3 #include <boost/shared_ptr.hpp>
9 #include "alg/annotation_colors.hpp"
10 #include "alg/sequence.hpp"
11 #include "alg/glsequence.hpp"
12 #include "alg/sequence_location.hpp"
13 #include "alg/track_region.hpp"
15 //! Manage rendering a collection of glSequences
20 GlSeqBrowser(const GlSeqBrowser&);
22 //! setup the opengl canvas
24 //! called when our screen canvas is resized
25 void resizeGL(int width, int height);
29 //! select a region (using canvas coordinates)
30 void selectRegion(int top, int left, int bottom, int right);
35 //! max world left coordinate
37 //! max world right coordinate
39 // return how wide is a pixel in world coordinates?
40 float get_pixel_width() const;
42 void setViewportCenter(float x);
43 //! return world coordinate of the left side of the viewport
44 float viewportLeft() const;
45 //! return world coordinate of the center of the viewport
46 float viewportCenter() const;
47 //! return world coordinate of the right side of the viewport
48 float viewportRight() const;
49 //! return height of the viewport in world coordinates
50 float viewportHeight() const;
51 //! return width of the viewport in world coordinates
52 float viewportWidth() const;
54 //! return viewport height in pixels
55 int viewportPixelHeight() const;
56 //! return viewport width in pixels
57 int viewportPixelWidth() const;
59 //! zoom out far enough to show the full size of the sequence
61 //! zoom in to a reasonable sequence view
62 double zoomToSequence();
63 //! set the current zoom level in (base pairs / pix )
64 //! its a double as zoom levels of [0.01, 1.0] make nice sequence views
65 void setZoom(double zoom_level);
66 //! returns the current zoom level as basepairs per pixel
68 //! center the provided path in the current viewport
69 void centerOnPath(const std::vector<int>&);
71 void setColorMapper(boost::shared_ptr<AnnotationColors> cm);
72 const AnnotationColors& colorMapper();
74 //! clear our tracks and connections
76 //! clear everything related to a selection
77 void clear_selection();
79 //! add a sequence to the back of our track container (makes copy of s)
80 void push_sequence(const Sequence& s);
81 //! add a sequence to the back of our track container
82 void push_sequence(boost::shared_ptr<Sequence> s);
83 //! add a glsequence to the back of our track container
84 void push_sequence(GlSequence s);
85 //! add a glsequence to the back of our track container
86 void push_sequence(boost::shared_ptr<GlSequence> gs);
87 //! return our track container
88 const std::vector<boost::shared_ptr<GlSequence> >& sequences() const;
90 //! clear all the line segments between all the sequences
93 void link(const std::vector<int>& path, const std::vector<bool>& isRC, int length);
94 //! set selected paths (it'd be nice if this could be a templated function)
95 void setSelectedPaths(std::vector<int> c);
96 //! returns the index of pathids based on order added by link
97 const std::set<int>& selectedPaths() const;
99 //! set selected tracks (it'd be nice if this could be a templated function)
100 void appendSelectedTrack(GLuint track_index, int left, int right);
102 //! return list of selected tracks
103 std::list<TrackRegion> selectedTracks() const;
105 //! copy sequence from selected track using formating function
107 size_t copySelectedTracks(std::list<Item>& result,
108 Item (*format_track)(const Sequence& s, int left, int right));
109 //! copy sequence from selected tracks as FASTA sequences
110 /*! \return number of base pairs copied
112 size_t copySelectedTracksAsFasta(std::string& copy_buffer);
113 //! copy sequence from selected tracks as a list of sequences
114 /*! \return number of base pairs copied
116 size_t copySelectedTracksAsSequences(std::list<Sequence>& result);
117 //! copy sequence from selected tracks as plain sequences
118 /*! \return number of base pairs copied
120 size_t copySelectedTracksAsString(std::string& copy_buffer);
122 //! copy tracks as a sequence and its coordinates
123 size_t copySelectedTracksAsSeqLocation(std::list<SequenceLocation>& result);
126 //! Provide a logical name for a type discriminator for our glName stack
127 enum FeatureType { MussaTrack, MussaSegment };
129 //! a useful point class
130 template<class T> struct point {
134 point(T x_, T y_):x(x_), y(y_) {}
137 //! a useful rectangle, where 0,0 is in the lower left
138 template<class T> struct rect {
145 rect(T t, T l, T b, T r) : top(t), left(l), bottom(b), right(r) {}
146 T width() { return right - left; }
147 T height() { return top - bottom; }
148 void clear() { top=0; left=0; bottom=0; right=0; }
157 // each integer represents an index into our list of paths
158 std::set<int> path_ids;
160 Segment() : start(0.0, 0.0), end(0.0, 0.0), reversed(false), length(0) {}
161 Segment(float x1, float y1, float x2, float y2, bool isRC, int length_)
162 : start(x1, y1), end(x2, y2), reversed(isRC), length(length_) {}
165 //! data structure holding our line segments
166 /*! the vector is of size track_container.size()-1
167 * it's indexed by the pair x1, x2 (the two x coordinates between
170 typedef std::pair<int, int> segment_key;
171 typedef std::map<segment_key, Segment> pair_segment_map;
172 typedef std::vector<pair_segment_map> path_segment_map_vector;
173 path_segment_map_vector path_segments;
176 //! recalculate the viewable world
177 /*! depending on the size of our canvas, our zoom level and
178 * how far we've been offset
180 void update_viewport(float center, double new_zoom);
182 //! determine where all the tracks should be placed
183 void update_layout();
185 //! convert opengl selections into the list of paths we should highlight
186 void processSelection(GLuint hits,
189 const rect<float>& r);
191 //! master scene drawing function
192 /*! draw is broken out for the opengl selection code
195 //! draw glsequence tracks
196 void draw_tracks() const;
197 //! draw line segments between tracks
198 void draw_segments() const;
199 //! draw selection box
200 void draw_selection() const;
202 //! number of pixels to reserve around the edges of our canvas
203 const int border_width;
204 //! the current viewable region (world coord)
205 rect<float> cur_ortho;
206 //! how many pixels our viewport is (screen coord)
207 point<int> viewport_size;
208 //! the center of our current viewport (world coord) (used for scrollbar)
209 float viewport_center;
211 boost::shared_ptr<AnnotationColors> color_mapper;
212 //! counter for each path added to us via connect
216 //! container of all the GlSequences loaded into our scene
217 std::vector<boost::shared_ptr<GlSequence> > track_container;
218 //! where to draw our box (world coordinates)
219 rect<float> selectedRegion;
220 //! true if we have a selection
222 //! indicate which paths are selected
223 std::set<int> selected_paths;
224 //! which track is selected (it only makes sense to have one track selected).
225 std::list<TrackRegion> selected_tracks;
226 typedef std::list<TrackRegion>::iterator selected_track_iterator;