BLAST (Basic Local Alignment Search Tool)
[ALGORITHMS]

Collaboration diagram for BLAST (Basic Local Alignment Search Tool):

Classes
class	CBl2Seq
	Runs the BLAST algorithm between 2 sequences. More...
class	CBlastAdvancedProteinOptionsHandle
	Handle to the Advanced BLASTP options. More...
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...
class	CBlastSystemException
	Defines system exceptions occurred while running BLAST. More...
class	CBlastException
	Defines BLAST error codes (user errors included). More...
class	CBlastNucleotideOptionsHandle
	Handle to the nucleotide-nucleotide options to the BLAST algorithm. More...
class	CBlastOptions
	Encapsulates ALL the BLAST algorithm's options. More...
class	CBlastOptionsBuilder
	Class to build CBlastOptionsHandle from blast4 ASN objects. More...
class	CBlastOptionsFactory
	Creates BlastOptionsHandle objects with default values for the programs/tasks requested. More...
class	CBlastOptionsHandle
	Handle to the options to the BLAST algorithm. More...
class	CBlastProteinOptionsHandle
	Handle to the protein-protein options to the BLAST algorithm. More...
class	CBlastAncillaryData
	Class used to return ancillary data from a blast search, i.e. More...
class	CSearchResults
	Search Results for One Query. More...
class	CSearchResultSet
	Search Results for All Queries. More...
class	CBlastRPSOptionsHandle
	Handle to the rpsblast options to the BLAST algorithm. More...
class	IBlastSeqInfoSrc
	Abstract base class to encapsulate retrieval of sequence identifiers. More...
class	CBlastxOptionsHandle
	Handle to the translated nucleotide-protein options to the BLAST algorithm. More...
class	CDiscNucleotideOptionsHandle
	Handle to the nucleotide-nucleotide options to the discontiguous BLAST algorithm. More...
class	CEffectiveSearchSpaceCalculator
	Auxiliary class to compute the effective search space. More...
class	CBlastHSPListQueueData
	Data structure for the queue implementation of BlastHSPStream. More...
class	CLocalBlast
	Class to perform a BLAST search on local BLAST databases Note that PHI-BLAST can be run using this class also, one only need to configure it as a regular blastp or blastn search and set the pattern in the CBlastOptionsHandle object. More...
class	CLocalDbAdapter
	Interface to create a BlastSeqSrc suitable for use in CORE BLAST from a a variety of BLAST database/subject representations. More...
class	CLocalSeqSearch
	Local sequence search. More...
class	CLocalPssmSearch
class	CLocalSearchFactory
	Factory for CLocalSearch. More...
class	CPsiBlastInputClustalW
	This class is a concrete strategy for IPssmInputData which converts the CLUSTALW-style output containing a multiple sequence alignment into the data structures needed by the PSSM engine. More...
class	CObjMgr_QueryFactory
	NCBI C++ Object Manager dependant implementation of IQueryFactory. More...
class	CObjMgrFree_QueryFactory
	NCBI C++ Object Manager free implementation of IQueryFactory. More...
class	CPHIBlastNuclOptionsHandle
	Handle to the nuclein PHI BLAST options. More...
class	CPHIBlastProtOptionsHandle
	Handle to the protein PHI BLAST options. More...
class	CBlastPrelimSearch
	Search class to perform the preliminary stage of the BLAST search. More...
class	CPsiBlastInputFreqRatios
	Implements the interface to retrieve data for the last 2 stages of the PSSM creation. More...
class	CPsiBlastInputData
	This class is a concrete strategy for IPssmInputData, and it implements the traditional PSI-BLAST algorithm for building a multiple sequence alignment from a list of pairwise alignments using the C++ object manager. More...
class	CPsiBl2Seq
	Runs a single iteration of the PSI-BLAST algorithm between 2 sequences. More...
class	CPsiBlast
	Runs a single iteration of the PSI-BLAST algorithm on a BLAST database. More...
struct	CSeqIdComparator
	Returns true if a < b, else false. More...
class	CPsiBlastIterationState
	Represents the iteration state in PSI-BLAST. More...
class	CPSIBlastOptionsHandle
	Handle to the protein-protein options to the BLAST algorithm. More...
class	CPssmEngineException
	Exception class for the CPssmEngine class. More...
class	CPssmEngine
	Computes a PSSM as specified in PSI-BLAST. More...
class	CScorematPssmConverter
	Auxiliary class to convert data encoded in the PSSM to CNcbiMatrix. More...
struct	IPssmInput_Base
	Base class for the IPssmInputData and IPssmInputFreqRatios interfaces, provided to avoid duplicating the methods that are common to both interfaces. More...
struct	IPssmInputData
	Abstract base class to encapsulate the source(s) and pre-processing of PSSM input data as well as options to the PSI-BLAST PSSM engine. More...
struct	IPssmInputFreqRatios
	Interface used to retrieve the PSSM frequency ratios to allow for "restart" processing in PSI-BLAST: Given a preliminary. More...
class	ILocalQueryData
	Provides access (not ownership) to the C structures used to configure local BLAST search class implementations. More...
class	IRemoteQueryData
class	IQueryFactory
	Source of query sequence data for BLAST Provides an interface for search classes to retrieve sequence data to be used in local/remote searches without coupling them to the actual means of retrieving the data. More...
class	CRemoteBlastException
	Exception class for the CRemoteBlast class. More...
class	CRemoteBlast
	API for Remote Blast Requests. More...
class	CRemoteSeqSearch
	Remote Sequence Search. More...
class	CRemotePssmSearch
	Remote Sequence Search. More...
class	CRemoteSearchFactory
	Factory for CRemoteSearch. More...
class	CBlastRPSInfo
	Wrapper class to manage the BlastRPSInfo structure, as currently there aren't any allocation or deallocation functions for this structure in the CORE of BLAST. More...
class	CRPSTBlastnOptionsHandle
	Handle to the options for translated nucleotide-RPS blast. More...
class	CImportStrategy
	Class to return parts of the CBlast4_request, or data associated with a CBlast4_request, such as options. More...
class	CSeqDbSeqInfoSrc
	Implementation of the IBlastSeqInfoSrc interface to encapsulate retrieval of sequence identifiers and lengths from a BLAST database. More...
class	CSeqVecSeqInfoSrc
	Implementation of the IBlastSeqInfoSrc interface to encapsulate retrieval of sequence identifiers and lengths from a vector of Seq-locs. More...
class	CStructWrapper< TData >
class	CThreadable
	Class that supports setting the number of threads to use with a given algorithm. More...
class	CSetupFactory
	Auxiliary class to create the various C structures to set up the preliminary and/or traceback stages of the search. More...
struct	SInternalData
	Lightweight wrapper to enclose C structures needed for running the preliminary and traceback stages of the BLAST search. More...
struct	SDatabaseScanData
	Structure to hold results of the preliminary (databases scanning phase) part of the search that are needed for the traceback. More...
class	CTBlastnOptionsHandle
	Handle to the protein-translated nucleotide options to the BLAST algorithm. More...
class	CTBlastxOptionsHandle
	Handle to the translated nucleotide-translated nucleotide options to the BLAST algorithm. More...
class	CBlastTracebackSearch
class	CSearchException
	Exception class. More...
class	CSearchDatabase
	Blast Search Subject. More...
class	ISearch
	Single Iteration Blast Database Search. More...
class	ISeqSearch
	Single Iteration Search of Sequence(s) Against Blast Database(s). More...
class	IPssmSearch
	Experimental interface (since this does not provide a full interface to PSI-BLAST). More...
class	ISearchFactory
	Factory for ISearch. More...
class	CBlastVersion
	Keeps track of the version of the BLAST engine in the NCBI C++ toolkit. More...
class	CReference
	Class to keep track of the various BLAST references. More...
class	CBlastServicesException
	RemoteServicesException. More...
class	CBlastServices
	API for Remote Blast Services. More...
class	CBlastSeqVectorFromCSeq_data
	Implementation of the IBlastSeqVector interface which obtains data from a CSeq_data object. More...
class	CBlastQuerySourceBioseqSet
	Implements the IBlastQuerySource interface using a CBioseq_set as data source. More...
struct	TQueryMessagesLessComparator
struct	TQueryMessagesEqualComparator
struct	SBlastSetupData
	Return type of BlastSetupPreliminarySearch. More...
struct	SIndexedDbNewArgs
	This structure is used to transfer arguments to s_IDbSrcNew(). More...
class	CIndexedDb
	This class is responsible for loading indices and doing the actual seed search. More...
class	CPreSearchThread
	One thread of the indexed seed search. More...
class	CBlastOptionsMemento
	Class that allows the transfer of data structures from the CBlastOptionsLocal class to either the BLAST preliminary or traceback search classes. More...
class	CEffectiveSearchSpacesMemento
	Memento class to save, replace out, and restore the effective search space options of the CBlastOptions object passed to its constructor. More...
class	CBlastQuerySourceOM
	Implements the object manager dependant version of the IBlastQuerySource. More...
class	CBlastSeqVectorOM
	Implementation of the IBlastSeqVector interface which obtains data from a CSeq_loc and a CScope relying on the CSeqVector class. More...
class	CBlastOptionsRemote
	Encapsulates all blast input parameters. More...
class	CBlastOptionsLocal
	Encapsulates all blast input parameters. More...
struct	SBlastSequence
	Structure to store sequence data and its length for use in the CORE of BLAST (it's a malloc'ed array of Uint1 and its length) FIXME: do not confuse with blast_seg.c's SSequence. More...
class	IBlastQuerySource
	Lightweight wrapper around an indexed sequence container. More...
class	IBlastSeqVector
	Lightweight wrapper around sequence data which provides a CSeqVector-like interface to the data. More...
class	CBlastQueryFilteredFrames
	Collection of BlastSeqLoc lists for filtering processing. More...
class	CFilteringMemento
	Memento class to save, null out, and restore the filtering options of the CBlastOptionsMemento object passed to its constructor This prevents side effects (like filtering the query sequence) to occur during calculation of the effective search space. More...
class	CObjMgr_LocalQueryData
	Provides access (not ownership) to the C structures used to configure local BLAST search class implementations. More...
class	CObjMgr_RemoteQueryData
class	CObjMgrFree_LocalQueryData
class	CObjMgrFree_RemoteQueryData
class	CPrelimSearchRunner
	Functor to run the preliminary stage of the BLAST search. More...
class	CPrelimSearchThread
	Thread class to run the preliminary stage of the BLAST search. More...
class	CPsiBlastAlignmentProcessor
	Auxiliary class to retrieve sequence identifiers its position in the alignment which are below the inclusion evalue threshold. More...
class	CPsiBlastValidate
	Auxialiry class containing static methods to validate PSI-BLAST search components. More...
class	CPsiBlastImpl
	Implementation class for PSI-BLAST (database search and 2 sequences). More...
struct	SNcbiMatrix2DoubleMatrix
	Auxiliary class to convert from a CNcbiMatrix into a double** as required by the C API. More...
class	CBlastRPSAuxInfo
	Wrapper class to manage the BlastRPSAuxInfo structure, as currently there aren't any allocation or deallocation functions for this structure in the CORE of BLAST. More...
class	CRpsAuxFile
	This class represents the .aux file in a RPS-BLAST file, which contains information about the scoring matrix to be used during the RPS-BLAST search, the scaling factor, an array of K statistical values (karlin_k), as well as various fields that are currently unused. More...
class	CRpsMmappedFile
	Encapsulates logic of mmap'ing and performing sanity checks on RPS-BLAST database files. More...
class	CRpsLookupTblFile
	This class represents the .loo file in a RPS-BLAST file, which contains the pre-computed lookup table. More...
class	CRpsPssmFile
	This class represents the .rps file in a RPS-BLAST file, which contains the PSSMs for the database. More...
class	CBioseqSeqInfoSrc
	Implementation of the IBlastSeqInfoSrc interface to encapsulate retrieval of sequence identifiers and lengths from a CBioseq/CBioseq_set object. More...
class	CMultiSeqInfo
	Contains information about all sequences in a set. More...
struct	SMultiSeqSrcNewArgs
	Encapsulates the arguments needed to initialize multi-sequence source. More...
class	CQueryFactoryInfo
	Contains information about all sequences in a set. More...
struct	SQueryFactorySrcNewArgs
	Encapsulates the arguments needed to initialize multi-sequence source. More...
struct	SSeqDB_SeqSrc_Data
	Simple container to support SeqSrc-local data. More...
class	CSeqDbSrcNewArgs
	Encapsulates the arguments needed to initialize CSeqDB. More...
class	CQuerySplitter
	Class responsible for splitting query sequences and providing data to the BLAST search class to search a split query chunk. More...
class	CContextTranslator
	Auxiliary class to provide convenient and efficient access to conversions between contexts local to query split chunks and the absolute (full, unsplit) query. More...
class	CQueryDataPerChunk
	Auxiliary class to determine information about the query that was split into chunks. More...
class	CSplitQueryBlk
	Wrapper class around SSplitQueryBlk structure. 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.
#define	BLAST2NA_SIZE   4
	Size of compressed nucleic acid alphabet.
#define	BLASTNA_SIZE   16
	Size of nucleic acid alphabet.
#define	BLASTAA_SIZE   28
	Size of aminoacid alphabet.
#define	BLASTNA_SEQ_CODE   99
	Identifies the blastna alphabet, for use in blast only.
#define	BLASTAA_SEQ_CODE   11
	== Seq_code_ncbistdaa
#define	NCBI4NA_SEQ_CODE   4
	== Seq_code_ncbi4na
#define	SMALLEST_EVALUE   1.0e-180
	Threshold below which e-values are saved as 0.
#define	GAP_VALUE   -1
	Value in the Dense-seg indicating a gap.
#define	GAP_IN_ALIGNMENT   ((Uint4)-1)
	Representation of GAP in Seq-align.
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[]).
typedef CStructWrapper< BlastScoreBlk >	TBlastScoreBlk
typedef CStructWrapper< LookupTableWrap >	TLookupTableWrap
typedef CStructWrapper< BlastDiagnostics >	TBlastDiagnostics
typedef CStructWrapper< BlastHSPStream >	TBlastHSPStream
typedef CStructWrapper< BlastSeqSrc >	TBlastSeqSrc
typedef CStructWrapper< SPHIPatternSearchBlk >	TSPHIPatternSearchBlk
typedef list< CRef< objects::CBlast4_error > >	TErrorList
	Error value type used by Blast4 ASN.1 objects.
typedef SSeqDB_SeqSrc_Data	TSeqDBData
typedef COpenRange< TSeqPos >	TChunkRange
	Range describing a query chunk.
Enumerations
enum	EBlastEncoding {   eBlastEncodingProtein = 0, eBlastEncodingNucleotide = 1, eBlastEncodingNcbi4na = 2, eBlastEncodingNcbi2na = 3,   eBlastEncodingError = 255 }
	Different types of sequence encodings for sequence retrieval from the BLAST database. More...
enum	EBlastOptIdx {   eBlastOpt_Program = 100, eBlastOpt_WordThreshold, eBlastOpt_LookupTableType, eBlastOpt_WordSize,   eBlastOpt_AlphabetSize, eBlastOpt_MBTemplateLength, eBlastOpt_MBTemplateType, eBlastOpt_FilterString,   eBlastOpt_MaskAtHash, eBlastOpt_DustFiltering, eBlastOpt_DustFilteringLevel, eBlastOpt_DustFilteringWindow,   eBlastOpt_DustFilteringLinker, eBlastOpt_SegFiltering, eBlastOpt_SegFilteringWindow, eBlastOpt_SegFilteringLocut,   eBlastOpt_SegFilteringHicut, eBlastOpt_RepeatFiltering, eBlastOpt_RepeatFilteringDB, eBlastOpt_StrandOption,   eBlastOpt_QueryGeneticCode, eBlastOpt_WindowSize, eBlastOpt_SeedContainerType, eBlastOpt_SeedExtensionMethod,   eBlastOpt_XDropoff, eBlastOpt_GapXDropoff, eBlastOpt_GapXDropoffFinal, eBlastOpt_GapTrigger,   eBlastOpt_GapExtnAlgorithm, eBlastOpt_HitlistSize, eBlastOpt_MaxNumHspPerSequence, eBlastOpt_CullingLimit,   eBlastOpt_EvalueThreshold, eBlastOpt_CutoffScore, eBlastOpt_PercentIdentity, eBlastOpt_SumStatisticsMode,   eBlastOpt_LongestIntronLength, eBlastOpt_GappedMode, eBlastOpt_MatrixName, eBlastOpt_MatrixPath,   eBlastOpt_MatchReward, eBlastOpt_MismatchPenalty, eBlastOpt_GapOpeningCost, eBlastOpt_GapExtensionCost,   eBlastOpt_FrameShiftPenalty, eBlastOpt_OutOfFrameMode, eBlastOpt_DbLength, eBlastOpt_DbSeqNum,   eBlastOpt_EffectiveSearchSpace, eBlastOpt_DbGeneticCode, eBlastOpt_PHIPattern, eBlastOpt_InclusionThreshold,   eBlastOpt_PseudoCount, eBlastOpt_GapTracebackAlgorithm, eBlastOpt_CompositionBasedStats, eBlastOpt_SmithWatermanMode,   eBlastOpt_UnifiedP, eBlastOpt_WindowMaskerDatabase, eBlastOpt_WindowMaskerTaxId, eBlastOpt_ForceMbIndex,   eBlastOpt_MbIndexName, eBlastOpt_BestHitScoreEdge, eBlastOpt_BestHitOverhang }
	Index of remote BLAST options. More...
enum	ESentinelType { eSentinels, eNoSentinels }
	Allows specification of whether sentinel bytes should be used or not. More...
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.
MT_LOCK	Blast_CMT_LOCKInit (void)
	Initialize a mutex locking mechanism for BLAST.
void	GetSequenceLengthAndId (const IBlastSeqInfoSrc *seqinfo_src, int oid, CRef< objects::CSeq_id > &seqid, TSeqPos *length)
	Retrieves subject sequence Seq-id and length.
void	GetFilteredRedundantGis (const IBlastSeqInfoSrc &sisrc, int oid, vector< int > &gis)
	Get GIs for a sequence in a redundant database.
BlastHSPStream *	Blast_HSPListCQueueInit ()
	Function to initialize a queue HSP stream.
CRef< objects::CPssmWithParameters >	PsiBlastComputePssmFromAlignment (const objects::CBioseq &query, CConstRef< objects::CSeq_align_set > alignment, CRef< objects::CScope > database_scope, const CPSIBlastOptionsHandle &opts_handle, CConstRef< CBlastAncillaryData > ancillary_data, PSIDiagnosticsRequest *diagnostics_req=0)
	Computes a PSSM from the result of a PSI-BLAST iteration.
objects::EBlast4_frame_type	FrameNumber2NetworkFrame (int frame, EBlastProgramType program)
	Converts the return value of CSeqLocInfo::GetFrame into the Blast4-frame-type field.
CSeqLocInfo::ETranslationFrame	NetworkFrame2FrameNumber (objects::EBlast4_frame_type frame, EBlastProgramType program)
	Converts Blast4-frame-type into CSeqLocInfo::ETranslationFrame.
EBlastProgramType	NetworkProgram2BlastProgramType (const string &program, const string &service)
	Function to convert from program and service name into the CORE BLAST program type This is based on the values set in the various CBlastOptionsHandle subclasses (look for SetRemoteProgramAndService_Blast3 in include tree).
CRef< objects::CBlast4_request >	ExtractBlast4Request (CNcbiIstream &in)
	Extract a Blast4-request (a.k.a.
void	Blast_FindRepeatFilterLoc (TSeqLocVector &query_loc, const CBlastOptionsHandle *opts_handle)
	Finds repeats locations for a given set of sequences.
void	Blast_FindRepeatFilterLoc (TSeqLocVector &query, const char *filter_db)
	Overloaded version of the function above which takes the name of the repeats filtering database to use, and a TSeqLocVector.
void	Blast_FindRepeatFilterLoc (CBlastQueryVector &query, const char *filter_db)
	Overloaded version of the function above which takes the name of the repeats filtering database to use, and a CBlastQueryVector.
BlastSeqSrc *	MultiSeqBlastSeqSrcInit (TSeqLocVector &seq_vector, EBlastProgramType program)
	Initialize the sequence source structure.
BlastSeqSrc *	SeqDbBlastSeqSrcInit (const string &dbname, bool is_prot, Uint4 first_seq=0, Uint4 last_seq=0, int filtering_algorithm=-1)
	Initialize the sequence source structure.
BlastSeqSrc *	SeqDbBlastSeqSrcInit (CSeqDB *seqdb, int filtering_algorithm=-1)
	Initialize the sequence source structure using an existing SeqDB object.
template<class TData>
CStructWrapper< TData > *	WrapStruct (TData *obj, TData *(*del)(TData *))
	Auxiliary function to create a CStructWrapper for a pointer to an object.
void	SmithWatermanScoreWithTraceback (EBlastProgramType program_number, const Uint1 *A, Int4 a_size, const Uint1 *B, Int4 b_size, BlastHSP *template_hsp, BlastHSPList *hsp_list, const BlastScoringParameters *score_params, const BlastHitSavingParameters *hit_params, BlastGapAlignStruct *gap_align, Int4 start_shift, Int4 cutoff)
	Find all local alignments between two (unpacked) sequences, using the Smith-Waterman algorithm, then save the list of alignments found.
Int2	BLAST_SmithWatermanGetGappedScore (EBlastProgramType program_number, BLAST_SequenceBlk *query, BlastQueryInfo *query_info, BLAST_SequenceBlk *subject, BlastGapAlignStruct *gap_align, const BlastScoringParameters *score_params, const BlastExtensionParameters *ext_params, const BlastHitSavingParameters *hit_params, BlastInitHitList *init_hitlist, BlastHSPList **hsp_list_ptr, BlastGappedStats *gapped_stats, Boolean *fence_hit)
	Performs score-only Smith-Waterman gapped alignment of the subject sequence with all contexts in the query.
Int4	BLAST_FindBestNucleotideWordSize (double min_percent_identity, Int4 min_align_length)
	Given a minimum amount of identity and the minimum desired length of nucleotide alignments, find the largest blastn word size that will find random instances of those alignments with high probability.
	USING_SCOPE (objects)
void	ThrowIfInvalidTask (const string &task)
	Validates that the task provided is indeed a valid task, otherwise throws a CBlastException.
string	EProgramToTaskName (EProgram p)
	Convert a EProgram enumeration value to a task name (as those used in the BLAST command line binaries).
EBlastProgramType	EProgramToEBlastProgramType (EProgram p)
	Convert EProgram to EBlastProgramType.
EProgram	ProgramNameToEnum (const std::string &program_name)
	Map a string into an element of the ncbi::blast::EProgram enumeration (except eBlastProgramMax).
template<class Position>
CRange< Position >	Map (const CRange< Position > &target, const CRange< Position > &range)
static pair< BlastSeqLoc *, bool >	s_GetBlastnMask (const BlastMaskLoc *mask, unsigned int query_index)
	Return the masked locations for a given query as well as whether the linked list's elements should be reverted or not (true in the case of negative only strand) The first element of the returned pair is the linked list of masked locations The second element of the returned pair is true if the linked list needs to be reversed.
static void	s_ConvertBlastnMasks (const CPacked_seqint::Tdata &query_intervals, const BlastMaskLoc *mask, TSeqLocInfoVector &retval)
	Convert EBlastTypeBlastn CORE masks into TSeqLocInfoVector.
CRef< objects::CBioseq_set >	TSeqLocVector2Bioseqs (const TSeqLocVector &input)
	Convert a TSeqLocVector to a CBioseq_set.
CConstRef< objects::CSeq_loc >	CreateWholeSeqLocFromIds (const list< CRef< objects::CSeq_id > > seqids)
	Create a single CSeq_loc of type whole from the first id in the list.
void	Blast_Message2TSearchMessages (const Blast_Message *blmsg, const BlastQueryInfo *query_info, TSearchMessages &messages)
	Converts the Blast_Message structure into a TSearchMessages object.
string	BlastErrorCode2String (Int2 error_code)
	Returns a string containing a human-readable interpretation of the error_code passed as this function's argument.
CRef< SBlastSetupData >	BlastSetupPreliminarySearch (CRef< IQueryFactory > query_factory, CRef< CBlastOptions > options, bool is_multi_threaded=false)
	Set up internal data structures used by the BLAST CORE engine.
CRef< SBlastSetupData >	BlastSetupPreliminarySearchEx (CRef< IQueryFactory > qf, CRef< CBlastOptions > options, CConstRef< CPssmWithParameters > pssm, BlastSeqSrc *seqsrc, bool is_multi_threaded)
	Extended interface to set up internal data structures used by the BLAST CORE engine.
void	BuildBlastAncillaryData (EBlastProgramType program, const vector< CConstRef< CSeq_id > > &query_ids, const BlastScoreBlk *sbp, const BlastQueryInfo *qinfo, const TSeqAlignVector &alignments, const EResultType result_type, CSearchResultSet::TAncillaryVector &retval)
	Builds an CSearchResultSet::TAncillaryVector.
CRef< CSearchResultSet >	BlastBuildSearchResultSet (const vector< CConstRef< CSeq_id > > &query_ids, const BlastScoreBlk *sbp, const BlastQueryInfo *qinfo, EBlastProgramType program, const TSeqAlignVector &alignments, TSearchMessages &messages, const vector< TSeqLocInfoVector > &subj_masks, const TSeqLocInfoVector *query_masks=NULL, const EResultType result_type=ncbi::blast::eDatabaseSearch)
	Build a CSearchResultSet from internal BLAST data structures.
static BlastSeqSrc *	s_IDbSrcNew (BlastSeqSrc *retval, void *args)
	Construct a new instance of index based subject sequence source.
static BlastSeqSrc *	s_CloneSrcNew (BlastSeqSrc *retval, void *args)
	Construct a copy of BlastSeqSrc structure.
static unsigned long	s_MB_IdbGetResults (void *idb_v, Int4 oid_i, Int4 chunk_i, BlastInitHitList *init_hitlist)
	Get the seed search results for a give subject id and chunk number.
	USING_SCOPE (ncbi::objects)
	USING_SCOPE (ncbi::blastdbindex)
int	MinIndexWordSize ()
	Get minimal word size accepted by indexing library.
static void	NullPreSearch (BlastSeqSrc *, LookupTableWrap *, BLAST_SequenceBlk *, BlastSeqLoc *, LookupTableOptions *, BlastInitialWordOptions *)
	No-op presearch function.
static void	NullSetQueryInfo (BlastSeqSrc *, LookupTableWrap *, CRef< CBlastSeqLocWrap >)
	No-op callback for setting query info.
static void	NullRunSearch (BlastSeqSrc *, BLAST_SequenceBlk *, LookupTableOptions *, BlastInitialWordOptions *)
	No-op callback to run indexed search.
static void	NullSetNumThreads (BlastSeqSrc *seq_src, size_t)
	No-op callback to set the number of threads for indexed search.
static void	IndexedDbSetNumThreads (BlastSeqSrc *seq_src, size_t n_threads)
	Set the number of treads for indexed search.
static void	IndexedDbRunSearch (BlastSeqSrc *seq_src, BLAST_SequenceBlk *queries, LookupTableOptions *lut_options, BlastInitialWordOptions *word_options)
	Run indexed search.
static void	IndexedDbSetQueryInfo (BlastSeqSrc *seq_src, LookupTableWrap *lt_wrap, CRef< CBlastSeqLocWrap > locs_wrap)
	Set information about unmasked query segments.
static void	IndexedDbPreSearch (BlastSeqSrc *seq_src, LookupTableWrap *lt_wrap, BLAST_SequenceBlk *queries, BlastSeqLoc *locs, LookupTableOptions *lut_options, BlastInitialWordOptions *word_options)
	Callback that is called for index based seed search.
BlastSeqSrc *	DbIndexSeqSrcInit (const string &indexname, BlastSeqSrc *db)
	Wrap a BlastSeqSrc object db by another object that provides index based seed searching.
BlastSeqSrc *	CloneSeqSrcInit (BlastSeqSrc *src)
	Creates a clone of a BlastSeqSrc structure.
void	CloneSeqSrc (BlastSeqSrc *dst, BlastSeqSrc *src)
	Copies the contents of src to dst.
DbIndexPreSearchFnType	GetDbIndexPreSearchFn ()
	Return the appropriate pre-search callback.
DbIndexSetQueryInfoFnType	GetDbIndexSetQueryInfoFn ()
	Return the appropriate callback to set query information in the index.
DbIndexRunSearchFnType	GetDbIndexRunSearchFn ()
	Return the appropriate callback to run indexed seed search.
DbIndexSetNumThreadsFnType	GetDbIndexSetNumThreadsFn ()
	Return the appropriate callback to set the number of threads for indexed seed search.
END_NCBI_SCOPE	USING_SCOPE (ncbi)
	USING_SCOPE (ncbi::blast)
static BlastSeqSrc *	s_GetForwardSeqSrc (void *handle)
	C language wrapper around CIndexedDb::GetDb().
static void *	s_GetForwardSeqDb (void *handle)
	C language wrapper around CIndexedDb::GetSeqDb().
static Int4	s_IDbGetNumSeqs (void *handle, void *x)
	Forwards the call to CIndexedDb::db_.
static Int4	s_IDbGetNumSeqsStats (void *handle, void *x)
	Forwards the call to CIndexedDb::db_.
static Int4	s_IDbGetMaxLength (void *handle, void *x)
	Forwards the call to CIndexedDb::db_.
static Int4	s_IDbGetAvgLength (void *handle, void *x)
	Forwards the call to CIndexedDb::db_.
static Int8	s_IDbGetTotLen (void *handle, void *x)
	Forwards the call to CIndexedDb::db_.
static Int8	s_IDbGetTotLenStats (void *handle, void *x)
	Forwards the call to CIndexedDb::db_.
static const char *	s_IDbGetName (void *handle, void *x)
	Forwards the call to CIndexedDb::db_.
static Boolean	s_IDbGetIsProt (void *handle, void *x)
	Forwards the call to CIndexedDb::db_.
static Int2	s_IDbGetSequence (void *handle, BlastSeqSrcGetSeqArg *seq_arg)
	Forwards the call to CIndexedDb::db_.
static Int4	s_IDbGetSeqLen (void *handle, void *x)
	Forwards the call to CIndexedDb::db_.
static Int4	s_IDbIteratorNext (void *handle, BlastSeqSrcIterator *itr)
	Forwards the call to CIndexedDb::db_ but skip over the ones for which no results were poduces by pre-search.
static void	s_IDbReleaseSequence (void *handle, BlastSeqSrcGetSeqArg *getseq_arg)
	Forwards the call to CIndexedDb::db_.
static void	s_IDbResetChunkIterator (void *handle)
	Forwards the call to CIndexedDb::db_.
static BlastSeqSrc *	s_IDbSrcFree (BlastSeqSrc *seq_src)
	Destroy the sequence source.
static BlastSeqSrc *	s_IDbSrcCopy (BlastSeqSrc *seq_src)
	Fill the BlastSeqSrc data with a copy of its own contents.
static void	s_IDbSrcInit (BlastSeqSrc *retval, CIndexedDb::TThreadLocal *idb)
	Initialize the BlastSeqSrc data structure with the appropriate callbacks.
void	SetupQueryInfo (TSeqLocVector &queries, EBlastProgramType prog, objects::ENa_strand strand_opt, BlastQueryInfo **qinfo)
	Allocates the query information structure and fills the context offsets, in case of multiple queries, frames or strands.
void	SetupQueryInfo (const CBlastQueryVector &queries, EBlastProgramType prog, objects::ENa_strand strand_opt, BlastQueryInfo **qinfo)
