include/algo/blast/api/blast_aux.hpp File Reference

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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.

#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 <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...
class	CAutomaticGenCodeSingleton
	Initializes and uninitializes the genetic code singleton as if it was an automatic variable. More...
class	CBLAST_SequenceBlk
	Wrapper class for struct_name. More...
class	CBlastQueryInfo
	Wrapper class for struct_name. More...
class	CQuerySetUpOptions
	Wrapper class for struct_name. More...
class	CLookupTableOptions
	Wrapper class for struct_name. More...
class	CLookupTableWrap
	Wrapper class for struct_name. More...
class	CBlastInitialWordOptions
	Wrapper class for struct_name. More...
class	CBlastInitialWordParameters
	Wrapper class for struct_name. More...
class	CBlast_ExtendWord
	Wrapper class for struct_name. More...
class	CBlastExtensionOptions
	Wrapper class for struct_name. More...
class	CBlastExtensionParameters
	Wrapper class for struct_name. More...
class	CBlastHitSavingOptions
	Wrapper class for struct_name. More...
class	CBlastHitSavingParameters
	Wrapper class for struct_name. More...
class	CPSIBlastOptions
	Wrapper class for struct_name. More...
class	CBlastDatabaseOptions
	Wrapper class for struct_name. More...
class	CBlastScoreBlk
	Wrapper class for struct_name. More...
class	CBlastScoringOptions
	Wrapper class for struct_name. More...
class	CBlastScoringParameters
	Wrapper class for struct_name. More...
class	CBlastEffectiveLengthsOptions
	Wrapper class for struct_name. More...
class	CBlastEffectiveLengthsParameters
	Wrapper class for struct_name. More...
class	CBlastGapAlignStruct
	Wrapper class for struct_name. More...
class	CBlastHSPResults
	Wrapper class for struct_name. More...
class	CPSIMsa
	Wrapper class for struct_name. More...
class	CPSIMatrix
	Wrapper class for struct_name. More...
class	CPSIDiagnosticsRequest
	Wrapper class for struct_name. More...
class	CPSIDiagnosticsResponse
	Wrapper class for struct_name. More...
class	CBlastSeqSrc
	Wrapper class for struct_name. More...
class	CBlastSeqSrcIterator
	Wrapper class for struct_name. More...
class	CBlast_Message
	Wrapper class for struct_name. More...
class	CBlastMaskLoc
	Wrapper class for struct_name. More...
class	CBlastSeqLoc
	Wrapper class for struct_name. More...
class	CSBlastProgress
	Wrapper class for struct_name. More...
Defines
#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.
#define	TYPEDEF_AUTOPTR_ARRAYDELETER(type)   typedef AutoPtr<type, ArrayDeleter<type> > TAuto ## type ## ArrayPtr
	Uses delete [] operator - for C++ arrays.
#define	DECLARE_AUTO_CLASS_WRAPPER(struct_name, free_func)
	Declares class to handle deallocating of the structure using the appropriate function.
Typedefs
typedef AutoPtr< Uint1, CDeleter< Uint1 > >	TAutoUint1Ptr
	Declares TAutoUint1Ptr (for Uint1 arrays allocated with malloc/calloc).
typedef AutoPtr< Char, CDeleter< Char > >	TAutoCharPtr
	Declares TAutoCharPtr (for Char arrays allocated with malloc/calloc).
typedef AutoPtr< Uint1, ArrayDeleter< Uint1 > >	TAutoUint1ArrayPtr
	Declares TAutoUint1ArrayPtr (for Uint1 arrays allocated with new[]).
Functions
string	Blast_ProgramNameFromType (EBlastProgramType program)
	Returns a string program name, given a blast::EBlastProgramType enumeration.
BlastSeqLoc *	CSeqLoc2BlastSeqLoc (const objects::CSeq_loc *slp)
	Converts a CSeq_loc into a BlastSeqLoc structure used in NewBlast.
TAutoUint1ArrayPtr	FindGeneticCode (int genetic_code)
	Retrieves the requested genetic code in Ncbistdaa format.
bool	IsLocalId (const objects::CSeq_id *seqid)
	Returns true if the CSeq_id is a local id.
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.
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.
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.

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