GlSequence::GlSequence(const Sequence &s,
boost::shared_ptr<AnnotationColors> cm)
: Sequence(s),
- seq_x(0.0),
- seq_y(0.0),
- seq_z(1.0),
- seq_height(12.0),
color_mapper(cm),
- drawColor(new Color(0.0, 0.0, 0.0)),
char_pix_per_world_unit(2.5)
{
+ seq->setDrawable(default_drawable());
}
GlSequence::GlSequence(const GlSequence &s)
: Sequence(s),
- seq_x(s.seq_x),
- seq_y(s.seq_y),
- seq_z(s.seq_z),
- seq_height(s.seq_height),
color_mapper(s.color_mapper),
- drawColor(s.drawColor),
char_pix_per_world_unit(s.char_pix_per_world_unit)
{
+ seq->setDrawable(copy_drawable(s.seq->drawable()));
}
GlSequence::GlSequence(const GlSequence *s)
: Sequence(s),
- seq_x(s->seq_x),
- seq_y(s->seq_y),
- seq_z(s->seq_z),
- seq_height(s->seq_height),
color_mapper(s->color_mapper),
- drawColor(s->drawColor),
char_pix_per_world_unit(s->char_pix_per_world_unit)
{
+ seq->setDrawable(copy_drawable(s->seq->drawable()));
+}
+
+GlSequence::GlSequence(const GlSequenceRef s)
+ : Sequence( (SequenceRef)s ),
+ color_mapper(s->color_mapper),
+ char_pix_per_world_unit(s->char_pix_per_world_unit)
+{
+ seq->setDrawable(copy_drawable(s->seq->drawable()));
}
GlSequence &GlSequence::operator=(const GlSequence & s)
{
if (this != &s) {
Sequence::operator=(s);
- seq_x = s.seq_x;
- seq_y = s.seq_y;
- seq_z = s.seq_z;
- seq_height = s.seq_height;
+ seq->setDrawable(copy_drawable(s.seq->drawable()));
color_mapper = s.color_mapper;
- drawColor = s.drawColor;
assert(char_pix_per_world_unit == s.char_pix_per_world_unit);
}
return *this;
}
-void GlSequence::setX(GLfloat value)
+DrawableRef GlSequence::default_drawable()
{
- seq_x = value;
+ ColorRef c(new Color(0.0, 0.0, 0.0));
+ DrawableRef d(new Drawable(0.0, 0.0, 1.0, 12.0, c));
+ return d;
}
-GLfloat GlSequence::x() const
+DrawableRef GlSequence::copy_drawable(DrawableRef old_d)
{
- return seq_x;
+ ColorRef c(old_d->color());
+ DrawableRef d(new Drawable(old_d));
+ // use the same color
+ d->setColor(c);
+ return d;
}
-GLfloat GlSequence::right() const
+void GlSequence::setX(float value)
{
- return size()+seq_x;
+ seq->drawable()->setX(value);
+}
+
+float GlSequence::x() const
+{
+ return seq->drawable()->x();
}
void GlSequence::setY(GLfloat value)
{
- seq_y = value;
+ seq->drawable()->setY(value);
}
-GLfloat GlSequence::y() const
+float GlSequence::y() const
{
- return seq_y;
+ return seq->drawable()->y();
}
-GLfloat GlSequence::height() const
+float GlSequence::z() const
{
- return seq_height;
+ return seq->drawable()->z();
+}
+
+float GlSequence::height() const
+{
+ return seq->drawable()->height();
+}
+
+GLfloat GlSequence::right() const
+{
+ return size()+x();
}
GLfloat GlSequence::size() const
Sequence::size_type GlSequence::leftbase(GLfloat left) const
{
- left = ceil(left - seq_x);
+ left = ceil(left - x());
if (left < 0)
return 0;
else if (left > Sequence::size() )
Sequence::size_type GlSequence::rightbase(GLfloat right) const
{
- right = floor(right) - seq_x;
+ right = floor(right) - x();
if (right > Sequence::size())
return Sequence::size();
else if ( right < 0)
{
GlSequence new_seq(*this);
new_seq.seq = seq->subseq(start, count);
+ // make sure our subseq has a drawable attached to it
+ // perhaps we should figure out correct x,y,z,h coords
+ DrawableRef d(default_drawable());
