make Substitution nucleotide[Value] properties read-only

Author: bhaller

EidosScribe/EidosHelpController.mm

@@ -1289,6 +1289,8 @@ - (void)drawRow:(NSInteger)rowIndex clipRect:(NSRect)clipRect
 						   @"nucleotideBased =>",
 						   @"nucleotide <–>",
 						   @"nucleotideValue <–>",
+						   @"nucleotide =>",
+						   @"nucleotideValue =>",
 						   @"mutationMatrix =>",
 						   @"–\u00A0setMutationMatrix()",
 						   @"–\u00A0ancestralNucleotides()",

QtSLiM/help/SLiMHelpClasses.html

@@ -1353,9 +1353,9 @@
 <p class="p4">The tick in which this mutation fixed.</p>
 <p class="p3">mutationType =&gt; (object&lt;MutationType&gt;$)</p>
 <p class="p4">The <span class="s1">MutationType</span> from which this mutation was drawn.</p>
-<p class="p5"><span class="s3">nucleotide &lt;–&gt; (string$)</span></p>
+<p class="p5"><span class="s3">nucleotide =&gt; (string$)</span></p>
 <p class="p6"><span class="s3">A </span><span class="s4">string</span><span class="s3"> representing the nucleotide associated with this mutation; this will be </span><span class="s4">"A"</span><span class="s3">, </span><span class="s4">"C"</span><span class="s3">, </span><span class="s4">"G"</span><span class="s3">, or </span><span class="s4">"T"</span><span class="s3">.<span class="Apple-converted-space">  </span>If the mutation is not nucleotide-based, this property is unavailable.</span></p>
-<p class="p5"><span class="s3">nucleotideValue &lt;–&gt; (integer$)</span></p>
+<p class="p5"><span class="s3">nucleotideValue =&gt; (integer$)</span></p>
 <p class="p6"><span class="s3">An </span><span class="s4">integer</span><span class="s3"> representing the nucleotide associated with this mutation; this will be </span><span class="s4">0</span><span class="s3"> (A), </span><span class="s4">1</span><span class="s3"> (C), </span><span class="s4">2</span><span class="s3"> (G), or </span><span class="s4">3</span><span class="s3"> (T).<span class="Apple-converted-space">  </span>If the mutation is not nucleotide-based, this property is unavailable.</span></p>
 <p class="p3">originTick =&gt; (integer$)</p>
 <p class="p4">The tick in which this mutation arose.</p>

SLiMgui/SLiMHelpClasses.rtf

@@ -14056,7 +14056,7 @@ Note that this method is only for use in nonWF models, in which migration is man
 \pard\pardeftab720\li720\fi-446\ri720\sb180\sa60\partightenfactor0
 
 \f3\fs18 \cf2 \expnd0\expndtw0\kerning0
-nucleotide <\'96> (string$)\
+nucleotide => (string$)\
 \pard\pardeftab720\li547\ri720\sb60\sa60\partightenfactor0
 
 \f4\fs20 \cf2 A 
@@ -14072,7 +14072,7 @@ nucleotide <\'96> (string$)\
 \f4\fs20 .  If the mutation is not nucleotide-based, this property is unavailable.\
 \pard\pardeftab720\li720\fi-446\ri720\sb180\sa60\partightenfactor0
 
-\f3\fs18 \cf2 nucleotideValue <\'96> (integer$)\
+\f3\fs18 \cf2 nucleotideValue => (integer$)\
 \pard\pardeftab720\li547\ri720\sb60\sa60\partightenfactor0
 
 \f4\fs20 \cf2 An 

VERSIONS

@@ -80,6 +80,7 @@ multitrait branch:
 		Mutation: add +setHemizygousDominanceForTrait([Nio<Trait> traits = NULL], [Nif dominance = NULL]) method
 		Mutation: add read-write <trait-name>HemizygousDominance property to Mutation
 		Substitution: add read-only <trait-name>HemizygousDominance property
+	policy change: the nucleotide and nucleotideValue properties of Substitution are now read-only (I think it was a bug that they were ever read-write...?)
 
