Public Types |
| enum | Errtype_ {
OK = 0,
FILEERR,
FORMATERR,
TITLEERR,
IDERR,
ANNOTERR,
SEQERR,
TYPEERR
} |
| | I/O error types. More...
|
| enum | Formatflags_ {
UNKNOWN = 0,
FASTA = 1,
GCG = 2,
PIR = 4,
SWISS = 8,
EMBL = 16,
ANYFORMAT = 31
} |
| | available I/O formats. More...
|
Static Public Methods |
| const char* | error_str (Errtype_ Err) |
| | error_str(), format_str(): return a const char ptr to a human-readable short description of the various enums.
|
| const char* | format_str (Formatflags_ F) |
Protected Methods |
| | Bioseqio_ () |
| | Create an empty I/O object. More...
|
| | Bioseqio_ (const Bioseqio_ &B) |
| | copy ctor: we do not copy the buffer (see above).
|
| Bioseqio_& | operator= (const Bioseqio_ &B) |
| | assignment: buffer not overwritten! essentially, this is a null operation.
|
| virtual | ~Bioseqio_ () |
| | dtor.
|
| char* | buffer () |
| char& | buffer (size_t Idx) |
| void | make_buffer () |
| | the rest of the I/O methods.
|
| bool | fetch_buffer (istream &Inf) |
| int | clean_seq (string &S, int Type, bool Nocase, bool GapsOK=false) const |
| Errtype_ | read_fasta (istream &Inf, string &Id, string &Title, string &Seq) |
| Errtype_ | read_pir (istream &Inf, string &Id, string &Title, string &Annot, string &Seq) |
| Errtype_ | read_gcg (istream &Inf, string &Id, string &Annot, string &Seq, int &Gcglen, int &Gcgcheck, char &Typechar) |
| Errtype_ | read_swiss (istream &Inf, string &Id, string &Annot, string &Seq, int &Swlen, int &Mw, unsigned int &Crc32) |
| Errtype_ | read_embl (istream &Inf, string &Id, string &Annot, string &Seq, int &Embllen, int Acgtx[5]) |
Static Protected Methods |
| int | autodetect_type (const string &S) |
| Errtype_ | write_fasta (ostream &Outf, const string &ID, const string &Title, const string &Seq) |
| Errtype_ | write_pir (ostream &Outf, const string &ID, const string &Title, const string &Annot, const string &Seq) |
| Errtype_ | write_gcg (ostream &Outf, const string &ID, const string &Title, const string &Annot, const string &Seq, Monomer_::Type_ Type) |
| Errtype_ | write_swiss (ostream &Outf, const string &ID, const string &Title, const string &Annot, const string &Seq) |
| Errtype_ | write_embl (ostream &Outf, const string &ID, const string &Title, const string &Annot, const string &Seq, Monomer_::Type_ Type) |
| int | gcg_checksum (const string &S) |
| const char* | current_datestr () |
| int | mol_weight (const string &S) |
| void | BuildCRCTable (unsigned int CRCTable[256]) |
| unsigned int | crc_32 (const string &buffer) |
| void | count_bases (const string &S, int Acgtx[5], bool Isdna) |
| bool | compare_basecount (const string &S, const int Acgtx[5], bool Isdna) |
Private Attributes |
| char* | Buffer |
| | I/O buffer.
|
Static Private Methods |
| void | parse_title (const char *Strc, string &Tok1, string &Rest) |
| void | swissembl_comment (ostream &Outf, const string &S) |
Static Private Attributes |
| const int | BUFFERSIZE |
| | and its size.
|
Defines the I/O methods for some popular formats.
1.2.6 written by Dimitri van Heesch,
© 1997-2001