(psi_opts.
Empty()) {
163 "Options for CLocalPssmSearch are not PSI-BLAST");
170 CPsiBlastpsiblast(query_factory, dbadapter, psi_opts);
User-defined methods of the data storage class.
User-defined methods of the data storage class.
EProgram
This enumeration is to evolve into a task/program specific list that specifies sets of default parame...
Defines BLAST error codes (user errors included)
Class to perform a BLAST search on local BLAST databases Note that PHI-BLAST can be run using this cl...
Interface to create a BlastSeqSrc suitable for use in CORE BLAST from a a variety of BLAST database/s...
NCBI C++ Object Manager free implementation of IQueryFactory.
Handle to the protein-protein options to the BLAST algorithm.
Runs a single iteration of the PSI-BLAST algorithm on a BLAST database.
CRef< CSearchResultSet > Run()
Run the PSI-BLAST engine for one iteration.
virtual CRef< CSearchResultSet > Run()
Run the search.
virtual void SetQueryFactory(CRef< IQueryFactory > query_factory)
Set the factory which will return the queries to search for.
CRef< CLocalBlast > m_LocalBlast
Local database search class.
CRef< CBlastOptionsHandle > m_SearchOpts
Search options.
CConstRef< CSearchDatabase > m_Subject
Subject database.
virtual CRef< ISeqSearch > GetSeqSearch()
Get an object to manage a local sequence search.
CRef< CBlastOptionsHandle > m_SearchOpts
Search configuration.
virtual void SetOptions(CRef< CBlastOptionsHandle > options)
Configure this search.
CRef< objects::CPssmWithParameters > m_Pssm
Search queries.
CRef< CSearchResultSet > Run()
Executes the search.
static CBlastOptionsHandle * Create(EProgram program, EAPILocality locality=CBlastOptions::eLocal)
Creates an options handle object configured with default options for the requested program,...
virtual CRef< CBlastOptionsHandle > GetOptions(EProgram)
Get an options handle for a search of the specified type.
CRef< IQueryFactory > m_QueryFactory
Factory which provides the query data to be populated in m_Queries.
virtual CRef< CSearchResultSet > Run()
Run a single iteration of the search.
virtual CRef< IPssmSearch > GetPssmSearch()
Get an object to manage a remote PSSM search.
CConstRef< CSearchDatabase > m_Database
BLAST database for the search class to use.
static void Pssm(const objects::CPssmWithParameters &pssm, bool require_scores=false)
Perform validation on the PSSM.
virtual void SetQuery(CRef< objects::CPssmWithParameters > pssm)
Set the PSSM with which to search the database.
virtual void SetSubject(CConstRef< CSearchDatabase > subject)
Set the databases to search.
virtual void SetSubject(CConstRef< CSearchDatabase > subject)
Set the databases to search.
virtual void SetOptions(CRef< CBlastOptionsHandle > options)
Configure the search.
#define NCBI_THROW(exception_class, err_code, message)
Generic macro to throw an exception, given the exception class, error code and message string.
bool Empty(void) const THROWS_NONE
Check if CConstRef is empty â not pointing to any object which means having a null value.
void Reset(void)
Reset reference object.
void Reset(void)
Reset reference object.
bool Empty(void) const THROWS_NONE
Check if CRef is empty â not pointing to any object, which means having a null value.
#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.
Implementation of the uniform BLAST search interface for searching locally installed BLAST databases.
NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...
Declares CPsiBlast, the C++ API for the PSI-BLAST engine.
Declarations of auxiliary functions/classes for PSI-BLAST.
Implementation of the BlastSeqSrc interface using the C++ BLAST databases API.
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