recombination() callbacks can now have a chromosome specifier

Author: bhaller

QtSLiM/QtSLiMScriptTextEdit.cpp

@@ -989,7 +989,7 @@ void QtSLiMTextEdit::updateStatusFieldFromSelection(void)
             else if (callName == "recombination")
             {
                 static EidosCallSignature_CSP callbackSig = nullptr;
-                if (!callbackSig) callbackSig = EidosCallSignature_CSP((new EidosFunctionSignature("recombination", nullptr, kEidosValueMaskLogical | kEidosValueMaskSingleton))->AddObject_OS("subpop", gSLiM_Subpopulation_Class, gStaticEidosValueNULLInvisible));
+                if (!callbackSig) callbackSig = EidosCallSignature_CSP((new EidosFunctionSignature("recombination", nullptr, kEidosValueMaskLogical | kEidosValueMaskSingleton))->AddObject_OS("subpop", gSLiM_Subpopulation_Class, gStaticEidosValueNULLInvisible)->AddIntString_OSN("chromosome", gStaticEidosValueNULLInvisible));
                 signature = callbackSig;
             }
             else if (callName == "survival")

QtSLiM/help/SLiMHelpCallbacks.html

@@ -189,8 +189,8 @@
 <p class="p1"><i>5.13.6<span class="Apple-converted-space">  </span>ITEM: 7. </i><span class="s1"><i>recombination()</i></span><i> callbacks</i></p>
 <p class="p2">Typically, a simulation sets up a recombination map at the beginning of the run with <span class="s1">initializeRecombinationRate()</span>, and that map is used for the duration of the run.<span class="Apple-converted-space">  </span>Less commonly, the recombination map is changed dynamically from tick to tick, with <span class="s1">Chromosome</span>’s method <span class="s1">setRecombinationRate()</span>; but still, a single recombination map applies for all individuals of a species in a given tick.<span class="Apple-converted-space">  </span>However, in unusual circumstances a simulation may need to modify the way that recombination works on an individual basis; for this, the <span class="s1">recombination()</span> callback mechanism is provided.<span class="Apple-converted-space">  </span>This can be useful for models involving chromosomal inversions that prevent recombination within a region for some individuals, for example, or for models of the evolution of recombination.</p>
 <p class="p2">A <span class="s1">recombination()</span> callback is defined with a syntax much like that of other callbacks:</p>
-<p class="p3">[id] [t1 [: t2]] recombination([&lt;subpop-id&gt;]) { ... }</p>
-<p class="p2">The <span class="s1">recombination()</span> callback will be called during the generation of every gamete during the tick(s) in which it is active.<span class="Apple-converted-space">  </span>It may optionally be restricted to apply only to gametes generated by parents in a specified subpopulation, using the <span class="s1">&lt;subpop-id&gt;</span> specifier.<span class="Apple-converted-space">  </span>(In multispecies models, the definition must be preceded by a <span class="s1">species</span> specification as usual.)</p>
+<p class="p3">[id] [t1 [: t2]] recombination([&lt;subpop-id&gt; [, &lt;chromosome-id&gt;]]) { ... }</p>
+<p class="p2">The <span class="s1">recombination()</span> callback will be called during the generation of every gamete during the tick(s) in which it is active.<span class="Apple-converted-space">  </span>It may optionally be restricted to apply only to gametes generated by parents in a specified subpopulation, using the <span class="s1">&lt;subpop-id&gt;</span> specifier.<span class="Apple-converted-space">  </span>In addition, in multi-chromosome models it may optionally be restricted to apply only to a specified chromosome, using the <span class="s1">&lt;chromosome-id&gt;</span> specifier, which may be either the <span class="s1">id</span> or the <span class="s1">symbol</span> of a chromosome defined in the species.<span class="Apple-converted-space">  </span>(In multispecies models, the definition must be preceded by a <span class="s1">species</span> specification as usual.)</p>
 <p class="p2">When a <span class="s1">recombination()</span> callback is called, a parent has already been chosen to generate a gamete, and candidate recombination breakpoints for use in recombining the parental haplosomes have been drawn.<span class="Apple-converted-space">  </span>The relevant haplosomes of the focal parent are provided to the callback, as is the focal parent itself (as an <span class="s1">Individual</span> object) and the subpopulation in which it resides.<span class="Apple-converted-space">  </span>Furthermore, the proposed breakpoints are provided to the callback.<span class="Apple-converted-space">  </span>The callback may modify these breakpoints in order to change the breakpoints used, in which case it must return <span class="s1">T</span> to indicate that changes were made, or it may leave the proposed breakpoints unmodified, in which case it must return <span class="s1">F</span>.<span class="Apple-converted-space">  </span>(The behavior of SLiM is undefined if the callback returns the wrong <span class="s1">logical</span> value.)</p>
 <p class="p2">In addition to the standard SLiM globals, then, a <span class="s1">recombination()</span> callback is supplied with additional information passed through “pseudo-parameters”:</p>
 <p class="p9"><span class="s1">individual</span><span class="Apple-tab-span">	</span>The focal parent that is generating a gamete</p>

