add per-trait effect size and dominance to Substitution

Author: bhaller

VERSIONS

@@ -59,6 +59,7 @@ multitrait branch:
 	make code completion work for the new dynamic properties on Species and Individual generated by initializeTrait()
 	shift from a single global mutation block into per-species mutation blocks, and make a new C++ class, MutationBlock, to encapsulate this
 		this is a forced move because we want the mutation block to have a separate buffer of per-trait state for mutations, and the number of traits varies among species
+	add effect size and dominance coefficient properties to Mutation and Substitution (but not hooked up to the simulation yet)
 
 
 version 5.1 (Eidos version 4.1):

core/mutation.cpp

@@ -70,7 +70,7 @@ mutation_type_ptr_(p_mutation_type_ptr), position_(p_position), selection_coeff_
 		Trait *trait = species.Traits()[trait_index];
 		TraitType traitType = trait->Type();
 
-		traitInfoRec->mutation_effect_ = selection_coeff_;
+		traitInfoRec->effect_size_ = selection_coeff_;
 		traitInfoRec->dominance_coeff_ = dominance_coeff_;
 
 		if (traitType == TraitType::kMultiplicative)
@@ -168,7 +168,7 @@ mutation_type_ptr_(p_mutation_type_ptr), position_(p_position), selection_coeff_
 		Trait *trait = species.Traits()[trait_index];
 		TraitType traitType = trait->Type();
 
-		traitInfoRec->mutation_effect_ = selection_coeff_;
+		traitInfoRec->effect_size_ = selection_coeff_;
 		traitInfoRec->dominance_coeff_ = dominance_coeff_;
 
 		if (traitType == TraitType::kMultiplicative)

core/mutation.h

@@ -59,7 +59,7 @@ typedef int32_t MutationIndex;
 // with a number of records per mutation that is determined when it is constructed.
 typedef struct _MutationTraitInfo
 {
-	slim_effect_t mutation_effect_;			// selection coefficient (s) or additive effect (a)
+	slim_effect_t effect_size_;				// selection coefficient (s) or additive effect (a)
 	slim_effect_t dominance_coeff_;			// dominance coefficient (h), inherited from MutationType by default
 
 	// We cache values used in the fitness calculation code, for speed.  These are the final fitness effects of this mutation

core/mutation_type.cpp

@@ -87,9 +87,9 @@ self_symbol_(EidosStringRegistry::GlobalStringIDForString(SLiMEidosScript::IDStr
 	all_pure_neutral_DFE_ = ((p_dfe_type == DFEType::kFixed) && (p_dfe_parameters[0] == 0.0));
 
 	// set up DE entries for all traits
-	int64_t trait_count = species_.TraitCount();
+	int trait_count = species_.TraitCount();
 
-	for (int64_t trait_index = 0; trait_index < trait_count; trait_index++)
+	for (int trait_index = 0; trait_index < trait_count; trait_index++)
 	{
 		EffectDistributionInfo ed_info;
 

core/species.cpp

@@ -609,7 +609,7 @@ void Species::GetTraitIndicesFromEidosValue(std::vector<int64_t> &trait_indices,
 {
 	EidosValueType traits_value_type = traits_value->Type();
 	int traits_value_count = traits_value->Count();
-	int64_t trait_count = TraitCount();
+	int trait_count = TraitCount();
 
 	switch (traits_value_type)
 	{
@@ -2825,7 +2825,7 @@ void Species::CreateAndPromulgateMutationBlock(void)
 		EIDOS_TERMINATION << "ERROR (Species::CreateAndPromulgateMutationBlock): (internal error) a mutation block has already been allocated." << EidosTerminate();
 
 	// first we make a new MutationBlock object for ourselves
-	mutation_block_ = new MutationBlock(*this, (int)TraitCount());
+	mutation_block_ = new MutationBlock(*this, TraitCount());
 
 	// then we promulgate it to the masses, so that they have it on hand (avoiding the non-local memory access
 	// of getting it from us), since it is referred to very actively in many places

core/species.h

@@ -448,7 +448,7 @@ class Species : public EidosDictionaryUnretained
 
 	// Trait configuration and access
 	inline __attribute__((always_inline)) const std::vector<Trait *> &Traits(void)	{ return traits_; }
-	inline __attribute__((always_inline)) int64_t TraitCount(void)	{ return (int64_t)traits_.size(); }
+	inline __attribute__((always_inline)) int TraitCount(void)	{ return (int)traits_.size(); }
 	Trait *TraitFromName(const std::string &p_name) const;
 	inline __attribute__((always_inline)) Trait *TraitFromStringID(EidosGlobalStringID p_string_id) const
 	{

core/substitution.cpp

@@ -23,6 +23,7 @@
 #include "eidos_call_signature.h"
 #include "eidos_property_signature.h"
 #include "species.h"
+#include "mutation_block.h"
 
