1 #ifndef _MUSSAWINDOW_H_
2 #define _MUSSAWINDOW_H_
11 #include "qui/MussaAlignedWindow.hpp"
12 #include "qui/motif_editor/MotifEditor.hpp"
13 #include "qui/seqbrowser/SequenceBrowserWidget.hpp"
14 #include "qui/ThresholdWidget.hpp"
20 class MussaWindow : public QMainWindow
25 MussaWindow(Mussa* analysis=0, QWidget *parent=0);
28 //! display an about box, contemplating the politics of the author list
31 //! \defgroup AnalysisFunctions Components related to running analyses
33 //! open a window to collect the information needed to create a new analysis
34 void createNewAnalysis();
35 //! launch a sub analysis
36 void createSubAnalysis();
39 //! \defgroup MotifHandling Handling of motif lists
48 //! load a mussa parameter file (which specifies an analysis to run)
50 //! load a previously run analysis
51 void loadSavedAnalysis();
52 //! set the soft threshold used by the Nway_Path algorithm
53 void setSoftThreshold(int thres);
55 void showMussaToolbar();
57 //! open new window showing our alignment
58 void viewMussaAlignment();
61 void changedAnnotations();
65 std::list<MussaAlignedWindow *> aligned_windows;
66 MotifEditor *motif_editor;
68 // display our wonderful mussa output
69 SequenceBrowserWidget browser;
72 ThresholdWidget threshold;
78 QAction *createNewAnalysisAction;
79 QAction *createSubAnalysisAction;
80 QAction *editMotifsAction;
81 QAction *loadMotifListAction;
82 QAction *loadMupaAction;
83 QAction *loadSavedAnalysisAction;
84 QAction *saveMotifListAction;
85 QAction *showMussaViewToolbarAction;
86 QAction *toggleMotifsAction;
87 QAction *saveBrowserPixmapAction;
88 QAction *whatsThisAction;
89 QAction *viewMussaAlignmentAction;
91 //! initialze the actions
93 //! initialize this windows menu object
95 //! stub function to fill in QActions
96 void NotImplementedBox();
99 //! update the SequenceBrowser with our analysis
100 void updateAnalysis();
101 //! update the view of conserved windows
103 //! update annotations?
104 void updateAnnotations();