1 #ifndef _MUSSAWINDOW_H_
2 #define _MUSSAWINDOW_H_
5 #include <boost/shared_ptr.hpp>
9 #include <QProgressDialog>
13 #include "qui/MussaAlignedWindow.hpp"
14 #include "qui/motif_editor/MotifEditor.hpp"
15 #include "qui/mussa_setup_dialog/MussaSetupDialog.hpp"
16 #include "qui/seqbrowser/SequenceBrowserWidget.hpp"
17 #include "qui/SubanalysisWindow.hpp"
18 #include "qui/ThresholdWidget.hpp"
19 #include "qui/ZoomWidget.hpp"
26 class QAssistantClient;
28 class MussaWindow : public QMainWindow
33 MussaWindow(Mussa* analysis=0, QWidget *parent=0);
35 //! reset any attached window
38 //! switch to a new analysis
39 void setAnalysis(Mussa *new_analysis);
41 //! display an about box, contemplating the politics of the author list
44 //! \defgroup AnalysisFunctions Components related to running analyses
46 //! open a window to collect the information needed to create a new analysis
47 void createNewAnalysis();
48 //! launch a sub analysis
49 void createSubAnalysis();
54 //! \defgroup MotifHandling Handling of motif lists
63 //! load a mussa parameter file (which specifies an analysis to run)
65 //! load a previously run analysis
66 void loadSavedAnalysis();
67 //! set the soft threshold used by the Nway_Path algorithm
68 void setSoftThreshold(int thres);
69 //! update progress bar
70 void updateProgress(const std::string& description, int cur, int max);
72 //! open a new mussa window so one can compare analyses
73 void newMussaWindow();
75 void showMussaToolbar();
77 //! open new window showing our alignment
78 void viewMussaAlignment();
80 //! display mussagl manual
83 void assistantError(const QString message);
86 void changedAnnotations();
90 std::list<boost::shared_ptr<MussaAlignedWindow> > aligned_windows;
91 MotifEditor *motif_editor;
92 MussaSetupDialog setup_analysis_dialog;
93 SubanalysisWindow subanalysis_window;
95 // display our wonderful mussa output
96 SequenceBrowserWidget browser;
99 ThresholdWidget threshold;
100 QProgressDialog *progress_dialog;
102 QAction *aboutAction;
103 QAction *closeAction;
104 QAction *createNewAnalysisAction;
105 QAction *createSubAnalysisAction;
106 QAction *saveAnalysisAction;
107 QAction *editMotifsAction;
108 QAction *loadMotifListAction;
109 QAction *loadMupaAction;
110 QAction *loadSavedAnalysisAction;
111 QAction *mussaManualAssistantAction;
112 QAction *newMussaWindowAction;
113 QAction *saveMotifListAction;
114 QAction *showMussaViewToolbarAction;
115 QAction *toggleMotifsAction;
116 QAction *saveBrowserPixmapAction;
117 QAction *whatsThisAction;
118 QAction *viewMussaAlignmentAction;
120 QAssistantClient *manualAssistant;
122 //! initialze the actions
124 //! initialize this windows menu object
125 void setupMainMenu();
126 //! initialize assistant client
127 void setupAssistant();
128 //! stub function to fill in QActions
129 void NotImplementedBox();
132 //! update the SequenceBrowser with our analysis
133 void updateAnalysis();
134 //! update the view of conserved windows
136 //! update annotations?
137 void updateAnnotations();