more optimization flag cleanup

Author: bhaller

core/chromosome.cpp

@@ -1045,11 +1045,6 @@ MutationIndex Chromosome::DrawNewMutation(std::pair<slim_position_t, GenomicElem
 
 	// addition to the main registry and the muttype registries will happen if the new mutation clears the stacking policy
 
-	// BCH 1/4/2025: For simplicity we assume that this mutation will be added, and call NoteNonNeutralMutation()
-	// here.  The worst that will happen is that the simulation will shift to non-neutral unnecessarily.
-	if (!mutation->is_neutral_)
-		species_.NoteNonNeutralMutation(mutation);
-	
 	return new_mut_index;
 }
 
@@ -1447,11 +1442,6 @@ MutationIndex Chromosome::DrawNewMutationExtended(std::pair<slim_position_t, Gen
 
 	// addition to the main registry and the muttype registries will happen if the new mutation clears the stacking policy
 
-	// BCH 1/4/2025: For simplicity we assume that this mutation will be added, and call NoteNonNeutralMutation()
-	// here.  The worst that will happen is that the simulation will shift to non-neutral unnecessarily.
-	if (!mutation->is_neutral_)
-		species_.NoteNonNeutralMutation(mutation);
-	
 	return new_mut_index;
 }
 

core/community.cpp

@@ -2610,6 +2610,9 @@ void Community::AllSpecies_CheckIntegrity(void)
 		// Check the integrity of all substitution objects
 		for (Substitution *sub : species->population_.substitutions_)
 			sub->SelfConsistencyCheck(" in AllSpecies_CheckIntegrity()");
+		
+		// Check the integrity of Species optimization flags
+		species->CheckOptimizationFlags();
 	}
 #endif
 }

core/genomic_element_type.cpp

@@ -345,8 +345,8 @@ void GenomicElementType::SetProperty(EidosGlobalStringID p_property_id, const Ei
 			if (!color_.empty())
 				Eidos_GetColorComponents(color_, &color_red_, &color_green_, &color_blue_);
 
-			// tweak a flag to make SLiMgui update
-			species_.community_.genomic_element_types_changed_ = true;
+			// let the species know that our configuration has changed
+			species_.AutogenerationConfigurationChanged();
 
 			return;
 		}
@@ -410,9 +410,6 @@ EidosValue_SP GenomicElementType::ExecuteMethod_setMutationFractions(EidosGlobal
 			mutation_types.emplace_back(mutation_type_ptr);
 			mutation_fractions.emplace_back(proportion);
 
-			// let the mutation type know that it is being used
-			mutation_type_ptr->used_in_GEType_ = true;
-			
 			// check whether the mutation type is non-neutral; if so, the species is now considered non-neutral
 			// (because we expect that a non-neutral mutation will be generated by this genomic element type)
 			// see also Species::ExecuteContextFunction_initializeGenomicElementType() for the same logic
@@ -429,7 +426,7 @@ EidosValue_SP GenomicElementType::ExecuteMethod_setMutationFractions(EidosGlobal
 	InitializeDraws();
 
 	// Notify interested parties of the change
-	species_.community_.genomic_element_types_changed_ = true;
+	species_.AutogenerationConfigurationChanged();
 
 	return gStaticEidosValueVOID;
 }

core/haplosome.cpp

@@ -2583,9 +2583,8 @@ EidosValue_SP Haplosome_Class::ExecuteMethod_addMutations(EidosGlobalStringID p_
 
 						// No need to add the mutation to the registry; how would the user ever get a Mutation that was not already in it?
 
