move strand into seqspan

[mussa.git] / alg / sequence.hpp

diff --git a/alg/sequence.hpp b/alg/sequence.hpp
index 4b93ef132d81b93e924e153965407b32585c7851..80aa49f75e17bcf9ca572de2d9b8c53658ea31af 100644 (file)
--- a/alg/sequence.hpp
+++ b/alg/sequence.hpp
@@ -103,13 +103,14 @@ public:
   typedef SeqString::const_reference const_reference;
   typedef SeqString::size_type size_type;
   static const size_type npos = SeqString::npos;
-  enum strand_type { UnknownStrand, PlusStrand, MinusStrand, BothStrand };
                       
-  Sequence(AlphabetRef a = reduced_nucleic_alphabet);
+  Sequence(AlphabetRef a = reduced_dna_alphabet);
   Sequence(const char* seq, 
-           AlphabetRef a = reduced_nucleic_alphabet);
+           AlphabetRef a = reduced_dna_alphabet,
+           SeqSpan::strand_type strand = SeqSpan::PlusStrand);
   Sequence(const std::string& seq,
-           AlphabetRef a = reduced_nucleic_alphabet);
+           AlphabetRef a = reduced_dna_alphabet,
+           SeqSpan::strand_type strand = SeqSpan::PlusStrand);
   Sequence(const Sequence& seq);
   Sequence(const Sequence *);
   Sequence(const SeqSpanRef&); 
@@ -125,10 +126,10 @@ public:
 
   //! set sequence to a (sub)string containing nothing but AGCTN
   void set_filtered_sequence(const std::string& seq,
-                             AlphabetRef a, 
+                             AlphabetRef a=reduced_dna_alphabet, 
                              size_type start=0,
                              size_type count=npos,
-                             strand_type strand=UnknownStrand);
+                             SeqSpan::strand_type strand=SeqSpan::PlusStrand);
 
   //! retrive element at specific position
   const_reference at(size_type i) const { return seq->at(i); }
@@ -159,7 +160,9 @@ public:
   size_type stop() const { return seq->parentStop(); }
 
   //! return a subsequence, copying over any appropriate annotation
-  Sequence subseq(size_type start=0, size_type count = npos) const;
+  Sequence subseq(size_type start=0, 
+                  size_type count = npos,
+                  SeqSpan::strand_type strand = SeqSpan::SameStrand) const;
   //! reverse a character
   std::string create_reverse_map() const;
   //! return a reverse compliment (this needs to be improved?)
@@ -234,8 +237,6 @@ public:
   
 protected:  
   SeqSpanRef seq;
-  //! strand orientation
-  strand_type strand;
   //! fasta header
   std::string header;
   //! species name
@@ -259,7 +260,6 @@ protected:
   template<class Archive>
   void serialize(Archive& ar, const unsigned int /*version*/) {
     ar & BOOST_SERIALIZATION_NVP(seq);
-    ar & BOOST_SERIALIZATION_NVP(strand);
     ar & BOOST_SERIALIZATION_NVP(header);
     ar & BOOST_SERIALIZATION_NVP(species);
     ar & BOOST_SERIALIZATION_NVP(annots);