NCBI C++ ToolKit
Classes | Macros | Typedefs | Enumerations | Functions | Variables
BLAST (Basic Local Alignment Search Tool)
+ Collaboration diagram for BLAST (Basic Local Alignment Search Tool):

Classes

class  CBl2Seq
 Runs the BLAST algorithm between 2 sequences. More...
 
class  CBlastAdvancedProteinOptionsHandle
 Handle to the Advanced BLASTP options. More...
 
class  CFrameFinder
 Function object to assist in finding all CSeqLocInfo objects which corresponds to a given frame. More...
 
struct  CConstRefCSeqId_LessThan
 
class  CAutomaticGenCodeSingleton
 Initializes and uninitializes the genetic code singleton as if it was an automatic variable (to facilitate use in our unit tests and in the CBlastOptions object). More...
 
class  CBLAST_SequenceBlk
 Wrapper class for BLAST_SequenceBlk . More...
 
class  CBlastQueryInfo
 Wrapper class for BlastQueryInfo . More...
 
class  CQuerySetUpOptions
 Wrapper class for QuerySetUpOptions . More...
 
class  CLookupTableOptions
 Wrapper class for LookupTableOptions . More...
 
class  CLookupTableWrap
 Wrapper class for LookupTableWrap . More...
 
class  CBlastInitialWordOptions
 Wrapper class for BlastInitialWordOptions . More...
 
class  CBlastInitialWordParameters
 Wrapper class for BlastInitialWordParameters . More...
 
class  CBlast_ExtendWord
 Wrapper class for Blast_ExtendWord . More...
 
class  CBlastExtensionOptions
 Wrapper class for BlastExtensionOptions . More...
 
class  CBlastExtensionParameters
 Wrapper class for BlastExtensionParameters . More...
 
class  CBlastHitSavingOptions
 Wrapper class for BlastHitSavingOptions . More...
 
class  CBlastHitSavingParameters
 Wrapper class for BlastHitSavingParameters . More...
 
class  CPSIBlastOptions
 Wrapper class for PSIBlastOptions . More...
 
class  CBlastDatabaseOptions
 Wrapper class for BlastDatabaseOptions . More...
 
class  CBlastScoreBlk
 Wrapper class for BlastScoreBlk . More...
 
class  CBlastScoringOptions
 Wrapper class for BlastScoringOptions . More...
 
class  CBlastScoringParameters
 Wrapper class for BlastScoringParameters . More...
 
class  CBlastEffectiveLengthsOptions
 Wrapper class for BlastEffectiveLengthsOptions . More...
 
class  CBlastEffectiveLengthsParameters
 Wrapper class for BlastEffectiveLengthsParameters . More...
 
class  CBlastGapAlignStruct
 Wrapper class for BlastGapAlignStruct . More...
 
class  CBlastHSPResults
 Wrapper class for BlastHSPResults . More...
 
class  CPSIMsa
 Wrapper class for PSIMsa . More...
 
class  CPSIMatrix
 Wrapper class for PSIMatrix . More...
 
class  CPSIDiagnosticsRequest
 Wrapper class for PSIDiagnosticsRequest . More...
 
class  CPSIDiagnosticsResponse
 Wrapper class for PSIDiagnosticsResponse . More...
 
class  CBlastSeqSrc
 Wrapper class for BlastSeqSrc . More...
 
class  CBlastSeqSrcIterator
 Wrapper class for BlastSeqSrcIterator . More...
 
class  CBlast_Message
 Wrapper class for Blast_Message . More...
 
class  CBlastMaskLoc
 Wrapper class for BlastMaskLoc . More...
 
class  CBlastSeqLoc
 Wrapper class for BlastSeqLoc . More...
 
class  CSBlastProgress
 Wrapper class for SBlastProgress . More...
 
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  CBlastpKmerOptionsHandle
 Handle to the KMER BLASTP options. More...
 
class  CBlastxOptionsHandle
 Handle to the translated nucleotide-protein options to the BLAST algorithm. More...
 
class  IPssmInputCdd
 Interface for strategy to pre-process multiple alignment of conserved domains matches as input data for PSSM engine. More...
 
class  CCddInputData
 Strategy for pre-processing RPS-BLAST matches for PSSM computation. More...
 
class  CDeltaBlast
 A simple realization of the DELTA-BLAST algorithm: seacrch domain database, compute PSSM, search sequence database. More...
 
class  CDeltaBlastOptionsHandle
 Handle to the protein-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  CMagicBlast
 BLAST RNA-Seq mapper. More...
 
class  CMagicBlastResults
 Magic-BLAST results for a single query/read or a pair of reads. More...
 
class  CMagicBlastResultSet
 Results of Magic-BLAST mapping. More...
 
class  CMagicBlastOptionsHandle
 Handle to the nucleotide mapping options to the BLAST algorithm. 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...
 
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...
 
struct  CImportStrategyData
 This is the "mutable" data for CImportStrategy. More...
 
class  CImportStrategy
 Class to return parts of the CBlast4_request, or data associated with a CBlast4_request, such as options. More...
 
class  CExportStrategy
 
struct  SPatternUnit
 
class  CSeedTop
 
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  CIgBlastVersion
 Keeps track of the version of IgBLAST in the NCBI C++ toolkit. More...
 
class  CIgBlastOptions
 
class  CIgAnnotation
 
class  CIgAnnotationInfo
 
class  CIgBlastResults
 
class  CIgBlast
 
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...
 
class  CIndexedDb
 This class is responsible for loading indices and doing the actual seed search. More...
 
class  CIndexedDb_Old
 Index wrapper for old style MegaBLAST indexing functionality. More...
 
class  CIndexedDb_New
 Index wrapper for new style MegaBLAST indexing functionality. 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...
 
struct  SBlast4ParamFinder
 Finder class for matching CBlast4_parameter. 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...
 
struct  seq_align_pairs_first
 
struct  compare_alignments_fwrev_first
 
struct  compare_alignments_revfw_first
 
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  CNcbiMatrix< T >
 
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  CRpsFreqsFile
 This class represents the .wcounts file in a RPS-BLAST file, which contains the weighted residue frequencies for the database. More...
 
class  CRpsObsrFile
 This class represents the .obsr file in a RPS-BLAST file, which contains the numbers of independent observations for the database. More...
 
class  CRpsFreqRatiosFile
 This class represents the .freq file in a RPS-BLAST file, which contains the frequency ratios 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...
 
class  CAutoNcbiConfigFile
 Auxiliary class to write temporary NCBI configuration files in the local directory for the purpose of testing the CBlastScopeSource configuration class via this file (and override any other installed NCBI configuration files) More...
 
class  CBlastScopeSourceWrapper
 RAII class for the CBlastScopeSource. More...
 

Macros

#define TYPEDEF_AUTOPTR_CDELETER(type)   typedef AutoPtr<type, CDeleter<type> > TAuto ## type ## Ptr
 Uses C Deleter (free) - used in functions that deal with CORE BLAST. More...
 
#define TYPEDEF_AUTOPTR_ARRAYDELETER(type)   typedef AutoPtr<type, ArrayDeleter<type> > TAuto ## type ## ArrayPtr
 Uses delete [] operator - for C++ arrays. More...
 
#define DECLARE_AUTO_CLASS_WRAPPER(struct_name, free_func)
 Declares class to handle deallocating of the structure using the appropriate function. More...
 
#define BLAST2NA_SIZE   4
 Size of compressed nucleic acid alphabet. More...
 
#define BLASTNA_SIZE   16
 Size of nucleic acid alphabet. More...
 
#define BLASTAA_SIZE   28
 Size of aminoacid alphabet. More...
 
#define BLASTNA_SEQ_CODE   99
 Identifies the blastna alphabet, for use in blast only. More...
 
#define BLASTAA_SEQ_CODE   11
 == Seq_code_ncbistdaa More...
 
#define NCBI4NA_SEQ_CODE   4
 == Seq_code_ncbi4na More...
 
#define NCBI_MODULE   NETBLAST
 
#define SMALLEST_EVALUE   1.0e-180
 Threshold below which e-values are saved as 0. More...
 
#define GAP_VALUE   -1
 Value in the Dense-seg indicating a gap. More...
 
#define GAP_IN_ALIGNMENT   ((Uint4)-1)
 Representation of GAP in Seq-align. More...
 
#define GAP_IN_ALIGNMENT   ((Uint4)-1)
 Representation of GAP in Seq-align. More...
 
#define NCBI_MODULE   NETBLAST
 

Typedefs

typedef AutoPtr< Uint1, CDeleter< Uint1 > > TAutoUint1Ptr
 Declares TAutoUint1Ptr (for Uint1 arrays allocated with malloc/calloc) More...
 
typedef AutoPtr< Char, CDeleter< Char > > TAutoCharPtr
 Declares TAutoCharPtr (for Char arrays allocated with malloc/calloc) More...
 
typedef AutoPtr< Uint1, ArrayDeleter< Uint1 > > TAutoUint1ArrayPtr
 Declares TAutoUint1ArrayPtr (for Uint1 arrays allocated with new[]) More...
 
typedef CStructWrapper< BlastScoreBlkTBlastScoreBlk
 
typedef CStructWrapper< LookupTableWrapTLookupTableWrap
 
typedef CStructWrapper< BlastDiagnosticsTBlastDiagnostics
 
typedef CStructWrapper< BlastHSPStreamTBlastHSPStream
 
typedef CStructWrapper< BlastSeqSrcTBlastSeqSrc
 
typedef CStructWrapper< SPHIPatternSearchBlkTSPHIPatternSearchBlk
 
typedef list< CRef< objects::CBlast4_error > > TErrorList
 Error value type used by Blast4 ASN.1 objects. More...
 
typedef SSeqDB_SeqSrc_Data TSeqDBData
 
typedef COpenRange< TSeqPosTChunkRange
 Range describing a query chunk. More...
 

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  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. More...
 
BlastSeqLocCSeqLoc2BlastSeqLoc (const objects::CSeq_loc *slp)
 Converts a CSeq_loc into a BlastSeqLoc structure used in NewBlast. More...
 
TAutoUint1ArrayPtr FindGeneticCode (int genetic_code)
 Retrieves the requested genetic code in Ncbistdaa format. More...
 
bool IsLocalId (const objects::CSeq_id *seqid)
 Returns true if the CSeq_id is a local id. More...
 
TMaskedQueryRegions PackedSeqLocToMaskedQueryRegions (CConstRef< objects::CSeq_loc > sloc, EBlastProgramType program, bool assume_both_strands=false)
 Auxiliary function to convert a Seq-loc describing masked query regions to a TMaskedQueryRegions object. More...
 
CRef< objects::CSeq_loc > MaskedQueryRegionsToPackedSeqLoc (const TMaskedQueryRegions &sloc)
 Interface to build a CSeq-loc from a TMaskedQueryRegion; note that conversion conversion in this direction can be lossy. More...
 
void LoadSequencesToScope (objects::CScope::TIds &ids, vector< TSeqRange > &ranges, CRef< objects::CScope > &scope)
 This method retrieve sequence data in bulk to scope @ids seq id list [in] @ranges seq range list [in] @scope sconfigured with data loader for retrieving seqs [in] | retrieved bioseqs [out]. More...
 
void Blast_GetSeqLocInfoVector (EBlastProgramType program, const objects::CPacked_seqint &queries, const BlastMaskLoc *mask, TSeqLocInfoVector &mask_v)
 Converts a BlastMaskLoc internal structure into an object returned by the C++ API. More...
 
MT_LOCK Blast_CMT_LOCKInit (void)
 Initialize a mutex locking mechanism for BLAST. More...
 
void GetSequenceLengthAndId (const IBlastSeqInfoSrc *seqinfo_src, int oid, CRef< objects::CSeq_id > &seqid, TSeqPos *length)
 Retrieves subject sequence Seq-id and length. More...
 
void GetFilteredRedundantGis (const IBlastSeqInfoSrc &sisrc, int oid, vector< TGi > &gis)
 Get GIs for a sequence in a redundant database. More...
 
void GetFilteredRedundantSeqids (const IBlastSeqInfoSrc &sisrc, int oid, vector< string > &seqids, bool use_gis=true)
 Get Seqids for a sequence in a redundant database. More...
 
