add subpopulationsWithNames() to Community

QtSLiM/help/SLiMHelpClasses.html

@@ -5,7 +5,7 @@
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   <meta name="Generator" content="Cocoa HTML Writer">
-  <meta name="CocoaVersion" content="2299.5">
+  <meta name="CocoaVersion" content="2299.77">
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@@ -221,6 +221,8 @@
 <p class="p6">Find and return the <span class="s1">Species</span> objects with <span class="s1">id</span> values matching the values in <span class="s1">ids</span>.<span class="Apple-converted-space">  </span>If no matching <span class="s1">Species</span> object can be found with a given <span class="s1">id</span>, an error results.</p>
 <p class="p5">– (object&lt;Subpopulation&gt;)subpopulationsWithIDs(integer ids)</p>
 <p class="p6">Find and return the <span class="s1">Subpopulation</span> objects with <span class="s1">id</span> values matching the values in <span class="s1">ids</span>.<span class="Apple-converted-space">  </span>If no matching <span class="s1">Subpopulation</span> object can be found with a given <span class="s1">id</span>, an error results.</p>
+<p class="p5">– (object&lt;Subpopulation&gt;)subpopulationsWithNames(string names)</p>
+<p class="p6">Find and return the <span class="s1">Subpopulation</span> objects with <span class="s1">name</span> values matching the values in <span class="s1">names</span>.<span class="Apple-converted-space">  </span>If no matching <span class="s1">Subpopulation</span> object can be found with a given name, an error results.</p>
 <p class="p5">– (float$)usage(void)</p>
 <p class="p6">Return the current memory usage of the simulation.<span class="Apple-converted-space">  </span>The specifics of what is totalled up should not be relied upon as it may change from version to version of SLiM.<span class="Apple-converted-space">  </span>This method is primarily useful for understanding where the memory usage of a simulation predominantly resides, for debugging or optimization.<span class="Apple-converted-space">  </span>Note that it does not capture <i>all</i> memory usage by the process; rather, it summarizes the memory usage by SLiM and Eidos in directly allocated objects and buffers.<span class="Apple-converted-space">  </span>To see details of this internal memory usage, use the <span class="s1">Community</span> method <span class="s1">outputUsage()</span>.<span class="Apple-converted-space">  </span>To get the <i>total</i> memory usage of the running process (either current or peak), use the Eidos function <span class="s1">usage()</span>.</p>
 <p class="p1"><b>5.4<span class="Apple-converted-space">  </span>Class Genome</b></p>

SLiMgui/SLiMHelpClasses.rtf

@@ -1352,6 +1352,20 @@ Note that new script blocks can also be created and scheduled using the
 \f4\fs20 , an error results.\
 \pard\pardeftab397\li720\fi-446\ri720\sb180\sa60\partightenfactor0
 
+\f3\fs18 \cf2 \'96\'a0(object<Subpopulation>)subpopulationsWithNames(string\'a0names)\
+\pard\pardeftab720\li547\ri720\sb60\sa60\partightenfactor0
+
+\f4\fs20 \cf2 Find and return the 
+\f3\fs18 Subpopulation
+\f4\fs20  objects with 
+\f3\fs18 name
+\f4\fs20  values matching the values in 
+\f3\fs18 names
+\f4\fs20 .  If no matching 
+\f3\fs18 Subpopulation
+\f4\fs20  object can be found with a given name, an error results.\
+\pard\pardeftab397\li720\fi-446\ri720\sb180\sa60\partightenfactor0
+
 \f3\fs18 \cf2 \'96\'a0(float$)usage(void)\
 \pard\pardeftab720\li547\ri720\sb60\sa60\partightenfactor0
 

VERSIONS

@@ -7,6 +7,8 @@ Note that not every commit will be logged here; that is what the Github commit h
 
 development head (in the master branch):
 	fixed a bug in calcWattersonsTheta(): the value calculated would be incorrect if a window (start/end) was specified
+	added TOC I and TOC II to the PDF index of the SLiM manual; removed the bottom-of-page links section, which made search difficult
+	add subpopulationsWithNames() method to Community, to facilitate being able to use user-defined names for subpops
 
 
 version 4.2.2 (Eidos version 3.2.2):

core/community.cpp

@@ -1233,6 +1233,19 @@ Subpopulation *Community::SubpopulationWithID(slim_objectid_t p_subpop_id)
 	return nullptr;
 }
 
+Subpopulation *Community::SubpopulationWithName(const std::string &p_subpop_name)
+{
+	for (Species *species : all_species_)
+	{
+		Subpopulation *found_subpop = species->SubpopulationWithName(p_subpop_name);
+
+		if (found_subpop)
+			return found_subpop;
+	}
+
+	return nullptr;
+}
+
 MutationType *Community::MutationTypeWithID(slim_objectid_t p_muttype_id)
 {
 	for (Species *species : all_species_)

core/community.h

@@ -219,6 +219,7 @@ class Community : public EidosDictionaryUnretained
 	bool SubpopulationNameInUse(const std::string &p_subpop_name);					// not whether a SLiM subpop with this name currently exists, but whether the name is "in use"
 