QtSLiM/help/SLiMHelpClasses.html

@@ -922,14 +922,20 @@ A
 \f2\fs22  callback is defined with a syntax much like that of other callbacks:\
 \pard\tx990\tx1260\tx1530\tx1800\tx2070\tx2340\tx2610\tx2880\tx3150\tx3420\pardeftab720\li547\ri720\sb180\sa180\partightenfactor0
 
-\f3\fs18 \cf2 [id] [t1 [: t2]] recombination([<subpop-id>]) \{ ... \}\
+\f3\fs18 \cf2 [id] [t1 [: t2]] recombination([<subpop-id> [, <chromosome-id>]]) \{ ... \}\
 \pard\pardeftab397\fi274\ri720\sb40\sa40\partightenfactor0
 
 \f2\fs22 \cf2 The 
 \f3\fs18 recombination()
 \f2\fs22  callback will be called during the generation of every gamete during the tick(s) in which it is active.  It may optionally be restricted to apply only to gametes generated by parents in a specified subpopulation, using the 
 \f3\fs18 <subpop-id>
-\f2\fs22  specifier.  (In multispecies models, the definition must be preceded by a 
+\f2\fs22  specifier.  In addition, in multi-chromosome models it may optionally be restricted to apply only to a specified chromosome, using the 
+\f3\fs18 <chromosome-id>
+\f2\fs22  specifier, which may be either the 
+\f3\fs18 id
+\f2\fs22  or the 
+\f3\fs18 symbol
+\f2\fs22  of a chromosome defined in the species.  (In multispecies models, the definition must be preceded by a 
 \f3\fs18 species
 \f2\fs22  specification as usual.)\
 When a 

SLiMgui/SLiMHelpCallbacks.rtf

@@ -9056,16 +9056,16 @@ After this call, the fitness values used for all purposes in SLiM will be the ne
 
 \f3\fs18 \cf0 \'96\'a0(object<SLiMEidosBlock>$)registerRecombinationCallback(Nis$\'a0id, string$\'a0source, [Nio<Subpopulation>$\'a0subpop
 \f5 \'a0
-\f3 =\'a0NULL], [Ni$\'a0start\'a0=\'a0NULL], [Ni$\'a0end\'a0=\'a0NULL])\
+\f3 =\'a0NULL], [Ni$\'a0start\'a0=\'a0NULL], [Ni$\'a0end\'a0=\'a0NULL]\cf2 , [Niso<Chromosome>$\'a0chromosome\'a0=\'a0NULL]\cf0 )\
 \pard\pardeftab720\li547\ri720\sb60\sa60\partightenfactor0
 
-\f4\fs20 \cf0 Register a block of Eidos source code, represented as the 
+\f4\fs20 \cf2 Register a block of Eidos source code, represented as the 
 \f3\fs18 string
 \f4\fs20  singleton 
 \f3\fs18 source
 \f4\fs20 , as an Eidos 
 \f3\fs18 recombination()
-\f4\fs20  callback in the current simulation\cf2  (specific to the target species)\cf0 , with optional subpopulation 
+\f4\fs20  callback in the current simulation (specific to the target species), with optional subpopulation 
 \f3\fs18 subpop
 \f4\fs20  (which may be an 
 \f3\fs18 integer
@@ -9075,7 +9075,19 @@ After this call, the fitness values used for all purposes in SLiM will be the ne
 \f3\fs18 start
 \f4\fs20  and 
 \f3\fs18 end
-\f4\fs20  ticks all limiting its applicability.  The script block will be given identifier 
+\f4\fs20  ticks all limiting its applicability.  In multi-chromosome models, parameter 
+\f3\fs18 chromosome
+\f4\fs20 , if non-
+\f3\fs18 NULL
+\f4\fs20 , may specify a chromosome to which the callback will apply (as either an 
+\f3\fs18 integer
+\f4\fs20  id, a 
+\f3\fs18 string
+\f4\fs20  symbol, or a 
+\f3\fs18 Chromosome
+\f4\fs20  object); otherwise, 
+\f3\fs18 NULL
+\f4\fs20  indicates that the callback applies to all chromosomes.  The script block will be given identifier 
 \f3\fs18 id
 \f4\fs20  (specified as an 
 \f3\fs18 integer
@@ -9089,10 +9101,9 @@ After this call, the fitness values used for all purposes in SLiM will be the ne
 \f3\fs18 SLiMEidosBlock
 \f4\fs20  objects, and is active immediately; it 
 \f1\i may
-\f4\i0  be eligible to execute in the current tick.  The new 
+\f4\i0  be eligible to execute in the current tick (see section 26.11 for details).  The new 
 \f3\fs18 SLiMEidosBlock
-\f4\fs20  will be defined as a global variable immediately by this method, and will also be returned by this method.
-\f5 \
+\f4\fs20  will be defined as a global variable immediately by this method (see section 25.13), and will also be returned by this method.\
 \pard\pardeftab720\li720\fi-446\ri720\sb180\sa60\partightenfactor0
 
