multitrait changes

CMakeLists.txt

@@ -417,7 +417,7 @@ if(BUILD_SLIMGUI)
   file(GLOB_RECURSE QTSLIM_SOURCES ${PROJECT_SOURCE_DIR}/QtSLiM/*.cpp ${PROJECT_SOURCE_DIR}/QtSLiM/*.qrc ${PROJECT_SOURCE_DIR}/eidos/*.cpp)
   add_executable(${TARGET_NAME_SLIMGUI} "${QTSLIM_SOURCES}" "${SLIM_SOURCES}")
   set_target_properties( ${TARGET_NAME_SLIMGUI} PROPERTIES LINKER_LANGUAGE CXX)
-  target_compile_definitions( ${TARGET_NAME_SLIMGUI} PRIVATE EIDOSGUI=1 SLIMGUI=1)
+  target_compile_definitions( ${TARGET_NAME_SLIMGUI} PRIVATE EIDOS_GUI=1 SLIMGUI=1)
   target_include_directories(${TARGET_NAME_SLIMGUI} PUBLIC ${GSL_INCLUDES} "${PROJECT_SOURCE_DIR}/QtSLiM" "${PROJECT_SOURCE_DIR}/eidos" "${PROJECT_SOURCE_DIR}/core" "${PROJECT_SOURCE_DIR}/treerec" "${PROJECT_SOURCE_DIR}/treerec/tskit/kastore")
 
   # Qt dependencies, which depend on the Qt version used.  For Qt6, we also need C++17; the last -std flag supplied ought to take priority.

EidosScribe/EidosHelpController.mm

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

EidosScribe/EidosHelpFunctions.rtf

@@ -3650,8 +3650,8 @@ Regarding how values in
 \f1\fs18 x
 \f3\fs20  according to which sorting should be done.  This must be a simple property name; it cannot be a property path.  For example, to sort a 
 \f1\fs18 Mutation
-\f3\fs20  vector by the selection coefficients of the mutations, you would simply pass 
-\f1\fs18 "selectionCoeff"
+\f3\fs20  vector by the dominance coefficients of the mutations, you would simply pass 
+\f1\fs18 "dominance"
 \f3\fs20 , including the quotes, for 
 \f1\fs18 property
 \f2\fs20 .

EidosScribe/EidosTextView.mm

@@ -2005,7 +2005,7 @@ - (NSMutableArray *)completionsForKeyPathEndingInTokenIndex:(int)lastDotTokenInd
 		else
 		{
 			// We have a property; look up its signature and get the class
-			const EidosPropertySignature *property_signature = key_path_class->SignatureForProperty(identifier_id);
+			const EidosPropertySignature *property_signature = key_path_class->SignatureForProperty_TYPE_INTERPRETER(identifier_id);
 
 			if (!property_signature)
 				return nil;			// no signature, so the class does not support the property given
@@ -2023,7 +2023,7 @@ - (NSMutableArray *)completionsForKeyPathEndingInTokenIndex:(int)lastDotTokenInd
 	const EidosClass *terminus = key_path_class;
 
 	// First, a sorted list of globals
-	for (auto symbol_sig : *terminus->Properties())
+	for (auto symbol_sig : terminus->Properties_TYPE_INTERPRETER())
 	{
 		if (!symbol_sig->deprecated_)
 			[candidates addObject:[NSString stringWithUTF8String:symbol_sig->property_name_.c_str()]];
@@ -2337,6 +2337,9 @@ - (void)_completionHandlerWithRangeForCompletion:(NSRange *)baseRange completion
 			std::cout << "Eidos AST:\n" << parse_stream.str() << std::endl << std::endl;
 #endif
 
+			// Clear out dynamic property signatures kept by EidosClass, since we're starting a new type-interpretation pass.
+			EidosClass::ClearDynamicSignatures();
+
 			EidosTypeInterpreter typeInterpreter(script, *typeTablePtr, *functionMapPtr, *callTypeTablePtr);
 
 			typeInterpreter.TypeEvaluateInterpreterBlock_AddArgumentCompletions(&argumentCompletions, script_string.length());	// result not used

