[Avida-SVN] r3518 - branches/topology-manager/source/main
pakanati at myxo.css.msu.edu
pakanati at myxo.css.msu.edu
Fri Oct 30 21:45:29 PDT 2009
Author: pakanati
Date: 2009-10-31 00:45:29 -0400 (Sat, 31 Oct 2009)
New Revision: 3518
Modified:
branches/topology-manager/source/main/cTopologyManager.cc
branches/topology-manager/source/main/cWorld.h
Log:
Broken topology manager update again...
Modified: branches/topology-manager/source/main/cTopologyManager.cc
===================================================================
--- branches/topology-manager/source/main/cTopologyManager.cc 2009-10-30 21:34:56 UTC (rev 3517)
+++ branches/topology-manager/source/main/cTopologyManager.cc 2009-10-31 04:45:29 UTC (rev 3518)
@@ -203,14 +203,15 @@
}
+/*
cTopologyManager::InitiateTop()
{
}
+*/
-
/*! Compete all demes with each other based on the given vector of fitness values.
This form of compete demes uses fitness-proportional selection on a vector of deme
@@ -914,7 +915,8 @@
@todo Fix lineage label on injected genomes.
@todo Different strategies for non-random placement.
*/
-void cTopologyManager::SeedDeme(cDeme& deme, cGenome& genome) {
+void cTopologyManager::SeedDeme(cDeme& deme, cGenome& genome)
+{
// Kill all the organisms in the deme.
deme.KillAll();
@@ -926,7 +928,8 @@
}
}
-void cTopologyManager::SeedDeme(cDeme& _deme, cGenotype& _genotype) {
+void cTopologyManager::SeedDeme(cDeme& _deme, cGenotype& _genotype)
+{
// Kill all the organisms in the deme.
_deme.KillAll();
_deme.ClearFounders();
@@ -945,7 +948,8 @@
All organisms in the target deme are terminated, and a subset of the organisms in
the source will be cloned to the target. Returns whether target deme was successfully seeded.
*/
-bool cTopologyManager::SeedDeme(cDeme& source_deme, cDeme& target_deme) {
+bool cTopologyManager::SeedDeme(cDeme& source_deme, cDeme& target_deme)
+{
cRandom& random = m_world->GetRandom();
bool successfully_seeded = true;
@@ -1512,7 +1516,7 @@
// then we might do something like this... (untested)
//organism->SetPhenotype(*_phenotype);
// Re-initialize the time-slice for this new organism.
- //AdjustSchedule(_cell_id, organism->GetPhenotype().GetMerit());
+ //AdjustSchedule(_cell_id, organism->GetPhenotype().GetMerit());ana
// For now, just copy the generation...
organism->GetPhenotype().SetGeneration( _phenotype->GetGeneration() );
@@ -1543,7 +1547,8 @@
already. Used for replicating multiple organisms from the source to the
target deme in a sensible fashion.
*/
-int cTopologyManager::DemeSelectInjectionCell(cDeme& deme, int sequence) {
+int cTopologyManager::DemeSelectInjectionCell(cDeme& deme, int sequence)
+{
int cellid = -1;
assert(sequence < deme.GetSize()); // cannot inject a sequence bigger then the deme
@@ -1756,7 +1761,8 @@
InjectClone( cell2_id, *(cell_array[cell1_id].GetOrganism()) );
}
-void cTopologyManager::AddDemePred(cString type, int times) {
+void cTopologyManager::AddDemePred(cString type, int times)
+{
if(type == "EventReceivedCenter") {
for (int deme_id = 0; deme_id < deme_array.GetSize(); deme_id++) {
deme_array[deme_id].AddEventReceivedCenterPred(times);
@@ -1798,7 +1804,8 @@
}
// Print out all statistics about individual demes
-void cTopologyManager::PrintDemeAllStats() {
+void cTopologyManager::PrintDemeAllStats()
+{
PrintDemeFitness();
PrintDemeLifeFitness();
PrintDemeMerit();
@@ -1816,7 +1823,8 @@
}
}
-void cTopologyManager::PrintDemeTestamentStats(const cString& filename) {
+void cTopologyManager::PrintDemeTestamentStats(const cString& filename)
+{
cStats& stats = m_world->GetStats();
cDataFile& df = m_world->GetDataFile(filename);
@@ -1835,7 +1843,8 @@
stats.SumEnergyTestamentToNeighborOrganisms().Clear();
