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NCBI C++ ToolKit: include/algo/cobalt/hit.hpp Source File

kMinHitSize = 2;

(

seq1_index,

seq2_index)

: m_SeqIndex1(seq1_index), m_SeqIndex2(seq2_index),

m_Score(0), m_SeqRange1(0,0), m_SeqRange2(0,0) {}

: m_SeqIndex1(seq1_index), m_SeqIndex2(seq2_index),

m_EditScript(hsp->gap_info) { VerifyHit(); }

(

seq1_index,

seq2_index,

score,

objects::CDense_seg& denseg);

(

seq1_index,

seq2_index,

score,

objects::CDense_diag& dendiag);

(

seq1_index,

seq2_index,

: m_SeqIndex1(seq1_index), m_SeqIndex2(seq2_index),

m_SeqRange1(seq_range1), m_SeqRange2(seq_range2),

m_EditScript(edit_script) { VerifyHit(); }

(

= 0;

< (

)m_SubHit.size();

++)

m_SubHit[

];

GetRangeFromSeq2(

seq_range2,

& traceback_range);

GetRangeFromSeq1(

seq_range1,

& traceback_range);

ResolveSubHitConflicts(

& seq1,

User-defined methods of the data storage class.

Definitions used by all COBALT aligner components.

Structures and API used for saving BLAST hits.

Interface for the traceback from blast hits.

A generalized representation of a pairwise alignment.

TSubHit & GetSubHit()

Retrieve a list of subhits.

CHit(int seq1_index, int seq2_index, int score, const objects::CDense_seg &denseg)

Create an alignment from a Dense_seg.

vector< CHit * > m_SubHit

Subhits for this alignment.

CHit(int seq1_index, int seq2_index, TRange seq_range1, TRange seq_range2, int score, CEditScript edit_script)

Create an alignment with all specified parameters.

CEditScript m_EditScript

Traceback for this alignment.

void InsertSubHit(CHit *hit)

Add a to a CHit's list of subhits.

CHit(int seq1_index, int seq2_index, BlastHSP *hsp)

Create an alignment from a BLAST hit.

CHit(int seq1_index, int seq2_index, int score, const objects::CDense_diag &dendiag)

Create an alignment from a Dense_diag.

int m_Score

Score of alignment.

CEditScript & GetEditScript()

Retrieve the traceback associated with a CHit.

int m_SeqIndex1

Numerical identifier for first sequence in alignment.

int m_SeqIndex2

Numerical identifier for second sequence in alignment.

TRange m_SeqRange1

The range of offsets on the first sequence.

CHit(int seq1_index, int seq2_index)

Create an empty alignment.

TRange m_SeqRange2

The range of offsets on the second sequence.

bool HasSubHits()

Query if a CHit has a hierarchy of subhits available.

vector< CHit * > TSubHit

Hits can be grouped hierarchically.

Class for representing protein sequences.

Definitions of structures used for saving traceback information.

#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.

#define NCBI_COBALT_EXPORT

unsigned int

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

Interface for CSequence class.

Structure holding all information about an HSP.

Interface for CEditScript class.

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