PARALLEL

@@ -71,7 +71,7 @@ PARALLEL changes (now in the master branch, but disabled):
 	add support for parallel reproduction with tree-sequence recording
 	add parallel reproduction in nonWF models, with no callbacks (recombination(), mutation()) active - modifyChild() callbacks are legal but cannot access child haplosomes since they are deferred
 		this is achieved by passing defer=T to addCrossed(), addCloned(), addSelfed(), addMultiRecombinant(), or addRecombinant()
-	thread-safety work - break in backward reproducibility for scripts that use a type 's' DFE, because the code path for that shifted
+	thread-safety work - break in backward reproducibility for scripts that use a type 's' DES, because the code path for that shifted
 	algorithm change for nearestNeighbors() and nearestNeighborsOfPoint(), when count is >1 and <N; the old algorithm was not thread-safe, and was inefficient; breaks backward reproducibility for the relevant case
 		the break in backward reproducibility is because the old algorithm returned the neighbors in a scrambled order, whereas the new algorithm returns them in sorted order; the order is not documented, so both are compliant
 	add max thread counts for each parallel loop, allowing flexible customization both by Eidos and by the user

QtSLiM/QtSLiMAppDelegate.cpp

@@ -245,7 +245,7 @@ QtSLiMAppDelegate::QtSLiMAppDelegate(QObject *p_parent) : QObject(p_parent)
 
     // This lambda (1) ensures that visible top-level windows remain on screen;
     // (2) raises the active window to the front on the appropriate screen, if appropriate.
-    auto ensureOnScreen = [this]() {
+    auto ensureOnScreen = []() {
         const auto topLevels = QApplication::topLevelWidgets();
         QWidget *active = qApp->activeWindow();
         for (QWidget *w : topLevels)

QtSLiM/QtSLiMChromosomeWidget.cpp

@@ -480,7 +480,7 @@ void QtSLiMChromosomeWidgetController::runChromosomeContextMenuAtPoint(QPoint p_
                         MutationType *muttype = muttype_iter.second;
                         slim_objectid_t muttype_id = muttype->mutation_type_id_;
 
-                        if ((muttype->dfe_type_ != DFEType::kFixed) || (muttype->dfe_parameters_[0] != 0.0))
+                        if (muttype->IsPureNeutralDES())
                             displayMuttypes_.emplace_back(muttype_id);
                     }
                 }

QtSLiM/QtSLiMChromosomeWidget_GL.cpp

@@ -30,6 +30,8 @@
 #include <algorithm>
 #include <vector>
 
+#include "mutation_block.h"
+
 
 //
 //  OpenGL-based drawing; maintain this in parallel with the Qt-based drawing!
@@ -175,10 +177,12 @@ void QtSLiMChromosomeWidget::glDrawMutations(QRect &interiorRect, Chromosome *ch
     static std::vector<const Mutation *> mutations;
     mutations.resize(0);
 
+    MutationBlock *mutation_block = displaySpecies->SpeciesMutationBlock();
+    Mutation *mut_block_ptr = mutation_block->mutation_buffer_;
+
     {
         int registry_size;
         const MutationIndex *registry = pop.MutationRegistry(&registry_size);
-        Mutation *mut_block_ptr = gSLiM_Mutation_Block;
         slim_chromosome_index_t chromosome_index = chromosome->Index();
 
         for (int registry_index = 0; registry_index < registry_size; ++registry_index)
@@ -218,7 +222,10 @@ void QtSLiMChromosomeWidget::glDrawMutations(QRect &interiorRect, Chromosome *ch
             }
             else
             {
-                RGBForSelectionCoeff(static_cast<double>(mutation->selection_coeff_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
+                // FIXME MULTITRAIT: should be a way to choose which trait is being used for colors in the chromosome view!
+                MutationTraitInfo *mut_trait_info = mutation_block->TraitInfoForMutation(mutation);
+
+                RGBForEffectSize(static_cast<double>(mut_trait_info[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
             }
 