 \f3\fs18 \cf0 \'96\'a0(object<SLiMEidosBlock>$)registerReproductionCallback(Nis$\'a0id, string$\'a0source, [Nio<Subpopulation>$\'a0subpop
@@ -9272,7 +9283,9 @@ Register a block of Eidos source code, represented as the
 \f3\fs18 NULL
 \f4\fs20 , may specify a required value for the 
 \f3\fs18 id
-\f4\fs20  property of the mutations to be returned.  Parameter chromosome, if non-
+\f4\fs20  property of the mutations to be returned.  Parameter 
+\f3\fs18 chromosome
+\f4\fs20 , if non-
 \f3\fs18 NULL
 \f4\fs20 , may specify a chromosome with which the mutations returned must be associated (as either an 
 \f3\fs18 integer

SLiMgui/SLiMHelpClasses.rtf

@@ -4223,7 +4223,7 @@ - (void)updateStatusFieldFromSelection
 			static EidosCallSignature_CSP callbackSig = nullptr;
 
 			if (!callbackSig)
-				callbackSig = EidosCallSignature_CSP((new EidosFunctionSignature("recombination", nullptr, kEidosValueMaskLogical | kEidosValueMaskSingleton))->AddObject_OS("subpop", gSLiM_Subpopulation_Class, gStaticEidosValueNULLInvisible));
+				callbackSig = EidosCallSignature_CSP((new EidosFunctionSignature("recombination", nullptr, kEidosValueMaskLogical | kEidosValueMaskSingleton))->AddObject_OS("subpop", gSLiM_Subpopulation_Class, gStaticEidosValueNULLInvisible)->AddIntString_OSN("chromosome", gStaticEidosValueNULLInvisible));
 
 			sig = callbackSig.get();
 		}

SLiMgui/SLiMWindowController.mm

@@ -107,6 +107,8 @@ development head (in the master branch):
 		update calcHeterozygosity() for multi-chromosome support (but it assesses heterozygosity for only a single chromosome, for now)
 		new PAR (pseudo-autosomal region) recipe for section 15.23, replacing the old recipe in section 14.5 (which will be moved to SLiM-Extras for posterity)
 		new recipe 9.11 (Ne estimation) with a new multichrom-aware version of function estimateNe_Heterozygosity() that requires the chromosome to be supplied
+		recombination() callbacks can now be optionally declared with a chromosome specifier (id or symbol), to apply to just one chromosome
+			registerRecombinationCallback() now takes an optional chromosome parameter to specify that focal chromosome
 
 
 version 4.3 (Eidos version 3.3):

VERSIONS

@@ -1709,7 +1709,7 @@ void Chromosome::DrawBreakpoints(Individual *p_parent, Haplosome *p_haplosome1,
 	{
 		parent_sex = p_parent->sex_;
 		parent_subpop = p_parent->subpopulation_;
-		recombination_callbacks = species_.CallbackBlocksMatching(community_.Tick(), SLiMEidosBlockType::SLiMEidosRecombinationCallback, -1, -1, parent_subpop->subpopulation_id_);
+		recombination_callbacks = species_.CallbackBlocksMatching(community_.Tick(), SLiMEidosBlockType::SLiMEidosRecombinationCallback, -1, -1, parent_subpop->subpopulation_id_, id_);
 
