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NCBI C++ ToolKit: src/algo/blast/unit_tests/api/neutral_seqalign.hpp Source File

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(make_pair(query_gi, subj_gi)) {}

Class to contain the gis of the aligned sequences.

CAlignedGis(std::pair< TGi, TGi > gis)

CAlignedGis(TGi query_gi, TGi subj_gi)

std::pair< TGi, TGi > m_Gis

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

ENa_strand

strand of nucleic acid

Magic spell ;-) needed for some weird compilers... very empiric.

Miscellaneous common-use basic types and functionality.

const int kInvalidIntValue

std::vector< SeqAlign > TSeqAlignSet

Vector of neutral sequence alignments.

std::list< SeqLoc > TSeqLocList

ncbi::objects::ENa_strand TStrand

const double kInvalidDoubleValue

Neutral sequence alignment (for representing an HSP in BLAST)

int GetNumSegments() const

Return the number of segments in the HSP.

std::vector< TSeqPos > lengths

Lengths of aligned segments.

double bit_score

HSP bit score.

int num_ident

Number of identical residues.

double evalue

HSP evalue.

CAlignedGis sequence_gis

Gis of the aligned sequences.

SeqAlign()

Default constructor, initializes all fields to kInvalid*Value or empty.

std::vector< int > starts

Query/Subject starting offsets.

int query_strand

Strand of the query sequence.

int subject_strand

Strand of the subject sequence.

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