collect/source/classification/cGenotype.cc 2007-06-06 02:10:08 UTC (rev 1647)
@@ -135,13 +135,14 @@
sum_merit.Subtract(in.GetDouble());
}
-void cGenotype::SetParent(cGenotype * parent, cGenotype * parent2)
+void cGenotype::SetParent(cGenotype* parent, cGenotype* parent2)
{
birth_data.parent_genotype = parent;
birth_data.parent2_genotype = parent2;
+ if (parent == NULL) return;
+
// If we have a real parent genotype, collect other data about parent.
- if (parent == NULL) return;
birth_data.ancestor_ids[0] = parent->GetID();
birth_data.ancestor_ids[2] = parent->GetAncestorID(0);
birth_data.ancestor_ids[3] = parent->GetAncestorID(1);
@@ -151,8 +152,7 @@
birth_data.ancestor_ids[5] = parent2->GetAncestorID(1);
}
- birth_data.parent_distance =
- cGenomeUtil::FindEditDistance(genome, parent->genome);
+ birth_data.parent_distance = cGenomeUtil::FindEditDistance(genome, parent->genome);
birth_data.parent_species = parent->GetSpecies();
birth_data.gene_depth = parent->GetDepth() + 1;
birth_data.lineage_label = parent->GetLineageLabel();
Modified: branches/collect/source/classification/cGenotypeControl.cc
===================================================================
--- branches/collect/source/classification/cGenotypeControl.cc 2007-06-06 01:51:15 UTC (rev 1646)
+++ branches/collect/source/classification/cGenotypeControl.cc 2007-06-06 02:10:08 UTC (rev 1647)
@@ -85,12 +85,9 @@
void cGenotypeControl::Remove(cGenotype & in_genotype)
{
- if (size == 1) {
- best = NULL;
- }
- if (&in_genotype == best) {
- best = best->GetNext();
- }
+ if (size == 1) best = NULL;
+ if (&in_genotype == best) best = best->GetNext();
+ if (&in_genotype == coalescent) coalescent = NULL;
in_genotype.GetNext()->SetPrev(in_genotype.GetPrev());
in_genotype.GetPrev()->SetNext(in_genotype.GetNext());
@@ -140,9 +137,7 @@
// Test to see if any updating needs to be done...
// Don't update active coalescent genotype, or if there is more than
// one offspring.
- if (coalescent != NULL &&
- (coalescent->GetNumOrganisms() > 0 ||
- coalescent->GetNumOffspringGenotypes() > 1)) {
+ if (coalescent != NULL && (coalescent->GetNumOrganisms() > 0 || coalescent->GetNumOffspringGenotypes() > 1)) {
return coalescent->GetDepth();
}
@@ -150,14 +145,13 @@
if (best == NULL) return -1;
// Find the new point...
- cGenotype * test_gen = best;
- cGenotype * found_gen = best;
- cGenotype * parent_gen = best->GetParentGenotype();
+ cGenotype* test_gen = best;
+ cGenotype* found_gen = best;
+ cGenotype* parent_gen = best->GetParentGenotype();
while (parent_gen != NULL) {
// See if this genotype should be the new found genotype...
- if (test_gen->GetNumOrganisms() > 0 ||
- test_gen->GetNumOffspringGenotypes() > 1) {
+ if (test_gen->GetNumOrganisms() > 0 || test_gen->GetNumOffspringGenotypes() > 1) {
found_gen = test_gen;
}
Modified: branches/collect/source/classification/cGenotype_BirthData.cc
===================================================================
--- branches/collect/source/classification/cGenotype_BirthData.cc 2007-06-06 01:51:15 UTC (rev 1646)
+++ branches/collect/source/classification/cGenotype_BirthData.cc 2007-06-06 02:10:08 UTC (rev 1647)
@@ -25,9 +25,6 @@
#include "cGenotype_BirthData.h"
-#include "defs.h"
-
-
cGenotype_BirthData::cGenotype_BirthData(int in_update_born)
: update_born(in_update_born)
, parent_distance(-1)
Modified: branches/collect/source/classification/cGenotype_BirthData.h
===================================================================
--- branches/collect/source/classification/cGenotype_BirthData.h 2007-06-06 01:51:15 UTC (rev 1646)
+++ branches/collect/source/classification/cGenotype_BirthData.h 2007-06-06 02:10:08 UTC (rev 1647)
@@ -53,9 +53,9 @@
int lineage_label; // Unique label for the lineage of this genotype.
int update_deactivated; // If not, when did it get deactivated?