BlastHSPStreamBlast_HSPListCQueueInit ()
 Function to initialize a queue HSP stream. More...
 
size_t SplitQuery_GetChunkSize (EProgram program)
 Returns the optimal chunk size for a given task. More...
 
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. More...
 
objects::EBlast4_frame_type FrameNumber2NetworkFrame (int frame, EBlastProgramType program)
 Converts the return value of CSeqLocInfo::GetFrame into the Blast4-frame-type field. More...
 
CSeqLocInfo::ETranslationFrame NetworkFrame2FrameNumber (objects::EBlast4_frame_type frame, EBlastProgramType program)
 Converts Blast4-frame-type into CSeqLocInfo::ETranslationFrame. More...
 
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) More...
 
CRef< objects::CBlast4_request > ExtractBlast4Request (CNcbiIstream &in)
 Extract a Blast4-request (a.k.a. More...
 
void FlattenBioseqSet (const CBioseq_set &bss, list< CRef< CBioseq > > &seqs)
 
void Blast_FindRepeatFilterLoc (TSeqLocVector &query_loc, const CBlastOptionsHandle *opts_handle)
 Finds repeats locations for a given set of sequences. More...
 
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. More...
 
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. More...
 
BlastSeqSrcMultiSeqBlastSeqSrcInit (TSeqLocVector &seq_vector, EBlastProgramType program, bool dbscan_mode=false)
 Initialize the sequence source structure. More...
 
BlastSeqSrcSeqDbBlastSeqSrcInit (const string &dbname, bool is_prot, Uint4 first_seq=0, Uint4 last_seq=0, Int4 mask_algo_id=-1, ESubjectMaskingType mask_type=eNoSubjMasking)
 Initialize the sequence source structure. More...
 
BlastSeqSrcSeqDbBlastSeqSrcInit (CSeqDB *seqdb, Int4 mask_algo_id=-1, ESubjectMaskingType mask_type=eNoSubjMasking)
 Initialize the sequence source structure using an existing SeqDB object. More...
 
template<class TData >
CStructWrapper< TData > * WrapStruct (TData *obj, TData *(*del)(TData *))
 Auxiliary function to create a CStructWrapper for a pointer to an object. More...
 
void GetTaxIdWithWindowMaskerSupport (set< int > &supported_taxids)
 This function returns a list of NCBI taxonomy IDs for which there exists windowmasker masking data to support organism specific filtering. More...
 
string WindowMaskerTaxidToDb (int taxid)
 Get the windowmasker file path for a given taxid. More...
 
string WindowMaskerTaxidToDb (const string &window_masker_path, int taxid)
 Get the windowmasker file path for a given taxid and base path. More...
 
int WindowMaskerPathInit (const string &window_masker_path)
 Initialize the path to the windowmasker data files. More...
 
void WindowMaskerPathReset ()
 Resets the path to the windowmasker data files. More...
 
string WindowMaskerPathGet ()
 Retrieves the path to the windowmasker data files. More...
 
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. More...
 
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. More...
 
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. More...
 
CRef< objects::CBlast4_archive > BlastBuildArchive (blast::IQueryFactory &queries, blast::CBlastOptionsHandle &options_handle, const CSearchResultSet &results, CRef< CSearchDatabase > search_db, unsigned int num_iters=0)
 Returns a blast archive object. More...
 
CRef< objects::CBlast4_archive > BlastBuildArchive (blast::IQueryFactory &queries, blast::CBlastOptionsHandle &options_handle, const CSearchResultSet &results, blast::IQueryFactory &subjects)
 Returns a blast archive object. More...
 
CRef< objects::CBlast4_archive > BlastBuildArchive (objects::CPssmWithParameters &pssm, blast::CBlastOptionsHandle &options_handle, const CSearchResultSet &results, CRef< CSearchDatabase > search_db, unsigned int num_iters=0)
 Returns a blast archive object. More...
 
 USING_SCOPE (objects)
 
CRef< CSeq_align_setCreateEmptySeq_align_set (void)
 Constructs an empty Seq-align-set containing an empty discontinuous seq-align, and appends it to a previously constructed Seq-align-set. More...
 
 DEFINE_CLASS_STATIC_FAST_MUTEX (CAutomaticGenCodeSingleton::sm_Mutex)
 
void ThrowIfInvalidTask (const string &task)
 Validates that the task provided is indeed a valid task, otherwise throws a CBlastException. More...
 
string EProgramToTaskName (EProgram p)
 Convert a EProgram enumeration value to a task name (as those used in the BLAST command line binaries) More...
 
EBlastProgramType EProgramToEBlastProgramType (EProgram p)
 Convert EProgram to EBlastProgramType. More...
 
EProgram ProgramNameToEnum (const std::string &program_name)
 Map a string into an element of the ncbi::blast::EProgram enumeration (except eBlastProgramMax). More...
 
template<class Position >
CRange< Position > Map (const CRange< Position > &target, const CRange< Position > &range)
 
static pair< BlastSeqLoc *, bools_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. More...
 
static void s_ConvertBlastnMasks (const CPacked_seqint::Tdata &query_intervals, const BlastMaskLoc *mask, TSeqLocInfoVector &retval)
 Convert EBlastTypeBlastn CORE masks into TSeqLocInfoVector. More...
 
CRef< objects::CBioseq_set > TSeqLocVector2Bioseqs (const TSeqLocVector &input)
 
void LoadSequencesToScope (CScope::TIds &ids, vector< TSeqRange > &ranges, CRef< CScope > &scope)
 
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. More...
 
void Blast_Message2TSearchMessages (const Blast_Message *blmsg, const BlastQueryInfo *query_info, TSearchMessages &messages)
 Converts the Blast_Message structure into a TSearchMessages object. More...
 
string BlastErrorCode2String (Int2 error_code)
 Returns a string containing a human-readable interpretation of the error_code passed as this function's argument. More...
 
CRef< SBlastSetupDataBlastSetupPreliminarySearch (CRef< IQueryFactory > query_factory, CRef< CBlastOptions > options, size_t num_threads=1)
 Set up internal data structures used by the BLAST CORE engine. More...
 
CRef< SBlastSetupDataBlastSetupPreliminarySearchEx (CRef< IQueryFactory > qf, CRef< CBlastOptions > options, CConstRef< CPssmWithParameters > pssm, BlastSeqSrc *seqsrc, size_t num_threads)
 Extended interface to set up internal data structures used by the BLAST CORE engine. More...
 
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. More...
 
CRef< CSearchResultSetBlastBuildSearchResultSet (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. More...
 
static unsigned long s_MB_IdbGetResults (Int4 oid_i, Int4 chunk_i, BlastInitHitList *init_hitlist)
 Get the seed search results for a give subject id and chunk number. More...
 
static int s_MB_IdbCheckOid (Int4 oid, Int4 *last_vol_oid)
 
static void s_MB_IdxEndSearchIndication (Int4 last_vol_id)
 
 USING_SCOPE (ncbi::objects)
 
 USING_SCOPE (ncbi::blastdbindex)
 
int MinIndexWordSize ()
 Get the minimum acceptable word size to use with indexed search. More...
 
static void NullSetUsingThreads (bool)
 No-op callback for setting concurrency state. More...
 
static void NullSetNumThreads (size_t)
 No-op callback for setting the number of threads. More...
 
static void NullSetQueryInfo (LookupTableWrap *, CRef< CBlastSeqLocWrap >)
 No-op callback for setting query info. More...
 
static void NullRunSearch (BLAST_SequenceBlk *, LookupTableOptions *, BlastInitialWordOptions *)
 No-op callback to run indexed search. More...
 
static void IndexedDbRunSearch (BLAST_SequenceBlk *queries, LookupTableOptions *lut_options, BlastInitialWordOptions *word_options)
 Run indexed search. More...
 
static void IndexedDbSetUsingThreads (bool multiple_threads)
 Set state of concurrency in the index structure. More...
 
static void IndexedDbSetNumThreads (size_t n_threads)
 Set the number of concurrent search threads in the index structure. More...
 
static void IndexedDbSetQueryInfo (LookupTableWrap *lt_wrap, CRef< CBlastSeqLocWrap > locs_wrap)
 Set information about unmasked query segments. More...
 
std::string DbIndexInit (const string &indexname, bool old_style, bool &partial)
 
void SetUpDbIndexCallbacks (void)
 
void ClearDbIndexCallbacks (void)
 
DbIndexSetUsingThreadsFnType GetDbIndexSetUsingThreadsFn ()
 Return the appropriate callback to set the concurrency state in the index structure. More...
 
DbIndexSetNumThreadsFnType GetDbIndexSetNumThreadsFn ()
 Return the appropriate callback to set the number of threads in the index structure. More...
 
DbIndexSetQueryInfoFnType GetDbIndexSetQueryInfoFn ()
 Return the appropriate callback to set query information in the index. More...
 
DbIndexRunSearchFnType GetDbIndexRunSearchFn ()
 Return the appropriate callback to run indexed seed search. More...
 
 USING_SCOPE (ncbi)
 
 USING_SCOPE (ncbi::blast)
 
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. More...
 
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. More...
 
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. More...
 
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. More...
 
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. More...
 
CRef< objects::CPacked_seqint > TSeqLocVector2Packed_seqint (const TSeqLocVector &sequences)
 Converts a TSeqLocVector into a CPacked_seqint. More...
 
void s_Ncbi4naToNcbi2na (const string &ncbi4na, int base_length, unsigned char *ncbi2na)
 
static void s_MergeCBlast4_parameters (const objects::CBlast4_parameters *aopts, const objects::CBlast4_parameters *popts, const objects::CBlast4_parameters *fopts, objects::CBlast4_parameters &retval)
 Convenience function to merge all lists into one object to facilitate invoking AdjustProgram. More...
 
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 void s_InitializeGumbelBlk (Blast_GumbelBlk *src, Blast_GumbelBlk **dest)
 
static CConstRef< CSeq_ids_ExtractSeqId (CConstRef< CSeq_align_set > align_set)
 Find the first alignment in a set of blast results, and. More...
 
static ENa_strand s_Frame2Strand (short frame)
 Converts a frame into the appropriate strand. More...
 
static int s_GetCurrPos (int &pos, int pos2advance)
 Advances position in a sequence, according to an edit script instruction. More...
 
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. More...
 
static Int4 s_GetProteinFrameLength (Int4 nuc_length, Int2 frame)
 Finds length of a protein frame given a nucleotide length and a frame number. More...
 
static void s_CollectSeqAlignData (const BlastHSP *hsp, const GapEditScript *esp, unsigned int first, unsigned int nsegs, CDense_seg::TStarts &starts, CDense_seg::TLens &lengths, CDense_seg::TStrands &strands, Int4 query_length, Int4 subject_length, bool translate1, bool translate2)
 Fills vectors of start positions, lengths and strands for all alignment segments. More...
 
static void s_CreateDenseg (CDense_seg &dense_seg, CRef< CSeq_id > master, CRef< CSeq_id > slave, CDense_seg::TStarts &starts, CDense_seg::TLens &lengths, CDense_seg::TStrands &strands)
 Creates a Dense-seg object from the starts, lengths and strands vectors and two Seq-ids. More...
 
static CSeq_align::C_Segs::TStd s_CreateStdSegs (CRef< CSeq_id > master, CRef< CSeq_id > slave, CDense_seg::TStarts &starts, CDense_seg::TLens &lengths, CDense_seg::TStrands &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. More...
 
