Make MussaWindow UI objects pointers

It appears to me that Qt seems to like UI widgets that are attached to
it to be pointers as it'll sometimes handle freeing said pointer, which is
bad when its a statically allocated member of a class.

So this patch tries to make most of the UI objects associated with
MussaWindow pointers (I had to convert some elements of the
SequenceBrowserWidget as MussaWindow was storing references to them.)

diff --git a/qui/MussaAlignedWindow.cpp b/qui/MussaAlignedWindow.cpp
index d54ef3d445a3fc49d745216e05fa512de311165a..f418b02e8e7626e088030e4ff513153a90a0b8f4 100644 (file)
--- a/qui/MussaAlignedWindow.cpp
+++ b/qui/MussaAlignedWindow.cpp
@@ -63,7 +63,7 @@ void MussaAlignedWindow::setupMenus()
   newMenu->addAction(saveBrowserPixmapAction);
 
   newMenu = menuBar()->addMenu(tr("&Edit"));
-  newMenu->addAction(&browser.getCopySelectedSequenceAsFastaAction());
+  newMenu->addAction(browser.getCopySelectedSequenceAsFastaAction());
 }
 
 void MussaAlignedWindow::setupAlignmentMenus()

diff --git a/qui/MussaWindow.cpp b/qui/MussaWindow.cpp
index 6b0e8a7e9e07614ea9e596e12bde4a2dfd4660eb..a079974dd5666005aef4d0f49171fa4dc6735cff 100644 (file)
--- a/qui/MussaWindow.cpp
+++ b/qui/MussaWindow.cpp
@@ -34,11 +34,12 @@ MussaWindow::MussaWindow(Mussa *analysis_, QWidget *parent) :
   analysis(analysis_),
   default_dir(QDir::home().absolutePath().toStdString(), fs::native),
   motif_editor(0),
-  setup_analysis_dialog(this),
-  browser(this),
-  mussaViewTB("Path Views"),
-  zoom(),
-  threshold(),
+  setup_analysis_dialog(new MussaSetupDialog(this)),
+  subanalysis_window(new SubanalysisWindow),
+  browser(new SequenceBrowserWidget(this)),  
+  mussaViewTB(new QToolBar("Path Views")),
+  zoom(new ZoomWidget),
+  threshold(new ThresholdWidget),
   progress_dialog(0),
   aboutAction(0),
   closeAction(0),
@@ -66,28 +67,28 @@ MussaWindow::MussaWindow(Mussa *analysis_, QWidget *parent) :
   // a segfault when using WhatsThis feature with 
   // opengl widget.
   //scene->setWhatsThis(tr("Mussa in OpenGL!"));
-  setCentralWidget(&browser);
+  setCentralWidget(browser);
   // well updatePosition isn't quite right as we really just need
   // to call update()
-  connect(this, SIGNAL(changedAnnotations()), &browser, SLOT(update()));
+  connect(this, SIGNAL(changedAnnotations()), browser, SLOT(update()));
 
-  //mussaViewTB.addAction(toggleMotifsAction);
-  mussaViewTB.addWidget(&zoom);
+  //mussaViewTB->addAction(toggleMotifsAction);
+  mussaViewTB->addWidget(zoom);
   
-  connect(&zoom, SIGNAL(valueChanged(double)), 
-          &browser, SLOT(setZoom(double)));
+  connect(zoom, SIGNAL(valueChanged(double)), 
+          browser, SLOT(setZoom(double)));
   
   // threshold range is set in updateAnalysis
   
   //scene->setClipPlane(20);
   // FIXME: for when we get the paths drawn at the appropriate depth
-  //connect(&threshold, SIGNAL(thresholdChanged(int)),
+  //connect(threshold, SIGNAL(thresholdChanged(int)),
   //        this, SLOT(setClipPlane(int)));
-  connect(&threshold, SIGNAL(thresholdChanged(int)),
+  connect(threshold, SIGNAL(thresholdChanged(int)),
           this, SLOT(setSoftThreshold(int)));
-  mussaViewTB.addWidget(&threshold);
+  mussaViewTB->addWidget(threshold);
 
