add Species.chromosome back in, as a singleton alias for chromosomes

Author: bhaller

QtSLiM/QtSLiMWindow.cpp

@@ -2001,11 +2001,11 @@ bool QtSLiMWindow::checkTerminationForAutofix(QString terminationMessage)
 
     if (terminationMessage.contains("property chromosome is not defined for object element type Species") &&
             (selectionString == "chromosome"))
-        return offerAndExecuteAutofix(selection, "chromosomes", "The `chromosome` property of Species has been renamed to `chromosomes`.", terminationMessage);
+        return offerAndExecuteAutofix(selection, "chromosomes", "The `chromosome` property of Species has been renamed to `chromosomes`.", terminationMessage);     // actually, this property was left in, for now
 
     if (terminationMessage.contains("property chromosomeType is not defined for object element type Species") &&
             (selectionString == "chromosomeType"))
-        return offerAndExecuteAutofix(selection, "chromosomes.type", "The `chromosomeType` property of Species has been removed; it is now accessed as `chromosomes.type`.", terminationMessage);
+        return offerAndExecuteAutofix(selection, "chromosome.type", "The `chromosomeType` property of Species has been removed; it is now accessed as `chromosome.type`.", terminationMessage);
 
     if (terminationMessage.contains("undefined identifier genome") &&
             (selectionString == "genome"))

QtSLiM/help/SLiMHelpClasses.html

@@ -880,6 +880,8 @@
 <p class="p2"><i>5.16.1<span class="Apple-converted-space">  </span></i><span class="s1"><i>Species</i></span><i> properties</i></p>
 <p class="p5">avatar =&gt; (string$)</p>
 <p class="p6">The avatar string used to represent this species in SLiMgui.<span class="Apple-converted-space">  </span>Outside of SLiMgui, this property still exists, but is not used by SLiM.<span class="Apple-converted-space">  </span>Avatars are typically one-character strings, often using an emoji that symbolizes the species.<span class="Apple-converted-space">  </span>This property is read-only; its value should be set with the <span class="s1">avatar</span> parameter of <span class="s1">initializeSpecies()</span>.</p>
+<p class="p5">chromosome =&gt; (object&lt;Chromosome&gt;$)</p>
+<p class="p6">The <span class="s1">Chromosome</span> object used by the species.<span class="Apple-converted-space">  </span>This property may only be accessed in a single-chromosome model; if there are multiple chromosomes (or none), the <span class="s1">chromosomes</span> property must be used instead.</p>
 <p class="p5">chromosomes =&gt; (object&lt;Chromosome&gt;)</p>
 <p class="p6">The <span class="s1">Chromosome</span> objects used by the species, in the order in which they were defined.<span class="Apple-converted-space">  </span>See also the <span class="s1">sexChromosomes</span> property.</p>
 <p class="p5">color =&gt; (string$)</p>

SLiMgui/SLiMHelpClasses.rtf

@@ -7858,6 +7858,16 @@ The density scale of the kernel has no effect and will be normalized; this is th
 \f4\fs20 .\
 \pard\pardeftab720\li720\fi-446\ri720\sb180\sa60\partightenfactor0
 
+\f3\fs18 \cf2 chromosome => (object<Chromosome>$)\
+\pard\pardeftab720\li547\ri720\sb60\sa60\partightenfactor0
+
+\f4\fs20 \cf2 The 
+\f3\fs18 Chromosome
+\f4\fs20  object used by the species.  This property may only be accessed in a single-chromosome model; if there are multiple chromosomes (or none), the 
+\f3\fs18 chromosomes
+\f4\fs20  property must be used instead.\
+\pard\pardeftab720\li720\fi-446\ri720\sb180\sa60\partightenfactor0
+
 \f3\fs18 \cf2 chromosomes => (object<Chromosome>)\
 \pard\pardeftab720\li547\ri720\sb60\sa60\partightenfactor0
 

VERSIONS

@@ -141,6 +141,7 @@ development head (in the master branch):
 		split chapter 15 (nonWF models) into two chapters, involving a great deal of renumbering, reorganizing, and rewriting
 		add a [Niso<Chromosome]$ chromosome] parameter to relatedness(), to allow relatedness to be assessed for any model chromosome; extended to all chromosome types
 		disable defer=T for all nonWF reproduction methods; it now does the same thing as defer=F (and is documented as having that possibility)
+		add a chromosome property back onto Species, accessible only in single-chromosome models; this makes porting models forward a little easier
 
 
 version 4.3 (Eidos version 3.3):

