Store Sequence sequence location in a shared_ptr class

[mussa.git] / qui / MussaWindow.hpp

diff --git a/qui/MussaWindow.hpp b/qui/MussaWindow.hpp
index acec825b11fa3161a5b1cbc3750424f74e935ce7..f02f0917c299392c1600b9ba68db8a02b79f2884 100644 (file)
--- a/qui/MussaWindow.hpp
+++ b/qui/MussaWindow.hpp
@@ -4,6 +4,7 @@
 #include <list>
 #include <boost/shared_ptr.hpp>
 
+#include <QCloseEvent>
 #include <QDir>
 #include <QMainWindow>
 #include <QPixmap>
@@ -15,7 +16,7 @@
 #include "qui/motif_editor/MotifEditor.hpp"
 #include "qui/mussa_setup_dialog/MussaSetupDialog.hpp"
 #include "qui/seqbrowser/SequenceBrowserWidget.hpp"
-#include "qui/SubanalysisWindow.hpp"
+#include "qui/subanalysis/SubanalysisWindow.hpp"
 #include "qui/ThresholdWidget.hpp"
 #include "qui/ZoomWidget.hpp"
 
@@ -25,6 +26,9 @@ class QLabel;
 class QStringList;
 class Mussa;
 class QAssistantClient;
+class MussaWindow;
+
+typedef boost::shared_ptr<MussaWindow> MussaWindowRef;
 
 class MussaWindow : public QMainWindow
 {
@@ -33,6 +37,7 @@ class MussaWindow : public QMainWindow
 public: 
   MussaWindow(MussaRef analysis, QWidget *parent=0);
 
+public:
   //! reset any attached window
   void clear();
 
@@ -79,7 +84,7 @@ public slots:
   //! set the soft threshold used by the Nway_Path algorithm
   void setSoftThreshold(int thres);
   //! update progress bar
-  void updateProgress(const std::string& description, int cur, int max);
+  void updateProgress(const QString& description, int cur, int max);
 
   //! open a new mussa window so one can compare analyses
   void newMussaWindow();
@@ -106,7 +111,7 @@ protected:
   MussaRef analysis;
   //! the default directory we should loand and save from
   boost::shared_ptr<QDir> default_dir;
-  std::list<boost::shared_ptr<MussaAlignedWindow> > aligned_windows;
+  std::list<MussaAlignedWindowRef> aligned_windows;
   MotifEditor *motif_editor;
   MussaSetupDialog *setup_analysis_dialog;
   SubanalysisWindowRef subanalysis_window;
@@ -145,6 +150,8 @@ protected:
   void closeEvent(QCloseEvent *event);
   //! initialize this windows menu object
   void setupMainMenu();
+  //! initialize all of our widgets
+  void setupWidgets();
   //! initialize assistant client
   void setupAssistant();
   //! stub function to fill in QActions