X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=mussa.git;a=blobdiff_plain;f=alg%2Fglsequence.hpp;h=7882d23a9340db77cbea53fdd2a3893726f46660;hp=4d93d15b66969aea13f3a51026352c58c9524a4a;hb=292ef077dafe705f4b367c426839d7154f464148;hpb=f2858f72af9cbe3258229bda254f186f279c5c8c

diff --git a/alg/glsequence.hpp b/alg/glsequence.hpp
index 4d93d15..7882d23 100644
--- a/alg/glsequence.hpp
+++ b/alg/glsequence.hpp
@@ -35,6 +35,8 @@ public:
   static DrawableRef default_drawable();
   static DrawableRef copy_drawable(DrawableRef s);
   
+  //! search through sequence and add an annotation highlighting all the non AGCT characters
+  void add_annotations_for_undefined_sequence(Drawable::draw_func_ptr draw=0);
   //! set our starting x (horizontal) coordinate
   void setX(float x);
   //! get our starting x (horizontal) coordinate
@@ -105,6 +107,12 @@ protected:
   AnnotationColorsRef color_mapper;
   const GLfloat char_pix_per_world_unit;
 
+  //! initalize a SeqSpanRef covering start, count
+  SeqSpanRef GlSequence::make_undefined_sequence_annotation(
+    Drawable::draw_func_ptr draw,
+    size_type start,
+    size_type count);
+
   //! Return the pixel width of the opengl viewport.
   static int get_viewport_width_in_pixels();
   //! draw a from left to right +/- height/2