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NCBI C++ ToolKit: src/objects/seqalign/Sparse_seg.cpp Source File

58

(*aln_it)->Validate(full_test);

88 "CSparse_seg::GetSeq_id(): " 89 "can not get seq-id for the row requested."

);

113 "CSparse_seg::GetSeqStrand(): " 114 "can not get strand for the row requested."

);

122 bool

first_row =

true

;

131 else if

( start < total_start ) {

152 "CSparse_seg::GetSeqStart(): " 153 "can not get seq start for the row requested."

);

161 bool

first_row =

true

;

166

stop += align.

GetLens

().back() - 1;

171 else if

( stop > total_stop ) {

184

stop += align.

GetLens

().back() - 1;

190

stop += align.

GetLens

().front() - 1;

196 "CSparse_seg::GetSeqStop(): " 197 "can not get seq stop for the row requested."

);

205 bool

first_row =

true

;

206 TSeqPos

total_start = 0, total_stop = 0;

211

stop += align.

GetLens

().back() - 1;

218 if

( start < total_start ) {

221 if

( stop > total_stop ) {

236

stop += align.

GetLens

().back() - 1;

243

stop += align.

GetLens

().front() - 1;

249 "CSparse_seg::GetSeqRange(): " 250 "can not get seq range for the row requested."

);

bool IsForward(ENa_strand s)

User-defined methods of the data storage class.

ENa_strand GetSeqStrand(TDim row) const

CRange< TSeqPos > GetSeqRange(TDim row) const

TDim CheckNumRows(void) const

void Validate(bool full_test=false) const

Validators.

TSeqPos GetSeqStart(TDim row) const

const CSeq_id & GetSeq_id(TDim row) const

TSeqPos GetSeqStop(TDim row) const

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

vector< CRef< CSparse_align > > TRows

const TFirst_id & GetFirst_id(void) const

Get the First_id member data.

const TSecond_starts & GetSecond_starts(void) const

Get the Second_starts member data.

const TLens & GetLens(void) const

Get the Lens member data.

bool IsSetSecond_strands(void) const

Check if a value has been assigned to Second_strands data member.

const TFirst_starts & GetFirst_starts(void) const

Get the First_starts member data.

const TRow_scores & GetRow_scores(void) const

Get the Row_scores member data.

const TSecond_strands & GetSecond_strands(void) const

Get the Second_strands member data.

const TSecond_id & GetSecond_id(void) const

Get the Second_id member data.

const TRows & GetRows(void) const

Get the Rows member data.

bool IsSetRow_scores(void) const

per-row scores Check if a value has been assigned to Row_scores data member.

ENa_strand

strand of nucleic acid

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

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

#define _SEQALIGN_ASSERT(expr)

#define row(bind, expected)

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