new MutationBlock class for per-species mutation storage

Author: bhaller

QtSLiM/QtSLiMAppDelegate.cpp

@@ -244,7 +244,7 @@ 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_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!
@@ -178,7 +180,7 @@ void QtSLiMChromosomeWidget::glDrawMutations(QRect &interiorRect, Chromosome *ch
     {
         int registry_size;
         const MutationIndex *registry = pop.MutationRegistry(&registry_size);
-        Mutation *mut_block_ptr = gSLiM_Mutation_Block;
+        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)

QtSLiM/QtSLiMChromosomeWidget_QT.cpp

@@ -24,6 +24,8 @@
 
 #include <QtDebug>
 
+#include "mutation_block.h"
+
 #include <map>
 #include <algorithm>
 #include <vector>
@@ -174,7 +176,7 @@ void QtSLiMChromosomeWidget::qtDrawMutations(QRect &interiorRect, Chromosome *ch
     {
         int registry_size;
         const MutationIndex *registry = pop.MutationRegistry(&registry_size);
-        Mutation *mut_block_ptr = gSLiM_Mutation_Block;
+        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)

QtSLiM/QtSLiMGraphView.cpp

@@ -48,6 +48,7 @@
 #include "subpopulation.h"
 #include "haplosome.h"
 #include "mutation_run.h"
+#include "mutation_block.h"
 
 
 QFont QtSLiMGraphView::labelFontOfPointSize(double size)
@@ -2551,7 +2552,7 @@ size_t QtSLiMGraphView::tallyGUIMutationReferences(slim_objectid_t subpop_id, in
     Population &population = graphSpecies->population_;
     size_t subpop_total_haplosome_count = 0;
 
-    Mutation *mut_block_ptr = gSLiM_Mutation_Block;
+    Mutation *mut_block_ptr = graphSpecies->SpeciesMutationBlock()->mutation_buffer_;
 
     {
         int registry_size;
@@ -2618,7 +2619,7 @@ size_t QtSLiMGraphView::tallyGUIMutationReferences(const std::vector<Haplosome *
 
     Population &population = graphSpecies->population_;
 
-	Mutation *mut_block_ptr = gSLiM_Mutation_Block;
+	Mutation *mut_block_ptr = graphSpecies->SpeciesMutationBlock()->mutation_buffer_;
 
     {
         int registry_size;

QtSLiM/QtSLiMGraphView_1DPopulationSFS.cpp

@@ -23,6 +23,8 @@
 
 #include <string>
 
+#include "mutation_block.h"
+
 
 QtSLiMGraphView_1DPopulationSFS::QtSLiMGraphView_1DPopulationSFS(QWidget *p_parent, QtSLiMWindow *controller) : QtSLiMGraphView(p_parent, controller)
 {
@@ -89,9 +91,10 @@ double *QtSLiMGraphView_1DPopulationSFS::populationSFS(int mutationTypeCount)
 	Population &pop = graphSpecies->population_;
 
 	pop.TallyMutationReferencesAcrossPopulation(/* p_clock_for_mutrun_experiments */ false);	// update tallies; usually this will just use the cache set up by Population::MaintainRegistry()
-	
-	Mutation *mut_block_ptr = gSLiM_Mutation_Block;
-	slim_refcount_t *refcount_block_ptr = gSLiM_Mutation_Refcounts;
+    
+    MutationBlock *mutation_block = graphSpecies->SpeciesMutationBlock();
+	Mutation *mut_block_ptr = mutation_block->mutation_buffer_;
+    slim_refcount_t *refcount_block_ptr = mutation_block->refcount_buffer_;
     int registry_size;
     const MutationIndex *registry = pop.MutationRegistry(&registry_size);
 
@@ -101,7 +104,7 @@ double *QtSLiMGraphView_1DPopulationSFS::populationSFS(int mutationTypeCount)
         Chromosome *mut_chromosome = graphSpecies->Chromosomes()[mutation->chromosome_index_];
         double totalHaplosomeCount = ((mut_chromosome->total_haplosome_count_ == 0) ? 1 : mut_chromosome->total_haplosome_count_);   // prevent a zero count from producing NAN frequencies below
 
-		slim_refcount_t mutationRefCount = *(refcount_block_ptr + mutation->BlockIndex());
+		slim_refcount_t mutationRefCount = *(refcount_block_ptr + mutation_block->IndexInBlock(mutation));
 		double mutationFrequency = mutationRefCount / totalHaplosomeCount;
 		int mutationBin = static_cast<int>(floor(mutationFrequency * binCount));
 		int mutationTypeIndex = mutation->mutation_type_ptr_->mutation_type_index_;

QtSLiM/QtSLiMGraphView_1DSampleSFS.cpp

@@ -33,6 +33,7 @@
 #include "QtSLiMWindow.h"
 #include "subpopulation.h"
 #include "mutation_type.h"
+#include "mutation_block.h"
 
