Member List

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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()