-						// BCH 1/4/2025: the mutation is already in the system, so for now we don't need to note it
-						//if (!mut_to_add->is_neutral_)
-						//	species->NoteNonNeutralMutation(mut_to_add);
+						// BCH 1/4/2025: the mutation is already in the system, so its effects have been
+						// noted; no call to NoteChangedMutation(mut_to_add) is needed
 					}
 				}
 			}
@@ -2964,10 +2963,6 @@ EidosValue_SP Haplosome_Class::ExecuteMethod_addNewMutation(EidosGlobalStringID
 				if (p_method_id == gID_addNewDrawnMutation)
 				{
 					new_mut = new (mut_block_ptr + new_mut_index) Mutation(mutation_type_ptr, chromosome->Index(), position, origin_subpop_id, origin_tick, (int8_t)nucleotide);
-					
-					// this mutation will be added to the simulation somewhere, so tell the species about it
-					if (!new_mut->is_neutral_)
-						species->NoteNonNeutralMutation(new_mut);
 				}
 				else	// (p_method_id == gID_addNewMutation)
 				{
@@ -2984,10 +2979,6 @@ EidosValue_SP Haplosome_Class::ExecuteMethod_addNewMutation(EidosGlobalStringID
 					// FIXME MULTITRAIT: This needs to pass in a whole vector of effects and dominance coefficients now... and hemizygous dominance...
 					// FIXME MULTITRAIT this code will also now need to handle the independent dominance case
 					new_mut = new (mut_block_ptr + new_mut_index) Mutation(mutation_type_ptr, chromosome->Index(), position, static_cast<slim_effect_t>(selection_coeff), mutation_type_ptr->DefaultDominanceForTrait(0), origin_subpop_id, origin_tick, (int8_t)nucleotide);
-					
-					// this mutation will be added to the simulation somewhere, so tell the species about it
-					if (!new_mut->is_neutral_)
-						species->NoteNonNeutralMutation(new_mut);
 				}
 
 				// add to the registry, return value, haplosome, etc.
@@ -3484,10 +3475,6 @@ EidosValue_SP Haplosome_Class::ExecuteMethod_readHaplosomesFromMS(EidosGlobalStr
 		// FIXME MULTITRAIT this code will also now need to handle the independent dominance case
 		Mutation *new_mut = new (mut_block_ptr + new_mut_index) Mutation(mutation_type_ptr, chromosome->Index(), position, static_cast<slim_effect_t>(selection_coeff), mutation_type_ptr->DefaultDominanceForTrait(0), subpop_index, origin_tick, nucleotide);
 
-		// this mutation will be added to the simulation somewhere, so tell the species about it
-		if (!new_mut->is_neutral_)
-			species.NoteNonNeutralMutation(new_mut);
-		
 		// add it to our local map, so we can find it when making haplosomes, and to the population's mutation registry
 		pop.MutationRegistryAdd(new_mut);
 		mutation_indices.emplace_back(new_mut_index);
@@ -4136,10 +4123,6 @@ EidosValue_SP Haplosome_Class::ExecuteMethod_readHaplosomesFromVCF(EidosGlobalSt
 				new_mut = new (mut_block_ptr + new_mut_index) Mutation(mutation_type_ptr, chromosome->Index(), mut_position, selection_coeff, dominance_coeff, subpop_index, origin_tick, nucleotide);
 			}
 
-			// this mutation will be added to the simulation somewhere, so tell the species about it
-			if (!new_mut->is_neutral_)
-				species->NoteNonNeutralMutation(new_mut);
-			
 			// add it to our local map, so we can find it when making haplosomes, and to the population's mutation registry
 			pop.MutationRegistryAdd(new_mut);
 			alt_allele_mut_indices.emplace_back(new_mut_index);
@@ -4391,7 +4374,6 @@ EidosValue_SP Haplosome_Class::ExecuteMethod_removeMutations(EidosGlobalStringID
 		// Construct a vector of mutations to remove that is sorted by position
 		std::vector<Mutation *> mutations_to_remove;
 		Mutation * const *mutations_data = (Mutation * const *)mutations_value->ObjectData();
-		slim_trait_index_t trait_count = species->TraitCount();
 
 		for (int value_index = 0; value_index < mutations_count; ++value_index)
 		{
@@ -4405,20 +4387,12 @@ EidosValue_SP Haplosome_Class::ExecuteMethod_removeMutations(EidosGlobalStringID
 
 			mutations_to_remove.emplace_back(mut);
 
