return *this;
}
-/*
-Sequence::operator std::string()
-{
- std::string s(seq.begin(), seq.end());
- return s;
-}
-
-Sequence::operator std::string() const
-{
- std::string s(seq.begin(), seq.end());
- return s;
-}
-*/
-
static void multiplatform_getline(std::istream& in, std::string& line)
{
line.clear();
}
void Sequence::set_filtered_sequence(const std::string &old_seq,
- std::string::size_type start,
+ std::string::size_type start,
std::string::size_type count)
{
char conversionTable[257];
const char *Sequence::c_str() const
{
- return seq->c_str();
+ if (seq)
+ return seq->c_str();
+ else
+ return 0;
}
Sequence::const_iterator Sequence::begin() const
//! assignment to constant sequences
Sequence &operator=(const Sequence&);
- // dangerous since they create large copies
- //operator std::string();
- //operator std::string() const;
-
friend std::ostream& operator<<(std::ostream&, const Sequence&);
friend bool operator<(const Sequence&, const Sequence&);
friend bool operator==(const Sequence&, const Sequence&);
private:
boost::shared_ptr<seq_string> seq;
std::string header;
+ //! species name
std::string species;
+ //! 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;