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NCBI C++ ToolKit: include/algo/gnomon/gnomon_model.hpp Source File

()

{

m_len; }

(IsDeletion() &&

() >=

&&

() <=

+1) ||

((IsInsertion() || IsMismatch()) &&

() <=

&&

<=

()+

()-1);

(m_loc != fsi.m_loc)

m_loc < fsi.m_loc;

(m_type != fsi.m_type)

m_type < fsi.m_type;

(m_len != fsi.m_len)

m_len < fsi.m_len;

m_indelv < fsi.m_indelv;

(m_indelv.empty() || (

)m_indelv.length() ==

);

(m_indelv.empty() || m_type != eIns);

((IsDeletion() || IsMismatch()) && GetInDelV().

())

m_indelv.insert( m_indelv.end(),

(),

);

<

Res>

<

Res>

m_fsplice(fs), m_ssplice(ss), m_fsplice_sig(fsig), m_ssplice_sig(ssig), m_ident(ident), m_seq(seq), m_source(src), m_range(

,s)

(m_seq.empty() || m_range.Empty());

!(*

== p);

(

d) { m_range.SetFrom( m_range.GetFrom() +d ); }

(

d) { m_range.SetTo( m_range.GetTo() +d ); }

(

score,

open=

);

(

==(stp))

(

includeall =

)

;

eNotForChaining = 64,

TypeToString(

);

eBestPlacement = 512,

eUnknownOrientation = 1024,

eConsistentCoverage = 2048,

eUnmodifiedAlign = 8192,

eChangedByFilter = 16384,

eLeftConfirmed = 65536,

eRightConfirmed = 131072,

eLeftFlexible = 262144,

eRightFlexible = 524288,

eExcludedReadthrough = 1048576

m_type(

), m_id(id), m_status(0), m_ident(0), m_weight(1), m_expecting_hole(

), m_strand(s), m_geneid(0), m_rank_in_gene(0), m_trusted_group(0) {}

AddGgapExon(

ident,

& seq,

& src,

infront);

AddNormalExon(

exon,

& fs,

& ss,

ident,

infront);

m_edge_reading_frames.clear();

(

,

& f_sig,

& s_sig) { m_exons[

].m_fsplice_sig = f_sig; m_exons[

].m_ssplice_sig = s_sig; }

ReverseComplementModel();

ExtendLeft(

amount);

ExtendRight(

amount);

Extend(

&

,

ensure_cds_invariant =

);

RemoveShortHolesAndRescore(

& gnomon);

AlignLen()

;

RecalculateLimits();

RealCdsLen()

;

SetCdsInfo(

& cds_info);

CombineCdsInfo(

&

,

ensure_cds_invariant =

);

CombineCdsInfo(

& cds_info,

ensure_cds_invariant =

);

Limits().IntersectingWith(

.Limits());

()

{

m_ident; }

()

{

m_weight; }

plusstrand = Strand() ==

;

(notreversed == plusstrand) ?

:

;

()

{

m_type; }

&

() {

m_status; }

&

()

{

m_status; }

(

& comment) { m_comment = comment; }

(

& comment) { m_comment +=

+ comment; }

()

{

m_cds_info.Score(); }

(

= 1;

< Exons().size(); ++

)

(!Exons()[

-1].m_ssplice || !Exons()[

].m_fsplice)

()

{

m_cds_info.HasStart(); }

()

{

m_cds_info.HasStop (); }

()

{

HasStart() && HasStop() && Continuous(); }

()

{

FullCds() && (!Open5primeEnd() || ConfirmedStart()); }

( !(OpenCds()&&ConfirmedStart()) );

(ReadingFrame().

