NCBI C++ ToolKit
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Search Toolkit Book for CPsiBlastImpl

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

#include "psiblast_impl.hpp"
(Private to src/algo/blast/api.)

+ Inheritance diagram for CPsiBlastImpl:
+ Collaboration diagram for CPsiBlastImpl:

Public Member Functions

 CPsiBlastImpl (CRef< objects::CPssmWithParameters > pssm, CRef< CLocalDbAdapter > subject, CConstRef< CPSIBlastOptionsHandle > options)
 Constructor for restarting PSI-BLAST iterations with a previously generated PSSM. More...
 
 CPsiBlastImpl (CRef< IQueryFactory > query, CRef< CLocalDbAdapter > subject, CConstRef< CBlastProteinOptionsHandle > options)
 Constructor to handle the first iteration of PSI-BLAST when the query is a protein sequence or when the performing an object manager free BLAST 2 Sequences search. More...
 
CRef< CSearchResultSetRun ()
 Run the PSI-BLAST engine for one iteration. More...
 
void SetPssm (CConstRef< objects::CPssmWithParameters > pssm)
 This method allows the same object to be reused when performing multiple iterations. More...
 
CConstRef< objects::CPssmWithParameters > GetPssm () const
 Accessor for the most recently used PSSM. More...
 
void SetResultType (EResultType type)
 Set the desired result type. More...
 
- Public Member Functions inherited from CThreadable
 CThreadable (void)
 Default ctor. More...
 
virtual ~CThreadable (void)
 Our virtual destructor. More...
 
virtual void SetNumberOfThreads (size_t nthreads)
 Mutator for the number of threads. More...
 
size_t GetNumberOfThreads (void) const
 Accessor for the number of threads to use. More...
 
bool IsMultiThreaded (void) const
 Returns true if more than 1 thread is specified. More...
 

Private Member Functions

 CPsiBlastImpl (const CPsiBlastImpl &rhs)
 Prohibit copy constructor. More...
 
CPsiBlastImploperator= (const CPsiBlastImpl &rhs)
 Prohibit assignment operator. More...
 
void x_Validate ()
 Perform sanity checks on input parameters. More...
 
void x_CreatePssmScoresFromFrequencyRatios ()
 Computes the PSSM scores in case these are not available in the PSSM. More...
 
void x_ExtractQueryFromPssm ()
 Auxiliary function to get the query sequence data from the ASN.1 PSSM Post-condition: (m_Query.Empty() == false) More...
 

Private Attributes

CRef< objects::CPssmWithParameters > m_Pssm
 PSSM to be used as query. More...
 
CRef< IQueryFactorym_Query
 Query sequence (either extracted from PSSM or provided in constructor) More...
 
CRef< CLocalDbAdapterm_Subject
 PSI-BLAST subject abstraction. More...
 
CConstRef< CBlastOptionsHandlem_OptsHandle
 Options to use. More...
 
CRef< CSearchResultSetm_Results
 Holds a reference to the results. More...
 
EResultType m_ResultType
 Specifies how the results should be produced. More...
 

Additional Inherited Members

- Public Types inherited from CThreadable
enum  { kMinNumThreads = 1 }
 Never have less than 1 thread. More...
 
- Protected Attributes inherited from CThreadable
size_t m_NumThreads
 Keep track of how many threads should be used. More...
 

Detailed Description

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

Definition at line 62 of file psiblast_impl.hpp.


The documentation for this class was generated from the following files:
Modified on Sat May 25 14:18:12 2024 by modify_doxy.py rev. 669887