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. More...
 
static void s_ValidateExon (const CSpliced_exon &exon, const CSeq_id &product_id, const CSeq_id &genomic_id)
 
void MakeSplicedSeg (CSpliced_seg &spliced_seg, CRef< CSeq_id > product_id, CRef< CSeq_id > genomic_id, int product_length, const HSPChain *chain)
 Convert a spliced alignmeny in BlastHSPChain into Spliced_seg. More...
 
static CRef< CSeq_aligns_CreateSeqAlign (CRef< CSeq_id > master, CRef< CSeq_id > slave, CDense_seg::TStarts starts, CDense_seg::TLens lengths, CDense_seg::TStrands 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. More...
 
static CRef< CSeq_aligns_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. More...
 
static CRef< CSeq_aligns_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. More...
 
static CRef< CScores_MakeScore (const string &ident_string, double d, int i, bool is_integer)
 Creates and initializes CScore with a given name, and with integer or double value. More...
 
static size_t s_CalculateScoreVectorSize (const BlastHSP *hsp, const vector< string > &seqid_list)
 Computes the exact size of a CSeq_align::TScore for a given HSP. More...
 
static void s_BuildScoreList (const BlastHSP *hsp, CSeq_align::TScore &scores, const vector< string > &seqid_list, Int4 query_length)
 Creates a list of score objects for a Seq-align, given an HSP structure. More...
 
static void s_AddUserObjectToSeqAlign (CRef< CSeq_align > &seqalign, const vector< string > &seqid_list)
 Produce UserObject with Seq-ids to limit formatting to ("use_this_gi") More...
 
static void s_AddScoresToSeqAlign (CRef< CSeq_align > &seqalign, const BlastHSP *hsp, const vector< string > &seqid_list, Int4 query_length)
 Given an HSP structure, creates a list of scores and inserts them into a Seq-align. More...
 
CRef< CDense_diagx_UngappedHSPToDenseDiag (BlastHSP *hsp, CRef< CSeq_id > query_id, CRef< CSeq_id > subject_id, Int4 query_length, Int4 subject_length, const vector< string > &seqid_list)
 Creates a Dense-diag object from HSP information and sequence identifiers for a non-translated ungapped search. More...
 
CRef< CStd_segx_UngappedHSPToStdSeg (BlastHSP *hsp, CRef< CSeq_id > query_id, CRef< CSeq_id > subject_id, Int4 query_length, Int4 subject_length, const vector< string > &seqid_list)
 Creates a Std-seg object from HSP information and sequence identifiers for a translated ungapped search. More...
 
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< string > &seqid_list, vector< CRef< CSeq_align > > &sa_vector)
 Creates a Seq-align from an HSP list for an ungapped search. More...
 
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< string > &seqid_list, vector< CRef< CSeq_align > > &sa_vector)
 This is called for each query and each subject in a BLAST search. More...
 
void RemapToQueryLoc (CRef< CSeq_align > sar, const CSeq_loc &query)
 Remaps Seq-align offsets relative to the query Seq-loc. More...
 
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. More...
 
CRef< CSeq_align_setBlastHitList2SeqAlign_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. More...
 
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. More...
 
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 ... More...
 
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. More...
 
CRef< CStd_segx_NonTranslatedHSPToStdSeg (BlastHSP *hsp, CRef< CSeq_id > query_id, CRef< CSeq_id > subject_id, Int4 query_length, Int4 subject_length, const vector< string > &seqid_list)
 Creates a Std-seg object from HSP information and sequence identifiers for a non-translated ungapped search. More...
 
void BLASTPrelminSearchHitListToStdSeg (EBlastProgramType program, BlastHitList *hit_list, const CSeq_loc &query_loc, TSeqPos query_length, const IBlastSeqInfoSrc *subject_seqinfo, list< CRef< CStd_seg > > &seg_list)
 
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. More...
 
void SetupQueryInfo_OMF (const IBlastQuerySource &queries, EBlastProgramType prog, objects::ENa_strand strand_opt, BlastQueryInfo **qinfo)
 ObjMgr Free version of SetupQueryInfo. More...
 
void SetupQueries_OMF (IBlastQuerySource &queries, BlastQueryInfo *qinfo, BLAST_SequenceBlk **seqblk, EBlastProgramType prog, objects::ENa_strand strand_opt, TSearchMessages &messages)
 ObjMgr Free version of SetupQueries. More...
 
void SetupSubjects_OMF (IBlastQuerySource &subjects, EBlastProgramType program, vector< BLAST_SequenceBlk * > *seqblk_vec, unsigned int *max_subjlen)
 Object manager free version of SetupSubjects. More...
 
SBlastSequence GetSequence_OMF (IBlastSeqVector &sv, EBlastEncoding encoding, objects::ENa_strand strand, ESentinelType sentinel, std::string *warnings=0)
 Object manager free version of GetSequence. More...
 
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. More...
 
SBlastSequence CompressNcbi2na (const SBlastSequence &source)
 Compresses the sequence data passed in to the function from 1 base per byte to 4 bases per byte. More...
 
Uint1 GetSentinelByte (EBlastEncoding encoding) THROWS((CBlastException))
 Convenience function to centralize the knowledge of which sentinel bytes we use for supported encodings. More...
 
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. More...
 
unsigned int GetNumberOfContexts (EBlastProgramType p)
 Returns the number of contexts for a given BLAST program. More...
 
EBlastEncoding GetQueryEncoding (EBlastProgramType program)
 Returns the encoding for the sequence data used in BLAST for the query. More...
 
EBlastEncoding GetSubjectEncoding (EBlastProgramType program)
 Returns the encoding for the sequence data used in BLAST2Sequences for the subject. More...
 
BLAST_SequenceBlkSafeSetupQueries (IBlastQuerySource &queries, const CBlastOptions *options, BlastQueryInfo *query_info, TSearchMessages &messages)
 Wrapper around SetupQueries. More...
 
BlastQueryInfoSafeSetupQueryInfo (const IBlastQuerySource &queries, const CBlastOptions *options)
 Wrapper around SetupQueryInfo. More...
 
char * BlastFindMatrixPath (const char *matrix_name, Boolean is_prot)
 Returns the path to a specified matrix. More...
 
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. More...
 
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. More...
 
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. More...
 
static void s_ComputeStartEndContexts (ENa_strand strand, int num_contexts, int &start, int &end)
 Calculate the starting and ending contexts for a given strand. More...
 
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. More...
 
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. More...
 
static CRef< CBlastQueryFilteredFramess_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. More...
 
static void s_InvalidateQueryContexts (BlastQueryInfo *qinfo, int query_index)
 Mark the contexts corresponding to the query identified by query_index as invalid. More...
 
static void s_SeqLoc2MaskedSubjRanges (const CSeq_loc *slp, const CSeq_loc *range, Int4 total_length, CSeqDB::TSequenceRanges &output)
 
static bool s_IsValidResidue (Uint1 res)
 Tests if a number represents a valid residue. More...
 
static SBlastSequence GetSequenceProtein (IBlastSeqVector &sv, string *warnings=0)
 Protein sequences are always encoded in eBlastEncodingProtein and always have sentinel bytes around sequence data. More...
 
static SBlastSequence GetSequenceCompressedNucleotide (IBlastSeqVector &sv)
 Auxiliary function to retrieve plus strand in compressed (ncbi4na) format. More...
 
static SBlastSequence GetSequenceSingleNucleotideStrand (IBlastSeqVector &sv, EBlastEncoding encoding, objects::ENa_strand strand, ESentinelType sentinel)
 Auxiliary function to retrieve a single strand of a nucleotide sequence. More...
 
static SBlastSequence GetSequenceNucleotideBothStrands (IBlastSeqVector &sv, EBlastEncoding encoding, ESentinelType sentinel)
 Auxiliary function to retrieve both strands of a nucleotide sequence. More...
 
char * s_GetCStringOfMatrixPath (string &full_path, const string &matrix_name)
 Get the path to the matrix, without the actual matrix name. More...
 
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. More...
 
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. More...
 
static CRef< CSeq_loc_Mappers_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. More...
 
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. More...
 
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. More...
 
static IBlastSeqInfoSrcs_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. More...
 
static void s_CheckForBlastSeqSrcErrors (const BlastSeqSrc *seqsrc)
 Checks if the BlastSeqSrc initialization succeeded. More...
 
static void s_ComputeBtopAndIdentity (const HSPChain *chain, string &btop, string &md_tag, double &perc_id)
 
static CRef< CSeq_aligns_CreateSeqAlign (const HSPChain *chain, CRef< ILocalQueryData > &qdata, CRef< IBlastSeqInfoSrc > &seqinfo_src, const BlastQueryInfo *query_info)
 
static const char kGapChar ('-')
 The representation of a gap in ASCII format. More...
 
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. More...
 
static bool s_AreSequencesEqual (const CNCBIstdaa &sequence, Uint1 *query)
 Returns true iff sequence is identical to query. More...
 
static CRef< CBioseq_sets_QueryVectorToBioseqSet (const CBlastQueryVector &queries)
 Produces a BioseqSet from a CBlastQueryVector. More...
 
static CRef< CBioseq_sets_TSeqLocVectorToBioseqSet (const TSeqLocVector *queries)
 Produces a BioseqSet from a TSeqLocVector. More...
 
static IRemoteQueryData::TSeqLocs s_TSeqLocVectorToTSeqLocs (const TSeqLocVector *queries)
 Produces a vector of SeqLocs from a TSeqLocVector. More...
 
static IRemoteQueryData::TSeqLocs s_QueryVectorToTSeqLocs (const CBlastQueryVector &queries)
 Produces a vector of SeqLocs from a CBlastQueryVector. More...
 
static EBlastProgramType s_GuessProgram (CConstRef< CSeq_loc > mask)
 Auxiliary function to help guess the program type from a CSeq-loc. More...
 
static IRemoteQueryData::TSeqLocs s_ConstBioseqSetToSeqLocs (CConstRef< CBioseq_set > bioseq_set)
 Convert a constant reference to a Bioseq-set to IRemoteQueryData::TSeqLocs. More...
 
CRef< CBioseq_setx_BioseqSetFromBioseq (const CBioseq &bioseq)
 Auxiliary function to convert a CBioseq into a CRef<CBioseq_set> More...
 
void s_FixNumIdent (BlastHSPList *hsp_list, bool gapped_calculation)
 
void s_GetBitScores (BlastHitList *hit_list, bool gapped_calculation, const BlastScoreBlk *sbp)
 
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. More...
 
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. More...
 
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) More...
 
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. More...
 
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. More...
 
static double s_GetEvalue (const CScore &score)
 Returns the evalue from this score object. More...
 
static double s_GetBitScore (const CScore &score)
 Returns the bit_score from this score object. More...
 
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. More...
 
static void s_CheckAgainstNullData (IPssmInputData *pssm_input_msa)
 This function makes sure that none of the required data is returned as NULL or "empty". More...
 
static void s_CheckAgainstNullData (IPssmInputFreqRatios *pssm_input_freqratios)
 This function makes sure that none of the required data is returned as NULL or "empty". More...
 
static void s_Validate (IPssmInputData *pssm_input_msa)
 Performs validation on data provided before invoking the CORE PSSM engine. More...
 
static void s_Validate (IPssmInputCdd *pssm_input)
 Performs validation on data provided before invoking the CORE PSSM engine. More...
 
static void s_Validate (IPssmInputFreqRatios *pssm_input_fr)
 Performs validation on data provided before invoking the CORE PSSM engine. More...
 
static bool s_SearchPending (CRef< objects::CBlast4_reply > reply)
 Determine whether the search is still running. More...
 
static CRef< CBlast4_masks_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. More...
 
static const string kNoRIDSpecified ("Cannot fetch query info: No RID was specified.")
 
static const string kNoArchiveFile ("Cannot fetch query info: No archive file.")
 
static void s_ExtractQueryIdsFromBioseqSet (const CBioseq_set &bss, CSearchResultSet::TQueryIdVector &query_ids)
 Extract the query IDs from a CBioseq_set. More...
 
static CRef< CBlast4_request_bodys_BuildSearchInfoRequest (const string &rid, const string &name, const string &value)
 
static CRef< CSearchResultSets_BuildResultsRemote (CRemoteBlast &rb)
 Build a result set from results in a remote blast search. More...
 
static TSeqAlignVector s_SplitAlignVectorBySubjects (TSeqAlignVector seqaligns)
 CRemoteBlast does not separate each hit to the query in discontinuous Seq-aligns, so we do it here. More...
 
static CSeq_locs_BlastSeqLoc2CSeqloc (const CSeq_loc &query, CScope *scope, BlastSeqLoc *loc_list)
 Convert a list of mask locations to a CSeq_loc object. More...
 
static CSeq_locs_BlastSeqLoc2CSeqloc (SSeqLoc &query, BlastSeqLoc *loc_list)
 Convert a list of mask locations to a CSeq_loc object. More...
 
