Member List

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# gnProteinSequence Member List

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

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 &lt, vector< gnBaseFeature * > &feature_vector) const | gnSequence | `[inline, virtual]`
getContainedFeatures(const gnLocation &lt, 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 &lt, 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 |