             int height_adjust = mutationTickRect.height() - static_cast<int>(ceil((mutationRefCount / totalHaplosomeCount) * interiorRect.height()));
@@ -234,9 +241,9 @@ void QtSLiMChromosomeWidget::glDrawMutations(QRect &interiorRect, Chromosome *ch
 	{
 		// We have a lot of mutations, so let's try to be smarter.  It's hard to be smarter.  The overhead from allocating the NSColors and such
 		// is pretty negligible; practially all the time is spent in NSRectFill().  Unfortunately, NSRectFillListWithColors() provides basically
-		// no speedup; Apple doesn't appear to have optimized it.  So, here's what I came up with.  For each mutation type that uses a fixed DFE,
+		// no speedup; Apple doesn't appear to have optimized it.  So, here's what I came up with.  For each mutation type that uses a fixed DES,
 		// and thus a fixed color, we can do a radix sort of mutations into bins corresponding to each pixel in our displayed image.  Then we
-		// can draw each bin just once, making one bar for the highest bar in that bin.  Mutations from non-fixed DFEs, and mutations which have
+		// can draw each bin just once, making one bar for the highest bar in that bin.  Mutations from non-fixed DESs, and mutations which have
 		// had their selection coefficient changed, will be drawn at the end in the usual (slow) way.
 		int displayPixelWidth = interiorRect.width();
 		int16_t *heightBuffer = static_cast<int16_t *>(malloc(static_cast<size_t>(displayPixelWidth) * sizeof(int16_t)));
@@ -254,21 +261,22 @@ void QtSLiMChromosomeWidget::glDrawMutations(QRect &interiorRect, Chromosome *ch
 		for (auto mutationTypeIter : mut_types)
 		{
 			MutationType *mut_type = mutationTypeIter.second;
+            EffectDistributionInfo &DES_info = mut_type->effect_distributions_[0];	// FIXME MULTITRAIT
 
 			if (mut_type->mutation_type_displayed_)
 			{
 				if (draw_muttypes_sequentially)
 				{
 					bool mut_type_fixed_color = !mut_type->color_.empty();
 
-					// We optimize fixed-DFE mutation types only, and those using a fixed color set by the user
-					if ((mut_type->dfe_type_ == DFEType::kFixed) || mut_type_fixed_color)
+					// We optimize fixed-DES mutation types only, and those using a fixed color set by the user
+					if ((DES_info.DES_type_ == DESType::kFixed) || mut_type_fixed_color)
 					{
-						slim_selcoeff_t mut_type_selcoeff = (mut_type_fixed_color ? 0.0 : static_cast<slim_selcoeff_t>(mut_type->dfe_parameters_[0]));
+						slim_effect_t mut_type_effect = (mut_type_fixed_color ? 0.0 : static_cast<slim_effect_t>(DES_info.DES_parameters_[0]));
 
 						EIDOS_BZERO(heightBuffer, static_cast<size_t>(displayPixelWidth) * sizeof(int16_t));
 