() || (!OpenCds() && FullCds()));

(Strand() ==

? OpenLeftEnd() : OpenRightEnd());

()

{

m_cds_info.OpenCds(); }

(

includeall =

)

{

m_cds_info.PStop(includeall); }

isNMD(

limit = 50)

;

GetInDels(

fs_only)

;

GetCdsDnaSequence (

& contig_sequence)

;

GetProtein (

& contig_sequence)

;

HasCompatibleOverlap(

&

,

min_overlap = 2)

;

MutualExtension(

&

)

;

{

Strand()==

.Strand() && Limits()==

.Limits() && Exons() ==

.Exons() && FrameShifts()==

.FrameShifts() &&

GetCdsInfo().PStops() ==

.GetCdsInfo().PStops() &&

() ==

.Type() && Status() ==

.Status(); }

IdenticalAlign(

) &&

()==

.Type() && m_id==

.m_id && m_support==

.m_support;

list< CRef<CSeq_id> >&

()

{

m_trusted_mrna; }

list< CRef<CSeq_id> >&

()

{

m_trusted_prot; }

RemoveExtraFShifts(

left,

right);

TrimEdgesToFrameInOtherAlignGaps(

& exons_with_gaps);

CdsInvariant(

check_start_stop =

)

;

(fsi_begin != fsi_end) {

(fsi_begin->Loc() == orig_a && !fsi_begin->IsMismatch()) {

(!fsi_begin->IsInsertion());

TInDels::const_iterator fs = fsi_end-1;

(fs->Loc() == orig_b+1 && fs->IsDeletion())

<

In,

Out>

(

In& original_sequence,

& edited_sequence,

includeholes =

)

;

mrange.MoveOrigin(shift);

left_type,

right_type,

& left_edit_extra_seq,

& right_edit_extra_seq);

ResetAlignMap();

RecalculateAlignMap(

.GetFrom(),

.GetTo());

RecalculateAlignMap(hole.

()+1, hole.

()-1);

TargetAccession()

;

(

objects::CSeq_id&

) { m_target_id.Reset(&

); }

()

{

m_alignmap.TargetLen(); }

PolyALen()

;

RecalculateAlignMap(

left,

right);

(

& cntg) : m_contig(cntg) {}

<

Model>

m_limits.CombineWith(

.Limits());

this->push_back(

);

m_limits.CombineWith(c.

());

this->splice(list<Model>::end(),c);

list<Model>::clear();

m_limits.SetFrom(

);

m_limits.SetTo( second );

<

Cluster>

(

Cluster::TModel&

) {

clust.Splice(

Cluster&

(*it));

Cluster&

(*this->insert(second,Cluster(clust.Limits()))).Splice(clust);

<

B

irectionalIterator>

(BidirectionalIterator

(

);

!=

; ++

)

<

Model>

left = algn.Limits().GetFrom();

(

= 1;

< algn.Exons().

(); ++

) {

(!algn.Exons()[

-1].m_ssplice || !algn.Exons()[

].m_fsplice) {

(!parts.empty() && settrimflags) {

parts.back().Status() &= ~

::eRightTrimmed;

left = algn.

()[

].GetFrom();

(!parts.empty()) {

parts.back().Status() &= ~

::eRightTrimmed;

TSignedSeqPos GetTo() const

const string & GetMismatch() const

TSignedSeqPos GetExtendedFrom() const

void SetEdgeFrom(SMapRangeEdge from)

EEdgeType GetTypeTo() const

string GetExtraSeqFrom() const

void MoveOrigin(TSignedSeqPos shift)

bool operator<(const SMapRange &mr) const

TSignedSeqPos GetExtraTo() const

string GetExtraSeqTo() const

SMapRangeEdge GetEdgeFrom() const

TSignedSeqPos GetFrom() const

TSignedSeqPos GetExtraFrom() const

SMapRangeEdge GetEdgeTo() const

TSignedSeqPos GetExtendedTo() const

EEdgeType GetTypeFrom() const

void SetEdgeTo(SMapRangeEdge to)

SMapRange(SMapRangeEdge from, SMapRangeEdge to, const string &mism)

CAlignMap(TSignedSeqPos orig_a, TSignedSeqPos orig_b, TInDels::const_iterator fsi_begin, const TInDels::const_iterator fsi_end)

TSignedSeqPos FShiftedMove(TSignedSeqPos orig_pos, int len) const

static int FindLowerRange(const vector< CAlignMap::SMapRange > &a, TSignedSeqPos p)

