more auto and const usage cleanup

Author: bhaller

core/chromosome.cpp

@@ -454,7 +454,7 @@ void Chromosome::InitializeDraws(void)
 	{
 		last_position_ = 0;
 
-		for (GenomicElement *genomic_element : genomic_elements_)
+		for (const GenomicElement *genomic_element : genomic_elements_)
 		{ 
 			if (genomic_element->end_position_ > last_position_)
 				last_position_ = genomic_element->end_position_;
@@ -1915,7 +1915,7 @@ void Chromosome::DrawBreakpoints(Individual *p_parent, Haplosome *p_haplosome1,
 #endif
 }
 
-size_t Chromosome::MemoryUsageForMutationMaps(void)
+size_t Chromosome::MemoryUsageForMutationMaps(void) const
 {
 	size_t usage = 0;
 
@@ -1937,7 +1937,7 @@ size_t Chromosome::MemoryUsageForMutationMaps(void)
 	return usage;
 }
 
-size_t Chromosome::MemoryUsageForRecombinationMaps(void)
+size_t Chromosome::MemoryUsageForRecombinationMaps(void) const
 {
 	size_t usage = 0;
 
@@ -1956,7 +1956,7 @@ size_t Chromosome::MemoryUsageForRecombinationMaps(void)
 	return usage;
 }
 
-size_t Chromosome::MemoryUsageForAncestralSequence(void)
+size_t Chromosome::MemoryUsageForAncestralSequence(void) const
 {
 	size_t usage = 0;
 
@@ -2172,15 +2172,15 @@ void Chromosome::CheckMutationRegistry(bool p_check_haplosomes)
 
 		for (const std::pair<const slim_objectid_t,Subpopulation*> &subpop_pair : species_.population_.subpops_)
 		{
-			Subpopulation *subpop = subpop_pair.second;
+			const Subpopulation *subpop = subpop_pair.second;
 
-			for (Individual *ind : subpop->parent_individuals_)
+			for (const Individual *ind : subpop->parent_individuals_)
 			{
-				Haplosome **haplosomes = ind->haplosomes_;
+				const Haplosome * const *haplosomes = ind->haplosomes_;
 
 				for (int haplosome_index = 0; haplosome_index < haplosome_count_per_individual; haplosome_index++)
 				{
-					Haplosome *haplosome = haplosomes[haplosome_index];
+					const Haplosome *haplosome = haplosomes[haplosome_index];
 
 					int mutrun_count = haplosome->mutrun_count_;
 

core/chromosome.h

@@ -319,7 +319,7 @@ class Chromosome : public EidosDictionaryRetained
 	~Chromosome(void);
 
 	// mutation registry
-	inline const MutationIndex *MutationRegistry(int *registry_count)
+	inline const MutationIndex *MutationRegistry(int *registry_count) const
 	{
 		*registry_count = mutation_registry_.size();
 		return mutation_registry_.begin_pointer_const();
@@ -332,7 +332,7 @@ class Chromosome : public EidosDictionaryRetained
 
 	void CheckMutationRegistry(bool p_check_haplosomes);		// check the registry for any bad entries (i.e. zombies, mutations with an incorrect state_)
 	inline void SetMutationRegistryNeedsCheck(void) { registry_needs_consistency_check_ = true; }
-	inline bool MutationRegistryNeedsCheck(void) { return registry_needs_consistency_check_; }
+	inline bool MutationRegistryNeedsCheck(void) const { return registry_needs_consistency_check_; }
 
 	// accessors
 	inline __attribute__((always_inline)) int64_t ID(void) const	{ return id_; }
@@ -404,9 +404,9 @@ class Chromosome : public EidosDictionaryRetained
 	void RecombinationMapConfigError(void) const __attribute__((__noreturn__)) __attribute__((cold)) __attribute__((analyzer_noreturn));
 