-						// Scan through the mutation list for mutations of this type with the right selcoeff
+						// Scan through the mutation list for mutations of this type with the right effect
                         for (int mutation_index = 0; mutation_index < (int)mutations.size(); ++mutation_index)
 						{
                             const Mutation *mutation = mutations[mutation_index];
@@ -277,8 +285,11 @@ void QtSLiMChromosomeWidget::glDrawMutations(QRect &interiorRect, Chromosome *ch
 #pragma GCC diagnostic ignored "-Wfloat-equal"
 #pragma clang diagnostic push
 #pragma clang diagnostic ignored "-Wfloat-equal"
-                            // We do want to do an exact floating-point equality compare here; we want to see whether the mutation's selcoeff is unmodified from the fixed DFE
-							if ((mutation->mutation_type_ptr_ == mut_type) && (mut_type_fixed_color || (mutation->selection_coeff_ == mut_type_selcoeff)))
+                            // We do want to do an exact floating-point equality compare here; we want to see whether the mutation's effect is unmodified from the fixed DES
+                            // FIXME MULTITRAIT: should be a way to choose which trait is being used for colors in the chromosome view!
+                            MutationTraitInfo *mut_trait_info = mutation_block->TraitInfoForMutation(mutation);
+
+                            if ((mutation->mutation_type_ptr_ == mut_type) && (mut_type_fixed_color || (mut_trait_info[0].effect_size_ == mut_type_effect)))
 #pragma clang diagnostic pop
 #pragma GCC diagnostic pop
 							{
@@ -309,7 +320,7 @@ void QtSLiMChromosomeWidget::glDrawMutations(QRect &interiorRect, Chromosome *ch
 						}
 						else
 						{
-							RGBForSelectionCoeff(static_cast<double>(mut_type_selcoeff), &colorRed, &colorGreen, &colorBlue, scalingFactor);
+							RGBForEffectSize(static_cast<double>(mut_type_effect), &colorRed, &colorGreen, &colorBlue, scalingFactor);
 						}
 
 						for (int binIndex = 0; binIndex < displayPixelWidth; ++binIndex)
@@ -366,7 +377,11 @@ void QtSLiMChromosomeWidget::glDrawMutations(QRect &interiorRect, Chromosome *ch
                         int height_adjust = mutationTickRect.height() - static_cast<int>(ceil((mutationRefCount / totalHaplosomeCount) * interiorRect.height()));
 
                         mutationTickRect.setTop(mutationTickRect.top() + height_adjust);
-						RGBForSelectionCoeff(static_cast<double>(mutation->selection_coeff_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
+
+                        // FIXME MULTITRAIT: should be a way to choose which trait is being used for colors in the chromosome view!
+                        MutationTraitInfo *mut_trait_info = mutation_block->TraitInfoForMutation(mutation);
+
+						RGBForEffectSize(static_cast<double>(mut_trait_info[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
 
 						SLIM_GL_DEFCOORDS(mutationTickRect);
 						SLIM_GL_PUSHRECT();
@@ -418,8 +433,11 @@ void QtSLiMChromosomeWidget::glDrawMutations(QRect &interiorRect, Chromosome *ch
                         mutationTickRect.setTop(mutationTickRect.top() + interiorRect.height() - barHeight);
 
 						const Mutation *mutation = mutationBuffer[binIndex];
-
-						RGBForSelectionCoeff(static_cast<double>(mutation->selection_coeff_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
+
+                        // FIXME MULTITRAIT: should be a way to choose which trait is being used for colors in the chromosome view!
+                        MutationTraitInfo *mut_trait_info = mutation_block->TraitInfoForMutation(mutation);
+
+						RGBForEffectSize(static_cast<double>(mut_trait_info[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
 
 						SLIM_GL_DEFCOORDS(mutationTickRect);
 						SLIM_GL_PUSHRECT();
@@ -486,7 +504,8 @@ void QtSLiMChromosomeWidget::glDrawFixedSubstitutions(QRect &interiorRect, Chrom
 					}
 					else
 					{
-						RGBForSelectionCoeff(static_cast<double>(substitution->selection_coeff_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
+                        // FIXME MULTITRAIT: should be a way to choose which trait is being used for colors in the chromosome view!
+						RGBForEffectSize(static_cast<double>(substitution->trait_info_[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
 					}
 				}
 
@@ -565,7 +584,8 @@ void QtSLiMChromosomeWidget::glDrawFixedSubstitutions(QRect &interiorRect, Chrom
 					}
 					else
 					{
-						RGBForSelectionCoeff(static_cast<double>(substitution->selection_coeff_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
+                        // FIXME MULTITRAIT: should be a way to choose which trait is being used for colors in the chromosome view!
+						RGBForEffectSize(static_cast<double>(substitution->trait_info_[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
 					}
 
                     mutationTickRect.setX(interiorRect.x() + binIndex);