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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/seqinfosrc__seqvec_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/blast/api/seqinfosrc_seqvec.cpp Source File

51  if

(seqv.size() == 0) {

53  "Empty sequence vector for id and length retrieval"

);

65  "Index out of range for id retrieval"

);

68

list < CRef<CSeq_id> > seqid_list;

75

seqid_list.push_back(seqid_ref);

83  "Index out of range for Seq-loc retrieval"

);

92  "Index out of range for length retrieval"

);

111  const

vector <TSeqRange>& target_ranges,

117  for

(

size_t

ir=0; ir< target_ranges.size(); ir++) {

121

retval.push_back(sli);

134

vector<TSeqRange> ranges;

135

ranges.push_back(target_range);

136  return GetMasks

(index, ranges, retval);

140  const

vector<TSeqRange>& target_ranges,

146  if

(

mask

.Empty() || target_ranges.empty()) {

150  if

(

mask

->IsInt()) {

152

target_ranges, kFrame, retval);

153

}

else if

(

mask

->IsPacked_int()) {

159  "Type of mask not supported"

);

162  return

(retval.empty() ?

false

:

true

);

Declares the BLAST exception class.

ncbi::TMaskedQueryRegions mask

Defines BLAST error codes (user errors included)

structure for seqloc info

Implementation of the IBlastSeqInfoSrc interface to encapsulate retrieval of sequence identifiers and...

Collection of masked regions for a single query sequence.

TSeqLocVector m_SeqVec

Vector of subject sequence locations to get information from.

virtual bool GetMasks(Uint4 index, const TSeqRange &target_range, TMaskedSubjRegions &retval) const

Retrieves the subject masks for the corresponding index.

virtual Uint4 GetLength(Uint4 index) const

Retrieve sequence length given its index in the vector.

static void s_SeqIntervalToSeqLocInfo(CRef< CSeq_interval > interval, const vector< TSeqRange > &target_ranges, const CSeqLocInfo::ETranslationFrame frame, TMaskedSubjRegions &retval)

virtual size_t Size() const

Returns the size of the underlying container of sequences.

virtual ~CSeqVecSeqInfoSrc()

Destructor.

virtual list< CRef< objects::CSeq_id > > GetId(Uint4 index) const

Retrieve a sequence identifier given its index in the vector.

virtual bool HasGiList() const

Is the subject restricted by a GI list? (Always returns false).

virtual CConstRef< objects::CSeq_loc > GetSeqLoc(Uint4 index) const

Method to retrieve the sequence location given its ordinal number.

#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.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

void Reset(void)

Reset reference object.

uint32_t Uint4

4-byte (32-bit) unsigned integer

bool IntersectingWith(const TThisType &r) const

static TThisType GetEmpty(void)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define USING_SCOPE(ns)

Use the specified namespace.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

list< CRef< CSeq_interval > > Tdata

TFrom GetFrom(void) const

Get the From member data.

TTo GetTo(void) const

Get the To member data.

Defines a concrete strategy for the IBlastSeqInfoSrc interface for sequence identifiers retrieval fro...

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

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