Merge pull request #256 from EliasH-E/docu-branch

Added more documentation

Author: anyaevostinar

source/sgp_mode/GenomeLibrary.h

@@ -265,6 +265,15 @@ class ProgramBuilder : emp::vector<sgpl::Instruction<Spec>> {
     Add("SharedIO");
   }
 
+
+   /**
+     * Input: The number of steal instructions to add.
+     *
+     * Output: None.
+     *
+     * Purpose: Spread out steal instructions throughout the organim's genome in order to allow stealing 
+     * during a symbiont's entire genome and not just in one place. Without the spread of instructions symbionts were unable to steal regularly and died.
+     */
   void AddStartSteal(int steal_count){
 
     if(steal_count > 0){
@@ -283,6 +292,14 @@ class ProgramBuilder : emp::vector<sgpl::Instruction<Spec>> {
 
   }
 
+  /**
+     * Input: The number of donate instructions to add.
+     *
+     * Output: None.
+     *
+     * Purpose: Spread out donate instructions throughout the organim's genome in order to allow donations 
+     * during a symbiont's entire genome and not just in one place. Without the spread of instructions symbionts were unable to donate regularly.
+     */
   void AddStartDonate(int donate_count){
 
     if(donate_count > 0){

source/sgp_mode/HealthHost.h

@@ -53,17 +53,40 @@ class HealthHost : public SGPHost {
         random, GetWorld(), sgp_config, GetCPU().GetProgram(), GetIntVal());
     return host_baby;
   }
+
+    /**
+     * Input: An integer amount for the number of updates that are being transferred
+     *
+     * Output: None.
+     *
+     * Purpose: To change the number of cycles a host is set to give/be given.
+     */
     void CycleTransfer(int amount) override {
       cycles_given += amount;
     }
 
+    /**
+     * Input: None.
+     *
+     * Output: A integer for the amount of cycles the host is set to give/be given.
+     *
+     * Purpose: For symbionts to check if their host already owes cycles.
+     */
     int GetCyclesGiven(){
       return cycles_given;
     }
 
+     /**
+     * Input: None.
+     *
+     * Output: The string 'HealthHost', which is the name of this organism
+     *
+     * Purpose: Allows tests to check that an organism is of the proper type. 
+     */
     std::string const GetName() override{
       return "HealthHost";
     }
+    
     /** 
      * Input: The location of the host.
      * 
@@ -201,4 +224,4 @@ class HealthHost : public SGPHost {
 };
 
 
-#endif // HEALTHHOST_H
+#endif // HEALTHHOST_H

source/sgp_mode/SGPWorldSetup.cc

@@ -7,6 +7,14 @@
 #include "SGPSymbiont.h"
 #include "SGPWorld.h"
 
+
+/**
+ * Input: A pointer to a long for the number of hosts to add to the world
+ *
+ * Output: None
+ *
+ * Purpose: Adds a number of hosts of a set type to the world. 
+ */
 void SGPWorld::SetupHosts(unsigned long *POP_SIZE) {
   for (size_t i = 0; i < *POP_SIZE; i++) {
     emp::Ptr<SGPHost> new_org;
@@ -59,6 +67,14 @@ void SGPWorld::SendToGraveyard(emp::Ptr<Organism> org) {
   SymWorld::SendToGraveyard(org);
 }
 
+
+/**
+ * Input: An id for the the parent symbiont and a pointer to that symbiont. 
+ *
+ * Output: The id of a host that can be infected by the symbiont
+ *
+ * Purpose: Searches through up to 10 hosts in the world to find a host that the symbiont can infect. 
+ */
 int SGPWorld::GetNeighborHost (size_t id, emp::Ptr<Organism> symbiont){
   // Attempt to find host that matches some tasks
   for (int i = 0; i < 10; i++) {
@@ -129,7 +145,14 @@ bool SGPWorld::TaskMatchCheck(emp::Ptr<Organism> sym_parent, emp::Ptr<Organism>
 }
 
 
-
+ /**
+  * Input: Pointers to a symbiont offspring and the position of the symbiont's parent. 
+  *
+  * Output: Returns a WorldPosition pointer, a valid one for succesful 
+  * infection and an invalid for a failed infection
+  *
+  * Purpose: To get the location of where the symbiont offpsring can be added to. 
+  */
 emp::WorldPosition SGPWorld::SymDoBirth(emp::Ptr<Organism> sym_baby, emp::WorldPosition parent_pos) {
    size_t i = parent_pos.GetPopID();
     emp::Ptr<Organism> parent = GetOrgPtr(i)->GetSymbionts()[parent_pos.GetIndex()-1];