get rid of subpop haplosome vectors

SLiMgui/GraphView_MutationFrequencyTrajectory.mm

@@ -316,12 +316,11 @@ - (void)fetchDataForFinishedTick
 		{
 			Subpopulation *subpop = subpop_pair.second;
 
-			slim_popsize_t subpop_haplosome_count = 2 * subpop->parent_subpop_size_;
-			std::vector<Haplosome *> &subpop_haplosome = subpop->parent_haplosomes_;
-
-			for (int i = 0; i < subpop_haplosome_count; i++)
+			for (Individual *ind : subpop->parent_individuals_)
+			{
+			for (int haplosome_index = 0; haplosome_index <= 1; ++haplosome_index)
 			{
-				Haplosome &haplosome = *subpop_haplosome[i];
+				Haplosome &haplosome = *((haplosome_index == 0) ? ind->haplosome1_ : ind->haplosome2_);
 
 				if (!haplosome.IsNull())
 				{
@@ -345,6 +344,7 @@ - (void)fetchDataForFinishedTick
 					subpop_total_haplosome_count++;
 				}
 			}
+			}
 		}
 	}
 

SLiMgui/SLiMHaplotypeManager.mm

@@ -108,10 +108,20 @@ - (instancetype)initWithClusteringMethod:(SLiMHaplotypeClusteringMethod)clusteri
 		[self setSubpopCount:(int)selected_subpops.size()];
 
 		// Fetch haplosomes and figure out what we're going to plot; note that we plot only non-null haplosomes
+#warning we need a focal chromosome here; we can't align non-homologous haplosomes
 		for (Subpopulation *subpop : selected_subpops)
-			for (Haplosome *haplosome : subpop->parent_haplosomes_)
+		{
+			for (Individual *ind : subpop->parent_individuals_)
+			{
+			for (int haplosome_index = 0; haplosome_index <= 1; ++haplosome_index)
+			{
+				Haplosome *haplosome = ((haplosome_index == 0) ? ind->haplosome1_ : ind->haplosome2_);
+
 				if (!haplosome->IsNull())
 					haplosomes.emplace_back(haplosome);
+			}
+			}
+		}
 
 		// If a sample is requested, select that now; sampleSize <= 0 means no sampling
 		if ((sampleSize > 0) && ((int)haplosomes.size() > sampleSize))

core/haplosome.cpp

@@ -4138,8 +4138,19 @@ EidosValue_SP Haplosome_Class::ExecuteMethod_removeMutations(EidosGlobalStringID
 			{
 				// Mark all non-null haplosomes in the simulation that are not among the target haplosomes
 				for (auto subpop_pair : species->population_.subpops_)
-					for (Haplosome *haplosome : subpop_pair.second->parent_haplosomes_)
+				{
+					Subpopulation *subpop = subpop_pair.second;
+
+					for (Individual *ind : subpop->parent_individuals_)
+					{
+					for (int haplosome_index = 0; haplosome_index <= 1; ++haplosome_index)
+					{
+						Haplosome *haplosome = ((haplosome_index == 0) ? ind->haplosome1_ : ind->haplosome2_);
+
 						haplosome->scratch_ = (haplosome->IsNull() ? 0 : 1);
+					}
+					}
+				}
 
 				for (int haplosome_index = 0; haplosome_index < target_size; ++haplosome_index)
 					targets_data[haplosome_index]->scratch_ = 0;
@@ -4161,13 +4172,24 @@ EidosValue_SP Haplosome_Class::ExecuteMethod_removeMutations(EidosGlobalStringID
 
 				// Loop through those haplosomes and log the new derived state at each (unique) position
 				for (auto subpop_pair : species->population_.subpops_)
-					for (Haplosome *haplosome : subpop_pair.second->parent_haplosomes_)
+				{
+					Subpopulation *subpop = subpop_pair.second;
+
+					for (Individual *ind : subpop->parent_individuals_)
+					{
+					for (int haplosome_index = 0; haplosome_index <= 1; ++haplosome_index)
+					{
+						Haplosome *haplosome = ((haplosome_index == 0) ? ind->haplosome1_ : ind->haplosome2_);
+
 						if (haplosome->scratch_ == 1)
 						{
 							for (slim_position_t position : unique_positions)
 								species->RecordNewDerivedState(haplosome, position, *haplosome->derived_mutation_ids_at_position(position));
 							haplosome->scratch_ = 0;
 						}
+					}
+					}
+				}
 			}
 		}
 

core/individual.cpp

@@ -86,6 +86,14 @@ Individual::Individual(Subpopulation *p_subpopulation, slim_popsize_t p_individu
 #endif
 }
 
+Individual::~Individual(void)
+{
+	// BCH 10/6/2024: Individual now owns the haplosomes inside it (a policy change for multichrom)
+	// This means the subpopulation_ pointer must be valid at this point!
+	subpopulation_->FreeSubpopHaplosome(haplosome1_);
+	subpopulation_->FreeSubpopHaplosome(haplosome2_);
+}
+
 static inline bool _InPedigree(slim_pedigreeid_t A, slim_pedigreeid_t A_P1, slim_pedigreeid_t A_P2, slim_pedigreeid_t A_G1, slim_pedigreeid_t A_G2, slim_pedigreeid_t A_G3, slim_pedigreeid_t A_G4, slim_pedigreeid_t B)
 {
 	if (B == -1)

core/individual.h

@@ -132,7 +132,7 @@ class Individual : public EidosDictionaryUnretained
 										// that confuses interpretation; note that individual_cached_fitness_OVERRIDE_ is not relevant to this
 #endif
 
-	Haplosome *haplosome1_, *haplosome2_;	// NOT OWNED; must correspond to the entries in the Subpopulation we live in
+	Haplosome *haplosome1_, *haplosome2_;	// OWNED; must correspond to the entries in the Subpopulation we live in
 	slim_age_t age_;					// nonWF only: the age of the individual, in cycles; -1 in WF models
 
 	slim_popsize_t index_;				// the individual index in that subpop (0-based, and not multiplied by 2)
@@ -150,7 +150,7 @@ class Individual : public EidosDictionaryUnretained
 	Individual& operator= (const Individual &p_original) = delete;						// no copy construction
 	Individual(void) = delete;															// no null construction
 	Individual(Subpopulation *p_subpopulation, slim_popsize_t p_individual_index, Haplosome *p_haplosome1, Haplosome *p_haplosome2, IndividualSex p_sex, slim_age_t p_age, double p_fitness, float p_mean_parent_age);
-	inline virtual ~Individual(void) override { }
+	virtual ~Individual(void) override;
 
 	inline __attribute__((always_inline)) void ClearColor(void) { color_set_ = false; }