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

[mussa.git] / qui / MussaAlignedWindow.hpp

diff --git a/qui/MussaAlignedWindow.hpp b/qui/MussaAlignedWindow.hpp
index 452ac0e5bea391e48ba588a0a69d391833e8cd08..28d43d6e8e2fe82d03c244fb1eef1efc50d8a358 100644 (file)
--- a/qui/MussaAlignedWindow.hpp
+++ b/qui/MussaAlignedWindow.hpp
@@ -5,14 +5,16 @@
 
 #include <boost/shared_ptr.hpp>
 
+#include <QDir>
 #include <QMainWindow>
 #include <QMenu>
 #include <QToolBar>
 #include "alg/mussa.hpp"
 #include "qui/IntAction.hpp"
 #include "qui/ZoomWidget.hpp"
+#include "qui/ThresholdWidget.hpp"
 #include "qui/seqbrowser/SequenceBrowserWidget.hpp"
-#include "qui/SubanalysisWindow.hpp"
+#include "qui/subanalysis/SubanalysisWindow.hpp"
 
 //! Show sequence alignments
 class MussaAlignedWindow : public QMainWindow
@@ -27,7 +29,9 @@ public:
    *         sequence portions from both the mussa window and the sequence view window
    *  \param parent is the typical Qt pointer to a parent widget
    */ 
-  MussaAlignedWindow(MussaRef analysis, const std::set<int>& paths, 
+  MussaAlignedWindow(MussaRef analysis, 
+                     boost::shared_ptr<QDir> default_dir,
+                     const std::set<int>& paths, 
                      SubanalysisWindowRef window, QWidget *parent=0);
 
 public slots:
@@ -40,6 +44,11 @@ public slots:
 
   //! just force updating the window
   void update();
+  
+  //! set the title based on the analysis
+  void updateTitle();
+  //! display how many base pairs were copied on the status bar
+  void showBasePairsCopied(size_t);
 
 protected:
   // figure out what Alignments we have (needed for setupAlignmentMenus)
@@ -52,7 +61,8 @@ protected:
   void setupAlignmentMenus();
   void computeMatchLines();
   
-  MussaRef analysis;  
+  MussaRef analysis;
+  boost::shared_ptr<QDir> default_dir;
   //std::vector<Sequence> sequences;
   //const std::set<int>& selected_paths;
   std::vector<ConservedPath> selected_paths;
@@ -68,6 +78,7 @@ protected:
   std::vector <IntAction *> pick_actions;
   std::vector <IntAction *> view_actions;
   ZoomWidget *zoom;
+  ThresholdWidget *threshold_widget;
   QToolBar *alignTB;
 };