1 #ifndef _GL_SEQUENCE_H_
2 #define _GL_SEQUENCE_H_
4 #include <boost/shared_ptr.hpp>
6 #include "alg/annotation_colors.hpp"
7 #include "alg/sequence.hpp"
8 #include "alg/color.hpp"
9 // isn't it lovely how the header file can live in different places?
11 #include <OpenGL/gl.h>
17 typedef boost::shared_ptr<GlSequence> GlSequenceRef;
19 //! Manage rendering a mussa sequence track
20 /*! The idea is this will keep track of the location of where the sequence
21 * is being rendered, and handle displaying annotations on that track
23 class GlSequence : public Sequence
26 GlSequence(const Sequence & s,
27 boost::shared_ptr<AnnotationColors> cm);
28 GlSequence(const GlSequence & s);
29 GlSequence(const GlSequence *);
30 //! Make a new GlSequence, using a copy of SeqSpan
31 GlSequence(const GlSequenceRef);
33 GlSequence &operator=(const GlSequence &s);
35 static DrawableRef default_drawable();
36 static DrawableRef copy_drawable(DrawableRef s);
38 //! search through sequence and add an annotation highlighting all the non AGCT characters
39 void add_annotations_for_undefined_sequence(Drawable::draw_func_ptr draw=0);
40 //! set our starting x (horizontal) coordinate
42 //! get our starting x (horizontal) coordinate
44 //! set our current y (vertical) position
46 //! get our current y (vertical) position
48 //! get our current z (depth) position
50 //! how thick (high) the track we're drawing is
53 //! set our default draw color
54 void setColor(ColorRef &c );
55 //! return our draw color
56 const ColorRef color() const;
57 //! return our draw color
59 //! return our annotation color mapper
60 AnnotationColorsRef colorMapper() { return color_mapper; }
63 /*! left and right are the edges of the current viewport
65 void draw(GLfloat left, GLfloat right) const;
67 //! get our right (horizontal) coordinate (size-x)
69 //! how long is our sequence track? (computed from the sequence)
72 //! return the left (lowest) base index that is fully visible
73 Sequence::size_type leftbase(GLfloat left) const;
74 //! return one past rightmost (highest ) base index that is fully visible
75 //! done mostly so all the iterator logic continues to work correctly.
76 Sequence::size_type rightbase(GLfloat right) const;
78 //! provide an iterator to the sequence starting at world coordinate left
79 Sequence::const_iterator region_begin(GLfloat left, GLfloat right) const;
80 //! provide an iterator to the sequence ending at world coordinate right
81 Sequence::const_iterator region_end(GLfloat left, GLfloat right) const;
83 //! return a subsequence as a GlSequence (instead of a Sequence subsequence)
84 GlSequence subseq(size_type start, size_type count) const;
86 //! how big is a pixel in world coordinats
87 GLfloat pixelWidth(GLfloat, GLfloat) const;
88 //! how big is a pixel in world coordinats (specifying viewport size)
89 GLfloat pixelWidth(GLfloat, GLfloat, int) const;
91 //! are we close enough that it would make sense to view the base pairs?
92 bool is_sequence_renderable(GLfloat left, GLfloat right) const;
93 //! are we close enough that it would make sense to view the base pairs?
94 /*! though we don't actually check to see if there's sequence in our
95 * view, just that there's enough pixels to render something if
97 * \param[in] left the left edge of the viewable region in world coordinates
98 * \param[in] right the right edge of the viewable region in world
100 * \param[in] pixel_width allow setting the current viewport pixel width
102 bool is_sequence_renderable(GLfloat, GLfloat, int) const;
104 friend bool operator==(const GlSequence &left, const GlSequence &right);
107 AnnotationColorsRef color_mapper;
108 const GLfloat char_pix_per_world_unit;
110 //! initalize a SeqSpanRef covering start, count
111 SeqSpanRef make_undefined_sequence_annotation(
112 Drawable::draw_func_ptr draw,
116 //! Return the pixel width of the opengl viewport.
117 static int get_viewport_width_in_pixels();
118 //! draw a from left to right +/- height/2
119 void draw_box(GLfloat world_left, GLfloat world_right, GLfloat left, GLfloat right, GLfloat height, GLfloat z) const;
120 //! draw sequence as a bar
121 void draw_track(GLfloat, GLfloat) const;
122 void draw_annotations(GLfloat, GLfloat) const;
123 //! render a sequence as ATGC
124 /*! left and right are the current edges of the viewable world
126 void draw_sequence(GLfloat, GLfloat) const;