TSignedSeqRange ShrinkToRealPointsOnEdited(TSignedSeqRange edited_range) const

TSignedSeqRange MapRangeOrigToEdited(TSignedSeqRange orig_range, bool withextras=true) const

void MoveOrigin(TSignedSeqPos shift)

int FShiftedLen(TSignedSeqPos a, TSignedSeqPos b, bool withextras=true) const

void InsertOneToOneRange(TSignedSeqPos orig_start, TSignedSeqPos edited_start, TSignedSeqPos len, const string &mism, TSignedSeqPos left_orige, TSignedSeqPos left_edite, TSignedSeqPos right_orige, TSignedSeqPos right_edite, EEdgeType left_type, EEdgeType right_type, const string &left_edit_extra_seq, const string &right_edit_extra_seq)

static TSignedSeqRange MapRangeAtoB(const vector< CAlignMap::SMapRange > &a, const vector< CAlignMap::SMapRange > &b, TSignedSeqRange r, ERangeEnd lend, ERangeEnd rend)

vector< SMapRange > m_edited_ranges

CAlignMap(TSignedSeqPos orig_a, TSignedSeqPos orig_b)

TSignedSeqPos InsertIndelRangesForInterval(TSignedSeqPos orig_a, TSignedSeqPos orig_b, TSignedSeqPos edit_a, TInDels::const_iterator fsi_begin, TInDels::const_iterator fsi_end, EEdgeType type_a, EEdgeType type_b, const string &gseq_a, const string &gseq_b)

TSignedSeqRange MapRangeEditedToOrig(TSignedSeqRange edited_range, bool withextras=true) const

static TSignedSeqRange MapRangeAtoB(const vector< CAlignMap::SMapRange > &a, const vector< CAlignMap::SMapRange > &b, TSignedSeqRange r, bool withextras)

TSignedSeqPos MapOrigToEdited(TSignedSeqPos orig_pos) const

void EditedSequence(const In &original_sequence, Out &edited_sequence, bool includeholes=false) const

TSignedSeqPos MapEditedToOrig(TSignedSeqPos edited_pos) const

TSignedSeqRange ShrinkToRealPoints(TSignedSeqRange orig_range, bool snap_to_codons=false) const

int FShiftedLen(TSignedSeqRange ab, ERangeEnd lend, ERangeEnd rend) const

static TSignedSeqPos MapAtoB(const vector< CAlignMap::SMapRange > &a, const vector< CAlignMap::SMapRange > &b, TSignedSeqPos p, ERangeEnd move_mode)

EStrand Orientation() const

TSignedSeqRange MapRangeOrigToEdited(TSignedSeqRange orig_range, ERangeEnd lend, ERangeEnd rend) const

vector< SMapRange > m_orig_ranges

virtual void Clip(TSignedSeqRange limits, EClipMode mode, bool ensure_cds_invariant=true)

CConstRef< objects::CSeq_id > m_target_id

CConstRef< objects::CSeq_id > GetTargetId() const

virtual void CutExons(TSignedSeqRange hole)

virtual CAlignMap GetAlignMap() const

void SetTargetId(const objects::CSeq_id &id)

CAlignModel(const objects::CSeq_align &seq_align)

void Cut(TSignedSeqRange hole)

CCDSInfo MapFromEditedToOrig(const CAlignMap &amap) const

bool PStop(bool includeall=true) const

void SetStart(TSignedSeqRange r, bool confirmed=false)

CCDSInfo MapFromOrigToEdited(const CAlignMap &amap) const

TSignedSeqRange MaxCdsLimits() const

void Set5PrimeCdsLimit(TSignedSeqPos p)

CCDSInfo(bool gcoords=true)

void Remap(const CRangeMapper &mapper)

bool IsMappedToGenome() const

void SetScore(double score, bool open=false)

bool m_genomic_coordinates

TSignedSeqRange m_reading_frame_from_proteins

TSignedSeqRange Start() const

bool ConfirmedStart() const

TSignedSeqRange m_reading_frame

void Clip(TSignedSeqRange limits)

void AddPStop(SPStop stp)

