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