x_InitSubject(
subject, options.GetPointer());
User-defined methods of the data storage class.
@ eSequenceComparison
Seq-aligns in the BLAST 2 Sequence style (one alignment per query-subject pair)
Defines BLAST error codes (user errors included)
Handle to the options to the BLAST algorithm.
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.
Runs a single iteration of the PSI-BLAST algorithm between 2 sequences.
Implementation class for PSI-BLAST (database search and 2 sequences).
Source of query sequence data for BLAST Provides an interface for search classes to retrieve sequence...
CRef< CLocalDbAdapter > m_Subject
Reference to a BLAST subject/database object.
class CPsiBlastImpl * m_Impl
Implementation class.
void SetResultType(EResultType type)
Set the desired result type.
CPsiBl2Seq(CRef< objects::CPssmWithParameters > pssm, CRef< IQueryFactory > subject, CConstRef< CPSIBlastOptionsHandle > options)
Constructor to compare a PSSM against protein sequences.
~CPsiBl2Seq()
Destructor.
CRef< CSearchResultSet > Run()
Run the PSI-BLAST 2 Sequences engine.
void x_InitSubject(CRef< IQueryFactory > subject, const CBlastOptionsHandle *options)
Auxiliary method to initialize the subject.
CRef< CSearchResultSet > Run()
Run the PSI-BLAST engine for one iteration.
#define NCBI_THROW(exception_class, err_code, message)
Generic macro to throw an exception, given the exception class, error code and message string.
TObjectType * GetPointer(void) const THROWS_NONE
Get pointer,.
void Reset(void)
Reset reference object.
#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.
Declares CPsiBl2Seq, the C++ API for the PSI-BLAST 2 Sequences engine.
Defines implementation class for PSI-BLAST and PSI-BLAST 2 Sequences.
Declares the CPSIBlastOptionsHandle class.
NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...
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