- cGenotype * parent_genotype; // Pointer to parent genotype...
- cGenotype * parent2_genotype; // Pointer to secondary parent genotype...
- cSpecies * parent_species;
+ cGenotype* parent_genotype; // Pointer to parent genotype...
+ cGenotype* parent2_genotype; // Pointer to secondary parent genotype...
+ cSpecies* parent_species;
int num_offspring_genotypes; // Num offspring genotypes still in memory.
// Ancestral IDs. This array contains all of the information about the
Modified: branches/collect/source/main/cPopulation.cc
===================================================================
--- branches/collect/source/main/cPopulation.cc 2007-06-06 01:51:15 UTC (rev 1646)
+++ branches/collect/source/main/cPopulation.cc 2007-06-06 02:10:08 UTC (rev 1647)
@@ -2445,7 +2445,8 @@
phenotype.SetMerit( cMerit(new_genotype->GetTestMerit(ctx)) );
- cerr<<"initial energy: " << phenotype.GetStoredEnergy() <<endl<<"initial Merit: "<<phenotype.GetMerit().GetDouble()<<endl;
+ // @DMB - this appears to be debugging output
+ //cerr<<"initial energy: " << phenotype.GetStoredEnergy() <<endl<<"initial Merit: "<<phenotype.GetMerit().GetDouble()<<endl;
// @CAO are these really needed?
phenotype.SetLinesCopied( new_genotype->GetTestCopiedSize(ctx) );
Added: branches/collect/tests/demes_germline/expected/data/archive/100-aaaaa.org
===================================================================
--- branches/collect/tests/demes_germline/expected/data/archive/100-aaaaa.org (rev 0)
+++ branches/collect/tests/demes_germline/expected/data/archive/100-aaaaa.org 2007-06-06 02:10:08 UTC (rev 1647)
@@ -0,0 +1,134 @@
+# Tue Jun 5 22:14:22 2007
+# Filename........: archive/100-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...........: 97.000000
+# Gestation Time..: 389
+# Fitness.........: 0.249357
+# Errors..........: 0
+# Genome Size.....: 100
+# Copied Size.....: 100
+# Executed Size...: 97
+# Offspring.......: SELF
+#
+# Tasks Performed:
+# not 0 (0.000000)
+# nand 0 (0.000000)
+# and 0 (0.000000)
+# orn 0 (0.000000)
+# or 0 (0.000000)
+# andn 0 (0.000000)
+# nor 0 (0.000000)
+# xor 0 (0.000000)
+# equ 0 (0.000000)
+
+
+h-alloc
+h-search
+nop-C
+nop-A
+mov-head
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+h-search
+h-copy
+if-label
+nop-C
+nop-A
+h-divide
+mov-head
+nop-A
+nop-B
Added: branches/collect/tests/demes_germline/expected/data/average.dat
===================================================================
--- branches/collect/tests/demes_germline/expected/data/average.dat (rev 0)
+++ branches/collect/tests/demes_germline/expected/data/average.dat 2007-06-06 02:10:08 UTC (rev 1647)
@@ -0,0 +1,30 @@
+# Avida Average Data
+# Tue Jun 5 22:14:21 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 97.000000 389.000000 0.000000 0.000000 100.000000 100.000000 97.000000 1.000000 101.000000 101.000000 0.000000 0.000000 0.000000 0.000000 0.000000
+10 97 389 0 0 100 100 97 100 0 0 0 0 0 0 0
+20 97 389 0.249357 0 100.015 100 97 3.57143 0 0 0.285 1 0.128671 0 0
+30 95.7848 387.223 0.247028 0 100.005 99.4987 95.7848 2.2067 0 0 0.594937 1.98734 0.123768 0 0
+40 96.51 364.63 0 0 100 100 96.51 3.125 0 0 0.01 0 0 -1 0
