NCBI C++ ToolKit
Classes | Macros | Typedefs | Functions
blast_aux.hpp File Reference

Contains C++ wrapper classes to structures in algo/blast/core as well as some auxiliary functions to convert CSeq_loc to/from BlastMask structures. More...

#include <corelib/ncbistd.hpp>
#include <corelib/ddumpable.hpp>
#include <corelib/ncbifile.hpp>
#include <corelib/metareg.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <util/range.hpp>
#include <objects/seq/seqlocinfo.hpp>
#include <objects/blast/Blast4_error.hpp>
#include <objmgr/scope.hpp>
#include <algo/blast/api/blast_types.hpp>
#include <algo/blast/api/blast_exception.hpp>
#include <algo/blast/core/blast_query_info.h>
#include <algo/blast/core/blast_util.h>
#include <algo/blast/core/blast_options.h>
#include <algo/blast/core/blast_filter.h>
#include <algo/blast/core/blast_extend.h>
#include <algo/blast/core/blast_gapalign.h>
#include <algo/blast/core/blast_hits.h>
#include <algo/blast/core/blast_psi.h>
#include <algo/blast/core/blast_hspstream.h>
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Classes

struct  Deleter< BlastHSPStream >
 
class  CFrameFinder
 Function object to assist in finding all CSeqLocInfo objects which corresponds to a given frame. More...
 
struct  CConstRefCSeqId_LessThan
 
class  CAutomaticGenCodeSingleton
 Initializes and uninitializes the genetic code singleton as if it was an automatic variable (to facilitate use in our unit tests and in the CBlastOptions object). More...
 
class  CBlastAppDiagHandler
 Class to capture message from diag handler. More...
 
class  CBLAST_SequenceBlk
 Wrapper class for BLAST_SequenceBlk . More...
 
class  CBlastQueryInfo
 Wrapper class for BlastQueryInfo . More...
 
class  CQuerySetUpOptions
 Wrapper class for QuerySetUpOptions . More...
 
class  CLookupTableOptions
 Wrapper class for LookupTableOptions . More...
 
class  CLookupTableWrap
 Wrapper class for LookupTableWrap . More...
 
class  CBlastInitialWordOptions
 Wrapper class for BlastInitialWordOptions . More...
 
class  CBlastInitialWordParameters
 Wrapper class for BlastInitialWordParameters . More...
 
class  CBlast_ExtendWord
 Wrapper class for Blast_ExtendWord . More...
 
class  CBlastExtensionOptions
 Wrapper class for BlastExtensionOptions . More...
 
class  CBlastExtensionParameters
 Wrapper class for BlastExtensionParameters . More...
 
class  CBlastHitSavingOptions
 Wrapper class for BlastHitSavingOptions . More...
 
class  CBlastHitSavingParameters
 Wrapper class for BlastHitSavingParameters . More...
 
class  CPSIBlastOptions
 Wrapper class for PSIBlastOptions . More...
 
class  CBlastDatabaseOptions
 Wrapper class for BlastDatabaseOptions . More...
 
class  CBlastScoreBlk
 Wrapper class for BlastScoreBlk . More...
 
class  CBlastScoringOptions
 Wrapper class for BlastScoringOptions . More...
 
class  CBlastScoringParameters
 Wrapper class for BlastScoringParameters . More...
 
class  CBlastEffectiveLengthsOptions
 Wrapper class for BlastEffectiveLengthsOptions . More...
 
class  CBlastEffectiveLengthsParameters
 Wrapper class for BlastEffectiveLengthsParameters . More...
 
class  CBlastGapAlignStruct
 Wrapper class for BlastGapAlignStruct . More...
 
class  CBlastHSPResults
 Wrapper class for BlastHSPResults . More...
 
class  CPSIMsa
 Wrapper class for PSIMsa . More...
 
class  CPSIMatrix
 Wrapper class for PSIMatrix . More...
 
class  CPSIDiagnosticsRequest
 Wrapper class for PSIDiagnosticsRequest . More...
 
