Merge pull request #188 from K-Johnson-Horrigan/dev-branch

SymWorld Setup() method

source/SymAnimate.h

@@ -188,7 +188,7 @@ class SymAnimate : public UI::Animate {
     random.ResetSeed(config.SEED());
     world.SetRandom(random);
 
-    worldSetup(&world, &config);
+    world.Setup();
 
     p = world.GetPop();
 

source/default_mode/DataNodes.h

@@ -238,9 +238,11 @@ emp::DataMonitor<int>& SymWorld::GetHostCountDataNode() {
     data_node_hostcount.New();
     OnUpdate([this](size_t){
       data_node_hostcount -> Reset();
-      for (size_t i = 0; i< pop.size(); i++)
-        if(IsOccupied(i))
+      for (size_t i = 0; i< pop.size(); i++){
+        if (IsOccupied(i)){
           data_node_hostcount->AddDatum(1);
+        }
+      }
     });
   }
   return *data_node_hostcount;
@@ -289,9 +291,11 @@ emp::DataMonitor<int>& SymWorld::GetCountHostedSymsDataNode(){
     data_node_hostedsymcount.New();
     OnUpdate([this](size_t){
       data_node_hostedsymcount->Reset();
-      for (size_t i = 0; i< pop.size(); i++)
-        if (IsOccupied(i))
+      for (size_t i = 0; i< pop.size(); i++){
+        if (IsOccupied(i)){
           data_node_hostedsymcount->AddDatum(pop[i]->GetSymbionts().size());
+        }
+      }
     });
   }
   return *data_node_hostedsymcount;
@@ -312,9 +316,11 @@ emp::DataMonitor<int>& SymWorld::GetCountFreeSymsDataNode(){
     data_node_freesymcount.New();
     OnUpdate([this](size_t){
       data_node_freesymcount->Reset();
-      for (size_t i = 0; i< pop.size(); i++)
-        if (sym_pop[i])
+      for (size_t i = 0; i< pop.size(); i++){
+        if (sym_pop[i]){
           data_node_freesymcount->AddDatum(1);
+        }
+      }
     });
   }
   return *data_node_freesymcount;
@@ -366,9 +372,11 @@ emp::DataMonitor<double, emp::data::Histogram>& SymWorld::GetHostIntValDataNode(
     data_node_hostintval.New();
     OnUpdate([this](size_t){
       data_node_hostintval->Reset();
-      for (size_t i = 0; i< pop.size(); i++)
-        if (IsOccupied(i))
+      for (size_t i = 0; i< pop.size(); i++){
+        if (IsOccupied(i)){
           data_node_hostintval->AddDatum(pop[i]->GetIntVal());
+        }
+      }
     });
   }
   data_node_hostintval->SetupBins(-1.0, 1.1, 21);

source/default_mode/Host.h

@@ -102,7 +102,10 @@ class Host: public Organism {
   double _intval =0.0, emp::vector<emp::Ptr<Organism>> _syms = {},
   emp::vector<emp::Ptr<Organism>> _repro_syms = {},
   double _points = 0.0) : interaction_val(_intval), syms(_syms), repro_syms(_repro_syms), points(_points), random(_random), my_world(_world), my_config(_config) {
-    if ( _intval > 1 || _intval < -1) {
+    if (_intval == -2) {
+      interaction_val = random->GetDouble(-1, 1);
+    }
+    if (interaction_val > 1 || interaction_val < -1) {
        throw "Invalid interaction value. Must be between -1 and 1";  // Exception for invalid interaction value
      };
    }