TMaskedQueryRegions s_BlastSeqLoc2MaskedRegions (const CSeq_loc &query, CScope *scope, BlastSeqLoc *loc_list, EBlastProgramType program)
 Convert a list of mask locations to TMaskedQueryRegions. More...
 
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. More...
 
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. More...
 
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. More...
 
static CRef< CBlastOptionsHandles_CreateRepeatsSearchOptions ()
 Create an options handle with the defaults set for a search for repeats. More...
 
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 *)
 The following functions interact with the C API, and have to be declared extern "C". More...
 
static Int4 s_MultiSeqGetMinLength (void *multiseq_handle, void *)
 Retrieves the length of the longest sequence in the BlastSeqSrc. More...
 
static Int4 s_MultiSeqGetAvgLength (void *multiseq_handle, void *)
 Retrieves the length of the longest sequence in the BlastSeqSrc. More...
 
static Int4 s_MultiSeqGetNumSeqs (void *multiseq_handle, void *)
 Retrieves the number of sequences in the BlastSeqSrc. More...
 
static Int4 s_MultiSeqGetNumSeqsStats (void *, void *)
 Returns zero as this implementation does not support alias files. More...
 
static Int8 s_MultiSeqGetTotLen (void *multiseq_handle, void *)
 Returns total length in db scan mode. More...
 
static Int8 s_MultiSeqGetTotLenStats (void *, void *)
 Returns 0 as this implementation does not use alias files. More...
 
static const char * s_MultiSeqGetName (void *, void *)
 Always returns NcbiEmptyCStr. More...
 
static Boolean s_MultiSeqGetIsProt (void *multiseq_handle, void *)
 Answers whether this object is for protein or nucleotide sequences. More...
 
static Int2 s_MultiSeqGetSequence (void *multiseq_handle, BlastSeqSrcGetSeqArg *args)
 Retrieves the sequence for a given index, in a given encoding. More...
 
static void s_MultiSeqReleaseSequence (void *, BlastSeqSrcGetSeqArg *args)
 Deallocates the uncompressed sequence buffer if necessary. More...
 
static Int4 s_MultiSeqGetSeqLen (void *multiseq_handle, void *args)
 Retrieve length of a given sequence. More...
 
static Int2 s_MultiSeqGetNextChunk (void *multiseq_handle, BlastSeqSrcIterator *itr)
 Mirrors the database iteration interface. More...
 
static void s_MultiSeqResetChunkIter (void *)
 Resets the internal bookmark iterator (N/A in this case) More...
 
static Int4 s_MultiSeqIteratorNext (void *multiseq_handle, BlastSeqSrcIterator *itr)
 Gets the next sequence index, given a BlastSeqSrc pointer. More...
 
static BlastSeqSrcs_MultiSeqSrcFree (BlastSeqSrc *seq_src)
 Multi sequence source destructor: frees its internal data structure. More...
 
static BlastSeqSrcs_MultiSeqSrcCopy (BlastSeqSrc *seq_src)
 Multi-sequence sequence source copier: creates a new reference to the CMultiSeqInfo object and copies the rest of the BlastSeqSrc structure. More...
 
static BlastSeqSrcs_MultiSeqSrcNew (BlastSeqSrc *retval, void *args)
 Multi-sequence source constructor. More...
 
static Int4 s_QueryFactoryGetMaxLength (void *multiseq_handle, void *)
 The following functions interact with the C API, and have to be declared extern "C". More...
 
static Int4 s_QueryFactoryGetMinLength (void *multiseq_handle, void *)
 Retrieves the length of the longest sequence in the BlastSeqSrc. More...
 
static Int4 s_QueryFactoryGetAvgLength (void *multiseq_handle, void *)
 Retrieves the average length of the sequence in the BlastSeqSrc. More...
 
static Int4 s_QueryFactoryGetNumSeqs (void *multiseq_handle, void *)
 Retrieves the number of sequences in the BlastSeqSrc. More...
 
static Int4 s_QueryFactoryGetNumSeqsStats (void *, void *)
 Returns zero as this implementation does not use an alias file. More...
 
static Int8 s_QueryFactoryGetTotLen (void *, void *)
 Returns 0 as total length, indicating that this is NOT a database! More...
 
static Int8 s_QueryFactoryGetTotLenStats (void *, void *)
 Returns 0 as total statistic length, as this implementation does not use alias files. More...
 
static const char * s_QueryFactoryGetName (void *, void *)
 Always returns NcbiEmptyCStr. More...
 
static Boolean s_QueryFactoryGetIsProt (void *multiseq_handle, void *)
 Answers whether this object is for protein or nucleotide sequences. More...
 
static Int2 s_QueryFactoryGetSequence (void *multiseq_handle, BlastSeqSrcGetSeqArg *args)
 Retrieves the sequence for a given index, in a given encoding. More...
 
static void s_QueryFactoryReleaseSequence (void *, BlastSeqSrcGetSeqArg *args)
 Deallocates the uncompressed sequence buffer if necessary. More...
 
static Int4 s_QueryFactoryGetSeqLen (void *multiseq_handle, void *args)
 Retrieve length of a given sequence. More...
 
static Int2 s_QueryFactoryGetNextChunk (void *multiseq_handle, BlastSeqSrcIterator *itr)
 Mirrors the database iteration interface. More...
 
static void s_QueryFactoryResetChunkIter (void *)
 Resets the internal bookmark iterator (N/A in this case) More...
 
static Int4 s_QueryFactoryIteratorNext (void *multiseq_handle, BlastSeqSrcIterator *itr)
 Gets the next sequence index, given a BlastSeqSrc pointer. More...
 
static BlastSeqSrcs_QueryFactorySrcFree (BlastSeqSrc *seq_src)
 Multi sequence source destructor: frees its internal data structure. More...
 
static BlastSeqSrcs_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. More...
 
static BlastSeqSrcs_QueryFactorySrcNew (BlastSeqSrc *retval, void *args)
 Multi-sequence source constructor. More...
 
static BlastSeqSrcs_QueryFactoryBlastSeqSrcInit (CRef< IQueryFactory > query_factory, const TSeqLocVector &subj_seqs, EBlastProgramType program)
 
BlastSeqSrcQueryFactoryBlastSeqSrcInit (CRef< IQueryFactory > query_factory, EBlastProgramType program)
 Initialize the sequence source structure from a query factory. More...
 
BlastSeqSrcQueryFactoryBlastSeqSrcInit (const TSeqLocVector &subj_seqs, EBlastProgramType program)
 Initialize the sequence source structure from a TSeqLocVector. More...
 
 USING_SCOPE (blast)
 
static Int4 s_SeqDbGetMaxLength (void *seqdb_handle, void *)
 Retrieves the length of the longest sequence in the BlastSeqSrc. More...
 
static Int4 s_SeqDbGetMinLength (void *seqdb_handle, void *)
 Retrieves the length of the shortest sequence in the BlastSeqSrc. More...
 
static void s_SeqDbSetNumberOfThreads (void *seqdb_handle, int n)
 Setting number of threads in MT mode. More...
 
static Int4 s_SeqDbGetNumSeqs (void *seqdb_handle, void *)
 Retrieves the number of sequences in the BlastSeqSrc. More...
 
static Int4 s_SeqDbGetNumSeqsStats (void *seqdb_handle, void *)
 Retrieves the number of sequences from alias file to be used for. More...
 
static Int8 s_SeqDbGetTotLen (void *seqdb_handle, void *)
 Retrieves the total length of all sequences in the BlastSeqSrc. More...
 
static Int8 s_SeqDbGetTotLenStats (void *seqdb_handle, void *)
 Retrieves the total length of all sequences from alias file. More...
 
static Int4 s_SeqDbGetAvgLength (void *seqdb_handle, void *ignoreme)
 Retrieves the average length of sequences in the BlastSeqSrc. More...
 
static const char * s_SeqDbGetName (void *seqdb_handle, void *)
 Retrieves the name of the BLAST database. More...
 
static Boolean s_SeqDbGetIsProt (void *seqdb_handle, void *)
 Checks whether database is protein or nucleotide. More...
 
static Boolean s_SeqDbGetSupportsPartialFetching (void *seqdb_handle, void *)
 Determine if partial fetching should be enabled. More...
 
static void s_SeqDbSetRanges (void *seqdb_handle, BlastSeqSrcSetRangesArg *args)
 Set sequence ranges for partial fetching. More...
 
static Int2 s_SeqDbGetSequence (void *seqdb_handle, BlastSeqSrcGetSeqArg *args)
 Retrieves the sequence meeting the criteria defined by its second argument. More...
 
static void s_SeqDbReleaseSequence (void *seqdb_handle, BlastSeqSrcGetSeqArg *args)
 Returns the memory allocated for the sequence buffer to the CSeqDB interface. More...
 
static Int4 s_SeqDbGetSeqLen (void *seqdb_handle, void *args)
 Retrieve length of a given database sequence. More...
 
static Int2 s_SeqDbGetNextChunk (void *seqdb_handle, BlastSeqSrcIterator *itr)
 Assigns next chunk of the database to the sequence source iterator. More...
 
static Int4 s_SeqDbIteratorNext (void *seqdb_handle, BlastSeqSrcIterator *itr)
 Finds the next not searched ordinal id in the iteration over BLAST database. More...
 
static void s_SeqDbResetChunkIterator (void *seqdb_handle)
 Resets CSeqDB's internal chunk bookmark. More...
 
static BlastSeqSrcs_SeqDbSrcFree (BlastSeqSrc *seq_src)
 SeqDb sequence source destructor: frees its internal data structure. More...
 
static BlastSeqSrcs_SeqDbSrcCopy (BlastSeqSrc *seq_src)
 SeqDb sequence source copier: creates a new reference to the CSeqDB object and copies the rest of the BlastSeqSrc structure. More...
 
static void s_InitNewSeqDbSrc (BlastSeqSrc *retval, TSeqDBData *datap)
 Initializes the data structure and function pointers in a SeqDb based BlastSeqSrc. More...
 
static BlastSeqSrcs_SeqDbSrcSharedNew (BlastSeqSrc *retval, void *args)
 Populates a BlastSeqSrc, creating a new reference to the already existing SeqDb object. More...
 
static BlastSeqSrcs_SeqDbSrcNew (BlastSeqSrc *retval, void *args)
 SeqDb sequence source constructor. More...
 
static CRef< CPacked_seqints_LocalQueryData2Packed_seqint (ILocalQueryData &query_data)
 Auxiliary function to extract the Seq-ids from the ILocalQueryData and bundle them in a Packed-seqint. More...
 
size_t SplitQuery_GetOverlapChunkSize (EBlastProgramType program)
 Size of the region that overlaps in between each query chunk. More...
 
bool SplitQuery_ShouldSplit (EBlastProgramType program, size_t chunk_size, size_t concatenated_query_length, size_t num_queries)
 Determines if the input query sequence(s) should be split because it. More...
 
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. More...
 
void SplitQuery_SetEffectiveSearchSpace (CRef< CBlastOptions > options, CRef< IQueryFactory > full_query_fact, CRef< SInternalData > full_data)
 this might supercede the function below... More...
 