 	// Memory usage tallying, for outputUsage()
-	size_t MemoryUsageForMutationMaps(void);
-	size_t MemoryUsageForRecombinationMaps(void);
-	size_t MemoryUsageForAncestralSequence(void);
+	size_t MemoryUsageForMutationMaps(void) const;
+	size_t MemoryUsageForRecombinationMaps(void) const;
+	size_t MemoryUsageForAncestralSequence(void) const;
 
 	// Make a null haplosome, which is associated with an individual, but has no associated chromosome, or
 	// make a non-null haplosome, which is associated with an individual and has an associated chromosome
@@ -422,7 +422,7 @@ class Chromosome : public EidosDictionaryRetained
 	void SetUpMutationRunContexts(void);
 
 #ifndef _OPENMP
-	inline int ChromosomeMutationRunContextCount(void) { return 1; }
+	inline int ChromosomeMutationRunContextCount(void) const { return 1; }
 	inline __attribute__((always_inline)) MutationRunContext &ChromosomeMutationRunContextForThread(__attribute__((unused)) int p_thread_num)
 	{
 #if DEBUG
@@ -440,7 +440,7 @@ class Chromosome : public EidosDictionaryRetained
 		return mutation_run_context_SINGLE_;
 	}
 #else
-	inline int ChromosomeMutationRunContextCount(void) { return mutation_run_context_COUNT_; }
+	inline int ChromosomeMutationRunContextCount(void) const { return mutation_run_context_COUNT_; }
 	inline __attribute__((always_inline)) MutationRunContext &ChromosomeMutationRunContextForThread(int p_thread_num)
 	{
 #if DEBUG

core/community.cpp

@@ -204,7 +204,7 @@ void Community::InitializeFromFile(std::istream &p_infile)
 	std::vector<std::string> explicit_species_decl_names;		// names from "species <name> initialize()" declarations
 	int implied_species_decl_count = 0;							// number of "initialize()" seen without "species <name>"
 
-	for (EidosASTNode *script_block_node : root_node->children_)
+	for (const EidosASTNode *script_block_node : root_node->children_)
 	{
 		if (script_block_node->token_->token_type_ == EidosTokenType::kTokenIdentifier)
 		{
@@ -326,7 +326,7 @@ void Community::InitializeFromFile(std::istream &p_infile)
 	bool last_spec_is_ticks_all = false;	// "ticks all" is a special syntax; there is no species named "all" so it must be tracked with a separate flag
 	bool last_spec_is_species_all = false;	// "species all" is a special syntax; there is no species named "all" so it must be tracked with a separate flag
 
-	for (EidosASTNode *script_block_node : root_node->children_)
+	for (const EidosASTNode *script_block_node : root_node->children_)
 	{
 		if ((script_block_node->token_->token_type_ == EidosTokenType::kTokenIdentifier) && (script_block_node->children_.size() == 1))
 		{
@@ -493,7 +493,7 @@ void Community::ValidateScriptBlockCaches(void)
 
 #if DEBUG_BLOCK_REG_DEREG
 		std::cout << "   ValidateScriptBlockCaches() recaching, AllScriptBlocks() is:" << std::endl;
-		for (SLiMEidosBlock *script_block : script_blocks)
+		for (const SLiMEidosBlock *script_block : script_blocks)
 		{
 			std::cout << "      ";
 			script_block->Print(std::cout);
@@ -547,7 +547,7 @@ void Community::ValidateScriptBlockCaches(void)
 
 #if DEBUG_BLOCK_REG_DEREG
 		std::cout << "   ValidateScriptBlockCaches() recached, late() events cached are:" << std::endl;
-		for (SLiMEidosBlock *script_block : cached_late_events_)
+		for (const SLiMEidosBlock *script_block : cached_late_events_)
 		{
 			std::cout << "      ";
 			script_block->Print(std::cout);
@@ -1095,7 +1095,7 @@ void Community::AddScriptBlock(SLiMEidosBlock *p_script_block, EidosInterpreter
 
