Member List

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# gnSequence Member List

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

- addFeature(gnBaseFeature *feature) `[inline, virtual]`
- addHeader(const uint32 contigI, gnBaseHeader *header, const uint32 headerI) `[virtual]`
- append(const gnSequence &seq) `[inline, virtual]`
- assign(gnSequence &seq) `[inline, virtual]`
- Clone() const `[virtual]`
- comparator `[private]`
- compare(const gnSequence &seq) const `[virtual]`
- compare(const string &str) const `[virtual]`
- contig(const uint32 contigI) const
- contigByBase(const gnSeqI baseI) const
- contigByName(string &contigName) const `[virtual]`
- contigIndexByBase(const gnSeqI baseI) const
- contigIndexByName(string &contigName) const `[virtual]`
- contigLength(const uint32 contigI) const `[virtual]`
- contigListLength() const
- contigListSize() const
- contigName(const uint32 contigI) const `[virtual]`
- contigStart(const uint32 contigI) const `[virtual]`
- erase(const gnSeqI offset=0, const gnSeqI length=GNSEQI_END) `[virtual]`
- filter_list `[private]`
- find(const gnSequence &search, const gnSeqI offset=0) const `[virtual]`
- getBrokenFeatures(const gnLocation &lt, vector< gnBaseFeature *> &feature_vector) const `[inline, virtual]`
- getContainedFeatures(const gnLocation &lt, vector< gnBaseFeature *> &feature_vector, vector< uint32 > &index_vector) const `[inline, virtual]`
- getFeature(const uint32 featureI) const `[inline, virtual]`
- getFeatureListLength() const `[inline, virtual]`
- getFilterList() const `[inline, virtual]`
- getHeader(const uint32 contigI, const uint32 headerI) const `[virtual]`
- getHeaderListLength(const uint32 contigI) const `[virtual]`
- getIntersectingFeatures(const gnLocation &lt, vector< gnBaseFeature *> &feature_vector, vector< uint32 > &index_vector) const `[inline, virtual]`
- GetSeqC(const gnSeqI offset) const `[virtual]`
- GetSpec() const `[inline, virtual]`
- globalToLocal(uint32 &contigI, gnSeqI &baseI) const `[virtual]`
- globalToSource(uint32 &contigI, gnSeqI &baseI) const `[virtual]`
- gnClone() `[inline]`
- gnSequence()
- gnSequence(const gnSeqC *seq)
- gnSequence(const string &str)
- gnSequence(const gnGenomeSpec &gngs)
- gnSequence(const gnFragmentSpec &gnfs)
- gnSequence(const gnContigSpec &gncs)
- gnSequence(gnSeqC *bases, const gnSeqI length)
- gnSequence(const gnSequence &seq)
- insert(const gnSeqI offset, const gnSeqC *bases, const gnSeqI length) `[virtual]`
- insert(const gnSeqI offset, const gnSequence &seq) `[inline, virtual]`
- insert(const gnSeqI offset, const gnGenomeSpec &gnbs) `[virtual]`
- isCircular() const `[inline, virtual]`
- isReverseComplement(const uint32 contigI=ALL_CONTIGS) `[virtual]`
- length() const `[inline, virtual]`
- LoadSource(const string sourcename) `[virtual]`
- localToGlobal(const uint32 contigI, gnSeqI &baseI) const `[virtual]`
- localToSource(uint32 &contigI, gnSeqI &baseI) const `[virtual]`
- merge(const gnSeqI startI, const gnSeqI endI) `[virtual]`
- mergeContigs(const uint32 startC, const uint32 endC) `[virtual]`
- operator!=(const gnSequence &seq) const `[inline]`
- operator+(const gnSequence &seq) const
- operator+=(const gnSequence &seq) `[inline]`
- operator<(const gnSequence &seq) const `[inline]`
- operator<<(std::ostream &os, const gnSequence &gns) `[friend]`
- operator<=(const gnSequence &seq) const `[inline]`
- operator=(const gnSequence &seq)
- operator=(gnSequence &seq) `[inline]`
- operator==(const gnSequence &seq) const `[inline]`
- operator>(const gnSequence &seq) const `[inline]`
- operator>=(const gnSequence &seq) const `[inline]`
- operator>>(std::istream &is, gnSequence &gns) `[friend]`
- operator[](const gnSeqI offset) const
- removeFeature(const uint32 featureI) `[inline, virtual]`
- removeHeader(const uint32 contigI, const uint32 headerI) `[virtual]`
- setCircular(const boolean value) `[inline, virtual]`
- setContigName(const uint32 contigI, const string &contig_name) `[virtual]`
- setFilter(const gnBaseFilter *filt) `[inline, virtual]`
- setFilterList(list< const gnBaseFilter *> &filt_list) `[inline, virtual]`
- setReverseComplement(const boolean revComp, const uint32 contigI=ALL_CONTIGS) `[virtual]`
- SetSpec(gnGenomeSpec *s) `[inline, virtual]`
- size() const `[inline, virtual]`
- spec `[private]`
- splitContig(const gnSeqI splitI, const uint32 contigI=ALL_CONTIGS) `[virtual]`
- subseq(const gnSeqI offset, const gnSeqI length) const
- ToArray(gnSeqC *pSeqC, gnSeqI length, const gnSeqI offset=1) const `[virtual]`
- ToString(const gnSeqI length=GNSEQI_END, const gnSeqI offset=1) const `[virtual]`
- ToString(string &str, const gnSeqI length=GNSEQI_END, const gnSeqI offset=1) const `[virtual]`
- ~gnClone() `[inline, virtual]`
- ~gnSequence()