-  addToolBar(&mussaViewTB);
+  addToolBar(mussaViewTB);
 
   statusBar()->showMessage("Welcome to mussa", 2000);
   connect(analysis, SIGNAL(progress(const std::string&, int, int)),
@@ -194,7 +195,7 @@ void MussaWindow::setupActions()
   //Save pixel map action
   saveBrowserPixmapAction = new QAction(tr("Save to image..."), this);
   connect(saveBrowserPixmapAction, (SIGNAL(triggered())),
-         &browser, SLOT(promptSaveBrowserPixmap()));
+         browser, SLOT(promptSaveBrowserPixmap()));
   saveBrowserPixmapAction->setIcon(QIcon(":/icons/image2.png"));
 
   viewMussaAlignmentAction = new QAction(tr("View sequence alignment"), this);
@@ -242,7 +243,7 @@ void MussaWindow::setupMainMenu()
 
   newMenu = menuBar()->addMenu(tr("&Edit"));
   newMenu->addAction(editMotifsAction);
-  newMenu->addAction(&browser.getCopySelectedSequenceAsFastaAction());
+  newMenu->addAction(browser->getCopySelectedSequenceAsFastaAction());
   newMenu->addAction(createSubAnalysisAction);
  
   newMenu = menuBar()->addMenu(tr("&View"));
@@ -256,9 +257,11 @@ void MussaWindow::setupMainMenu()
   newMenu->addAction(aboutAction);
 
   // add some extra features to the context menu
-  QMenu& popupMenu = browser.getPopupMenu();
-  popupMenu.addAction(viewMussaAlignmentAction);
-  popupMenu.addAction(createSubAnalysisAction);
+  QMenu *popupMenu = browser->getPopupMenu();
+  if (popupMenu) {
+    popupMenu->addAction(viewMussaAlignmentAction);
+    popupMenu->addAction(createSubAnalysisAction);
+  }
 }
 
 void MussaWindow::setupAssistant()
@@ -289,7 +292,7 @@ void MussaWindow::about()
 void MussaWindow::clear()
 {
   aligned_windows.clear();
-  browser.clear();
+  browser->clear();
 }
 
 void MussaWindow::createNewAnalysis()
@@ -299,9 +302,9 @@ void MussaWindow::createNewAnalysis()
     // but this should work for the moment.
     if (not isClearingAnalysisSafe()) return;
 
-    if (setup_analysis_dialog.exec()) {
+    if (setup_analysis_dialog->exec()) {
       Mussa *m = 0;
-      m = setup_analysis_dialog.getMussa();
+      m = setup_analysis_dialog->getMussa();
       setAnalysis(m);
     }
   } catch(mussa_error e) {
@@ -313,8 +316,8 @@ void MussaWindow::createNewAnalysis()
 void MussaWindow::createSubAnalysis()
 {
   list<SequenceLocation> result;
-  SequenceLocationModel& model = subanalysis_window.getModel();
-  browser.copySelectedTracksAsSeqLocation(result);
+  SequenceLocationModel& model = subanalysis_window->getModel();
+  browser->copySelectedTracksAsSeqLocation(result);
   for(list<SequenceLocation>::iterator result_itor = result.begin();
       result_itor != result.end();
       ++result_itor)
@@ -322,8 +325,8 @@ void MussaWindow::createSubAnalysis()
     model.push_back(*result_itor);
   }
 
-  if (not subanalysis_window.isVisible()) {
-    subanalysis_window.show();
+  if (not subanalysis_window->isVisible()) {
+    subanalysis_window->show();
   }
 }
 
@@ -557,10 +560,10 @@ void MussaWindow::setSoftThreshold(int threshold)
 
 void MussaWindow::showMussaToolbar()
 {
-  if (mussaViewTB.isVisible())
-    mussaViewTB.hide();
+  if (mussaViewTB->isVisible())
+    mussaViewTB->hide();
   else
-    mussaViewTB.show();
+    mussaViewTB->show();
 }
 
 void MussaWindow::toggleMotifs()
@@ -597,7 +600,7 @@ void MussaWindow::NotImplementedBox()
 
 void MussaWindow::viewMussaAlignment()
 {
-  const set<int>& selected_paths = browser.selectedPaths();
+  const set<int>& selected_paths = browser->selectedPaths();
   if (selected_paths.size() == 0 ) {
     QMessageBox::warning(this, 
                          QObject::tr("mussa"),
@@ -617,13 +620,17 @@ void MussaWindow::viewMussaAlignment()
                         
