incorporate drawable and annotations

[mussa.git] / alg / seq_span.hpp

diff --git a/alg/seq_span.hpp b/alg/seq_span.hpp
index 5a2da1268d3a62cf807f323d7e39bb450fea5841..f5e574814c532b7ea95246695fc837e7d534bd40 100644 (file)
--- a/alg/seq_span.hpp
+++ b/alg/seq_span.hpp
@@ -2,6 +2,7 @@
 #define SEQ_SPAN_HPP_
 
 #include <string>
+#include <map>
 
 #include <boost/serialization/base_object.hpp>
 #include <boost/serialization/export.hpp>
@@ -18,6 +19,8 @@
 
 //! These classes provide for the internal implementation for the Sequence class
 #include "seq.hpp"
+#include "annotations.hpp"
+#include "drawable.hpp"
 
 class SeqSpan;
 typedef boost::shared_ptr<SeqSpan> SeqSpanRef;
@@ -128,11 +131,16 @@ public:
   std::string sequence() const; 
   //! are both sequences derived from the same sequence tree?
   static bool isFamily(const SeqSpan& a, const SeqSpan& b);
+
+  //! access annotations dictionary
+  AnnotationsRef annotations() const { return seq_annotations; }
+  //! set annotations dictionary
+  void setAnnotations(AnnotationsRef a) { seq_annotations = a; }
+  //! get data for drawing
+  DrawableRef drawable() const { return seq_drawable; }
+  //! store drawing data
+  void setDrawable(DrawableRef d) { seq_drawable = d; }
   
-  //! fill in our rc_seq variable 
-  void initialize_rc_seq() const;
-  
-  friend class Sequence;
 private:
   //! do not statically initialize, only create with new
   SeqSpan() {};
@@ -148,10 +156,18 @@ protected:
   
   //! keep a reference to who our parent span is 
   SeqSpanRef parent;
-
+  
   //! hold a reverse complement version of our sequence if needed
-  SeqStringRef rc_seq;
+  SeqStringRef rc_seq;  
+  //! fill in our rc_seq variable 
+  void initialize_rc_seq() const;
   
+  //! annotations provides a python-dictionary like place for metadata
+  AnnotationsRef seq_annotations;
+  //! store information needed for drawing
+  DrawableRef seq_drawable;
+  
+  friend class Sequence;
   // boost::serialization support
   friend class boost::serialization::access;
   template<class Archive>