remove C++ selection_coeff_ and dominance_coeff_ ivars

Author: bhaller

QtSLiM/QtSLiMChromosomeWidget_GL.cpp

@@ -177,10 +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 = displaySpecies->SpeciesMutationBlock()->mutation_buffer_;
         slim_chromosome_index_t chromosome_index = chromosome->Index();
 
         for (int registry_index = 0; registry_index < registry_size; ++registry_index)
@@ -220,7 +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);
+                
+                RGBForSelectionCoeff(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()));
@@ -281,7 +286,10 @@ void QtSLiMChromosomeWidget::glDrawMutations(QRect &interiorRect, Chromosome *ch
 #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)))
+                            // 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)))
 #pragma clang diagnostic pop
 #pragma GCC diagnostic pop
 							{
@@ -369,7 +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);
+                        
+						RGBForSelectionCoeff(static_cast<double>(mut_trait_info[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
 
 						SLIM_GL_DEFCOORDS(mutationTickRect);
 						SLIM_GL_PUSHRECT();
@@ -421,8 +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);
+                        
+						RGBForSelectionCoeff(static_cast<double>(mut_trait_info[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
 
 						SLIM_GL_DEFCOORDS(mutationTickRect);
 						SLIM_GL_PUSHRECT();
@@ -489,7 +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!
+						RGBForSelectionCoeff(static_cast<double>(substitution->trait_info_[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
 					}
 				}
 
@@ -568,7 +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!
+						RGBForSelectionCoeff(static_cast<double>(substitution->trait_info_[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
 					}
 
                     mutationTickRect.setX(interiorRect.x() + binIndex);

QtSLiM/QtSLiMChromosomeWidget_QT.cpp

@@ -173,10 +173,12 @@ void QtSLiMChromosomeWidget::qtDrawMutations(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 = displaySpecies->SpeciesMutationBlock()->mutation_buffer_;
         slim_chromosome_index_t chromosome_index = chromosome->Index();
 
         for (int registry_index = 0; registry_index < registry_size; ++registry_index)
@@ -216,7 +218,10 @@ void QtSLiMChromosomeWidget::qtDrawMutations(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);
+                
+                RGBForSelectionCoeff(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()));
@@ -277,7 +282,10 @@ void QtSLiMChromosomeWidget::qtDrawMutations(QRect &interiorRect, Chromosome *ch
 #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)))
+                            // 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)))
 #pragma clang diagnostic pop
 #pragma GCC diagnostic pop
 							{
@@ -365,7 +373,11 @@ void QtSLiMChromosomeWidget::qtDrawMutations(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);
+                        
+						RGBForSelectionCoeff(static_cast<double>(mut_trait_info[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
 
 						SLIM_GL_DEFCOORDS(mutationTickRect);
 						SLIM_GL_PUSHRECT();
@@ -417,8 +429,11 @@ void QtSLiMChromosomeWidget::qtDrawMutations(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);
+                        
+						RGBForSelectionCoeff(static_cast<double>(mut_trait_info[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
 
 						SLIM_GL_DEFCOORDS(mutationTickRect);
 						SLIM_GL_PUSHRECT();
@@ -485,7 +500,8 @@ void QtSLiMChromosomeWidget::qtDrawFixedSubstitutions(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!
+						RGBForSelectionCoeff(static_cast<double>(substitution->trait_info_[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
 					}
 				}
 
@@ -564,7 +580,7 @@ void QtSLiMChromosomeWidget::qtDrawFixedSubstitutions(QRect &interiorRect, Chrom
 					}
 					else
 					{
-						RGBForSelectionCoeff(static_cast<double>(substitution->selection_coeff_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
+						RGBForSelectionCoeff(static_cast<double>(substitution->trait_info_[0].effect_size_), &colorRed, &colorGreen, &colorBlue, scalingFactor);
 					}
 
                     mutationTickRect.setX(interiorRect.x() + binIndex);

QtSLiM/QtSLiMHaplotypeManager.cpp

@@ -481,7 +481,8 @@ void QtSLiMHaplotypeManager::configureMutationInfoBuffer(Chromosome *chromosome)
 	mutationPositions = static_cast<slim_position_t *>(malloc(sizeof(slim_position_t) * mutationIndexCount));
 