 void MussaWindow::updateAnalysis()
 {
-  threshold.setRange(analysis->get_threshold(),analysis->get_window());
-
   const Mussa::vector_sequence_type& seqs = analysis->sequences();
-  browser.setSequences(seqs, analysis->colorMapper());
+  browser->setSequences(seqs, analysis->colorMapper());
+  assert(browser->sequences().size() == analysis->size());
+
+  // setRange eventually emits something that causes updateLinks to be called
+  // but it's possible for us to not have had a chance to set out sequences
+  // yet.
+  threshold->setRange(analysis->get_threshold(),analysis->get_window());
   updateLinks();
-  browser.zoomOut();
-  zoom.setValue(browser.zoom());
+  browser->zoomOut();
+  zoom->setValue(browser->zoom());
 }
 
 void MussaWindow::updateAnnotations()
@@ -631,12 +638,17 @@ void MussaWindow::updateAnnotations()
   // motifs were changed in the sequences by 
   // Mussa::update_sequences_motifs
   emit changedAnnotations();
-  browser.update();
+  browser->update();
 }
 
 void MussaWindow::updateLinks()
 {
-  browser.clear_links();
+  if(browser->sequences().size() == 0) {
+    // we don't have any sequences load so we have no business setting links
+    return;
+  }
+
+  browser->clear_links();
   bool reversed = false;
   const NwayPaths& nway = analysis->paths();
 
@@ -674,9 +686,9 @@ void MussaWindow::updateLinks()
       normalized_path.push_back(x);
       rc_flags.push_back(reversed);
     }
-    browser.link(normalized_path, rc_flags, path_itor->window_size);
+    browser->link(normalized_path, rc_flags, path_itor->window_size);
   }
-  browser.update();
+  browser->update();
 }
 
 void 

diff --git a/qui/MussaWindow.hpp b/qui/MussaWindow.hpp
index d81d027b621debb87be8603f2424128113b7247c..83692d394fdc9fd30e852959e1d64c6ec8183982 100644 (file)
--- a/qui/MussaWindow.hpp
+++ b/qui/MussaWindow.hpp
@@ -99,14 +99,14 @@ protected:
   boost::filesystem::path default_dir;
   std::list<boost::shared_ptr<MussaAlignedWindow> > aligned_windows;
   MotifEditor *motif_editor;
-  MussaSetupDialog setup_analysis_dialog;
-  SubanalysisWindow subanalysis_window;
+  MussaSetupDialog *setup_analysis_dialog;
+  boost::shared_ptr<SubanalysisWindow> subanalysis_window;
 
   // display our wonderful mussa output
-  SequenceBrowserWidget browser;
-  QToolBar mussaViewTB;
-  ZoomWidget zoom;
-  ThresholdWidget threshold;
+  SequenceBrowserWidget *browser;
+  QToolBar *mussaViewTB;
+  ZoomWidget *zoom;
+  ThresholdWidget *threshold;
   QProgressDialog *progress_dialog;
 
   QAction *aboutAction;

diff --git a/qui/seqbrowser/SequenceBrowser.cpp b/qui/seqbrowser/SequenceBrowser.cpp
index 3d31f7f748bbb0bfaa29f95f40cdf53f1e38e639..fbfc124d3d33fbb5e96d36172f12930dee19c055 100644 (file)
--- a/qui/seqbrowser/SequenceBrowser.cpp
+++ b/qui/seqbrowser/SequenceBrowser.cpp
@@ -20,21 +20,21 @@ using namespace std;
 SequenceBrowser::SequenceBrowser(QWidget *parent)
   : QGLWidget(parent),
     rubberBand(0),
-    popupMenu(this),
-    copySelectedSequenceAsFastaAction(tr("&Copy as Fasta"), this)
+    popupMenu(new QMenu(this)),
+    copySelectedSequenceAsFastaAction(new QAction(tr("&Copy as Fasta"), this))
 { 
-  connect(&copySelectedSequenceAsFastaAction, SIGNAL(triggered()), 
+  connect(copySelectedSequenceAsFastaAction, SIGNAL(triggered()), 
           this, SLOT(copySelectedSequenceAsFasta()));
-  copySelectedSequenceAsFastaAction.setShortcut(Qt::CTRL | Qt::Key_C);
-  popupMenu.addAction(&copySelectedSequenceAsFastaAction);
+  copySelectedSequenceAsFastaAction->setShortcut(Qt::CTRL | Qt::Key_C);
+  popupMenu->addAction(copySelectedSequenceAsFastaAction);
 }
 