TSignedSeqRange Cds() const

void CombineWith(const CCDSInfo &another_cds_info)

TSignedSeqRange ReadingFrame() const

TSignedSeqRange m_max_cds_limits

TSignedSeqRange ProtReadingFrame() const

void SetStop(TSignedSeqRange r, bool confirmed=false)

const TPStops & PStops() const

bool ConfirmedStop() const

void Clear5PrimeCdsLimit()

void SetReadingFrame(TSignedSeqRange r, bool protein=false)

bool operator==(const CCDSInfo &another) const

TSignedSeqRange Stop() const

void SetSplices(int i, const string &f_sig, const string &s_sig)

const list< CRef< CSeq_id > > & TrustedProt() const

bool operator<(const CGeneModel &a) const

const unsigned int & Status() const

bool GoodEnoughToBeAnnotation() const

void SetTrustedCds(const TSignedSeqRange &r)

bool Open5primeEnd() const

int FShiftedLen(TSignedSeqPos a, TSignedSeqPos b, bool withextras=true) const

virtual void CutExons(TSignedSeqRange hole)

bool IntersectingWith(const CGeneModel &a) const

EStrand Orientation() const

void InsertTrustedProt(CRef< CSeq_id > g)

list< CRef< CSeq_id > > m_trusted_mrna

TSignedSeqRange TrustedCds() const

void SetRankInGene(int rank)

bool IdenticalAlign(const CGeneModel &a) const

const CSupportInfoSet & Support() const

bool OpenRightEnd() const

const TExons & Exons() const

vector< CCDSInfo > * SetEdgeReadingFrames()

bool LeftComplete() const

TSignedSeqRange ReadingFrame() const

const TInDels & FrameShifts() const

list< CRef< CSeq_id > > m_trusted_prot

bool RightComplete() const

CGeneModel(EStrand s=ePlus, Int8 id=0, int type=0)

CSupportInfoSet m_support

TSignedSeqRange m_trusted_cds

void SetStrand(EStrand s)

void ReplaceSupport(const CSupportInfoSet &support_set)

virtual void Clip(TSignedSeqRange limits, EClipMode mode, bool ensure_cds_invariant=true)

bool ConfirmedStop() const

void InsertTrustedmRNA(CRef< CSeq_id > g)

bool AddSupport(const CSupportInfo &support)

TSignedSeqRange Limits() const

const list< CRef< CSeq_id > > & TrustedmRNA() const

void AddComment(const string &comment)

const CCDSInfo & GetCdsInfo() const

const string & GetComment() const

bool operator==(const CGeneModel &a) const

vector< CModelExon > TExons

const string & ProteinHit() const

bool ConfirmedStart() const

const vector< CCDSInfo > * GetEdgeReadingFrames() const

vector< CCDSInfo > m_edge_reading_frames

void SetTrustedGroup(int tgr)

bool PStop(bool includeall=true) const

void SetComment(const string &comment)

const SSource & GetSource() const

void SetStatus(EStatus s)

TSignedSeqPos Loc() const

bool operator==(const CInDelInfo &fsi) const

EStatus GetStatus() const

void Init(TSignedSeqPos l, int len, EType type, const string &v, const SSource &s)

void SetLoc(TSignedSeqPos l)

bool operator<(const CInDelInfo &fsi) const

bool operator!=(const CInDelInfo &fsi) const

bool IntersectingWith(TSignedSeqPos a, TSignedSeqPos b) const

CInDelInfo(TSignedSeqPos l, int len, EType type, const string &v=kEmptyStr, const SSource &s=SSource())

set< Cluster >::iterator Titerator

void Insert(const typename Cluster::TModel &a)

CModelCluster(TSignedSeqRange limits)

void Insert(const Model &a)

void Init(TSignedSeqPos first, TSignedSeqPos second)

CModelCluster(int f=numeric_limits< int >::max(), int s=0)

