Mark real sequence instead of Ns

[mussa.git] / alg / glsequence.cpp

diff --git a/alg/glsequence.cpp b/alg/glsequence.cpp
index 6c8b12b80410418e2e8bc2c0ec537a574724283a..c77c29b5369a4acf5ab72d2981c16e3f2d403d08 100644 (file)
--- a/alg/glsequence.cpp
+++ b/alg/glsequence.cpp
@@ -85,7 +85,7 @@ SeqSpanRef GlSequence::make_undefined_sequence_annotation(
   return empty_seq;
 }
 
-void GlSequence::add_annotations_for_undefined_sequence(Drawable::draw_func_ptr draw)
+void GlSequence::add_annotations_for_defined_sequence(Drawable::draw_func_ptr draw)
 {
   Sequence::const_iterator start_i = begin();
   Sequence::const_iterator seq_i = begin();
@@ -95,7 +95,7 @@ void GlSequence::add_annotations_for_undefined_sequence(Drawable::draw_func_ptr
   for(; seq_i != end_i; ++seq_i)
   {
     // need a better set of characters to serch for
-    if (*seq_i == 'N' or *seq_i == 'n') {
+    if (not (*seq_i == 'N' or *seq_i == 'n')) {
       if (start_block_i == end_i) {
         start_block_i = seq_i;
       }
@@ -280,7 +280,8 @@ void GlSequence::draw(GLfloat left, GLfloat right) const
 
 void GlSequence::draw_box(GLfloat world_left, GLfloat world_right,
                           GLfloat left, GLfloat right, 
-                          GLfloat height, GLfloat y, GLfloat z)
+                          GLfloat height, GLfloat y, GLfloat z,
+                          GLint primitive)
 {
   GLfloat pixel_width = pixelWidth(world_left, world_right);
   GLfloat offset = height/2.0;
@@ -291,7 +292,7 @@ void GlSequence::draw_box(GLfloat world_left, GLfloat world_right,
   if ((right-left) < pixel_width) {
     right = left + pixel_width;
   }
-  glBegin(GL_QUADS);
+  glBegin(primitive);
     glVertex3f(left,  top,    z);
     glVertex3f(left,  bottom, z);
     glVertex3f(right, bottom, z);
@@ -303,7 +304,7 @@ void GlSequence::draw_track(GLfloat left, GLfloat right) const
 {
   glColor3fv(color()->get());
   // draw main sequence track
-  draw_box(left, right, x(), x()+Sequence::size(), height(), y(), 0.0);
+  draw_box(left, right, x(), x()+Sequence::size(), height(), y(), 0.0, GL_LINE_LOOP);
 }
 
 void GlSequence::draw_annotations(GLfloat left, GLfloat right) const
@@ -465,8 +466,22 @@ void draw_narrow_track(SeqSpanRef s, float left, float right)
   float z( (parent_draw) ? parent_draw->z() : 10 );
   float height( (parent_draw) ? parent_draw->height() : default_height ); 
 
-  glColor3f(1.0, 1.0, 1.0);
-  float hsmall = height * 3.0/4.0;
+  glColor3f(0.0, 0.0, 0.0);
+  float hsmall = height * 0.5;
   GlSequence::draw_box(left, right, x+s->start(), x+s->stop(), 
                        hsmall, y, z+10);
+}
+
+void draw_track(SeqSpanRef s, float left, float right)
+{
+  SeqSpanRef parent(s->parent());
+  DrawableRef parent_draw(parent->drawable());
+  float x( (parent_draw) ? parent_draw->x() : 0);
+  float y( (parent_draw) ? parent_draw->y() : 0);
+  float z( (parent_draw) ? parent_draw->z() : 10 );
+  float height( (parent_draw) ? parent_draw->height() : default_height ); 
+
+  glColor3f(0.0, 0.0, 0.0);
+  GlSequence::draw_box(left, right, x+s->start(), x+s->stop(), 
+                       height, y, z+10);
 }
\ No newline at end of file