	Allocates the query information structure and fills the context offsets, in case of multiple queries, frames or strands.
void	SetupQueries (TSeqLocVector &queries, BlastQueryInfo *qinfo, BLAST_SequenceBlk **seqblk, EBlastProgramType prog, objects::ENa_strand strand_opt, TSearchMessages &messages)
	Populates BLAST_SequenceBlk with sequence data for use in CORE BLAST.
void	SetupSubjects (TSeqLocVector &subjects, EBlastProgramType program, vector< BLAST_SequenceBlk * > *seqblk_vec, unsigned int *max_subjlen)
	Sets up internal subject data structure for the BLAST search.
SBlastSequence	GetSequence (const objects::CSeq_loc &sl, EBlastEncoding encoding, objects::CScope *scope, objects::ENa_strand strand=objects::eNa_strand_plus, ESentinelType sentinel=eSentinels, std::string *warnings=NULL)
	Retrieves a sequence using the object manager.
CRef< objects::CPacked_seqint >	TSeqLocVector2Packed_seqint (const TSeqLocVector &sequences)
	Converts a TSeqLocVector into a CPacked_seqint.
static void	s_BlastMessageToException (Blast_Message **blmsg_ptr, const string &default_msg)
int	x_safe_strcmp (const char *a, const char *b)
int	x_safe_memcmp (const void *a, const void *b, size_t size)
bool	x_QuerySetupOptions_cmp (const QuerySetUpOptions *a, const QuerySetUpOptions *b)
bool	x_LookupTableOptions_cmp (const LookupTableOptions *a, const LookupTableOptions *b)
bool	x_BlastDatabaseOptions_cmp (const BlastDatabaseOptions *a, const BlastDatabaseOptions *b)
bool	x_BlastScoringOptions_cmp (const BlastScoringOptions *a, const BlastScoringOptions *b)
bool	x_BlastEffectiveLengthsOptions_cmp (const BlastEffectiveLengthsOptions *a, const BlastEffectiveLengthsOptions *b)
static void	s_InitializeKarlinBlk (Blast_KarlinBlk *src, Blast_KarlinBlk **dest)
static CConstRef< CSeq_id >	s_ExtractSeqId (CConstRef< CSeq_align_set > align_set)
	Find the first alignment in a set of blast results, and.
static ENa_strand	s_Frame2Strand (short frame)
	Converts a frame into the appropriate strand.
static int	s_GetCurrPos (int &pos, int pos2advance)
	Advances position in a sequence, according to an edit script instruction.
static TSeqPos	s_GetAlignmentStart (int &curr_pos, int num, ENa_strand strand, bool translate, int length, int original_length, short frame)
	Finds the starting position of a sequence segment in an alignment, given an editing script.
static Int4	s_GetProteinFrameLength (Int4 nuc_length, Int2 frame)
	Finds length of a protein frame given a nucleotide length and a frame number.
static void	s_CollectSeqAlignData (const BlastHSP *hsp, const GapEditScript *esp, unsigned int first, unsigned int nsegs, vector< TSignedSeqPos > &starts, vector< TSeqPos > &lengths, vector< ENa_strand > &strands, Int4 query_length, Int4 subject_length, bool translate1, bool translate2)
	Fills vectors of start positions, lengths and strands for all alignment segments.
static void	s_CreateDenseg (CDense_seg &dense_seg, CRef< CSeq_id > master, CRef< CSeq_id > slave, vector< TSignedSeqPos > &starts, vector< TSeqPos > &lengths, vector< ENa_strand > &strands)
	Creates a Dense-seg object from the starts, lengths and strands vectors and two Seq-ids.
static CSeq_align::C_Segs::TStd	s_CreateStdSegs (CRef< CSeq_id > master, CRef< CSeq_id > slave, vector< TSignedSeqPos > &starts, vector< TSeqPos > &lengths, vector< ENa_strand > &strands, bool translate_master, bool translate_slave)
	Creates a Std-seg object from the starts, lengths and strands vectors and two Seq-ids for a translated search.
static void	s_CorrectUASequence (BlastHSP *hsp)
	Checks if any decline-to-align segments immediately follow an insertion or deletion, and swaps any such segments so indels are always to the right of the decline-to-align segments.
static CRef< CSeq_align >	s_CreateSeqAlign (CRef< CSeq_id > master, CRef< CSeq_id > slave, vector< TSignedSeqPos > starts, vector< TSeqPos > lengths, vector< ENa_strand > strands, bool translate_master, bool translate_slave)
	Creates a Seq-align for a single HSP from precalculated vectors of start positions, lengths and strands of segments, sequence identifiers and other information.
static CRef< CSeq_align >	s_BlastHSP2SeqAlign (EBlastProgramType program, BlastHSP *hsp, CRef< CSeq_id > id1, CRef< CSeq_id > id2, Int4 query_length, Int4 subject_length)
	Converts a traceback editing block to a Seq-align, provided the 2 sequence identifiers.
static CRef< CSeq_align >	s_OOFBlastHSP2SeqAlign (EBlastProgramType program, BlastHSP *hsp, CRef< CSeq_id > query_id, CRef< CSeq_id > subject_id, Int4 query_length, Int4 subject_length)
	This function is used for out-of-frame traceback conversion Converts an OOF editing script chain to a Seq-align of type Std-seg.
static CRef< CScore >	s_MakeScore (const string &ident_string, double d=0.0, int i=0)
	Creates and initializes CScore with a given name, and with integer or double value.
static size_t	s_CalculateScoreVectorSize (const BlastHSP *hsp, const vector< int > &gi_list)
	Computes the exact size of a CSeq_align::TScore for a given HSP.
static void	s_BuildScoreList (const BlastHSP *hsp, CSeq_align::TScore &scores, const vector< int > &gi_list)
	Creates a list of score objects for a Seq-align, given an HSP structure.
static void	s_AddScoresToSeqAlign (CRef< CSeq_align > &seqalign, const BlastHSP *hsp, const vector< int > &gi_list)
	Given an HSP structure, creates a list of scores and inserts them into a Seq-align.
CRef< CDense_diag >	x_UngappedHSPToDenseDiag (BlastHSP *hsp, CRef< CSeq_id > query_id, CRef< CSeq_id > subject_id, Int4 query_length, Int4 subject_length, const vector< int > &gi_list)
	Creates a Dense-diag object from HSP information and sequence identifiers for a non-translated ungapped search.
CRef< CStd_seg >	x_UngappedHSPToStdSeg (BlastHSP *hsp, CRef< CSeq_id > query_id, CRef< CSeq_id > subject_id, Int4 query_length, Int4 subject_length, const vector< int > &gi_list)
	Creates a Std-seg object from HSP information and sequence identifiers for a translated ungapped search.
void	BLASTUngappedHspListToSeqAlign (EBlastProgramType program, BlastHSPList *hsp_list, CRef< CSeq_id > query_id, CRef< CSeq_id > subject_id, Int4 query_length, Int4 subject_length, const vector< int > &gi_list, vector< CRef< CSeq_align > > &sa_vector)
	Creates a Seq-align from an HSP list for an ungapped search.
void	BLASTHspListToSeqAlign (EBlastProgramType program, BlastHSPList *hsp_list, CRef< CSeq_id > query_id, CRef< CSeq_id > subject_id, Int4 query_length, Int4 subject_length, bool is_ooframe, const vector< int > &gi_list, vector< CRef< CSeq_align > > &sa_vector)
	This is called for each query and each subject in a BLAST search.
static CRef< CSeq_align_set >	s_CreateEmptySeq_align_set ()
void	RemapToQueryLoc (CRef< CSeq_align > sar, const CSeq_loc &query)
	Remaps Seq-align offsets relative to the query Seq-loc.
static void	s_RemapToSubjectLoc (CRef< CSeq_align > &subj_aligns, const CSeq_loc &subj_loc)
	Remap subject alignment if its location specified the reverse strand or a starting location other than the beginning of the sequence.
CRef< CSeq_align_set >	BlastHitList2SeqAlign_OMF (const BlastHitList *hit_list, EBlastProgramType prog, const CSeq_loc &query_loc, TSeqPos query_length, const IBlastSeqInfoSrc *seqinfo_src, bool is_gapped, bool is_ooframe, TSeqLocInfoVector &subj_masks)
TSeqAlignVector	PhiBlastResults2SeqAlign_OMF (const BlastHSPResults *results, EBlastProgramType prog, class ILocalQueryData &query, const IBlastSeqInfoSrc *seqinfo_src, const SPHIQueryInfo *pattern_info, vector< TSeqLocInfoVector > &subj_masks)
static void	s_AdjustNegativeSubjFrameInBlastn (ENa_strand subj_strand, EBlastProgramType program, BlastHSPList *hsp_list)
	This function changes the subject frame for HSPs if the program is blastn and the subject was specified with a negative strand.
static TSeqAlignVector	s_BLAST_OneSubjectResults2CSeqAlign (const BlastHSPResults *results, ILocalQueryData &query_data, const IBlastSeqInfoSrc &seqinfo_src, EBlastProgramType prog, Uint4 subj_idx, bool is_gapped, bool is_ooframe, vector< TSeqLocInfoVector > &subj_masks)
	Extracts results from the BlastHSPResults structure for only one subject sequence, identified by its index, and converts them into a vector of CSeq_align_set objects.
static TSeqAlignVector	s_TransposeSeqAlignVector (const TSeqAlignVector &alnvec, const size_t num_queries, const size_t num_subjects)
	Transpose the (linearly organized) seqalign set matrix from (q1 s1 q2 s1 .
static TSeqAlignVector	s_BlastResults2SeqAlignSequenceCmp_OMF (const BlastHSPResults *results, EBlastProgramType prog, class ILocalQueryData &query_data, const IBlastSeqInfoSrc *seqinfo_src, bool is_gapped, bool is_ooframe, vector< TSeqLocInfoVector > &subj_masks)
static TSeqAlignVector	s_BlastResults2SeqAlignDatabaseSearch_OMF (const BlastHSPResults *results, EBlastProgramType prog, class ILocalQueryData &query, const IBlastSeqInfoSrc *seqinfo_src, bool is_gapped, bool is_ooframe, vector< TSeqLocInfoVector > &subj_masks)
TSeqAlignVector	LocalBlastResults2SeqAlign (BlastHSPResults *hsp_results, ILocalQueryData &local_data, const IBlastSeqInfoSrc &seqinfo_src, EBlastProgramType program, bool gapped, bool oof_mode, vector< TSeqLocInfoVector > &subj_masks, EResultType result_type=eDatabaseSearch)
	Convert traceback output into Seq-align format.
CSeq_align_set *	CreateEmptySeq_align_set (CSeq_align_set *sas)
	Constructs an empty Seq-align-set containing an empty discontinuous seq-align, and appends it to a previously constructed Seq-align-set.
void	GetSequenceLengthAndId (const blast::IBlastSeqInfoSrc *seqinfo_src, int oid, CRef< CSeq_id > &seqid, TSeqPos *length)
objects::ENa_strand	BlastSetup_GetStrand (const objects::CSeq_loc &query_seqloc, EBlastProgramType program, objects::ENa_strand strand_option)
	Choose between a Seq-loc specified query strand and the strand obtained from the CBlastOptions.
void	SetupQueryInfo_OMF (const IBlastQuerySource &queries, EBlastProgramType prog, objects::ENa_strand strand_opt, BlastQueryInfo **qinfo)
	ObjMgr Free version of SetupQueryInfo.
void	SetupQueries_OMF (IBlastQuerySource &queries, BlastQueryInfo *qinfo, BLAST_SequenceBlk **seqblk, EBlastProgramType prog, objects::ENa_strand strand_opt, TSearchMessages &messages)
	ObjMgr Free version of SetupQueries.
void	SetupSubjects_OMF (IBlastQuerySource &subjects, EBlastProgramType program, vector< BLAST_SequenceBlk * > *seqblk_vec, unsigned int *max_subjlen)
	Object manager free version of SetupSubjects.
SBlastSequence	GetSequence_OMF (IBlastSeqVector &sv, EBlastEncoding encoding, objects::ENa_strand strand, ESentinelType sentinel, std::string *warnings=0)
	Object manager free version of GetSequence.
TSeqPos	CalculateSeqBufferLength (TSeqPos sequence_length, EBlastEncoding encoding, objects::ENa_strand strand=objects::eNa_strand_unknown, ESentinelType sentinel=eSentinels) THROWS((CBlastException))
	Calculates the length of the buffer to allocate given the desired encoding, strand (if applicable) and use of sentinel bytes around sequence.
SBlastSequence	CompressNcbi2na (const SBlastSequence &source)
	Compresses the sequence data passed in to the function from 1 base per byte to 4 bases per byte.
Uint1	GetSentinelByte (EBlastEncoding encoding) THROWS((CBlastException))
	Convenience function to centralize the knowledge of which sentinel bytes we use for supported encodings.
string	FindBlastDbPath (const char *dbname, bool is_prot)
	Returns the path (including a trailing path separator) to the location where the BLAST database can be found.
unsigned int	GetNumberOfContexts (EBlastProgramType p)
	Returns the number of contexts for a given BLAST program.
EBlastEncoding	GetQueryEncoding (EBlastProgramType program)
	Returns the encoding for the sequence data used in BLAST for the query.
EBlastEncoding	GetSubjectEncoding (EBlastProgramType program)
	Returns the encoding for the sequence data used in BLAST2Sequences for the subject.
BLAST_SequenceBlk *	SafeSetupQueries (IBlastQuerySource &queries, const CBlastOptions *options, BlastQueryInfo *query_info, TSearchMessages &messages)
	Wrapper around SetupQueries.
BlastQueryInfo *	SafeSetupQueryInfo (const IBlastQuerySource &queries, const CBlastOptions *options)
	Wrapper around SetupQueryInfo.
char *	BlastFindMatrixPath (const char *matrix_name, Boolean is_prot)
	Returns the path to a specified matrix.
static void	s_QueryInfo_SetContext (BlastQueryInfo *qinfo, Uint4 index, Uint4 length)
	Set field values for one element of the context array of a concatenated query.
static objects::ENa_strand	s_BlastSetup_GetStrand (objects::ENa_strand seqloc_strand, EBlastProgramType program, objects::ENa_strand strand_opt)
	Internal function to choose between the strand specified in a Seq-loc (which specified the query strand) and the strand obtained from the CBlastOptions.
static void	s_AdjustFirstContext (BlastQueryInfo *query_info, EBlastProgramType prog, ENa_strand strand_opt, const IBlastQuerySource &queries)
	Adjust first context depending on the first query strand.
static void	s_ComputeStartEndContexts (ENa_strand strand, int num_contexts, int &start, int &end)
	Calculate the starting and ending contexts for a given strand.
static void	s_AddMask (EBlastProgramType prog, BlastMaskLoc *mask, int query_index, CBlastQueryFilteredFrames &seqloc_frames, ENa_strand strand, TSeqPos query_length)
	Adds seqloc_frames to mask.
static void	s_RestrictSeqLocs_Multiframe (CBlastQueryFilteredFrames &frame_to_bsl, const IBlastQuerySource &queries, int query_index, const BlastQueryInfo *qinfo)
	Restricts the masked locations in frame_to_bsl for the case when the BLAST program requires the query to be translated into multiple frames.
static CRef< CBlastQueryFilteredFrames >	s_GetRestrictedBlastSeqLocs (IBlastQuerySource &queries, int query_index, const BlastQueryInfo *qinfo, EBlastProgramType program)
	Extract the masking locations for a single query into a CBlastQueryFilteredFrames object and adjust the masks so that they correspond to the range specified by the Seq-loc in queries.
static void	s_InvalidateQueryContexts (BlastQueryInfo *qinfo, int query_index)
	Mark the contexts corresponding to the query identified by query_index as invalid.
static void	s_SeqLoc2MaskedSubjRanges (const CSeq_loc *slp, CSeqDB::TSequenceRanges &output)
static bool	s_IsValidResidue (Uint1 res)
	Tests if a number represents a valid residue.
static SBlastSequence	GetSequenceProtein (IBlastSeqVector &sv, string *warnings=0)
	Protein sequences are always encoded in eBlastEncodingProtein and always have sentinel bytes around sequence data.
static SBlastSequence	GetSequenceCompressedNucleotide (IBlastSeqVector &sv)
	Auxiliary function to retrieve plus strand in compressed (ncbi4na) format.
static SBlastSequence	GetSequenceSingleNucleotideStrand (IBlastSeqVector &sv, EBlastEncoding encoding, objects::ENa_strand strand, ESentinelType sentinel)
	Auxiliary function to retrieve a single strand of a nucleotide sequence.
static SBlastSequence	GetSequenceNucleotideBothStrands (IBlastSeqVector &sv, EBlastEncoding encoding, ESentinelType sentinel)
	Auxiliary function to retrieve both strands of a nucleotide sequence.
char *	s_GetCStringOfMatrixPath (string &full_path, const string &matrix_name)
	Get the path to the matrix, without the actual matrix name.
static bool	BlastDbFileExists (string &path, bool is_prot)
	Checks if a BLAST database exists at a given file path: looks for an alias file first, then for an index file.
static set< CSeqLocInfo::ETranslationFrame >	s_GetAllAvailableFrames ()
	Auxiliary function to retrieve all available frames.
void	Blast_FindDustFilterLoc (TSeqLocVector &query, const CBlastNucleotideOptionsHandle *nucl_handle)
	Finds dust locations for a given set of sequences by calling the the symmetric dust lib.
static CRef< CSeq_loc_Mapper >	s_CreateSeqLocMapper (CSeq_id &query_id, const CSeq_loc *target_seqloc, CScope *scope)
	Auxiliary function to create CSeq_loc_Mapper from a copy of the target Seq-loc.
void	s_CombineDustMasksWithUserProvidedMasks (CSeqVector &data, CConstRef< CSeq_loc > seqloc, CRef< CScope > scope, CRef< CSeq_id > query_id, CRef< CSeq_loc > &orig_query_mask, Uint4 level, Uint4 window, Uint4 linker)
void	Blast_FindDustFilterLoc (TSeqLocVector &query, Uint4 level=CSymDustMasker::DEFAULT_LEVEL, Uint4 window=CSymDustMasker::DEFAULT_WINDOW, Uint4 linker=CSymDustMasker::DEFAULT_LINKER)
	Overloaded version of the function above which takes the filtering implementation's arguments directly, TSeqLocVector version.
void	Blast_FindDustFilterLoc (CBlastQueryVector &query, Uint4 level=CSymDustMasker::DEFAULT_LEVEL, Uint4 window=CSymDustMasker::DEFAULT_WINDOW, Uint4 linker=CSymDustMasker::DEFAULT_LINKER)
	Overloaded version of the function above which takes the filtering implementation's arguments directly, CBlastQueryVector version.
static IBlastSeqInfoSrc *	s_InitSeqInfoSrc (const BlastSeqSrc *seqsrc)
	FIXME: this should be removed as soon as we safely can We will be able to do this once we are guaranteed that every constructor to CLocalBlast takes or can construct a IBlastSeqInfoSrc on it's own.
static void	s_CheckForBlastSeqSrcErrors (const BlastSeqSrc *seqsrc)
	Checks if the BlastSeqSrc initialization succeeded Exceptions: CBlastException  if BlastSeqSrc initialization failed.
static CRef< CSeqDbSeqInfoSrc >	s_InitCSeqDbSeqInfoSrc (CRef< CSeqDB > dbhandle, int filtering_algorithm)
static const char	kGapChar ('-')
	The representation of a gap in ASCII format.
static void	s_GetQuerySequenceData (const CBioseq &bioseq, size_t query_length, CNCBIstdaa &retval)
	Auxiliary function to retrieve the sequence data in NCBI-stdaa format from the bioseq.
static bool	s_AreSequencesEqual (const CNCBIstdaa &sequence, Uint1 *query)
	Returns true iff sequence is identical to query.
static CRef< CBioseq_set >	s_QueryVectorToBioseqSet (const CBlastQueryVector &queries)
	Produces a BioseqSet from a CBlastQueryVector.
static CRef< CBioseq_set >	s_TSeqLocVectorToBioseqSet (const TSeqLocVector *queries)
	Produces a BioseqSet from a TSeqLocVector.
static IRemoteQueryData::TSeqLocs	s_TSeqLocVectorToTSeqLocs (const TSeqLocVector *queries)
	Produces a vector of SeqLocs from a TSeqLocVector.
static IRemoteQueryData::TSeqLocs	s_QueryVectorToTSeqLocs (const CBlastQueryVector &queries)
	Produces a vector of SeqLocs from a CBlastQueryVector.
static EBlastProgramType	s_GuessProgram (CConstRef< CSeq_loc > mask)
	Auxiliary function to help guess the program type from a CSeq-loc.
static IRemoteQueryData::TSeqLocs	s_ConstBioseqSetToSeqLocs (CConstRef< CBioseq_set > bioseq_set)
	Convert a constant reference to a Bioseq-set to IRemoteQueryData::TSeqLocs.
CRef< CBioseq_set >	x_BioseqSetFromBioseq (const CBioseq &bioseq)
	Auxiliary function to convert a CBioseq into a CRef<CBioseq_set>.
void	PsiBlastSetupScoreBlock (BlastScoreBlk *score_blk, CConstRef< objects::CPssmWithParameters > pssm, TSearchMessages &messages, CConstRef< CBlastOptions > options)
	Setup CORE BLAST score block structure with data from the scoremat PSSM.
template<class T>
void	Convert2Matrix (const list< T > &source, CNcbiMatrix< T > &dest, bool by_row, SIZE_TYPE num_rows, SIZE_TYPE num_columns)
	Convert a list of values into a CNcbiMatrix.
void	PsiBlastAddAncillaryPssmData (objects::CPssmWithParameters &pssm, int gap_open, int gap_extend)
	Even though the query sequence and the matrix gap costs are not a product of the PSSM engine, set them as they are required for the PSI-BLAST (query sequence) and RPS-BLAST/formatrpsdb (gap costs).
static void	s_AdjustFrequencyRatiosMatrixToMatchScoreMatrix (objects::CPssmWithParameters &pssm)
	After creating the PSSM from frequency ratios, adjust the frequency ratios matrix to match the dimensions of the score matrix.
void	PsiBlastComputePssmScores (CRef< objects::CPssmWithParameters > pssm, const CBlastOptions &opts)
	Given a PSSM with frequency ratios and options, invoke the PSSM engine to compute the scores.
static double	s_GetEvalue (const CScore &score)
	Returns the evalue from this score object.
static double	s_GetBitScore (const CScore &score)
	Returns the bit_score from this score object.
double	GetLowestEvalue (const objects::CDense_seg::TScores &scores, double *bit_score=NULL)
	Returns the lowest score from the list of scores in CDense_seg::TScores.
static void	s_CheckAgainstNullData (IPssmInputData *pssm_input_msa)
	This function makes sure that none of the required data is returned as NULL or "empty".
static void	s_CheckAgainstNullData (IPssmInputFreqRatios *pssm_input_freqratios)
	This function makes sure that none of the required data is returned as NULL or "empty".
static void	s_Validate (IPssmInputData *pssm_input_msa)
	Performs validation on data provided before invoking the CORE PSSM engine.
static void	s_Validate (IPssmInputFreqRatios *pssm_input_fr)
	Performs validation on data provided before invoking the CORE PSSM engine.
static bool	s_SearchPending (CRef< objects::CBlast4_reply > reply)
	Determine whether the search is still running.
static CRef< CBlast4_mask >	s_CreateBlastMask (const CPacked_seqint &packed_int, EBlastProgramType program)
	Creates a Blast4-mask which is supposed to contain all masked locations for a given query sequence and frame, all of which are in the packed_int argument.
static void	s_FlattenBioseqSet (const CBioseq_set &bss, list< CRef< CBioseq > > &seqs)
static const string	kNoRIDSpecified ("Cannot fetch query info: No RID was specified.")
static const string	kNoArchiveFile ("Cannot fetch query info: No archive file.")
static void	s_ExtractQueryIdsFromBioseqSet (const CBioseq_set &bss, CSearchResultSet::TQueryIdVector &query_ids)
	Extract the query IDs from a CBioseq_set.
static CRef< CSearchResultSet >	s_BuildResultsRemote (CRemoteBlast &rb)
	Build a result set from results in a remote blast search.
static TSeqAlignVector	s_SplitAlignVectorBySubjects (TSeqAlignVector seqaligns)
	CRemoteBlast does not separate each hit to the query in discontinuous Seq-aligns, so we do it here.
static CSeq_loc *	s_BlastSeqLoc2CSeqloc (const CSeq_loc &query, CScope *scope, BlastSeqLoc *loc_list)
	Convert a list of mask locations to a CSeq_loc object.
static CSeq_loc *	s_BlastSeqLoc2CSeqloc (SSeqLoc &query, BlastSeqLoc *loc_list)
	Convert a list of mask locations to a CSeq_loc object.
TMaskedQueryRegions	s_BlastSeqLoc2MaskedRegions (const CSeq_loc &query, CScope *scope, BlastSeqLoc *loc_list, EBlastProgramType program)
	Convert a list of mask locations to TMaskedQueryRegions.
static void	s_SeqAlignToBlastSeqLoc (const CSeq_align_set &alignment, BlastSeqLoc **locs)
	Build a list of BlastSeqLoc's from a set of Dense-seg contained in a Seq-align-set.
static void	s_FillMaskLocFromBlastResults (TSeqLocVector &query, const CSearchResultSet &results)
	Fills the mask locations in the query SSeqLoc structures, as if it was a lower case mask, given the results of a BLAST search against a database of repeats.
static void	s_FillMaskLocFromBlastResults (CBlastQueryVector &query, const CSearchResultSet &results, EBlastProgramType program)
	Fills the mask locations in the BlastSearchQuery structures, as if it was a lower case mask, given the results of a BLAST search against a database of repeats.
static CRef< CBlastOptionsHandle >	s_CreateRepeatsSearchOptions ()
	Create an options handle with the defaults set for a search for repeats.
static void	s_SeqIntervalToSeqLocInfo (CRef< CSeq_interval > interval, const vector< TSeqRange > &target_ranges, const CSeqLocInfo::ETranslationFrame frame, TMaskedSubjRegions &retval)
static Int4	s_MultiSeqGetMaxLength (void *multiseq_handle, void *)
	Retrieves the length of the longest sequence in the BlastSeqSrc.
static Int4	s_MultiSeqGetAvgLength (void *multiseq_handle, void *)
	Retrieves the length of the longest sequence in the BlastSeqSrc.
static Int4	s_MultiSeqGetNumSeqs (void *multiseq_handle, void *)
	Retrieves the number of sequences in the BlastSeqSrc.
static Int4	s_MultiSeqGetNumSeqsStats (void *, void *)
	Returns zero as this implementation does not support alias files.
static Int8	s_MultiSeqGetTotLen (void *, void *)
	Returns 0 as total length, indicating that this is NOT a database!
static Int8	s_MultiSeqGetTotLenStats (void *, void *)
	Returns 0 as this implementation does not use alias files.
static const char *	s_MultiSeqGetName (void *, void *)
	Always returns NcbiEmptyCStr.
static Boolean	s_MultiSeqGetIsProt (void *multiseq_handle, void *)
	Answers whether this object is for protein or nucleotide sequences.
static Int2	s_MultiSeqGetSequence (void *multiseq_handle, BlastSeqSrcGetSeqArg *args)
	Retrieves the sequence for a given index, in a given encoding.
static void	s_MultiSeqReleaseSequence (void *, BlastSeqSrcGetSeqArg *args)
	Deallocates the uncompressed sequence buffer if necessary.
static Int4	s_MultiSeqGetSeqLen (void *multiseq_handle, void *args)
	Retrieve length of a given sequence.
static Int2	s_MultiSeqGetNextChunk (void *multiseq_handle, BlastSeqSrcIterator *itr)
	Mirrors the database iteration interface.
static void	s_MultiSeqResetChunkIter (void *)
	Resets the internal bookmark iterator (N/A in this case).
static Int4	s_MultiSeqIteratorNext (void *multiseq_handle, BlastSeqSrcIterator *itr)
	Gets the next sequence index, given a BlastSeqSrc pointer.
static BlastSeqSrc *	s_MultiSeqSrcFree (BlastSeqSrc *seq_src)
	Multi sequence source destructor: frees its internal data structure.
static BlastSeqSrc *	s_MultiSeqSrcNew (BlastSeqSrc *retval, void *args)
	Multi-sequence source constructor.
static Int4	s_QueryFactoryGetMaxLength (void *multiseq_handle, void *)
	Retrieves the length of the longest sequence in the BlastSeqSrc.
static Int4	s_QueryFactoryGetAvgLength (void *multiseq_handle, void *)
	Retrieves the average length of the sequence in the BlastSeqSrc.
static Int4	s_QueryFactoryGetNumSeqs (void *multiseq_handle, void *)
	Retrieves the number of sequences in the BlastSeqSrc.
static Int4	s_QueryFactoryGetNumSeqsStats (void *, void *)
	Returns zero as this implementation does not use an alias file.
static Int8	s_QueryFactoryGetTotLen (void *, void *)
	Returns 0 as total length, indicating that this is NOT a database!
static Int8	s_QueryFactoryGetTotLenStats (void *, void *)
	Returns 0 as total statistic length, as this implementation does not use alias files.
static const char *	s_QueryFactoryGetName (void *, void *)
	Always returns NcbiEmptyCStr.
static Boolean	s_QueryFactoryGetIsProt (void *multiseq_handle, void *)
	Answers whether this object is for protein or nucleotide sequences.
static Int2	s_QueryFactoryGetSequence (void *multiseq_handle, BlastSeqSrcGetSeqArg *args)
	Retrieves the sequence for a given index, in a given encoding.
static void	s_QueryFactoryReleaseSequence (void *, BlastSeqSrcGetSeqArg *args)
	Deallocates the uncompressed sequence buffer if necessary.
static Int4	s_QueryFactoryGetSeqLen (void *multiseq_handle, void *args)
	Retrieve length of a given sequence.
static Int2	s_QueryFactoryGetNextChunk (void *multiseq_handle, BlastSeqSrcIterator *itr)
	Mirrors the database iteration interface.
static void	s_QueryFactoryResetChunkIter (void *)
	Resets the internal bookmark iterator (N/A in this case).
static Int4	s_QueryFactoryIteratorNext (void *multiseq_handle, BlastSeqSrcIterator *itr)
	Gets the next sequence index, given a BlastSeqSrc pointer.
static BlastSeqSrc *	s_QueryFactorySrcFree (BlastSeqSrc *seq_src)
	Multi sequence source destructor: frees its internal data structure.
static BlastSeqSrc *	s_QueryFactorySrcCopy (BlastSeqSrc *seq_src)
	Multi-sequence sequence source copier: creates a new reference to the CQueryFactoryInfo object and copies the rest of the BlastSeqSrc structure.
static BlastSeqSrc *	s_QueryFactorySrcNew (BlastSeqSrc *retval, void *args)
	Multi-sequence source constructor.
static BlastSeqSrc *	s_QueryFactoryBlastSeqSrcInit (CRef< IQueryFactory > query_factory, const TSeqLocVector &subj_seqs, EBlastProgramType program)
BlastSeqSrc *	QueryFactoryBlastSeqSrcInit (CRef< IQueryFactory > query_factory, EBlastProgramType program)
	Initialize the sequence source structure from a query factory.
BlastSeqSrc *	QueryFactoryBlastSeqSrcInit (const TSeqLocVector &subj_seqs, EBlastProgramType program)
	Initialize the sequence source structure from a TSeqLocVector.
	USING_SCOPE (blast)
static Int4	s_SeqDbGetMaxLength (void *seqdb_handle, void *)
	Retrieves the length of the longest sequence in the BlastSeqSrc.
static void	s_SeqDbSetNumberOfThreads (void *seqdb_handle, int n)
	Setting number of threads in MT mode.
static Int4	s_SeqDbGetNumSeqs (void *seqdb_handle, void *)
	Retrieves the number of sequences in the BlastSeqSrc.
static Int4	s_SeqDbGetNumSeqsStats (void *seqdb_handle, void *)
static Int8	s_SeqDbGetTotLen (void *seqdb_handle, void *)
	Retrieves the total length of all sequences in the BlastSeqSrc.
static Int8	s_SeqDbGetTotLenStats (void *seqdb_handle, void *)
static Int4	s_SeqDbGetAvgLength (void *seqdb_handle, void *ignoreme)
	Retrieves the average length of sequences in the BlastSeqSrc.
static const char *	s_SeqDbGetName (void *seqdb_handle, void *)
	Retrieves the name of the BLAST database.
static Boolean	s_SeqDbGetIsProt (void *seqdb_handle, void *)