+50 96.51 364.63 0 0 100 100 96.51 3.125 0 0 0.01 0 0 -1 0
+60 96.6477 376.104 0.240143 0 100.01 100 96.6477 2.29762 0 0 0.279793 0.963731 -0.0994681 -1 0
+70 95.587 379.742 0.242971 0 100 99.4538 95.587 2.06742 0 0 0.521739 1.92935 -0.0806159 -1 0
+80 96.78 341.19 0 0 100 100 96.78 2.27273 0 0 0 0 0 -1 0
+90 96.78 341.19 0 0 100 100 96.78 2.27273 0 0 0 0 0 -1 0
+100 96.5745 362.968 0.232594 0 100.016 100 96.5745 2 0 0 0.265957 0.93617 -0.0339842 -1 0
Added: branches/collect/tests/demes_germline/expected/data/count.dat
===================================================================
--- branches/collect/tests/demes_germline/expected/data/count.dat (rev 0)
+++ branches/collect/tests/demes_germline/expected/data/count.dat 2007-06-06 02:10:08 UTC (rev 1647)
@@ -0,0 +1,30 @@
+# Avida count data
+# Tue Jun 5 22:14:21 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 0 101 1 101 1 1 1 0 0
+10 3000 100 1 1 0 0 0 0 0 0 100 100 100 0 0
+20 6000 200 56 2 0 0 0 0 0 0 143 100 200 0 0
+30 11850 395 179 2 0 0 0 0 0 0 212 200 395 0 0
+40 3000 100 32 1 0 0 0 0 0 0 100 100 100 0 0
+50 3000 100 32 1 0 0 0 0 0 0 100 100 100 0 0
+60 5790 193 84 1 0 0 0 0 0 0 140 100 193 0 0
+70 11040 368 178 6 0 0 0 0 0 0 219 193 368 0 0
+80 3000 100 44 2 0 0 0 0 0 0 100 100 100 0 0
+90 3000 100 44 2 0 0 0 0 0 0 100 100 100 0 0
+100 5640 188 94 5 0 0 0 0 0 0 137 100 188 0 0
Added: branches/collect/tests/demes_germline/expected/data/detail-100.pop
===================================================================
--- branches/collect/tests/demes_germline/expected/data/detail-100.pop (rev 0)
+++ branches/collect/tests/demes_germline/expected/data/detail-100.pop 2007-06-06 02:10:08 UTC (rev 1647)
@@ -0,0 +1,111 @@
+#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 72 551 100 97 389 0.249357 -1 -1 0 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+590 -1 -1 4 4 100 87 377 0.230769 79 -1 0 rucavccccccccccccccccccccccccccccccccccccccccccdccccccccccccccccccccccccccyccccccccccccccccutycasvab
+623 -1 -1 4 4 100 97 388 0.25 79 -1 0 rucavccccccccccccmcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+620 -1 -1 3 3 100 97 388 0.25 79 -1 0 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccqcccccccutycasvab
+571 -1 -1 2 2 100 0 0 0 79 -1 0 ruyavcccccccccccccsccccccccccccccccccccccccccccccccccccccccccccccccccccpcccccccccccccccccccutycasvab
+613 -1 -1 2 2 100 97 388 0.25 79 -1 0 rucavcccccccccccccccccccccccccccccccccccccccccccccccbcccccccccccccccccccccccccccoccccccccccutycasvab
+577 -1 -1 2 3 100 97 388 0.25 79 -1 0 rucavccccccccccccccccccccccccccccccccccccpcccccccscccccccccccccccccccccccccccccccccccccccccutycasvab
+584 -1 -1 2 2 100 97 385 0.251948 79 -1 0 rucavcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccczcccccctccutycasvab
+585 -1 -1 2 2 100 97 385 0.251948 79 -1 0 rucavcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccczcrcccctccutycasvab
+598 -1 -1 2 2 100 97 387 0.250646 79 -1 0 rucavccccccccccccccccccqccccccccccccccccccccccccccccccccccccccccccccccccccccccccczcccccccccutycasvab
+604 -1 -1 2 2 100 97 388 0.25 79 -1 0 rucavcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccfccccccccccccccccccccccutycasvab
