|
Collaboration diagram for BLAST (Basic Local Alignment Search Tool):
|
|
Classes | |
| class | CBl2Seq |
| Runs the BLAST algorithm between 2 sequences. More... | |
| class | CBlastAdvancedProteinOptionsHandle |
| Handle to the Advanced BLASTP options. More... | |
| class | CSeqLocInfo |
| structure for seqloc info More... | |
| class | TMaskedQueryRegions |
| Collection of masked regions for a single query sequence. 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 | 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... | |
| struct | SSeqIdKey |
| Auxiliary type to embed a CConstRef<CSeq_id> in STL containers that require operator< to be defined. 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 | 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... | |
| 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 | CRemoteServices |
| API for Remote Blast Services. 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 | CQuerySplitter |
| Class responsible for splitting query sequences and providing data to the BLAST search class to search a split query chunk. 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 | 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 | CSeqIdComparator |
| 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 | 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 TMaskedQueryRegions | TMaskedSubjRegions |
| TMaskedSubjRegions defined as synonym to TMaskedQueryRegions. | |
| typedef vector< TMaskedQueryRegions > | TSeqLocInfoVector |
| Collection of masked regions for all queries in a BLAST search. | |
| 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 } |
| 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; this method always throws an exception, because 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, CConstRef< 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, const vector< int > &filtering_algorithms=vector< int >()) |
| Initialize the sequence source structure. | |
| BlastSeqSrc * | SeqDbBlastSeqSrcInit (CSeqDB *seqdb, const vector< int > &filtering_algorithms=vector< int >()) |
| 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, Uint1 *A, Int4 a_size, 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. | |
| IBlastSeqInfoSrc * | InitSeqInfoSrc (const BlastSeqSrc *seqsrc) |
| Initializes the IBlastSeqInfoSrc from data obtained from the BlastSeqSrc (for database searches only, uses CSeqDB). | |
| IBlastSeqInfoSrc * | InitSeqInfoSrc (CSeqDB *seqdb) |
| Initializes the IBlastSeqInfoSrc from an existing CSeqDB object. | |
| CConstRef< CSeq_loc > | CreateWholeSeqLocFromIds (const list< CRef< CSeq_id > > seqids) |
| 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) |
| 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. | |
| 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. | |
| 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. | |