	Checks whether database is protein or nucleotide.
static Int2	s_SeqDbGetSequence (void *seqdb_handle, BlastSeqSrcGetSeqArg *args)
	Retrieves the sequence meeting the criteria defined by its second argument.
static void	s_SeqDbReleaseSequence (void *seqdb_handle, BlastSeqSrcGetSeqArg *args)
	Returns the memory allocated for the sequence buffer to the CSeqDB interface.
static Int4	s_SeqDbGetSeqLen (void *seqdb_handle, void *args)
	Retrieve length of a given database sequence.
static Int2	s_SeqDbGetNextChunk (void *seqdb_handle, BlastSeqSrcIterator *itr)
	Assigns next chunk of the database to the sequence source iterator.
static Int4	s_SeqDbIteratorNext (void *seqdb_handle, BlastSeqSrcIterator *itr)
	Finds the next not searched ordinal id in the iteration over BLAST database.
static void	s_SeqDbResetChunkIterator (void *seqdb_handle)
	Resets CSeqDB's internal chunk bookmark.
static BlastSeqSrc *	s_SeqDbSrcFree (BlastSeqSrc *seq_src)
	SeqDb sequence source destructor: frees its internal data structure.
static BlastSeqSrc *	s_SeqDbSrcCopy (BlastSeqSrc *seq_src)
	SeqDb sequence source copier: creates a new reference to the CSeqDB object and copies the rest of the BlastSeqSrc structure.
static void	s_InitNewSeqDbSrc (BlastSeqSrc *retval, TSeqDBData *datap)
	Initializes the data structure and function pointers in a SeqDb based BlastSeqSrc.
static BlastSeqSrc *	s_SeqDbSrcSharedNew (BlastSeqSrc *retval, void *args)
	Populates a BlastSeqSrc, creating a new reference to the already existing SeqDb object.
static BlastSeqSrc *	s_SeqDbSrcNew (BlastSeqSrc *retval, void *args)
	SeqDb sequence source constructor.
static CRef< CPacked_seqint >	s_LocalQueryData2Packed_seqint (ILocalQueryData &query_data)
	Auxiliary function to extract the Seq-ids from the ILocalQueryData and bundle them in a Packed-seqint.
size_t	SplitQuery_GetOverlapChunkSize (EBlastProgramType program)
	Size of the region that overlaps in between each query chunk.
size_t	SplitQuery_GetChunkSize (EProgram program)
	Returns the optimal chunk size for a given task.
bool	SplitQuery_ShouldSplit (EBlastProgramType program, size_t chunk_size, size_t concatenated_query_length, size_t num_queries)
	is supported by the current implementation.
Uint4	SplitQuery_CalculateNumChunks (EBlastProgramType program, size_t *chunk_size, size_t concatenated_query_length, size_t num_queries)
	Calculate the number of chunks that a query will be split into based upon query length, chunk_size and program.
void	SplitQuery_SetEffectiveSearchSpace (CRef< CBlastOptions > options, CRef< IQueryFactory > full_query_fact, CRef< SInternalData > full_data)
	this might supercede the function below...
CRef< SInternalData >	SplitQuery_CreateChunkData (CRef< IQueryFactory > qf, CRef< CBlastOptions > options, CRef< SInternalData > full_data, bool is_multi_threaded=false)
	Function used by search class to retrieve a query factory for a given chunk.
ostream &	operator<< (ostream &out, const CContextTranslator &rhs)
template<class T>
string	s_PrintVector (const vector< T > &data2print)
	Auxiliary function to print a vector.
ostream &	operator<< (ostream &out, const CSplitQueryBlk &rhs)
CSeqMasker *	s_BuildSeqMasker (const string &lstat)
void	s_BuildMaskedRanges (CSeqMasker::TMaskList &masks, const CSeq_loc &seqloc, CSeq_id &query_id, TMaskedQueryRegions *mqr, CRef< CSeq_loc > *psl)
template<class TQueries>
void	Blast_FindWindowMaskerLoc_Fwd (TQueries &query, const CBlastOptions *opts)
template<class TQueries>
void	Blast_FindWindowMaskerLoc_Fwd (TQueries &query, const CBlastOptionsHandle *opts_handle)
void	Blast_FindWindowMaskerLoc (CBlastQueryVector &query, const CBlastOptions *opts_handle)
	Find Window Masker filtered locations using a BlastOptions.
void	Blast_FindWindowMaskerLoc (TSeqLocVector &query, const CBlastOptions *opts)
	Find Window Masker filtered locations using BlastOptions.
void	Blast_FindWindowMaskerLoc (CBlastQueryVector &query, const CBlastOptionsHandle *opts_handle)
	Find Window Masker filtered locations using a BlastOptionsHandle.
void	Blast_FindWindowMaskerLoc (TSeqLocVector &query, const CBlastOptionsHandle *opts_handle)
	Find Window Masker filtered locations using a BlastOptionsHandle.
void	Blast_FindWindowMaskerLoc (CBlastQueryVector &query, const string &lstat)
	Find Window Masker filtered locations by database name.
void	Blast_FindWindowMaskerLoc (TSeqLocVector &query, const string &lstat)
	Find Window Masker filtered locations on TSeqLocVector by database name.
static void	s_VersionNumberTransform (const string &a, vector< int > &b)
static bool	s_VersionNumberLess (const string &a, const string &b)
static string	s_FindPathToWM (void)
	Find the path to the window masker files, first checking the environment variable WINDOW_MASKER_PATH, then the section WINDOW_MASKER, label WINDOW_MASKER_PATH in the NCBI configuration file.
static string	s_WindowMaskerTaxidToDb (int taxid)
void	Blast_FindWindowMaskerLocTaxId (CBlastQueryVector &query, int taxid)
	Find Window Masker filtered locations by taxonomic ID.
void	Blast_FindWindowMaskerLocTaxId (TSeqLocVector &query, int taxid)
	Find Window Masker filtered locations on a TSeqLocVector by Taxid.
static void	s_ProcessErrorsFromReply (CRef< objects::CBlast4_reply > reply, string &errors, string &warnings)
	Process error messages from a reply object.
static EBlast4_residue_type	s_SeqTypeToResidue (char p, string &errors)
void	CBl2Seq::SetQuery (const SSeqLoc &query)
	Set the query.
const SSeqLoc &	CBl2Seq::GetQuery () const
	Retrieve the query sequence.
void	CBl2Seq::SetQueries (const TSeqLocVector &queries)
	Set a vector of query sequences for a concatenated search.
const TSeqLocVector &	CBl2Seq::GetQueries () const
	Retrieve a vector of query sequences.
void	CBl2Seq::SetSubject (const SSeqLoc &subject)
	Set the subject sequence.
const SSeqLoc &	CBl2Seq::GetSubject () const
	Retrieve the subject sequence.
void	CBl2Seq::SetSubjects (const TSeqLocVector &subjects)
	Set a vector of subject sequences.
const TSeqLocVector &	CBl2Seq::GetSubjects () const
	Retrieve a vector of subject sequences.
CBlastOptionsHandle &	CBl2Seq::SetOptionsHandle ()
	Set the options handle.
const CBlastOptionsHandle &	CBl2Seq::GetOptionsHandle () const
	Retrieve the options handle.
BlastDiagnostics *	CBl2Seq::GetDiagnostics () const
	Retrieves the diagnostics information returned from the engine.
NCBI_DEPRECATED BlastHSPResults *	CBl2Seq::GetResults () const
	Retrieves the list of HSP results from the engine (to be used after RunWithoutSeqalignGeneration() method).
void	CBl2Seq::GetMessages (TSearchMessages &messages) const
	Returns error messages/warnings.
TInterruptFnPtr	CBl2Seq::SetInterruptCallback (TInterruptFnPtr fnptr, void *user_data=NULL)
	Set a function callback to be invoked by the CORE of BLAST to allow interrupting a BLAST search in progress.
void	CBl2Seq::GetAncillaryResults (CSearchResultSet::TAncillaryVector &retval) const
	Get the ancillary results for a BLAST search (to be used with the Run() method).
void	CBl2Seq::GetFilteredSubjectRegions (vector< TSeqLocInfoVector > &retval) const
	Retrieves regions filtered on the subject sequence(s).
int	CLocalDbAdapter::GetFilteringAlgorithm () const
	Retrieve the database filtering algorithm.
const char *	CPHIBlastNuclOptionsHandle::GetPHIPattern () const
	Retrieves the pattern string option.
void	CPHIBlastNuclOptionsHandle::SetPHIPattern (const char *p)
	Sets the pattern string option.
const char *	CPHIBlastProtOptionsHandle::GetPHIPattern () const
	Retrieves the pattern string option.
void	CPHIBlastProtOptionsHandle::SetPHIPattern (const char *p)
	Sets the pattern string option.
TSearchMessages	CBlastPrelimSearch::GetSearchMessages () const
	Retrieve any error/warning messages that occurred during the search.
TSeqLocInfoVector	CBlastPrelimSearch::GetFilteredQueryRegions () const
	Retrieve the filtered/masked query regions.
virtual void	CThreadable::SetNumberOfThreads (size_t nthreads)
	Mutator for the number of threads.
size_t	CThreadable::GetNumberOfThreads (void) const
	Accessor for the number of threads to use.
bool	CThreadable::IsMultiThreaded (void) const
	Returns true if more than 1 thread is specified.
	CBlastSeqVectorFromCSeq_data::CBlastSeqVectorFromCSeq_data (const objects::CSeq_data &seq_data, TSeqPos length)
	Parametrized constructor.
virtual void	CBlastSeqVectorFromCSeq_data::SetCoding (objects::CSeq_data::E_Choice c)
	Sets the encoding for the sequence data. Two encodings are really necessary: ncbistdaa and ncbi4na, both use 1 byte per residue/base
virtual TSeqPos	CBlastSeqVectorFromCSeq_data::x_Size () const
	Method which retrieves the size of the sequence vector, as described in the size() method above.
virtual Uint1	CBlastSeqVectorFromCSeq_data::operator[] (TSeqPos pos) const
	Allows index-based access to the sequence data.
virtual SBlastSequence	CBlastSeqVectorFromCSeq_data::GetCompressedPlusStrand ()
	Returns the compressed nucleotide data for the plus strand, still occupying one base per byte.
virtual void	CBlastSeqVectorFromCSeq_data::x_SetPlusStrand ()
	Method which does the work for setting the plus strand of the nucleotide sequence data.
virtual void	CBlastSeqVectorFromCSeq_data::x_SetMinusStrand ()
	Method which does the work for setting the minus strand of the nucleotide sequence data.
void	CBlastSeqVectorFromCSeq_data::x_ComplementData ()
	Complements the data in m_SequenceData in place.
CSeqUtil::ECoding	CBlastSeqVectorFromCSeq_data::x_Encoding_CSeq_data2CSeqUtil (objects::CSeq_data::E_Choice c)
	Auxiliary function to map the description of the encoding in CSeq_data::EChoice to CSeqUtil::ECoding.
	CBlastQuerySourceBioseqSet::CBlastQuerySourceBioseqSet (const objects::CBioseq_set &bss, bool is_prot)
	Parametrized constructor for a Bioseq-set.
	CBlastQuerySourceBioseqSet::CBlastQuerySourceBioseqSet (const objects::CBioseq &bioseq, bool is_prot)
	Parametrized constructor for a Bioseq.
virtual objects::ENa_strand	CBlastQuerySourceBioseqSet::GetStrand (int index) const
	Return strand for a sequence.
virtual TSeqPos	CBlastQuerySourceBioseqSet::Size () const
	Return the number of elements in the sequence container.
virtual CConstRef< objects::CSeq_loc >	CBlastQuerySourceBioseqSet::GetMask (int index)
	Return the filtered (masked) regions for a sequence.
virtual TMaskedQueryRegions	CBlastQuerySourceBioseqSet::GetMaskedRegions (int index)
	Return the filtered (masked) regions for a sequence.
virtual CConstRef< objects::CSeq_loc >	CBlastQuerySourceBioseqSet::GetSeqLoc (int index) const
	Return the CSeq_loc associated with a sequence.
virtual const objects::CSeq_id *	CBlastQuerySourceBioseqSet::GetSeqId (int index) const
	Return the sequence identifier associated with a sequence.
virtual Uint4	CBlastQuerySourceBioseqSet::GetGeneticCodeId (int index) const
	Retrieve the genetic code associated with a sequence.
virtual SBlastSequence	CBlastQuerySourceBioseqSet::GetBlastSequence (int index, EBlastEncoding encoding, objects::ENa_strand strand, ESentinelType sentinel, string *warnings=0) const
	Return the sequence data for a sequence.
virtual TSeqPos	CBlastQuerySourceBioseqSet::GetLength (int index) const
	Return the length of a sequence.
virtual string	CBlastQuerySourceBioseqSet::GetTitle (int index) const
	Return the title of a sequence.
void	CBlastQuerySourceBioseqSet::x_BioseqSanityCheck (const objects::CBioseq &bs)
	Auxiliary method to do some sanity checks on the input Bioseqs.
	CBl2Seq::CBl2Seq (const SSeqLoc &query, const SSeqLoc &subject, EProgram p)
	Constructor to compare 2 sequences with default options.
	CBl2Seq::CBl2Seq (const SSeqLoc &query, const SSeqLoc &subject, CBlastOptionsHandle &opts)
	Constructor to compare 2 sequences with specified options.
	CBl2Seq::CBl2Seq (const SSeqLoc &query, const TSeqLocVector &subjects, EProgram p)
	Constructor to compare query against all subject sequences with default options.
	CBl2Seq::CBl2Seq (const SSeqLoc &query, const TSeqLocVector &subjects, CBlastOptionsHandle &opts)
	Constructor to compare query against all subject sequences with specified options.
	CBl2Seq::CBl2Seq (const TSeqLocVector &queries, const TSeqLocVector &subjects, EProgram p)
	Constructor to allow query concatenation with default options.
	CBl2Seq::CBl2Seq (const TSeqLocVector &queries, const TSeqLocVector &subjects, CBlastOptionsHandle &opts)
	Constructor to allow query concatenation with specified options.
void	CBl2Seq::x_Init (const TSeqLocVector &queries, const TSeqLocVector &subjs)
	Common initialization code for all c-tors.
virtual	CBl2Seq::~CBl2Seq ()
	Destructor.
void	CBl2Seq::x_ResetQueryDs ()
	Resets query data structures.
void	CBl2Seq::x_ResetSubjectDs ()
	Resets subject data structures.
virtual TSeqAlignVector	CBl2Seq::Run ()
	Perform BLAST search Assuming N queries and M subjects, the structure of the returned vector is as follows, with types indicated in parenthesis: TSeqAlignVector = [ {Results for query 1 and subject 1 (Seq-align-set)}, {Results for query 1 and subject 2 (Seq-align-set)}, .
void	CBl2Seq::x_BuildAncillaryData (const TSeqAlignVector &alignments)
	Populate the internal m_AncillaryData member.
static void	CBl2Seq::x_SimplifyTSeqLocVector (const TSeqLocVector &slv, vector< CConstRef< objects::CSeq_id > > &query_ids)
	Convert the TSeqLocVector to a vector of Seq-ids.
CRef< CSearchResultSet >	CBl2Seq::RunEx ()
	Performs the same functionality as Run(), but it returns a different data type.
virtual NCBI_DEPRECATED void	CBl2Seq::RunWithoutSeqalignGeneration ()
	Runs the search but does not produce seqalign output (useful if the raw search results are needed, rather than a set of complete Seq-aligns).
virtual void	CBl2Seq::SetupSearch ()
	Process the queries, do setup, and build the lookup table.
virtual void	CBl2Seq::RunFullSearch ()
	Creates a BlastHSPStream and calls the engine.
virtual TSeqAlignVector	CBl2Seq::x_Results2SeqAlign ()
	Return a seqalign list for each query/subject pair, even if it is empty.
TSeqLocInfoVector	CBl2Seq::GetFilteredQueryRegions () const
	Retrieves regions filtered on the query/queries.
	CBlastAdvancedProteinOptionsHandle::CBlastAdvancedProteinOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
	Creates object with default options set.
void	CBlastAdvancedProteinOptionsHandle::SetGappedExtensionDefaults ()
	Overrides SetGappedExtensionDefaults for advanced blastp options.
void	CBlastAdvancedProteinOptionsHandle::SetQueryOptionDefaults ()
	Overrides SetQueryOptionDefaults for advanced blastp options to disable filtering.
virtual void	CQuerySetUpOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CBLAST_SequenceBlk::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CBlastQueryInfo::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CLookupTableOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CLookupTableWrap::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CBlastInitialWordOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CBlastInitialWordParameters::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CBlast_ExtendWord::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CBlastExtensionOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CBlastExtensionParameters::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CBlastHitSavingOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CBlastHitSavingParameters::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CPSIBlastOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CBlastGapAlignStruct::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CBlastEffectiveLengthsOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CBlastEffectiveLengthsParameters::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CBlastScoreBlk::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CBlastScoringOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CBlastScoringParameters::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CBlastDatabaseOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CPSIMsa::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CPSIMatrix::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CPSIDiagnosticsRequest::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CPSIDiagnosticsResponse::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CBlastSeqSrc::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
virtual void	CBlastSeqSrcIterator::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CBlast_Message::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CBlastHSPResults::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CBlastMaskLoc::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CBlastSeqLoc::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
virtual void	CSBlastProgress::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information.
	CAutomaticGenCodeSingleton::CAutomaticGenCodeSingleton ()
	Default constructor.
	CAutomaticGenCodeSingleton::~CAutomaticGenCodeSingleton ()
	destructor
void	TQueryMessages::SetQueryId (const string &id)
	Set the query id as a string.
string	TQueryMessages::GetQueryId () const
	Get the query id as a string.
void	TQueryMessages::Combine (const TQueryMessages &other)
	Combine other messages with these.
bool	TSearchMessages::HasMessages () const
string	TSearchMessages::ToString () const
	Converts messages to a string, which is returned.
void	TSearchMessages::Combine (const TSearchMessages &other_msgs)
	Combine another set of search messages with this one.
void	TSearchMessages::RemoveDuplicates ()
	Find and remove redundant messages.
void	TSearchMessages::AddMessageAllQueries (EBlastSeverity severity, int error_id, const string &message)
	Add a message for all queries.
	CIndexedDb::CIndexedDb (const string &indexname, BlastSeqSrc *db)
	Object constructor.
void	CIndexedDb::SetNumThreads (size_t n_threads)
	Set the number of threads for indexed search.
	CIndexedDb::~CIndexedDb ()
	Object destructor.
virtual void *	CPreSearchThread::Main (void)
	Main procedure of the thread.
void	CIndexedDb::PreSearch (BLAST_SequenceBlk *queries, BlastSeqLoc *locs, LookupTableOptions *lut_options, BlastInitialWordOptions *word_options)
	Invoke the seed search procedure on each of the loaded indices.
unsigned long	CIndexedDb::GetResults (CDbIndex::TSeqNum oid, CDbIndex::TSeqNum chunk, BlastInitHitList *init_hitlist) const
	Return results corresponding to a given subject sequence and chunk.
	CBlastNucleotideOptionsHandle::CBlastNucleotideOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
	Creates object with default options set.
virtual void	CBlastNucleotideOptionsHandle::SetDefaults ()
	Sets Defaults.
void	CBlastNucleotideOptionsHandle::SetTraditionalBlastnDefaults ()
	Sets TraditionalBlastnDefaults.
void	CBlastNucleotideOptionsHandle::SetTraditionalMegablastDefaults ()
	Sets TraditionalMegablastDefaults.
virtual void	CBlastNucleotideOptionsHandle::SetLookupTableDefaults ()
	Overrides LookupTableDefaults for nucleotide options.
virtual void	CBlastNucleotideOptionsHandle::SetMBLookupTableDefaults ()
	Overrides MBLookupTableDefaults for nucleotide options.
virtual void	CBlastNucleotideOptionsHandle::SetQueryOptionDefaults ()
	Overrides QueryOptionDefaults for nucleotide options.
virtual void	CBlastNucleotideOptionsHandle::SetInitialWordOptionsDefaults ()
	Overrides InitialWordOptionsDefaults for nucleotide options.
virtual void	CBlastNucleotideOptionsHandle::SetMBInitialWordOptionsDefaults ()
	Overrides MBInitialWordOptionsDefaults for nucleotide options.
virtual void	CBlastNucleotideOptionsHandle::SetGappedExtensionDefaults ()
	Overrides GappedExtensionDefaults for nucleotide options.
virtual void	CBlastNucleotideOptionsHandle::SetMBGappedExtensionDefaults ()
	Overrides MBGappedExtensionDefaults for nucleotide options.
virtual void	CBlastNucleotideOptionsHandle::SetScoringOptionsDefaults ()
	Overrides ScoringOptionsDefaults for nucleotide options.
virtual void	CBlastNucleotideOptionsHandle::SetMBScoringOptionsDefaults ()
	Overrides MBScoringOptionsDefaults for nucleotide options.
virtual void	CBlastNucleotideOptionsHandle::SetHitSavingOptionsDefaults ()
	Overrides HitSavingOptionsDefaults for nucleotide options.
virtual void	CBlastNucleotideOptionsHandle::SetMBHitSavingOptionsDefaults ()
	Overrides MBHitSavingOptionsDefaults for nucleotide options.
virtual void	CBlastNucleotideOptionsHandle::SetEffectiveLengthsOptionsDefaults ()
	Overrides EffectiveLengthsOptionsDefaults for nucleotide options.
virtual void	CBlastNucleotideOptionsHandle::SetSubjectSequenceOptionsDefaults ()
	Overrides SubjectSequenceOptionsDefaults for nucleotide options.
	CBlastQuerySourceOM::CBlastQuerySourceOM (TSeqLocVector &v, EBlastProgramType prog)
	Constructor which takes a TSeqLocVector.
	CBlastQuerySourceOM::CBlastQuerySourceOM (TSeqLocVector &v, const CBlastOptions *opts)
	Constructor which takes a TSeqLocVector.
	CBlastQuerySourceOM::CBlastQuerySourceOM (CBlastQueryVector &v, EBlastProgramType prog)
	Constructor which takes a CBlastQueryVector.
	CBlastQuerySourceOM::CBlastQuerySourceOM (CBlastQueryVector &v, const CBlastOptions *opts)
	Constructor which takes a CBlastQueryVector.
void	CBlastQuerySourceOM::x_AutoDetectGeneticCodes (void)
	Tries to extract the genetic code using the CScope, if it succeeds, it supercedes what's specified in the {SSeqLoc,CBlastSearchQuery}genetic_code_id field.
void	CBlastQuerySourceOM::x_CalculateMasks ()
	Performs filtering on the query sequences to calculate the masked locations.
virtual	CBlastQuerySourceOM::~CBlastQuerySourceOM ()
	dtor which determines if the internal pointer to its data should be deleted or not.
virtual objects::ENa_strand	CBlastQuerySourceOM::GetStrand (int i) const
	Return strand for a sequence.
virtual TMaskedQueryRegions	CBlastQuerySourceOM::GetMaskedRegions (int i)
	Return the filtered (masked) regions for a sequence.
virtual CConstRef< objects::CSeq_loc >	CBlastQuerySourceOM::GetMask (int i)
	Return the filtered (masked) regions for a sequence.
virtual CConstRef< objects::CSeq_loc >	CBlastQuerySourceOM::GetSeqLoc (int i) const
	Return the CSeq_loc associated with a sequence.
virtual const objects::CSeq_id *	CBlastQuerySourceOM::GetSeqId (int index) const
	Return the sequence identifier associated with a sequence.
virtual Uint4	CBlastQuerySourceOM::GetGeneticCodeId (int index) const
	Retrieve the genetic code associated with a sequence.
virtual SBlastSequence	CBlastQuerySourceOM::GetBlastSequence (int i, EBlastEncoding encoding, objects::ENa_strand strand, ESentinelType sentinel, string *warnings=0) const
	Return the sequence data for a sequence.
virtual TSeqPos	CBlastQuerySourceOM::GetLength (int i) const
	Return the length of a sequence.
virtual string	CBlastQuerySourceOM::GetTitle (int index) const
	Return the title of a sequence.
virtual TSeqPos	CBlastQuerySourceOM::Size () const
	Return the number of elements in the sequence container.
	CBlastOptionsBuilder::CBlastOptionsBuilder (const string &program, const string &service, CBlastOptions::EAPILocality locality=CBlastOptions::eLocal)
	Constructor.
static EProgram	CBlastOptionsBuilder::ComputeProgram (const string &program, const string &service)
	Compute the EProgram value to use for this search.
void	CBlastOptionsBuilder::x_ProcessOneOption (CBlastOptionsHandle &opts, objects::CBlast4_parameter &p)
	Apply the value of one option to the CBlastOptionsHandle.
void	CBlastOptionsBuilder::x_ProcessOptions (CBlastOptionsHandle &opts, const TValueList *L)
	Apply the value of all options to the CBlastOptionsHandle.
void	CBlastOptionsBuilder::x_ApplyInteractions (CBlastOptionsHandle &boh)
	Apply values directly to BlastOptions object.
static EProgram	CBlastOptionsBuilder::AdjustProgram (const TValueList *L, EProgram program, const string &program_string)
	Adjust the EProgram based on option values.
CRef< CBlastOptionsHandle >	CBlastOptionsBuilder::GetSearchOptions (const objects::CBlast4_parameters *aopts, const objects::CBlast4_parameters *popts, string *task_name=NULL)
	Build and return options as a CBlastOptionsHandle.
bool	CBlastOptionsBuilder::HaveEntrezQuery ()
	Check whether an Entrez query is specified.
string	CBlastOptionsBuilder::GetEntrezQuery ()
	Get the Entrez query.
bool	CBlastOptionsBuilder::HaveFirstDbSeq ()
	Check whether an OID range start point is specified.
int	CBlastOptionsBuilder::GetFirstDbSeq ()
	Get the OID range start point.
bool	CBlastOptionsBuilder::HaveFinalDbSeq ()
	Check whether an OID range end point is specified.
int	CBlastOptionsBuilder::GetFinalDbSeq ()
	Get the OID range end point.
bool	CBlastOptionsBuilder::HaveGiList ()
	Check whether a GI list is specified.
list< int >	CBlastOptionsBuilder::GetGiList ()
	Get the GI list.
bool	CBlastOptionsBuilder::HasDbFilteringAlgorithmId ()
	Check whether a database filtering algorithm ID is specified.
int	CBlastOptionsBuilder::GetDbFilteringAlgorithmId ()
	Get the database filtering algorithm ID.
bool	CBlastOptionsBuilder::HaveNegativeGiList ()
	Check whether a negative GI list is specified.
list< int >	CBlastOptionsBuilder::GetNegativeGiList ()
	Get the negative GI list.
bool	CBlastOptionsBuilder::HaveQueryMasks ()
	Check whether query masks are specified.
TMaskList	CBlastOptionsBuilder::GetQueryMasks ()
	Get the query masks.
void	CBlastOptionsBuilder::SetIgnoreUnsupportedOptions (bool ignore)
	Set the 'ignore unsupported options' flag.
	CBlastOptions::CBlastOptions (EAPILocality locality=eLocal)
	Constructor which allows specification of local or remote version of the options (might change in the future).
	CBlastOptions::~CBlastOptions ()
	Destructor.
CRef< CBlastOptions >	CBlastOptions::Clone () const
	Explicit deep copy of the Blast options object.
EAPILocality	CBlastOptions::GetLocality () const
	Return the locality used when the object was created.
void	CBlastOptionsRemote::SetValue (EBlastOptIdx opt, const EProgram &x)
void	CBlastOptionsRemote::SetValue (EBlastOptIdx opt, const int &x)
void	CBlastOptionsRemote::SetValue (EBlastOptIdx opt, const double &x)
void	CBlastOptionsRemote::SetValue (EBlastOptIdx opt, const char *x)
void	CBlastOptionsRemote::SetValue (EBlastOptIdx opt, const TSeqLocVector &x)
void	CBlastOptionsRemote::SetValue (EBlastOptIdx opt, const ESeedContainerType &x)
void	CBlastOptionsRemote::SetValue (EBlastOptIdx opt, const bool &x)
void	CBlastOptionsRemote::SetValue (EBlastOptIdx opt, const Int8 &x)
const CBlastOptionsMemento *	CBlastOptions::CreateSnapshot () const
	Create a snapshot of the state of this object for internal use of its data structures (BLAST C++ APIs only).
bool	CBlastOptions::operator== (const CBlastOptions &rhs) const
bool	CBlastOptions::operator!= (const CBlastOptions &rhs) const
bool	CBlastOptions::Validate () const
	Validate the options.
EProgram	CBlastOptions::GetProgram () const
	Returns the task this object is best suited for.
EBlastProgramType	CBlastOptions::GetProgramType () const
	Returns the CORE BLAST notion of program type.
void	CBlastOptions::SetProgram (EProgram p)
	Sets the task this object is best suited for.
double	CBlastOptions::GetWordThreshold () const
	Returns WordThreshold.
void	CBlastOptions::SetWordThreshold (double w)
	Sets WordThreshold.
ELookupTableType	CBlastOptions::GetLookupTableType () const
void	CBlastOptions::SetLookupTableType (ELookupTableType type)
int	CBlastOptions::GetWordSize () const
void	CBlastOptions::SetWordSize (int ws)
unsigned char	CBlastOptions::GetMBTemplateLength () const
	Megablast only lookup table options.
void	CBlastOptions::SetMBTemplateLength (unsigned char len)
unsigned char	CBlastOptions::GetMBTemplateType () const
void	CBlastOptions::SetMBTemplateType (unsigned char type)
void	CBlastOptions::ClearFilterOptions ()
NCBI_DEPRECATED char *	CBlastOptions::GetFilterString () const
	Return the filtering string used.
NCBI_DEPRECATED void	CBlastOptions::SetFilterString (const char *f, bool clear=true)
bool	CBlastOptions::GetMaskAtHash () const
void	CBlastOptions::SetMaskAtHash (bool val=true)
bool	CBlastOptions::GetDustFiltering () const
void	CBlastOptions::SetDustFiltering (bool val=true)
int	CBlastOptions::GetDustFilteringLevel () const
void	CBlastOptions::SetDustFilteringLevel (int m)
int	CBlastOptions::GetDustFilteringWindow () const
void	CBlastOptions::SetDustFilteringWindow (int m)
int	CBlastOptions::GetDustFilteringLinker () const
void	CBlastOptions::SetDustFilteringLinker (int m)
bool	CBlastOptions::GetSegFiltering () const
void	CBlastOptions::SetSegFiltering (bool val=true)
int	CBlastOptions::GetSegFilteringWindow () const
void	CBlastOptions::SetSegFilteringWindow (int m)
double	CBlastOptions::GetSegFilteringLocut () const
void	CBlastOptions::SetSegFilteringLocut (double m)
double	CBlastOptions::GetSegFilteringHicut () const
void	CBlastOptions::SetSegFilteringHicut (double m)
bool	CBlastOptions::GetRepeatFiltering () const
	Returns true if repeat filtering is on.
void	CBlastOptions::SetRepeatFiltering (bool val=true)
	Turns on repeat filtering using the default repeat database, namely kDefaultRepeatFilterDb.
const char *	CBlastOptions::GetRepeatFilteringDB () const
	Returns the name of the repeat filtering database to use.
void	CBlastOptions::SetRepeatFilteringDB (const char *db)
	Sets the repeat filtering database to use.