 	Subpopulation *SubpopulationWithID(slim_objectid_t p_subpop_id);
+	Subpopulation *SubpopulationWithName(const std::string &p_subpop_name);
 	MutationType *MutationTypeWithID(slim_objectid_t p_muttype_id);
 	GenomicElementType *GenomicElementTypeWithID(slim_objectid_t p_getype_id);
 	SLiMEidosBlock *ScriptBlockWithID(slim_objectid_t p_script_block_id);
@@ -366,6 +367,7 @@ class Community : public EidosDictionaryUnretained
 	EidosValue_SP ExecuteMethod_scriptBlocksWithIDs(EidosGlobalStringID p_method_id, const std::vector<EidosValue_SP> &p_arguments, EidosInterpreter &p_interpreter);
 	EidosValue_SP ExecuteMethod_speciesWithIDs(EidosGlobalStringID p_method_id, const std::vector<EidosValue_SP> &p_arguments, EidosInterpreter &p_interpreter);
 	EidosValue_SP ExecuteMethod_subpopulationsWithIDs(EidosGlobalStringID p_method_id, const std::vector<EidosValue_SP> &p_arguments, EidosInterpreter &p_interpreter);
+	EidosValue_SP ExecuteMethod_subpopulationsWithNames(EidosGlobalStringID p_method_id, const std::vector<EidosValue_SP> &p_arguments, EidosInterpreter &p_interpreter);
 	EidosValue_SP ExecuteMethod_outputUsage(EidosGlobalStringID p_method_id, const std::vector<EidosValue_SP> &p_arguments, EidosInterpreter &p_interpreter);
 	EidosValue_SP ExecuteMethod_registerFirstEarlyLateEvent(EidosGlobalStringID p_method_id, const std::vector<EidosValue_SP> &p_arguments, EidosInterpreter &p_interpreter);
 	EidosValue_SP ExecuteMethod_registerInteractionCallback(EidosGlobalStringID p_method_id, const std::vector<EidosValue_SP> &p_arguments, EidosInterpreter &p_interpreter);

core/community_eidos.cpp

@@ -556,6 +556,7 @@ EidosValue_SP Community::ExecuteInstanceMethod(EidosGlobalStringID p_method_id,
 		case gID_scriptBlocksWithIDs:			return ExecuteMethod_scriptBlocksWithIDs(p_method_id, p_arguments, p_interpreter);
 		case gID_speciesWithIDs:				return ExecuteMethod_speciesWithIDs(p_method_id, p_arguments, p_interpreter);
 		case gID_subpopulationsWithIDs:			return ExecuteMethod_subpopulationsWithIDs(p_method_id, p_arguments, p_interpreter);
+		case gID_subpopulationsWithNames:		return ExecuteMethod_subpopulationsWithNames(p_method_id, p_arguments, p_interpreter);
 		case gID_outputUsage:					return ExecuteMethod_outputUsage(p_method_id, p_arguments, p_interpreter);
 		case gID_registerFirstEvent:
 		case gID_registerEarlyEvent:
@@ -872,6 +873,30 @@ EidosValue_SP Community::ExecuteMethod_subpopulationsWithIDs(EidosGlobalStringID
 	return EidosValue_SP(vec);
 }
 