+612 -1 -1 2 2 100 97 387 0.250646 79 -1 0 rucavccccccccccccccccccccccoccccccccccccccccccccccccccccccccccccccccccccccccccccccccmbcccccutycasvab
+611 -1 -1 2 2 100 97 387 0.250646 79 -1 0 rucavccccccccccccccccccccccoccccccccccccccccccccccccccccccccccccccccccccccccccccccccmccccccutycasvab
+605 -1 -1 2 2 100 88 378 0.232804 79 -1 0 rucavcccccccccccccccccbcccccccccccccccccccccccccccccccccccccccccccccfccccccucccccccccccccccutycasvab
+603 -1 -1 2 2 100 97 389 0.249357 79 -1 0 rucavcccccccccccccccccccccccaccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+609 -1 -1 2 2 100 97 388 0.25 79 -1 0 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccocccccutycasvab
+587 -1 -1 2 2 100 97 388 0.25 79 -1 0 rucavccccccccccccdcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+591 -1 -1 2 2 100 87 378 0.230159 79 -1 0 rucavccccccccccccccccccccccccccccccccccccycccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+615 -1 -1 2 2 100 88 379 0.23219 79 -1 0 rucavccccccccccccucccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+573 -1 -1 1 1 100 88 377 0.233422 79 -1 0 rucavcccccccccccccccuccccccccccccccccncccccccccccccccccccdcccccccccccccccccccccccccccccccccutycasvab
+574 -1 -1 1 1 100 97 387 0.250646 79 -1 0 rucavccccccccccccccccccccccccccccccccccccccccccccccecccccccccccccccccccccccccciccccccccccccutycasvab
+575 -1 -1 1 1 100 96 385 0.249351 79 -1 0 rucavccccccccccccccccccccqcccccccccccccccccccccccccecccccccccccccccccccccccccciccccccccccccutycasvab
+579 -1 -1 1 1 100 0 0 0 79 -1 0 hucavcccccccccccccccccccccccxccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+580 -1 -1 1 1 100 97 388 0.25 79 -1 0 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccncccccccccccutycasvab
+581 -1 -1 1 1 100 97 388 0.25 79 -1 0 rucavcccccccccccccccccccccccccccccccccccccccccccccccccccccccclcccccccccccccccccccccccccccccutycasvab
+583 -1 -1 1 1 100 0 0 0 79 -1 0 rucabcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccclcccccutycasvab
+588 -1 -1 1 1 100 0 0 0 79 -1 0 rucavccccccccccccdcccjcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccstycasvab
+589 -1 -1 1 1 100 97 388 0.25 79 -1 0 rucavcccwccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+592 -1 -1 1 1 100 97 388 0.25 79 -1 0 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccciccccccccccccccccccccutycasvab
+593 -1 -1 1 1 100 97 387 0.250646 79 -1 0 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccciccccccccccccclccccccutycasvab
+594 -1 -1 1 1 100 0 0 0 79 -1 0 rucavccccccccccccccccccccccccccchccccccccccccccccccccccccccccccccccccccccccccccccccccccckccutycasveb
+597 -1 -1 1 1 100 0 0 0 79 -1 0 rupavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+602 -1 -1 1 1 100 97 387 0.250646 79 -1 0 rucavcccccccccccccccccccccccccccccccccccccccccccccccccccccccccdccccxcccccccccccccccccccccccutycasvab
+586 -1 -1 1 2 100 97 387 0.250646 79 -1 0 rucavccccccccccccccgccccgccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+606 -1 -1 1 1 100 97 388 0.25 79 -1 0 rucavcccccccccccccccccccccccccccccccccccczcccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+607 -1 -1 1 1 100 0 0 0 79 -1 0 rqcavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+608 -1 -1 1 1 100 97 389 0.249357 79 -1 0 rucavccccccccccccccccccccccccccccccccccccccccccccccbcccccccccccccccccccccccccccccccccccccccutycasvab