TSignedSeqRange Limits() const

void Splice(CModelCluster &c)

bool operator<(const CModelCluster &c) const

bool operator==(const CModelExon &p) const

CInDelInfo::SSource m_source

CModelExon(TSignedSeqPos f=0, TSignedSeqPos s=0, bool fs=false, bool ss=false, const string &fsig="", const string &ssig="", double ident=0, const string &seq="", const CInDelInfo::SSource &src=CInDelInfo::SSource())

bool operator<(const CModelExon &p) const

TSignedSeqPos GetFrom() const

const TSignedSeqRange & Limits() const

void Remap(const CRangeMapper &mapper)

TSignedSeqPos GetTo() const

TSignedSeqRange & Limits()

bool operator!=(const CModelExon &p) const

virtual TSignedSeqRange operator()(TSignedSeqRange r, bool withextras=true) const =0

bool operator==(const CSupportInfo &s) const

CSupportInfo(Int8 model_id, bool core=false)

bool operator<(const CSupportInfo &s) const

EResidue(EResidueNames e)

const_iterator upper_bound(const key_type &key) const

const_iterator lower_bound(const key_type &key) const

Include a standard set of the NCBI C++ Toolkit most basic headers.

bool Empty(const CNcbiOstrstream &src)

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

static DLIST_TYPE *DLIST_NAME() last(DLIST_LIST_TYPE *list)

static const TDS_WORD limits[]

vector< TResidue > CResidueVec

bool Precede(TSignedSeqRange l, TSignedSeqRange r)

set< CSupportInfo > CSupportInfoSet

TResidue Complement(TResidue c)

CModelCluster< CAlignModel > TAlignModelCluster

const char *const k_aa_table

CModelCluster< CGeneModel > TGeneModelCluster

list< CAlignModel > TAlignModelList

CModelClusterSet< TAlignModelCluster > TAlignModelClusterSet

CNcbiOstream & operator<<(CNcbiOstream &s, const setcontig &c)

CNcbiIstream & operator>>(CNcbiIstream &s, const getcontig &c)

bool Include(TSignedSeqRange big, TSignedSeqRange small)

const EResidue k_toMinus[5]

void ReverseComplement(const BidirectionalIterator &first, const BidirectionalIterator &last)

CModelClusterSet< TGeneModelCluster > TGeneModelClusterSet

list< CGeneModel > TGeneModelList

bool IsStopCodon(const Res *seq, int strand=ePlus)

EStrand OtherStrand(EStrand s)

vector< CInDelInfo > TInDels

objects::CSeqVectorTypes::TResidue TResidue

bool Enclosed(TSignedSeqRange big, TSignedSeqRange small)

void MapAlignsToOrigContig(TAlignModelList &aligns, const TInDels &corrections, int contig_size)

list< Model > GetAlignParts(const Model &algn, bool settrimflags)

bool IsStartCodon(const Res *seq, int strand=ePlus)

int TSignedSeqPos

Type for signed sequence position.

int64_t Int8

8-byte (64-bit) signed integer

bool NotEmpty(void) const

bool operator<(const TThisType &r) const

static TThisType GetEmpty(void)

static position_type GetWholeFrom(void)

CRange< TSignedSeqPos > TSignedSeqRange

static TThisType GetWhole(void)

static position_type GetWholeTo(void)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

#define NCBI_XALGOGNOMON_EXPORT

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

unsigned int

A callback function used to compare two keys in a database.

constexpr bool empty(list< Ts... >) noexcept

const struct ncbi::grid::netcache::search::fields::SIZE size

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

void Out(T t, int w, CNcbiOstream &to=cout)

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

bool operator<(const SMapRangeEdge &mre) const

SMapRangeEdge(TSignedSeqPos p, TSignedSeqPos e=0, EEdgeType t=eBoundary, const string &seq=kEmptyStr)

bool operator==(const SMapRangeEdge &mre) const

SPStop(TSignedSeqRange r, EStatus s)

bool operator<(const SPStop &stp) const

setcontig(const string &cntg)

int g(Seg_Gsm *spe, Seq_Mtf *psm, Thd_Gsm *tdg)

void AddExon(CRef< CSeq_entry > seq, const string &number, TSeqPos start)

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