 #if DEBUG_BLOCK_REG_DEREG
 	std::cout << "Tick " << tick_ << ": AddScriptBlock() just added a block, script_blocks_ is:" << std::endl;
-	for (SLiMEidosBlock *script_block : script_blocks_)
+	for (const SLiMEidosBlock *script_block : script_blocks_)
 	{
 		std::cout << "      ";
 		script_block->Print(std::cout);
@@ -1124,7 +1124,7 @@ void Community::DeregisterScheduledScriptBlocks(void)
 	if (scheduled_deregistrations_.size())
 	{
 		std::cout << "Tick " << tick_ << ": DeregisterScheduledScriptBlocks() planning to remove:" << std::endl;
-		for (SLiMEidosBlock *script_block : scheduled_deregistrations_)
+		for (const SLiMEidosBlock *script_block : scheduled_deregistrations_)
 		{
 			std::cout << "      ";
 			script_block->Print(std::cout);
@@ -1167,7 +1167,7 @@ void Community::DeregisterScheduledScriptBlocks(void)
 	if (scheduled_deregistrations_.size())
 	{
 		std::cout << "Tick " << tick_ << ": DeregisterScheduledScriptBlocks() after removal:" << std::endl;
-		for (SLiMEidosBlock *script_block : script_blocks_)
+		for (const SLiMEidosBlock *script_block : script_blocks_)
 		{
 			std::cout << "      ";
 			script_block->Print(std::cout);
@@ -1186,7 +1186,7 @@ void Community::DeregisterScheduledInteractionBlocks(void)
 	if (scheduled_interaction_deregs_.size())
 	{
 		std::cout << "Tick " << tick_ << ": DeregisterScheduledInteractionBlocks() planning to remove:" << std::endl;
-		for (SLiMEidosBlock *script_block : scheduled_interaction_deregs_)
+		for (const SLiMEidosBlock *script_block : scheduled_interaction_deregs_)
 		{
 			std::cout << "      ";
 			script_block->Print(std::cout);
@@ -1229,7 +1229,7 @@ void Community::DeregisterScheduledInteractionBlocks(void)
 	if (scheduled_interaction_deregs_.size())
 	{
 		std::cout << "Tick " << tick_ << ": DeregisterScheduledInteractionBlocks() after removal:" << std::endl;
-		for (SLiMEidosBlock *script_block : script_blocks_)
+		for (const SLiMEidosBlock *script_block : script_blocks_)
 		{
 			std::cout << "      ";
 			script_block->Print(std::cout);
@@ -1269,12 +1269,12 @@ bool Community::SubpopulationIDInUse(slim_objectid_t p_subpop_id)
 	// been used, or is reserved for use in some way by, by any SLiM species or by any tree sequence.
 
 	// First check our own data structures; we now do not allow reuse of subpop ids, even disjoint in time
-	for (Species *species : all_species_)
+	for (const Species *species : all_species_)
 		if (species->used_subpop_ids_.find(p_subpop_id) != species->used_subpop_ids_.end())
 			return true;
 
 	// Then have each species check for a conflict with its tree-sequence population table
-	for (Species *species : all_species_)
+	for (const Species *species : all_species_)
 		if (species->_SubpopulationIDInUse(p_subpop_id))
 			return true;
 
@@ -1287,7 +1287,7 @@ bool Community::SubpopulationNameInUse(const std::string &p_subpop_name)
 	// been used, or is reserved for use in some way by, by any SLiM species or by any tree sequence.
 