 		// SPECIES CONSISTENCY CHECK
 		if (&p_parent->subpopulation_->species_ != &species_)

core/chromosome.cpp

@@ -557,7 +557,7 @@ void Community::ValidateScriptBlockCaches(void)
 	}
 }
 
-std::vector<SLiMEidosBlock*> Community::ScriptBlocksMatching(slim_tick_t p_tick, SLiMEidosBlockType p_event_type, slim_objectid_t p_mutation_type_id, slim_objectid_t p_interaction_type_id, slim_objectid_t p_subpopulation_id, Species *p_species)
+std::vector<SLiMEidosBlock*> Community::ScriptBlocksMatching(slim_tick_t p_tick, SLiMEidosBlockType p_event_type, slim_objectid_t p_mutation_type_id, slim_objectid_t p_interaction_type_id, slim_objectid_t p_subpopulation_id, int64_t p_chromosome_id, Species *p_species)
 {
 	if (!script_block_types_cached_)
 		ValidateScriptBlockCaches();
@@ -639,6 +639,15 @@ std::vector<SLiMEidosBlock*> Community::ScriptBlocksMatching(slim_tick_t p_tick,
 				continue;
 		}
 
+		// check that the chromosome id matches, if requested
+		if (p_chromosome_id != -1)
+		{
+			int64_t chromosome_id = script_block->chromosome_id_;
+			
+			if ((chromosome_id != -1) && (p_chromosome_id != chromosome_id))
+				continue;
+		}
+		
 		// check that the species matches; this check is always on, nullptr means check that the species is nullptr
 		if (p_species != script_block->species_spec_)
 			continue;
@@ -1032,6 +1041,9 @@ void Community::AddScriptBlock(SLiMEidosBlock *p_script_block, EidosInterpreter
 		if (p_script_block->subpopulation_id_ != -1)
 			EIDOS_TERMINATION << "ERROR (Community::AddScriptBlock): (internal error) script block for a non-callback or initialize() callback has subpopulation_id_ set." << EidosTerminate(p_error_token);
 
+		if (p_script_block->chromosome_id_ != -1)
+			EIDOS_TERMINATION << "ERROR (Community::AddScriptBlock): (internal error) script block for a non-callback or initialize() callback has chromosome_id_ set." << EidosTerminate(p_error_token);
+		
 		if (p_script_block->interaction_type_id_ != -1)
 			EIDOS_TERMINATION << "ERROR (Community::AddScriptBlock): (internal error) script block for a non-callback or initialize() callback has interaction_type_id_ set." << EidosTerminate(p_error_token);
 
@@ -2143,7 +2155,7 @@ void Community::AllSpecies_RunInitializeCallbacks(void)
 	// The zero tick is handled here by shared code, since it is the same for WF and nonWF models
 
 	// execute user-defined function blocks first; no need to profile this, it's just the definitions not the executions
-	std::vector<SLiMEidosBlock*> function_blocks = ScriptBlocksMatching(-1, SLiMEidosBlockType::SLiMEidosUserDefinedFunction, -1, -1, -1, nullptr);
+	std::vector<SLiMEidosBlock*> function_blocks = ScriptBlocksMatching(-1, SLiMEidosBlockType::SLiMEidosUserDefinedFunction, -1, -1, -1, -1, nullptr);
 
 	for (auto script_block : function_blocks)
 		ExecuteFunctionDefinitionBlock(script_block);
@@ -2232,7 +2244,7 @@ void Community::RunInitializeCallbacks(void)
 	num_modeltype_declarations_ = 0;
 
 	// execute `species all` initialize() callbacks, which should always have a tick of 0 set
-	std::vector<SLiMEidosBlock*> init_blocks = ScriptBlocksMatching(0, SLiMEidosBlockType::SLiMEidosInitializeCallback, -1, -1, -1, nullptr);
+	std::vector<SLiMEidosBlock*> init_blocks = ScriptBlocksMatching(0, SLiMEidosBlockType::SLiMEidosInitializeCallback, -1, -1, -1, -1, nullptr);
 
 	for (auto script_block : init_blocks)
 		ExecuteEidosEvent(script_block);
@@ -2470,7 +2482,7 @@ bool Community::_RunOneTickWF(void)
 #endif
 
 		cycle_stage_ = SLiMCycleStage::kWFStage0ExecuteFirstScripts;
-		std::vector<SLiMEidosBlock*> first_blocks = ScriptBlocksMatching(tick_, SLiMEidosBlockType::SLiMEidosEventFirst, -1, -1, -1, nullptr);
+		std::vector<SLiMEidosBlock*> first_blocks = ScriptBlocksMatching(tick_, SLiMEidosBlockType::SLiMEidosEventFirst, -1, -1, -1, -1, nullptr);
 
 		for (auto script_block : first_blocks)
 			ExecuteEidosEvent(script_block);
@@ -2498,7 +2510,7 @@ bool Community::_RunOneTickWF(void)
 #endif
 