}
-void cTopologyManager::PrintCurrentMeanDemeDensity(const cString& filename) {
+void cTopologyManager::PrintCurrentMeanDemeDensity(const cString& filename)
+{
cDoubleSum demeDensity;
demeDensity.Clear();
const int num_demes = deme_array.GetSize();
@@ -1852,7 +1861,8 @@
}
// Print some stats about the energy sharing behavior of each deme
-void cTopologyManager::PrintDemeEnergySharingStats() {
+void cTopologyManager::PrintDemeEnergySharingStats()
+{
const int num_demes = deme_array.GetSize();
cStats& stats = m_world->GetStats();
cDataFile & df_donor = m_world->GetDataFile("deme_energy_sharing.dat");
@@ -1906,7 +1916,8 @@
// Print some stats about the distribution of energy among the cells in a deme
// If a cell is occupied, the amount returned is that of the organism in that cell
// If a cell is not occupied, the amount returned is the amount of energy resource in the cell
-void cTopologyManager::PrintDemeEnergyDistributionStats() {
+void cTopologyManager::PrintDemeEnergyDistributionStats()
+{
const int num_demes = deme_array.GetSize();
cStats& stats = m_world->GetStats();
cString comment;
@@ -1956,7 +1967,8 @@
// Print some stats about the distribution of energy among the organism in a deme
// If a cell is occupied, the amount returned is that of the organism in that cell
// If a cell is not occupied, 0 energy is returned for that cell.
-void cTopologyManager::PrintDemeOrganismEnergyDistributionStats() {
+void cTopologyManager::PrintDemeOrganismEnergyDistributionStats()
+{
const int num_demes = deme_array.GetSize();
cStats& stats = m_world->GetStats();
cString comment;
@@ -2003,7 +2015,8 @@
} //End PrintDemeOrganismEnergyDistributionStats()
-void cTopologyManager::PrintDemeDonor() {
+void cTopologyManager::PrintDemeDonor()
+{
cStats& stats = m_world->GetStats();
const int num_demes = deme_array.GetSize();
cDataFile & df_donor = m_world->GetDataFile("deme_donor.dat");
@@ -2028,7 +2041,8 @@
df_donor.Endl();
}
-void cTopologyManager::PrintDemeFitness() {
+void cTopologyManager::PrintDemeFitness()
+{
cStats& stats = m_world->GetStats();
const int num_demes = deme_array.GetSize();
cDataFile & df_fit = m_world->GetDataFile("deme_fitness.dat");
@@ -2053,7 +2067,8 @@
df_fit.Endl();
}
-void cTopologyManager::PrintDemeTotalAvgEnergy() {
+void cTopologyManager::PrintDemeTotalAvgEnergy()
+{
cStats& stats = m_world->GetStats();
const int num_demes = deme_array.GetSize();
cDataFile & df_fit = m_world->GetDataFile("deme_totalAvgEnergy.dat");
@@ -2070,7 +2085,8 @@
df_fit.Endl();
}
-void cTopologyManager::PrintDemeGestationTime() {
+void cTopologyManager::PrintDemeGestationTime()
+{
cStats& stats = m_world->GetStats();
const int num_demes = deme_array.GetSize();
cDataFile & df_gest = m_world->GetDataFile("deme_gest_time.dat");
@@ -2095,7 +2111,8 @@
df_gest.Endl();
}
-void cTopologyManager::PrintDemeInstructions() {
+void cTopologyManager::PrintDemeInstructions()
+{
cStats& stats = m_world->GetStats();
const int num_demes = deme_array.GetSize();
const int num_inst = m_world->GetNumInstructions();
@@ -2132,7 +2149,8 @@
}
}
-void cTopologyManager::PrintDemeLifeFitness() {
+void cTopologyManager::PrintDemeLifeFitness()
+{
cStats& stats = m_world->GetStats();
const int num_demes = deme_array.GetSize();
cDataFile & df_life_fit = m_world->GetDataFile("deme_lifetime_fitness.dat");
@@ -2157,7 +2175,8 @@
df_life_fit.Endl();
}
-void cTopologyManager::PrintDemeMerit() {
+void cTopologyManager::PrintDemeMerit()
+{
cStats& stats = m_world->GetStats();
const int num_demes = deme_array.GetSize();
cDataFile & df_merit = m_world->GetDataFile("deme_merit.dat");
@@ -2182,7 +2201,8 @@
df_merit.Endl();
}
-void cTopologyManager::PrintDemeMutationRate() {
