initializeMutationType() sets the DES for all traits; naming shifts

Author: bhaller

EidosScribe/EidosHelpFunctions.rtf

@@ -3519,8 +3519,8 @@ This is quite similar to a function in R of the same name; note, however, that E
 \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 .
@@ -6748,8 +6748,9 @@ Named
 \f1\fs18 c()
 \f3\fs20  function (including the possibility of type promotion).\
 Since this function can be hard to understand at first, here is an example:\
+\pard\pardeftab397\li547\ri720\sb60\sa60\partightenfactor0
 
-\f1\fs18 sapply(1:10, "if (applyValue % 2) applyValue ^ 2; else NULL;");\
+\f1\fs18 \cf2 sapply(1:10, "if (applyValue % 2) applyValue ^ 2; else NULL;");\
 \pard\pardeftab397\li547\ri720\sb60\sa60\partightenfactor0
 
 \f3\fs20 \cf2 \kerning1\expnd0\expndtw0 This produces the output 

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/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->IsPureNeutralDFE())
+                        if (muttype->IsPureNeutralDES())
                             displayMuttypes_.emplace_back(muttype_id);
                     }
                 }

QtSLiM/QtSLiMChromosomeWidget_GL.cpp

@@ -225,7 +225,7 @@ void QtSLiMChromosomeWidget::glDrawMutations(QRect &interiorRect, Chromosome *ch
                 // 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);
 
-                RGBForSelectionCoeff(static_cast<double>(mut_trait_info[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
+                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()));
@@ -241,9 +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)));
@@ -261,22 +261,22 @@ void QtSLiMChromosomeWidget::glDrawMutations(QRect &interiorRect, Chromosome *ch
 		for (auto mutationTypeIter : mut_types)
 		{
 			MutationType *mut_type = mutationTypeIter.second;
-            EffectDistributionInfo &ed_info = mut_type->effect_distributions_[0];	// FIXME MULTITRAIT
+            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 ((ed_info.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_effect_t mut_type_selcoeff = (mut_type_fixed_color ? 0.0 : static_cast<slim_effect_t>(ed_info.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];
@@ -285,11 +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
+                            // 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_selcoeff)))
+                            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
 							{
@@ -320,7 +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)
@@ -381,7 +381,7 @@ void QtSLiMChromosomeWidget::glDrawMutations(QRect &interiorRect, Chromosome *ch
                         // 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);
 
-						RGBForSelectionCoeff(static_cast<double>(mut_trait_info[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
+						RGBForEffectSize(static_cast<double>(mut_trait_info[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
 
 						SLIM_GL_DEFCOORDS(mutationTickRect);
 						SLIM_GL_PUSHRECT();
@@ -437,7 +437,7 @@ void QtSLiMChromosomeWidget::glDrawMutations(QRect &interiorRect, Chromosome *ch
                         // 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);
 
-						RGBForSelectionCoeff(static_cast<double>(mut_trait_info[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
+						RGBForEffectSize(static_cast<double>(mut_trait_info[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
 
 						SLIM_GL_DEFCOORDS(mutationTickRect);
 						SLIM_GL_PUSHRECT();
@@ -505,7 +505,7 @@ void QtSLiMChromosomeWidget::glDrawFixedSubstitutions(QRect &interiorRect, Chrom
 					else
 					{
                         // FIXME MULTITRAIT: should be a way to choose which trait is being used for colors in the chromosome view!
-						RGBForSelectionCoeff(static_cast<double>(substitution->trait_info_[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
+						RGBForEffectSize(static_cast<double>(substitution->trait_info_[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
 					}
 				}
 
@@ -585,7 +585,7 @@ void QtSLiMChromosomeWidget::glDrawFixedSubstitutions(QRect &interiorRect, Chrom
 					else
 					{
                         // FIXME MULTITRAIT: should be a way to choose which trait is being used for colors in the chromosome view!
-						RGBForSelectionCoeff(static_cast<double>(substitution->trait_info_[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
+						RGBForEffectSize(static_cast<double>(substitution->trait_info_[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
 					}
 
                     mutationTickRect.setX(interiorRect.x() + binIndex);

QtSLiM/QtSLiMChromosomeWidget_QT.cpp

@@ -221,7 +221,7 @@ void QtSLiMChromosomeWidget::qtDrawMutations(QRect &interiorRect, Chromosome *ch
                 // 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);
 