int	CBlastOptions::GetWindowMaskerTaxId () const
	Returns the tax id used for the windowmasker database to use, if set via SetWindowMaskerTaxId (otherwise, returns 0).
void	CBlastOptions::SetWindowMaskerTaxId (int taxid)
	Sets the tax id to select an appropriate windowmasker database Conversion algorithm from tax id to database name is specific to NCBI, will not work outside NCBI.
const char *	CBlastOptions::GetWindowMaskerDatabase () const
	Return the name of the windowmasker database to use.
void	CBlastOptions::SetWindowMaskerDatabase (const char *db)
	Sets the windowmasker database to use.
objects::ENa_strand	CBlastOptions::GetStrandOption () const
void	CBlastOptions::SetStrandOption (objects::ENa_strand s)
int	CBlastOptions::GetQueryGeneticCode () const
void	CBlastOptions::SetQueryGeneticCode (int gc)
int	CBlastOptions::GetWindowSize () const
void	CBlastOptions::SetWindowSize (int w)
int	CBlastOptions::GetOffDiagonalRange () const
void	CBlastOptions::SetOffDiagonalRange (int r)
double	CBlastOptions::GetXDropoff () const
void	CBlastOptions::SetXDropoff (double x)
double	CBlastOptions::GetGapXDropoff () const
void	CBlastOptions::SetGapXDropoff (double x)
double	CBlastOptions::GetGapXDropoffFinal () const
void	CBlastOptions::SetGapXDropoffFinal (double x)
double	CBlastOptions::GetGapTrigger () const
void	CBlastOptions::SetGapTrigger (double g)
EBlastPrelimGapExt	CBlastOptions::GetGapExtnAlgorithm () const
void	CBlastOptions::SetGapExtnAlgorithm (EBlastPrelimGapExt a)
EBlastTbackExt	CBlastOptions::GetGapTracebackAlgorithm () const
void	CBlastOptions::SetGapTracebackAlgorithm (EBlastTbackExt a)
ECompoAdjustModes	CBlastOptions::GetCompositionBasedStats () const
void	CBlastOptions::SetCompositionBasedStats (ECompoAdjustModes mode)
bool	CBlastOptions::GetSmithWatermanMode () const
void	CBlastOptions::SetSmithWatermanMode (bool m=true)
int	CBlastOptions::GetUnifiedP () const
void	CBlastOptions::SetUnifiedP (int u=0)
int	CBlastOptions::GetHitlistSize () const
void	CBlastOptions::SetHitlistSize (int s)
int	CBlastOptions::GetMaxNumHspPerSequence () const
void	CBlastOptions::SetMaxNumHspPerSequence (int m)
int	CBlastOptions::GetCullingLimit () const
void	CBlastOptions::SetCullingLimit (int s)
double	CBlastOptions::GetBestHitOverhang () const
void	CBlastOptions::SetBestHitOverhang (double overhang)
double	CBlastOptions::GetBestHitScoreEdge () const
void	CBlastOptions::SetBestHitScoreEdge (double score_edge)
double	CBlastOptions::GetEvalueThreshold () const
void	CBlastOptions::SetEvalueThreshold (double eval)
int	CBlastOptions::GetCutoffScore () const
void	CBlastOptions::SetCutoffScore (int s)
double	CBlastOptions::GetPercentIdentity () const
void	CBlastOptions::SetPercentIdentity (double p)
int	CBlastOptions::GetMinDiagSeparation () const
void	CBlastOptions::SetMinDiagSeparation (int d)
bool	CBlastOptions::GetSumStatisticsMode () const
	Sum statistics options.
void	CBlastOptions::SetSumStatisticsMode (bool m=true)
int	CBlastOptions::GetLongestIntronLength () const
	for linking HSPs with uneven gaps
void	CBlastOptions::SetLongestIntronLength (int l)
	for linking HSPs with uneven gaps
bool	CBlastOptions::GetGappedMode () const
	Returns true if gapped BLAST is set, false otherwise.
void	CBlastOptions::SetGappedMode (bool m=true)
const char *	CBlastOptions::GetMatrixName () const
void	CBlastOptions::SetMatrixName (const char *matrix)
int	CBlastOptions::GetMatchReward () const
void	CBlastOptions::SetMatchReward (int r)
int	CBlastOptions::GetMismatchPenalty () const
void	CBlastOptions::SetMismatchPenalty (int p)
int	CBlastOptions::GetGapOpeningCost () const
void	CBlastOptions::SetGapOpeningCost (int g)
int	CBlastOptions::GetGapExtensionCost () const
void	CBlastOptions::SetGapExtensionCost (int e)
int	CBlastOptions::GetFrameShiftPenalty () const
void	CBlastOptions::SetFrameShiftPenalty (int p)
bool	CBlastOptions::GetOutOfFrameMode () const
void	CBlastOptions::SetOutOfFrameMode (bool m=true)
Int8	CBlastOptions::GetDbLength () const
void	CBlastOptions::SetDbLength (Int8 l)
unsigned int	CBlastOptions::GetDbSeqNum () const
void	CBlastOptions::SetDbSeqNum (unsigned int n)
Int8	CBlastOptions::GetEffectiveSearchSpace () const
void	CBlastOptions::SetEffectiveSearchSpace (Int8 eff)
void	CBlastOptions::SetEffectiveSearchSpace (const vector< Int8 > &eff)
int	CBlastOptions::GetDbGeneticCode () const
void	CBlastOptions::SetDbGeneticCode (int gc)
const char *	CBlastOptions::GetPHIPattern () const
void	CBlastOptions::SetPHIPattern (const char *pattern, bool is_dna)
double	CBlastOptions::GetInclusionThreshold () const
void	CBlastOptions::SetInclusionThreshold (double u)
int	CBlastOptions::GetPseudoCount () const
void	CBlastOptions::SetPseudoCount (int u)
void	CBlastOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Allows to dump a snapshot of the object.
void	CBlastOptions::DoneDefaults () const
TBlast4Opts *	CBlastOptions::GetBlast4AlgoOpts ()
bool	CBlastOptions::GetUseIndex () const
bool	CBlastOptions::GetForceIndex () const
bool	CBlastOptions::GetMBIndexLoaded () const
const string	CBlastOptions::GetIndexName () const
void	CBlastOptions::SetUseIndex (bool use_index=true, const string &index_name="", bool force_index=false)
void	CBlastOptions::SetMBIndexLoaded (bool index_loaded=true)
QuerySetUpOptions *	CBlastOptions::GetQueryOpts () const
	Returns QuerySetUpOptions for eLocal objects, NULL for eRemote.
LookupTableOptions *	CBlastOptions::GetLutOpts () const
	Returns LookupTableOptions for eLocal objects, NULL for eRemote.
BlastInitialWordOptions *	CBlastOptions::GetInitWordOpts () const
	Returns BlastInitialWordOptions for eLocal objects, NULL for eRemote.
BlastExtensionOptions *	CBlastOptions::GetExtnOpts () const
	Returns BlastExtensionOptions for eLocal objects, NULL for eRemote.
BlastHitSavingOptions *	CBlastOptions::GetHitSaveOpts () const
	Returns BlastHitSavingOptions for eLocal objects, NULL for eRemote.
PSIBlastOptions *	CBlastOptions::GetPSIBlastOpts () const
	Returns PSIBlastOptions for eLocal objects, NULL for eRemote.
BlastDatabaseOptions *	CBlastOptions::GetDbOpts () const
	Returns BlastDatabaseOptions for eLocal objects, NULL for eRemote.
BlastScoringOptions *	CBlastOptions::GetScoringOpts () const
	Returns BlastScoringOptions for eLocal objects, NULL for eRemote.
BlastEffectiveLengthsOptions *	CBlastOptions::GetEffLenOpts () const
	Returns BlastEffectiveLengthsOptions for eLocal objects, NULL for eRemote.
void	CBlastOptions::x_Throwx (const string &msg) const
	Auxiliary to throw CBlastExceptions.
void	CBlastOptions::SetDefaultsMode (bool dmode)
	If this is true, remote options will ignore "Set" calls.
bool	CBlastOptions::GetDefaultsMode () const
void	CBlastOptions::x_DoDeepCopy (const CBlastOptions &opts)
	Perform a "deep copy" of Blast options.
	CBlastOptionsHandle::CBlastOptionsHandle (EAPILocality locality)
	Default c-tor.
virtual void	CBlastOptionsHandle::SetDefaults ()
	Resets the state of the object to all default values.
bool	CBlastOptionsHandle::Validate () const
	Validate the options contained in this object.
char *	CBlastOptionsHandle::GetFilterString () const
	Returns FilterString.
void	CBlastOptionsHandle::SetFilterString (const char *f, bool clear=true)
	Sets FilterString.
static CBlastOptionsHandle *	CBlastOptionsFactory::Create (EProgram program, EAPILocality locality=CBlastOptions::eLocal)
	Creates an options handle object configured with default options for the requested program, throws an exception if an unsupported program is requested.
static set< string >	CBlastOptionsFactory::GetTasks (ETaskSets choice=eAll)
	Retrieve the set of supported tasks.
static string	CBlastOptionsFactory::GetDocumentation (const string &task_name)
	Return the documentation for the provided task.
static CBlastOptionsHandle *	CBlastOptionsFactory::CreateTask (string task, EAPILocality locality=CBlastOptions::eLocal)
	Creates an options handle object configured with default options for the requested task, throws an exception if an unsupported task is requested.
	CBlastOptionsLocal::CBlastOptionsLocal ()
	CBlastOptionsLocal::~CBlastOptionsLocal ()
	CBlastOptionsLocal::CBlastOptionsLocal (const CBlastOptionsLocal &optsLocal)
	Copy constructor.
CBlastOptionsLocal &	CBlastOptionsLocal::operator= (const CBlastOptionsLocal &optsLocal)
	Assignment operator.
void	CBlastOptionsLocal::x_DoDeepCopy (const CBlastOptionsLocal &optsLocal)
	Perform a "deep copy" of local Blast options.
static void	CBlastOptionsLocal::x_Copy_CQuerySetUpOptions (CQuerySetUpOptions &queryOptsDst, const CQuerySetUpOptions &queryOptsSrc)
	Get a copy of CQuerySetUpOptions.
static void	CBlastOptionsLocal::x_Copy_CLookupTableOptions (CLookupTableOptions &lutOptsDst, const CLookupTableOptions &lutOptsSrc)
	Get a copy of CLookupTableOptions.
static void	CBlastOptionsLocal::x_Copy_CBlastInitialWordOptions (CBlastInitialWordOptions &initWordOptsDst, const CBlastInitialWordOptions &initWordOptsSrc)
	Get a copy of CBlastInitialWordOptions.
static void	CBlastOptionsLocal::x_Copy_CBlastExtensionOptions (CBlastExtensionOptions &extnOptsDst, const CBlastExtensionOptions &extnOptsSrc)
	Get a copy of CBlastExtensionOptions.
static void	CBlastOptionsLocal::x_Copy_CBlastHitSavingOptions (CBlastHitSavingOptions &hitSaveOptsDst, const CBlastHitSavingOptions &hitSaveOptsSrc)
	Get a copy of CBlastHitSavingOptions.
static void	CBlastOptionsLocal::x_Copy_CPSIBlastOptions (CPSIBlastOptions &psiBlastOptsDst, const CPSIBlastOptions &psiBlastOptsSrc)
	Get a copy of CPSIBlastOptions.
static void	CBlastOptionsLocal::x_Copy_CBlastDatabaseOptions (CBlastDatabaseOptions &dbOptsDst, const CBlastDatabaseOptions &dbOptsSrc)
	Get a copy of CBlastDatabaseOptions.
static void	CBlastOptionsLocal::x_Copy_CBlastScoringOptions (CBlastScoringOptions &scoringOptsDst, const CBlastScoringOptions &scoringOptsSrc)
	Get a copy of CBlastScoringOptions.
static void	CBlastOptionsLocal::x_Copy_CBlastEffectiveLengthsOptions (CBlastEffectiveLengthsOptions &effLenOptsDst, const CBlastEffectiveLengthsOptions &effLenOptsSrc)
	Get a copy of CBlastEffectiveLengthsOptions.
void	CBlastOptionsLocal::SetDbGeneticCode (int gc)
EBlastProgramType	CBlastOptionsLocal::GetProgramType () const
bool	CBlastOptionsLocal::Validate () const
	Validate the options.
void	CBlastOptionsLocal::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Allows to dump a snapshot of the object.
bool	CBlastOptionsLocal::operator== (const CBlastOptionsLocal &rhs) const
bool	CBlastOptionsLocal::operator!= (const CBlastOptionsLocal &rhs) const
EProgram	CBlastOptionsLocal::GetProgram () const
	Accessors/Mutators for individual options.
void	CBlastOptionsLocal::SetProgram (EProgram p)
const char *	CBlastOptionsLocal::GetMatrixName () const
void	CBlastOptionsLocal::SetMatrixName (const char *matrix)
double	CBlastOptionsLocal::GetWordThreshold () const
void	CBlastOptionsLocal::SetWordThreshold (double w)
ELookupTableType	CBlastOptionsLocal::GetLookupTableType () const
void	CBlastOptionsLocal::SetLookupTableType (ELookupTableType type)
int	CBlastOptionsLocal::GetWordSize () const
void	CBlastOptionsLocal::SetWordSize (int ws)
unsigned char	CBlastOptionsLocal::GetMBTemplateLength () const
	Megablast only lookup table options.
void	CBlastOptionsLocal::SetMBTemplateLength (unsigned char len)
unsigned char	CBlastOptionsLocal::GetMBTemplateType () const
void	CBlastOptionsLocal::SetMBTemplateType (unsigned char type)
char *	CBlastOptionsLocal::GetFilterString () const
void	CBlastOptionsLocal::SetFilterString (const char *f)
bool	CBlastOptionsLocal::GetMaskAtHash () const
void	CBlastOptionsLocal::SetMaskAtHash (bool val=true)
bool	CBlastOptionsLocal::GetDustFiltering () const
void	CBlastOptionsLocal::SetDustFiltering (bool val=true)
int	CBlastOptionsLocal::GetDustFilteringLevel () const
void	CBlastOptionsLocal::SetDustFilteringLevel (int m)
int	CBlastOptionsLocal::GetDustFilteringWindow () const
void	CBlastOptionsLocal::SetDustFilteringWindow (int m)
int	CBlastOptionsLocal::GetDustFilteringLinker () const
void	CBlastOptionsLocal::SetDustFilteringLinker (int m)
bool	CBlastOptionsLocal::GetSegFiltering () const
void	CBlastOptionsLocal::SetSegFiltering (bool val=true)
int	CBlastOptionsLocal::GetSegFilteringWindow () const
void	CBlastOptionsLocal::SetSegFilteringWindow (int m)
double	CBlastOptionsLocal::GetSegFilteringLocut () const
void	CBlastOptionsLocal::SetSegFilteringLocut (double m)
double	CBlastOptionsLocal::GetSegFilteringHicut () const
void	CBlastOptionsLocal::SetSegFilteringHicut (double m)
bool	CBlastOptionsLocal::GetRepeatFiltering () const
void	CBlastOptionsLocal::SetRepeatFiltering (bool val=true)
const char *	CBlastOptionsLocal::GetRepeatFilteringDB () const
void	CBlastOptionsLocal::SetRepeatFilteringDB (const char *db)
int	CBlastOptionsLocal::GetWindowMaskerTaxId () const
void	CBlastOptionsLocal::SetWindowMaskerTaxId (int taxid)
const char *	CBlastOptionsLocal::GetWindowMaskerDatabase () const
void	CBlastOptionsLocal::SetWindowMaskerDatabase (const char *db)
objects::ENa_strand	CBlastOptionsLocal::GetStrandOption () const
void	CBlastOptionsLocal::SetStrandOption (objects::ENa_strand s)
int	CBlastOptionsLocal::GetQueryGeneticCode () const
void	CBlastOptionsLocal::SetQueryGeneticCode (int gc)
int	CBlastOptionsLocal::GetWindowSize () const
void	CBlastOptionsLocal::SetWindowSize (int w)
int	CBlastOptionsLocal::GetOffDiagonalRange () const
void	CBlastOptionsLocal::SetOffDiagonalRange (int r)
double	CBlastOptionsLocal::GetXDropoff () const
void	CBlastOptionsLocal::SetXDropoff (double x)
double	CBlastOptionsLocal::GetGapTrigger () const
void	CBlastOptionsLocal::SetGapTrigger (double g)
double	CBlastOptionsLocal::GetGapXDropoff () const
void	CBlastOptionsLocal::SetGapXDropoff (double x)
double	CBlastOptionsLocal::GetGapXDropoffFinal () const
void	CBlastOptionsLocal::SetGapXDropoffFinal (double x)
EBlastPrelimGapExt	CBlastOptionsLocal::GetGapExtnAlgorithm () const
void	CBlastOptionsLocal::SetGapExtnAlgorithm (EBlastPrelimGapExt a)
EBlastTbackExt	CBlastOptionsLocal::GetGapTracebackAlgorithm () const
void	CBlastOptionsLocal::SetGapTracebackAlgorithm (EBlastTbackExt a)
ECompoAdjustModes	CBlastOptionsLocal::GetCompositionBasedStats () const
void	CBlastOptionsLocal::SetCompositionBasedStats (ECompoAdjustModes mode)
bool	CBlastOptionsLocal::GetSmithWatermanMode () const
void	CBlastOptionsLocal::SetSmithWatermanMode (bool m=true)
int	CBlastOptionsLocal::GetUnifiedP () const
void	CBlastOptionsLocal::SetUnifiedP (int u=0)
int	CBlastOptionsLocal::GetHitlistSize () const
void	CBlastOptionsLocal::SetHitlistSize (int s)
int	CBlastOptionsLocal::GetMaxNumHspPerSequence () const
void	CBlastOptionsLocal::SetMaxNumHspPerSequence (int m)
int	CBlastOptionsLocal::GetCullingLimit () const
void	CBlastOptionsLocal::SetCullingLimit (int s)
double	CBlastOptionsLocal::GetBestHitScoreEdge () const
void	CBlastOptionsLocal::SetBestHitScoreEdge (double score_edge)
double	CBlastOptionsLocal::GetBestHitOverhang () const
void	CBlastOptionsLocal::SetBestHitOverhang (double s)
double	CBlastOptionsLocal::GetEvalueThreshold () const
void	CBlastOptionsLocal::SetEvalueThreshold (double eval)
int	CBlastOptionsLocal::GetCutoffScore () const
void	CBlastOptionsLocal::SetCutoffScore (int s)
double	CBlastOptionsLocal::GetPercentIdentity () const
void	CBlastOptionsLocal::SetPercentIdentity (double p)
int	CBlastOptionsLocal::GetMinDiagSeparation () const
void	CBlastOptionsLocal::SetMinDiagSeparation (int d)
bool	CBlastOptionsLocal::GetSumStatisticsMode () const
	Sum statistics options.
void	CBlastOptionsLocal::SetSumStatisticsMode (bool m=true)
int	CBlastOptionsLocal::GetLongestIntronLength () const
void	CBlastOptionsLocal::SetLongestIntronLength (int l)
bool	CBlastOptionsLocal::GetGappedMode () const
	Returns true if gapped BLAST is set, false otherwise.
void	CBlastOptionsLocal::SetGappedMode (bool m=true)
int	CBlastOptionsLocal::GetMatchReward () const
void	CBlastOptionsLocal::SetMatchReward (int r)
int	CBlastOptionsLocal::GetMismatchPenalty () const
void	CBlastOptionsLocal::SetMismatchPenalty (int p)
int	CBlastOptionsLocal::GetGapOpeningCost () const
void	CBlastOptionsLocal::SetGapOpeningCost (int g)
int	CBlastOptionsLocal::GetGapExtensionCost () const
void	CBlastOptionsLocal::SetGapExtensionCost (int e)
int	CBlastOptionsLocal::GetFrameShiftPenalty () const
void	CBlastOptionsLocal::SetFrameShiftPenalty (int p)
bool	CBlastOptionsLocal::GetOutOfFrameMode () const
void	CBlastOptionsLocal::SetOutOfFrameMode (bool m=true)
Int8	CBlastOptionsLocal::GetDbLength () const
void	CBlastOptionsLocal::SetDbLength (Int8 l)
unsigned int	CBlastOptionsLocal::GetDbSeqNum () const
void	CBlastOptionsLocal::SetDbSeqNum (unsigned int n)
Int8	CBlastOptionsLocal::GetEffectiveSearchSpace () const
void	CBlastOptionsLocal::SetEffectiveSearchSpace (Int8 eff)
void	CBlastOptionsLocal::SetEffectiveSearchSpace (const vector< Int8 > &eff)
int	CBlastOptionsLocal::GetDbGeneticCode () const
const char *	CBlastOptionsLocal::GetPHIPattern () const
double	CBlastOptionsLocal::GetInclusionThreshold () const
void	CBlastOptionsLocal::SetInclusionThreshold (double incthr)
int	CBlastOptionsLocal::GetPseudoCount () const
void	CBlastOptionsLocal::SetPseudoCount (int ps)
void	CBlastOptionsLocal::SetPHIPattern (const char *pattern, bool is_dna)
bool	CBlastOptionsLocal::GetUseIndex () const
bool	CBlastOptionsLocal::GetForceIndex () const
bool	CBlastOptionsLocal::GetMBIndexLoaded () const
const string	CBlastOptionsLocal::GetIndexName () const
void	CBlastOptionsLocal::SetMBIndexLoaded (bool index_loaded=true)
void	CBlastOptionsLocal::SetUseIndex (bool use_index=true, const string &index_name="", bool force_index=false)
	CBlastProteinOptionsHandle::CBlastProteinOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
	Creates object with default options set.
virtual void	CBlastProteinOptionsHandle::SetLookupTableDefaults ()
	Overrides LookupTableDefaults for protein options.
virtual void	CBlastProteinOptionsHandle::SetQueryOptionDefaults ()
	Overrides QueryOptionDefaults for protein options.
virtual void	CBlastProteinOptionsHandle::SetInitialWordOptionsDefaults ()
	Overrides InitialWordOptionsDefaults for protein options.
virtual void	CBlastProteinOptionsHandle::SetGappedExtensionDefaults ()
	Overrides GappedExtensionDefaults for protein options.
virtual void	CBlastProteinOptionsHandle::SetScoringOptionsDefaults ()
	Overrides ScoringOptionsDefaults for protein options.
virtual void	CBlastProteinOptionsHandle::SetHitSavingOptionsDefaults ()
	Overrides HitSavingOptionsDefaults for protein options.
virtual void	CBlastProteinOptionsHandle::SetEffectiveLengthsOptionsDefaults ()
	Overrides EffectiveLengthsOptionsDefaults for protein options.
virtual void	CBlastProteinOptionsHandle::SetSubjectSequenceOptionsDefaults ()
	Overrides SubjectSequenceOptionsDefaults for protein options.
	CBlastAncillaryData::CBlastAncillaryData (EBlastProgramType program_type, int query_number, const BlastScoreBlk *sbp, const BlastQueryInfo *query_info)
	constructor
	CBlastAncillaryData::CBlastAncillaryData (pair< double, double > lambda, pair< double, double > k, pair< double, double > h, Int8 effective_search_space, bool is_psiblast=false)
	Parametrized constructor taking pairs of values for ungapped and gapped Karlin-Altschul parameters as well as the effective search space.
	CBlastAncillaryData::~CBlastAncillaryData ()
	Destructor.
void	CBlastAncillaryData::do_copy (const CBlastAncillaryData &other)
	Workhorse for copy constructor and assignment operator.
	CSearchResults::CSearchResults (CConstRef< objects::CSeq_id > query, CRef< objects::CSeq_align_set > align, const TQueryMessages &errs, CRef< CBlastAncillaryData > ancillary_data, const TMaskedQueryRegions *query_masks=NULL, const string &rid=kEmptyStr, const SPHIQueryInfo *phi_query_info=NULL)
	Constructor.
	CSearchResults::~CSearchResults ()
	Our destructor.
void	CSearchResults::GetMaskedQueryRegions (TMaskedQueryRegions &flt_query_regions) const
	Retrieve the query regions which were masked by BLAST.
void	CSearchResults::SetMaskedQueryRegions (const TMaskedQueryRegions &flt_query_regions)
	Mutator for the masked query regions, intended to be used by internal BLAST APIs to populate this object.
TQueryMessages	CSearchResults::GetErrors (int min_severity=eBlastSevError) const
	Accessor for the error/warning messsages for this query.
string	CSearchResults::GetErrorStrings () const
	Retrieve a string with the query identifier followed by the errors produced, returns a empty string if HasErrors() returns false.
string	CSearchResults::GetWarningStrings () const
	Retrieve a string with the query identifier followed by the warnings produced, returns a empty string if HasWarnings() returns false.
bool	CSearchResults::HasErrors () const
	Returns true if there are errors among the results for this object.
bool	CSearchResults::HasWarnings () const
	Returns true if there are warnings among the results for this object.
bool	CSearchResults::HasAlignments () const
	Return true if there are any alignments for this query.
CConstRef< objects::CSeq_id >	CSearchResults::GetSeqId () const
	Accessor for the query's sequence identifier.
void	CSearchResults::GetSubjectMasks (TSeqLocInfoVector &subj_masks) const
	Retrieve the masked locations for the subject sequences in the contained alignment.
void	CSearchResults::SetSubjectMasks (const TSeqLocInfoVector &subj_masks)
	Set the masked locations for the subject sequences in the contained alignment.
CSearchResults &	CSearchResultSet::GetResults (size_type qi, size_type si)
	Retrieve results for a query-subject pair contained by this object.
const CSearchResults &	CSearchResultSet::GetResults (size_type qi, size_type si) const
	Retrieve results for a query-subject pair.
CConstRef< CSearchResults >	CSearchResultSet::operator[] (const objects::CSeq_id &ident) const
	Allow array-like access with CSeq_id indices to const CSearchResults contained by this object.
CRef< CSearchResults >	CSearchResultSet::operator[] (const objects::CSeq_id &ident)
	Allow array-like access with CSeq_id indices to CSearchResults contained by this object.
	CSearchResultSet::CSearchResultSet (EResultType res_type=eDatabaseSearch)
	Simplest constructor.
	CSearchResultSet::CSearchResultSet (TQueryIdVector ids, TSeqAlignVector aligns, TSearchMessages msg_vec, TAncillaryVector ancillary_data=TAncillaryVector(), const TSeqLocInfoVector *masks=NULL, EResultType res_type=eDatabaseSearch, const SPHIQueryInfo *phi_query_info=NULL)
	Parametrized constructor.
	CSearchResultSet::CSearchResultSet (TSeqAlignVector aligns, TSearchMessages msg_vec, EResultType res_type=eDatabaseSearch)
	Parametrized constructor.
void	CSearchResultSet::SetFilteredQueryRegions (const TSeqLocInfoVector &masks)
	Sets the filtered query regions.
void	CSearchResultSet::x_Init (TQueryIdVector &queries, TSeqAlignVector aligns, TSearchMessages msg_vec, TAncillaryVector ancillary_data, const TSeqLocInfoVector *query_masks, const SPHIQueryInfo *phi_query_info=NULL)
	Initialize the result set.
void	CSearchResultSet::push_back (value_type &element)
	Add a value to the back of this container.
void	CSearchResultSet::SetRID (const string &rid)
	Sets the RID for these results.
	CBlastRPSOptionsHandle::CBlastRPSOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
	Creates object with default options set.
virtual void	CBlastRPSOptionsHandle::SetLookupTableDefaults ()
	Overrides LookupTableDefaults for RPS-BLAST options.
virtual void	CBlastRPSOptionsHandle::SetQueryOptionDefaults ()
	Overrides QueryOptionDefaults for RPS-BLAST options.
virtual void	CBlastRPSOptionsHandle::SetInitialWordOptionsDefaults ()
	Overrides InitialWordOptionsDefaults for RPS-BLAST options.
virtual void	CBlastRPSOptionsHandle::SetGappedExtensionDefaults ()
	Overrides GappedExtensionDefaults for RPS-BLAST options.
virtual void	CBlastRPSOptionsHandle::SetScoringOptionsDefaults ()
	Overrides ScoringOptionsDefaults for RPS-BLAST options.
virtual void	CBlastRPSOptionsHandle::SetHitSavingOptionsDefaults ()
	Overrides HitSavingOptionsDefaults for RPS-BLAST options.
virtual void	CBlastRPSOptionsHandle::SetEffectiveLengthsOptionsDefaults ()
	Overrides EffectiveLengthsOptionsDefaults for RPS-BLAST options.
virtual void	CBlastRPSOptionsHandle::SetSubjectSequenceOptionsDefaults ()
	Overrides SubjectSequenceOptionsDefaults for RPS-BLAST options.
bool	CBlastQueryFilteredFrames::x_NeedsTrans ()
	Returns true if this program needs coordinate translation.
	CBlastQueryFilteredFrames::CBlastQueryFilteredFrames (EBlastProgramType program)
	Construct container for frame values and BlastSeqLocs for the specified search program.
	CBlastQueryFilteredFrames::CBlastQueryFilteredFrames (EBlastProgramType program, const TMaskedQueryRegions &mqr)
	Construct container for frame values and BlastSeqLocs from a TMaskedQueryRegions vector.
	CBlastQueryFilteredFrames::~CBlastQueryFilteredFrames ()
	Destructor; frees any BlastSeqLoc lists not released by the caller.
void	CBlastQueryFilteredFrames::Release (int frame)
	Release the BlastSeqLocs for a given frame.
void	CBlastQueryFilteredFrames::UseProteinCoords (TSeqPos dna_length)
	Adjusts all stored masks from nucleotide to protein offsets.
const set< ETranslationFrame > &	CBlastQueryFilteredFrames::ListFrames ()
	Returns the list of frame values for which this object contains masking information.
bool	CBlastQueryFilteredFrames::Empty ()
	Returns true if this object contains any masking information.
void	CBlastQueryFilteredFrames::x_VerifyFrame (int frame)
	Verify the specified frame value.
bool	CBlastQueryFilteredFrames::QueryHasMultipleFrames () const
	Check whether the query is multiframe for this type of search.
void	CBlastQueryFilteredFrames::AddSeqLoc (const objects::CSeq_interval &intv, int frame)
	Add a masked interval to the specified frame.
BlastSeqLoc **	CBlastQueryFilteredFrames::operator[] (int frame)
	Access the BlastSeqLocs for a given frame.
	CBlastxOptionsHandle::CBlastxOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
	Creates object with default options set.
void	CBlastxOptionsHandle::SetLookupTableDefaults ()
	Overrides LookupTableDefaults for blastx options.
void	CBlastxOptionsHandle::SetQueryOptionDefaults ()
	Overrides QueryOptionDefaults for blastx options.
void	CBlastxOptionsHandle::SetScoringOptionsDefaults ()
	Overrides ScoringOptionsDefaults for blastx options.
void	CBlastxOptionsHandle::SetHitSavingOptionsDefaults ()
	Overrides HitSavingOptionsDefaults for blastx options.
	CDiscNucleotideOptionsHandle::CDiscNucleotideOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
	Creates object with default options set.
void	CDiscNucleotideOptionsHandle::SetMBLookupTableDefaults ()
	Sets MBLookupTableDefaults.
void	CDiscNucleotideOptionsHandle::SetMBInitialWordOptionsDefaults ()
	Sets MBInitialWordOptionsDefaults.
void	CDiscNucleotideOptionsHandle::SetMBGappedExtensionDefaults ()
	Sets MBGappedExtensionDefaults.
void	CDiscNucleotideOptionsHandle::SetMBScoringOptionsDefaults ()
	Sets MBScoringOptionsDefaults.
void	CDiscNucleotideOptionsHandle::SetTraditionalBlastnDefaults ()
	NOTE: Unavailable for discontiguous megablast Exceptions: CBlastException  if this is called on an object configured for discontiguous megablast.
	CEffectiveSearchSpaceCalculator::CEffectiveSearchSpaceCalculator (CRef< IQueryFactory > query_factory, const CBlastOptions &options, Int4 db_num_seqs, Int8 db_num_bases, BlastScoreBlk *sbp=NULL)
	Constructor.
Int8	CEffectiveSearchSpaceCalculator::GetEffSearchSpace (size_t query_index=0) const
	Retrieve the effective search space calculated for a given query.
Int8	CEffectiveSearchSpaceCalculator::GetEffSearchSpaceForContext (size_t ctx_index) const
	Retrieve the effective search space calculated for a given query context.
BlastQueryInfo *	CEffectiveSearchSpaceCalculator::GetQueryInfo () const
	Retrieve the BlastQueryInfo structure that stores the effective search spaces for all queries.
	CLocalBlast::CLocalBlast (CRef< IQueryFactory > query_factory, CRef< CBlastOptionsHandle > opts_handle, const CSearchDatabase &dbinfo)
	Constructor with database description.
	CLocalBlast::CLocalBlast (CRef< IQueryFactory > query_factory, CRef< CBlastOptionsHandle > opts_handle, CRef< CLocalDbAdapter > db)
	Constructor with subject adapter (.
	CLocalBlast::CLocalBlast (CRef< IQueryFactory > query_factory, CRef< CBlastOptionsHandle > opts_handle, BlastSeqSrc *seqsrc, CRef< IBlastSeqInfoSrc > seqInfoSrc)
	Constructor with database description.
CRef< CSearchResultSet >	CLocalBlast::Run ()
	Executes the search.
	CLocalDbAdapter::CLocalDbAdapter (const CSearchDatabase &dbinfo)
	Constructor.
	CLocalDbAdapter::CLocalDbAdapter (CRef< CSeqDB > seqdb, int filtering_algorithm=-1)
	Constructor.
	CLocalDbAdapter::CLocalDbAdapter (CRef< IQueryFactory > subject_sequences, CConstRef< CBlastOptionsHandle > opts_handle)
	Constructor.
	CLocalDbAdapter::CLocalDbAdapter (BlastSeqSrc *seqSrc, CRef< IBlastSeqInfoSrc > seqInfoSrc)
	Constructor taking custom BlastSeqSrc and IBlastSeqInfoSrc objects.
virtual	CLocalDbAdapter::~CLocalDbAdapter ()
	Destructor.
void	CLocalDbAdapter::ResetBlastSeqSrcIteration ()