-QMenu &SequenceBrowser::getPopupMenu()
+QMenu *SequenceBrowser::getPopupMenu()
 {
   return popupMenu;
 }
 
-QAction &SequenceBrowser::getCopySelectedSequenceAsFastaAction()
+QAction *SequenceBrowser::getCopySelectedSequenceAsFastaAction()
 {
   return copySelectedSequenceAsFastaAction;
 }
@@ -105,7 +105,7 @@ void SequenceBrowser::clear()
 
 void SequenceBrowser::displayContextMenu(const QPoint& point)
 {
-  popupMenu.popup(point);
+  popupMenu->popup(point);
 }
 
 void SequenceBrowser::push_sequence(boost::shared_ptr<Sequence> s)

diff --git a/qui/seqbrowser/SequenceBrowser.hpp b/qui/seqbrowser/SequenceBrowser.hpp
index 7ada6124d2cab26c56e2c84a0fe60f9ff41c8076..8d1ef65a0c611ba90076b5b54d1c7c481db7cb94 100644 (file)
--- a/qui/seqbrowser/SequenceBrowser.hpp
+++ b/qui/seqbrowser/SequenceBrowser.hpp
@@ -34,9 +34,9 @@ public:
   void push_sequence(boost::shared_ptr<GlSequence>);
 
   //! return the popup menu for the glcanvas (reference stored internally)
-  QMenu &getPopupMenu();
+  QMenu *getPopupMenu();
   //! return our copy actioy (reference stored internally)
-  QAction &getCopySelectedSequenceAsFastaAction();
+  QAction *getCopySelectedSequenceAsFastaAction();
 
 public slots:
   void copySelectedSequenceAsFasta();
@@ -71,7 +71,7 @@ protected:
   void stopSelecting(QMouseEvent *);
   /* \@} */
 
-  QMenu popupMenu;
-  QAction copySelectedSequenceAsFastaAction;
+  QMenu *popupMenu;
+  QAction *copySelectedSequenceAsFastaAction;
 };
 #endif

diff --git a/qui/seqbrowser/SequenceBrowserWidget.cpp b/qui/seqbrowser/SequenceBrowserWidget.cpp
index 615291347b8872942b47455ffde77d76476859c5..0ce3030d48a9265226228d5f4f0e484740dd3490 100644 (file)
--- a/qui/seqbrowser/SequenceBrowserWidget.cpp
+++ b/qui/seqbrowser/SequenceBrowserWidget.cpp
@@ -51,12 +51,12 @@ void SequenceBrowserWidget::clear()
   right_sidebar.clear();
 }
 
-QMenu &SequenceBrowserWidget::getPopupMenu()
+QMenu *SequenceBrowserWidget::getPopupMenu()
 {
   return scrollable_browser.browser().getPopupMenu();
 }
 
-QAction &SequenceBrowserWidget::getCopySelectedSequenceAsFastaAction()
+QAction *SequenceBrowserWidget::getCopySelectedSequenceAsFastaAction()
 {
   return scrollable_browser.browser().getCopySelectedSequenceAsFastaAction();
 }

diff --git a/qui/seqbrowser/SequenceBrowserWidget.hpp b/qui/seqbrowser/SequenceBrowserWidget.hpp
index 332fa1bf0f4c05d6c9268dfde508e9c76d4ca9c5..fedb86f6accb8e0e2af22c79a8e3c7bcb2257215 100644 (file)
--- a/qui/seqbrowser/SequenceBrowserWidget.hpp
+++ b/qui/seqbrowser/SequenceBrowserWidget.hpp
@@ -20,9 +20,9 @@ public:
   SequenceBrowserWidget(QWidget *parent=0);
 
   //! return the popup menu for the glcanvas (reference stored internally)
-  QMenu &getPopupMenu();
+  QMenu *getPopupMenu();
   //! return our copy actioy (reference stored internally)
-  QAction &getCopySelectedSequenceAsFastaAction();
+  QAction *getCopySelectedSequenceAsFastaAction();
 
   //! copy selected track regions into a list of SequenceLocations
   void copySelectedTracksAsSeqLocation(std::list<SequenceLocation>& );