mRNAModel Member List

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

advanceGeneId()	RNAModel	[inline, static]
advanceId()	RNAModel	[inline, static]
advancePosOnExon(int pos, unsigned int d) const	Noschain
after(const Range &r) const	Range
append(mRNAModel &mod, int &comment)	mRNAModel
RNAModel::append(Noschain &mod)	RNAModel
asDelimitedString(const char sep=':', const char rsep[]=",") const	Noschain
asDelimitedString(const char sep=':', const char rsep=',') const	Noschain
Range::asDelimitedString(const char delimiter[]=",") const	Range
Range::asDelimitedString(const char delimiter=',') const	Range
assignCurrentGeneId()	RNAModel	[inline]
assignNewGeneId()	RNAModel	[inline]
assignNewId()	RNAModel	[inline]
b	Range	[protected]
before(const Range &r) const	Range
begin() const	Range	[inline]
beginUpdate(int len)	Range	[inline]
cdsb	mRNAModel	[protected]
CDSChain() const	mRNAModel
CDSDirection() const	mRNAModel	[inline]
cdse	mRNAModel	[protected]
CDSFraction() const	mRNAModel	[inline]
CDSFractionGenomic() const	mRNAModel	[inline]
CDSFractionRNA() const	mRNAModel	[inline]
CDSLength() const	mRNAModel	[inline]
CDSOnewayChain() const	mRNAModel
CDSOnewayChain(Noschain &ch) const	mRNAModel
CDSRange() const	mRNAModel	[inline]
CDSSeq() const	mRNAModel	[inline]
CDSSequence() const	mRNAModel
clear()	Noschain	[inline]
combine(const Range &r)	Range
commonExons(const Noschain &eg) const	Noschain
commonIntrons(const Noschain &nc) const	Noschain
compare(const Range &r) const	Range
compare(const Range *r) const	Range	[inline]
compareByDirection(const Noschain &nc) const	Noschain
Range::compareByDirection(const Range &r) const	Range
compareChainAndFix(Noschain &nc, int &edit)	Noschain
compareDirectional(const Range &r) const	Range
complete() const	mRNAModel	[inline]
contain(const Range &r, bool sameDirection=true) const	Range
contain(int p) const	Range
containIntron(int p1, int p2) const	Noschain	[inline]
copyReverse() const	Range	[inline]
copyShrinkBothEnds(int del) const	Range
currentGeneId()	RNAModel	[inline, static]
currentId()	RNAModel	[inline, static]
direction() const	Range	[inline]
directionAgree() const	Noschain
directionalLess(const Range &r) const	Range	[inline]
distance(const Range &r) const	Range
e	Range	[protected]
empty() const	Noschain	[inline]
end() const	Range	[inline]
endUpdate(int len)	Range	[inline]
exonContain(const Noschain &nc, bool samedirection=false) const	Noschain
exonheader	RNAModel	[static]
exonid	RNAModel	[protected, static]
exonIndex(int p) const	Noschain
exonIndex(const Range &r) const	Noschain
exonIntersectFraction(const Noschain &nc) const	Noschain
exonIntersectLength(const Noschain &nc) const	Noschain
exonLength() const	RNAModel	[inline]
exonOnlyChain(Noschain &eoc) const	Noschain
exonOnlyChain() const	Noschain
exonOverlap(const Noschain &nc) const	Noschain
exonOverlapLength(const Noschain &nc) const	Noschain
exons	Noschain	[protected]
extendEnd(const Noschain &nc)	Noschain
firstExon() const	Noschain	[inline]
FivePrimeUTR() const	mRNAModel	[inline]
FivePrimeUTRLength() const	mRNAModel	[inline]
fixAndBuild(const vector< int > &bb, const vector< int > &ee, char strand)	Noschain
forceFuse(const Range &r)	Range
frame	mRNAModel	[protected]
fuse(const Range &r)	Range
gcdsb	mRNAModel	[protected]
gcdse	mRNAModel	[protected]
geneid	RNAModel	[protected, static]
geneId() const	RNAModel	[inline]
genid	RNAModel	[protected]
genomicCDSBegin() const	mRNAModel	[inline]