+			// Note the removal; it might affect our caching, even if the mutation is neutral
+			species->NoteChangedMutation(mut);
+			
 			// If we're not already aware of having removed a non-neutral mutation, check on that now
-			if (!any_nonneutral_removed)
-			{
-				MutationTraitInfo *mut_trait_info = mutation_block->TraitInfoForMutation(mut);
-				
-				for (slim_trait_index_t trait_index = 0; trait_index < trait_count; ++trait_index)
-				{
-					if (mut_trait_info[trait_index].effect_size_ != (slim_effect_t)0.0)
-					{
-						any_nonneutral_removed = true;
-						break;
-					}
-				}
-			}
+			if (!mut->is_neutral_for_all_traits_)
+				any_nonneutral_removed = true;
 		}
 
 		std::sort(mutations_to_remove.begin(), mutations_to_remove.end(), [ ](Mutation *i1, Mutation *i2) {return i1->position_ < i2->position_;});

core/individual.cpp

@@ -1430,7 +1430,7 @@ EidosValue_SP Individual::GetProperty(EidosGlobalStringID p_property_id)
 			}
 
 			Subpopulation *subpop = subpopulation_;
-			double fitness = subpop->individual_cached_fitness_OVERRIDE_ ? subpop->individual_cached_fitness_OVERRIDE_value_ : cached_fitness_UNSAFE_;
+			double fitness = subpop->individual_cached_fitness_OVERRIDE_ ? subpop->individual_cached_fitness_OVERRIDE_value_ : (double)cached_fitness_UNSAFE_;
 
 			return EidosValue_SP(new (gEidosValuePool->AllocateChunk()) EidosValue_Float(fitness));
 		}
@@ -1955,7 +1955,7 @@ EidosValue *Individual::GetProperty_Accelerated_cachedFitness(EidosGlobalStringI
 			{
 				Individual *ind = (Individual *)(p_values[value_index]);
 
-				float_result->set_float_no_check(ind->cached_fitness_UNSAFE_, value_index);
+				float_result->set_float_no_check((double)ind->cached_fitness_UNSAFE_, value_index);
 			}
 		}
 	}
@@ -1965,7 +1965,7 @@ EidosValue *Individual::GetProperty_Accelerated_cachedFitness(EidosGlobalStringI
 		{
 			Individual *ind = (Individual *)(p_values[value_index]);
 			Subpopulation *subpop = ind->subpopulation_;
-			double fitness = (subpop->individual_cached_fitness_OVERRIDE_ ? subpop->individual_cached_fitness_OVERRIDE_value_ : ind->cached_fitness_UNSAFE_);
+			double fitness = (subpop->individual_cached_fitness_OVERRIDE_ ? subpop->individual_cached_fitness_OVERRIDE_value_ : (double)ind->cached_fitness_UNSAFE_);
 
 			float_result->set_float_no_check(fitness, value_index);
 		}
@@ -5493,6 +5493,7 @@ EidosValue_SP Individual_Class::ExecuteMethod_readIndividualsFromVCF(EidosGlobal
 				if (info_mutids.size() > 0)
 				{
 					// a mutation ID was supplied; we use it blindly, having checked above that we are in the case where this is legal
+					// FIXME MULTITRAIT: This needs to pass in a whole vector of effects and dominance coefficients now...
 					slim_mutationid_t mut_mutid = info_mutids[alt_allele_index];
 
 					new_mut = new (mut_block_ptr + new_mut_index) Mutation(mut_mutid, mutation_type_ptr, chromosome->Index(), mut_position, selection_coeff, dominance_coeff, subpop_index, origin_tick, nucleotide);
@@ -5504,10 +5505,6 @@ EidosValue_SP Individual_Class::ExecuteMethod_readIndividualsFromVCF(EidosGlobal
 					new_mut = new (mut_block_ptr + new_mut_index) Mutation(mutation_type_ptr, chromosome->Index(), mut_position, selection_coeff, dominance_coeff, subpop_index, origin_tick, nucleotide);
 				}
 
-				// all mutations seen here will be added to the simulation somewhere, so tell the species about it
-				if (!new_mut->is_neutral_)
-					species->NoteNonNeutralMutation(new_mut);
-				
 				// add it to our local map, so we can find it when making haplosomes, and to the population's mutation registry
 				pop.MutationRegistryAdd(new_mut);
 				alt_allele_mut_indices.emplace_back(new_mut_index);