+//	*********************	– (object<Subpopulation>)subpopulationsWithNames(string names)
+//
+EidosValue_SP Community::ExecuteMethod_subpopulationsWithNames(EidosGlobalStringID p_method_id, const std::vector<EidosValue_SP> &p_arguments, EidosInterpreter &p_interpreter)
+{
+#pragma unused (p_method_id, p_interpreter)
+	EidosValue *names_value = p_arguments[0].get();
+	int names_count = names_value->Count();
+	const std::string *names_data = names_value->StringData();
+	EidosValue_Object *vec = (new (gEidosValuePool->AllocateChunk()) EidosValue_Object(gSLiM_Subpopulation_Class))->resize_no_initialize_RR(names_count);
+
+	for (int name_index = 0; name_index < names_count; name_index++)
+	{
+		const std::string &name = names_data[name_index];
+		Subpopulation *object = SubpopulationWithName(name);
+
+		if (!object)
+			EIDOS_TERMINATION << "ERROR (Community::ExecuteMethod_subpopulationsWithNames): subpopulationsWithNames() did not find a subpopulation with name " << name << "." << EidosTerminate();
+
+		vec->set_object_element_no_check_NORR(object, name_index);
+	}
+
+	return EidosValue_SP(vec);
+}
+
 //	*********************	– (void)outputUsage(void)
 //
 EidosValue_SP Community::ExecuteMethod_outputUsage(EidosGlobalStringID p_method_id, const std::vector<EidosValue_SP> &p_arguments, EidosInterpreter &p_interpreter)
@@ -1396,6 +1421,7 @@ const std::vector<EidosMethodSignature_CSP> *Community_Class::Methods(void) cons
 		methods->emplace_back((EidosInstanceMethodSignature *)(new EidosInstanceMethodSignature(gStr_simulationFinished, kEidosValueMaskVOID)));
 		methods->emplace_back((EidosInstanceMethodSignature *)(new EidosInstanceMethodSignature(gStr_speciesWithIDs, kEidosValueMaskObject, gSLiM_Species_Class))->AddInt("ids"));
 		methods->emplace_back((EidosInstanceMethodSignature *)(new EidosInstanceMethodSignature(gStr_subpopulationsWithIDs, kEidosValueMaskObject, gSLiM_Subpopulation_Class))->AddInt("ids"));
+		methods->emplace_back((EidosInstanceMethodSignature *)(new EidosInstanceMethodSignature(gStr_subpopulationsWithNames, kEidosValueMaskObject, gSLiM_Subpopulation_Class))->AddString("names"));
 		methods->emplace_back((EidosInstanceMethodSignature *)(new EidosInstanceMethodSignature(gEidosStr_usage, kEidosValueMaskFloat | kEidosValueMaskSingleton)));
 
 		std::sort(methods->begin(), methods->end(), CompareEidosCallSignatures);

core/slim_globals.cpp

@@ -1310,6 +1310,7 @@ const std::string &gStr_mutationTypesWithIDs = EidosRegisteredString("mutationTy
 const std::string &gStr_scriptBlocksWithIDs = EidosRegisteredString("scriptBlocksWithIDs", gID_scriptBlocksWithIDs);
 const std::string &gStr_speciesWithIDs = EidosRegisteredString("speciesWithIDs", gID_speciesWithIDs);
 const std::string &gStr_subpopulationsWithIDs = EidosRegisteredString("subpopulationsWithIDs", gID_subpopulationsWithIDs);
+const std::string &gStr_subpopulationsWithNames = EidosRegisteredString("subpopulationsWithNames", gID_subpopulationsWithNames);
 const std::string &gStr_individualsWithPedigreeIDs = EidosRegisteredString("individualsWithPedigreeIDs", gID_individualsWithPedigreeIDs);
 const std::string &gStr_killIndividuals = EidosRegisteredString("killIndividuals", gID_killIndividuals);
 const std::string &gStr_mutationCounts = EidosRegisteredString("mutationCounts", gID_mutationCounts);

core/slim_globals.h

@@ -904,6 +904,7 @@ extern const std::string &gStr_mutationTypesWithIDs;
 extern const std::string &gStr_scriptBlocksWithIDs;
 extern const std::string &gStr_speciesWithIDs;
 extern const std::string &gStr_subpopulationsWithIDs;
+extern const std::string &gStr_subpopulationsWithNames;
 extern const std::string &gStr_individualsWithPedigreeIDs;
 extern const std::string &gStr_killIndividuals;
 extern const std::string &gStr_mutationCounts;
@@ -1320,6 +1321,7 @@ enum _SLiMGlobalStringID : int {
 	gID_scriptBlocksWithIDs,
 	gID_speciesWithIDs,
 	gID_subpopulationsWithIDs,
+	gID_subpopulationsWithNames,
 	gID_individualsWithPedigreeIDs,
 	gID_killIndividuals,
 	gID_mutationCounts,

core/species.cpp

@@ -1787,6 +1787,16 @@ void Species::DeleteAllMutationRuns(void)
 	}
 }
 
+Subpopulation *Species::SubpopulationWithName(const std::string &p_subpop_name) {
+	for (auto subpop_iter : population_.subpops_)
+	{
+		Subpopulation *subpop = subpop_iter.second;
+		if (subpop->name_ == p_subpop_name)
+			return subpop;
+	}
+	return nullptr;
+}
+
 
 //
 // Running cycles

core/species.h

@@ -516,6 +516,7 @@ class Species : public EidosDictionaryUnretained
 		auto id_iter = population_.subpops_.find(p_subpop_id);
 		return (id_iter == population_.subpops_.end()) ? nullptr : id_iter->second;
 	}
+	Subpopulation *SubpopulationWithName(const std::string &p_subpop_name);
 	inline MutationType *MutationTypeWithID(slim_objectid_t p_muttype_id) {
 		auto id_iter = mutation_types_.find(p_muttype_id);
 		return (id_iter == mutation_types_.end()) ? nullptr : id_iter->second;