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...
BlastSeqLoc *	CSeqLoc2BlastSeqLoc (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.