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