 	// Copy the information we need on each mutation in use
-	Mutation *mut_block_ptr = graphSpecies->SpeciesMutationBlock()->mutation_buffer_;
+    MutationBlock *mutation_block = graphSpecies->SpeciesMutationBlock();
+	Mutation *mut_block_ptr = mutation_block->mutation_buffer_;
 
 	for (const MutationIndex *reg_ptr = registry; reg_ptr != reg_end_ptr; ++reg_ptr)
 	{
@@ -493,6 +494,10 @@ void QtSLiMHaplotypeManager::configureMutationInfoBuffer(Chromosome *chromosome)
 
 		haplo_mut->position_ = mut_position;
 		*(mutationPositions + mut_index) = mut_position;
+        
+        // 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(mut);
+        slim_effect_t selection_coeff = mut_trait_info[0].effect_size_;
 
 		if (!mut_type->color_.empty())
 		{
@@ -502,10 +507,10 @@ void QtSLiMHaplotypeManager::configureMutationInfoBuffer(Chromosome *chromosome)
 		}
 		else
 		{
-			RGBForSelectionCoeff(static_cast<double>(mut->selection_coeff_), &haplo_mut->red_, &haplo_mut->green_, &haplo_mut->blue_, scalingFactor);
+			RGBForSelectionCoeff(static_cast<double>(selection_coeff), &haplo_mut->red_, &haplo_mut->green_, &haplo_mut->blue_, scalingFactor);
 		}
 
-		haplo_mut->neutral_ = (mut->selection_coeff_ == 0.0f);
+		haplo_mut->neutral_ = (selection_coeff == 0.0f);
 
 		haplo_mut->display_ = mut_type->mutation_type_displayed_;
 	}

QtSLiM/help/SLiMHelpClasses.html

@@ -1327,6 +1327,8 @@
 <p class="p6">The <span class="s1">Chromosome</span> object with which the mutation is associated.</p>
 <p class="p5">dominance =&gt; (float)</p>
 <p class="p6">The dominance coefficient(s) of the mutation, carried over from the original mutation object.<span class="Apple-converted-space">  </span>In a multi-trait model, this property provides the dominance coefficients for all of the traits (in the order in which the traits were defined).<span class="Apple-converted-space">  </span>For more control, see the <span class="s1">dominanceForTrait()</span> method.<span class="Apple-converted-space">  </span>Also note that dynamic properties are defined for each trait in the model; if there is a trait named <span class="s1">height</span>, for example, then <span class="s1">Substitution</span> objects will have a dynamic property named <span class="s1">heightDominance</span> to access the dominance for that trait.</p>
+<p class="p5">effect =&gt; (float)</p>
+<p class="p6">The selection coefficient(s) of the mutation, carried over from the original mutation object.<span class="Apple-converted-space">  </span>In a multi-trait model, this property provides the effect sizes for all of the traits (in the order in which the traits were defined).<span class="Apple-converted-space">  </span>For more control, see the <span class="s1">effectForTrait()</span> method.<span class="Apple-converted-space">  </span>Also note that dynamic properties are defined for each trait in the model; if there is a trait named <span class="s1">height</span>, for example, then <span class="s1">Substitution</span> objects will have a dynamic property named <span class="s1">heightEffect</span> to access the effect for that trait.</p>
 <p class="p3">id =&gt; (integer$)</p>
 <p class="p4">The identifier for this mutation.<span class="Apple-converted-space">  </span>Each mutation created during a run receives an immutable identifier that will be unique across the duration of the run, and that identifier is carried over to the <span class="s1">Substitution</span> object when the mutation fixes.</p>
 <p class="p3">fixationTick =&gt; (integer$)</p>
@@ -1341,8 +1343,6 @@
 <p class="p4">The tick in which this mutation arose.</p>
 <p class="p3">position =&gt; (integer$)</p>
 <p class="p4">The position in the chromosome of this mutation.</p>
-<p class="p3">selectionCoeff =&gt; (float$)</p>
-<p class="p4">The selection coefficient of the mutation, drawn from the distribution of fitness effects of its <span class="s1">MutationType</span><span class="s2">.</span></p>
 <p class="p3">subpopID &lt;–&gt; (integer$)</p>
 <p class="p4">The identifier of the subpopulation in which this mutation arose.<span class="Apple-converted-space">  </span>This value is carried over from the <span class="s1">Mutation</span> object directly; if a “tag” value was used in the <span class="s1">Mutation</span> object, that value will carry over to the corresponding <span class="s1">Substitution</span> object.<span class="Apple-converted-space">  </span>The <span class="s1">subpopID</span> in <span class="s1">Substitution</span> is a read-write property to allow it to be used as a “tag” in the same way, if the origin subpopulation identifier is not needed.</p>
 <p class="p3">tag &lt;–&gt; (integer$)</p>