Update mussa to build on ubuntu 10.04 with qt 4.6.2 +boost 1.40.0.1

[mussa.git] / qui / MussaWindow.hpp

diff --git a/qui/MussaWindow.hpp b/qui/MussaWindow.hpp
index d81d027b621debb87be8603f2424128113b7247c..bba3106191748925ffb57bc83c77b2ee7878ff3c 100644 (file)
--- a/qui/MussaWindow.hpp
+++ b/qui/MussaWindow.hpp
@@ -4,17 +4,20 @@
 #include <list>
 #include <boost/shared_ptr.hpp>
 
+#include <QCloseEvent>
+#include <QDir>
 #include <QMainWindow>
 #include <QPixmap>
 #include <QProgressDialog>
 #include <QSpinBox>
 #include <QToolBar>
+#include <QProcess>
 
 #include "qui/MussaAlignedWindow.hpp"
 #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"
 
@@ -24,19 +27,23 @@ class QLabel;
 class QStringList;
 class Mussa;
 class QAssistantClient;
+class MussaWindow;
+
+typedef boost::shared_ptr<MussaWindow> MussaWindowRef;
 
 class MussaWindow : public QMainWindow
 {
   Q_OBJECT
 
 public: 
-  MussaWindow(Mussa* analysis=0, QWidget *parent=0);
+  MussaWindow(MussaRef analysis, QWidget *parent=0);
 
+public:
   //! reset any attached window
   void clear();
 
   //! switch to a new analysis
-  void setAnalysis(Mussa *new_analysis);
+  void setAnalysis(MussaRef new_analysis);
 
   //! ask the user what to do if we're going to lose data
   //! returns true if getting rid of this analysis is safe
@@ -56,6 +63,10 @@ public slots:
   void saveAnalysis();
   //! save an analysis after prompting for new name
   void saveAnalysisAs();
+  //! set the window modified flag
+  void updateAnalysisModified(bool);
+  //! try to conver the mussa analysis_path to a title
+  void updateTitle();
   //\@}
 
   //! \defgroup MotifHandling Handling of motif lists
@@ -74,12 +85,15 @@ 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();
 
   void showMussaToolbar();
+  //! display how many base pairs were copied on the status bar
+  void showBasePairsCopied(size_t);
+
 
   //! open new window showing our alignment
   void viewMussaAlignment();
@@ -91,22 +105,23 @@ public slots:
 
 signals:
   void changedAnnotations();
+  void changedMotifs();
 
 protected:
-  //! reference to our analysis
-  Mussa *analysis;
+  //! shared_ptr to our analysis
+  MussaRef analysis;
   //! the default directory we should loand and save from
-  boost::filesystem::path default_dir;
-  std::list<boost::shared_ptr<MussaAlignedWindow> > aligned_windows;
+  boost::shared_ptr<QDir> default_dir;
+  std::list<MussaAlignedWindowRef> aligned_windows;
   MotifEditor *motif_editor;
-  MussaSetupDialog setup_analysis_dialog;
-  SubanalysisWindow subanalysis_window;
+  MussaSetupDialog *setup_analysis_dialog;
+  SubanalysisWindowRef 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;
@@ -128,7 +143,8 @@ protected:
   QAction *whatsThisAction;
   QAction *viewMussaAlignmentAction;
 
-  QAssistantClient *manualAssistant;
+  //QAssistantClient *manualAssistant;
+  QProcess *assistantProcess;
 
   //! initialze the actions
   void setupActions();
@@ -136,6 +152,8 @@ 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