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RazorBack::Gapseq_ Member List

This is the complete list of members for RazorBack::Gapseq_, including all inherited members.

• annot() const [inline]
• annot() [inline]
• annot(const string &A) [inline]
• ANNOTERR enum value [protected]
• ANYFORMAT enum value [protected]
• at_1(size_t Idx) const [virtual]
• at_1(size_t Idx, char C) [virtual]
• at_3(size_t Idx) const [virtual]
• at_3(size_t Idx, const char *Ccc) [virtual]
• autodetect_type(const string &S) [protected, static]
• Bioseq_(Monomer_::Type_ Mt=Monomer_::PROT) [inline, explicit]
• Bioseq_(const char *Codes) [inline, explicit]
• Bioseq_(const Bioseq_ &B) [inline]
• 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]
• chg_monomer() [inline, protected]
• 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]
• EMBL enum value [protected]
• error_str(Errtype_ Err) [protected, static]
• Errtype_ enum name [protected]
• FASTA enum value [protected]
• fetch_buffer(istream &Inf) [protected]
• FILEERR enum value [protected]
• format_str(Formatflags_ F) [protected, static]
• FORMATERR enum value [protected]
• Formatflags_ enum name [protected]
• GAP [static]
• GAP3 [static]
• Gaplen [private]
• Gaplist [private]
• gapped_sequence(bool Gcg=false) const
• gapped_sequence(const string &Gseq, int Mtype=Monomer_::UNKNOWN)
• Gapseq_(Monomer_::Type_ Mt=Monomer_::PROT) [inline, explicit]
• Gapseq_(const char *Codes) [inline, explicit]
• Gapseq_(const Bioseq_ &B) [inline]
• Gapseq_(const Gapseq_ &G) [inline]
• GCG enum value [protected]
• gcg_checksum(const string &S) [protected, static]
• GCG_ENDGAP [static]
• GCG_ENDGAP3 [static]
• GCG_GAP [static]
• GCG_GAP3 [static]
• gross_length() const [inline]
• gross_pos(size_t Net) const
• id() const [inline]
• id() [inline]
• id(const string &I) [inline]
• IDERR enum value [protected]
• insert_gaps(size_t Idx, size_t N)
• is_legal(char C) const [inline, virtual]
• is_legal(const char *Ccc) const [inline, virtual]
• is_legal(const string &S) const [inline]
• is_legal(int Mt, char C) const [protected, virtual]
• length() const [inline]
• lowercase()
• make_buffer() [inline, protected]
• mol_weight(const string &S) [protected, static]
• monomer() const [inline]
• net_length() const [inline]
• net_pos(size_t Gross) const
• nocase() const [inline]
• nocase(bool N) [inline]
• OK enum value [protected]
• operator=(const Bioseqio_ &B) [inline, protected]
• operator[](size_t Idx) const [inline]
• operator[](size_t Idx) [inline]
• PIR enum value [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_pir(istream &Inf, string &Id, string &Title, string &Annot, string &Seq) [protected]
• read_seq(istream &Inf, int Type=Monomer_::USER, int Format=ANYFORMAT) [virtual]
• read_swiss(istream &Inf, string &Id, string &Annot, string &Seq, int &Swlen, int &Mw, unsigned int &Crc32) [protected]
• remove_gaps(size_t Idx)
• remove_gaps() [inline]
• seq() const [inline]
• seq(const string &S) [inline, virtual]
• SEQERR enum value [protected]
• sequence() [inline, protected]
• SWISS enum value [protected]
• title() const [inline]
• title() [inline]
• title(const string &T) [inline]
• TITLEERR enum value [protected]
• TYPEERR enum value [protected]
• UNKNOWN enum value [protected]
• uppercase()
• 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_pir(ostream &Outf, const string &ID, const string &Title, const string &Annot, const string &Seq) [protected, static]
• write_seq(ostream &Outf, int Format) const [virtual]
• 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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