 #include <iostream>
 #include <algorithm>
@@ -40,11 +41,38 @@ Substitution::Substitution(Mutation &p_mutation, slim_tick_t p_fixation_tick) :
 {
 	AddKeysAndValuesFrom(&p_mutation);
 	// No call to ContentsChanged() here; we know we use Dictionary not DataFrame, and Mutation already vetted the dictionary
+	
+	// Copy per-trait information over from the mutation object
+	Species &species = mutation_type_ptr_->species_;
+	MutationBlock *mutation_block = species.SpeciesMutationBlock();
+	MutationIndex mut_index = mutation_block->IndexInBlock(&p_mutation);
+	MutationTraitInfo *mut_trait_info = mutation_block->TraitInfoIndex(mut_index);
+	int trait_count = species.TraitCount();
+	
+	trait_info_ = (SubstitutionTraitInfo *)malloc(trait_count * sizeof(SubstitutionTraitInfo));
+	
+	for (int trait_index = 0; trait_index < trait_count; trait_index++)
+	{
+		trait_info_[trait_index].effect_size_ = mut_trait_info[trait_index].effect_size_;
+		trait_info_[trait_index].dominance_coeff_ = mut_trait_info[trait_index].dominance_coeff_;
+	}
 }
 
 Substitution::Substitution(slim_mutationid_t p_mutation_id, MutationType *p_mutation_type_ptr, slim_chromosome_index_t p_chromosome_index, slim_position_t p_position, slim_effect_t p_selection_coeff, slim_effect_t p_dominance_coeff, slim_objectid_t p_subpop_index, slim_tick_t p_tick, slim_tick_t p_fixation_tick, int8_t p_nucleotide) :
 mutation_type_ptr_(p_mutation_type_ptr), position_(p_position), selection_coeff_(static_cast<slim_effect_t>(p_selection_coeff)), dominance_coeff_(static_cast<slim_effect_t>(p_dominance_coeff)), subpop_index_(p_subpop_index), origin_tick_(p_tick), fixation_tick_(p_fixation_tick), chromosome_index_(p_chromosome_index), nucleotide_(p_nucleotide), mutation_id_(p_mutation_id), tag_value_(SLIM_TAG_UNSET_VALUE)
 {
+	// FIXME MULTITRAIT: This code path is hit when loading substitutions from an output file, also needs to initialize the multitrait info; this is just a
+	// placeholder.  The file being read in ought to specify per-trait values, which hasn't happened yet, so there are lots of details to be worked out...
+	Species &species = mutation_type_ptr_->species_;
+	int trait_count = species.TraitCount();
+	
+	trait_info_ = (SubstitutionTraitInfo *)malloc(trait_count * sizeof(SubstitutionTraitInfo));
+	
+	for (int trait_index = 0; trait_index < trait_count; trait_index++)
+	{
+		trait_info_[trait_index].effect_size_ = 0.0;
+		trait_info_[trait_index].dominance_coeff_ = 0.0;
+	}
 }
 
 void Substitution::PrintForSLiMOutput(std::ostream &p_out) const

core/substitution.h

@@ -37,6 +37,18 @@
 
 extern EidosClass *gSLiM_Substitution_Class;
 
+// This structure contains all of the information about how a substitution influenced a particular trait: in particular, its
+// effect size and dominance coefficient.  Each substitution keeps this information for each trait in its species, and since
+// the number of traits is determined at runtime, the size of this data -- the number of SubstitutionTraitInfo records kept
+// by each substitution -- is also determined at runtime.  This is parallel to the MutationTraitInfo struct for mutations,
+// but keeps less information since it is not used during fitness evaluation.  Also unlike Mutation, which keeps all this
+// in a block maintained by MutationBlock, we simply make a malloced block for each substitution; substitution is relatively
+// rare and substitutions don't go away once created, so there is no need to overcomplicate this design.
+typedef struct _SubstitutionTraitInfo
+{
+	slim_effect_t effect_size_;				// selection coefficient (s) or additive effect (a)
+	slim_effect_t dominance_coeff_;			// dominance coefficient (h), inherited from MutationType by default
+} SubstitutionTraitInfo;
 
 class Substitution : public EidosDictionaryRetained
 {
@@ -59,14 +71,17 @@ class Substitution : public EidosDictionaryRetained
 	const slim_mutationid_t mutation_id_;		// a unique id for each mutation, used to track mutations
 	slim_usertag_t tag_value_;					// a user-defined tag value
 
+	// Per-trait information
+	SubstitutionTraitInfo *trait_info_;			// OWNED: a malloced block of per-trait information
+	
 	Substitution(const Substitution&) = delete;							// no copying
 	Substitution& operator=(const Substitution&) = delete;				// no copying
 	Substitution(void) = delete;										// no null construction
 	Substitution(Mutation &p_mutation, slim_tick_t p_fixation_tick);	// construct from the mutation that has fixed, and the tick in which it fixed
 	Substitution(slim_mutationid_t p_mutation_id, MutationType *p_mutation_type_ptr, slim_chromosome_index_t p_chromosome_index, slim_position_t p_position, slim_effect_t p_selection_coeff, slim_effect_t p_dominance_coeff, slim_objectid_t p_subpop_index, slim_tick_t p_tick, slim_tick_t p_fixation_tick, int8_t p_nucleotide);
 
-	// a destructor is needed now that we inherit from EidosDictionaryRetained; we want it to be as minimal as possible, though, and inline
-	inline virtual ~Substitution(void) override { }
+	// a destructor is needed now that we inherit from EidosDictionaryRetained; we want it to be as minimal as possible, though
+	inline virtual ~Substitution(void) override { free(trait_info_); trait_info_ = nullptr; }
 
 	void PrintForSLiMOutput(std::ostream &p_out) const;
 	void PrintForSLiMOutput_Tag(std::ostream &p_out) const;