+610 -1 -1 1 1 100 0 0 0 79 -1 0 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccocccccutybasvab
+617 -1 -1 1 1 100 97 388 0.25 79 -1 0 rucavcccccnccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+256 -1 -1 1 4 100 0 0 0 39 -1 0 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycaswab
+619 -1 -1 1 1 100 97 386 0.251295 79 -1 0 rucavcccccccccccccccccccccccccccccccccccccctcccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+621 -1 -1 1 1 100 97 388 0.25 79 -1 0 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccccncccccccccccccccccccccccccccccutycasvab
+614 -1 -1 1 2 100 0 0 0 79 -1 0 rxcavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+622 -1 -1 1 1 100 0 0 0 79 -1 0 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvtb
+624 586 1 1 1 100 0 0 0 91 -1 1 rucavccccccccccccccgccycgccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+625 1 1 1 1 100 97 389 0.249357 91 -1 1 rucavcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccchcccccccutycasvab
+626 581 1 1 1 100 0 0 0 92 -1 1 rucavcccccccccccccccccccccccccccccccccccccccccccccccccccccccclcccccccccccccccccucccccccccccutycasvab
+627 608 1 1 1 100 0 0 0 92 -1 1 rucavccccccccccccccccccccccccccccccccccccccccccccccbcccccccccccccccccccccccccccccccccccccccueycasvab
+628 1 2 1 1 99 97 389 0.249357 92 -1 1 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccbccccutycasvab
+629 1 2 1 1 100 97 389 0.249357 92 -1 1 rucavccccckccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasval
+630 1 1 1 1 100 97 389 0.249357 92 -1 1 rucavcccccccccccccccccccgccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+631 606 1 1 1 100 0 0 0 92 -1 1 rucavcccccccccccccccccccccccccccccccccccczccccccccccccccccccccccchcccccccccccccccccccccccccutycasvab
+632 1 3 1 1 99 97 389 0.249357 92 -1 1 rucavccccccccdccccccvcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+633 1 1 1 1 101 97 389 0.249357 92 -1 1 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccfccccccccccccccccccccccutycasvab
+634 580 1 1 1 100 0 0 0 92 -1 1 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccncccccccccccutylasvab
+635 1 1 1 1 100 97 389 0.249357 92 -1 1 rucavcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccvccccccccccccccccutycasvab
+636 587 1 1 1 99 0 0 0 92 -1 1 rucavccccccccccccdccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+637 1 2 1 1 100 97 389 0.249357 92 -1 1 rucavccczccccccccccccccccccccccccccccccccccccqcccccccccccccccccccccccccccccccccccccccccccccutycasvab
+638 1 1 1 1 100 97 389 0.249357 92 -1 1 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccclccccccccccccccccccccccutycasvab
+639 1 1 1 1 100 97 389 0.249357 92 -1 1 rucavcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccaccccccccccccccccccutycasvab
+640 1 1 1 1 101 97 389 0.249357 92 -1 1 rucavccccccccccccccccccccccccccccccccccccccccclcccccccccccccccccccccccccccccccccccccccccccccutycasvab
