gnFASSource Member List

This is the complete list of members for gnFASSource, including all inherited members.

Clone() constgnFASSource [inline, virtual]
Close()gnFileSource [virtual]
DetermineNewlineType()gnFileSource [protected]
GetContig(const uint32 i) constgnFASSource
GetContigID(const string &name) constgnFASSource [virtual]
GetContigListLength() constgnFASSource [inline, virtual]
GetContigName(const uint32 i) constgnFASSource [virtual]
GetContigSeqLength(const uint32 i) constgnFASSource [virtual]
GetFileContig(const uint32 contigI) constgnFASSource [virtual]
GetFilter() constgnFileSource [inline, virtual]
GetOpenString() constgnFileSource [inline, virtual]
GetSpec() constgnFASSource [virtual]
gnBaseSource()gnBaseSource [inline]
gnClone()gnClone [inline]
gnFASSource()gnFASSource
gnFASSource(const gnFASSource &s)gnFASSource
gnFileSource()gnFileSource [inline]
gnFileSource(const gnFileSource &gnfs)gnFileSource
HasContig(const string &name) constgnFASSource [virtual]
m_contigListgnFASSource [private]
m_ifstreamgnFileSource [protected]
m_newlineSizegnFileSource [protected]
m_newlineTypegnFileSource [protected]
m_openStringgnFileSource [protected]
m_pFiltergnFileSource [protected]
Open(string openString)gnFileSource [virtual]
Open()gnFileSource [virtual]
ParseStream(istream &fin)gnFASSource [private, virtual]
Read(const uint64 pos, char *buf, gnSeqI &bufLen)gnFileSource [virtual]
SeqRead(const gnSeqI start, char *buf, gnSeqI &bufLen, const uint32 contigI=ALL_CONTIGS)gnFASSource [virtual]
SeqSeek(const gnSeqI start, const uint32 contigI, uint64 &startPos, uint64 &readableBytes)gnFASSource [private]
SeqStartPos(const gnSeqI start, gnFileContig &contig, uint64 &startPos, uint64 &readableBytes)gnFASSource [private]
SetFilter(gnFilter *filter)gnFileSource [inline, virtual]
Write(gnSequence &sequence, const string &filename, boolean write_coords=true, boolean enforce_unique_names=true)gnFASSource [static]
Write(gnSequence &sequence, ostream &m_ostream, boolean write_coords=true, boolean enforce_unique_names=true)gnFASSource [static]
Write(gnBaseSource *source, const string &filename)gnFASSource [static]
~gnBaseSource()gnBaseSource [inline, virtual]
~gnClone()gnClone [inline, virtual]
~gnFASSource()gnFASSource
~gnFileSource()gnFileSource [inline, virtual]


Generated on Mon Feb 14 19:29:50 2005 for libGenome by doxygen 1.3.8