8 #include "alg/annotation_colors.hpp"
9 #include "alg/sequence.hpp"
10 #include "alg/glsequence.hpp"
12 //! Manage rendering a collection of glSequences
17 GlSeqBrowser(const GlSeqBrowser&);
19 //! setup the opengl canvas
21 //! called when our screen canvas is resized
22 void resizeGL(int width, int height);
26 //! select a region (using canvas coordinates)
27 void selectRegion(int top, int left, int bottom, int right);
32 //! max world left coordinate
34 //! max world right coordinate
37 void setViewportCenter(float x);
38 //! return world coordinate of the left side of the viewport
39 float viewportLeft() const;
40 //! return world coordinate of the center of the viewport
41 float viewportCenter() const;
42 //! return world coordinate of the right side of the viewport
43 float viewportRight() const;
44 //! return height of the viewport in world coordinates
45 float viewportHeight() const;
46 //! return width of the viewport in world coordinates
47 float viewportWidth() const;
49 //! zoom out far enough to show the full size of the sequence
51 //! zoom in to a reasonable sequence view
52 double zoomToSequence();
53 //! set the current zoom level in (base pairs / pix )
54 //! its a double as zoom levels of [0.01, 1.0] make nice sequence views
55 void setZoom(double zoom_level);
56 //! returns the current zoom level as basepairs per pixel
58 //! center the provided path in the current viewport
59 void centerOnPath(const std::vector<int>&);
61 void setColorMapper(AnnotationColors& cm);
62 AnnotationColors& colorMapper();
64 //! clear our tracks and connections
66 //! clear everything related to a selection
67 void clear_selection();
69 //! add a sequence to the back of our track container
70 void push_sequence(const Sequence &s);
71 //! add a glsequence to the back of our track container
72 void push_sequence(GlSequence &s);
73 //! return our track container
74 const std::vector<GlSequence>& sequences() const;
76 //! clear all the line segments between all the sequences
79 void link(const std::vector<int>& path, const std::vector<bool>& isRC, int length);
80 //! returns the index of pathids based on order added by link
81 const std::set<int>& selectedPaths() const;
82 //! define our function for formating sequence copy
83 typedef std::string format_track(const Sequence& s, int left, int right);
84 //! copy sequence from selected track using formating function
85 void copySelectedTracks(std::string& copy_buffer, format_track func);
86 //! copy sequence from selected tracks as plain sequences
87 void copySelectedTracksAsString(std::string& copy_buffer);
88 //! copy sequence from selected tracks as FASTA sequences
89 void copySelectedTracksAsFasta(std::string& copy_buffer);
92 //! Provide a logical name for a type discriminator for our glName stack
93 enum FeatureType { MussaTrack, MussaSegment };
95 //! a useful point class
96 template<class T> struct point {
100 point(T x_, T y_):x(x_), y(y_) {}
103 //! a useful rectangle, where 0,0 is in the lower left
104 template<class T> struct rect {
111 rect(T t, T l, T b, T r) : top(t), left(l), bottom(b), right(r) {}
112 T width() { return right - left; }
113 T height() { return top - bottom; }
114 void clear() { top=0; left=0; bottom=0; right=0; }
122 std::set<int> path_ids;
124 Segment() : start(0.0, 0.0), end(0.0, 0.0) {}
125 Segment(float x1, float y1, float x2, float y2, bool isRC)
126 : start(x1, y1), end(x2, y2), reversed(isRC) {}
129 //! data structure holding our line segments
130 /*! the vector is of size track_container.size()-1
131 * it's indexed by the pair x1, x2 (the two x coordinates between
134 typedef std::pair<int, int> segment_key;
135 typedef std::map<segment_key, Segment> pair_segment_map;
136 typedef std::vector<pair_segment_map> path_segment_map_vector;
137 path_segment_map_vector path_segments;
145 TrackRegion():track_id(0), left(0), right(0) {};
146 TrackRegion(const TrackRegion& o)
147 : track_id(o.track_id), left(o.left), right(o.right) {}
148 TrackRegion(GLuint id, int l, int r)
149 : track_id(id), left(l), right(r) {}
150 void set(GLuint id, int l, int r) { track_id = id; left=l; right=r; };
154 //! recalculate the viewable world
155 /*! depending on the size of our canvas, our zoom level and
156 * how far we've been offset
158 void update_viewport(float center, double new_zoom);
160 //! determine where all the tracks should be placed
161 void update_layout();
163 //! convert opengl selections into the list of paths we should highlight
164 void processSelection(GLuint hits,
167 const rect<float>& r);
169 //! master scene drawing function
170 /*! draw is broken out for the opengl selection code
173 //! draw glsequence tracks
174 void draw_tracks() const;
175 //! draw line segments between tracks
176 void draw_segments() const;
177 //! draw selection box
178 void draw_selection() const;
180 //! number of pixels to reserve around the edges of our canvas
181 const int border_width;
182 //! the current viewable region (world coord)
183 rect<float> cur_ortho;
184 //! how many pixels our viewport is (screen coord)
185 point<int> viewport_size;
186 //! the center of our current viewport (world coord) (used for scrollbar)
187 float viewport_center;
189 AnnotationColors color_mapper;
190 //! container of all the GlSequences loaded into our scene
191 std::vector<GlSequence> track_container;
192 //! counter for each path added to us via connect
196 //! where to draw our box (world coordinates)
197 rect<float> selectedRegion;
198 //! true if we have a selection
200 //! indicate which paths are selected
201 std::set<int> selected_paths;
202 //! which track is selected (it only makes sense to have one track selected).
203 std::list<TrackRegion> selected_tracks;
204 typedef std::list<TrackRegion>::iterator selected_track_iterator;