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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/Packed__seqint_8cpp_source.html below:

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

(

, ival->GetFrom(), ival->GetTo(), strand);

length += (**i).GetLength();

().back() :

().front();

().front() :

().back();

().back() :

().front();

().front() :

().back();

( (*i)->IsSetStrand() )

;

( !(*i)->IsSetStrand() )

;

strand_set =

;

= &((*i)->GetId());

}

(!strand_set) {

}

(istrand != strand) {

().push_back(new_ival);

ival.

().Assign(

);

(ivals.begin(), ivals.end(), back_inserter(

()));

(*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.

void ResetStrand(void)

Reset the strand to 'not set'.

bool IsPartialStop(ESeqLocExtremes ext) const

void SetPartialStart(bool val, ESeqLocExtremes ext)

TSeqPos GetStop(ESeqLocExtremes ext) 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)

void FlipStrand(void)

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

bool IsTruncatedStart(ESeqLocExtremes ext) const

check if parts of the seq-loc are missing

void AddIntervals(const CPacked_seqint &ivals)

void SetTruncatedStop(bool val, ESeqLocExtremes ext)

TSeqPos GetStart(ESeqLocExtremes ext) const

TSeqPos GetLength(void) const

void SetPartialStop(bool val, ESeqLocExtremes ext)

bool IsPartialStart(ESeqLocExtremes ext) const

bool IsReverseStrand(void) const

CSeq_interval * SetStopInt(ESeqLocExtremes ext)

const CSeq_interval * GetStopInt(ESeqLocExtremes ext) const

const CSeq_interval * GetStartInt(ESeqLocExtremes ext) const

bool IsSetStrand(EIsSetStrand flag=eIsSetStrand_Any) const

bool IsTruncatedStop(ESeqLocExtremes ext) const

vector< CRange< TSeqPos > > TRanges

CSeq_interval * SetStartInt(ESeqLocExtremes ext)

ENa_strand GetStrand(void) const

void SetStrand(ENa_strand strand)

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

void AddInterval(const CSeq_interval &ival)

for convenience

bool IsTruncatedStop(ESeqLocExtremes ext) const

bool IsPartialStop(ESeqLocExtremes ext) 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 GetStart(ESeqLocExtremes ext) const

bool IsPartialStart(ESeqLocExtremes ext) const

bool IsTruncatedStart(ESeqLocExtremes ext) const

check if parts of the seq-loc are missing

TSeqPos GetStop(ESeqLocExtremes ext) const

void SetTruncatedStop(bool val, ESeqLocExtremes ext)

void SetPartialStart(bool val, ESeqLocExtremes ext)

void SetPartialStop(bool val, ESeqLocExtremes ext)

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.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

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

Set object to copy of another one.

E_SIC Compare(const CSeq_id &sid2) const

Compare() - more general.

@ e_YES

SeqIds compared, but are different.

#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.

list< CRef< CSeq_interval > > Tdata

ENa_strand

strand of nucleic acid

const Tdata & Get(void) const

Get the member data.

Tdata & Set(void)

Assign a value to data member.

void SetId(TId &value)

Assign a value to Id data member.

void SetFrom(TFrom value)

Assign a value to From data member.

void SetStrand(TStrand value)

Assign a value to Strand data member.

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

Useful/utility classes and methods.

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

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