 
 version 5.1 (Eidos version 4.1):

core/substitution.cpp

@@ -516,32 +516,6 @@ void Substitution::SetProperty(EidosGlobalStringID p_property_id, const EidosVal
 	// All of our strings are in the global registry, so we can require a successful lookup
 	switch (p_property_id)
 	{
-		case gID_nucleotide:
-		{
-			const std::string &nucleotide = ((EidosValue_String &)p_value).StringRefAtIndex_NOCAST(0, nullptr);
-			
-			if (nucleotide_ == -1)
-				EIDOS_TERMINATION << "ERROR (Substitution::SetProperty): property nucleotide is only defined for nucleotide-based substitutions." << EidosTerminate();
-			
-			if (nucleotide == gStr_A)		nucleotide_ = 0;
-			else if (nucleotide == gStr_C)	nucleotide_ = 1;
-			else if (nucleotide == gStr_G)	nucleotide_ = 2;
-			else if (nucleotide == gStr_T)	nucleotide_ = 3;
-			else EIDOS_TERMINATION << "ERROR (Substitution::SetProperty): property nucleotide may only be set to 'A', 'C', 'G', or 'T'." << EidosTerminate();
-			return;
-		}
-		case gID_nucleotideValue:
-		{
-			int64_t nucleotide = p_value.IntAtIndex_NOCAST(0, nullptr);
-			
-			if (nucleotide_ == -1)
-				EIDOS_TERMINATION << "ERROR (Substitution::SetProperty): property nucleotideValue is only defined for nucleotide-based substitutions." << EidosTerminate();
-			if ((nucleotide < 0) || (nucleotide > 3))
-				EIDOS_TERMINATION << "ERROR (Substitution::SetProperty): property nucleotideValue may only be set to 0 (A), 1 (C), 2 (G), or 3 (T)." << EidosTerminate();
-			
-			nucleotide_ = (int8_t)nucleotide;
-			return;
-		}
 		case gID_subpopID:
 		{
 			slim_objectid_t value = SLiMCastToObjectidTypeOrRaise(p_value.IntAtIndex_NOCAST(0, nullptr));
@@ -706,8 +680,8 @@ const std::vector<EidosPropertySignature_CSP> *Substitution_Class::Properties(vo
 		properties->emplace_back((EidosPropertySignature *)(new EidosPropertySignature(gStr_dominance,			true,	kEidosValueMaskFloat)));
 		properties->emplace_back((EidosPropertySignature *)(new EidosPropertySignature(gStr_hemizygousDominance,true,	kEidosValueMaskFloat)));
 		properties->emplace_back((EidosPropertySignature *)(new EidosPropertySignature(gStr_subpopID,			false,	kEidosValueMaskInt | kEidosValueMaskSingleton))->DeclareAcceleratedGet(Substitution::GetProperty_Accelerated_subpopID));
-		properties->emplace_back((EidosPropertySignature *)(new EidosPropertySignature(gStr_nucleotide,			false,	kEidosValueMaskString | kEidosValueMaskSingleton))->DeclareAcceleratedGet(Substitution::GetProperty_Accelerated_nucleotide));
-		properties->emplace_back((EidosPropertySignature *)(new EidosPropertySignature(gStr_nucleotideValue,	false,	kEidosValueMaskInt | kEidosValueMaskSingleton))->DeclareAcceleratedGet(Substitution::GetProperty_Accelerated_nucleotideValue));
+		properties->emplace_back((EidosPropertySignature *)(new EidosPropertySignature(gStr_nucleotide,			true,	kEidosValueMaskString | kEidosValueMaskSingleton))->DeclareAcceleratedGet(Substitution::GetProperty_Accelerated_nucleotide));
+		properties->emplace_back((EidosPropertySignature *)(new EidosPropertySignature(gStr_nucleotideValue,	true,	kEidosValueMaskInt | kEidosValueMaskSingleton))->DeclareAcceleratedGet(Substitution::GetProperty_Accelerated_nucleotideValue));
 		properties->emplace_back((EidosPropertySignature *)(new EidosPropertySignature(gStr_originTick,			true,	kEidosValueMaskInt | kEidosValueMaskSingleton))->DeclareAcceleratedGet(Substitution::GetProperty_Accelerated_originTick));
 		properties->emplace_back((EidosPropertySignature *)(new EidosPropertySignature(gStr_fixationTick,		true,	kEidosValueMaskInt | kEidosValueMaskSingleton))->DeclareAcceleratedGet(Substitution::GetProperty_Accelerated_fixationTick));
 		properties->emplace_back((EidosPropertySignature *)(new EidosPropertySignature(gStr_tag,				false,	kEidosValueMaskInt | kEidosValueMaskSingleton))->DeclareAcceleratedGet(Substitution::GetProperty_Accelerated_tag));