1 #ifndef _MUSSAWINDOW_H_
2 #define _MUSSAWINDOW_H_
11 #include "qui/MussaAlignedWindow.hpp"
12 #include "qui/motif_editor/MotifEditor.hpp"
13 #include "qui/mussa_setup_dialog/MussaSetupDialog.hpp"
14 #include "qui/seqbrowser/SequenceBrowserWidget.hpp"
15 #include "qui/ThresholdWidget.hpp"
16 #include "qui/ZoomWidget.hpp"
23 class MussaWindow : public QMainWindow
28 MussaWindow(Mussa* analysis=0, QWidget *parent=0);
30 //! switch to a new analysis
31 void setAnalysis(Mussa *new_analysis);
33 //! display an about box, contemplating the politics of the author list
36 //! \defgroup AnalysisFunctions Components related to running analyses
38 //! open a window to collect the information needed to create a new analysis
39 void createNewAnalysis();
40 //! launch a sub analysis
41 void createSubAnalysis();
44 //! \defgroup MotifHandling Handling of motif lists
53 //! load a mussa parameter file (which specifies an analysis to run)
55 //! load a previously run analysis
56 void loadSavedAnalysis();
57 //! set the soft threshold used by the Nway_Path algorithm
58 void setSoftThreshold(int thres);
60 void showMussaToolbar();
62 //! open new window showing our alignment
63 void viewMussaAlignment();
66 void changedAnnotations();
70 std::list<MussaAlignedWindow *> aligned_windows;
71 MotifEditor *motif_editor;
72 MussaSetupDialog setup_analysis_dialog;
74 // display our wonderful mussa output
75 SequenceBrowserWidget browser;
78 ThresholdWidget threshold;
82 QAction *createNewAnalysisAction;
83 QAction *createSubAnalysisAction;
84 QAction *editMotifsAction;
85 QAction *loadMotifListAction;
86 QAction *loadMupaAction;
87 QAction *loadSavedAnalysisAction;
88 QAction *saveMotifListAction;
89 QAction *showMussaViewToolbarAction;
90 QAction *toggleMotifsAction;
91 QAction *saveBrowserPixmapAction;
92 QAction *whatsThisAction;
93 QAction *viewMussaAlignmentAction;
95 //! initialze the actions
97 //! initialize this windows menu object
99 //! stub function to fill in QActions
100 void NotImplementedBox();
103 //! update the SequenceBrowser with our analysis
104 void updateAnalysis();
105 //! update the view of conserved windows
107 //! update annotations?
108 void updateAnnotations();