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() constgnSequence [virtual]
comparatorgnProteinSequence [private]
compare(const gnSequence &seq) constgnSequence [virtual]
compare(const string &str) constgnSequence [virtual]
contig(const uint32 contigI) constgnSequence
contigByBase(const gnSeqI baseI) constgnSequence
contigByName(string &contigName) constgnSequence [virtual]
contigIndexByBase(const gnSeqI baseI) constgnSequence
contigIndexByName(string &contigName) constgnSequence [virtual]
contigLength(const uint32 contigI) constgnSequence [virtual]
contigListLength() constgnSequence
contigListSize() constgnSequence
contigName(const uint32 contigI) constgnSequence [virtual]
contigStart(const uint32 contigI) constgnSequence [virtual]
erase(const gnSeqI offset=0, const gnSeqI length=GNSEQI_END)gnSequence [virtual]
filter_listgnProteinSequence [private]
find(const gnSequence &search, const gnSeqI offset=0) constgnSequence [virtual]
getBrokenFeatures(const gnLocation &lt, vector< gnBaseFeature * > &feature_vector) constgnSequence [inline, virtual]
getContainedFeatures(const gnLocation &lt, vector< gnBaseFeature * > &feature_vector, vector< uint32 > &index_vector) constgnSequence [inline, virtual]
getFeature(const uint32 featureI) constgnSequence [inline, virtual]
getFeatureListLength() constgnSequence [inline, virtual]
getFilterList() constgnSequence [inline, virtual]
getHeader(const uint32 contigI, const uint32 headerI) constgnSequence [virtual]
getHeaderListLength(const uint32 contigI) constgnSequence [virtual]
getIntersectingFeatures(const gnLocation &lt, vector< gnBaseFeature * > &feature_vector, vector< uint32 > &index_vector) constgnSequence [inline, virtual]
GetSeqC(const gnSeqI offset) constgnSequence [virtual]
GetSpec() constgnSequence [inline, virtual]
globalToLocal(uint32 &contigI, gnSeqI &baseI) constgnSequence [virtual]
globalToSource(uint32 &contigI, gnSeqI &baseI) constgnSequence [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() constgnSequence [inline, virtual]
isReverseComplement(const uint32 contigI=ALL_CONTIGS)gnSequence [virtual]
length() constgnSequence [inline, virtual]
LoadSource(const string sourcename)gnSequence [virtual]
localToGlobal(const uint32 contigI, gnSeqI &baseI) constgnSequence [virtual]
localToSource(uint32 &contigI, gnSeqI &baseI) constgnSequence [virtual]
merge(const gnSeqI startI, const gnSeqI endI)gnSequence [virtual]
mergeContigs(const uint32 startC, const uint32 endC)gnSequence [virtual]
operator!=(const gnSequence &seq) constgnSequence [inline]
operator+(const gnSequence &seq) constgnSequence
operator+=(const gnSequence &seq)gnSequence [inline]
operator<(const gnSequence &seq) constgnSequence [inline]
operator<<(std::ostream &os, const gnSequence &gns)gnSequence [friend]
operator<=(const gnSequence &seq) constgnSequence [inline]
operator=(const gnSequence &seq)gnSequence
operator=(gnSequence &seq)gnSequence [inline]
operator==(const gnSequence &seq) constgnSequence [inline]
operator>(const gnSequence &seq) constgnSequence [inline]
operator>=(const gnSequence &seq) constgnSequence [inline]
operator>>(std::istream &is, gnSequence &gns)gnSequence [friend]
operator[](const gnSeqI offset) constgnSequence
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() constgnSequence [inline, virtual]
specgnProteinSequence [private]
splitContig(const gnSeqI splitI, const uint32 contigI=ALL_CONTIGS)gnSequence [virtual]
subseq(const gnSeqI offset, const gnSeqI length) constgnSequence
ToArray(gnSeqC *pSeqC, gnSeqI length, const gnSeqI offset=1) constgnSequence [virtual]
ToString(const gnSeqI length=GNSEQI_END, const gnSeqI offset=1) constgnSequence [virtual]
ToString(string &str, const gnSeqI length=GNSEQI_END, const gnSeqI offset=1) constgnSequence [virtual]
~gnClone()gnClone [inline, virtual]
~gnSequence()gnSequence


Generated on Mon Feb 14 19:29:55 2005 for libGenome by doxygen 1.3.8