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NCBI C++ ToolKit: src/objects/seqloc/Seq_loc_mix.cpp Source File

( (*it)->GetStrand() )

;

( !(*it)->GetStrand() )

;

strand_set =

;

((*it)->IsNull() || (*it)->IsEmpty()) {

* iid = (*it)->GetId();

}

(!strand_set) {

}

(istrand != strand) {

( !other.

() ) {

().push_back(loc);

( !other.

() ) {

().push_back(loc);

pnt.

().Assign(

);

ival.

().Assign(

);

().push_back(loc);

(*it)->SetStrand(strand);

(*it)->ResetStrand();

ESeqLocExtremes

Used to determine the meaning of a location's Start/Stop positions.

@ eExtreme_Positional

numerical value

EIsSetStrand

Flag used by IsSetStrand() to switch between any/all modes.

@ eIsSetStrand_All

Check if all parts have strand.

@ eIsSetStrand_Any

Check if any part has strand.

bool IsReverseStrand(void) const

void SetPartialStart(bool val, ESeqLocExtremes ext)

void AddInterval(const CSeq_id &id, TSeqPos from, TSeqPos to, ENa_strand strand=eNa_strand_unknown)

const CSeq_loc * GetLastLoc(ENullSegType null_seg=eNullSegAllow) const

bool IsTruncatedStop(ESeqLocExtremes ext) const

CSeq_loc * SetStartLoc(ESeqLocExtremes ext, ENullSegType null_seg=eNullSegAllow)

const CSeq_loc * GetStopLoc(ESeqLocExtremes ext, ENullSegType null_seg=eNullSegAllow) const

void SetPartialStop(bool val, ESeqLocExtremes ext)

void ResetStrand(void)

Reset the strand to 'not set'.

bool IsSetStrand(EIsSetStrand flag=eIsSetStrand_Any) const

void SetTruncatedStart(bool val, ESeqLocExtremes ext)

set / remove e_Lim fuzz on start or stop (tl/tr - indicating removed parts of the seq-loc)

TSeqPos GetStop(ESeqLocExtremes ext) const

void AddSeqLoc(const CSeq_loc &other)

bool IsPartialStart(ESeqLocExtremes ext) const

CSeq_loc * SetStopLoc(ESeqLocExtremes ext, ENullSegType null_seg=eNullSegAllow)

ENa_strand GetStrand(void) const

CSeq_loc * SetLastLoc(ENullSegType null_seg=eNullSegAllow)

TSeqPos GetStart(ESeqLocExtremes ext) const

bool IsPartialStop(ESeqLocExtremes ext) const

void SetStrand(ENa_strand strand)

Set the strand for all of the location's ranges.

CSeq_loc * SetFirstLoc(ENullSegType null_seg=eNullSegAllow)

const CSeq_loc * GetStartLoc(ESeqLocExtremes ext, ENullSegType null_seg=eNullSegAllow) const

bool IsTruncatedStart(ESeqLocExtremes ext) const

check if parts of the seq-loc are missing

const CSeq_loc * GetFirstLoc(ENullSegType null_seg=eNullSegAllow) const

void FlipStrand(void)

Flip the strand (e.g. plus to minus)

void SetTruncatedStop(bool val, ESeqLocExtremes ext)

static vector< string > arr

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define NON_CONST_REVERSE_ITERATE(Type, Var, Cont)

Non constant version of REVERSE_ITERATE macro.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

#define REVERSE_ITERATE(Type, Var, Cont)

ITERATE macro to reverse sequence through container elements.

E_SIC Compare(const CSeq_id &sid2) const

Compare() - more general.

@ e_YES

SeqIds compared, but are different.

void SetTruncatedStart(bool val, ESeqLocExtremes ext)

set / remove e_Lim fuzz on start or stop (tl/tr - indicating removed parts of the seq-loc)

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Override Assign() to incorporate cache invalidation.

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

bool IsTruncatedStop(ESeqLocExtremes ext) const

bool IsTruncatedStart(ESeqLocExtremes ext) const

check if parts of the seq-loc are missing

void SetPartialStart(bool val, ESeqLocExtremes ext)

set / remove e_Lim fuzz on start or stop (lt/gt - indicating partial interval)

void SetPartialStop(bool val, ESeqLocExtremes ext)

bool IsPartialStop(ESeqLocExtremes ext) const

void SetTruncatedStop(bool val, ESeqLocExtremes ext)

TSeqPos GetStop(ESeqLocExtremes ext) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

void SetTo(TTo value)

Assign a value to To data member.

void SetPoint(TPoint value)

Assign a value to Point data member.

void SetId(TId &value)

Assign a value to Id data member.

bool IsMix(void) const

Check if variant Mix is selected.

ENa_strand

strand of nucleic acid

void SetId(TId &value)

Assign a value to Id data member.

void SetStrand(TStrand value)

Assign a value to Strand data member.

list< CRef< CSeq_loc > > Tdata

void SetFrom(TFrom value)

Assign a value to From data member.

const Tdata & Get(void) const

Get the member data.

Tdata & Set(void)

Assign a value to data member.

bool IsNull(void) const

Check if variant Null is selected.

void SetStrand(TStrand value)

Assign a value to Strand data member.

const TMix & GetMix(void) const

Get the variant data.

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

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