CRef< SInternalDataSplitQuery_CreateChunkData (CRef< IQueryFactory > qf, CRef< CBlastOptions > options, CRef< SInternalData > full_data, size_t num_threaded=1)
 Function used by search class to retrieve a query factory for a given chunk. More...
 
ostream & operator<< (ostream &out, const CContextTranslator &rhs)
 
template<class T >
string s_PrintVector (const vector< T > &data2print)
 Auxiliary function to print a vector. More...
 
ostream & operator<< (ostream &out, const CSplitQueryBlk &rhs)
 
static bool s_IsNumericId (const string &id)
 
static string s_WINDOW_MASKER_STAT_FILE_NAME ("wmasker.obinary")
 
static string s_WINDOW_MASKER_PATH (kEmptyStr)
 
 DEFINE_STATIC_MUTEX (InitMutex)
 
CSeqMaskers_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. More...
 
void Blast_FindWindowMaskerLoc (TSeqLocVector &query, const CBlastOptions *opts)
 Find Window Masker filtered locations using BlastOptions. More...
 
void Blast_FindWindowMaskerLoc (CBlastQueryVector &query, const CBlastOptionsHandle *opts_handle)
 Find Window Masker filtered locations using a BlastOptionsHandle. More...
 
void Blast_FindWindowMaskerLoc (TSeqLocVector &query, const CBlastOptionsHandle *opts_handle)
 Find Window Masker filtered locations using a BlastOptionsHandle. More...
 
void Blast_FindWindowMaskerLoc (CBlastQueryVector &query, const string &lstat)
 Find Window Masker filtered locations by database name. More...
 
void Blast_FindWindowMaskerLoc (TSeqLocVector &query, const string &lstat)
 Find Window Masker filtered locations on TSeqLocVector by database name. More...
 
static string s_FindPathToWM (void)
 Find the path to the window masker files, first checking the (optionally set) value passed to the WindowMaskerPathInit function, then the environment variable WINDOW_MASKER_PATH, then the section WINDOW_MASKER, label WINDOW_MASKER_PATH in the NCBI configuration file. More...
 
void Blast_FindWindowMaskerLocTaxId (CBlastQueryVector &query, int taxid)
 Find Window Masker filtered locations by taxonomic ID. More...
 
void Blast_FindWindowMaskerLocTaxId (TSeqLocVector &query, int taxid)
 Find Window Masker filtered locations on a TSeqLocVector by Taxid. More...
 
static void s_OldGetTaxIdWithWindowMaskerSupport (set< int > &supported_taxids)
 
static CRef< CBlast4_ka_blocks_Convert_to_CBlast_ka_block (const Blast_KarlinBlk *kablk, bool gapped)
 
static CRef< objects::CBlast4_archive > s_BuildArchiveAll (CRef< CExportStrategy > export_strategy, blast::CBlastOptionsHandle &options_handle, const CSearchResultSet &results)
 
static void s_ReadLinesFromFile (const string &fn, vector< string > &lines)
 
static bool s_CompareSeqAlignByScoreAndName (const CRef< CSeq_align > &x, const CRef< CSeq_align > &y)
 
static bool s_IsSeqAlignAsGood (const CRef< CSeq_align > &x, const CRef< CSeq_align > &y)
 
static string s_RemoveLocalPrefix (const string &sid)
 
static string s_MakeTopHitsId (const CSeq_align_set::Tdata &align_list, int num_align)
 
static bool s_SeqAlignInSet (CSeq_align_set::Tdata &align_list, CRef< CSeq_align > &align)
 
static bool s_CompareSeqAlignByEvalue (const CRef< CSeq_align > &x, const CRef< CSeq_align > &y)
 
static bool s_CompareSeqAlignByScore (const CRef< CSeq_align > &x, const CRef< CSeq_align > &y)
 
static bool s_DJNotCompatible (const CSeq_align &d, const CSeq_align &j, bool ms, int margin)
 
static void s_ProcessErrorsFromReply (CRef< objects::CBlast4_reply > reply, string &errors, string &warnings)
 Process error messages from a reply object. More...
 
static void s_GetSeqsFromReply (CRef< objects::CBlast4_reply > reply, CBlastServices::TBioseqVector &bioseqs, string &errors, string &warnings)
 Get bioseqs from a sequence fetching reply. More...
 
static EBlast4_residue_type s_SeqTypeToResidue (char p, string &errors)
 
static CRef< objects::CBlast4_request > s_BuildGetSeqRequest (CBlastServices::TSeqIdVector &seqids, const string &database, char seqtype, bool skip_seq_data, bool target_only, string &errors)
 Build Sequence Fetching Request. More...
 
static void s_GetSequences (CBlastServices::TSeqIdVector &seqids, const string &database, char seqtype, bool skip_seq_data, bool target_only, CBlastServices::TBioseqVector &bioseqs, string &errors, string &warnings, bool verbose)
 Main function to issue a Blast4-get-sequences-request and collect its results from the remote BLAST server. More...
 
static CRef< objects::CBlast4_request > s_BuildGetSeqPartsRequest (const CBlastServices::TSeqIntervalVector &seqids, const string &database, char seqtype, string &errors)
 Build Sequence Parts Fetching Request. More...
 
static void s_GetPartsFromReply (CRef< objects::CBlast4_reply > reply, CBlastServices::TSeqIdVector &ids, CBlastServices::TSeqDataVector &seq_data, string &errors, string &warnings)
 Extract information from the get-seq-parts reply object. More...
 
void CBl2Seq::SetQuery (const SSeqLoc &query)
 Set the query. More...
 
const SSeqLocCBl2Seq::GetQuery () const
 Retrieve the query sequence. More...
 
void CBl2Seq::SetQueries (const TSeqLocVector &queries)
 Set a vector of query sequences for a concatenated search. More...
 
const TSeqLocVectorCBl2Seq::GetQueries () const
 Retrieve a vector of query sequences. More...
 
void CBl2Seq::SetSubject (const SSeqLoc &subject)
 Set the subject sequence. More...
 
const SSeqLocCBl2Seq::GetSubject () const
 Retrieve the subject sequence. More...
 
void CBl2Seq::SetSubjects (const TSeqLocVector &subjects)
 Set a vector of subject sequences. More...
 
const TSeqLocVectorCBl2Seq::GetSubjects () const
 Retrieve a vector of subject sequences. More...
 
CBlastOptionsHandleCBl2Seq::SetOptionsHandle ()
 Set the options handle. More...
 
const CBlastOptionsHandleCBl2Seq::GetOptionsHandle () const
 Retrieve the options handle. More...
 
BlastDiagnosticsCBl2Seq::GetDiagnostics () const
 Retrieves the diagnostics information returned from the engine. More...
 
void CBl2Seq::GetMessages (TSearchMessages &messages) const
 Returns error messages/warnings. More...
 
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. More...
 
void CBl2Seq::GetAncillaryResults (CSearchResultSet::TAncillaryVector &retval) const
 Get the ancillary results for a BLAST search (to be used with the Run() method) More...
 
TSearchMessages CLocalBlast::GetSearchMessages () const
 Retrieve any error/warning messages that occurred during the search. More...
 
int CLocalDbAdapter::GetFilteringAlgorithm ()
 Retrieve the database filtering algorithm. More...
 
const char * CPHIBlastNuclOptionsHandle::GetPHIPattern () const
 Retrieves the pattern string option. More...
 
void CPHIBlastNuclOptionsHandle::SetPHIPattern (const char *p)
 Sets the pattern string option. More...
 
const char * CPHIBlastProtOptionsHandle::GetPHIPattern () const
 Retrieves the pattern string option. More...
 
void CPHIBlastProtOptionsHandle::SetPHIPattern (const char *p)
 Sets the pattern string option. More...
 
TSearchMessages CBlastPrelimSearch::GetSearchMessages () const
 Retrieve any error/warning messages that occurred during the search. More...
 
TSeqLocInfoVector CBlastPrelimSearch::GetFilteredQueryRegions () const
 Retrieve the filtered/masked query regions. More...
 
TInterruptFnPtr CBlastPrelimSearch::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. More...
 
virtual void CThreadable::SetNumberOfThreads (size_t nthreads)
 Mutator for the number of threads. More...
 
size_t CThreadable::GetNumberOfThreads (void) const
 Accessor for the number of threads to use. More...
 
bool CThreadable::IsMultiThreaded (void) const
 Returns true if more than 1 thread is specified. More...
 
TSearchMessages CBlastTracebackSearch::GetSearchMessages () const
 Retrieve any error/warning messages that occurred during the search. More...
 
 CBlastSeqVectorFromCSeq_data::CBlastSeqVectorFromCSeq_data (const objects::CSeq_data &seq_data, TSeqPos length)
 Parametrized constructor. More...
 
virtual void CBlastSeqVectorFromCSeq_data::SetCoding (objects::CSeq_data::E_Choice c)
 @inheritDoc More...
 
virtual TSeqPos CBlastSeqVectorFromCSeq_data::x_Size () const
 @inheritDoc More...
 
virtual Uint1 CBlastSeqVectorFromCSeq_data::operator[] (TSeqPos pos) const
 @inheritDoc More...
 
virtual SBlastSequence CBlastSeqVectorFromCSeq_data::GetCompressedPlusStrand ()
 @inheritDoc More...
 
virtual void CBlastSeqVectorFromCSeq_data::x_SetPlusStrand ()
 @inheritDoc More...
 
virtual void CBlastSeqVectorFromCSeq_data::x_SetMinusStrand ()
 @inheritDoc More...
 
void CBlastSeqVectorFromCSeq_data::x_ComplementData ()
 Complements the data in m_SequenceData in place. More...
 
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. More...
 
 CBlastQuerySourceBioseqSet::CBlastQuerySourceBioseqSet (const objects::CBioseq_set &bss, bool is_prot)
 Parametrized constructor for a Bioseq-set. More...
 
 CBlastQuerySourceBioseqSet::CBlastQuerySourceBioseqSet (const objects::CBioseq &bioseq, bool is_prot)
 Parametrized constructor for a Bioseq. More...
 
virtual objects::ENa_strand CBlastQuerySourceBioseqSet::GetStrand (int index) const
 Return strand for a sequence. More...
 
virtual TSeqPos CBlastQuerySourceBioseqSet::Size () const
 Return the number of elements in the sequence container. More...
 
virtual CConstRef< objects::CSeq_loc > CBlastQuerySourceBioseqSet::GetMask (int index)
 Return the filtered (masked) regions for a sequence. More...
 
virtual TMaskedQueryRegions CBlastQuerySourceBioseqSet::GetMaskedRegions (int index)
 Return the filtered (masked) regions for a sequence. More...
 
virtual CConstRef< objects::CSeq_loc > CBlastQuerySourceBioseqSet::GetSeqLoc (int index) const
 Return the CSeq_loc associated with a sequence. More...
 
virtual const objects::CSeq_id * CBlastQuerySourceBioseqSet::GetSeqId (int index) const
 Return the sequence identifier associated with a sequence. More...
 
virtual Uint4 CBlastQuerySourceBioseqSet::GetGeneticCodeId (int index) const
 Retrieve the genetic code associated with a sequence. More...
 
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. More...
 
virtual TSeqPos CBlastQuerySourceBioseqSet::GetLength (int index) const
 Return the length of a sequence. More...
 
virtual string CBlastQuerySourceBioseqSet::GetTitle (int index) const
 Return the title of a sequence. More...
 
virtual bool CBlastQuerySourceBioseqSet::IsFirstOfAPair (int index) const
 Is this sequence followed by a mate (for mapping short reads) More...
 
virtual int CBlastQuerySourceBioseqSet::GetSegmentInfo (int index) const
 Get segment information (for mapping paired short reads) More...
 
void CBlastQuerySourceBioseqSet::x_BioseqSanityCheck (const objects::CBioseq &bs)
 Auxiliary method to do some sanity checks on the input Bioseqs. More...
 
 CBl2Seq::CBl2Seq (const SSeqLoc &query, const SSeqLoc &subject, EProgram p)
 Constructor to compare 2 sequences with default options. More...
 
void CBl2Seq::x_InitCLocalBlast ()
 Common initialization of the CLocalBlast object. More...
 
 CBl2Seq::CBl2Seq (const SSeqLoc &query, const SSeqLoc &subject, CBlastOptionsHandle &opts)
 Constructor to compare 2 sequences with specified options. More...
 
