multichrom fixes for the haplotype plot

Author: bhaller

QtSLiM/QtSLiMChromosomeWidget.cpp

@@ -569,19 +569,48 @@ Chromosome *QtSLiMChromosomeWidget::focalChromosome(void)
 {
     Species *focalSpecies = focalDisplaySpecies();
 
-    if (focalSpecies && focalChromosomeSymbol_.length())
+    if (focalSpecies)
     {
-        Chromosome *chromosome = focalSpecies->ChromosomeFromSymbol(focalChromosomeSymbol_);
-        
-        if (isOverview_ && !chromosome)
+        if (focalChromosomeSymbol_.length())
+        {
+            Chromosome *chromosome = focalSpecies->ChromosomeFromSymbol(focalChromosomeSymbol_);
+            
+            if (isOverview_ && !chromosome)
+            {
+                // The focal chromosome apparently no longer exists, but we want to keep
+                // trying to focus on it if it comes back (e.g., after a recycle), so we
+                // do not reset or forget the focal chromosome symbol here; we only reset
+                // the symbol to "" in setFocalDisplaySpecies() and setFocalChromosome().
+                // However, if the focal species has chromosomes (and they don't match),
+                // then apparently we're waiting for something that won't happen; give up
+                // and switch.
+                if (focalSpecies->Chromosomes().size() > 1)
+                {
+                    focalChromosomeSymbol_ = "";
+                    return nullptr;
+                }
+                else if (focalSpecies->Chromosomes().size() == 1)
+                {
+                    Chromosome *chromosome = focalSpecies->Chromosomes()[0];
+                    
+                    focalChromosomeSymbol_ = chromosome->Symbol();
+                    return chromosome;
+                }
+            }
+            
+            return chromosome;
+        }
+        else if (focalSpecies->Chromosomes().size() == 1)
         {
-            // the focal chromosome apparently no longer exists, but we want to keep
-            // trying to focus on it if it comes back (e.g., after a recycle), so we
-            // do not reset or forget the focal chromosome symbol here; we only reset
-            // the symbol to "" in setFocalDisplaySpecies() and setFocalChromosome()
+            // The species has just one chromosome, so there is no visual difference
+            // between that chromosome being selected vs. not selected.  However, we
+            // want to return that chromosome to the caller, so if it is not selected,
+            // we fix that here and return it.
+            Chromosome *chromosome = focalSpecies->Chromosomes()[0];
+            
+            focalChromosomeSymbol_ = chromosome->Symbol();
+            return chromosome;
         }
-        
-        return chromosome;
     }
 
     return nullptr;

QtSLiM/QtSLiMHaplotypeManager.cpp

@@ -35,6 +35,7 @@
 #include <QFileDialog>
 #include <QStandardPaths>
 #include <QLabel>
+#include <QMessageBox>
 #include <QDebug>
 
 #include <vector>
@@ -51,7 +52,40 @@
 // This class method runs a plot options dialog, and then produces a haplotype plot with a progress panel as it is being constructed
 void QtSLiMHaplotypeManager::CreateHaplotypePlot(QtSLiMChromosomeWidgetController *controller)
 {
+    QtSLiMWindow *slimWindow = controller->slimWindow();
+    
+    if (!slimWindow)
+        return;
+    
     Species *displaySpecies = controller->focalDisplaySpecies();
+    
+    if (!displaySpecies)
+    {
+        QMessageBox messageBox(slimWindow);
+        messageBox.setText("Haplotype Plot");
+        messageBox.setInformativeText("A single species must be chosen to create a haplotype plot; the plot will be based upon the selected species.");
+        messageBox.setIcon(QMessageBox::Warning);
+        messageBox.setWindowModality(Qt::WindowModal);
+        messageBox.exec();
+        return;
+    }
+    
+    // We need a single chromosome to work with; QtSLiMHaplotypeManager creates a haplotype
+    // plot for one chromosome, which makes sense since haplosomes assort independently.
+    // If we can't get a single chromosome, then we tell the user to select a chromosome.
+    Chromosome *chromosome = slimWindow->focalChromosome();
+    
+    if (!chromosome)
+    {
+        QMessageBox messageBox(slimWindow);
+        messageBox.setText("Haplotype Plot");
+        messageBox.setInformativeText("A single chromosome must be chosen to create a haplotype plot; the plot will be based upon the selected chromosome.");
+        messageBox.setIcon(QMessageBox::Warning);
+        messageBox.setWindowModality(Qt::WindowModal);
+        messageBox.exec();
+        return;
+    }
+    
     QtSLiMHaplotypeOptions optionsPanel(controller->slimWindow());
 
     int result = optionsPanel.exec();
@@ -63,9 +97,6 @@ void QtSLiMHaplotypeManager::CreateHaplotypePlot(QtSLiMChromosomeWidgetControlle
         QtSLiMHaplotypeManager::ClusteringOptimization clusteringOptimization = optionsPanel.clusteringOptimization();
 
         // First generate the haplotype plot data, with a progress panel
-        // FIXME MULTICHROM this code path should work with all of the chromosomes, probably...
-        Chromosome *chromosome = &displaySpecies->TheChromosome();
-        
         QtSLiMHaplotypeManager *haplotypeManager = new QtSLiMHaplotypeManager(nullptr, clusteringMethod, clusteringOptimization, controller,
                                                                               displaySpecies, chromosome, QtSLiMRange(0,0), haplosomeSampleSize, true);
 
@@ -214,6 +245,9 @@ QtSLiMHaplotypeManager::QtSLiMHaplotypeManager(QObject *p_parent, ClusteringMeth
 
     title.append(QString(", tick %1").arg(community->Tick()));
 
+    if (displaySpecies->Chromosomes().size() > 1)
+        title.append(QString(", chromosome '%2'").arg(QString::fromStdString(chromosome->Symbol())));
+    
     titleString = title;
     subpopCount = static_cast<int>(selected_subpops.size());
 

QtSLiM/QtSLiMWindow.cpp

@@ -2236,6 +2236,25 @@ Species *QtSLiMWindow::focalDisplaySpecies(void)
 	return nullptr;
 }
 
+Chromosome *QtSLiMWindow::focalChromosome(void)
+{
+    // There needs to be a focal display species to answer this question; if
+    // we are on the "all" tab in a multispecies model, there are multiple
+    // focal chromosomes, so we return nullptr.
+    Species *species = focalDisplaySpecies();
+    
+    if (!species)
+        return nullptr;
+    
+    // If there is one focal display species, then the first overview widget
+    // if the one being displayed (see updateChromosomeViewSetup()).
+    QtSLiMChromosomeWidget *overviewWidget = chromosomeOverviewWidgets[0];
+    
+    Chromosome *chromosome = overviewWidget->focalChromosome();
+    
+    return chromosome;
+}
+
 void QtSLiMWindow::selectedSpeciesChanged(void)
 {
     // We don't want to react to automatic tab changes as we are adding or removing tabs from the species bar

QtSLiM/QtSLiMWindow.h

@@ -185,6 +185,8 @@ class QtSLiMWindow : public QMainWindow
     void setScriptStringAndInitializeSimulation(std::string string);
 
     Species *focalDisplaySpecies(void);
+    Chromosome *focalChromosome(void);
+    
     void updateOutputViews(void);
     void updateTickCounter(void);
     void updateSpeciesBar(void);