class  CPSIDiagnosticsResponse
 Wrapper class for PSIDiagnosticsResponse . More...
 
class  CBlastSeqSrc
 Wrapper class for BlastSeqSrc . More...
 
class  CBlastSeqSrcIterator
 Wrapper class for BlastSeqSrcIterator . More...
 
class  CBlast_Message
 Wrapper class for Blast_Message . More...
 
class  CBlastMaskLoc
 Wrapper class for BlastMaskLoc . More...
 
class  CBlastSeqLoc
 Wrapper class for BlastSeqLoc . More...
 
class  CSBlastProgress
 Wrapper class for SBlastProgress . More...
 

Macros

#define TYPEDEF_AUTOPTR_CDELETER(type)   typedef AutoPtr<type, CDeleter<type> > TAuto ## type ## Ptr
 Uses C Deleter (free) - used in functions that deal with CORE BLAST. More...
 
#define TYPEDEF_AUTOPTR_ARRAYDELETER(type)   typedef AutoPtr<type, ArrayDeleter<type> > TAuto ## type ## ArrayPtr
 Uses delete [] operator - for C++ arrays. More...
 
#define DECLARE_AUTO_CLASS_WRAPPER(struct_name, free_func)
 Declares class to handle deallocating of the structure using the appropriate function. More...
 

Typedefs

typedef AutoPtr< Uint1, CDeleter< Uint1 > > TAutoUint1Ptr
 Declares TAutoUint1Ptr (for Uint1 arrays allocated with malloc/calloc) More...
 
typedef AutoPtr< Char, CDeleter< Char > > TAutoCharPtr
 Declares TAutoCharPtr (for Char arrays allocated with malloc/calloc) More...
 
typedef AutoPtr< Uint1, ArrayDeleter< Uint1 > > TAutoUint1ArrayPtr
 Declares TAutoUint1ArrayPtr (for Uint1 arrays allocated with new[]) More...
 

Functions

string Blast_ProgramNameFromType (EBlastProgramType program)
 Returns a string program name, given a blast::EBlastProgramType enumeration. More...
 
BlastSeqLocCSeqLoc2BlastSeqLoc (const objects::CSeq_loc *slp)
 Converts a CSeq_loc into a BlastSeqLoc structure used in NewBlast. More...
 
TAutoUint1ArrayPtr FindGeneticCode (int genetic_code)
 Retrieves the requested genetic code in Ncbistdaa format. More...
 
bool IsLocalId (const objects::CSeq_id *seqid)
 Returns true if the CSeq_id is a local id. More...
 
TMaskedQueryRegions PackedSeqLocToMaskedQueryRegions (CConstRef< objects::CSeq_loc > sloc, EBlastProgramType program, bool assume_both_strands=false)
 Auxiliary function to convert a Seq-loc describing masked query regions to a TMaskedQueryRegions object. More...
 
CRef< objects::CSeq_loc > MaskedQueryRegionsToPackedSeqLoc (const TMaskedQueryRegions &sloc)
 Interface to build a CSeq-loc from a TMaskedQueryRegion; note that conversion conversion in this direction can be lossy. More...
 
void LoadSequencesToScope (objects::CScope::TIds &ids, vector< TSeqRange > &ranges, CRef< objects::CScope > &scope)
 This method retrieve sequence data in bulk to scope @ids seq id list [in] @ranges seq range list [in] @scope sconfigured with data loader for retrieving seqs [in] | retrieved bioseqs [out]. More...
 
void Blast_GetSeqLocInfoVector (EBlastProgramType program, const objects::CPacked_seqint &queries, const BlastMaskLoc *mask, TSeqLocInfoVector &mask_v)
 Converts a BlastMaskLoc internal structure into an object returned by the C++ API. More...
 

Detailed Description

Contains C++ wrapper classes to structures in algo/blast/core as well as some auxiliary functions to convert CSeq_loc to/from BlastMask structures.

Definition in file blast_aux.hpp.

Modified on Fri Mar 01 10:04:51 2024 by modify_doxy.py rev. 669887