typedef SeqString::const_reference const_reference;
typedef SeqString::size_type size_type;
static const size_type npos = SeqString::npos;
+
+ typedef std::list<motif> MotifList;
+ typedef boost::shared_ptr<MotifList> MotifListRef;
Sequence(AlphabetRef a = reduced_dna_alphabet);
Sequence(const char* seq,
//! 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);
//! 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;