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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]

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