+641 1 1 1 1 100 97 389 0.249357 92 -1 1 rucavcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccdccccccccccccccccccutycasvab
+642 1 1 1 1 100 97 389 0.249357 92 -1 1 rucavcccccccccccccccccccccccccccccccctcccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+643 1 2 1 1 101 97 389 0.249357 92 -1 1 rucavccccccccccchcccccccccccccccccccccccccccccccccccccccccccccccccccccccpcccccccccccccccccccutycasvab
+644 574 1 1 1 100 0 0 0 92 -1 1 rucavcccccccccccccccccccccccccccccctcccccccccccccccecccccccccccccccccccccccccciccccccccccccutycasvab
+645 617 1 1 1 100 0 0 0 92 -1 1 rucavcccccnccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccbcccccutycasvab
+646 1 1 1 1 100 97 389 0.249357 92 -1 1 rucavcccccccccccccccccccccccccccccccccccccccccccccccccccccccccwccccccccccccccccccccccccccccutycasvab
+647 621 4 1 1 99 0 0 0 92 -1 1 rucavcccccccccccccccccccccccccccccgccccccccccccccccccccscccccnccccccccccccccyccccccccccccccutycasva
+648 1 1 1 1 100 97 389 0.249357 93 -1 1 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccpcccccccccccccccccutycasvab
+649 575 2 1 1 100 0 0 0 93 -1 1 zucavccccccccccccccccccccqcccccccccccccccccccccccccecccccccccccciccccccccccccciccccccccccccutycasvab
+650 1 2 1 1 100 97 389 0.249357 93 -1 1 rucavcccccccccccccucccccccccccccccccccbccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+651 620 1 1 1 101 97 388 0.25 93 -1 1 rucavcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccqcccccccutycasvab
+652 1 1 1 1 100 97 389 0.249357 93 -1 1 rucavccccbcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+653 1 1 1 1 100 97 389 0.249357 93 -1 1 rucavccccccccccccccccccccccccccccjcccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+654 1 1 1 1 100 97 389 0.249357 93 -1 1 rucavcccccccccccccccccccccccccccccckcccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+655 1 2 1 1 100 97 389 0.249357 93 -1 1 rucavcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccclcccccccccccccccccccccctccutycasvab
+656 619 1 1 1 100 0 0 0 93 -1 1 rucavccccccccccccccccccpccccccccccccccccccctcccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+657 1 1 1 1 100 97 389 0.249357 93 -1 1 rucavccccccccccccccdcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+658 1 1 1 1 100 97 389 0.249357 93 -1 1 rucavccccicccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+659 1 2 1 1 100 97 389 0.249357 93 -1 1 rucavcccccccccccrccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccdcutycasvab
+660 1 3 1 1 100 97 389 0.249357 93 -1 1 rucavcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccocccccmccccccccccccccccccutyccsvab
+661 1 1 1 1 101 97 389 0.249357 93 -1 1 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccdccutycasvab
+662 602 1 1 1 100 0 0 0 93 -1 1 rucadcccccccccccccccccccccccccccccccccccccccccccccccccccccccccdccccxcccccccccccccccccccccccutycasvab
+663 1 1 1 1 100 97 389 0.249357 93 -1 1 rucavcccccccccccccccccccccccccccccccccccccccccccuccccccccccccccccccccccccccccccccccccccccccutycasvab
+664 1 3 1 1 100 97 389 0.249357 93 -1 1 rucavcpcccccccccjccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutkcasvab
+665 592 2 1 1 100 0 0 0 93 -1 1 rucavcccccccccccccccccccoccccccccccccfcccccccccccccccccccccccccccccccciccccccccccccccccccccutycasvab
