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gnSEQSource Member List This is the complete list of members for gnSEQSource, including all inherited members. BaseCount(const string &bases, gnSeqI &a_count, gnSeqI &c_count, gnSeqI &g_count, gnSeqI &t_count, gnSeqI &other_count) [private, static] Clone() const [inline, virtual] Close() [virtual] Filler(uint32 length) [private, static] FormatString(string &data, uint32 offset, uint32 width) [private, static] GetContigID(const string &name) const [virtual] GetContigListLength() const [inline, virtual] GetContigName(const uint32 i) const [virtual] GetContigSeqLength(const uint32 i) const [virtual] GetFileContig(const uint32 contigI) const [virtual] GetFilter() const [inline, virtual] GetOpenString() const [inline, virtual] GetSpec() const [inline, virtual] gnBaseSource() [inline] gnClone() [inline] gnFileSource() [inline] gnFileSource(const gnFileSource &gnfs) gnSEQSource() gnSEQSource(const gnSEQSource &s) HasContig(const string &name) const [virtual] m_contigList [private] m_ifstream [protected] m_newlineSize [protected] m_newlineType [protected] m_openString [protected] m_pFilter [protected] m_spec [private] Open(string openString) [virtual] Open() [virtual] ParseStream(istream &fin) [private, virtual] Read(const uint64 pos, char *buf, uint32 &bufLen) [virtual] SeqRead(const gnSeqI start, char *buf, uint32 &bufLen, const uint32 contigI=ALL_CONTIGS) [virtual] SeqSeek(const gnSeqI start, const uint32 &contigI, uint64 &startPos, uint64 &readableBytes) [private] SeqStartPos(const gnSeqI start, gnFileContig &contig, uint64 &startPos, uint64 &readableBytes) [private] SetFilter(gnFilter *filter) [inline, virtual] Write(gnSequence &sequence, const string &filename) [inline, static] Write(gnBaseSource *source, const string &filename) [inline, static] Write(gnGenomeSpec *spec, const string &filename) [static] ~gnBaseSource() [inline, virtual] ~gnClone() [inline, virtual] ~gnFileSource() [inline, virtual] ~gnSEQSource()