 	// First check our own data structures; we now do not allow reuse of subpop names, even disjoint in time
-	for (Species *species : all_species_)
+	for (const Species *species : all_species_)
 		if (species->used_subpop_names_.count(p_subpop_name))
 			return true;
 
@@ -1298,7 +1298,7 @@ bool Community::SubpopulationNameInUse(const std::string &p_subpop_name)
 
 Subpopulation *Community::SubpopulationWithID(slim_objectid_t p_subpop_id)
 {
-	for (Species *species : all_species_)
+	for (const Species *species : all_species_)
 	{
 		Subpopulation *found_subpop = species->SubpopulationWithID(p_subpop_id);
 
@@ -1311,7 +1311,7 @@ Subpopulation *Community::SubpopulationWithID(slim_objectid_t p_subpop_id)
 
 Subpopulation *Community::SubpopulationWithName(const std::string &p_subpop_name)
 {
-	for (Species *species : all_species_)
+	for (const Species *species : all_species_)
 	{
 		Subpopulation *found_subpop = species->SubpopulationWithName(p_subpop_name);
 
@@ -1324,7 +1324,7 @@ Subpopulation *Community::SubpopulationWithName(const std::string &p_subpop_name
 
 MutationType *Community::MutationTypeWithID(slim_objectid_t p_muttype_id)
 {
-	for (Species *species : all_species_)
+	for (const Species *species : all_species_)
 	{
 		MutationType *found_muttype = species->MutationTypeWithID(p_muttype_id);
 
@@ -1337,7 +1337,7 @@ MutationType *Community::MutationTypeWithID(slim_objectid_t p_muttype_id)
 
 GenomicElementType *Community::GenomicElementTypeWithID(slim_objectid_t p_getype_id)
 {
-	for (Species *species : all_species_)
+	for (const Species *species : all_species_)
 	{
 		GenomicElementType *found_getype = species->GenomicElementTypeWithID(p_getype_id);
 
@@ -2043,7 +2043,7 @@ void Community::FlagUnevaluatedScriptBlockTickRanges()
 
 	std::vector<SLiMEidosBlock*> &script_blocks = AllScriptBlocks();
 
-	for (SLiMEidosBlock *script_block : script_blocks)
+	for (const SLiMEidosBlock *script_block : script_blocks)
 	{
 		if ((script_block->type_ != SLiMEidosBlockType::SLiMEidosInitializeCallback) &&
 			!script_block->tick_range_evaluated_)
@@ -2063,7 +2063,7 @@ slim_tick_t Community::FirstTick(void)
 
 	// Figure out our first tick; it is the earliest tick in which an Eidos event is set up to run,
 	// since an Eidos event that adds a subpopulation is necessary to get things started
-	for (SLiMEidosBlock *script_block : script_blocks)
+	for (const SLiMEidosBlock *script_block : script_blocks)
 	{
 		if ((script_block->type_ == SLiMEidosBlockType::SLiMEidosEventFirst) ||
 			(script_block->type_ == SLiMEidosBlockType::SLiMEidosEventEarly) ||
@@ -2105,7 +2105,7 @@ slim_tick_t Community::EstimatedLastTick(void)
 	// The estimate is derived from the last tick in which an Eidos block is registered.
 	// Any block type works, since the simulation could plausibly be stopped within a callback.
 	// However, blocks that do not specify an end tick don't count.
-	for (SLiMEidosBlock *script_block : script_blocks)
+	for (const SLiMEidosBlock *script_block : script_blocks)
 	{
 		if (script_block->tick_range_is_sequence_)
 		{
@@ -2235,7 +2235,7 @@ bool Community::_RunOneTick(void)
 		gSLiMScheduling << "# tick " << tick_ << ": ";
 		bool first_species = true;
 
-		for (Species *species : all_species_)
+		for (const Species *species : all_species_)
 		{
 			if (!first_species)
 				gSLiMScheduling << ", ";
@@ -2360,7 +2360,7 @@ void Community::AllSpecies_RunInitializeCallbacks(void)
 	DeregisterScheduledScriptBlocks();
 