source/default_mode/SymWorld.h

@@ -394,11 +394,29 @@ class SymWorld : public emp::World<Organism>{
 
 
   /**
-   * Input: The pointer to an organism that will be injected into a host.
+     * Input: The pointer to a host that will be added to the world. This function assumes that the
+     * pop vector has not been resized to fit the world yet.
+     *
+     * Output: None
+     *
+     * Purpose: To add a host to the world.
+     */
+  void InjectHost(emp::Ptr<Organism> new_host) {
+    if (my_config->GRID()) {
+      AddOrgAt(new_host, emp::WorldPosition(GetRandomCellID()));
+    }
+    else {
+      AddOrgAt(new_host, pop.size());
+    }
+  }
+
+
+  /**
+   * Input: The pointer to an organism that will be injected into the world.
    *
    * Output: None
    *
-   * Purpose: To add a symbiont to a host's symbionts.
+   * Purpose: To add a symbiont to the world, either into a host or into a sym world cell.
    */
   void InjectSymbiont(emp::Ptr<Organism> new_sym){
     size_t new_loc;
@@ -449,6 +467,13 @@ class SymWorld : public emp::World<Organism>{
   emp::DataMonitor<double,emp::data::Histogram>& GetFreeSymInfectChanceDataNode();
   emp::DataMonitor<double,emp::data::Histogram>& GetHostedSymInfectChanceDataNode();
 
+  /**
+   * Definitions of setup functions, expanded in WorldSetup.cc
+   */
+  virtual void Setup();
+  virtual void SetupHosts(long unsigned int* POP_SIZE);
+  virtual void SetupSymbionts(long unsigned int* total_syms);
+
   /**
    * Input: The pointer to the symbiont that is moving, the WorldPosition of its
    * current location.

source/default_mode/Symbiont.h

@@ -95,8 +95,10 @@ class Symbiont: public Organism {
     infection_chance = my_config->SYM_INFECTION_CHANCE();
     if (infection_chance == -2) infection_chance = random->GetDouble(0,1); //randomized starting infection chance
     if (infection_chance > 1 || infection_chance < 0) throw "Invalid infection chance. Must be between 0 and 1"; //exception for invalid infection chance
-
-    if ( _intval > 1 || _intval < -1) {
+    if (_intval == -2) {
+      interaction_val = random->GetDouble(-1, 1);
+    }
+   if (interaction_val > 1 || interaction_val < -1) {
        throw "Invalid interaction value. Must be between -1 and 1";   // Exception for invalid interaction value
     };
   }

source/default_mode/WorldSetup.cc

@@ -2,71 +2,65 @@
 #define WORLD_SETUP_C
 
 #include "SymWorld.h"
-#include "../ConfigSetup.h"
 #include "Host.h"
 #include "Symbiont.h"
 
+/**
+ * Input: The number of hosts.
+ *
+ * Output: None.
+ *
+ * Purpose: To populate the world with hosts with appropriate phenotypes. 
+ */
+void SymWorld::SetupHosts(long unsigned int* POP_SIZE){ 
+  for (size_t i = 0; i < *POP_SIZE; i++) {
+    emp::Ptr<Host> new_org;
+    new_org.New(&GetRandom(), this, my_config, my_config->HOST_INT());
+    InjectHost(new_org);
+  }
 
-void worldSetup(emp::Ptr<SymWorld> world, emp::Ptr<SymConfigBase> my_config) {
-// params
-  emp::Random& random = world->GetRandom();
+}
 
+
+/**
+ * Input: The number of symbionts.
+ *
+ * Output: None.
+ *
+ * Purpose: To populate the world with symbionts with appropriate phenotypes.
+ */
+void SymWorld::SetupSymbionts(long unsigned int *total_syms) {
+  for (size_t j = 0; j < *total_syms; j++) {
+    emp::Ptr<Symbiont> new_sym = emp::NewPtr<Symbiont>(&GetRandom(), this, my_config, my_config->SYM_INT(), 0);
+    InjectSymbiont(new_sym);
+  }
+}
+
+/**
+ * Input: None.
+ *
+ * Output: None.
+ *
+ * Purpose: Prepare the world for an experiment by applying the configuration settings 
+ * and populating the world with hosts and symbionts.
+ */
+void SymWorld::Setup() {
   double start_moi = my_config->START_MOI();
   long unsigned int POP_SIZE;
   if (my_config->POP_SIZE() == -1) {
     POP_SIZE = my_config->GRID_X() * my_config->GRID_Y();
   } else {
     POP_SIZE = my_config->POP_SIZE();
   }
-  bool random_phen_host = false;
-  bool random_phen_sym = false;
-  if(my_config->HOST_INT() == -2 && !my_config->COMPETITION_MODE()) random_phen_host = true;
-  if(my_config->SYM_INT() == -2) random_phen_sym = true;
-
-  if (my_config->GRID() == 0) {world->SetPopStruct_Mixed(false);}
-  else world->SetPopStruct_Grid(my_config->GRID_X(), my_config->GRID_Y(), false);
-
-
-  double comp_host_1 = 0;
-  double comp_host_2 = 0.95;
-
-
-
-  //inject hosts
-  for (size_t i = 0; i < POP_SIZE; i++){
-    emp::Ptr<Host> new_org;
-
-    if (random_phen_host) {new_org.New(&random, world, my_config, random.GetDouble(-1, 1));
-    } else if (my_config->COMPETITION_MODE() && i%2==0) {
-        new_org.New(&random, world, my_config, comp_host_1);
-    } else if (my_config->COMPETITION_MODE() && i%2==1) {
-        new_org.New(&random, world, my_config, comp_host_2);
-    } else { new_org.New(&random, world, my_config, my_config->HOST_INT());
-    }
-    //Currently hacked because there isn't an AddOrg function, but there probably should be
-    if(my_config->GRID()) {
-      world->AddOrgAt(new_org, emp::WorldPosition(world->GetRandomCellID()));
-    } else {
-      world->AddOrgAt(new_org, world->size());
-    }
-    //world.Inject(*new_org);
-  }
 
