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gnFASSource Member List This is the complete list of members for gnFASSource, including all inherited members. Clone() const [inline, virtual] Close() [virtual] GetContig(const uint32 i) const GetContigID(const string &nameStr) 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 [virtual] gnBaseSource() [inline] gnClone() [inline] gnFASSource() gnFASSource(const gnFASSource &s) gnFileSource() [inline] gnFileSource(const gnFileSource &gnfs) HasContig(const string &nameStr) const [virtual] m_contigList [private] m_ifstream [protected] m_newlineSize [protected] m_newlineType [protected] m_openString [protected] m_pFilter [protected] 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, boolean write_coords=true, boolean enforce_unique_names=true) [static] Write(gnSequence &sequence, ostream &m_ostream, boolean write_coords=true, boolean enforce_unique_names=true) [static] Write(gnBaseSource *source, const string &filename) [static] ~gnBaseSource() [inline, virtual] ~gnClone() [inline, virtual] ~gnFASSource() ~gnFileSource() [inline, virtual]