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NCBI C++ ToolKit: src/algo/cobalt/phi.cpp Source File

: query_idx(seq), hit(range) {}

vector<int>& indices)

(queries.size() == indices.size());

num_queries = queries.size();

vector<CMultiAlignerOptions::CPattern>&

vector<SPatternHit> phi_hits;

* pattern = (

*)

[

].AsPointer();

(

j = 0; j < num_queries; j++) {

, phi_pattern);

(

k = 0; k < (size_t)twice_num_hits; k += 2) {

(

j = 0; j < (

)phi_hits.size() - 1; j++) {

(

k = j + 1; k < (

)phi_hits.size(); k++) {

(phi_hits[j].query_idx != phi_hits[k].query_idx) {

phi_hits[k].query_idx,

);

printf(

);

printf(

,

CLocalRange< TOffset > TRange

define for the fundamental building block of sequence ranges

Declares the BLAST exception class.

BlastScoreBlk * BlastScoreBlkFree(BlastScoreBlk *sbp)

Deallocates BlastScoreBlk as well as all associated structures.

BlastScoreBlk * BlastScoreBlkNew(Uint1 alphabet, Int4 number_of_contexts)

Allocates and initializes BlastScoreBlk.

Interface for the traceback from blast hits.

int Size() const

Retrieve number of hits in list.

void PurgeAllHits()

Delete all hits unconditionally.

CHit * GetHit(int index)

Retrieve a hit from the hitlist.

void AddToHitList(CHit *hit)

Append a hit to the hitlist.

A generalized representation of a pairwise alignment.

int m_Score

Score of alignment.

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.

TRange m_SeqRange2

The range of offsets on the second sequence.

const vector< CPattern > & GetCddPatterns(void) const

Get regular expression patterns for identification of conserved domains.

bool GetVerbose(void) const

Get verbose mode.

SProgress m_ProgressMonitor

@ eInterrupt

Alignment interruped through callback function.

CConstRef< CMultiAlignerOptions > m_Options

void x_FindPatternHits(const vector< const CSequence * > &queries, const vector< int > &indices)

Find PROSITE pattern hits on selected input sequences.

Interface for CMultiAligner.

#define BLASTAA_SEQ_CODE

== Seq_code_ncbistdaa

SBlastSequence GetSequence(const objects::CSeq_loc &sl, EBlastEncoding encoding, objects::CScope *scope, objects::ENa_strand strand=objects::eNa_strand_plus, ESentinelType sentinel=eSentinels, std::string *warnings=NULL)

Retrieves a sequence using the object manager.

#define NCBI_THROW(exception_class, err_code, message)

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

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

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

uint8_t Uint1

1-byte (8-bit) unsigned integer

int32_t Int4

4-byte (32-bit) signed integer

#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.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

unsigned int

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

#define FALSE

bool replacment for C indicating false.

Functions for finding pattern matches in sequence (PHI-BLAST).

Int4 FindPatternHits(Int4 *hitArray, const Uint1 *seq, Int4 len, Boolean is_dna, const SPHIPatternSearchBlk *patternSearch)

Find the places where the pattern matches seq; 3 different methods are used depending on the length o...

#define PHI_MAX_HIT

Maximal size of an array of pattern hits.

struct SPatternHit SPatternHit

Intermediate representation of a pattern hit.

Pseudo lookup table structure and database scanning functions used in PHI-BLAST.

SPHIPatternSearchBlk * SPHIPatternSearchBlkFree(SPHIPatternSearchBlk *pattern_blk)

Deallocate memory for the PHI BLAST lookup table.

Int2 SPHIPatternSearchBlkNew(char *pattern, Boolean is_dna, BlastScoreBlk *sbp, SPHIPatternSearchBlk **pattern_blk, Blast_Message **error_msg)

Initialize the pattern items structure, serving as a "pseudo" lookup table in a PHI BLAST search.

Structure used for scoring calculations.

Structure containing all auxiliary information needed in a pattern search.

Intermediate representation of a pattern hit.

SPatternHit(int seq, TRange range)

constructor

TRange hit

range on query sequence where hit occurs

int query_idx

query sequence containing the hit

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