genomicCDSBound() const	mRNAModel	[inline]
genomicCDSEnd() const	mRNAModel	[inline]
genomicCDSLength() const	mRNAModel	[inline]
genomicId() const	RNAModel	[inline]
genomicIndex(int mrnaidx) const	RNAModel
genomicLength() const	RNAModel	[inline]
genuine() const	mRNAModel	[inline]
getExons() const	Noschain	[inline]
getFrame() const	mRNAModel	[inline]
getGeneId() const	RNAModel	[inline]
getGenomicPointer() const	RNAModel	[inline]
getOid() const	RNAModel	[inline]
getProtein() const	mRNAModel	[inline]
getReverse() const	Range	[inline]
gid	RNAModel	[protected]
greaterByDirection(const Range &r) const	Range	[inline]
greaterByDirection(const Range *r) const	Range	[inline]
greaterByDirection(int p) const	Range	[inline]
growCDS3Prime(int len)	mRNAModel
growEnd(int icr)	Noschain
gseq	RNAModel	[protected]
guessStrand() const	mRNAModel
hasStart() const	mRNAModel	[inline]
hasStop() const	mRNAModel	[inline]
header	mRNAModel	[protected, static]
high() const	Range	[inline]
inside(const Range &r) const	Range	[inline]
insideExon(int p) const	Noschain	[inline]
insideExon(const Range &r, bool samedir=false) const	Noschain
intronBound(map< string, int > &spsite) const	RNAModel
intronLength() const	Noschain
introns() const	Noschain
intronsInside(const int len) const	Noschain
isDangle(const int intronlen=900, const int exonlen=27) const	Noschain
isMinus() const	Range	[inline]
isNull() const	Noschain	[inline, virtual]
isPlus() const	Range	[inline]
isPoint() const	Range	[inline]
isStar() const	mRNAModel	[inline]
jgiformat(char sep='\t') const	Noschain
jgiModelCol	mRNAModel	[static]
JGIModelRow(const char sep='\t') const	mRNAModel
jgiProteinCol	mRNAModel	[static]
JGIProteinRow(char sep='\t') const	mRNAModel
jgiTranscriptCol	mRNAModel	[static]
JGITranscriptRow(const char sep='\t') const	mRNAModel
largerEnd() const	Range	[inline]
lastExon() const	Noschain	[inline]
length() const	Range
less(const Range &r) const	Range	[inline]
lessByDirection(const Range &r) const	Range
lessByDirection(const Range *r) const	Range
lessByDirection(int p, char direc='+') const	Range
low() const	Range	[inline]
margin	Range	[protected, static]
marginFraction	Range	[protected, static]
maxIntron() const	Noschain
maxIntronLength() const	Noschain	[inline]
merge(const Range &r, bool sd=true)	Range
minIntron() const	Noschain
minIntronLength() const	Noschain	[inline]
minusContain(const Range &r) const	Range
minusOverlap(const Range &r) const	Range
minusplusContain(const Range &r) const	Range
minusplusOverlap(const Range &r) const	Range
modelheader	mRNAModel	[static]
modelidAsGeneid()	RNAModel	[inline]
mRNAModel()	mRNAModel	[inline]
mRNAModel(const Noschain &seg, const string &chrom, const string &gs)	mRNAModel	[explicit]
mRNAModel(const Noschain &seg, int gcdsb_, int gcdse_, const string &chrom, const string &gs, int fr=0)	mRNAModel	[explicit]
mRNAModel(const string &exstr, const string &gname, const string &gs, int oi, int gcb, int gce, int fr=0)	mRNAModel
mRNAModel(const string &exstr, const string &gname, const string &gs, int oi, int gcb, int gce, int gene_id, int fr=0)	mRNAModel
mRNAModel(const string &exstarts, const string &exends, char strand, int gcb, int gce, const string &gi, const string &genomic)	mRNAModel
mRNAModel(const string &exstarts, const string &exends, char strand, int gcb, int gce, const string &gi, const string &genomic, int oo)	mRNAModel
mRNAModel(const mRNAModel &mm)	mRNAModel	[inline]
name(const string &prefix)	mRNAModel	[inline]