 		cycle_stage_ = SLiMCycleStage::kWFStage1ExecuteEarlyScripts;
-		std::vector<SLiMEidosBlock*> early_blocks = ScriptBlocksMatching(tick_, SLiMEidosBlockType::SLiMEidosEventEarly, -1, -1, -1, nullptr);
+		std::vector<SLiMEidosBlock*> early_blocks = ScriptBlocksMatching(tick_, SLiMEidosBlockType::SLiMEidosEventEarly, -1, -1, -1, -1, nullptr);
 
 		for (auto script_block : early_blocks)
 			ExecuteEidosEvent(script_block);
@@ -2647,7 +2659,7 @@ bool Community::_RunOneTickWF(void)
 #endif
 
 		cycle_stage_ = SLiMCycleStage::kWFStage5ExecuteLateScripts;
-		std::vector<SLiMEidosBlock*> late_blocks = ScriptBlocksMatching(tick_, SLiMEidosBlockType::SLiMEidosEventLate, -1, -1, -1, nullptr);
+		std::vector<SLiMEidosBlock*> late_blocks = ScriptBlocksMatching(tick_, SLiMEidosBlockType::SLiMEidosEventLate, -1, -1, -1, -1, nullptr);
 
 		for (auto script_block : late_blocks)
 			ExecuteEidosEvent(script_block);
@@ -2806,7 +2818,7 @@ bool Community::_RunOneTickNonWF(void)
 #endif
 
 		cycle_stage_ = SLiMCycleStage::kNonWFStage0ExecuteFirstScripts;
-		std::vector<SLiMEidosBlock*> first_blocks = ScriptBlocksMatching(tick_, SLiMEidosBlockType::SLiMEidosEventFirst, -1, -1, -1, nullptr);
+		std::vector<SLiMEidosBlock*> first_blocks = ScriptBlocksMatching(tick_, SLiMEidosBlockType::SLiMEidosEventFirst, -1, -1, -1, -1, nullptr);
 
 		for (auto script_block : first_blocks)
 			ExecuteEidosEvent(script_block);
@@ -2934,7 +2946,7 @@ bool Community::_RunOneTickNonWF(void)
 #endif
 
 		cycle_stage_ = SLiMCycleStage::kNonWFStage2ExecuteEarlyScripts;
-		std::vector<SLiMEidosBlock*> early_blocks = ScriptBlocksMatching(tick_, SLiMEidosBlockType::SLiMEidosEventEarly, -1, -1, -1, nullptr);
+		std::vector<SLiMEidosBlock*> early_blocks = ScriptBlocksMatching(tick_, SLiMEidosBlockType::SLiMEidosEventEarly, -1, -1, -1, -1, nullptr);
 
 		for (auto script_block : early_blocks)
 			ExecuteEidosEvent(script_block);
@@ -3079,7 +3091,7 @@ bool Community::_RunOneTickNonWF(void)
 #endif
 
 		cycle_stage_ = SLiMCycleStage::kNonWFStage6ExecuteLateScripts;
-		std::vector<SLiMEidosBlock*> late_blocks = ScriptBlocksMatching(tick_, SLiMEidosBlockType::SLiMEidosEventLate, -1, -1, -1, nullptr);
+		std::vector<SLiMEidosBlock*> late_blocks = ScriptBlocksMatching(tick_, SLiMEidosBlockType::SLiMEidosEventLate, -1, -1, -1, -1, nullptr);
 
 		for (auto script_block : late_blocks)
 			ExecuteEidosEvent(script_block);

core/community.cpp

@@ -205,7 +205,7 @@ class Community : public EidosDictionaryUnretained
 
 	// Managing script blocks; these two methods should be used as a matched pair, bracketing each cycle stage that calls out to script
 	void ValidateScriptBlockCaches(void);
-	std::vector<SLiMEidosBlock*> ScriptBlocksMatching(slim_tick_t p_tick, SLiMEidosBlockType p_event_type, slim_objectid_t p_mutation_type_id, slim_objectid_t p_interaction_type_id, slim_objectid_t p_subpopulation_id, Species *p_species);
+	std::vector<SLiMEidosBlock*> ScriptBlocksMatching(slim_tick_t p_tick, SLiMEidosBlockType p_event_type, slim_objectid_t p_mutation_type_id, slim_objectid_t p_interaction_type_id, slim_objectid_t p_subpopulation_id, int64_t p_chromosome_id, Species *p_species);
 	std::vector<SLiMEidosBlock*> &AllScriptBlocks();
 	std::vector<SLiMEidosBlock*> AllScriptBlocksForSpecies(Species *p_species);
 	void OptimizeScriptBlock(SLiMEidosBlock *p_script_block);