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gnDNASequence Member List

This is the complete list of members for gnDNASequence, 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	gnDNASequence	`[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	gnDNASequence	`[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]`
gnDNASequence()	gnDNASequence	`[inline]`
gnDNASequence(const gnSeqC *seq)	gnDNASequence	`[inline]`
gnDNASequence(const string &str)	gnDNASequence	`[inline]`
gnDNASequence(const gnGenomeSpec &gngs)	gnDNASequence	`[inline]`
gnDNASequence(const gnFragmentSpec &gnfs)	gnDNASequence	`[inline]`
gnDNASequence(const gnContigSpec &gncs)	gnDNASequence	`[inline]`
gnDNASequence(gnSeqC *bases, const gnSeqI length)	gnDNASequence	`[inline]`
gnDNASequence(const gnDNASequence &seq)	gnDNASequence	`[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	gnDNASequence	`[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

Generated on Mon Feb 3 02:34:45 2003 for libGenome by

1.3-rc3