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NCBI C++ ToolKit: src/algo/blast/proteinkmer/demo/kblastthr.cpp Source File

(TSeqLocVector::iterator iter=tsl_v.begin(); iter!=tsl_v.end(); ++iter)

(neggilist && neggilist->

())

vector<SFormatResultValues> results_v;

(

*)

;

Produce formatted blast output for command line applications.

Declares the CBlastAdvancedProteinOptionsHandle class.

Interface for reading SRA sequences into blast input.

Interface for converting sources of sequence data into blast sequence input.

#define BLAST_DEFAULT_MATRIX

Default matrix name: BLOSUM62.

#define BLAST_GENETIC_CODE

Default genetic code for query and/or database.

Declares the CBlastProteinOptionsHandle class.

Declares CBlastScopeSource class to create properly configured CScope objects to invoke the BLAST dat...

void QueueResults(int batchNumber, vector< SFormatResultValues > results)

Queue results for printing.

CRef< CSearchDatabase > GetSearchDatabase() const

Retrieve the search database information.

This class formats the BLAST results for command line applications.

TSeqLocVector GetNextSeqLocBatch(CScope &scope)

Read and convert the next batch of sequences.

bool End()

Determine if we have reached the end of the BLAST input.

Threading class for BlastKmer searches.

void SetGiListLimit(CRef< CSeqDBGiList > list)

Limits output by GILIST.

void SetQuery(CRef< IQueryFactory > queryFactory)

Sets the queries. Overrides any queries already set.

CRef< CSearchResultSet > Run(void)

Run a KMER and then BLAST search.

virtual void * Main(void)

Derived (user-created) class must provide a real thread function.

CRef< CBlastDatabaseArgs > m_DbArgs

virtual ~CBlastKmerThread(void)

CBlastAsyncFormatThread * m_FormattingThr

CRef< CFormattingArgs > m_FormattingArgs

CRef< CBlastpKmerOptionsHandle > m_BlastOptsHandle

void AddQuery(CRef< CBlastSearchQuery > q)

Add a query to the set.

Class whose purpose is to create CScope objects which have data loaders added with different prioriti...

Handle to the KMER BLASTP options.

string GetCustomOutputFormatSpec() const

Retrieve for string that specifies the custom output format for tabular and comma-separated value.

EOutputFormat GetFormattedOutputChoice() const

Get the choice of formatted output.

TSeqPos GetNumAlignments() const

Number of alignments to show in traditional BLAST output.

TSeqPos GetNumDescriptions() const

Number of one-line descriptions to show in traditional BLAST output.

Interface to create a BlastSeqSrc suitable for use in CORE BLAST from a a variety of BLAST database/s...

NCBI C++ Object Manager dependant implementation of IQueryFactory.

void GetGiList(vector< TGi > &gis) const

Get the gi list.

bool NotEmpty() const

Return true if there are elements present.

SeqDB ID list for performing boolean set operations.

CRef< CSeqDBNegativeList > GetNegativeList()

Retrieve a negative GI list.

Operators to edit gaps in sequences.

const CRef< CSeqDBGiList > & GetNegativeGiList() const

Accessor for the negative gi list.

int GetCandidateSeqs() const

Gets the max number of candidate matches to process with BLAST.

int GetMinHits() const

Returns the number of hits to initiate calculation of Jaccard distance.

const CBlastOptions & GetOptions() const

Return the object which this object is a handle for.

CRef< CBlastOptions > Clone() const

Explicit deep copy of the Blast options object.

const CRef< CSeqDBGiList > & GetGiList() const

Accessor for the gi list.

void SetMinHits(int minhits=1)

Sets the number of hits ot initiate calculation of Jaccard distance.

void SetCandidateSeqs(int candidates=1000)

Sets the max number of candidate matches to process with BLAST @candidates max number of target seque...

void SetThresh(double thresh=0.1)

Sets Threshold for Jaccard distance.

double GetThresh() const

Returns threshold for Jaccard distance (range: 0-1)

void Reset(void)

Reset reference object.

void Lock(void)

Acquire mutex for the current thread with no nesting checks.

void Unlock(void)

Release mutex with no owner or nesting checks.

CRef< CBlastQueryVector > s_GetBlastQueryVector(TSeqLocVector &tsl_v)

Main class to perform a BLAST search on the local machine.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

Defines BLAST database access classes.

Defines exception class and several constants for SeqDB.

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

Implementation of the BlastSeqSrc interface for a vector of sequence locations.

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

Configuration structure for the CBlastScopeSource.

@ eUseNoDataLoaders

Do not add any data loaders.

Contains query, results and CBlastFormat for one batch.

Uniform BLAST Search Interface.

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