	This method should be called so that if the implementation has an internal "bookmark" of the chunks of the database it has assigned to different threads, this can be reset at the start of a PSI-BLAST iteration (or when reusing the same object to iterate over the database/subjects when the query is split).
BlastSeqSrc *	CLocalDbAdapter::MakeSeqSrc ()
	Retrieves or constructs the BlastSeqSrc.
CRef< CSeqDB >	CLocalDbAdapter::x_InitSeqDB (CConstRef< CSearchDatabase > dbinfo)
	Initialize a CSeqDB object from a CSearchDatabase object.
IBlastSeqInfoSrc *	CLocalDbAdapter::MakeSeqInfoSrc ()
	Retrieves or constructs the IBlastSeqInfoSrc.
bool	CLocalDbAdapter::IsProtein () const
	Returns true if this object represents protein or nucleotide sequences.
virtual CRef< ISeqSearch >	CLocalSearchFactory::GetSeqSearch ()
	Get an object to manage a local sequence search.
virtual CRef< IPssmSearch >	CLocalSearchFactory::GetPssmSearch ()
	Get an object to manage a remote PSSM search.
virtual CRef< CBlastOptionsHandle >	CLocalSearchFactory::GetOptions (EProgram)
	Get an options handle for a search of the specified type.
virtual CRef< CSearchResultSet >	CLocalSeqSearch::Run ()
	Run the search.
virtual void	CLocalSeqSearch::SetOptions (CRef< CBlastOptionsHandle > options)
	Configure the search.
virtual void	CLocalSeqSearch::SetSubject (CConstRef< CSearchDatabase > subject)
	Set the databases to search.
virtual void	CLocalSeqSearch::SetQueryFactory (CRef< IQueryFactory > query_factory)
	Set the factory which will return the queries to search for.
virtual void	CLocalPssmSearch::SetOptions (CRef< CBlastOptionsHandle > options)
	Configure this search.
virtual void	CLocalPssmSearch::SetSubject (CConstRef< CSearchDatabase > subject)
	Set the databases to search.
virtual void	CLocalPssmSearch::SetQuery (CRef< objects::CPssmWithParameters > pssm)
	Set the PSSM with which to search the database.
virtual CRef< CSearchResultSet >	CLocalPssmSearch::Run ()
	Run a single iteration of the search.
	CPsiBlastInputClustalW::CPsiBlastInputClustalW (CNcbiIstream &input_file, const PSIBlastOptions &opts, const char *matrix_name=NULL, const PSIDiagnosticsRequest *diags=NULL, const unsigned char *query=NULL, unsigned int query_length=0)
	Construct a concrete strategy, used to configure the CPssmEngine object.
virtual	CPsiBlastInputClustalW::~CPsiBlastInputClustalW ()
	virtual destructor
void	CPsiBlastInputClustalW::x_ReadAsciiMsa (CNcbiIstream &input_file)
	Reads the multiple sequence alignment from the input file.
void	CPsiBlastInputClustalW::x_ExtractQueryForPssm ()
	Extracts the query bioseq from m_SeqEntry.
void	CPsiBlastInputClustalW::Process ()
	The work to process the alignment is done here.
void	CPsiBlastInputClustalW::x_ValidateQueryInMsa ()
	Searches the query sequence (m_Query) in the aligned sequences (m_AsciiMsa) and moves the first instance it finds to the front of this data structure.
void	CPsiBlastInputClustalW::x_ExtractQueryFromMsa ()
	Extracts the query sequence from the multiple sequence alignment, assuming it's the first one, into m_Query.
void	CPsiBlastInputClustalW::x_CopyQueryToMsa ()
	Copies query sequence data to multiple alignment data structure.
void	CPsiBlastInputClustalW::x_ExtractAlignmentData ()
	Populates the multiple alignment data structure.
	CObjMgr_LocalQueryData::CObjMgr_LocalQueryData (TSeqLocVector *queries, const CBlastOptions *options)
	Ctor that takes a vector of SSeqLocs.
	CObjMgr_LocalQueryData::CObjMgr_LocalQueryData (CBlastQueryVector &queries, const CBlastOptions *options)
	Ctor that takes a CBlastQueryVector (preferred over TSeqLocVector).
virtual BLAST_SequenceBlk *	CObjMgr_LocalQueryData::GetSequenceBlk ()
	Accessor for the BLAST_SequenceBlk structure.
virtual BlastQueryInfo *	CObjMgr_LocalQueryData::GetQueryInfo ()
	Accessor for the BlastQueryInfo structure.
virtual size_t	CObjMgr_LocalQueryData::GetNumQueries ()
	Get the number of queries.
virtual CConstRef< CSeq_loc >	CObjMgr_LocalQueryData::GetSeq_loc (size_t index)
	Get the Seq_loc for the sequence indicated by index.
virtual size_t	CObjMgr_LocalQueryData::GetSeqLength (size_t index)
	Get the length of the sequence indicated by index.
	CObjMgr_RemoteQueryData::CObjMgr_RemoteQueryData (const TSeqLocVector *queries)
	Construct query data from a TSeqLocVector.
	CObjMgr_RemoteQueryData::CObjMgr_RemoteQueryData (CBlastQueryVector &queries)
	Construct query data from a CBlastQueryVector.
virtual CRef< objects::CBioseq_set >	CObjMgr_RemoteQueryData::GetBioseqSet ()
	Accessor for the CBioseq_set.
virtual TSeqLocs	CObjMgr_RemoteQueryData::GetSeqLocs ()
	Accessor for the TSeqLocs.
	CObjMgr_QueryFactory::CObjMgr_QueryFactory (TSeqLocVector &queries)
	ctor that takes a vector of SSeqLoc
	CObjMgr_QueryFactory::CObjMgr_QueryFactory (CBlastQueryVector &queries)
	ctor that takes a CBlastQueryVector (preferred)
vector< CRef< objects::CScope > >	CObjMgr_QueryFactory::ExtractScopes ()
	Retrieve the CScope objects associated with the query sequences associated with this object.
TSeqLocVector	CObjMgr_QueryFactory::GetTSeqLocVector ()
	Retrieves the TSeqLocVector used to construct this object or a conversion of the CBlastQueryVector provided.
TSeqLocInfoVector	CObjMgr_QueryFactory::ExtractUserSpecifiedMasks ()
	Retrieve any user specified masking locations.
CRef< ILocalQueryData >	CObjMgr_QueryFactory::x_MakeLocalQueryData (const CBlastOptions *opts)
	factory method to create an ILocalQueryData, only called if the data members above are not set
CRef< IRemoteQueryData >	CObjMgr_QueryFactory::x_MakeRemoteQueryData ()
	factory method to create an IRemoteQueryData, only called if the data members above are not set
	CObjMgrFree_LocalQueryData::CObjMgrFree_LocalQueryData (CConstRef< CBioseq_set > bioseq_set, const CBlastOptions *options)
virtual BLAST_SequenceBlk *	CObjMgrFree_LocalQueryData::GetSequenceBlk ()
	Accessor for the BLAST_SequenceBlk structure.
virtual BlastQueryInfo *	CObjMgrFree_LocalQueryData::GetQueryInfo ()
	Accessor for the BlastQueryInfo structure.
virtual size_t	CObjMgrFree_LocalQueryData::GetNumQueries ()
	Get the number of queries.
virtual CConstRef< CSeq_loc >	CObjMgrFree_LocalQueryData::GetSeq_loc (size_t index)
	Get the Seq_loc for the sequence indicated by index.
virtual size_t	CObjMgrFree_LocalQueryData::GetSeqLength (size_t index)
	Get the length of the sequence indicated by index.
	CObjMgrFree_RemoteQueryData::CObjMgrFree_RemoteQueryData (CConstRef< CBioseq_set > bioseq_set)
	Construct query data from a CBioseq_set.
virtual CRef< CBioseq_set >	CObjMgrFree_RemoteQueryData::GetBioseqSet ()
	Accessor for the CBioseq_set.
virtual TSeqLocs	CObjMgrFree_RemoteQueryData::GetSeqLocs ()
	Accessor for the TSeqLocs.
	CObjMgrFree_QueryFactory::CObjMgrFree_QueryFactory (CConstRef< objects::CBioseq > bioseq)
	Parametrized constructor taking a single Bioseq.
	CObjMgrFree_QueryFactory::CObjMgrFree_QueryFactory (CConstRef< objects::CBioseq_set > bioseq_set)
	Parametrized constructor taking a Bioseq-set.
CRef< ILocalQueryData >	CObjMgrFree_QueryFactory::x_MakeLocalQueryData (const CBlastOptions *opts)
	factory method to create an ILocalQueryData, only called if the data members above are not set
CRef< IRemoteQueryData >	CObjMgrFree_QueryFactory::x_MakeRemoteQueryData ()
	factory method to create an IRemoteQueryData, only called if the data members above are not set
	CPHIBlastNuclOptionsHandle::CPHIBlastNuclOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
	Creates object with default options set.
	CPHIBlastProtOptionsHandle::CPHIBlastProtOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
	Creates object with default options set.
	CBlastPrelimSearch::CBlastPrelimSearch (CRef< IQueryFactory > query_factory, CRef< CBlastOptions > options, const CSearchDatabase &dbinfo)
	Constructor which creates and manages a BLAST database handle for the caller.
	CBlastPrelimSearch::CBlastPrelimSearch (CRef< IQueryFactory > query_factory, CRef< CBlastOptions > options, CRef< CLocalDbAdapter > db)
	Constructor which creates BlastSeqSrc object from the already constructed BLAST database handle.
	CBlastPrelimSearch::CBlastPrelimSearch (CRef< IQueryFactory > query_factory, CRef< CBlastOptions > options, BlastSeqSrc *seqsrc, CConstRef< objects::CPssmWithParameters > pssm=null)
	Constructor which takes a PSSM and an already initialized BlastSeqSrc object.
virtual void	CBlastPrelimSearch::SetNumberOfThreads (size_t nthreads)
	Mutator for the number of threads. Parameters: nthreads  number of threads to use
void	CBlastPrelimSearch::x_Init (CRef< IQueryFactory > query_factory, CRef< CBlastOptions > options, CConstRef< objects::CPssmWithParameters > pssm, BlastSeqSrc *seqsrc)
	Internal initialization function Initializes internal data structures except the BlastSeqSrc.
int	CBlastPrelimSearch::x_LaunchMultiThreadedSearch (SInternalData &internal_data)
	Runs the preliminary search in multi-threaded mode.
CRef< SInternalData >	CBlastPrelimSearch::Run ()
	Borrow the internal data and results results.
int	CBlastPrelimSearch::CheckInternalData ()
	Checks that internal data is valid.
BlastHSPResults *	CBlastPrelimSearch::ComputeBlastHSPResults (BlastHSPStream *stream, Uint4 max_num_hsps=0, bool *rm_hsps=NULL) const
	Return HSPs in a structure other than the HSPStream? Provide conversion? How to combine this with CBlastTracebackStage?
	CPsiBlastInputData::CPsiBlastInputData (const unsigned char *query, unsigned int query_length, CConstRef< objects::CSeq_align_set > sset, CRef< objects::CScope > scope, const PSIBlastOptions &opts, const char *matrix_name=NULL, const PSIDiagnosticsRequest *diags=NULL)
	Construct a concrete strategy, used to configure the CPssmEngine object.
virtual	CPsiBlastInputData::~CPsiBlastInputData ()
	virtual destructor
void	CPsiBlastInputData::Process ()
	The work to process the alignment is done here.
void	CPsiBlastInputData::x_ExtractQueryForPssm ()
	Extracts the query bioseq from m_SeqAlignSet.
unsigned int	CPsiBlastInputData::x_CountAndSelectQualifyingAlignments ()
	Examines the sequence alignment and keeps track of those hits which have an HSP with an e-value below the inclusion threshold specified in the PSIBlastOptions structure.
unsigned int	CPsiBlastInputData::GetNumAlignedSequences () const
	Returns the number of sequences that make up the multiple sequence alignment Exceptions: CBlastException  if this number hasn't been calculated yet (need to invoke Process() first!).
PSIMsa *	CPsiBlastInputData::GetData ()
	Obtain the multiple sequence alignment structure.
unsigned char *	CPsiBlastInputData::GetQuery ()
	Get the query sequence used as master for the multiple sequence alignment in ncbistdaa encoding.
unsigned int	CPsiBlastInputData::GetQueryLength ()
	Get the query's length.
const PSIBlastOptions *	CPsiBlastInputData::GetOptions ()
	Obtain the options for the PSSM engine.
const char *	CPsiBlastInputData::GetMatrixName ()
	Obtain the name of the underlying matrix to use when building the PSSM.
const PSIDiagnosticsRequest *	CPsiBlastInputData::GetDiagnosticsRequest ()
	Obtain the diagnostics data that is requested from the PSSM engine.
void	CPsiBlastInputData::x_CopyQueryToMsa ()
	Copies query sequence data to multiple alignment data structure.
void	CPsiBlastInputData::x_ExtractAlignmentData ()
	Populates the multiple alignment data structure.
void	CPsiBlastInputData::x_ProcessDenseg (const objects::CDense_seg &denseg, unsigned int msa_index, double evalue, double bit_score)
	Iterates over the Dense-seg passed in and extracts alignment information to multiple alignment data structure.
static void	CPsiBlastInputData::x_GetSubjectSequence (const objects::CDense_seg &ds, objects::CScope &scope, string &sequence_data)
	Tries to fetch the sequence data for the subject for the segments specified in the Dense-seg.
	CPsiBl2Seq::CPsiBl2Seq (CRef< objects::CPssmWithParameters > pssm, CRef< IQueryFactory > subject, CConstRef< CPSIBlastOptionsHandle > options)
	Constructor to compare a PSSM against protein sequences.
	CPsiBl2Seq::CPsiBl2Seq (CRef< IQueryFactory > query, CRef< IQueryFactory > subject, CConstRef< CBlastProteinOptionsHandle > options)
	Constructor to compare protein sequences in an object manager-free manner.
void	CPsiBl2Seq::x_InitSubject (CRef< IQueryFactory > subject, const CBlastOptionsHandle *options)
	Auxiliary method to initialize the subject.
	CPsiBl2Seq::~CPsiBl2Seq ()
	Destructor.
CRef< CSearchResultSet >	CPsiBl2Seq::Run ()
	Run the PSI-BLAST 2 Sequences engine.
	CPsiBlast::CPsiBlast (CRef< IQueryFactory > query_factory, CRef< CLocalDbAdapter > blastdb, CConstRef< CPSIBlastOptionsHandle > options)
	Constructor to compare a single sequence against a database of protein sequences.
	CPsiBlast::CPsiBlast (CRef< objects::CPssmWithParameters > pssm, CRef< CLocalDbAdapter > blastdb, CConstRef< CPSIBlastOptionsHandle > options)
	Constructor to compare a PSSM against a database of protein sequences.
	CPsiBlast::~CPsiBlast ()
	Destructor.
void	CPsiBlast::SetPssm (CConstRef< objects::CPssmWithParameters > pssm)
	This method allows the same object to be reused when performing multiple iterations.
CConstRef< objects::CPssmWithParameters >	CPsiBlast::GetPssm () const
	Accessor for the most recently used PSSM.
CRef< CSearchResultSet >	CPsiBlast::Run ()
	Run the PSI-BLAST engine for one iteration.
static CNcbiMatrix< int > *	CScorematPssmConverter::GetScores (const objects::CPssmWithParameters &pssm)
	Returns matrix of BLASTAA_SIZE by query size (dimensions are opposite of what is stored in the BlastScoreBlk) containing scores.
static CNcbiMatrix< double > *	CScorematPssmConverter::GetFreqRatios (const objects::CPssmWithParameters &pssm)
	Returns matrix of BLASTAA_SIZE by query size (dimensions are opposite of what is stored in the BlastScoreBlk) containing frequency ratios.
static CNcbiMatrix< int > *	CScorematPssmConverter::GetResidueFrequencies (const objects::CPssmWithParameters &pssm)
	Returns matrix of BLASTAA_SIZE by query size (dimensions are opposite of what is stored in the BlastScoreBlk) containing the residue frequencies per position of the PSSM.
static CNcbiMatrix< double > *	CScorematPssmConverter::GetWeightedResidueFrequencies (const objects::CPssmWithParameters &pssm)
	Returns matrix of BLASTAA_SIZE by query size (dimensions are opposite of what is stored in the BlastScoreBlk) containing the weighted residue frequencies per position of the PSSM.
static void	CScorematPssmConverter::GetInformationContent (const objects::CPssmWithParameters &pssm, vector< double > &retval)
	Returns the information content per position of the PSSM.
static void	CScorematPssmConverter::GetGaplessColumnWeights (const objects::CPssmWithParameters &pssm, vector< double > &retval)
	Returns the gapless PSSM column weights for the provided PSSM.
static void	CScorematPssmConverter::GetSigma (const objects::CPssmWithParameters &pssm, vector< double > &retval)
	Data used in sequence weights computation.
static void	CScorematPssmConverter::GetIntervalSizes (const objects::CPssmWithParameters &pssm, vector< int > &retval)
	Length of the aligned regions per position of the query sequence.
static void	CScorematPssmConverter::GetNumMatchingSeqs (const objects::CPssmWithParameters &pssm, vector< int > &retval)
	Gets the number of matching sequences per position of the PSSM.
void	CPsiBlastAlignmentProcessor::operator() (const objects::CSeq_align_set &alignments, double evalue_inclusion_threshold, THitIdentifiers &output)
	Extract all the THitId which have evalues below the inclusion threshold.
static void	CPsiBlastValidate::Pssm (const objects::CPssmWithParameters &pssm, bool require_scores=false)
	Perform validation on the PSSM.
static void	CPsiBlastValidate::QueryFactory (CRef< IQueryFactory > query_factory, const CBlastOptionsHandle &opts_handle, EQueryFactoryType query_factory_type=eQFT_Query)
	Function to perform sanity checks on the query factory.
	CPsiBlastImpl::CPsiBlastImpl (CRef< objects::CPssmWithParameters > pssm, CRef< CLocalDbAdapter > subject, CConstRef< CPSIBlastOptionsHandle > options)
	Constructor for restarting PSI-BLAST iterations with a previously generated PSSM.
	CPsiBlastImpl::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.
void	CPsiBlastImpl::x_Validate ()
	Perform sanity checks on input parameters.
void	CPsiBlastImpl::x_CreatePssmScoresFromFrequencyRatios ()
	Computes the PSSM scores in case these are not available in the PSSM.
void	CPsiBlastImpl::x_ExtractQueryFromPssm ()
	Auxiliary function to get the query sequence data from the ASN.1 PSSM Post-condition: (m_Query.Empty() == false).
CRef< CSearchResultSet >	CPsiBlastImpl::Run ()
	Run the PSI-BLAST engine for one iteration.
void	CPsiBlastImpl::SetPssm (CConstRef< objects::CPssmWithParameters > pssm)
	This method allows the same object to be reused when performing multiple iterations.
void	CPsiBlastImpl::SetResultType (EResultType type)
	Set the desired result type.
CConstRef< objects::CPssmWithParameters >	CPsiBlastImpl::GetPssm () const
	Accessor for the most recently used PSSM.
	CPsiBlastIterationState::CPsiBlastIterationState (unsigned int num_iterations=1)
	Constructor.
	CPsiBlastIterationState::~CPsiBlastIterationState ()
	Destructor.
bool	CPsiBlastIterationState::HasMoreIterations () const
	Determines if more iterations are still needed.
bool	CPsiBlastIterationState::HasConverged ()
	Determines if the PSI-BLAST search has converged (i.e.
	CPsiBlastIterationState::operator bool ()
	Allow implicit conversion to a boolean value, returning true if there are more iterations to perform or false if iterations are done.
void	CPsiBlastIterationState::x_ThrowExceptionOnLogicError ()
	After the iteration state object has converged or exhausted its iterations, it shouldn't be modified, so it throws a CBlastException if this happens.
TSeqIds	CPsiBlastIterationState::GetPreviouslyFoundSeqIds () const
	Retrieve the set of Seq-id's found in the previous iteration.
void	CPsiBlastIterationState::Advance (const TSeqIds &list)
	Advance the iterator by passing it the list of Seq-ids which passed the inclusion criteria for the current iteration.
unsigned int	CPsiBlastIterationState::GetIterationNumber () const
	Return the number of the current iteration.
static void	CPsiBlastIterationState::GetSeqIds (CConstRef< objects::CSeq_align_set > seqalign, CConstRef< CPSIBlastOptionsHandle > opts, TSeqIds &retval)
	Extract the sequence ids from the sequence alignment which identify those sequences that will be used for PSSM construction.
	CPSIBlastOptionsHandle::CPSIBlastOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
	Creates object with default options set.
virtual void	CPSIBlastOptionsHandle::SetQueryOptionDefaults ()
	Override the parent class' default for filtering query sequence (i.e.
void	CPSIBlastOptionsHandle::SetPSIBlastDefaults ()
	Sets PSIBlastDefaults.
void	CPSIBlastOptionsHandle::SetPSITblastnDefaults ()
	Sets default options for psi tblastn search.
	CPssmEngine::CPssmEngine (IPssmInputData *input)
	Constructor to configure the PSSM engine with a PSSM input data strategy object Checks that no data returned by the IPssmInputData interface is NULL Exceptions: CPssmEngineException  if validation fails.
	CPssmEngine::CPssmEngine (IPssmInputFreqRatios *input)
	Constructor to perform the last 2 stages of the PSSM creation algorithm Checks that no data returned by the IPssmInputFreqRatios interface is NULL Exceptions: CPssmEngineException  if validation fails.
	CPssmEngine::~CPssmEngine ()
	Destructor.
static std::string	CPssmEngine::x_ErrorCodeToString (int error_code)
	Convert a PSSM return status into a string.
CRef< objects::CPssmWithParameters >	CPssmEngine::Run ()
	Runs the PSSM engine to compute the PSSM.
CRef< objects::CPssmWithParameters >	CPssmEngine::x_CreatePssmFromFreqRatios ()
	Using IPssmInputFreqRatios as a delegate to provide the input PSSM's frequency ratios, creates a PSSM using the CORE C PSSM engine API.
CRef< objects::CPssmWithParameters >	CPssmEngine::x_CreatePssmFromMsa ()
	Using IPssmInputData as a delegate to provide input data in the form of a multiple sequence alignment, creates a PSSM using the CORE C PSSM engine API.
static unsigned char *	CPssmEngine::x_GuardProteinQuery (const unsigned char *query, unsigned int query_length)
	Copies query sequence and adds protein sentinel bytes at the beginning and at the end of the sequence.
BlastQueryInfo *	CPssmEngine::x_InitializeQueryInfo (unsigned int query_length)
	Initialiazes the core BlastQueryInfo structure for a single protein sequence.
void	CPssmEngine::SetUngappedStatisticalParams (CConstRef< CBlastAncillaryData > ancillary_data)
	Sets the Karlin & Altschul parameters in the BlastScoreBlk to be used in PSSM generation.
void	CPssmEngine::x_InitializeScoreBlock (const unsigned char *query, unsigned int query_length, const char *matrix_name)
	Initializes the BlastScoreBlk data member required to run the PSSM engine.
unsigned char *	CPssmEngine::x_GetQuery () const
	Private interface to retrieve query sequence from its data source interface.
unsigned int	CPssmEngine::x_GetQueryLength () const
	Private interface to retrieve query length from its data source interface.
const char *	CPssmEngine::x_GetMatrixName () const
	Private interface to retrieve matrix name from its data source interface.
static CRef< objects::CPssmWithParameters >	CPssmEngine::x_PSIMatrix2Asn1 (const PSIMatrix *pssm, const char *matrix_name, const PSIBlastOptions *opts=NULL, const PSIDiagnosticsResponse *diagnostics=NULL)
	Converts the PSIMatrix structure into a ASN.1 CPssmWithParameters object.
CRef< ILocalQueryData >	IQueryFactory::MakeLocalQueryData (const CBlastOptions *opts)
	Creates and caches an ILocalQueryData.
CRef< IRemoteQueryData >	IQueryFactory::MakeRemoteQueryData ()
	Creates and caches an IRemoteQueryData.
void	ILocalQueryData::x_ValidateIndex (size_t index)
bool	ILocalQueryData::IsValidQuery (size_t index)
	Determine if a given query sequence is valid or not.
size_t	ILocalQueryData::GetSumOfSequenceLengths ()
	Compute the sum of all the sequence's lengths.
bool	ILocalQueryData::IsAtLeastOneQueryValid ()
	Determine if at least one query sequence is valid or not.
void	ILocalQueryData::GetQueryMessages (size_t index, TQueryMessages &qmsgs)
	Retrieve error/warning messages for a specific query.
void	ILocalQueryData::GetMessages (TSearchMessages &messages) const
	Retrieve all error/warning messages.
void	ILocalQueryData::FlushSequenceData ()
	Frees the cached sequence data structure (as this is usually the larger data structure).
void	CRemoteBlast::x_SearchErrors (CRef< objects::CBlast4_reply > reply)
	Iterate over error list, splitting into errors and warnings.
void	CRemoteBlast::x_CheckConfig (void)
	Verify that search object contains mandatory fields.
CRef< objects::CBlast4_request >	CRemoteBlast::GetSearchStrategy ()
	Fetch the search strategy for this object without submitting the search.
CRef< objects::CBlast4_reply >	CRemoteBlast::x_SendRequest (CRef< objects::CBlast4_request_body > body)
	Send a Blast4 request and get a reply.
CRef< objects::CBlast4_reply >	CRemoteBlast::x_GetSearchResults (void)
	Try to get the search results.
bool	CRemoteBlast::SubmitSync (int timeout)
	This submits the search (if necessary) and polls for results.
bool	CRemoteBlast::Submit (void)
	This submits the search (if necessary) and returns immediately.
ESearchStatus	CRemoteBlast::CheckStatus ()
	Returns the status of a previously submitted search/RID.
bool	CRemoteBlast::x_IsUnknownRID (void)
	Determine if this is an unknown RID.
bool	CRemoteBlast::CheckDone (void)
	Check whether the search has completed.
TGSRR *	CRemoteBlast::x_GetGSRR (void)
	Poll until done, return the CBlast4_get_search_results_reply.
CRef< objects::CSeq_align_set >	CRemoteBlast::GetAlignments (void)
	Get the seqalign set from the results.
TSeqAlignVector	CRemoteBlast::GetSeqAlignSets ()
	Get the seqalign vector from the results.
CRef< objects::CBlast4_phi_alignments >	CRemoteBlast::GetPhiAlignments (void)
	Get the results of a PHI-Align request, if PHI pattern was set.
TSeqLocInfoVector	CRemoteBlast::GetMasks (void)
	Get the queries' masked locations.
TGSRR::TMasks	CRemoteBlast::x_GetMasks (void)
	Get the query masks from the results.
TKarlinAltschulBlocks	CRemoteBlast::GetKABlocks (void)
	Get the Karlin/Altschul parameter blocks produced by the search.
list< string >	CRemoteBlast::GetSearchStats (void)
	Get the search statistics block as a list of strings.
CRef< objects::CPssmWithParameters >	CRemoteBlast::GetPSSM (void)
	Get the PSSM produced by the search.
EState	CRemoteBlast::x_GetState (void)
	Determine what state the search is in.
CRef< objects::CBlast4_request_body >	CRemoteBlast::x_GetBlast4SearchRequestBody ()
	Retrieve the request body for a search submission.
void	CRemoteBlast::x_SubmitSearch (void)
	Submit the search and process results (of submit action).
void	CRemoteBlast::x_CheckResults (void)
	Try to get and process results.
void	CRemoteBlast::x_PollUntilDone (EImmediacy poll_immed, int seconds)
	Poll until results are found, error occurs, or timeout expires.
void	CRemoteBlast::x_Init (CNcbiIstream &f)
	Uses the file to populate results.
void	CRemoteBlast::x_Init (CBlastOptionsHandle *algo_opts)
	Called by new search constructors: initialize a new search.
void	CRemoteBlast::x_Init (CBlastOptionsHandle *algo_opts, const string &program, const string &service)
	Called by new search constructors: initialize a new search.
void	CRemoteBlast::x_Init (const string &RID)
	Called by RID constructor: set up monitoring of existing search.
void	CRemoteBlast::x_SetAlgoOpts (void)
	Configure new search from options handle passed to constructor.
void	CRemoteBlast::x_SetOneParam (objects::CBlast4Field &field, const int *value)
	Set an integer parameter (not used yet).
void	CRemoteBlast::x_SetOneParam (objects::CBlast4Field &field, CRef< objects::CBlast4_mask > mask)
	Set a masking location for query.
void	CRemoteBlast::x_SetOneParam (objects::CBlast4Field &field, const list< int > *value)
	Set a list of integers.
void	CRemoteBlast::x_SetOneParam (objects::CBlast4Field &field, const char **value)
	Set a string parameter.
void	CRemoteBlast::SetQueries (CRef< objects::CBioseq_set > bioseqs)
	Set the query as a Bioseq_set.
void	CRemoteBlast::SetQueries (CRef< objects::CBioseq_set > bioseqs, const TSeqLocInfoVector &masking_locations)
	Set the query as a Bioseq_set along with the corresponding masking locations.
void	CRemoteBlast::SetQueryMasks (const TSeqLocInfoVector &masking_locations)
	Set the masking locations for queries.
void	CRemoteBlast::SetQueries (TSeqLocList &seqlocs)
	Set the query as a list of Seq_locs.
void	CRemoteBlast::SetQueries (TSeqLocList &seqlocs, const TSeqLocInfoVector &masking_locations)
	Set the query as a list of Seq_locs.
void	CRemoteBlast::x_SetMaskingLocationsForQueries (const TSeqLocInfoVector &masking_locations)
	Set the masking locations AFTER the queries have been set in the m_QSR field.
static objects::CBlast4_get_search_results_reply::TMasks	CRemoteBlast::ConvertToRemoteMasks (const TSeqLocInfoVector &masking_locations, EBlastProgramType program, vector< string > *warnings=NULL)
	Convert a TSeqLocInfoVector to a list< CRef<CBlast4_mask> > objects.
void	CRemoteBlast::x_QueryMaskingLocationsToNetwork ()
	Converts the provided query masking locations (if any) to the network representation following the BLAST 4 ASN.1 spec.
void	CRemoteBlast::SetQueries (CRef< objects::CPssmWithParameters > pssm)
	Set a PSSM query (as for PSI blast), which must include a bioseq set.
string	CRemoteBlast::GetErrors (void)
	This returns a string containing any errors that were produced by the search.
string	CRemoteBlast::GetWarnings (void)
	This returns any warnings encountered.
const vector< string > &	CRemoteBlast::GetWarningVector ()
	This returns any warnings encountered as a vector of strings.
const vector< string > &	CRemoteBlast::GetErrorVector ()
	This returns any errors encountered as a vector of strings.
	CRemoteBlast::CRemoteBlast (CNcbiIstream &f)
	Uses the file to populate results.
	CRemoteBlast::CRemoteBlast (const string &RID)
	Use the specified RID to get results for an existing search.
	CRemoteBlast::CRemoteBlast (CBlastOptionsHandle *any_opts)
	Create a search using any kind of options handle.
	CRemoteBlast::CRemoteBlast (CRef< IQueryFactory > queries, CRef< CBlastOptionsHandle > opts_handle, const CSearchDatabase &db)
	Create a sequence search and set options, queries, and database.
	CRemoteBlast::CRemoteBlast (CRef< IQueryFactory > queries, CRef< CBlastOptionsHandle > opts_handle, CRef< IQueryFactory > subjects)
	Create a search and set options, queries, and subject sequences.
void	CRemoteBlast::x_InitQueries (CRef< IQueryFactory > queries)
	Initialize queries based on a query factory.
void	CRemoteBlast::x_ExtractUserSpecifiedMasks (CRef< IQueryFactory > query_factory, TSeqLocInfoVector &masks)
	Extract the user specified masking locations from the query factory.
	CRemoteBlast::CRemoteBlast (CRef< objects::CPssmWithParameters > pssm, CRef< CBlastOptionsHandle > opts_handle, const CSearchDatabase &db)
	Create a PSSM search and set options, queries, and database.
void	CRemoteBlast::x_Init (CRef< CBlastOptionsHandle > opts_handle, const CSearchDatabase &db)