+ // and default to our current color
+ ColorRef c(color());
+ d->setColor(c);
+ new_seq.seq->setDrawable(d);
copy_children(new_seq, start, count);
return new_seq;
}
-//! set default track draw color
-void GlSequence::setColor(boost::shared_ptr<Color> &c)
+void GlSequence::setColor(ColorRef &c)
+{
+ seq->drawable()->setColor(c);
+}
+
+ColorRef GlSequence::color()
{
- drawColor = c;
+ return seq->drawable()->color();
}
-//! get default track draw color
-boost::shared_ptr<Color> GlSequence::color()
+const ColorRef GlSequence::color() const
{
- return drawColor;
+ return seq->drawable()->color();
}
int GlSequence::get_viewport_width_in_pixels()
{
GLfloat pixel_width = pixelWidth(world_left, world_right);
GLfloat offset = height/2.0;
- GLfloat top = seq_y + offset;
- GLfloat bottom = seq_y - offset;
+ GLfloat top = y() + offset;
+ GLfloat bottom = y() - offset;
// make our box be at least 1 pixel
if ((right-left) < pixel_width) {
void GlSequence::draw_track(GLfloat left, GLfloat right) const
{
- glColor3fv(drawColor->get());
+ glColor3fv(color()->get());
// draw main sequence track
- draw_box(left, right, seq_x, seq_x+Sequence::size(), seq_height, 0.0);
+ draw_box(left, right, x(), x()+Sequence::size(), height(), 0.0);
}
void GlSequence::draw_annotations(GLfloat left, GLfloat right) const
{
// draw annotations
- GLfloat annotation_z = seq_z + 10.0;
+ GLfloat annotation_z = z() + 10.0;
const std::list<annot>& annots = Sequence::annotations();
const std::list<motif>& motifs = Sequence::motifs();
for (std::list<annot>::const_iterator annot_itor = annots.begin();
++annot_itor)
{
glColor3f(0.0, 0.8, 0.0);
- draw_box(left, right, seq_x+annot_itor->begin, seq_x+annot_itor->end,
- seq_height, annotation_z);
+ draw_box(left, right, x()+annot_itor->begin, x()+annot_itor->end,
+ height(), annotation_z);
}
// if motifs?
for (std::list<motif>::const_iterator motifs_itor = motifs.begin();
++motifs_itor)
{
glColor3fv(color_mapper->lookup("motif", motifs_itor->sequence).get());
- draw_box(left, right, seq_x+motifs_itor->begin, seq_x+motifs_itor->end,
- seq_height, annotation_z+1.0);
+ draw_box(left, right, x()+motifs_itor->begin, x()+motifs_itor->end,
+ height(), annotation_z+1.0);
}
}
// FIXME: basically this needs to be greater than the number of annotations
const GLfloat z = 30;
glLineWidth(1);
- glColor3fv(drawColor->get());
+ glColor3fv(color()->get());
Sequence::const_iterator seq_itor = region_begin(left, right);
Sequence::const_iterator seq_end = region_end(left, right);
{
assert ( basepair < Sequence::size() );
glPushMatrix();
- glTranslatef( seq_x+leftbase(left) + basepair + glyph_margin, seq_y, 1.0 );
+ glTranslatef( x()+leftbase(left) + basepair + glyph_margin, y(), 1.0 );
glScalef(glyph_x_scale, 1.0, 1.0);
switch (*seq_itor) {
case 'A': case 'a':
bool operator==(const GlSequence &left, const GlSequence &right)
{
- return ( (left.seq_x == right.seq_x) and
- (left.seq_y == right.seq_y) and
- (left.seq_z == right.seq_z) and
- (left.seq_height == right.seq_height) and
- (left.drawColor == right.drawColor));
+ return ( (left.x() == right.x()) and
+ (left.y() == right.y()) and
+ (left.z() == right.z()) and
+ (left.height() == right.height()) and
+ (left.color() == right.color()));
}
projects / mussa.git / blobdiff