+void cTopologyManager::PrintDemeMutationRate()
+{
cStats& stats = m_world->GetStats();
const int num_demes = deme_array.GetSize();
cDataFile & df_mut_rates = m_world->GetDataFile("deme_mut_rates.dat");
@@ -2209,7 +2229,8 @@
df_mut_rates.Endl();
}
-void cTopologyManager::PrintDemeReceiver() {
+void cTopologyManager::PrintDemeReceiver()
+{
cStats& stats = m_world->GetStats();
const int num_demes = deme_array.GetSize();
cDataFile & df_receiver = m_world->GetDataFile("deme_receiver.dat");
@@ -2234,7 +2255,8 @@
df_receiver.Endl();
}
-void cTopologyManager::PrintDemeResource() {
+void cTopologyManager::PrintDemeResource()
+{
cStats& stats = m_world->GetStats();
const int num_demes = deme_array.GetSize();
cDataFile & df_resources = m_world->GetDataFile("deme_resources.dat");
@@ -2259,7 +2281,8 @@
}
// Write spatial energy data to a file that can easily be read into Matlab
-void cTopologyManager::PrintDemeSpatialEnergyData() const {
+void cTopologyManager::PrintDemeSpatialEnergyData() const
+{
int cellID = 0;
int update = m_world->GetStats().GetUpdate();
@@ -2288,7 +2311,8 @@
}
// Write spatial data to a file that can easily be read into Matlab
-void cTopologyManager::PrintDemeSpatialResData(const cResourceCount& res, const int i, const int deme_id) const {
+void cTopologyManager::PrintDemeSpatialResData(const cResourceCount& res, const int i, const int deme_id) const
+{
const char* tmpResName = res.GetResName(i);
cString tmpfilename = cStringUtil::Stringf( "deme_spatial_resource_%s.m", tmpResName );
cDataFile& df = m_world->GetDataFile(tmpfilename);
@@ -2308,7 +2332,8 @@
}
// Write spatial energy data to a file that can easily be read into Matlab
-void cTopologyManager::PrintDemeSpatialSleepData() const {
+void cTopologyManager::PrintDemeSpatialSleepData() const
+{
int cellID = 0;
cString tmpfilename = "deme_spatial_sleep.m";
cDataFile& df = m_world->GetDataFile(tmpfilename);
@@ -2336,7 +2361,8 @@
}
}
-void cTopologyManager::PrintDemeTasks() {
+void cTopologyManager::PrintDemeTasks()
+{
cStats& stats = m_world->GetStats();
const int num_demes = deme_array.GetSize();
const int num_task = environment.GetNumTasks();
@@ -2369,7 +2395,8 @@
df_task.Endl();
}
-void cTopologyManager::DumpDemeFounders(ofstream& fp) {
+void cTopologyManager::DumpDemeFounders(ofstream& fp)
+{
fp << "#filetype deme_founders" << endl
<< "#format deme_id num_founders genotype_ids" << endl
<< endl
@@ -2646,7 +2673,7 @@
schedule->SetChangeList(change_list);
}
-cChangeList *cPopulation::GetChangeList()
+cChangeList *cTopologyManager::GetChangeList()
{
return schedule->GetChangeList();
}
Modified: branches/topology-manager/source/main/cWorld.h
===================================================================
--- branches/topology-manager/source/main/cWorld.h 2009-10-30 21:34:56 UTC (rev 3517)
+++ branches/topology-manager/source/main/cWorld.h 2009-10-31 04:45:29 UTC (rev 3518)
@@ -137,11 +137,12 @@
// @DMB - Inherited from cAvidaDriver heritage
void GetEvents(cAvidaContext& ctx);
- cEventList* GetEventsList() { return m_event_list; }
+ cEventList* GetEventsList() { return m_event_list; }
// Save to archive
template<class Archive>
- void save(Archive & a, const unsigned int version) const {
+ void save(Archive & a, const unsigned int version) const
+ {
a.ArkvObj("m_analyze", m_analyze);
a.ArkvObj("m_conf", m_conf);
a.ArkvObj("m_ctx", m_ctx);
@@ -192,7 +193,8 @@
// Ask archive to handle loads and saves separately
template<class Archive>
- void serialize(Archive & a, const unsigned int version){
+ void serialize(Archive & a, const unsigned int version)
+ {
a.SplitLoadSave(*this, version);
}
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