	Initialize a search with a database and options handle.
	CRemoteBlast::~CRemoteBlast ()
	Destruct the search object.
void	CRemoteBlast::SetGIList (const list< Int4 > &gi_list)
	This restricts the subject database to this list of GIs (this is not supported yet on the server end).
void	CRemoteBlast::SetDbFilteringAlgorithmId (int algo_id)
	Sets the filtering algorithm ID to be applied to the BLAST database (not supported by server yet).
void	CRemoteBlast::SetNegativeGIList (const list< Int4 > &gi_list)
	This excludes the provided GIs from the subject database (this is not supported yet on the server end).
void	CRemoteBlast::x_SetDatabase (const string &x)
	Sets a subset (only m_Dbs) of what the public SetDatabase sets.
void	CRemoteBlast::SetDatabase (const string &x)
	Set the name of the database to search against.
void	CRemoteBlast::SetSubjectSequences (CRef< IQueryFactory > subj)
	Set a list of subject sequences to search against.
void	CRemoteBlast::SetSubjectSequences (const list< CRef< objects::CBioseq > > &subj)
	Set a list of subject sequences to search against.
void	CRemoteBlast::SetEntrezQuery (const char *x)
	Restrict search to sequences matching this Entrez query.
bool	CRemoteBlast::SubmitSync (void)
	This submits the search (if necessary) and polls for results.
const string &	CRemoteBlast::GetRID (void)
	Gets the request id (RID) associated with the search.
void	CRemoteBlast::SetVerbose (EDebugMode verb=eDebug)
	Adjust the debugging level.
const int	CRemoteBlast::x_DefaultTimeout (void)
	The default timeout is 3.5 hours.
void	CRemoteBlast::x_GetRequestInfo ()
	Fetch the request info (wait for completion if necessary).
void	CRemoteBlast::x_GetRequestInfoFromFile ()
	Fetch the requested info from an archive file.
void	CRemoteBlast::x_GetRequestInfoFromRID ()
	Fetch the requested info from splitd.
CRef< objects::CBlast4_database >	CRemoteBlast::GetDatabases ()
	Get the database used by the search.
bool	CRemoteBlast::IsDbSearch ()
	Return values states whether GetDatabases or GetSubjectSequences call should be used.
list< CRef< objects::CBioseq > >	CRemoteBlast::GetSubjectSequences ()
	Returns subject sequences if "bl2seq" mode used.
string	CRemoteBlast::GetProgram ()
	Get the program used for this search.
string	CRemoteBlast::GetService ()
	Get the service used for this search.
string	CRemoteBlast::GetCreatedBy ()
	Get the created-by string associated with this search.
CRef< objects::CBlast4_queries >	CRemoteBlast::GetQueries ()
	Get the queries used for this search.
CRef< CBlastOptionsHandle >	CRemoteBlast::GetSearchOptions ()
	Get the search options used for this search.
void	CRemoteBlast::x_ExtractQueryIds (CSearchResultSet::TQueryIdVector &query_ids)
	Extract the query IDs from the CBlast4_queries for a given search.
CRef< CSearchResultSet >	CRemoteBlast::GetResultSet ()
	Submit the search (if necessary) and return the results.
virtual CRef< ISeqSearch >	CRemoteSearchFactory::GetSeqSearch ()
	Get an object to manage a remote sequence search.
virtual CRef< IPssmSearch >	CRemoteSearchFactory::GetPssmSearch ()
	Get an object to manage a remote PSSM search.
virtual CRef< CBlastOptionsHandle >	CRemoteSearchFactory::GetOptions (EProgram)
	Get an options handle for a search of the specified type.
CRemoteBlast &	CRemoteSeqSearch::x_RemoteBlast ()
	Method to construct and run the remote blast search.
virtual CRef< CSearchResultSet >	CRemoteSeqSearch::Run ()
	Run the search.
virtual void	CRemoteSeqSearch::SetOptions (CRef< CBlastOptionsHandle > options)
	Configure the search.
virtual void	CRemoteSeqSearch::SetSubject (CConstRef< CSearchDatabase > subject)
	Set the databases to search.
virtual void	CRemoteSeqSearch::SetQueryFactory (CRef< IQueryFactory > query_factory)
	Set the factory which will return the queries to search for.
virtual void	CRemotePssmSearch::SetOptions (CRef< CBlastOptionsHandle > options)
	Configure the search.
virtual void	CRemotePssmSearch::SetSubject (CConstRef< CSearchDatabase > subject)
	Set the databases to search.
CRemoteBlast &	CRemotePssmSearch::x_RemoteBlast ()
	Method to construct and run the remote blast search.
virtual CRef< CSearchResultSet >	CRemotePssmSearch::Run ()
	Run the search.
virtual void	CRemotePssmSearch::SetQuery (CRef< objects::CPssmWithParameters > query)
	Set the query to search with.
	CBlastRPSAuxInfo::CBlastRPSAuxInfo (const string &matrix, int gap_open, int gap_extend, double scale_factor, const vector< double > &karlin_k)
	Parametrized constructor.
	CBlastRPSAuxInfo::~CBlastRPSAuxInfo ()
	Destructor.
const BlastRPSAuxInfo *	CBlastRPSAuxInfo::operator() () const
	Lend the caller the pointer to the data structure this object manages.
void	CBlastRPSAuxInfo::x_DoDestroy ()
	Deallocates the structure owned by this class.
	CRpsAuxFile::CRpsAuxFile (const string &filename_no_extn)
	Parametrized constructor.
CRef< CBlastRPSAuxInfo >	CRpsAuxFile::x_ReadFromFile (CNcbiIfstream &input)
	Auxiliary method to read the contents of the file into m_Data.
const BlastRPSAuxInfo *	CRpsAuxFile::operator() () const
	Lend the caller the pointer to the data structure this object manages.
	CRpsMmappedFile::CRpsMmappedFile (const string &filename)
	Parametrized constructor.
	CRpsLookupTblFile::CRpsLookupTblFile (const string &filename_no_extn)
	Parametrized constructor.
const BlastRPSLookupFileHeader *	CRpsLookupTblFile::operator() () const
	Lend the caller the pointer to the data structure this object manages.
	CRpsPssmFile::CRpsPssmFile (const string &filename_no_extn)
	Parametrized constructor.
const BlastRPSProfileHeader *	CRpsPssmFile::operator() () const
	Lend the caller the pointer to the data structure this object manages.
	CBlastRPSInfo::CBlastRPSInfo (const string &rps_dbname)
	Parametrized constructor.
	CBlastRPSInfo::~CBlastRPSInfo ()
	Destructor.
const BlastRPSInfo *	CBlastRPSInfo::operator() () const
	Accessor for the underlying C structure (managed by this class).
double	CBlastRPSInfo::GetScalingFactor () const
	Returns the scaling factor used to build RPS-BLAST database.
const char *	CBlastRPSInfo::GetMatrixName () const
	Returns the name of the scoring matrix used to build the RPS-BLAST database.
int	CBlastRPSInfo::GetGapOpeningCost () const
	Returns the gap opening cost associated with the scoring matrix above.
int	CBlastRPSInfo::GetGapExtensionCost () const
	Returns the gap extension cost associated with the scoring matrix above.
	CRPSTBlastnOptionsHandle::CRPSTBlastnOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
	Creates object with default options set.
void	CRPSTBlastnOptionsHandle::SetQueryOptionDefaults ()
	Overrides SubjectSequenceOptionsDefaults for RPS-TBLASTN options.
	CImportStrategy::CImportStrategy (CRef< objects::CBlast4_request > request)
	Constructor, imports the CBlast4_request.
CRef< blast::CBlastOptionsHandle >	CImportStrategy::GetOptionsHandle ()
	Builds and returns the OptionsHandle.
string	CImportStrategy::GetTask ()
	Fetches task, such as "megablast", "blastn", etc.
string	CImportStrategy::GetProgram () const
	Fetches program, one of blastn, blastp, blastx, tblastn, tblastx.
string	CImportStrategy::GetCreatedBy () const
	Returns ident field from a Blast4-request.
TSeqRange	CImportStrategy::GetQueryRange ()
	The start and stop on the query (if applicable).
string	CImportStrategy::GetService () const
	Fetches service, such as psiblast, plain, megablast.
CRef< objects::CBlast4_queries >	CImportStrategy::GetQueries ()
	The queries either as Bioseq, seqloc, or pssm.
CRef< objects::CBlast4_subject >	CImportStrategy::GetSubject ()
	Returns the target sequences.
objects::CBlast4_parameters &	CImportStrategy::GetAlgoOptions ()
	Options specific to blast searches (e.g, threshold, expect value).
objects::CBlast4_parameters &	CImportStrategy::GetProgramOptions ()
	Options for controlling program execution and database filtering.
	CBioseqSeqInfoSrc::CBioseqSeqInfoSrc (const objects::CBioseq &bs, bool is_prot)
	Parametrized constructor.
	CBioseqSeqInfoSrc::CBioseqSeqInfoSrc (const objects::CBioseq_set &bss, bool is_prot)
	Parametrized constructor.
virtual list< CRef< objects::CSeq_id > >	CBioseqSeqInfoSrc::GetId (Uint4 index) const
	Retrieve a sequence identifier given its index in the vector.
virtual CConstRef< objects::CSeq_loc >	CBioseqSeqInfoSrc::GetSeqLoc (Uint4 index) const
	Retrieve a sequence identifier given its index in the vector.
virtual Uint4	CBioseqSeqInfoSrc::GetLength (Uint4 index) const
	Retrieve sequence length given its index in the vector.
virtual size_t	CBioseqSeqInfoSrc::Size () const
	Returns the size of the underlying container of sequences.
virtual bool	CBioseqSeqInfoSrc::HasGiList () const
	Is the subject restricted by a GI list? (Always returns false).
virtual bool	CBioseqSeqInfoSrc::GetMasks (Uint4 index, const TSeqRange &target_range, TMaskedSubjRegions &retval) const
	Retrieves the subject masks for the corresponding index.
virtual bool	CBioseqSeqInfoSrc::GetMasks (Uint4 index, const vector< TSeqRange > &target_ranges, TMaskedSubjRegions &retval) const
	Retrieves the subject masks for the corresponding index.
	CSeqDbSeqInfoSrc::CSeqDbSeqInfoSrc (const string &dbname, bool is_protein)
	Constructor: includes initializing the CSeqDB object.
	CSeqDbSeqInfoSrc::CSeqDbSeqInfoSrc (ncbi::CSeqDB *seqdb)
	Constructor from an already existing CSeqDB object.
virtual	CSeqDbSeqInfoSrc::~CSeqDbSeqInfoSrc ()
	Our destructor.
virtual list< CRef< objects::CSeq_id > >	CSeqDbSeqInfoSrc::GetId (Uint4 oid) const
	Retrieve a sequence identifier given its ordinal number.
virtual CConstRef< objects::CSeq_loc >	CSeqDbSeqInfoSrc::GetSeqLoc (Uint4 oid) const
	Method to retrieve the sequence location given its ordinal number.
virtual Uint4	CSeqDbSeqInfoSrc::GetLength (Uint4 oid) const
	Retrieve sequence length given its ordinal number.
virtual size_t	CSeqDbSeqInfoSrc::Size () const
	Returns the size of the underlying container of sequences.
virtual bool	CSeqDbSeqInfoSrc::HasGiList () const
	Returns true if the subject is restricted by a GI list.
void	CSeqDbSeqInfoSrc::SetFilteringAlgorithmId (int algo_id)
	Sets the filtering algorithm ID used in the search.
virtual bool	CSeqDbSeqInfoSrc::GetMasks (Uint4 index, const TSeqRange &target_range, TMaskedSubjRegions &retval) const
	Retrieves the subject masks for the corresponding index.
virtual bool	CSeqDbSeqInfoSrc::GetMasks (Uint4 index, const vector< TSeqRange > &target_ranges, TMaskedSubjRegions &retval) const
	Retrieves the subject masks for the corresponding index.
virtual void	CSeqDbSeqInfoSrc::GarbageCollect ()
	Invoke CSeqDB's garbage collector.
	CSeqVecSeqInfoSrc::CSeqVecSeqInfoSrc (const TSeqLocVector &seqv)
	Constructor from a vector of sequence locations.
virtual	CSeqVecSeqInfoSrc::~CSeqVecSeqInfoSrc ()
	Destructor.
virtual list< CRef< objects::CSeq_id > >	CSeqVecSeqInfoSrc::GetId (Uint4 index) const
	Retrieve a sequence identifier given its index in the vector.
virtual CConstRef< objects::CSeq_loc >	CSeqVecSeqInfoSrc::GetSeqLoc (Uint4 index) const
	Method to retrieve the sequence location given its ordinal number.
virtual Uint4	CSeqVecSeqInfoSrc::GetLength (Uint4 index) const
	Retrieve sequence length given its index in the vector.
virtual size_t	CSeqVecSeqInfoSrc::Size () const
	Returns the size of the underlying container of sequences.
virtual bool	CSeqVecSeqInfoSrc::HasGiList () const
	Is the subject restricted by a GI list? (Always returns false).
virtual bool	CSeqVecSeqInfoSrc::GetMasks (Uint4 index, const TSeqRange &target_range, TMaskedSubjRegions &retval) const
	Retrieves the subject masks for the corresponding index.
virtual bool	CSeqVecSeqInfoSrc::GetMasks (Uint4 index, const vector< TSeqRange > &target_ranges, TMaskedSubjRegions &retval) const
	Retrieves the subject masks for the corresponding index.
Uint4	CMultiSeqInfo::GetMaxLength ()
	Setter and getter functions for the private fields.
void	CMultiSeqInfo::SetMaxLength (Uint4 val)
	Sets maximal length.
Uint4	CMultiSeqInfo::GetAvgLength ()
	Returns average length.
void	CMultiSeqInfo::SetAvgLength (Uint4 val)
	Sets average length.
bool	CMultiSeqInfo::GetIsProtein ()
	Answers whether sequences in this object are protein or nucleotide.
Uint4	CMultiSeqInfo::GetNumSeqs ()
	Returns number of sequences.
BLAST_SequenceBlk *	CMultiSeqInfo::GetSeqBlk (int index)
	Returns sequence block structure for one of the sequences.
	CMultiSeqInfo::CMultiSeqInfo (TSeqLocVector &seq_vector, EBlastProgramType program)
	Constructor from a vector of sequence location/scope pairs and a BLAST program type.
	CMultiSeqInfo::~CMultiSeqInfo ()
	Destructor.
	CQueryFactoryInfo::CQueryFactoryInfo (CRef< IQueryFactory > qf, EBlastProgramType program)
	Constructor from a vector of sequence location/scope pairs and a BLAST program type.
	CQueryFactoryInfo::CQueryFactoryInfo (const TSeqLocVector &subject_seqs, EBlastProgramType program)
	CQueryFactoryInfo::~CQueryFactoryInfo ()
	Destructor.
Uint4	CQueryFactoryInfo::GetMaxLength ()
	Setter and getter functions for the private fields.
Uint4	CQueryFactoryInfo::GetAvgLength ()
	Returns average length.
void	CQueryFactoryInfo::SetAvgLength (Uint4 val)
	Sets average length.
bool	CQueryFactoryInfo::GetIsProtein ()
	Answers whether sequences in this object are protein or nucleotide.
Uint4	CQueryFactoryInfo::GetNumSeqs ()
	Returns number of sequences.
BLAST_SequenceBlk *	CQueryFactoryInfo::GetSeqBlk (Uint4 index)
	Returns sequence block structure for one of the sequences.
static CRef< CBlastRPSInfo >	CSetupFactory::CreateRpsStructures (const string &rps_dbname, CRef< CBlastOptions > options)
	Initializes RPS-BLAST data structures.
static BlastScoreBlk *	CSetupFactory::CreateScoreBlock (const CBlastOptionsMemento *opts_memento, CRef< ILocalQueryData > query_data, BlastSeqLoc **lookup_segments, TSearchMessages &search_messages, TSeqLocInfoVector *masked_query_regions=NULL, const CBlastRPSInfo *rps_info=NULL)
	Initializes the BlastScoreBlk.
static LookupTableWrap *	CSetupFactory::CreateLookupTable (CRef< ILocalQueryData > query_data, const CBlastOptionsMemento *opts_memento, BlastScoreBlk *score_blk, CRef< CBlastSeqLocWrap > lookup_segments, const CBlastRPSInfo *rps_info=NULL, BlastSeqSrc *seqsrc=NULL)
	Initialize the lookup table.
static BlastDiagnostics *	CSetupFactory::CreateDiagnosticsStructure ()
	Create and initialize the BlastDiagnostics structure for single-threaded applications.
static BlastDiagnostics *	CSetupFactory::CreateDiagnosticsStructureMT ()
	Create and initialize the BlastDiagnostics structure for multi-threaded applications.
static BlastHSPStream *	CSetupFactory::CreateHspStream (const CBlastOptionsMemento *opts_memento, size_t number_of_queries, BlastHSPWriter *writer)
	Create and initialize the BlastHSPStream structure.
static BlastHSPWriter *	CSetupFactory::CreateHspWriter (const CBlastOptionsMemento *opts_memento, BlastQueryInfo *query_info)
	Create a writer to be registered for use by stream.
static BlastHSPPipe *	CSetupFactory::CreateHspPipe (const CBlastOptionsMemento *opts_memento, BlastQueryInfo *query_info)
	Create a pipe to be registered for use by stream.
static BlastSeqSrc *	CSetupFactory::CreateBlastSeqSrc (const CSearchDatabase &db)
	Create a BlastSeqSrc from a CSearchDatabase (uses CSeqDB).
static BlastSeqSrc *	CSetupFactory::CreateBlastSeqSrc (CSeqDB *db)
	Create a BlastSeqSrc from an existing CSeqDB object.
static void	CSetupFactory::InitializeMegablastDbIndex (BlastSeqSrc *seqsrc, CRef< CBlastOptions > options)
	Initialize a megablast BLAST database index.
	SInternalData::SInternalData ()
	Default ctor.
	SDatabaseScanData::SDatabaseScanData ()
	Default ctor.
	CContextTranslator::CContextTranslator (const CSplitQueryBlk &sqb, vector< CRef< IQueryFactory > > *query_chunk_factories=NULL, const CBlastOptions *options=NULL)
	Constructor.
int	CContextTranslator::GetAbsoluteContext (size_t chunk_num, Int4 context_in_chunk) const
	Get the context number in the absolute (i.e.
int	CContextTranslator::GetContextInChunk (size_t chunk_num, int absolute_context) const
	Get the context number in the split query chunk.
int	CContextTranslator::GetStartingChunk (size_t curr_chunk, Int4 context_in_chunk) const
	Get the chunk number where context_in_chunk starts (i.e.
	CQueryDataPerChunk::CQueryDataPerChunk (const CSplitQueryBlk &sqb, EBlastProgramType program, CRef< ILocalQueryData > local_query_data)
	Constructor.
size_t	CQueryDataPerChunk::GetQueryLength (int global_query_index) const
	Get the length of the query.
size_t	CQueryDataPerChunk::GetQueryLength (size_t chunk_num, int context_in_chunk) const
	Get the length of the query.
size_t	CQueryDataPerChunk::x_ContextInChunkToQueryIndex (int context_in_chunk) const
	Convert a context in a chunk to a query index (within the chunk).
int	CQueryDataPerChunk::GetLastChunk (size_t chunk_num, int context_in_chunk)
	get the last chunk where query identified with global_query_index is found
int	CQueryDataPerChunk::GetLastChunk (int global_query_index)
	get the last chunk where query identified with global_query_index is found
	CSplitQueryBlk::CSplitQueryBlk (Uint4 num_chunks)
	Constructor for wrapper class for SSplitQueryBlk.
	CSplitQueryBlk::~CSplitQueryBlk ()
	Destructor.
size_t	CSplitQueryBlk::GetNumChunks () const
	Retrieve the number of chunks.
size_t	CSplitQueryBlk::GetNumQueriesForChunk (size_t chunk_num) const
	Get the number of queries in a given chunk.
vector< size_t >	CSplitQueryBlk::GetQueryIndices (size_t chunk_num) const
	Get the indices of the queries contained in a given chunk.
vector< int >	CSplitQueryBlk::GetQueryContexts (size_t chunk_num) const
	Get the contexts of the queries contained in a given chunk.
vector< size_t >	CSplitQueryBlk::GetContextOffsets (size_t chunk_num) const
	Get the context offsets (corrections) of the queries contained in a given chunk.
TChunkRange	CSplitQueryBlk::GetChunkBounds (size_t chunk_num) const
	Get the boundaries of a chunk in the concatenated query.
void	CSplitQueryBlk::SetChunkBounds (size_t chunk_num, const TChunkRange &chunk_range)
	Set the boundaries of a chunk in the concatenated query.
void	CSplitQueryBlk::AddQueryToChunk (size_t chunk_num, Int4 query_index)
	Adds a query index to a given chunk.
void	CSplitQueryBlk::AddContextToChunk (size_t chunk_num, Int4 context_index)
	Adds a query context to a given chunk.
void	CSplitQueryBlk::AddContextOffsetToChunk (size_t chunk_num, Int4 context_offset)
	Adds a context offset (correction) to a given chunk.
SSplitQueryBlk *	CSplitQueryBlk::GetCStruct () const
	Returns the C structure managed by objects of this class.
void	CSplitQueryBlk::SetChunkOverlapSize (size_t size)
	Sets the size (# of bases/residues) of overlap between query chunks.
size_t	CSplitQueryBlk::GetChunkOverlapSize () const
	Gets the size (# of bases/residues) of overlap between query chunks.
	CTBlastnOptionsHandle::CTBlastnOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
	Creates object with default options set.
void	CTBlastnOptionsHandle::SetLookupTableDefaults ()
	Sets LookupTableDefaults for tblastn options.
void	CTBlastnOptionsHandle::SetScoringOptionsDefaults ()
	Sets ScoringOptionsDefaults for tblastn options.
void	CTBlastnOptionsHandle::SetHitSavingOptionsDefaults ()
	Sets HitSavingOptionsDefaults for tblastn options.
void	CTBlastnOptionsHandle::SetGappedExtensionDefaults ()
	Overrides SetGappedExtensionDefaults for tblastn options.
void	CTBlastnOptionsHandle::SetSubjectSequenceOptionsDefaults ()
	Sets SubjectSequenceOptionsDefaults for tblastn options.
	CTBlastxOptionsHandle::CTBlastxOptionsHandle (EAPILocality locality)
	Creates object with default options set.
void	CTBlastxOptionsHandle::SetLookupTableDefaults ()
	Overrides LookupTableDefaults for tblastx options.
void	CTBlastxOptionsHandle::SetQueryOptionDefaults ()
	Overrides QueryOptionDefaults for tblastx options.
void	CTBlastxOptionsHandle::SetScoringOptionsDefaults ()
	Overrides ScoringOptionsDefaults for tblastx options.
void	CTBlastxOptionsHandle::SetHitSavingOptionsDefaults ()
	Overrides HitSavingOptionsDefaults for tblastx options.
void	CTBlastxOptionsHandle::SetGappedExtensionDefaults ()
	Overrides GappedExtensionDefaults for tblastx options.
void	CTBlastxOptionsHandle::SetSubjectSequenceOptionsDefaults ()
	Overrides SubjectSequenceOptionsDefaults for tblastx options.
	CBlastTracebackSearch::CBlastTracebackSearch (CRef< IQueryFactory > qf, CRef< CBlastOptions > opts, BlastSeqSrc *seqsrc, CRef< IBlastSeqInfoSrc > seqinfosrc, CRef< TBlastHSPStream > hsps, CConstRef< objects::CPssmWithParameters > pssm=null)
	Create a BlastSeqSrc re-using an already created BlastSeqSrc.
	CBlastTracebackSearch::CBlastTracebackSearch (CRef< IQueryFactory > query_factory, CRef< SInternalData > internal_data, CRef< CBlastOptions > opts, CRef< IBlastSeqInfoSrc > seqinfosrc, TSearchMessages &search_msgs)
	Use the internal data and return value of the preliminary search to proceed with the traceback.
virtual	CBlastTracebackSearch::~CBlastTracebackSearch ()
	Destructor.
void	CBlastTracebackSearch::SetResultType (EResultType type)
	Specifies how the Seq-align-set returned as part of the results is formatted.
void	CBlastTracebackSearch::SetDBScanInfo (CRef< SDatabaseScanData > dbscan_info)
	Sets the m_DBscanInfo field.
void	CBlastTracebackSearch::x_Init (CRef< IQueryFactory > qf, CRef< CBlastOptions > opts, CConstRef< objects::CPssmWithParameters > pssm, const string &dbname, CRef< TBlastHSPStream > hsps)
	Common initialization performed when doing traceback only.
bool	CBlastTracebackSearch::x_IsSuitableForPartialFetching ()
	Determines if the search is suitable for partial fetching or not.
void	CBlastTracebackSearch::x_SetSubjectRangesForPartialFetching ()
	Sets up the underlying BLAST database object handle to retrieve subject sequences partially during the traceback processing.
CRef< CSearchResultSet >	CBlastTracebackSearch::Run ()
	Run the traceback search.
	CSearchDatabase::CSearchDatabase (const string &dbname, EMoleculeType mol_type)
	Simple constructor.
	CSearchDatabase::CSearchDatabase (const string &dbname, EMoleculeType mol_type, const string &entrez_query)
	Constructor with allows an entrez query to be specified.
	CSearchDatabase::CSearchDatabase (const string &dbname, EMoleculeType mol_type, const TGiList &gilist)
	Constructor with allows a gi list to be specified.
	CSearchDatabase::CSearchDatabase (const string &dbname, EMoleculeType mol_type, const string &entrez_query, const TGiList &gilist)
	Constructor with allows a gi list and an entrez query to be specified.
void	CSearchDatabase::SetDatabaseName (const string &dbname)
	Mutator for the database name.
string	CSearchDatabase::GetDatabaseName () const
	Accessor for the database name.
void	CSearchDatabase::SetMoleculeType (EMoleculeType mol_type)
	Mutator for the molecule type.
EMoleculeType	CSearchDatabase::GetMoleculeType () const
	Accessor for the molecule type.
void	CSearchDatabase::SetEntrezQueryLimitation (const string &entrez_query)
	Mutator for the entrez query.
string	CSearchDatabase::GetEntrezQueryLimitation () const
	Accessor for the entrez query.
void	CSearchDatabase::SetGiListLimitation (const TGiList &gilist)
	Mutator for the gi list.
TGiList &	CSearchDatabase::SetGiListLimitation ()
	Mutator for the gi list.
const TGiList &	CSearchDatabase::GetGiListLimitation () const
	Accessor for the gi list.
void	CSearchDatabase::SetFilteringAlgorithm (int filt_algorithm_id)
	Mutator for the filtering algorithm.
int	CSearchDatabase::GetFilteringAlgorithm () const
	Accessor for the filtering algorithm ID.
void	CSearchDatabase::SetNegativeGiListLimitation (const TGiList &gilist)
	Mutator for the negative gi list.
TGiList &	CSearchDatabase::SetNegativeGiListLimitation ()
	Mutator for the negative gi list.
const TGiList &	CSearchDatabase::GetNegativeGiListLimitation () const
	Accessor for the negative gi list.
static string	CReference::GetString (EPublication pub)
	Reference for requested publication.
static string	CReference::GetHTMLFreeString (EPublication pub)
	Reference for requested publication without umlaut.
static string	CReference::GetPubmedUrl (EPublication pub)
	Get Pubmed url for requested publication.
bool	CBlastServices::IsValidBlastDb (const string &dbname, bool is_protein)
	Returns true if the BLAST database specified exists in the NCBI servers.
CRef< objects::CBlast4_database_info >	CBlastServices::x_FindDbInfoFromAvailableDatabases (CRef< objects::CBlast4_database > blastdb)
	Look for a database matching this method's argument and returned detailed information about it.
vector< CRef< objects::CBlast4_database_info > >	CBlastServices::GetOrganismSpecificRepeatsDatabases ()
	Retrieve organism specific repeats databases.
void	CBlastServices::x_GetAvailableDatabases ()
	Retrieve the BLAST databases available for searching.
CRef< objects::CBlast4_database_info >	CBlastServices::GetDatabaseInfo (CRef< objects::CBlast4_database > blastdb)
	Retrieve detailed information for a given BLAST database.
static void	CBlastServices::GetSequencesInfo (TSeqIdVector &seqids, const string &database, char seqtype, TBioseqVector &bioseqs, string &errors, string &warnings, bool verbose=false)
	Seq-ids.
static void	CBlastServices::GetSequences (TSeqIdVector &seqids, const string &database, char seqtype, TBioseqVector &bioseqs, string &errors, string &warnings, bool verbose=false)
	Get a set of Bioseqs given an input set of Seq-ids.
static void	CBlastServices::GetSequenceParts (const TSeqIntervalVector &seqids, const string &database, char seqtype, TSeqIdVector &ids, TSeqDataVector &seq_data, string &errors, string &warnings, bool verbose=false)
static void	CBlastServices::x_GetPartsFromReply (CRef< objects::CBlast4_reply > reply, TSeqIdVector &ids, TSeqDataVector &seq_data, string &errors, string &warnings)
	Extract information from the get-seq-parts reply object.
static void	CBlastServices::x_GetSeqsFromReply (CRef< objects::CBlast4_reply > reply, TBioseqVector &bioseqs, string &errors, string &warnings)
	Get bioseqs from a sequence fetching reply.
static CRef< objects::CBlast4_request >	CBlastServices::x_BuildGetSeqRequest (TSeqIdVector &seqids, const string &database, char seqtype, bool skip_seq_data, string &errors)
	Build Sequence Fetching Request.
static void	CBlastServices::x_GetSequences (TSeqIdVector &seqids, const string &database, char seqtype, bool skip_seq_data, TBioseqVector &bioseqs, string &errors, string &warnings, bool verbose)
	Main function to issue a Blast4-get-sequences-request and collect its results from the remote BLAST server.
static CRef< objects::CBlast4_request >	CBlastServices::x_BuildGetSeqPartsRequest (const TSeqIntervalVector &seqid, const string &database, char seqtype, string &errors)
	Build Sequence Parts Fetching Request.
Variables
const Uint1	NCBI4NA_TO_BLASTNA []
	Translates between ncbi4na and blastna.
const Uint1	BLASTNA_TO_NCBI4NA []
	Translates between blastna and ncbi4na.
const Uint1	IUPACNA_TO_BLASTNA []
	Translates between iupacna and blastna.
const Uint1	IUPACNA_TO_NCBI4NA []
	Translates between iupacna and ncbi4na.
const Uint1	AMINOACID_TO_NCBISTDAA []
	Translates between ncbieaa and ncbistdaa.
const char	NCBISTDAA_TO_AMINOACID []
	Translates between ncbieaa and ncbistdaa.
const char	BLASTNA_TO_IUPACNA []
	Translates between blastna and iupacna.
const char	NCBI4NA_TO_IUPACNA []
	Translates between ncbi4na and iupacna.
const Uint1	kProtSentinel
	Sentinel byte for protein sequences.
const Uint1	kNuclSentinel
	Sentinel nibble for nucleotide sequences.
static DbIndexPreSearchFnType	PreSearchFn = &NullPreSearch
	Global pointer to the appropriate pre-search function, based on whether or not index search is enabled.
static DbIndexSetQueryInfoFnType	SetQueryInfoFn = &NullSetQueryInfo
	Global pointer to the appropriate callback to set query info, based on whether or not index search is enabled.
static DbIndexRunSearchFnType	RunSearchFn = &NullRunSearch
	Global pointer to the appropriate callback to run indexed search, based on whether or not index search is enabled.
static DbIndexSetNumThreadsFnType	SetNumThreadsFn = &NullSetNumThreads
	Global pointer to the appropriate to set number of threads for indexed search, based on whether or not index search is enabled.
static const int	kInvalidFilterValue = -1
static const TSeqPos	kBlastAlignmentDim = 2
	BLAST alignments have always 2 dimensions (i.e.
	USING_NCBI_SCOPE
static const string	kReferences [(int) CReference::eMaxPublications+1]
	References for the various BLAST publications.
static const string	kPubMedUrls [(int) CReference::eMaxPublications+1]
	Pubmed URLs to retrieve the references defined above.
static Uint4	CAutomaticGenCodeSingleton::m_RefCounter = 0
	Reference counter for this object so that the genetic code singleton is.
static TThreadDataSet	CIndexedDb::Thread_Data_Set
	Set of allocated TThreadLocal objects.
static const string	CRpsAuxFile::kExtension
	Extension associated with the RPS-BLAST database auxiliary file.
static const string	CRpsLookupTblFile::kExtension
	Extension associated with the RPS-BLAST database lookup table file.
static const string	CRpsPssmFile::kExtension
	Extension associated with the RPS-BLAST database PSSM file.