-                RGBForSelectionCoeff(static_cast<double>(mut_trait_info[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
+				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()));
@@ -237,9 +237,9 @@ void QtSLiMChromosomeWidget::qtDrawMutations(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)));
@@ -263,16 +263,16 @@ void QtSLiMChromosomeWidget::qtDrawMutations(QRect &interiorRect, Chromosome *ch
 				if (draw_muttypes_sequentially)
 				{
 					bool mut_type_fixed_color = !mut_type->color_.empty();
-                    EffectDistributionInfo &ed_info = mut_type->effect_distributions_[0];	// FIXME MULTITRAIT
+                    EffectDistributionInfo &DES_info = mut_type->effect_distributions_[0];	// FIXME MULTITRAIT
 
-					// We optimize fixed-DFE mutation types only, and those using a fixed color set by the user
-					if ((ed_info.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_effect_t mut_type_selcoeff = (mut_type_fixed_color ? 0.0 : static_cast<slim_effect_t>(ed_info.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];
@@ -281,11 +281,11 @@ void QtSLiMChromosomeWidget::qtDrawMutations(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
+                            // 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_selcoeff)))
+                            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
 							{
@@ -316,7 +316,7 @@ void QtSLiMChromosomeWidget::qtDrawMutations(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)
@@ -377,7 +377,7 @@ void QtSLiMChromosomeWidget::qtDrawMutations(QRect &interiorRect, Chromosome *ch
                         // 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);
 
-						RGBForSelectionCoeff(static_cast<double>(mut_trait_info[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
+						RGBForEffectSize(static_cast<double>(mut_trait_info[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
 
 						SLIM_GL_DEFCOORDS(mutationTickRect);
 						SLIM_GL_PUSHRECT();
@@ -433,7 +433,7 @@ void QtSLiMChromosomeWidget::qtDrawMutations(QRect &interiorRect, Chromosome *ch
                         // 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);
 
-						RGBForSelectionCoeff(static_cast<double>(mut_trait_info[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
+						RGBForEffectSize(static_cast<double>(mut_trait_info[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
 
 						SLIM_GL_DEFCOORDS(mutationTickRect);
 						SLIM_GL_PUSHRECT();
@@ -501,7 +501,7 @@ void QtSLiMChromosomeWidget::qtDrawFixedSubstitutions(QRect &interiorRect, Chrom
 					else
 					{
                         // FIXME MULTITRAIT: should be a way to choose which trait is being used for colors in the chromosome view!
-						RGBForSelectionCoeff(static_cast<double>(substitution->trait_info_[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
+						RGBForEffectSize(static_cast<double>(substitution->trait_info_[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
 					}
 				}
 
@@ -580,7 +580,7 @@ void QtSLiMChromosomeWidget::qtDrawFixedSubstitutions(QRect &interiorRect, Chrom
 					}
 					else
 					{
-						RGBForSelectionCoeff(static_cast<double>(substitution->trait_info_[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
+						RGBForEffectSize(static_cast<double>(substitution->trait_info_[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
 					}
 
                     mutationTickRect.setX(interiorRect.x() + binIndex);

QtSLiM/QtSLiMExtras.cpp

@@ -278,7 +278,7 @@ void RGBForFitness(double value, float *colorRed, float *colorGreen, float *colo
 	}
 }
 
-void RGBForSelectionCoeff(double value, float *colorRed, float *colorGreen, float *colorBlue, double scalingFactor)
+void RGBForEffectSize(double value, float *colorRed, float *colorGreen, float *colorBlue, double scalingFactor)
 {
 	// apply a scaling factor; this could be user-adjustible since different models have different relevant fitness ranges
 	value *= scalingFactor;
@@ -394,7 +394,7 @@ void QtSLiMColorScaleWidget::paintEvent(QPaintEvent * /*p_paintEvent*/)
         double sliverFraction = (x - (stripe2.left() + 1)) / (stripe2.width() - 3.0);
         double fitness = sliverFraction * 2.0 - 1;     // cover mutation effect values of -1.0 to 1.0
         float r, g, b;
-        RGBForSelectionCoeff(fitness, &r, &g, &b, scalingFactor);
+		RGBForEffectSize(fitness, &r, &g, &b, scalingFactor);
         painter.fillRect(sliver, QColor(round(r * 255), round(g * 255), round(b * 255)));
 
         //qDebug() << "x =" << x << " << sliverFraction =" << sliverFraction << " fitness =" << fitness;