 CBl2Seq::CBl2Seq (const SSeqLoc &query, const TSeqLocVector &subjects, EProgram p, bool dbscan_mode=false)
 Constructor to compare query against all subject sequences with default options. More...
 
 CBl2Seq::CBl2Seq (const SSeqLoc &query, const TSeqLocVector &subjects, CBlastOptionsHandle &opts, bool dbscan_mode=false)
 Constructor to compare query against all subject sequences with specified options. More...
 
 CBl2Seq::CBl2Seq (const TSeqLocVector &queries, const TSeqLocVector &subjects, EProgram p, bool dbscan_mode=false)
 Constructor to allow query concatenation with default options. More...
 
 CBl2Seq::CBl2Seq (const TSeqLocVector &queries, const TSeqLocVector &subjects, CBlastOptionsHandle &opts, bool dbscan_mode=false)
 Constructor to allow query concatenation with specified options. More...
 
void CBl2Seq::x_Init (const TSeqLocVector &queries, const TSeqLocVector &subjs)
 Common initialization code for all c-tors. More...
 
virtual CBl2Seq::~CBl2Seq ()
 Destructor. More...
 
void CBl2Seq::x_ResetInternalDs ()
 Clean up structures and results from any previous search. More...
 
static TSeqAlignVector CBl2Seq::CSearchResultSet2TSeqAlignVector (CRef< CSearchResultSet > res)
 Converts m_Results data member to a TSeqAlignVector. More...
 
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)}, ... More...
 
void CBl2Seq::x_BuildAncillaryData ()
 Populate the internal m_AncillaryData member. More...
 
CRef< CSearchResultSetCBl2Seq::RunEx ()
 Performs the same functionality as Run(), but it returns a different data type. More...
 
TSeqLocInfoVector CBl2Seq::GetFilteredQueryRegions () const
 Retrieves regions filtered on the query/queries. More...
 
void CBl2Seq::GetFilteredSubjectRegions (vector< TSeqLocInfoVector > &retval) const
 Retrieves regions filtered on the subject sequence(s) More...
 
 CBlastAdvancedProteinOptionsHandle::CBlastAdvancedProteinOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
 Creates object with default options set. More...
 
virtual void CBlastAdvancedProteinOptionsHandle::SetGappedExtensionDefaults ()
 Overrides SetGappedExtensionDefaults for advanced blastp options. More...
 
virtual void CBlastAdvancedProteinOptionsHandle::SetQueryOptionDefaults ()
 Overrides SetQueryOptionDefaults for advanced blastp options to disable filtering. More...
 
virtual void CQuerySetUpOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CBLAST_SequenceBlk::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CBlastQueryInfo::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CLookupTableOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CLookupTableWrap::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CBlastInitialWordOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CBlastInitialWordParameters::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CBlast_ExtendWord::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CBlastExtensionOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CBlastExtensionParameters::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CBlastHitSavingOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CBlastHitSavingParameters::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CPSIBlastOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CBlastGapAlignStruct::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CBlastEffectiveLengthsOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CBlastEffectiveLengthsParameters::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CBlastScoreBlk::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CBlastScoringOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CBlastScoringParameters::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CBlastDatabaseOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CPSIMsa::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CPSIMatrix::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CPSIDiagnosticsRequest::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CPSIDiagnosticsResponse::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CBlastSeqSrc::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CBlastSeqSrcIterator::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CBlast_Message::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CBlastHSPResults::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CBlastMaskLoc::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CBlastSeqLoc::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual void CSBlastProgress::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CAutomaticGenCodeSingleton::CAutomaticGenCodeSingleton (int genetic_code=0)
 Default constructor. More...
 
 CAutomaticGenCodeSingleton::~CAutomaticGenCodeSingleton ()
 destructor More...
 
void CAutomaticGenCodeSingleton::AddGeneticCode (int genetic_code)
 Add the genetic code to the genetic code singleton. More...
 
void TQueryMessages::SetQueryId (const string &id)
 Set the query id as a string. More...
 
string TQueryMessages::GetQueryId () const
 Get the query id as a string. More...
 
void TQueryMessages::Combine (const TQueryMessages &other)
 Combine other messages with these. More...
 
bool TSearchMessages::HasMessages () const
 
string TSearchMessages::ToString () const
 Converts messages to a string, which is returned. More...
 
void TSearchMessages::Combine (const TSearchMessages &other_msgs)
 Combine another set of search messages with this one. More...
 
void TSearchMessages::RemoveDuplicates ()
 Find and remove redundant messages. More...
 
void TSearchMessages::AddMessageAllQueries (EBlastSeverity severity, int error_id, const string &message)
 Add a message for all queries. More...
 
static void CIndexedDb_New::ParseDBNames (const std::string db_spec, TStrVec &db_names)
 Generate a list of BLAST database names from a single string. More...
 
static void CIndexedDb_New::EnumerateDbVolumes (const TStrVec &db_names, TStrVec &db_vols)
 Generate a list of leaf database volumes from a list of database names. More...
 
SIZE_TYPE CIndexedDb_New::GetNextUnusedOID (void) const
 Auxiliary function thet returns the oid value that is one more than the largest oid used so far. More...
 
void CIndexedDb_New::AddIndexInfo (const std::string &vol_name, bool &idx_not_resolved)
 
 CIndexedDb_New::CIndexedDb_New (const string &indexname, bool &partial)
 Object constructor. More...
 
virtual CIndexedDb_New::~CIndexedDb_New ()
 Object destructor. More...
 
void CIndexedDb_New::UpdateIndex (Int4 oid, Int4 *vol_idx)
 Update the seed sets, if necessary. More...
 
virtual int CIndexedDb_New::CheckOid (Int4 oid, Int4 *last_vol_id)
 Check whether any results were reported for a given subject sequence. More...
 
virtual void CIndexedDb_New::EndSearchIndication (Int4 last_vol_id)
 Function used by threads to indicate that they are done with iterating over the database sequences. More...
 
virtual void CIndexedDb_New::DoPreSearch (BLAST_SequenceBlk *queries, LookupTableOptions *lut_options, BlastInitialWordOptions *word_options)
 Run preliminary indexed search functionality. More...
 
virtual unsigned long CIndexedDb_New::GetResults (CDbIndex::TSeqNum oid, CDbIndex::TSeqNum chunk, BlastInitHitList *init_hitlist) const
 Return results corresponding to a given subject sequence and chunk. More...
 
 CIndexedDb_Old::CIndexedDb_Old (const string &indexname)
 Object constructor. More...
 
virtual CIndexedDb::~CIndexedDb ()
 Object destructor. More...
 
void CIndexedDb_Old::PreSearch (BLAST_SequenceBlk *queries, BlastSeqLoc *locs, LookupTableOptions *lut_options, BlastInitialWordOptions *word_options)
 Invoke the seed search procedure on each of the loaded indices. More...
 
virtual unsigned long CIndexedDb_Old::GetResults (CDbIndex::TSeqNum oid, CDbIndex::TSeqNum chunk, BlastInitHitList *init_hitlist) const
 Return results corresponding to a given subject sequence and chunk. More...
 
 CBlastNucleotideOptionsHandle::CBlastNucleotideOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
 Creates object with default options set. More...
 
 CBlastNucleotideOptionsHandle::CBlastNucleotideOptionsHandle (CRef< CBlastOptions > opt)
 Create Options Handle from Existing CBlastOptions Object. More...
 
virtual void CBlastNucleotideOptionsHandle::SetDefaults ()
 Sets Defaults. More...
 
void CBlastNucleotideOptionsHandle::SetTraditionalBlastnDefaults ()
 Sets TraditionalBlastnDefaults. More...
 
void CBlastNucleotideOptionsHandle::SetVecScreenDefaults ()
 Sets default options for VecScreen. More...
 
void CBlastNucleotideOptionsHandle::SetTraditionalMegablastDefaults ()
 Sets TraditionalMegablastDefaults. More...
 
virtual void CBlastNucleotideOptionsHandle::SetLookupTableDefaults ()
 Overrides LookupTableDefaults for nucleotide options. More...
 
virtual void CBlastNucleotideOptionsHandle::SetMBLookupTableDefaults ()
 Overrides MBLookupTableDefaults for nucleotide options. More...
 
virtual void CBlastNucleotideOptionsHandle::SetQueryOptionDefaults ()
 Overrides QueryOptionDefaults for nucleotide options. More...
 
virtual void CBlastNucleotideOptionsHandle::SetInitialWordOptionsDefaults ()
 Overrides InitialWordOptionsDefaults for nucleotide options. More...
 
virtual void CBlastNucleotideOptionsHandle::SetMBInitialWordOptionsDefaults ()
 Overrides MBInitialWordOptionsDefaults for nucleotide options. More...
 
virtual void CBlastNucleotideOptionsHandle::SetGappedExtensionDefaults ()
 Overrides GappedExtensionDefaults for nucleotide options. More...
 
virtual void CBlastNucleotideOptionsHandle::SetMBGappedExtensionDefaults ()
 Overrides MBGappedExtensionDefaults for nucleotide options. More...
 
virtual void CBlastNucleotideOptionsHandle::SetScoringOptionsDefaults ()
 Overrides ScoringOptionsDefaults for nucleotide options. More...
 
virtual void CBlastNucleotideOptionsHandle::SetMBScoringOptionsDefaults ()
 Overrides MBScoringOptionsDefaults for nucleotide options. More...
 
virtual void CBlastNucleotideOptionsHandle::SetHitSavingOptionsDefaults ()
 Overrides HitSavingOptionsDefaults for nucleotide options. More...
 
virtual void CBlastNucleotideOptionsHandle::SetMBHitSavingOptionsDefaults ()
 Overrides MBHitSavingOptionsDefaults for nucleotide options. More...
 
virtual void CBlastNucleotideOptionsHandle::SetEffectiveLengthsOptionsDefaults ()
 Overrides EffectiveLengthsOptionsDefaults for nucleotide options. More...
 
virtual void CBlastNucleotideOptionsHandle::SetSubjectSequenceOptionsDefaults ()
 Overrides SubjectSequenceOptionsDefaults for nucleotide options. More...
 
 CBlastQuerySourceOM::CBlastQuerySourceOM (TSeqLocVector &v, EBlastProgramType prog)
 Constructor which takes a TSeqLocVector. More...
 
 CBlastQuerySourceOM::CBlastQuerySourceOM (TSeqLocVector &v, const CBlastOptions *opts)
 Constructor which takes a TSeqLocVector. More...
 
 CBlastQuerySourceOM::CBlastQuerySourceOM (CBlastQueryVector &v, EBlastProgramType prog)
 Constructor which takes a CBlastQueryVector. More...
 
 CBlastQuerySourceOM::CBlastQuerySourceOM (CBlastQueryVector &v, const CBlastOptions *opts)
 Constructor which takes a CBlastQueryVector. More...
 
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. More...
 
void CBlastQuerySourceOM::x_CalculateMasks ()
 Performs filtering on the query sequences to calculate the masked locations. More...
 
virtual CBlastQuerySourceOM::~CBlastQuerySourceOM ()
 dtor which determines if the internal pointer to its data should be deleted or not. More...
 
virtual objects::ENa_strand CBlastQuerySourceOM::GetStrand (int i) const
 Return strand for a sequence. More...
 
virtual TMaskedQueryRegions CBlastQuerySourceOM::GetMaskedRegions (int i)
 Return the filtered (masked) regions for a sequence. More...
 
virtual CConstRef< objects::CSeq_loc > CBlastQuerySourceOM::GetMask (int i)
 Return the filtered (masked) regions for a sequence. More...
 
virtual CConstRef< objects::CSeq_loc > CBlastQuerySourceOM::GetSeqLoc (int i) const
 Return the CSeq_loc associated with a sequence. More...
 
virtual const objects::CSeq_id * CBlastQuerySourceOM::GetSeqId (int index) const
 Return the sequence identifier associated with a sequence. More...
 
virtual Uint4 CBlastQuerySourceOM::GetGeneticCodeId (int index) const
 Retrieve the genetic code associated with a sequence. More...
 