core/slim_globals.cpp

@@ -1224,7 +1224,6 @@ const std::string &gStr_geneConversionGCBias = EidosRegisteredString("geneConver
 const std::string &gStr_geneConversionNonCrossoverFraction = EidosRegisteredString("geneConversionNonCrossoverFraction", gID_geneConversionNonCrossoverFraction);
 const std::string &gStr_geneConversionMeanLength = EidosRegisteredString("geneConversionMeanLength", gID_geneConversionMeanLength);
 const std::string &gStr_geneConversionSimpleConversionFraction = EidosRegisteredString("geneConversionSimpleConversionFraction", gID_geneConversionSimpleConversionFraction);
-const std::string &gStr_chromosome = EidosRegisteredString("chromosome", gID_chromosome);
 const std::string &gStr_isNullHaplosome = EidosRegisteredString("isNullHaplosome", gID_isNullHaplosome);
 const std::string &gStr_mutations = EidosRegisteredString("mutations", gID_mutations);
 const std::string &gStr_uniqueMutations = EidosRegisteredString("uniqueMutations", gID_uniqueMutations);
@@ -1262,6 +1261,7 @@ const std::string &gStr_allMutationTypes = EidosRegisteredString("allMutationTyp
 const std::string &gStr_allScriptBlocks = EidosRegisteredString("allScriptBlocks", gID_allScriptBlocks);
 const std::string &gStr_allSpecies = EidosRegisteredString("allSpecies", gID_allSpecies);
 const std::string &gStr_allSubpopulations = EidosRegisteredString("allSubpopulations", gID_allSubpopulations);
+const std::string &gStr_chromosome = EidosRegisteredString("chromosome", gID_chromosome);
 const std::string &gStr_chromosomes = EidosRegisteredString("chromosomes", gID_chromosomes);
 const std::string &gStr_genomicElementTypes = EidosRegisteredString("genomicElementTypes", gID_genomicElementTypes);
 const std::string &gStr_lifetimeReproductiveOutput = EidosRegisteredString("lifetimeReproductiveOutput", gID_lifetimeReproductiveOutput);

core/slim_globals.h

@@ -797,7 +797,6 @@ extern const std::string &gStr_geneConversionGCBias;
 extern const std::string &gStr_geneConversionNonCrossoverFraction;
 extern const std::string &gStr_geneConversionMeanLength;
 extern const std::string &gStr_geneConversionSimpleConversionFraction;
-extern const std::string &gStr_chromosome;
 extern const std::string &gStr_isNullHaplosome;
 extern const std::string &gStr_mutations;
 extern const std::string &gStr_uniqueMutations;
@@ -835,6 +834,7 @@ extern const std::string &gStr_allMutationTypes;
 extern const std::string &gStr_allScriptBlocks;
 extern const std::string &gStr_allSpecies;
 extern const std::string &gStr_allSubpopulations;
+extern const std::string &gStr_chromosome;
 extern const std::string &gStr_chromosomes;
 extern const std::string &gStr_genomicElementTypes;
 extern const std::string &gStr_lifetimeReproductiveOutput;
@@ -1246,7 +1246,6 @@ enum _SLiMGlobalStringID : int {
 	gID_geneConversionNonCrossoverFraction,
 	gID_geneConversionMeanLength,
 	gID_geneConversionSimpleConversionFraction,
-	gID_chromosome,
 	gID_isNullHaplosome,
 	gID_mutations,
 	gID_uniqueMutations,
@@ -1284,6 +1283,7 @@ enum _SLiMGlobalStringID : int {
 	gID_allScriptBlocks,
 	gID_allSpecies,
 	gID_allSubpopulations,
+	gID_chromosome,
 	gID_chromosomes,
 	gID_genomicElementTypes,
 	gID_lifetimeReproductiveOutput,

core/species_eidos.cpp

@@ -1698,6 +1698,13 @@ EidosValue_SP Species::GetProperty(EidosGlobalStringID p_property_id)
 		{
 			return EidosValue_SP(new (gEidosValuePool->AllocateChunk()) EidosValue_String(avatar_));
 		}
+		case gID_chromosome:
+		{
+			if (chromosomes_.size() != 1)
+				EIDOS_TERMINATION << "ERROR (Species::GetProperty): property chromosome may only be accessed on a species that has exactly one chromosome; in all other cases the chromosomes property must be used, since it can return multiple chromosomes (or none)." << EidosTerminate();
+			
+			return EidosValue_SP(new (gEidosValuePool->AllocateChunk()) EidosValue_Object(chromosomes_[0], gSLiM_Chromosome_Class));
+		}
 		case gID_chromosomes:
 		{
 			EidosValue_Object *vec = new (gEidosValuePool->AllocateChunk()) EidosValue_Object(gSLiM_Chromosome_Class);
@@ -4135,6 +4142,7 @@ const std::vector<EidosPropertySignature_CSP> *Species_Class::Properties(void) c
 		properties = new std::vector<EidosPropertySignature_CSP>(*super::Properties());
 
 		properties->emplace_back((EidosPropertySignature *)(new EidosPropertySignature(gStr_avatar,					true,	kEidosValueMaskString | kEidosValueMaskSingleton)));
+		properties->emplace_back((EidosPropertySignature *)(new EidosPropertySignature(gStr_chromosome,				true,	kEidosValueMaskObject | kEidosValueMaskSingleton, gSLiM_Chromosome_Class)));
 		properties->emplace_back((EidosPropertySignature *)(new EidosPropertySignature(gStr_chromosomes,			true,	kEidosValueMaskObject, gSLiM_Chromosome_Class)));
 		properties->emplace_back((EidosPropertySignature *)(new EidosPropertySignature(gEidosStr_color,				true,	kEidosValueMaskString | kEidosValueMaskSingleton)));
 		properties->emplace_back((EidosPropertySignature *)(new EidosPropertySignature(gStr_description,			false,	kEidosValueMaskString | kEidosValueMaskSingleton)));