---

Define Documentation

#define BLAST2NA_SIZE   4

Size of compressed nucleic acid alphabet. Definition at line 91 of file blast_encoding.h.

#define BLASTAA_SEQ_CODE   11

== Seq_code_ncbistdaa Definition at line 98 of file blast_encoding.h. Referenced by _PSIComputeScoreProbabilities(), AascanTestFixture::AascanTestFixture(), BLAST_GetStandardAaProbabilities(), Blast_GetStdAlphabet(), BlastScoreBlkNew(), BlastSetup_ScoreBlkInit(), BOOST_AUTO_TEST_CASE(), AalookupTestFixture::FillLookupTable(), Kappa_compactSearchItemsNew(), s_FillScoreBlkWithBadKbp(), LinkHspTestFixture::setupScoreBlk(), and CMultiAligner::x_AssignDefaultResFreqs().

#define BLASTAA_SIZE   28

Size of aminoacid alphabet. Definition at line 93 of file blast_encoding.h. Referenced by _PSICalculateNormalizedSequenceWeights(), _PSIComputeScoreProbabilities(), _PSIMatrixFrequencyRatiosFree(), _PSIMatrixFrequencyRatiosNew(), _PSIPackedMsaNew(), Blast_FillResidueProbability(), BLAST_GetStandardAaProbabilities(), BlastAaLookupTableNew(), BlastCompressedAaLookupTableNew(), BlastScoreBlkNew(), BlastScoreBlkProteinMatrixLoad(), BlastScoreBlkProteinMatrixRead(), BOOST_AUTO_TEST_CASE(), CPssmInputTestData::FindNonIdenticalHighScoringResidue(), TestUtil::GetResidue(), AalookupTestFixture::GetSeqBlk(), GetStandardProbability(), Kappa_compactSearchItemsNew(), Kappa_posSearchItemsNew(), CRedoAlignmentTestFixture::loadPssmFromFile(), LookupTableWrapInit(), PsiBlastComputePssmScores(), s_AddNeighboringWords(), s_AdjustFrequencyRatiosMatrixToMatchScoreMatrix(), s_CompressedAddNeighboringWords(), s_GetAlignParams(), s_GetPosBasedStartFreqRatios(), s_GetQueryInfo(), s_IsValidResidue(), s_loadSortedMatrix(), SCompressedAlphabetNew(), CPssmInputTestData::SetupNearIdenticalHits(), CRedoAlignmentTestFixture::setupPositionBasedBlastScoreBlk(), and SPsiBlastScoreMatrixNew().

#define BLASTNA_SEQ_CODE   99

Identifies the blastna alphabet, for use in blast only. Definition at line 96 of file blast_encoding.h. Referenced by Blast_ScoreBlkMatrixFill(), BlastScoreBlkNew(), BlastScoreBlkProteinMatrixRead(), BlastSetup_ScoreBlkInit(), BOOST_AUTO_TEST_CASE(), LinkHspTestFixture::setupScoreBlk(), and CBlastExtendTestFixture::setupStructures().

#define BLASTNA_SIZE   16

Size of nucleic acid alphabet. Definition at line 92 of file blast_encoding.h. Referenced by BlastScoreBlkNew(), BlastScoreBlkNuclMatrixCreate(), and GetSequenceSingleNucleotideStrand().

#define DECLARE_AUTO_CLASS_WRAPPER (  struct_name, free_func   )

Value: /** Wrapper class for struct_name. */ \ \ class C##struct_name : public CObject \ { \ public: \ C##struct_name() : m_Ptr(NULL) {} \ C##struct_name(struct_name* p) : m_Ptr(p) {} \ virtual ~C##struct_name() { Reset(); } \ void Reset(struct_name* p = NULL) { \ if (m_Ptr) { \ free_func(m_Ptr); \ } \ m_Ptr = p; \ } \ struct_name* Release() { \ struct_name* retval = m_Ptr; \ m_Ptr = NULL; \ return retval; \ } \ struct_name* Get() const { return m_Ptr; } \ operator struct_name *() { return m_Ptr; } \ operator struct_name *() const { return m_Ptr; } \ struct_name* operator->() { return m_Ptr; } \ struct_name* operator->() const { return m_Ptr; } \ struct_name** operator&() { return &m_Ptr; } \ virtual void DebugDump(CDebugDumpContext ddc, unsigned int depth) const;\ private: \ struct_name* m_Ptr; \ } Declares class to handle deallocating of the structure using the appropriate function. Definition at line 215 of file blast_aux.hpp.

#define GAP_IN_ALIGNMENT   ((Uint4)-1)

Representation of GAP in Seq-align. Definition at line 74 of file psi_pssm_input.cpp. Referenced by BOOST_AUTO_TEST_CASE(), and CPsiBlastInputData::x_GetSubjectSequence().

#define GAP_VALUE   -1

Value in the Dense-seg indicating a gap. Definition at line 64 of file blast_seqalign.cpp. Referenced by s_CollectSeqAlignData(), and s_CreateStdSegs().

#define NCBI4NA_SEQ_CODE   4

== Seq_code_ncbi4na Definition at line 99 of file blast_encoding.h.

#define SMALLEST_EVALUE   1.0e-180

Threshold below which e-values are saved as 0. Definition at line 60 of file blast_seqalign.cpp. Referenced by s_BuildScoreList(), and s_CalculateScoreVectorSize().

#define TYPEDEF_AUTOPTR_ARRAYDELETER (  type   )     typedef AutoPtr<type, ArrayDeleter<type> > TAuto ## type ## ArrayPtr

Uses delete [] operator - for C++ arrays. Definition at line 90 of file blast_aux.hpp.

#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. Definition at line 86 of file blast_aux.hpp.

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Typedef Documentation

typedef AutoPtr< Char , CDeleter< Char > > TAutoCharPtr

Declares TAutoCharPtr (for Char arrays allocated with malloc/calloc). Definition at line 97 of file blast_aux.hpp.

typedef AutoPtr< Uint1 , ArrayDeleter< Uint1 > > TAutoUint1ArrayPtr

Declares TAutoUint1ArrayPtr (for Uint1 arrays allocated with new[]). Definition at line 99 of file blast_aux.hpp.

typedef AutoPtr< Uint1 , CDeleter< Uint1 > > TAutoUint1Ptr

Declares TAutoUint1Ptr (for Uint1 arrays allocated with malloc/calloc). Definition at line 95 of file blast_aux.hpp.

typedef CStructWrapper<BlastDiagnostics> TBlastDiagnostics

Definition at line 300 of file setup_factory.hpp.

typedef CStructWrapper<BlastHSPStream> TBlastHSPStream

Definition at line 301 of file setup_factory.hpp.

typedef CStructWrapper<BlastScoreBlk> TBlastScoreBlk

Definition at line 298 of file setup_factory.hpp.

typedef CStructWrapper<BlastSeqSrc> TBlastSeqSrc

Definition at line 302 of file setup_factory.hpp.

typedef COpenRange<TSeqPos> TChunkRange

Range describing a query chunk. Definition at line 50 of file split_query_blk.hpp.

typedef list< CRef<objects::CBlast4_error> > TErrorList

Error value type used by Blast4 ASN.1 objects. Definition at line 74 of file remote_blast.cpp.

typedef CStructWrapper<LookupTableWrap> TLookupTableWrap

Definition at line 299 of file setup_factory.hpp.

typedef SSeqDB_SeqSrc_Data TSeqDBData

Definition at line 101 of file seqsrc_seqdb.cpp.

typedef CStructWrapper<SPHIPatternSearchBlk> TSPHIPatternSearchBlk

Definition at line 303 of file setup_factory.hpp.

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Enumeration Type Documentation

enum EBlastEncoding

Different types of sequence encodings for sequence retrieval from the BLAST database. Enumerator: eBlastEncodingProtein  NCBIstdaa. eBlastEncodingNucleotide  Special encoding for preliminary stage of BLAST: permutation of NCBI4na. A.k.a.: BLASTNA encoding eBlastEncodingNcbi4na  NCBI4na. eBlastEncodingNcbi2na  NCBI2na. eBlastEncodingError  Error value for encoding. Definition at line 53 of file blast_encoding.h.

enum EBlastOptIdx

Index of remote BLAST options. Enumerator: eBlastOpt_Program  eBlastOpt_WordThreshold  eBlastOpt_LookupTableType  eBlastOpt_WordSize  eBlastOpt_AlphabetSize  eBlastOpt_MBTemplateLength  eBlastOpt_MBTemplateType  eBlastOpt_FilterString  eBlastOpt_MaskAtHash  eBlastOpt_DustFiltering  eBlastOpt_DustFilteringLevel  eBlastOpt_DustFilteringWindow  eBlastOpt_DustFilteringLinker  eBlastOpt_SegFiltering  eBlastOpt_SegFilteringWindow  eBlastOpt_SegFilteringLocut  eBlastOpt_SegFilteringHicut  eBlastOpt_RepeatFiltering  eBlastOpt_RepeatFilteringDB  eBlastOpt_StrandOption  eBlastOpt_QueryGeneticCode  eBlastOpt_WindowSize  eBlastOpt_SeedContainerType  eBlastOpt_SeedExtensionMethod  eBlastOpt_XDropoff  eBlastOpt_GapXDropoff  eBlastOpt_GapXDropoffFinal  eBlastOpt_GapTrigger  eBlastOpt_GapExtnAlgorithm  eBlastOpt_HitlistSize  eBlastOpt_MaxNumHspPerSequence  eBlastOpt_CullingLimit  eBlastOpt_EvalueThreshold  eBlastOpt_CutoffScore  eBlastOpt_PercentIdentity  eBlastOpt_SumStatisticsMode  eBlastOpt_LongestIntronLength  eBlastOpt_GappedMode  eBlastOpt_MatrixName  eBlastOpt_MatrixPath  eBlastOpt_MatchReward  eBlastOpt_MismatchPenalty  eBlastOpt_GapOpeningCost  eBlastOpt_GapExtensionCost  eBlastOpt_FrameShiftPenalty  eBlastOpt_OutOfFrameMode  eBlastOpt_DbLength  eBlastOpt_DbSeqNum  eBlastOpt_EffectiveSearchSpace  eBlastOpt_DbGeneticCode  eBlastOpt_PHIPattern  eBlastOpt_InclusionThreshold  eBlastOpt_PseudoCount  eBlastOpt_GapTracebackAlgorithm  eBlastOpt_CompositionBasedStats  eBlastOpt_SmithWatermanMode  eBlastOpt_UnifiedP  eBlastOpt_WindowMaskerDatabase  eBlastOpt_WindowMaskerTaxId  eBlastOpt_ForceMbIndex  eBlastOpt_MbIndexName  eBlastOpt_BestHitScoreEdge  eBlastOpt_BestHitOverhang  Definition at line 62 of file blast_options_cxx.cpp.

enum ESentinelType

Allows specification of whether sentinel bytes should be used or not. Enumerator: eSentinels  Use sentinel bytes. eNoSentinels  Do not use sentinel bytes. Definition at line 93 of file blast_setup.hpp.

---

Function Documentation

void CSplitQueryBlk::AddContextOffsetToChunk (  size_t  chunk_num, Int4  context_offset )  [inherited]

Adds a context offset (correction) to a given chunk. Parameters: chunk_num  desired chunk [in] context_offset  query context offset (correction) to be added [in] Definition at line 187 of file split_query_blk.cpp. References CSplitQueryBlk::m_SplitQueryBlk, and SplitQueryBlk_AddContextOffsetToChunk().

void CSplitQueryBlk::AddContextToChunk (  size_t  chunk_num, Int4  context_index )  [inherited]

Adds a query context to a given chunk. Parameters: chunk_num  desired chunk [in] context_index  context of the concatenated query to be added [in] Definition at line 177 of file split_query_blk.cpp. References CSplitQueryBlk::m_SplitQueryBlk, and SplitQueryBlk_AddContextToChunk().

void TSearchMessages::AddMessageAllQueries (  EBlastSeverity  severity, int  error_id, const string &  message )  [inherited]

Add a message for all queries. Parameters: severity  The severity of this message. [in] error_id  A number unique to this error. [in] message  A description of the error for the user. [in] Definition at line 1012 of file blast_aux.cpp. References eBlastSevWarning, kBlastMessageNoContext, and NON_CONST_ITERATE. Referenced by CBlastPrelimSearch::Run().

void CSplitQueryBlk::AddQueryToChunk (  size_t  chunk_num, Int4  query_index )  [inherited]

Adds a query index to a given chunk. Parameters: chunk_num  desired chunk [in] query_index  index of query to be added [in] Definition at line 167 of file split_query_blk.cpp. References CSplitQueryBlk::m_SplitQueryBlk, and SplitQueryBlk_AddQueryToChunk().

void CBlastQueryFilteredFrames::AddSeqLoc (  const objects::CSeq_interval &  intv, int  frame )  [inherited]

Add a masked interval to the specified frame. The specified interval of the specified frame is masked. This creates a BlastSeqLoc object inside this container for that frame, which will be freed at destruction time unless the client code calls Release() for that frame. Parameters: intv  The interval to mask. frame  The specific frame, expressed as a value from ETranslationFrame, on which this interval falls. Definition at line 1666 of file blast_setup_cxx.cpp. References _ASSERT, BlastSeqLocNew(), eBlastTypeBlastn, CSeqLocInfo::eFrameMinus1, CSeqLocInfo::eFramePlus1, set< Key, Compare >::empty(), CBlastQueryFilteredFrames::m_Frames, CBlastQueryFilteredFrames::m_Program, CBlastQueryFilteredFrames::m_Seqlocs, CBlastQueryFilteredFrames::m_SeqlocTails, and CBlastQueryFilteredFrames::x_VerifyFrame().

EProgram CBlastOptionsBuilder::AdjustProgram (  const TValueList *  L, EProgram  program, const string &  program_string )  [static, inherited]

Adjust the EProgram based on option values. The blast4 protocol uses a notion of program and service to represent the type of search to do. However, for some values of program and service, it is necessary to look at options values in order to determine the precise EProgram value. This is particularly true when dealing with discontiguous megablast for example. This method adjusts the program value based on the additional information found in these options. Parameters: L  The list of options used for this search. program  The EProgram suggested by program+service. program_string  The program as a string. Returns: The EProgram value as adjusted by options or the argument program if L is NULL Definition at line 458 of file blast_options_builder.cpp. References B4Param_MBTemplateLength, eDiscMegablast, CBlast4_value_Base::GetInteger(), CBlast4_parameter_Base::GetValue(), ITERATE, and CBlast4Field::Match(). Referenced by CBlastOptionsBuilder::GetSearchOptions().

void CPsiBlastIterationState::Advance (  const TSeqIds &  list  )  [inherited]

Advance the iterator by passing it the list of Seq-ids which passed the inclusion criteria for the current iteration. Definition at line 123 of file psiblast_iteration.cpp. References CPsiBlastIterationState::m_CurrentData, CPsiBlastIterationState::m_IterationsDone, CPsiBlastIterationState::m_PreviousData, and CPsiBlastIterationState::x_ThrowExceptionOnLogicError(). Referenced by BOOST_AUTO_TEST_CASE(), and RunNIterationsWithoutConverging().

MT_LOCK Blast_CMT_LOCKInit (  void   )

Initialize a mutex locking mechanism for BLAST. Definition at line 77 of file blast_mtlock.cpp. References BlastLockCleanup(), BlastLockHandler(), and MT_LOCK_Create(). Referenced by CSetupFactory::CreateDiagnosticsStructureMT(), CBlastPrelimSearch::SetNumberOfThreads(), and testHSPStream().

Int4 BLAST_FindBestNucleotideWordSize (  double  min_percent_identity, Int4  min_align_length )

Given a minimum amount of identity and the minimum desired length of nucleotide alignments, find the largest blastn word size that will find random instances of those alignments with high probability. Note that when blast is actually run, it is obviously still possible to find alignments that are shorter and/or have less identity than what is specified here. The returned word size is just a choice that makes it unlikely that ungapped blast will miss alignments that exceed *both* minimums. The algorithm used is described in Valer Gotea, Vamsi Veeramachaneni, and Wojciech Makalowski "Mastering seeds for genomic size nucleotide BLAST searches" Nucleic Acids Research, 2003, Vol 31, No. 23, pp 6935-6941 Parameters: min_percent_identity  How much identity is expected in random alignments. Less identity means the probability of finding such alignments is decreased [in] min_align_length  The smallest alignment length desired. Longer length gives blastn more leeway to find seeds and increases the computed probability that alignments will be found [in] Returns: The optimal word size, or zero if the optimization process failed Definition at line 441 of file blast_tune.c. References s_FindWordSize(), s_MatrixDataFree(), and s_MatrixDataInit().

void Blast_FindDustFilterLoc (  CBlastQueryVector &  query, Uint4  level = CSymDustMasker::DEFAULT_LEVEL, Uint4  window = CSymDustMasker::DEFAULT_WINDOW, Uint4  linker = CSymDustMasker::DEFAULT_LINKER )

Overloaded version of the function above which takes the filtering implementation's arguments directly, CBlastQueryVector version. Parameters: query  Vector of sequence locations. [in] [out] level  Dust filtering level argument [in] window  Dust filtering window argument [in] linker  Dust filtering linker argument [in] Definition at line 170 of file dust_filter.cpp. References eBlastTypeBlastn, CBioseq_Handle::eCoding_Iupac, CBlastQueryVector::GetMasks(), CBlastQueryVector::GetQuerySeqLoc(), CBlastQueryVector::GetScope(), PackedSeqLocToMaskedQueryRegions(), s_CombineDustMasksWithUserProvidedMasks(), CBlastQueryVector::SetMaskedRegions(), and CBlastQueryVector::Size().

void Blast_FindDustFilterLoc (  TSeqLocVector &  query, Uint4  level = CSymDustMasker::DEFAULT_LEVEL, Uint4  window = CSymDustMasker::DEFAULT_WINDOW, Uint4  linker = CSymDustMasker::DEFAULT_LINKER )

Overloaded version of the function above which takes the filtering implementation's arguments directly, TSeqLocVector version. Parameters: query  Vector of sequence locations. [in] [out] level  Dust filtering level argument [in] window  Dust filtering window argument [in] linker  Dust filtering linker argument [in] Definition at line 151 of file dust_filter.cpp. References CBioseq_Handle::eCoding_Iupac, NON_CONST_ITERATE, query, and s_CombineDustMasksWithUserProvidedMasks().

void Blast_FindDustFilterLoc (  TSeqLocVector &  query, const CBlastNucleotideOptionsHandle *  nucl_handle )

Finds dust locations for a given set of sequences by calling the the symmetric dust lib. The locations are saved in the respective fields of the SSeqLoc structures. If previous masks exist, they are combined with the new masks. Parameters: query  Vector of sequence locations. [in] [out] nucl_handle  options handle for blast search [in] Definition at line 65 of file dust_filter.cpp. Referenced by BOOST_AUTO_TEST_CASE(), CBl2Seq::SetupSearch(), CBlastQuerySourceOM::x_CalculateMasks(), and x_TestGetFilteredQueryRegions().

void Blast_FindRepeatFilterLoc (  CBlastQueryVector &  query, const char *  filter_db )

Overloaded version of the function above which takes the name of the repeats filtering database to use, and a CBlastQueryVector. Parameters: query  Vector of sequence locations. [in] [out] filter_db  Name of the BLAST database with repeats to use for filtering [in] Definition at line 378 of file repeats_filter_cxx.cpp. References CBlastQueryVector::AddQuery(), CSearchDatabase::eBlastDbIsNucleotide, CBlastQueryVector::GetQuerySeqLoc(), CBlastQueryVector::GetScope(), query, s_CreateRepeatsSearchOptions(), and CBlastQueryVector::Size().

void Blast_FindRepeatFilterLoc (  TSeqLocVector &  query, const char *  filter_db )

Overloaded version of the function above which takes the name of the repeats filtering database to use, and a TSeqLocVector. Parameters: query  Vector of sequence locations. [in] [out] filter_db  Name of the BLAST database with repeats to use for filtering [in] Definition at line 346 of file repeats_filter_cxx.cpp. References CSearchDatabase::eBlastDbIsNucleotide, and s_CreateRepeatsSearchOptions().

void Blast_FindRepeatFilterLoc (  TSeqLocVector &  query_loc, const CBlastOptionsHandle *  opts_handle )

Finds repeats locations for a given set of sequences. The locations are saved in the respective fields of the SSeqLoc structures. If previous masks exist, they are combined with the new masks. opts_handle will be downcast to CBlastNucleotideOptionsHandle and if that succeeds and repeat filtering is specified then it will be run, otherwise it just returns. Parameters: query_loc  Vector of sequence locations. [in] [out] opts_handle  options handle for blast search [in] Definition at line 332 of file repeats_filter_cxx.cpp. References CBlastNucleotideOptionsHandle::GetRepeatFiltering(), and CBlastNucleotideOptionsHandle::GetRepeatFilteringDB(). Referenced by BOOST_AUTO_TEST_CASE(), and CBl2Seq::SetupSearch().

void Blast_FindWindowMaskerLoc (  TSeqLocVector &  query, const string &  lstat )

Find Window Masker filtered locations on TSeqLocVector by database name. Parameters: query  These queries will be masked. [in|out] lstat  Filename of the WindowMasker database. [in] Definition at line 295 of file winmask_filter.cpp. References CBioseq_Handle::eCoding_Iupac, eNa_strand_both, eNa_strand_plus, eNa_strand_unknown, mask, NON_CONST_ITERATE, s_BuildMaskedRanges(), and s_BuildSeqMasker().

void Blast_FindWindowMaskerLoc (  CBlastQueryVector &  query, const string &  lstat )

Find Window Masker filtered locations by database name. Parameters: query  These queries will be masked. [in|out] lstat  Filename of the WindowMasker database. [in] Definition at line 259 of file winmask_filter.cpp. References CBioseq_Handle::eCoding_Iupac, eNa_strand_plus, CBlastQueryVector::GetBlastSearchQuery(), CBlastQueryVector::GetScope(), query, s_BuildMaskedRanges(), s_BuildSeqMasker(), and CBlastQueryVector::Size().

void Blast_FindWindowMaskerLoc (  TSeqLocVector &  query, const CBlastOptionsHandle *  opts_handle )

Find Window Masker filtered locations using a BlastOptionsHandle. Parameters: query  These queries will be masked. [in|out] opts_handle  This provides the database name or taxid. [in] Definition at line 245 of file winmask_filter.cpp. References Blast_FindWindowMaskerLoc_Fwd().

void Blast_FindWindowMaskerLoc (  CBlastQueryVector &  query, const CBlastOptionsHandle *  opts_handle )

Find Window Masker filtered locations using a BlastOptionsHandle. Parameters: query  These queries will be masked. [in|out] opts_handle  This provides the database name or taxid. [in] Definition at line 238 of file winmask_filter.cpp. References Blast_FindWindowMaskerLoc_Fwd(), and query.

void Blast_FindWindowMaskerLoc (  TSeqLocVector &  query, const CBlastOptions *  opts )

Find Window Masker filtered locations using BlastOptions. Parameters: query  These queries will be masked. [in|out] opts  This provides the database name or taxid. [in] Definition at line 231 of file winmask_filter.cpp. References Blast_FindWindowMaskerLoc_Fwd().

void Blast_FindWindowMaskerLoc (  CBlastQueryVector &  query, const CBlastOptions *  opts_handle )

Find Window Masker filtered locations using a BlastOptions. Parameters: query  These queries will be masked. [in|out] opts_handle  This provides the database name or taxid. [in] Definition at line 224 of file winmask_filter.cpp. References Blast_FindWindowMaskerLoc_Fwd(), and query. Referenced by Blast_FindWindowMaskerLoc_Fwd(), Blast_FindWindowMaskerLocTaxId(), and BOOST_AUTO_TEST_CASE().

template<class TQueries> void Blast_FindWindowMaskerLoc_Fwd (  TQueries &  query, const CBlastOptionsHandle *  opts_handle )

Definition at line 210 of file winmask_filter.cpp. References Blast_FindWindowMaskerLoc_Fwd(), and CBlastOptionsHandle::GetOptions().

template<class TQueries> void Blast_FindWindowMaskerLoc_Fwd (  TQueries &  query, const CBlastOptions *  opts )

Definition at line 195 of file winmask_filter.cpp. References Blast_FindWindowMaskerLoc(), and CBlastOptions::GetWindowMaskerDatabase(). Referenced by Blast_FindWindowMaskerLoc(), and Blast_FindWindowMaskerLoc_Fwd().

void Blast_FindWindowMaskerLocTaxId (  TSeqLocVector &  query, int  taxid )

Find Window Masker filtered locations on a TSeqLocVector by Taxid. Parameters: query  These queries will be masked. [in|out] taxid  This taxid will be used to find a database. [in] Definition at line 492 of file winmask_filter.cpp. References Blast_FindWindowMaskerLoc(), and s_WindowMaskerTaxidToDb().

void Blast_FindWindowMaskerLocTaxId (  CBlastQueryVector &  query, int  taxid )

Find Window Masker filtered locations by taxonomic ID. Parameters: query  These queries will be masked. [in|out] taxid  This taxid will be used to find a database. [in] Definition at line 485 of file winmask_filter.cpp. References Blast_FindWindowMaskerLoc(), and s_WindowMaskerTaxidToDb().

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. Parameters: program  Type of BLAST program [in] queries  Container of query ids and start/stop locations [in] mask  All masking locations [in] mask_v  Vector of per-query lists of mask locations in CSeqLocInfo form. [out] Definition at line 860 of file blast_aux.cpp. References _ASSERT, GetNumberOfContexts(), NStr::IntToString(), mask, and NCBI_THROW. Referenced by BOOST_AUTO_TEST_CASE(), and CBl2Seq::GetFilteredQueryRegions().