 	// compile results from initialization into our overall state
-	for (Species *species : all_species_)
+	for (const Species *species : all_species_)
 	{
 		const std::map<slim_objectid_t,MutationType*> &muttypes = species->MutationTypes();
 		const std::map<slim_objectid_t,GenomicElementType*> &getypes = species->GenomicElementTypes();
@@ -2548,15 +2548,15 @@ void Community::AllSpecies_CheckIntegrity(void)
 {
 #if DEBUG
 	// Check the integrity of all the information in the individuals and haplosomes of the parental population
-	for (Species *species : all_species_)
+	for (const Species *species : all_species_)
 		species->Species_CheckIntegrity();
 #endif
 
 #if DEBUG
 	// Check for species consistency across all of the objects in each species
 	for (size_t species_index = 0; species_index < all_species_.size(); ++species_index)
 	{
-		Species *species = all_species_[species_index];
+		const Species *species = all_species_[species_index];
 
 		if (&species->community_ != this)
 			EIDOS_TERMINATION << "ERROR (Community::AllSpecies_CheckIntegrity): (internal error) species->community_ mismatch." << EidosTerminate();
@@ -2567,7 +2567,7 @@ void Community::AllSpecies_CheckIntegrity(void)
 		if (species->species_id_ != (int)species_index)
 			EIDOS_TERMINATION << "ERROR (Community::AllSpecies_CheckIntegrity): (internal error) species->species_id_ mismatch." << EidosTerminate();
 
-		for (Chromosome *chromosome : species->Chromosomes())
+		for (const Chromosome *chromosome : species->Chromosomes())
 		{
 			if (&chromosome->species_ != species)
 				EIDOS_TERMINATION << "ERROR (Community::AllSpecies_CheckIntegrity): (internal error) chromosome->species_ mismatch." << EidosTerminate();
@@ -2576,7 +2576,7 @@ void Community::AllSpecies_CheckIntegrity(void)
 				EIDOS_TERMINATION << "ERROR (Community::AllSpecies_CheckIntegrity): (internal error) chromosome->community_ mismatch." << EidosTerminate();
 		}
 
-		Population &population = species->population_;
+		const Population &population = species->population_;
 		const std::map<slim_objectid_t,MutationType*> &muttypes = species->MutationTypes();
 		const std::map<slim_objectid_t,GenomicElementType*> &getypes = species->GenomicElementTypes();
 
@@ -2604,9 +2604,9 @@ void Community::AllSpecies_CheckIntegrity(void)
 		return;
 #endif
 
-	for (Species *species : all_species_)
+	for (const Species *species : all_species_)
 	{
-		for (Chromosome *chromosome : species->Chromosomes())
+		for (const Chromosome *chromosome : species->Chromosomes())
 		{
 			// Check the integrity of the mutation registry; all MutationIndex values should be in range
 			int registry_size;
@@ -2945,7 +2945,7 @@ bool Community::_RunOneTickWF(void)
 #if DEBUG
 		// now that fitness calculations are done, do a crosscheck of all trait values
 		// this is disabled by a global flag while we are running some self-tests
-		for (Species *species : all_species_)
+		for (const Species *species : all_species_)
 			species->CrosscheckAllTraitValues();
 #endif
 
@@ -3255,7 +3255,7 @@ bool Community::_RunOneTickNonWF(void)
 
 #if DEBUG
 		// now that fitness calculations are done, do a crosscheck of all trait values
-		for (Species *species : all_species_)
+		for (const Species *species : all_species_)
 			species->CrosscheckAllTraitValues();
 #endif
 
@@ -3502,7 +3502,7 @@ void Community::TabulateSLiMMemoryUsage_Community(SLiMMemoryUsage_Community *p_u
 	p_usage->mutationPerTraitBuffer = 0.0;
 	p_usage->mutationUnusedPoolSpace = 0.0;
 
-	for (Species *species : all_species_)
+	for (const Species *species : all_species_)
 	{
 		if (species->HasGenetics())
 		{