+666 593 1 1 1 100 0 0 0 93 -1 1 rucafccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccciccccccccccccclccccccutycasvab
+667 1 2 1 1 100 97 389 0.249357 93 -1 1 rucavcccccccccccccccccccccccccccccccccccccccccccccccccccccclcccccccccccccccccccccccccccccccutycajvab
+668 589 4 1 1 102 0 0 0 93 -1 1 aarucavccuwccccccccccccccccpcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+669 573 1 1 1 100 0 0 0 94 -1 1 rucavcccccccccccccccuccccccccccccccccncccccccccccccccccccdcccccccccccccccccccccccciccccccccutycasvab
+670 1 1 1 1 100 97 389 0.249357 94 -1 1 rucavcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccvccccccccccccccccccccutycasvab
+671 1 1 1 1 100 97 389 0.249357 94 -1 1 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycayvab
+672 1 1 1 1 100 97 389 0.249357 94 -1 1 rucavcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccxccccutycasvab
+673 1 2 1 1 100 97 389 0.249357 94 -1 1 kucavcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccoccccccccccutycasvab
Added: branches/collect/tests/demes_germline/expected/data/dominant.dat
===================================================================
--- branches/collect/tests/demes_germline/expected/data/dominant.dat (rev 0)
+++ branches/collect/tests/demes_germline/expected/data/dominant.dat 2007-06-06 02:10:08 UTC (rev 1647)
@@ -0,0 +1,30 @@
+# Avida Dominant Data
+# Tue Jun 5 22:14:21 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 100 0.000000 0.000000 1 0 0 0 0 0.000000 1 100-aaaaa
+10 0 0 0 0 100 0 0 100 0 0 0 0 0 1 100-aaaaa
+20 97 389 0.249357 0.00257069 100 100 97 143 0 0 0 0 0.249357 1 100-aaaaa
+30 97 389 0.249357 0.00257069 100 100 97 194 0 0 0 0 0.251295 1 100-aaaaa
+40 97 389 0.249357 0.00257069 100 100 97 69 0 0 0 0 0 1 100-aaaaa
+50 97 389 0.249357 0.00257069 100 100 97 69 0 0 0 0 0 1 100-aaaaa
+60 97 389 0.249357 0.00257069 100 100 97 102 0 0 0 0 0.251948 1 100-aaaaa
+70 97 389 0.249357 0.00257069 100 100 97 152 0 0 0 0 0.251948 1 100-aaaaa
+80 97 389 0.249357 0.00257069 100 100 97 53 0 0 0 0 0 1 100-aaaaa
+90 97 389 0.249357 0.00257069 100 100 97 53 0 0 0 0 0 1 100-aaaaa
+100 97 389 0.249357 0.00257069 100 100 97 72 0 0 0 0 0.251948 1 100-aaaaa
Added: branches/collect/tests/demes_germline/expected/data/historic-100.pop
===================================================================
--- branches/collect/tests/demes_germline/expected/data/historic-100.pop (rev 0)
+++ branches/collect/tests/demes_germline/expected/data/historic-100.pop 2007-06-06 02:10:08 UTC (rev 1647)
@@ -0,0 +1,17 @@
+#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
+
Added: branches/collect/tests/demes_germline/expected/data/resource.dat
===================================================================
--- branches/collect/tests/demes_germline/expected/data/resource.dat (rev 0)
+++ branches/collect/tests/demes_germline/expected/data/resource.dat 2007-06-06 02:10:08 UTC (rev 1647)
@@ -0,0 +1,17 @@
+# Avida resource data
+# Tue Jun 5 22:14:21 2007
+# First column gives the current update, all further columns give the quantity
+# of the particular resource at that update.