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. More...
 
virtual TSeqPos CBlastQuerySourceOM::GetLength (int i) const
 Return the length of a sequence. More...
 
virtual string CBlastQuerySourceOM::GetTitle (int index) const
 Return the title of a sequence. More...
 
virtual TSeqPos CBlastQuerySourceOM::Size () const
 Return the number of elements in the sequence container. More...
 
 CBlastOptionsBuilder::CBlastOptionsBuilder (const string &program, const string &service, CBlastOptions::EAPILocality locality=CBlastOptions::eLocal, bool ignore_unsupported_options=false)
 Constructor. More...
 
static EProgram CBlastOptionsBuilder::ComputeProgram (const string &program, const string &service)
 Compute the EProgram value to use for this search. More...
 
void CBlastOptionsBuilder::x_ProcessOneOption (CBlastOptionsHandle &opts, objects::CBlast4_parameter &p)
 Apply the value of one option to the CBlastOptionsHandle. More...
 
void CBlastOptionsBuilder::x_ProcessOptions (CBlastOptionsHandle &opts, const TValueList *L)
 Apply the value of all options to the CBlastOptionsHandle. More...
 
void CBlastOptionsBuilder::x_ApplyInteractions (CBlastOptionsHandle &boh)
 Apply values directly to BlastOptions object. More...
 
static EProgram CBlastOptionsBuilder::AdjustProgram (const TValueList *L, EProgram program, const string &program_string)
 Adjust the EProgram based on option values. More...
 
CRef< CBlastOptionsHandleCBlastOptionsBuilder::GetSearchOptions (const objects::CBlast4_parameters *aopts, const objects::CBlast4_parameters *popts, const objects::CBlast4_parameters *fopts, string *task_name=NULL)
 Build and return options as a CBlastOptionsHandle. More...
 
bool CBlastOptionsBuilder::HaveEntrezQuery ()
 Check whether an Entrez query is specified. More...
 
string CBlastOptionsBuilder::GetEntrezQuery ()
 Get the Entrez query. More...
 
bool CBlastOptionsBuilder::HaveFirstDbSeq ()
 Check whether an OID range start point is specified. More...
 
int CBlastOptionsBuilder::GetFirstDbSeq ()
 Get the OID range start point. More...
 
bool CBlastOptionsBuilder::HaveFinalDbSeq ()
 Check whether an OID range end point is specified. More...
 
int CBlastOptionsBuilder::GetFinalDbSeq ()
 Get the OID range end point. More...
 
bool CBlastOptionsBuilder::HaveGiList ()
 Check whether a GI list is specified. More...
 
list< TGiCBlastOptionsBuilder::GetGiList ()
 Get the GI list. More...
 
bool CBlastOptionsBuilder::HasDbFilteringAlgorithmId ()
 Check whether a database filtering algorithm ID is specified. More...
 
int CBlastOptionsBuilder::GetDbFilteringAlgorithmId ()
 Get the database filtering algorithm ID. More...
 
bool CBlastOptionsBuilder::HasDbFilteringAlgorithmKey ()
 Check whether a database filtering algorithm key is specified. More...
 
string CBlastOptionsBuilder::GetDbFilteringAlgorithmKey ()
 Get the database filtering algorithm key. More...
 
bool CBlastOptionsBuilder::HasSubjectMaskingType ()
 Get Subject Maksing Type (soft/hard) More...
 
ESubjectMaskingType CBlastOptionsBuilder::GetSubjectMaskingType ()
 
bool CBlastOptionsBuilder::HaveNegativeGiList ()
 Check whether a negative GI list is specified. More...
 
list< TGiCBlastOptionsBuilder::GetNegativeGiList ()
 Get the negative GI list. More...
 
bool CBlastOptionsBuilder::HaveQueryMasks ()
 Check whether query masks are specified. More...
 
TMaskList CBlastOptionsBuilder::GetQueryMasks ()
 Get the query masks. More...
 
void CBlastOptionsBuilder::SetIgnoreUnsupportedOptions (bool ignore)
 Set the 'ignore unsupported options' flag. More...
 
bool CBlastOptionsBuilder::HaveTaxidList ()
 
list< intCBlastOptionsBuilder::GetTaxidList ()
 Get the Tax list. More...
 
bool CBlastOptionsBuilder::HaveNegativeTaxidList ()
 Check whether a negative tax id list is specified. More...
 
list< intCBlastOptionsBuilder::GetNegativeTaxidList ()
 Get the negative tax id list. More...
 
 CBlastOptions::CBlastOptions (EAPILocality locality=eLocal)
 Constructor which allows specification of local or remote version of the options (might change in the future) More...
 
 CBlastOptions::~CBlastOptions ()
 Destructor. More...
 
CRef< CBlastOptionsCBlastOptions::Clone () const
 Explicit deep copy of the Blast options object. More...
 
EAPILocality CBlastOptions::GetLocality () const
 Return the locality used when the object was created. More...
 
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 CBlastOptionsMementoCBlastOptions::CreateSnapshot () const
 Create a snapshot of the state of this object for internal use of its data structures (BLAST C++ APIs only) More...
 
bool CBlastOptions::operator== (const CBlastOptions &rhs) const
 
bool CBlastOptions::operator!= (const CBlastOptions &rhs) const
 
bool CBlastOptions::Validate () const
 Validate the options. More...
 
EProgram CBlastOptions::GetProgram () const
 Accessors/Mutators for individual options. More...
 
EBlastProgramType CBlastOptions::GetProgramType () const
 Returns the CORE BLAST notion of program type. More...
 
void CBlastOptions::SetProgram (EProgram p)
 Sets the task this object is best suited for. More...
 
bool CBlastOptions::IsIterativeSearch () const
 
double CBlastOptions::GetWordThreshold () const
 Returns WordThreshold. More...
 
void CBlastOptions::SetWordThreshold (double w)
 Sets WordThreshold. More...
 
ELookupTableType CBlastOptions::GetLookupTableType () const
 
void CBlastOptions::SetLookupTableType (ELookupTableType type)
 
int CBlastOptions::GetWordSize () const
 
void CBlastOptions::SetWordSize (int ws)
 
Uint4 CBlastOptions::GetLookupTableStride () const
 
void CBlastOptions::SetLookupTableStride (Uint4 val)
 
bool CBlastOptions::GetLookupDbFilter (void) const
 
void CBlastOptions::SetLookupDbFilter (bool val)
 
Uint1 CBlastOptions::GetMaxDbWordCount (void) const
 Get maximum word count for lookup table word masking by database frequency. More...
 
void CBlastOptions::SetMaxDbWordCount (Uint1 num)
 Set maximum word count for lookup table word masking by database frequency. More...
 
unsigned char CBlastOptions::GetMBTemplateLength () const
 Megablast only lookup table options. More...
 
void CBlastOptions::SetMBTemplateLength (unsigned char len)
 
unsigned char CBlastOptions::GetMBTemplateType () const
 
void CBlastOptions::SetMBTemplateType (unsigned char type)
 
void CBlastOptions::ClearFilterOptions ()
 
char * CBlastOptions::GetFilterString () const
 Return the filtering string used. More...
 
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. More...
 
void CBlastOptions::SetRepeatFiltering (bool val=true)
 Turns on repeat filtering using the default repeat database, namely kDefaultRepeatFilterDb. More...
 
const char * CBlastOptions::GetRepeatFilteringDB () const
 Returns the name of the repeat filtering database to use. More...
 
void CBlastOptions::SetRepeatFilteringDB (const char *db)
 Sets the repeat filtering database to use. More...
 
int CBlastOptions::GetWindowMaskerTaxId () const
 Returns the tax id used for the windowmasker database to use, if set via SetWindowMaskerTaxId (otherwise, returns 0) More...
 
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. More...
 
const char * CBlastOptions::GetWindowMaskerDatabase () const
 Return the name of the windowmasker database to use. More...
 
void CBlastOptions::SetWindowMaskerDatabase (const char *db)
 Sets the windowmasker database to use. More...
 
bool CBlastOptions::GetReadQualityFiltering () const
 Returns true if next-generation read quality filtering is turned on. More...
 
void CBlastOptions::SetReadQualityFiltering (bool val=true)
 Turn on/off next-generation read quality filtering with deafult parameters. More...
 
double CBlastOptions::GetReadMaxFractionAmbiguous () const
 Get maximum fraction of ambiguous bases for next-generation read quality filtering. More...
 
void CBlastOptions::SetReadMaxFractionAmbiguous (double val)
 Set maximum fraction of ambiguous bases for next-generation read quality filtering. More...
 
int CBlastOptions::GetReadMinDimerEntropy () const
 Get minimum dimer entropy for next-generation read quality filtering. More...
 
void CBlastOptions::SetReadMinDimerEntropy (int val)
 Set minimum dimer entropy for next-generation read quality filtering. More...
 
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::GetMaxMismatches () const
 
void CBlastOptions::SetMaxMismatches (int m)
 
int CBlastOptions::GetMismatchWindow () const
 
void CBlastOptions::SetMismatchWindow (int w)
 
int CBlastOptions::GetHitlistSize () const
 
void CBlastOptions::SetHitlistSize (int s)
 
int CBlastOptions::GetMaxNumHspPerSequence () const
 
void CBlastOptions::SetMaxNumHspPerSequence (int m)
 
int CBlastOptions::GetMaxHspsPerSubject () const
 
void CBlastOptions::SetMaxHspsPerSubject (int m)
 
int CBlastOptions::GetCullingLimit () const
 
void CBlastOptions::SetCullingLimit (int s)
 
bool CBlastOptions::GetSubjectBestHit () const
 
void CBlastOptions::SetSubjectBestHit ()
 
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)
 
vector< double > CBlastOptions::GetCutoffScoreCoeffs () const
 
void CBlastOptions::SetCutoffScoreCoeffs (const vector< double > &c)
 
double CBlastOptions::GetPercentIdentity () const
 
void CBlastOptions::SetPercentIdentity (double p)
 
int CBlastOptions::GetMaxEditDistance () const
 
void CBlastOptions::SetMaxEditDistance (int e)
 
double CBlastOptions::GetQueryCovHspPerc () const
 
void CBlastOptions::SetQueryCovHspPerc (double p)
 
int CBlastOptions::GetMinDiagSeparation () const
 
void CBlastOptions::SetMinDiagSeparation (int d)
 
bool CBlastOptions::GetSumStatisticsMode () const
 Sum statistics options. More...
 
void CBlastOptions::SetSumStatisticsMode (bool m=true)
 
int CBlastOptions::GetLongestIntronLength () const
 for linking HSPs with uneven gaps More...
 
void CBlastOptions::SetLongestIntronLength (int l)
 for linking HSPs with uneven gaps More...
 
bool CBlastOptions::GetGappedMode () const
 Returns true if gapped BLAST is set, false otherwise. More...
 
void CBlastOptions::SetGappedMode (bool m=true)
 
int CBlastOptions::GetMaskLevel () const
 Masklevel filtering option -RMH-. More...
 
void CBlastOptions::SetMaskLevel (int s)
 
bool CBlastOptions::GetComplexityAdjMode () const
 Returns true if cross_match-like complexity adjusted. More...
 
void CBlastOptions::SetComplexityAdjMode (bool m=true)
 
double CBlastOptions::GetLowScorePerc () const
 Sets a low score to drop ungapped alignments if hit list is full. More...
 
void CBlastOptions::SetLowScorePerc (double p=0.0)
 
bool CBlastOptions::GetPaired () const
 
void CBlastOptions::SetPaired (bool p)
 
bool CBlastOptions::GetSpliceAlignments () const
 Splice HSPs for each query (for mappring RNA-Seq reads to a genome) More...
 
void CBlastOptions::SetSpliceAlignments (bool s)
 
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)
 
bool CBlastOptions::GetIgnoreMsaMaster () const
 
void CBlastOptions::SetIgnoreMsaMaster (bool val)
 
double CBlastOptions::GetDomainInclusionThreshold (void) const
 
void CBlastOptions::SetDomainInclusionThreshold (double th)
 
void CBlastOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Allows to dump a snapshot of the object. More...
 
void CBlastOptions::DoneDefaults () const
 
TBlast4OptsCBlastOptions::GetBlast4AlgoOpts ()
 
bool CBlastOptions::GetUseIndex () const
 
bool CBlastOptions::GetForceIndex () const
 
bool CBlastOptions::GetIsOldStyleMBIndex () 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, bool old_style_index=false)
 
void CBlastOptions::SetMBIndexLoaded (bool index_loaded=true)
 
QuerySetUpOptionsCBlastOptions::GetQueryOpts () const
 Returns QuerySetUpOptions for eLocal objects, NULL for eRemote. More...
 