-  //sets up the world size
-  world->Resize(my_config->GRID_X(), my_config->GRID_Y());
+  // set world structure (either mixed or a grid with some dimensions) and set synchronous generations to false
+  if (my_config->GRID() == 0) {SetPopStruct_Mixed(false);}
+  else SetPopStruct_Grid(my_config->GRID_X(), my_config->GRID_Y(), false);
 
-  //This loop must be outside of the host generation loop since otherwise
-  //syms try to inject into mostly empty spots at first
-  int total_syms = POP_SIZE * start_moi;
-  for (int j = 0; j < total_syms; j++){
-    double sym_int = 0;
-    if (random_phen_sym) {sym_int = random.GetDouble(-1,1);}
-    else {sym_int = my_config->SYM_INT();}
+  SetupHosts(&POP_SIZE);
 
-    emp::Ptr<Symbiont> new_sym = emp::NewPtr<Symbiont>(&random, world, my_config,
-      sym_int, 0);
-    world->InjectSymbiont(new_sym);
-  }
+  Resize(my_config->GRID_X(), my_config->GRID_Y());
+  long unsigned int total_syms = POP_SIZE * start_moi;
+  SetupSymbionts(&total_syms);
 }
-
 #endif

source/efficient_mode/EfficientWorld.h

@@ -26,6 +26,15 @@ class EfficientWorld : public SymWorld {
       if (data_node_efficiency) data_node_efficiency.Delete();
   }
 
+
+  /**
+  * Definitions of setup functions, expanded in EfficientWorldSetup.cc
+  */
+  void Setup();
+  void SetupHosts(long unsigned int* POP_SIZE);
+  void SetupSymbionts(long unsigned int* total_syms);
+
+
   /**
   * Input: None.
   *

source/efficient_mode/EfficientWorldSetup.cc

@@ -2,72 +2,48 @@
 #define EFFWORLD_SETUP_C
 
 #include "EfficientWorld.h"
-#include "../ConfigSetup.h"
 #include "EfficientSymbiont.h"
 #include "EfficientHost.h"
-#include "../default_mode/WorldSetup.cc"
 
