| Clone() const | gnRAWSource | [inline, virtual] |
| Close() | gnFileSource | [virtual] |
| DetermineNewlineType() | gnFileSource | [protected] |
| GetContigID(const string &name) const | gnRAWSource | [virtual] |
| GetContigListLength() const | gnRAWSource | [inline, virtual] |
| GetContigName(const uint32 i) const | gnRAWSource | [virtual] |
| GetContigSeqLength(const uint32 i) const | gnRAWSource | [virtual] |
| GetFileContig(const uint32 contigI) const | gnRAWSource | [virtual] |
| GetFilter() const | gnFileSource | [inline, virtual] |
| GetOpenString() const | gnFileSource | [inline, virtual] |
| GetSpec() const | gnRAWSource | [virtual] |
| gnBaseSource() | gnBaseSource | [inline] |
| gnClone() | gnClone | [inline] |
| gnFileSource() | gnFileSource | [inline] |
| gnFileSource(const gnFileSource &gnfs) | gnFileSource | |
| gnRAWSource() | gnRAWSource | |
| gnRAWSource(const gnRAWSource &s) | gnRAWSource | |
| HasContig(const string &name) const | gnRAWSource | [virtual] |
| m_contig | gnRAWSource | [private] |
| m_ifstream | gnFileSource | [protected] |
| m_newlineSize | gnFileSource | [protected] |
| m_newlineType | gnFileSource | [protected] |
| m_openString | gnFileSource | [protected] |
| m_pFilter | gnFileSource | [protected] |
| m_spec | gnRAWSource | [private] |
| Open(string openString) | gnFileSource | [virtual] |
| Open() | gnFileSource | [virtual] |
| ParseStream(istream &fin) | gnRAWSource | [private, virtual] |
| Read(const uint64 pos, char *buf, uint32 &bufLen) | gnFileSource | [virtual] |
| SeqRead(const gnSeqI start, char *buf, uint32 &bufLen, const uint32 contigI=ALL_CONTIGS) | gnRAWSource | [virtual] |
| SeqSeek(const gnSeqI start, const uint32 &contigI, uint64 &startPos, uint64 &readableBytes) | gnRAWSource | [private] |
| SeqStartPos(const gnSeqI start, gnFileContig &contig, uint64 &startPos, uint64 &readableBytes) | gnRAWSource | [private] |
| SetFilter(gnFilter *filter) | gnFileSource | [inline, virtual] |
| Write(gnSequence &sequence, const string &filename) | gnRAWSource | [static] |
| Write(gnBaseSource *source, const string &filename) | gnRAWSource | [inline, static] |
| ~gnBaseSource() | gnBaseSource | [inline, virtual] |
| ~gnClone() | gnClone | [inline, virtual] |
| ~gnFileSource() | gnFileSource | [inline, virtual] |
| ~gnRAWSource() | gnRAWSource | |