nextGeneId()	RNAModel	[inline, static]
nextId()	RNAModel	[inline, static]
Noschain()	Noschain	[inline]
Noschain(const string &exstarts, const string &exends, char strand)	Noschain
Noschain(const string &exstr)	Noschain
Noschain(const Noschain &eg)	Noschain
num3NoncodingExons() const	mRNAModel	[inline]
num5NoncodingExons() const	mRNAModel	[inline]
numberOfInternalStops() const	mRNAModel
numberOfRanges() const	Noschain	[inline]
objtype() const	mRNAModel	[inline, virtual]
oid	RNAModel	[protected]
onewayChain() const	Noschain
onewayChain(Noschain &owc) const	Noschain
operator!=(const Noschain &nc) const	Noschain	[inline]
Range::operator!=(const Range &r) const	Range	[inline]
operator+(int c) const	Noschain
operator+(int c, const Noschain &chain)	Noschain	[friend]
Range::operator+(int c, const Range &r)	Range	[friend]
operator+=(const Range &r)	Noschain
operator+=(int c)	Noschain
operator-(int c) const	Noschain
operator-(int c, const Noschain &chain)	Noschain	[friend]
Range::operator-(int c, const Range &r)	Range	[friend]
operator-=(int c)	Noschain
operator<(const Noschain &nc) const	Noschain
Range::operator<(const Range &r) const	Range	[inline]
operator<<(ostream &ous, const Noschain &nc)	Noschain	[friend]
Range::operator<<(ostream &ous, const Range &r)	Range	[friend]
operator=(const mRNAModel &mm)	mRNAModel
RNAModel::operator=(const RNAModel &rm)	RNAModel
Noschain::operator=(const Noschain &eg)	Noschain
Range::operator=(const Range &r)	Range
operator==(const Noschain &nc) const	Noschain	[inline]
Range::operator==(const Range &r) const	Range	[inline]
operator>(const Range &r) const	Range	[inline]
operator[](int idx)	Noschain	[inline]
operator[](int idx) const	Noschain	[inline]
outerRange() const	Noschain	[inline]
output(ostream &ous, const char delimiter[]="\t") const	Range	[inline]
output(ostream &ous, char delim='\t') const	Range	[inline]
overlap(const Range &r, bool sameDirection=true) const	Range
overlapFraction(const Range &r, bool sd=true) const	Range
overlay(const Range &r) const	Range
overlayFraction(const Range &r) const	Range
pep	mRNAModel	[protected]
plusContain(const Range &r) const	Range
plusminusContain(const Range &r) const	Range
plusminusOverlap(const Range &r) const	Range
plusOverlap(const Range &r) const	Range
print(ostream &ous) const	mRNAModel	[virtual]
printJGIModelRow(ostream &ous, const char sep='\t') const	mRNAModel
printJGITranscriptRow(ostream &ous, const char sep='\t') const	mRNAModel
printJGITranscriptRowNoId(ostream &ous, const char sep='\t') const	mRNAModel
proteinLength() const	mRNAModel	[inline]
proteinLengthNoTail() const	mRNAModel
proteinSequence() const	mRNAModel	[inline]
Range()	Range	[inline]
Range(int begin, int end)	Range	[inline]
Range(pair< int, int > p)	Range	[inline]
Range(const Range &r)	Range	[inline]
Range(int p)	Range	[inline]
reset()	mRNAModel	[virtual]
resetProtein()	mRNAModel	[inline]
resetRNA()	RNAModel	[inline]
resetRNACDS(int bb, int ee)	mRNAModel	[inline]
retreatPosOnExon(int pos, unsigned int d) const	Noschain
reverse(int newRNACDSB, int newRNACDSE)	mRNAModel
RNAModel::reverse()	RNAModel
rna	RNAModel	[protected]
RNACDSBound() const	mRNAModel	[inline]
RNACDSRange() const	mRNAModel	[inline]
RNAIndex(int gidx) const	RNAModel
RNALength() const	RNAModel	[inline]
RNAModel()	RNAModel	[inline]
RNAModel(const Noschain &seg, const string &chrom, const string &gs)	RNAModel	[inline, explicit]
RNAModel(const string &exstr, const string &gname, const string &gs, int oi)	RNAModel	[inline]