+# 1: Update
+
+0
+10
+20
+30
+40
+50
+60
+70
+80
+90
+100
Added: branches/collect/tests/demes_germline/expected/data/stats.dat
===================================================================
--- branches/collect/tests/demes_germline/expected/data/stats.dat (rev 0)
+++ branches/collect/tests/demes_germline/expected/data/stats.dat 2007-06-06 02:10:08 UTC (rev 1647)
@@ -0,0 +1,26 @@
+# Generic Statistics Data
+# Tue Jun 5 22:14:21 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 0.562358 0.562358 0.826353 0.826353 1 0.000000 0.000000 0 0 0
+10 0 0.562358 0.562358 0.826353 0.826353 0 0 0 0 0 0
+20 0 0.562405 0.562358 0.826462 0.826353 0 1.7334 0 0 0 0
+30 0.0093872 0.562374 0.562358 0.82639 0.826353 0 3.29336 0 0 0 0
+40 0 0.562358 0.562358 0.826353 0.826353 -217 1.68364 0 0 0 0
+50 0 0.562358 0.562358 0.826353 0.826353 0 1.68364 0 0 0 0
+60 0.0376539 0.562391 0.562358 0.826428 0.826353 0 2.76094 0 0 0 0
+70 0.0259437 0.562358 0.562358 0.826353 0.826353 0 3.67898 0 0 0 0
+80 0 0.562358 0.562358 0.826353 0.826353 -271 2.44546 0 0 0 0
+90 0 0.562358 0.562358 0.826353 0.826353 0 2.44546 0 0 0 0
+100 0.0695927 0.562408 0.562358 0.826469 0.826353 0 3.41144 0 0 0 0
Added: branches/collect/tests/demes_germline/expected/data/tasks.dat
===================================================================
--- branches/collect/tests/demes_germline/expected/data/tasks.dat (rev 0)
+++ branches/collect/tests/demes_germline/expected/data/tasks.dat 2007-06-06 02:10:08 UTC (rev 1647)
@@ -0,0 +1,26 @@
+# Avida tasks data
+# Tue Jun 5 22:14:21 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 0 0 0 0 0 0 0 0 0
+20 0 0 0 0 0 0 0 0 0
+30 0 0 0 0 0 0 0 0 0
+40 0 0 0 0 0 0 0 0 0
+50 0 0 0 0 0 0 0 0 0
+60 0 0 0 0 0 0 0 0 0
+70 0 0 0 0 0 0 0 0 0
+80 0 0 0 0 0 0 0 0 0
+90 0 0 0 0 0 0 0 0 0
+100 0 0 0 0 0 0 0 0 0
Added: branches/collect/tests/demes_germline/expected/data/tasks_exe.dat
===================================================================
--- branches/collect/tests/demes_germline/expected/data/tasks_exe.dat (rev 0)
+++ branches/collect/tests/demes_germline/expected/data/tasks_exe.dat 2007-06-06 02:10:08 UTC (rev 1647)
@@ -0,0 +1,26 @@
+# Avida tasks execution data
+# Tue Jun 5 22:14:21 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 0 0 0 0 0 0 0 0 0
+20 0 0 0 0 0 0 0 0 0
+30 0 0 0 0 0 0 0 0 0
+40 0 0 0 0 0 0 0 0 0
+50 0 0 0 0 0 0 0 0 0
+60 0 0 0 0 0 0 0 0 0
+70 0 0 0 0 0 0 0 0 0
+80 0 0 0 0 0 0 0 0 0
+90 0 0 0 0 0 0 0 0 0
+100 0 0 0 0 0 0 0 0 0
Added: branches/collect/tests/demes_germline/expected/data/tasks_quality.dat
===================================================================
--- branches/collect/tests/demes_germline/expected/data/tasks_quality.dat (rev 0)
+++ branches/collect/tests/demes_germline/expected/data/tasks_quality.dat 2007-06-06 02:10:08 UTC (rev 1647)
@@ -0,0 +1,34 @@
+# Avida tasks quality data
+# Tue Jun 5 22:14:21 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+30 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+40 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+50 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+80 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+90 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Added: branches/collect/tests/demes_germline/expected/data/time.dat
===================================================================
--- branches/collect/tests/demes_germline/expected/data/time.dat (rev 0)
+++ branches/collect/tests/demes_germline/expected/data/time.dat 2007-06-06 02:10:08 UTC (rev 1647)
@@ -0,0 +1,18 @@
+# Avida time data
+# Tue Jun 5 22:14:21 2007
+# 1: update
+# 2: avida time
+# 3: average generation
+# 4: num_executed?
+
+0 0.000000 0.000000 30
+10 0.103093 0 3000
+20 0.206186 1 6000
+30 0.310286 1.98734 11850
+40 0.414811 0 3000
+50 0.518428 0 3000
+60 0.621917 0.963731 5790
+70 0.72634 1.92935 11040
+80 0.831141 0 3000
+90 0.934468 0 3000
+100 1.03792 0.93617 5640
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