BlastHSPStream* Blast_HSPListCQueueInit (   )

Function to initialize a queue HSP stream.

void Blast_Message2TSearchMessages (  const Blast_Message *  blmsg, const BlastQueryInfo *  query_info, TSearchMessages &  messages )

Converts the Blast_Message structure into a TSearchMessages object. Definition at line 71 of file blast_aux_priv.cpp. References _ASSERT, Blast_Message::context, BlastQueryInfo::contexts, kBlastMessageNoContext, kQueryIndex, Blast_Message::message, Blast_Message::next, BlastQueryInfo::num_queries, BlastContextInfo::query_index, and Blast_Message::severity. Referenced by CSetupFactory::CreateLookupTable(), CSetupFactory::CreateScoreBlock(), and CBl2Seq::SetupSearch().

string Blast_ProgramNameFromType (  EBlastProgramType  program  )

Returns a string program name, given a blast::EBlastProgramType enumeration. Parameters: program  Enumerated program value [in] Returns: String program name. Definition at line 769 of file blast_aux.cpp. References BlastNumber2Program(), NcbiEmptyString, and sfree. Referenced by BOOST_AUTO_TEST_CASE(), CCmdLineBlastXMLReportData::GetBlastProgramName(), GetNumberOfContexts(), s_ImportPssm(), CCmdLineBlastXMLReportData::x_FillScoreMatrix(), and x_TestGetSeqLocInfoVector().

Int2 BLAST_SmithWatermanGetGappedScore (  EBlastProgramType  program_number, BLAST_SequenceBlk *  query, BlastQueryInfo *  query_info, BLAST_SequenceBlk *  subject, BlastGapAlignStruct *  gap_align, const BlastScoringParameters *  score_params, const BlastExtensionParameters *  ext_params, const BlastHitSavingParameters *  hit_params, BlastInitHitList *  init_hitlist, BlastHSPList **  hsp_list_ptr, BlastGappedStats *  gapped_stats, Boolean *  fence_hit )

Performs score-only Smith-Waterman gapped alignment of the subject sequence with all contexts in the query. Parameters: program_number  Type of BLAST program [in] query  The query sequence block [in] query_info  Query information structure, containing offsets into the concatenated sequence [in] subject  The subject sequence block [in] gap_align  The auxiliary structure for gapped alignment [in] score_params  Options and parameters related to scoring [in] ext_params  Options and parameters related to extensions [in] hit_params  Options related to saving hits [in] init_hitlist  List of initial HSPs (ignored) hsp_list_ptr  Structure containing all saved HSPs. Note that there will be at most one HSP for each context that contains a gapped alignment that exceeds a cutoff score. [out] gapped_stats  Return statistics (not filled if NULL) [out] fence_hit  Partial range support (not used for S/W). [in] Definition at line 634 of file blast_sw.c. References BLAST_FrameToContext(), Blast_HSPInit(), Blast_HSPListNew(), Blast_HSPListSaveHSP(), Blast_ProgramIsRpsBlast(), BlastHspNumMax(), BlastQueryInfo::contexts, BlastGappedCutoffs::cutoff_score, BlastHitSavingParameters::cutoffs, SBlastScoreMatrix::data, eBlastTypeBlastn, eBlastTypePhiBlastn, eBlastTypeRpsTblastn, BlastQueryInfo::first_context, BlastContextInfo::frame, BlastScoringParameters::gap_extend, BlastScoringParameters::gap_open, BlastContextInfo::is_valid, NUM_FRAMES, BlastHitSavingParameters::options, BlastScoreBlk::psi_matrix, SPsiBlastScoreMatrix::pssm, query, BlastContextInfo::query_length, BlastContextInfo::query_offset, s_NuclSmithWaterman(), s_SmithWatermanScoreOnly(), BlastGapAlignStruct::sbp, subject, and TRUE. Referenced by s_BlastSetUpAuxStructures().

CRef< CSearchResultSet > BlastBuildSearchResultSet (  const vector< CConstRef< CSeq_id > > &  query_ids, const BlastScoreBlk *  sbp, const BlastQueryInfo *  qinfo, EBlastProgramType  program, const TSeqAlignVector &  alignments, TSearchMessages &  messages, const vector< TSeqLocInfoVector > &  subj_masks, const TSeqLocInfoVector *  query_masks = NULL, const EResultType  result_type = ncbi::blast::eDatabaseSearch )

Build a CSearchResultSet from internal BLAST data structures. Parameters: query_masks  Masks for query sequences [in] subj_masks  Masks for subject sequences [in] Definition at line 284 of file blast_aux_priv.cpp. References Blast_ProgramIsPhiBlast(), and eSequenceComparison. Referenced by CBl2Seq::RunEx().

static bool BlastDbFileExists (  string &  path, bool  is_prot )  [static]

Checks if a BLAST database exists at a given file path: looks for an alias file first, then for an index file. Definition at line 1317 of file blast_setup_cxx.cpp. Referenced by FindBlastDbPath().

string BlastErrorCode2String (  Int2  error_code  )

Returns a string containing a human-readable interpretation of the error_code passed as this function's argument. Definition at line 116 of file blast_aux_priv.cpp. References Blast_MessageFree(), Blast_PerrorEx(), and Blast_Message::message. Referenced by CBl2Seq::RunFullSearch().

char * BlastFindMatrixPath (  const char *  matrix_name, Boolean  is_prot )

Returns the path to a specified matrix. This is the implementation of the GET_MATRIX_PATH callback. Parameters: matrix_name  matrix name (e.g., BLOSUM62) [in] is_prot  matrix is for proteins if TRUE [in] Returns: path to matrix, should be deallocated by user. Definition at line 1213 of file blast_setup_cxx.cpp. References BLASTMAT_DIR, CMetaRegistry::eName_RcOrIni, CNcbiEnvironment::Get(), CDir::GetCwd(), CNcbiApplication::GetEnvironment(), CDirEntry::GetPathSeparator(), CNcbiApplication::Instance(), CMetaRegistry::Load(), CDirEntry::MakePath(), CMetaRegistry::SEntry::registry, s_GetCStringOfMatrixPath(), strdup, and NStr::ToUpper(). Referenced by AascanTestFixture::AascanTestFixture(), BOOST_AUTO_TEST_CASE(), CPhiblastTestFixture::CPhiblastTestFixture(), CSetupFactory::CreateScoreBlock(), AalookupTestFixture::FillLookupTable(), InitializeBlastScoreBlk(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), LinkHspTestFixture::setupScoreBlk(), CBl2Seq::SetupSearch(), CBlastExtendTestFixture::setupStructures(), CPssmEngine::x_InitializeScoreBlock(), and CTracebackTestFixture::x_SetupMain().

CRef<CSeq_align_set> BlastHitList2SeqAlign_OMF (  const BlastHitList *  hit_list, EBlastProgramType  prog, const CSeq_loc &  query_loc, TSeqPos  query_length, const IBlastSeqInfoSrc *  seqinfo_src, bool  is_gapped, bool  is_ooframe, TSeqLocInfoVector &  subj_masks )

Definition at line 1264 of file blast_seqalign.cpp. References _ASSERT, Blast_HSPListSortByEvalue(), GetSequenceLengthAndId(), BlastHitList::hsplist_array, BlastHitList::hsplist_count, s_CreateEmptySeq_align_set(), and SerialAssign(). Referenced by PhiBlastResults2SeqAlign_OMF(), and s_BlastResults2SeqAlignDatabaseSearch_OMF().

void BLASTHspListToSeqAlign (  EBlastProgramType  program, BlastHSPList *  hsp_list, CRef< CSeq_id >  query_id, CRef< CSeq_id >  subject_id, Int4  query_length, Int4  subject_length, bool  is_ooframe, const vector< int > &  gi_list, vector< CRef< CSeq_align > > &  sa_vector )

This is called for each query and each subject in a BLAST search. Parameters: program  BLAST program [in] hsp_list  HSP list structure [in] query_id  Query sequence identifier [in] subject_id  Subject sequence identifier [in] query_length  Length of query sequence [in] subject_length  Length of subject sequence [in] is_ooframe  Was this a search with out-of-frame gapping? [in] gi_list  List of GIs for the subject sequence [in] sa_vector  Resulting Seq-align object [in|out] Definition at line 1191 of file blast_seqalign.cpp. References BlastHSPList::hsp_array, BlastHSPList::hspcnt, and s_OOFBlastHSP2SeqAlign().

objects::ENa_strand BlastSetup_GetStrand (  const objects::CSeq_loc &  query_seqloc, EBlastProgramType  program, objects::ENa_strand  strand_option )

Choose between a Seq-loc specified query strand and the strand obtained from the CBlastOptions. Parameters: query_seqloc  Seq-loc corresponding to a given query sequence [in] program  program type from the CORE's point of view [in] strand_option  strand as specified by the BLAST options [in] Definition at line 120 of file blast_setup_cxx.cpp. References s_BlastSetup_GetStrand(). Referenced by CQuerySplitter::x_ComputeQueryContextsForChunks().

CRef< SBlastSetupData > BlastSetupPreliminarySearch (  CRef< IQueryFactory >  query_factory, CRef< CBlastOptions >  options, bool  is_multi_threaded = false )

Set up internal data structures used by the BLAST CORE engine. Parameters: query_factory  source of query sequence data structures [in] options  BLAST options [in] is_multi_threaded  whether this search is multi-threaded or not [in] Definition at line 126 of file blast_aux_priv.cpp. References BlastSetupPreliminarySearchEx().

CRef< SBlastSetupData > BlastSetupPreliminarySearchEx (  CRef< IQueryFactory >  qf, CRef< CBlastOptions >  options, CConstRef< CPssmWithParameters >  pssm, BlastSeqSrc *  seqsrc, bool  is_multi_threaded )

Extended interface to set up internal data structures used by the BLAST CORE engine. Parameters: query_factory  source of query sequence data structures [in] options  BLAST options [in] pssm  PSSM [in] seqsrc  source of database/subject sequence data [in] is_multi_threaded  whether this search is multi-threaded or not [in] Definition at line 136 of file blast_aux_priv.cpp. References CSetupFactory::InitializeMegablastDbIndex(). Referenced by BlastSetupPreliminarySearch(), SplitQuery_CreateChunkData(), and CBlastPrelimSearch::x_Init().

void BLASTUngappedHspListToSeqAlign (  EBlastProgramType  program, BlastHSPList *  hsp_list, CRef< CSeq_id >  query_id, CRef< CSeq_id >  subject_id, Int4  query_length, Int4  subject_length, const vector< int > &  gi_list, vector< CRef< CSeq_align > > &  sa_vector )

Creates a Seq-align from an HSP list for an ungapped search. Parameters: program  BLAST program [in] hsp_list  HSP list structure [in] query_id  Query sequence identifier [in] subject_id  Subject sequence identifier [in] query_length  Length of the query [in] subject_length  Length of the subject [in] gi_list  List of GIs for the subject sequence. Definition at line 1129 of file blast_seqalign.cpp. References eBlastTypeBlastn, eBlastTypeBlastp, eBlastTypeRpsBlast, CSeq_align_Base::eType_diags, BlastHSPList::hsp_array, BlastHSPList::hspcnt, and x_UngappedHSPToDenseDiag().

void BuildBlastAncillaryData (  EBlastProgramType  program, const vector< CConstRef< CSeq_id > > &  query_ids, const BlastScoreBlk *  sbp, const BlastQueryInfo *  qinfo, const TSeqAlignVector &  alignments, const EResultType  result_type, CSearchResultSet::TAncillaryVector &  retval )

Builds an CSearchResultSet::TAncillaryVector. Parameters: program  BLAST program [in] query_ids  the sequence identifiers for the queries [in] sbp  BlastScoreBlk structure used during the search [in] qinfo  BlastQueryInfo structure used during the search [in] alignments  alignments that were the result of the search [in] result_type  are these results for bl2seq or a database search? [in] retval  the output of this function is returned through this parameter [in|out] Definition at line 243 of file blast_aux_priv.cpp. References Blast_ProgramIsPhiBlast(). Referenced by CBl2Seq::x_BuildAncillaryData().

TSeqPos CalculateSeqBufferLength (  TSeqPos  sequence_length, EBlastEncoding  encoding, objects::ENa_strand  strand = objects::eNa_strand_unknown, ESentinelType  sentinel = eSentinels )

Calculates the length of the buffer to allocate given the desired encoding, strand (if applicable) and use of sentinel bytes around sequence. Parameters: sequence_length  Length of the sequence [in] encoding  Desired encoding for calculation (supported encodings are listed in GetSequence()) [in] strand  Which strand to use for calculation [in] sentinel  Whether to include or not sentinels in calculation. Same criteria as GetSequence() applies [in] Returns: Length of the buffer to allocate to contain original sequence of length sequence_length for given encoding and parameter constraints. If the sequence_length is 0, the return value will be 0 too Exceptions: CBlastException  in case of unsupported encoding Definition at line 1109 of file blast_setup_cxx.cpp. References _ASSERT, COMPRESSION_RATIO, eBlastEncodingNcbi2na, eBlastEncodingNcbi4na, eBlastEncodingNucleotide, eBlastEncodingProtein, eNa_strand_both, eNa_strand_plus, eNa_strand_unknown, eNoSentinels, eSentinels, and NCBI_THROW. Referenced by CompressNcbi2na(), GetSequenceNucleotideBothStrands(), GetSequenceProtein(), and GetSequenceSingleNucleotideStrand().

CAutomaticGenCodeSingleton::CAutomaticGenCodeSingleton (   )  [inherited]

Default constructor. Definition at line 622 of file blast_aux.cpp. References BLAST_GENETIC_CODE, FindGeneticCode(), GenCodeSingletonAdd(), GenCodeSingletonFind(), GenCodeSingletonInit(), AutoPtr< X, Del >::get(), and CAutomaticGenCodeSingleton::m_RefCounter.

CBioseqSeqInfoSrc::CBioseqSeqInfoSrc (  const objects::CBioseq_set &  bss, bool  is_prot )  [inherited]

Parametrized constructor. Parameters: bss  CBioseq_set object from which to obtain the data [in] is_prot  true if sequences in bss argument are all proteins, else false [in] Definition at line 62 of file seqinfosrc_bioseq.cpp.

CBioseqSeqInfoSrc::CBioseqSeqInfoSrc (  const objects::CBioseq &  bs, bool  is_prot )  [inherited]

Parametrized constructor. Parameters: bs  CBioseq object from which to obtain the data [in] is_prot  true if sequence in bs argument is protein, else false [in] Definition at line 58 of file seqinfosrc_bioseq.cpp.

CBl2Seq::CBl2Seq (  const TSeqLocVector &  queries, const TSeqLocVector &  subjects, CBlastOptionsHandle &  opts )  [inherited]

Constructor to allow query concatenation with specified options. Definition at line 125 of file bl2seq.cpp. References CBl2Seq::m_OptsHandle, CRef< C, Locker >::Reset(), and CBl2Seq::x_Init().

CBl2Seq::CBl2Seq (  const TSeqLocVector &  queries, const TSeqLocVector &  subjects, EProgram  p )  [inherited]

Constructor to allow query concatenation with default options. Definition at line 117 of file bl2seq.cpp. References CBlastOptionsFactory::Create(), CBl2Seq::m_OptsHandle, CRef< C, Locker >::Reset(), and CBl2Seq::x_Init().

CBl2Seq::CBl2Seq (  const SSeqLoc &  query, const TSeqLocVector &  subjects, CBlastOptionsHandle &  opts )  [inherited]

Constructor to compare query against all subject sequences with specified options. Definition at line 106 of file bl2seq.cpp. References CBl2Seq::m_OptsHandle, query, CRef< C, Locker >::Reset(), and CBl2Seq::x_Init().

CBl2Seq::CBl2Seq (  const SSeqLoc &  query, const TSeqLocVector &  subjects, EProgram  p )  [inherited]

Constructor to compare query against all subject sequences with default options. Definition at line 95 of file bl2seq.cpp. References CBlastOptionsFactory::Create(), CBl2Seq::m_OptsHandle, query, CRef< C, Locker >::Reset(), and CBl2Seq::x_Init().

CBl2Seq::CBl2Seq (  const SSeqLoc &  query, const SSeqLoc &  subject, CBlastOptionsHandle &  opts )  [inherited]

Constructor to compare 2 sequences with specified options. Definition at line 82 of file bl2seq.cpp. References CBl2Seq::m_OptsHandle, query, CRef< C, Locker >::Reset(), subject, and CBl2Seq::x_Init().

CBl2Seq::CBl2Seq (  const SSeqLoc &  query, const SSeqLoc &  subject, EProgram  p )  [inherited]

Constructor to compare 2 sequences with default options. Definition at line 70 of file bl2seq.cpp. References CBlastOptionsFactory::Create().

CBlastAdvancedProteinOptionsHandle::CBlastAdvancedProteinOptionsHandle (  EAPILocality  locality = CBlastOptions::eLocal  )  [inherited]

Creates object with default options set. Definition at line 46 of file blast_advprot_options.cpp. References eBlastp.

CBlastAncillaryData::CBlastAncillaryData (  pair< double, double >  lambda, pair< double, double >  k, pair< double, double >  h, Int8  effective_search_space, bool  is_psiblast = false )  [inherited]

Parametrized constructor taking pairs of values for ungapped and gapped Karlin-Altschul parameters as well as the effective search space. Parameters: lambda  Pair of ungapped and gapped lambda (in that order) [in] k  Pair of ungapped and gapped k (in that order) [in] h  Pair of ungapped and gapped h (in that order) [in] effective_search_space  effective search space [in] is_psiblast  true if the statistical parameters are for PSI-BLAST [in] Definition at line 108 of file blast_results.cpp. References Blast_KarlinBlkNew(), Blast_KarlinBlk::H, Blast_KarlinBlk::K, Blast_KarlinBlk::Lambda, CBlastAncillaryData::m_GappedKarlinBlk, CBlastAncillaryData::m_PsiGappedKarlinBlk, CBlastAncillaryData::m_PsiUngappedKarlinBlk, CBlastAncillaryData::m_SearchSpace, and CBlastAncillaryData::m_UngappedKarlinBlk.

CBlastAncillaryData::CBlastAncillaryData (  EBlastProgramType  program_type, int  query_number, const BlastScoreBlk *  sbp, const BlastQueryInfo *  query_info )  [inherited]

constructor Parameters: program_type  Type of blast search [in] query_number  The index of the query for which information will be retrieved [in] sbp  Score block, containing Karlin parameters [in] query_info  Structure with per-context information [in] Definition at line 67 of file blast_results.cpp. References BLAST_GetNumberOfContexts(), BlastQueryInfo::contexts, and CBlastAncillaryData::m_SearchSpace.

CBlastNucleotideOptionsHandle::CBlastNucleotideOptionsHandle (  EAPILocality  locality = CBlastOptions::eLocal  )  [inherited]

Creates object with default options set. Definition at line 48 of file blast_nucl_options.cpp.

CBlastOptions::CBlastOptions (  EAPILocality  locality = eLocal  )  [inherited]

Constructor which allows specification of local or remote version of the options (might change in the future). Parameters: locality  specification of whether this type will be used with a remote or local BLAST search database class Definition at line 368 of file blast_options_cxx.cpp. References CBlastOptions::eBoth, CBlastOptions::eLocal, CBlastOptions::eRemote, CBlastOptions::m_Local, and CBlastOptions::m_Remote. Referenced by CBlastOptions::Clone().

CBlastOptionsBuilder::CBlastOptionsBuilder (  const string &  program, const string &  service, CBlastOptions::EAPILocality  locality = CBlastOptions::eLocal )  [inherited]

Constructor. This takes the program and service strings, using them to determine the type of CBlastOptionsHandle to return. Some of the name/value pairs also influence the type of blast options handle required. Parameters: program  Blast4 program string (e.g. blastn or blastp). service  Blast4 service string (e.g. plain or rpsblast). locality  Locality of the resulting object. Definition at line 48 of file blast_options_builder.cpp.

CBlastOptionsHandle::CBlastOptionsHandle (  EAPILocality  locality  )  [inherited]

Default c-tor. Definition at line 58 of file blast_options_handle.cpp.

CBlastOptionsLocal::CBlastOptionsLocal (  const CBlastOptionsLocal &  optsLocal  )  [inherited]

Copy constructor. Definition at line 77 of file blast_options_local_priv.cpp. References CBlastOptionsLocal::x_DoDeepCopy().

CBlastOptionsLocal::CBlastOptionsLocal (   )  [inherited]

Definition at line 53 of file blast_options_local_priv.cpp. References BlastDatabaseOptionsNew(), BlastEffectiveLengthsOptionsNew(), BlastQuerySetUpOptionsNew(), calloc(), eBlastNotSet, CBlastOptionsLocal::m_DbOpts, CBlastOptionsLocal::m_EffLenOpts, CBlastOptionsLocal::m_ExtnOpts, CBlastOptionsLocal::m_ForceMBIndex, CBlastOptionsLocal::m_HitSaveOpts, CBlastOptionsLocal::m_InitWordOpts, CBlastOptionsLocal::m_LutOpts, CBlastOptionsLocal::m_MBIndexLoaded, CBlastOptionsLocal::m_Program, CBlastOptionsLocal::m_PSIBlastOpts, CBlastOptionsLocal::m_QueryOpts, CBlastOptionsLocal::m_ScoringOpts, CBlastOptionsLocal::m_UseMBIndex, PSIBlastOptionsNew(), CBlastScoringOptions::Reset(), CBlastHitSavingOptions::Reset(), CBlastExtensionOptions::Reset(), CLookupTableOptions::Reset(), CBlastInitialWordOptions::Reset(), and CQuerySetUpOptions::Reset().

CBlastPrelimSearch::CBlastPrelimSearch (  CRef< IQueryFactory >  query_factory, CRef< CBlastOptions >  options, BlastSeqSrc *  seqsrc, CConstRef< objects::CPssmWithParameters >  pssm = null )  [inherited]

Constructor which takes a PSSM and an already initialized BlastSeqSrc object. Note: we don't own the BlastSeqSrc Definition at line 87 of file prelim_stage.cpp. References CBlastPrelimSearch::m_InternalData, CRef< C, Locker >::Reset(), and CBlastPrelimSearch::x_Init().

CBlastPrelimSearch::CBlastPrelimSearch (  CRef< IQueryFactory >  query_factory, CRef< CBlastOptions >  options, CRef< CLocalDbAdapter >  db )  [inherited]

Constructor which creates BlastSeqSrc object from the already constructed BLAST database handle. Note: we don't own the BlastSeqSrc Definition at line 76 of file prelim_stage.cpp. References CBlastPrelimSearch::m_InternalData, CRef< C, Locker >::Reset(), and CBlastPrelimSearch::x_Init().

CBlastPrelimSearch::CBlastPrelimSearch (  CRef< IQueryFactory >  query_factory, CRef< CBlastOptions >  options, const CSearchDatabase &  dbinfo )  [inherited]

Constructor which creates and manages a BLAST database handle for the caller. Note: we create a BlastSeqSrc using CSeqDB as its implementation Definition at line 64 of file prelim_stage.cpp. References BlastSeqSrcFree(), and CSetupFactory::CreateBlastSeqSrc().

CBlastProteinOptionsHandle::CBlastProteinOptionsHandle (  EAPILocality  locality = CBlastOptions::eLocal  )  [inherited]

Creates object with default options set. Definition at line 49 of file blast_prot_options.cpp. References eBlastp.

CBlastQueryFilteredFrames::CBlastQueryFilteredFrames (  EBlastProgramType  program, const TMaskedQueryRegions &  mqr )  [inherited]

Construct container for frame values and BlastSeqLocs from a TMaskedQueryRegions vector. Parameters: program  Search program value used [in] mqr  MaskedQueryRegions to convert [in] Definition at line 1470 of file blast_setup_cxx.cpp. References CBlastQueryFilteredFrames::m_TranslateCoords, and CBlastQueryFilteredFrames::x_NeedsTrans().

CBlastQueryFilteredFrames::CBlastQueryFilteredFrames (  EBlastProgramType  program  )  [inherited]

Construct container for frame values and BlastSeqLocs for the specified search program. Parameters: program  The type of search being done. Definition at line 1450 of file blast_setup_cxx.cpp. References CBlastQueryFilteredFrames::m_TranslateCoords, and CBlastQueryFilteredFrames::x_NeedsTrans().

CBlastQuerySourceBioseqSet::CBlastQuerySourceBioseqSet (  const objects::CBioseq &  bioseq, bool  is_prot )  [inherited]

Parametrized constructor for a Bioseq. Parameters: bioseq  bioseq from which to extract the data [in] is_prot  whether the bioseq argument contains a protein or nucleotide sequence [in] Definition at line 244 of file bioseq_extract_data_priv.cpp.

CBlastQuerySourceBioseqSet::CBlastQuerySourceBioseqSet (  const objects::CBioseq_set &  bss, bool  is_prot )  [inherited]

Parametrized constructor for a Bioseq-set. Parameters: bss  set of bioseqs from which to extract the data [in] is_prot  whether the bss argument contains protein or nucleotide sequences [in] Definition at line 232 of file bioseq_extract_data_priv.cpp. References ConstBegin(), and eDetectLoops.

CBlastQuerySourceOM::CBlastQuerySourceOM (  CBlastQueryVector &  v, const CBlastOptions *  opts )  [inherited]

Constructor which takes a CBlastQueryVector. This version will compute masking information with dust. Parameters: v  Object containing the queries, scopes and masking info [in] opts  BLAST algorithm options [in] Definition at line 103 of file blast_objmgr_tools.cpp. References CBlastQuerySourceOM::x_AutoDetectGeneticCodes().

CBlastQuerySourceOM::CBlastQuerySourceOM (  CBlastQueryVector &  v, EBlastProgramType  prog )  [inherited]

Constructor which takes a CBlastQueryVector. This version assumes the masking information (if any) was provided with the CBlastQueryVector. Parameters: v  Object containing the queries, scopes and masking info [in] prog  type of program to run [in] Definition at line 92 of file blast_objmgr_tools.cpp. References CBlastQuerySourceOM::x_AutoDetectGeneticCodes().

CBlastQuerySourceOM::CBlastQuerySourceOM (  TSeqLocVector &  v, const CBlastOptions *  opts )  [inherited]

Constructor which takes a TSeqLocVector. This version will compute masking information with dust. Parameters: v  vector of SSeqLoc structures containing the queries [in] opts  BLAST algorithm options [in] Note: that the v argument might be changed with the filtering locations Definition at line 81 of file blast_objmgr_tools.cpp. References CBlastQuerySourceOM::x_AutoDetectGeneticCodes().

CBlastQuerySourceOM::CBlastQuerySourceOM (  TSeqLocVector &  v, EBlastProgramType  prog )  [inherited]

Constructor which takes a TSeqLocVector. This version assumes the masking information (if any) was provided with the TSeqLocVector. Parameters: v  vector of SSeqLoc structures containing the queries [in] prog  program type of this search [in] Definition at line 70 of file blast_objmgr_tools.cpp.

CBlastRPSAuxInfo::CBlastRPSAuxInfo (  const string &  matrix, int  gap_open, int  gap_extend, double  scale_factor, const vector< double > &  karlin_k )  [inherited]

Parametrized constructor. Parameters: matrix  name of the scoring matrix used to build the RPS-BLAST database gap_open  gap opening cost gap_extend  gap extension cost scale_factor  scaling factor karlin_k  statistical K parameter calculated when building the RPS-BLAST database Definition at line 99 of file rps_aux.cpp. References _ASSERT, BlastRPSAuxInfo::gap_extend_penalty, BlastRPSAuxInfo::gap_open_penalty, BlastRPSAuxInfo::karlin_k, CBlastRPSAuxInfo::m_Data, NCBI_THROW, BlastRPSAuxInfo::orig_score_matrix, BlastRPSAuxInfo::scale_factor, strdup, and CBlastRPSAuxInfo::x_DoDestroy().

CBlastRPSInfo::CBlastRPSInfo (  const string &  rps_dbname  )  [inherited]

Parametrized constructor. Parameters: rps_dbname  name of the RPS-BLAST database Definition at line 362 of file rps_aux.cpp. References _ASSERT, BlastRPSInfo::aux_info, CSeqDB::eProtein, CSeqDB::FindVolumePaths(), BlastRPSInfo::lookup_header, CBlastRPSInfo::m_AuxFile, CBlastRPSInfo::m_LutFile, CBlastRPSInfo::m_PssmFile, CBlastRPSInfo::m_RpsInfo, NCBI_RETHROW, NCBI_THROW, BlastRPSInfo::profile_header, auto_ptr< X >::release(), CRef< C, Locker >::Reset(), and auto_ptr< X >::reset().

CBlastRPSOptionsHandle::CBlastRPSOptionsHandle (  EAPILocality  locality = CBlastOptions::eLocal  )  [inherited]

Creates object with default options set. Definition at line 48 of file blast_rps_options.cpp. References eRPSBlast.

CBlastSeqVectorFromCSeq_data::CBlastSeqVectorFromCSeq_data (  const objects::CSeq_data &  seq_data, TSeqPos  length )  [inherited]

Parametrized constructor. Parameters: seq_data  sequence data [in] length  length of the sequence data (not of the buffer containing the data!) [in] Definition at line 80 of file bioseq_extract_data_priv.cpp. References CSeqConvert::Convert(), CSeqUtil::e_Iupacaa, CSeq_data_Base::e_Iupacaa, CSeqUtil::e_Iupacna, CSeq_data_Base::e_Iupacna, CSeqUtil::e_Ncbi2na, CSeq_data_Base::e_Ncbi2na, CSeqUtil::e_Ncbi2na_expand, CSeqUtil::e_Ncbi4na, CSeq_data_Base::e_Ncbi4na, CSeqUtil::e_Ncbi4na_expand, CSeqUtil::e_Ncbieaa, CSeq_data_Base::e_Ncbieaa, CSeqUtil::e_Ncbistdaa, CSeq_data_Base::e_Ncbistdaa, eNa_strand_plus, NStr::IntToString(), NCBI_CURRENT_FUNCTION, and NCBI_THROW.

CBlastTracebackSearch::CBlastTracebackSearch (  CRef< IQueryFactory >  query_factory, CRef< SInternalData >  internal_data, CRef< CBlastOptions >  opts, CRef< IBlastSeqInfoSrc >  seqinfosrc, TSearchMessages &  search_msgs )  [inherited]

Use the internal data and return value of the preliminary search to proceed with the traceback. Definition at line 82 of file traceback_stage.cpp. References Blast_ProgramIsPhiBlast(), CRef< C, Locker >::GetPointer(), BlastUngappedStats::lookup_hits, CBlastTracebackSearch::m_InternalData, CBlastTracebackSearch::SetDBScanInfo(), and BlastDiagnostics::ungapped_stat.

CBlastTracebackSearch::CBlastTracebackSearch (  CRef< IQueryFactory >  qf, CRef< CBlastOptions >  opts, BlastSeqSrc *  seqsrc, CRef< IBlastSeqInfoSrc >  seqinfosrc, CRef< TBlastHSPStream >  hsps, CConstRef< objects::CPssmWithParameters >  pssm = null )  [inherited]

Create a BlastSeqSrc re-using an already created BlastSeqSrc. Note: We don't own the BlastSeqSrc Definition at line 64 of file traceback_stage.cpp. References BlastSeqSrcGetName().