RNAModel(const string &exstr, const string &gname, const string &gs, int oi, int gene_id)	RNAModel	[inline]
RNAModel(const string &exstarts, const string &exends, char strand, const string &gi, const string &genomic)	RNAModel	[inline]
RNAModel(const string &exstarts, const string &exends, char strand, const string &gi, const string &genomic, int oo)	RNAModel	[inline]
RNAModel(const RNAModel &rm)	RNAModel	[inline]
RNASequence() const	RNAModel	[inline]
RNAString() const	RNAModel	[inline]
rollbackId()	RNAModel	[inline, static]
sameDirection(const Range &r) const	Range
sameExons(const RNAModel &gm) const	RNAModel	[inline]
sameGene(const mRNAModel &mod) const	mRNAModel
samePeptide(const mRNAModel &mm) const	mRNAModel	[inline]
sameRNA(const RNAModel &rmd) const	RNAModel	[inline]
semiGenuine() const	mRNAModel	[inline]
seqGenomic() const	RNAModel
serialid	RNAModel	[protected, static]
set(const Range &r)	Noschain
Range::set(int be, int en)	Range	[inline]
setBegin(int nb)	Noschain
setChain(const Noschain &chain)	Noschain	[inline]
setEnd(int ne)	Noschain
setExons(const vector< Range > &ex)	Noschain	[inline]
setGeneId(const int gene_id)	RNAModel	[inline]
setGenomic(const string &gs)	RNAModel	[inline]
setGenomicCDS(int gb, int ge)	mRNAModel
setGenomicCDS(pair< int, int > gcr)	mRNAModel	[inline]
setGenomicId(const string &gg)	RNAModel	[inline]
setGenomicPointer(const string *gs)	RNAModel	[inline]
setId(int oi)	RNAModel	[inline, static]
setLongestCDSAndProtein()	mRNAModel
setMargin(const int mg)	Range	[inline, static]
setNextOid()	RNAModel	[inline]
setNull()	Noschain	[inline, virtual]
setOid(int oi)	RNAModel	[inline]
setProtein(const string &pseq)	mRNAModel	[inline]
setRNA(const string &rseq)	RNAModel	[inline]
setRNACDS(int bb, int ee)	mRNAModel
setShortestModel(int len)	mRNAModel	[inline, static]
sfCDSGenomic() const	mRNAModel
sfCDSTranscript() const	mRNAModel	[inline]
sfExonsGenomic() const	Noschain
sfExonsProtein() const	mRNAModel
sfExonsTranscript() const	Noschain
shortestmodel	mRNAModel	[static]
shortestpep	mRNAModel	[static]
show(ostream &ous) const	mRNAModel	[virtual]
similar(const Range &r, bool sameDirection=true) const	Range
similar(const Range &r, const int marg=20, const float frac=0.1, bool sameDirection=true) const	Range
smallerEnd() const	Range	[inline]
startEnd(char sep=',') const	Noschain
subchain(const Range &r) const	Noschain
subchain(int bg, int ed) const	Noschain	[inline]
subchainAfterPoint(int p) const	Noschain
subchainBeforePoint(int p) const	Noschain
subsequence(string &sub, const string &gs) const	Noschain
ThreePrimeUTR() const	mRNAModel	[inline]
ThreePrimeUTRLength() const	mRNAModel	[inline]
topology(const Range &r) const	Range
toString() const	Noschain
trimAfterPoint(const int p)	mRNAModel
trimBeforePoint(const int p)	mRNAModel
trimBeforePoint(const int gp, const int rp)	mRNAModel
trimCDSStop()	mRNAModel
trimCDSTail()	mRNAModel
updateOuterRange()	Noschain	[inline]
UTR3Sequence(string &seq) const	mRNAModel	[inline]
UTR3Sequence() const	mRNAModel	[inline]
utrlen3max	mRNAModel	[static]
utrlen5max	mRNAModel	[static]
UTRLength() const	mRNAModel	[inline]
valid() const	mRNAModel	[virtual]
writeExon(ostream &ous, char sep='\t') const	RNAModel
writeModelTable(ostream &ous, char sep='\t') const	mRNAModel
writetab(ostream &mod, ostream &ex, ostream &track, ostream &orna, ostream &oprt, char sep='\t') const	mRNAModel
~Noschain()	Noschain	[inline]
~Range()	Range	[inline]