-void efficientWorldSetup(emp::Ptr<EfficientWorld> world, emp::Ptr<SymConfigBase> my_config) {
-// params
-  emp::Random& random = world->GetRandom();
-
-  double start_moi = my_config->START_MOI();
-  long unsigned int POP_SIZE;
-  if (my_config->POP_SIZE() == -1) {
-    POP_SIZE = my_config->GRID_X() * my_config->GRID_Y();
-  } else {
-    POP_SIZE = my_config->POP_SIZE();
-  }
-  bool random_phen_host = false;
-  bool random_phen_sym = false;
-  if(my_config->HOST_INT() == -2 && !my_config->COMPETITION_MODE()) random_phen_host = true;
-  if(my_config->SYM_INT() == -2) random_phen_sym = true;
-
-  if(my_config->EFFICIENCY_MUT_RATE() == -1) my_config->EFFICIENCY_MUT_RATE(my_config->HORIZ_MUTATION_RATE());
-
-  if (my_config->GRID() == 0) {world->SetPopStruct_Mixed(false);}
-  else world->SetPopStruct_Grid(my_config->GRID_X(), my_config->GRID_Y(), false);
-// settings
-
-  double comp_host_1 = 0;
-  double comp_host_2 = 0.95;
-
-
-
-  //inject hosts
-  for (size_t i = 0; i < POP_SIZE; i++){
+/**
+ * Input: The number of efficient hosts.
+ *
+ * Output: None.
+ *
+ * Purpose: To populate the world with efficient hosts with appropriate phenotypes.
+ */
+void EfficientWorld::SetupHosts(long unsigned int* POP_SIZE) {
+  for (size_t i = 0; i < *POP_SIZE; i++) {
     emp::Ptr<EfficientHost> new_org;
-
-    if (random_phen_host) {new_org.New(&random, world, my_config, random.GetDouble(-1, 1));
-    } else if (my_config->COMPETITION_MODE() && i%2==0) {
-        new_org.New(&random, world, my_config, comp_host_1);
-    } else if (my_config->COMPETITION_MODE() && i%2==1) {
-        new_org.New(&random, world, my_config, comp_host_2);
-    } else { new_org.New(&random, world, my_config, my_config->HOST_INT());
-    }
-    //Currently hacked because there isn't an AddOrg function, but there probably should be
-    if(my_config->GRID()) {
-      world->AddOrgAt(new_org, emp::WorldPosition(world->GetRandomCellID()));
-    } else {
-      world->AddOrgAt(new_org, world->size());
-    }
-    //world.Inject(*new_org);
+    new_org.New(&GetRandom(), this, my_config, my_config->HOST_INT());
+    InjectHost(new_org);
   }
+}
 
-  //sets up the world size
-  world->Resize(my_config->GRID_X(), my_config->GRID_Y());
-
-  //This loop must be outside of the host generation loop since otherwise
-  //syms try to inject into mostly empty spots at first
-  int total_syms = POP_SIZE * start_moi;
-  for (int j = 0; j < total_syms; j++){
-    double sym_int = 0;
-    if (random_phen_sym) {sym_int = random.GetDouble(-1,1);}
-    else {sym_int = my_config->SYM_INT();}
-
-    emp::Ptr<EfficientSymbiont> new_sym = emp::NewPtr<EfficientSymbiont>(&random, world, my_config, sym_int, 0, 1);
-    world->InjectSymbiont(new_sym);
+/**
+ * Input: The number of efficient symbionts.
+ *
+ * Output: None.
+ *
+ * Purpose: To populate the world with efficient symbionts with appropriate phenotypes.
+ */
+void EfficientWorld::SetupSymbionts(long unsigned int* total_syms) {
+  for (size_t j = 0; j < *total_syms; j++) {
+    emp::Ptr<EfficientSymbiont> new_sym = emp::NewPtr<EfficientSymbiont>(&GetRandom(), this, my_config, my_config->SYM_INT(), 0, 1);
+    InjectSymbiont(new_sym);
   }
 }
 
+/**
+ * Input: None.
+ *
+ * Output: None.
+ *
+ * Purpose: Prepare the world for a simulation by applying the configuration settings
+ * and populating the world with efficient hosts and efficient symbionts.
+ */
+void EfficientWorld::Setup() {
+  if (my_config->EFFICIENCY_MUT_RATE() == -1) my_config->EFFICIENCY_MUT_RATE(my_config->HORIZ_MUTATION_RATE());
+  SymWorld::Setup();
+}
 #endif

source/lysis_mode/LysisWorld.h

@@ -37,6 +37,14 @@ class LysisWorld : public SymWorld {
     if (data_node_cfu) data_node_cfu.Delete();
   }
 
+
+  /**
+   * Definitions of setup functions, expanded in LysisWorldSetup.cc
+   */
+  void SetupHosts(long unsigned int* POP_SIZE);
+  void SetupSymbionts(long unsigned int* total_syms);
+
+
   /**
   * Input: None.
   *