{
std::string sequence;
- motif() : annot(), sequence("") {};
+ motif() : annot(), sequence("") {};
//! this constructor is for when we're adding motifs to our annotations
motif(int begin, std::string motif);
~motif();
};
BOOST_CLASS_EXPORT(motif);
+class Sequence;
+typedef boost::shared_ptr<Sequence> SequenceRef;
//! sequence track for mussa.
class Sequence
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 };
+
+ typedef std::list<motif> MotifList;
+ typedef boost::shared_ptr<MotifList> MotifListRef;
- 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);
+ //! make a new sequence, with the same SeqSpan
Sequence(const Sequence& seq);
+ //! make a new sequence, with the same SeqSpan
Sequence(const Sequence *);
- Sequence(const SeqSpanRef&);
+ //! Make a new sequence using a copy of SeqSpan
+ Sequence(const SequenceRef);
+ Sequence(const SeqSpanRef&);
~Sequence();
//! assignment to constant sequences
Sequence &operator=(const Sequence&);
//! 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); }
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?)
//! add an annotation to our list of annotations
void add_annotation(const annot& a);
const std::list<annot>& annotations() const;
- const std::list<motif>& motifs() const;
+ const MotifList& motifs() const;
//! add a motif to our list of motifs
void add_motif(const Sequence& a_motif);
protected:
SeqSpanRef seq;
- //! strand orientation
- strand_type strand;
//! fasta header
std::string header;
//! species name
//! store our oldstyle annotations
std::list<annot> annots;
//! a seperate list for motifs since we're currently not saving them
- std::list<motif> motif_list;
+ MotifListRef motif_list;
//! copy over all our annotation children
void copy_children(Sequence &, size_type start, size_type count) const;
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);