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; }
62 //! draw a from left to right +/- height/2
64 void draw_box(GLfloat world_left, GLfloat world_right,
65 GLfloat left, GLfloat right, GLfloat height,
66 GLfloat y, GLfloat z);
68 /*! left and right are the edges of the current viewport
70 void draw(GLfloat left, GLfloat right) const;
72 //! get our right (horizontal) coordinate (size-x)
74 //! how long is our sequence track? (computed from the sequence)
77 //! return the left (lowest) base index that is fully visible
78 Sequence::size_type leftbase(GLfloat left) const;
79 //! return one past rightmost (highest ) base index that is fully visible
80 //! done mostly so all the iterator logic continues to work correctly.
81 Sequence::size_type rightbase(GLfloat right) const;
83 //! provide an iterator to the sequence starting at world coordinate left
84 Sequence::const_iterator region_begin(GLfloat left, GLfloat right) const;
85 //! provide an iterator to the sequence ending at world coordinate right
86 Sequence::const_iterator region_end(GLfloat left, GLfloat right) const;
88 //! return a subsequence as a GlSequence (instead of a Sequence subsequence)
89 GlSequence subseq(size_type start, size_type count) const;
91 //! Return the pixel width of the opengl viewport.
92 static int get_viewport_width_in_pixels();
93 //! how big is a pixel in world coordinats
94 static GLfloat pixelWidth(GLfloat, GLfloat);
95 //! how big is a pixel in world coordinats (specifying viewport size)
96 static GLfloat pixelWidth(GLfloat, GLfloat, int);
98 //! are we close enough that it would make sense to view the base pairs?
99 bool is_sequence_renderable(GLfloat left, GLfloat right) const;
100 //! are we close enough that it would make sense to view the base pairs?
101 /*! though we don't actually check to see if there's sequence in our
102 * view, just that there's enough pixels to render something if
104 * \param[in] left the left edge of the viewable region in world coordinates
105 * \param[in] right the right edge of the viewable region in world
107 * \param[in] pixel_width allow setting the current viewport pixel width
109 bool is_sequence_renderable(GLfloat, GLfloat, int) const;
111 friend bool operator==(const GlSequence &left, const GlSequence &right);
114 AnnotationColorsRef color_mapper;
115 const GLfloat char_pix_per_world_unit;
117 //! initalize a SeqSpanRef covering start, count
118 SeqSpanRef make_undefined_sequence_annotation(
119 Drawable::draw_func_ptr draw,
123 //! draw sequence as a bar
124 void draw_track(GLfloat, GLfloat) const;
125 void draw_annotations(GLfloat, GLfloat) const;
126 //! render a sequence as ATGC
127 /*! left and right are the current edges of the viewable world
129 void draw_sequence(GLfloat, GLfloat) const;
132 void draw_narrow_track(SeqSpanRef ref, float left, float right);