Main Page Namespace List Class Hierarchy Alphabetical List Compound List File List Compound Members File Members
RazorBack::Alignment_ Member List
This is the complete list of members for RazorBack::Alignment_, including all inherited members.
- add_seq(const Gapseq_ &Seq)
- add_seq(const Gapseq_ &Seq, size_t Idx)
- Alignment_()
[inline]
- Alignment_(size_t N)
[inline, explicit]
- ANNOTERR enum value
[protected]
- ANYFORMAT enum value
- at(size_t Idx) const
- autodetect_type(const string &S)
[protected, static]
- Bioseqio_()
[inline, protected]
- Bioseqio_(const Bioseqio_ &B)
[inline, protected]
- buffer()
[inline, protected]
- buffer(size_t Idx)
[inline, protected]
- BuildCRCTable(unsigned int CRCTable[256])
[protected, static]
- clean_seq(string &S, int Type, bool Nocase, bool GapsOK=false) const
[protected]
- compare_basecount(const string &S, const int Acgtx[5], bool Isdna)
[protected, static]
- count_bases(const string &S, int Acgtx[5], bool Isdna)
[protected, static]
- crc_32(const string &buffer)
[protected, static]
- current_datestr()
[protected, static]
- Dirty
[mutable, private]
- EMBL enum value
[protected]
- error_str(Errtype_ Err)
[protected, static]
- Errtype_ enum name
[protected]
- FASTA enum value
- fetch_buffer(istream &Inf)
[protected]
- FILEERR enum value
[protected]
- find(const string &ID) const
- format_str(Formatflags_ F)
[protected, static]
- FORMATERR enum value
[protected]
- Formatflags_ enum name
- GCG enum value
- gcg_checksum(const string &S)
[protected, static]
- IDERR enum value
[protected]
- insert_gaps(size_t Seqidx, size_t Netpos, size_t Gaplen)
- make_buffer()
[inline, protected]
- max_len() const
[inline]
- Maxlen
[mutable, private]
- mmer_compat(const Monomer_ &Mseq, const Monomer_ &Mali) const
- mmer_compat(const Monomer_ &Mseq) const
[inline]
- mol_weight(const string &S)
[protected, static]
- monomer() const
[inline]
- Monomer
[private]
- OK enum value
[protected]
- operator=(const Bioseqio_ &B)
[inline, protected]
- operator[](size_t Idx) const
[inline]
- PIR enum value
- read_align(istream &Inf, int Type=Monomer_::USER, int Format=ANYFORMAT)
- read_concat(istream &Inf, int Type, int Format)
[protected]
- read_embl(istream &Inf, string &Id, string &Annot, string &Seq, int &Embllen, int Acgtx[5])
[protected]
- read_fasta(istream &Inf, string &Id, string &Title, string &Seq)
[protected]
- read_gcg(istream &Inf, string &Id, string &Annot, string &Seq, int &Gcglen, int &Gcgcheck, char &Typechar)
[protected]
- read_msf(istream &Inf)
[protected]
- read_pir(istream &Inf, string &Id, string &Title, string &Annot, string &Seq)
[protected]
- read_swiss(istream &Inf, string &Id, string &Annot, string &Seq, int &Swlen, int &Mw, unsigned int &Crc32)
[protected]
- remove_gaps(size_t Seqidx, size_t Netpos)
- remove_gaps(size_t Seqidx)
- remove_gaps()
- remove_seq(size_t Idx)
- remove_seq()
- seq_no() const
[inline]
- SEQERR enum value
[protected]
- Sequences
[private]
- set_maxlen() const
[protected]
- set_monomer_type(const Monomer_ &Mseq, Monomer_ &Mali)
[protected]
- set_monomer_type(const Monomer_ &Mseq)
[inline, protected]
- SWISS enum value
[protected]
- TITLEERR enum value
[protected]
- TYPEERR enum value
[protected]
- UNKNOWN enum value
- vertical_string(size_t Apos) const
- write_align(ostream &Outf, int Format) const
- write_concat(ostream &Outf, int Format) const
[protected]
- write_embl(ostream &Outf, const string &ID, const string &Title, const string &Annot, const string &Seq, Monomer_::Type_ Type)
[protected, static]
- write_fasta(ostream &Outf, const string &ID, const string &Title, const string &Seq)
[protected, static]
- write_gcg(ostream &Outf, const string &ID, const string &Title, const string &Annot, const string &Seq, Monomer_::Type_ Type)
[protected, static]
- write_msf(ostream &Outf) const
[protected]
- write_pir(ostream &Outf, const string &ID, const string &Title, const string &Annot, const string &Seq)
[protected, static]
- write_swiss(ostream &Outf, const string &ID, const string &Title, const string &Annot, const string &Seq)
[protected, static]
- ~Bioseqio_()
[inline, protected, virtual]
Generated at Wed Aug 21 09:33:44 2002 for The Razorback C++ Library: Bioinformatics by
1.2.6 written by Dimitri van Heesch,
© 1997-2001