 
 QtSLiMGraphView_1DSampleSFS::QtSLiMGraphView_1DSampleSFS(QWidget *p_parent, QtSLiMWindow *controller) : QtSLiMGraphView(p_parent, controller)
@@ -300,7 +301,7 @@ uint64_t *QtSLiMGraphView_1DSampleSFS::mutation1DSFS(void)
 
         // Tally into our bins
         sfs1dbuf_ = static_cast<uint64_t *>(calloc(histogramBinCount_, sizeof(uint64_t)));
-        Mutation *mut_block_ptr = gSLiM_Mutation_Block;
+        Mutation *mut_block_ptr = graphSpecies->SpeciesMutationBlock()->mutation_buffer_;
         int registry_size;
         const MutationIndex *registry = population.MutationRegistry(&registry_size);
 

QtSLiM/QtSLiMGraphView_2DPopulationSFS.cpp

@@ -27,6 +27,7 @@
 #include <vector>
 
 #include "mutation_type.h"
+#include "mutation_block.h"
 
 
 QtSLiMGraphView_2DPopulationSFS::QtSLiMGraphView_2DPopulationSFS(QWidget *p_parent, QtSLiMWindow *controller) : QtSLiMGraphView(p_parent, controller)
@@ -232,7 +233,7 @@ double *QtSLiMGraphView_2DPopulationSFS::mutation2DSFS(void)
 		return nullptr;
 
     // Get frequencies in subpop1 and subpop2
-    Mutation *mut_block_ptr = gSLiM_Mutation_Block;
+    Mutation *mut_block_ptr = graphSpecies->SpeciesMutationBlock()->mutation_buffer_;
     std::vector<slim_refcount_t> refcounts1, refcounts2;
     size_t subpop1_total_haplosome_count, subpop2_total_haplosome_count;
 

QtSLiM/QtSLiMGraphView_2DSampleSFS.cpp

@@ -33,6 +33,7 @@
 #include "QtSLiMWindow.h"
 #include "subpopulation.h"
 #include "mutation_type.h"
+#include "mutation_block.h"
 
 
 QtSLiMGraphView_2DSampleSFS::QtSLiMGraphView_2DSampleSFS(QWidget *p_parent, QtSLiMWindow *controller) : QtSLiMGraphView(p_parent, controller)
@@ -347,7 +348,7 @@ uint64_t *QtSLiMGraphView_2DSampleSFS::mutation2DSFS(void)
         int registry_size;
         const MutationIndex *registry = population.MutationRegistry(&registry_size);
         const MutationIndex *registry_iter_end = registry + registry_size;
-        Mutation *mut_block_ptr = gSLiM_Mutation_Block;
+        Mutation *mut_block_ptr = graphSpecies->SpeciesMutationBlock()->mutation_buffer_;
 
         // Find our subpops and mutation type
         Subpopulation *subpop1 = graphSpecies->SubpopulationWithID(selectedSubpopulation1ID_);

QtSLiM/QtSLiMGraphView_FrequencyTrajectory.cpp

@@ -30,6 +30,7 @@
 
 #include "QtSLiMWindow.h"
 #include "subpopulation.h"
+#include "mutation_block.h"
 
 
 QtSLiMGraphView_FrequencyTrajectory::QtSLiMGraphView_FrequencyTrajectory(QWidget *p_parent, QtSLiMWindow *controller) : QtSLiMGraphView(p_parent, controller)
@@ -137,7 +138,7 @@ void QtSLiMGraphView_FrequencyTrajectory::fetchDataForFinishedTick(void)
         subpop_total_haplosome_count = 1;  // refcounts will all be zero; prevent NAN values below, make them 0 instead
 
     // Now we can run through the mutations and use the tallies in gui_scratch_reference_count to update our histories
-    Mutation *mut_block_ptr = gSLiM_Mutation_Block;
+    Mutation *mut_block_ptr = graphSpecies->SpeciesMutationBlock()->mutation_buffer_;
 
     for (const MutationIndex *registry_iter = registry; registry_iter != registry_iter_end; ++registry_iter)
     {

QtSLiM/QtSLiMHaplotypeManager.cpp

@@ -46,6 +46,7 @@
 #include "eidos_globals.h"
 #include "subpopulation.h"
 #include "species.h"
+#include "mutation_block.h"
 
 
 const int QtSLiM_SubpopulationStripWidth = 5;
@@ -480,7 +481,7 @@ 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 = gSLiM_Mutation_Block;
+	Mutation *mut_block_ptr = graphSpecies->SpeciesMutationBlock()->mutation_buffer_;
 
 	for (const MutationIndex *reg_ptr = registry; reg_ptr != reg_end_ptr; ++reg_ptr)
 	{