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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/psiblast_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/blast/api/psiblast.cpp Source File

: m_Subject(blastdb), m_Impl(0)

: m_Subject(blastdb), m_Impl(0)

(

.IsSetDescr()) {

((*iter)->IsTitle()) {

query_descr += (*iter)->GetTitle();

alignment, database_scope,

User-defined methods of the data storage class.

Int2 PSIBlastOptionsNew(PSIBlastOptions **psi_options)

Initialize default options for PSI BLAST.

Implements the IBlastQuerySource interface using a CBioseq_set as data source.

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

Handle to the protein-protein options to the BLAST algorithm.

Wrapper class for PSIBlastOptions .

Implementation class for PSI-BLAST (database search and 2 sequences).

This class is a concrete strategy for IPssmInputData, and it implements the traditional PSI-BLAST alg...

Runs a single iteration of the PSI-BLAST algorithm on a BLAST database.

Computes a PSSM as specified in PSI-BLAST.

Source of query sequence data for BLAST Provides an interface for search classes to retrieve sequence...

TSeqPos length

Length of the buffer above (not necessarily sequence length!)

CRef< CSearchResultSet > Run()

Run the PSI-BLAST engine for one iteration.

class CPsiBlastImpl * m_Impl

Implementation class.

CConstRef< objects::CPssmWithParameters > GetPssm() const

Accessor for the most recently used PSSM.

size_t GetNumberOfThreads(void) const

Accessor for the number of threads to use.

CRef< objects::CPssmWithParameters > Run()

Runs the PSSM engine to compute the PSSM.

virtual void SetNumberOfThreads(size_t nthreads)

Mutator for the number of threads.

double GetInclusionThreshold() const

Returns InclusionThreshold.

PSIBlastOptions * Get() const

virtual SBlastSequence GetBlastSequence(int index, EBlastEncoding encoding, objects::ENa_strand strand, ESentinelType sentinel, string *warnings=0) const

Return the sequence data for a sequence.

TAutoUint1Ptr data

Sequence data.

const char * GetMatrixName() const

Returns MatrixName.

int GetGapExtensionCost() const

Returns GapExtensionCost.

void SetPssm(CConstRef< objects::CPssmWithParameters > pssm)

This method allows the same object to be reused when performing multiple iterations.

CConstRef< objects::CPssmWithParameters > GetPssm() const

Accessor for the most recently used PSSM.

CRef< objects::CPssmWithParameters > PsiBlastComputePssmFromAlignment(const objects::CBioseq &query, CConstRef< objects::CSeq_align_set > alignment, CRef< objects::CScope > database_scope, const CPSIBlastOptionsHandle &opts_handle, CConstRef< CBlastAncillaryData > ancillary_data, PSIDiagnosticsRequest *diagnostics_req=0)

Computes a PSSM from the result of a PSI-BLAST iteration.

void PsiBlastAddAncillaryPssmData(objects::CPssmWithParameters &pssm, int gap_open, int gap_extend)

Even though the query sequence and the matrix gap costs are not a product of the PSSM engine,...

CPsiBlast(CRef< IQueryFactory > query_factory, CRef< CLocalDbAdapter > blastdb, CConstRef< CPSIBlastOptionsHandle > options)

Constructor to compare a single sequence against a database of protein sequences.

void SetPssm(CConstRef< objects::CPssmWithParameters > pssm)

This method allows the same object to be reused when performing multiple iterations.

void SetUngappedStatisticalParams(CConstRef< CBlastAncillaryData > ancillary_data)

Sets the Karlin & Altschul parameters in the BlastScoreBlk to be used in PSSM generation.

int GetGapOpeningCost() const

Returns GapOpeningCost.

CRef< CSearchResultSet > Run()

Run the PSI-BLAST engine for one iteration.

CRef< CLocalDbAdapter > m_Subject

Reference to a BLAST subject/database object.

int GetPseudoCount() const

Returns PseudoCount.

@ eBlastEncodingProtein

NCBIstdaa.

@ eSentinels

Use sentinel bytes.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

element_type * get(void) const

Get pointer.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define USING_SCOPE(ns)

Use the specified namespace.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

list< CRef< CSeqdesc > > Tdata

Defines a concrete strategy to obtain PSSM input data for PSI-BLAST.

Declares CPsiBlast, the C++ API for the PSI-BLAST engine.

Declarations of auxiliary functions/classes for PSI-BLAST.

Defines implementation class for PSI-BLAST and PSI-BLAST 2 Sequences.

Declares the CPSIBlastOptionsHandle class.

C++ API for the PSI-BLAST PSSM engine.

double inclusion_ethresh

Minimum evalue for inclusion in PSSM calculation.

Int4 pseudo_count

Pseudocount constant.

Structure to allow requesting various diagnostics data to be collected by PSSM engine.

Structure to store sequence data and its length for use in the CORE of BLAST (it's a malloc'ed array ...

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