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NCBI C++ ToolKit: include/objects/seq/seq_align_mapper_base.hpp Source File

SetMapped(

);

GetSegStart(

)

;

vector<SAlignment_Row>

;

(

)

{

m_Dim; }

GetMaxDim(

)

;

x_Init(

& diags);

x_Init(

TStd& sseg);

x_ConvertAlign(

*

);

x_ConvertRow(

);

x_FillKnownStrands(

& strands)

;

TSegments::const_iterator& seg,

& last_exon_partial,

start_seg)

;

& last_exon_partial,

& single_gen_id,

& single_gen_str,

& single_prod_id,

& single_prod_str,

& partial)

;

x_HaveMixedSeqTypes(

)

;

x_HaveMixedStrand(

)

;

x_IsEmpty(

)

;

m_IsSetStrand(

),

bool SameOrientation(ENa_strand a, ENa_strand b)

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

CMappingRange - describes a single interval to interval mapping.

Class used to map seq-alignments.

CSeq_loc_Mapper_Base & m_LocMapper

CSeq_loc_Mapper_Base & GetLocMapper(void) const

CSeq_align::C_Segs::TDendiag TDendiag

vector< CRef< CSeq_align_Mapper_Base > > TSubAligns

size_t GetDim(void) const

Some of the following methods use only the first segment to get information about rows.

size_t GetMaxDim(void) const

Get max number of rows of all segments.

SAlignment_Segment::TScores TScores

vector< TScores > TScoresGroups

CConstRef< CSpliced_exon > m_OrigExon

vector< ENa_strand > TStrands

CRef< CSeq_align > m_DstAlign

CConstRef< CSeq_align > m_OrigAlign

TScoresGroups m_GroupScores

CSeq_align::C_Segs::TStd TStd

const TSegments & GetSegments() const

Get parsed segments.

list< SAlignment_Segment > TSegments

CSeq_loc_Mapper_Base –.

CSeq_align::C_Segs::TDendiag TDendiag

unsigned int TSeqPos

Type for sequence locations and lengths.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

E_Choice

Choice variants.

list< CRef< CStd_seg > > TStd

list< CRef< CDense_diag > > TDendiag

ENa_strand

strand of nucleic acid

unsigned int

A callback function used to compare two keys in a database.

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

#define row(bind, expected)

Single row of a single alignment segment.

ENa_strand m_Strand

Strand value.

TSeqPos m_Start

kInvalidSeqPos means gap

CSeq_id_Handle m_Id

Row's seq-id.

int GetSegStart(void) const

Get segment start or -1 if it's a gap.

bool m_IsSetStrand

Is strand set for the row?

bool SameStrand(const SAlignment_Row &r) const

Check if the query row has the same strand orientation.

bool m_Mapped

Flag indicating mapped rows.

void SetMapped(void)

Mark the row as mapped.

Structure to hold information about a single alignment segment.

vector< SAlignment_Row > TRows

TRows m_Rows

Segment rows.

vector< CRef< CScore > > TScores

TScores m_Scores

Scores for this segment.

CSpliced_exon_chunk::E_Choice TPartType

ssize_t m_ScoresGroupIdx

Group of scores.

bool m_HaveStrands

Do at least some rows have strand set?

int m_Len

Segment length.

int m_GroupIdx

Group of segments (e.g.

const value_slice::CValueConvert< value_slice::SRunTimeCP, FROM > Convert(const FROM &value)

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