set annotation draw function by type

[mussa.git] / alg / seq_span.hpp

diff --git a/alg/seq_span.hpp b/alg/seq_span.hpp
index 1752a7ad160ea862008c7117f08e6a195dc40a39..6635a10c9dfbd182f2dc0c50e70d01683b2041c9 100644 (file)
--- a/alg/seq_span.hpp
+++ b/alg/seq_span.hpp
@@ -58,7 +58,6 @@ public:
   enum strand_type { UnknownStrand, MinusStrand, PlusStrand, 
                      BothStrand, SameStrand, OppositeStrand, SingleStrand };
 
-public:
   SeqSpan(const SeqSpan &);
   SeqSpan(const SeqSpan *);
   explicit SeqSpan(const std::string &, 
@@ -123,7 +122,8 @@ public:
   size_type parentStop() const;
   //! set stop position relative to parent sequence
   void setParentStop(size_type);
-  size_type parentSize() const { return (parent) ? parent->size() : size(); }
+  size_type parentSize() const { return (parent_seq) ? parent_seq->size() : size(); }
+  SeqSpanRef parent() { return parent_seq; }
   
 
   //! return a subsequence, copying over any appropriate annotation
@@ -158,7 +158,7 @@ protected:
   strand_type seq_strand;
   
   //! keep a reference to who our parent span is 
-  SeqSpanRef parent;
+  SeqSpanRef parent_seq;
   
   //! hold a reverse complement version of our sequence if needed
   SeqStringRef rc_seq;  
@@ -179,7 +179,7 @@ protected:
     ar & BOOST_SERIALIZATION_NVP(seq_start);
     ar & BOOST_SERIALIZATION_NVP(seq_count);
     ar & BOOST_SERIALIZATION_NVP(seq_strand);
-    ar & BOOST_SERIALIZATION_NVP(parent);
+    ar & BOOST_SERIALIZATION_NVP(parent_seq);
   }
 };
 #endif /*SEQ_SPAN_HPP_*/