1 #ifndef MUSSA_ALIGNED_WINDOW_H
2 #define MUSSA_ALIGNED_WINDOW_H
8 #include "alg/mussa.hpp"
9 #include "qui/IntAction.hpp"
10 #include "qui/seqbrowser/SequenceBrowserWidget.hpp"
12 //! Show sequence alignments
13 class MussaAlignedWindow : public QMainWindow
18 //! construct an aligned window for an analysis and selected paths
19 MussaAlignedWindow(Mussa&, const std::set<int>&, QWidget *parent=0);
22 //! use selected_paths[pathid] to set the starting position of our sequence
23 void setAlignment(int pathid);
24 //! toggle whether or not to show the aligned basepairs of a window
25 void toggleViewAlignment(size_t alignment_index);
27 //! just force updating the window
31 void setSelectedPaths(Mussa &m, const std::set<int>& sel_paths);
32 //! set menus (must be called after setSelectedPaths)
34 void computeMatchLines();
37 //std::vector<Sequence> sequences;
38 //const std::set<int>& selected_paths;
39 std::vector<ExtendedConservedPath> selected_paths;
40 std::vector<bool> view_paths;
41 SequenceBrowserWidget browser;
42 QMenu pick_align_menu;
43 QMenu view_align_menu;
44 std::vector <IntAction *> pick_actions;
45 std::vector <IntAction *> view_actions;