LookupTableOptionsCBlastOptions::GetLutOpts () const
 Returns LookupTableOptions for eLocal objects, NULL for eRemote. More...
 
BlastInitialWordOptionsCBlastOptions::GetInitWordOpts () const
 Returns BlastInitialWordOptions for eLocal objects, NULL for eRemote. More...
 
BlastExtensionOptionsCBlastOptions::GetExtnOpts () const
 Returns BlastExtensionOptions for eLocal objects, NULL for eRemote. More...
 
BlastHitSavingOptionsCBlastOptions::GetHitSaveOpts () const
 Returns BlastHitSavingOptions for eLocal objects, NULL for eRemote. More...
 
PSIBlastOptionsCBlastOptions::GetPSIBlastOpts () const
 Returns PSIBlastOptions for eLocal objects, NULL for eRemote. More...
 
BlastDatabaseOptionsCBlastOptions::GetDbOpts () const
 Returns BlastDatabaseOptions for eLocal objects, NULL for eRemote. More...
 
BlastScoringOptionsCBlastOptions::GetScoringOpts () const
 Returns BlastScoringOptions for eLocal objects, NULL for eRemote. More...
 
BlastEffectiveLengthsOptionsCBlastOptions::GetEffLenOpts () const
 Returns BlastEffectiveLengthsOptions for eLocal objects, NULL for eRemote. More...
 
void CBlastOptions::x_Throwx (const string &msg) const
 Auxiliary to throw CBlastExceptions. More...
 
void CBlastOptions::SetDefaultsMode (bool dmode)
 If this is true, remote options will ignore "Set" calls. More...
 
bool CBlastOptions::GetDefaultsMode () const
 
void CBlastOptions::x_DoDeepCopy (const CBlastOptions &opts)
 Perform a "deep copy" of Blast options. More...
 
 CBlastOptionsHandle::CBlastOptionsHandle (EAPILocality locality)
 Default c-tor. More...
 
 CBlastOptionsHandle::CBlastOptionsHandle (CRef< CBlastOptions > opt)
 Create Options Handle from Existing CBlastOptions Object. More...
 
virtual void CBlastOptionsHandle::SetDefaults ()
 Resets the state of the object to all default values. More...
 
bool CBlastOptionsHandle::Validate () const
 Validate the options contained in this object. More...
 
char * CBlastOptionsHandle::GetFilterString () const
 Returns FilterString. More...
 
void CBlastOptionsHandle::SetFilterString (const char *f, bool clear=true)
 Sets FilterString. More...
 
static CBlastOptionsHandleCBlastOptionsFactory::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. More...
 
static set< stringCBlastOptionsFactory::GetTasks (ETaskSets choice=eAll)
 Retrieve the set of supported tasks. More...
 
static string CBlastOptionsFactory::GetDocumentation (const string &task_name)
 Return the documentation for the provided task. More...
 
static CBlastOptionsHandleCBlastOptionsFactory::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. More...
 
 CBlastOptionsLocal::CBlastOptionsLocal ()
 
 CBlastOptionsLocal::~CBlastOptionsLocal ()
 
 CBlastOptionsLocal::CBlastOptionsLocal (const CBlastOptionsLocal &optsLocal)
 Copy constructor. More...
 
CBlastOptionsLocalCBlastOptionsLocal::operator= (const CBlastOptionsLocal &optsLocal)
 Assignment operator. More...
 
void CBlastOptionsLocal::x_DoDeepCopy (const CBlastOptionsLocal &optsLocal)
 Perform a "deep copy" of local Blast options. More...
 
static void CBlastOptionsLocal::x_Copy_CQuerySetUpOptions (CQuerySetUpOptions &queryOptsDst, const CQuerySetUpOptions &queryOptsSrc)
 Get a copy of CQuerySetUpOptions. More...
 
static void CBlastOptionsLocal::x_Copy_CLookupTableOptions (CLookupTableOptions &lutOptsDst, const CLookupTableOptions &lutOptsSrc)
 Get a copy of CLookupTableOptions. More...
 
static void CBlastOptionsLocal::x_Copy_CBlastInitialWordOptions (CBlastInitialWordOptions &initWordOptsDst, const CBlastInitialWordOptions &initWordOptsSrc)
 Get a copy of CBlastInitialWordOptions. More...
 
static void CBlastOptionsLocal::x_Copy_CBlastExtensionOptions (CBlastExtensionOptions &extnOptsDst, const CBlastExtensionOptions &extnOptsSrc)
 Get a copy of CBlastExtensionOptions. More...
 
static void CBlastOptionsLocal::x_Copy_CBlastHitSavingOptions (CBlastHitSavingOptions &hitSaveOptsDst, const CBlastHitSavingOptions &hitSaveOptsSrc)
 Get a copy of CBlastHitSavingOptions. More...
 
static void CBlastOptionsLocal::x_Copy_CPSIBlastOptions (CPSIBlastOptions &psiBlastOptsDst, const CPSIBlastOptions &psiBlastOptsSrc)
 Get a copy of CPSIBlastOptions. More...
 
static void CBlastOptionsLocal::x_Copy_CBlastDatabaseOptions (CBlastDatabaseOptions &dbOptsDst, const CBlastDatabaseOptions &dbOptsSrc)
 Get a copy of CBlastDatabaseOptions. More...
 
static void CBlastOptionsLocal::x_Copy_CBlastScoringOptions (CBlastScoringOptions &scoringOptsDst, const CBlastScoringOptions &scoringOptsSrc)
 Get a copy of CBlastScoringOptions. More...
 
static void CBlastOptionsLocal::x_Copy_CBlastEffectiveLengthsOptions (CBlastEffectiveLengthsOptions &effLenOptsDst, const CBlastEffectiveLengthsOptions &effLenOptsSrc)
 Get a copy of CBlastEffectiveLengthsOptions. More...
 
void CBlastOptionsLocal::SetDbGeneticCode (int gc)
 
EBlastProgramType CBlastOptionsLocal::GetProgramType () const
 
bool CBlastOptionsLocal::Validate () const
 Validate the options. More...
 
void CBlastOptionsLocal::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Allows to dump a snapshot of the object. More...
 
bool CBlastOptionsLocal::operator== (const CBlastOptionsLocal &rhs) const
 
bool CBlastOptionsLocal::operator!= (const CBlastOptionsLocal &rhs) const
 
EProgram CBlastOptionsLocal::GetProgram () const
 Accessors/Mutators for individual options. More...
 
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)
 
Uint4 CBlastOptionsLocal::GetLookupTableStride () const
 Skip words after each collected one while creating a lookup table (currently only for megablast) More...
 
void CBlastOptionsLocal::SetLookupTableStride (Uint4 val)
 
unsigned char CBlastOptionsLocal::GetMBTemplateLength () const
 Megablast only lookup table options. More...
 
void CBlastOptionsLocal::SetMBTemplateLength (unsigned char len)
 
unsigned char CBlastOptionsLocal::GetMBTemplateType () const
 
void CBlastOptionsLocal::SetMBTemplateType (unsigned char type)
 
bool CBlastOptionsLocal::GetLookupDbFilter (void) const
 
void CBlastOptionsLocal::SetLookupDbFilter (bool val)
 
Uint1 CBlastOptionsLocal::GetMaxDbWordCount (void) const
 
void CBlastOptionsLocal::SetMaxDbWordCount (Uint1 val)
 
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)
 
bool CBlastOptionsLocal::GetReadQualityFiltering (void) const
 
void CBlastOptionsLocal::SetReadQualityFiltering (bool val=true)
 
double CBlastOptionsLocal::GetReadMaxFractionAmbiguous (void) const
 
void CBlastOptionsLocal::SetReadMaxFractionAmbiguous (double val)
 
int CBlastOptionsLocal::GetReadMinDimerEntropy (void) const
 
void CBlastOptionsLocal::SetReadMinDimerEntropy (int val)
 
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::GetMaxMismatches () const
 
void CBlastOptionsLocal::SetMaxMismatches (int m)
 
int CBlastOptionsLocal::GetMismatchWindow () const
 
void CBlastOptionsLocal::SetMismatchWindow (int w)
 
int CBlastOptionsLocal::GetHitlistSize () const
 
void CBlastOptionsLocal::SetHitlistSize (int s)
 
int CBlastOptionsLocal::GetMaxNumHspPerSequence () const
 
void CBlastOptionsLocal::SetMaxHspsPerSubject (int m)
 
int CBlastOptionsLocal::GetMaxHspsPerSubject () 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)
 
void CBlastOptionsLocal::SetSubjectBestHit ()
 
bool CBlastOptionsLocal::GetSubjectBestHit () const
 
double CBlastOptionsLocal::GetEvalueThreshold () const
 
void CBlastOptionsLocal::SetEvalueThreshold (double eval)
 
int CBlastOptionsLocal::GetCutoffScore () const
 
void CBlastOptionsLocal::SetCutoffScore (int s)
 
vector< double > CBlastOptionsLocal::GetCutoffScoreCoeffs () const
 
void CBlastOptionsLocal::SetCutoffScoreCoeffs (const vector< double > &c)
 
double CBlastOptionsLocal::GetPercentIdentity () const
 
void CBlastOptionsLocal::SetPercentIdentity (double p)
 
int CBlastOptionsLocal::GetMaxEditDistance () const
 
void CBlastOptionsLocal::SetMaxEditDistance (int e)
 
double CBlastOptionsLocal::GetQueryCovHspPerc () const
 
void CBlastOptionsLocal::SetQueryCovHspPerc (double p)
 
int CBlastOptionsLocal::GetMinDiagSeparation () const
 
void CBlastOptionsLocal::SetMinDiagSeparation (int d)
 
bool CBlastOptionsLocal::GetSumStatisticsMode () const
 Sum statistics options. More...
 
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. More...
 
void CBlastOptionsLocal::SetGappedMode (bool m=true)
 
int CBlastOptionsLocal::GetMaskLevel () const
 Masklevel filtering option -RMH-. More...
 
void CBlastOptionsLocal::SetMaskLevel (int s)
 
double CBlastOptionsLocal::GetLowScorePerc () const
 Sets low score percentages. More...
 
void CBlastOptionsLocal::SetLowScorePerc (double p=0.0)
 
bool CBlastOptionsLocal::GetPaired () const
 
void CBlastOptionsLocal::SetPaired (bool p)
 
bool CBlastOptionsLocal::GetSplice () const
 Splice HSPs for each query. More...
 
void CBlastOptionsLocal::SetSplice (bool p)
 
bool CBlastOptionsLocal::GetComplexityAdjMode () const
 Returns true if cross_match-like complexity adjusted. More...
 
void CBlastOptionsLocal::SetComplexityAdjMode (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)
 
bool CBlastOptionsLocal::GetIgnoreMsaMaster () const
 
void CBlastOptionsLocal::SetIgnoreMsaMaster (bool val)
 
void CBlastOptionsLocal::SetPHIPattern (const char *pattern, bool is_dna)
 
double CBlastOptionsLocal::GetDomainInclusionThreshold () const
 
void CBlastOptionsLocal::SetDomainInclusionThreshold (double incthr)
 
bool CBlastOptionsLocal::GetUseIndex () const
 
bool CBlastOptionsLocal::GetForceIndex () const
 
bool CBlastOptionsLocal::GetMBIndexLoaded () const
 
const string CBlastOptionsLocal::GetIndexName () const
 
void CBlastOptionsLocal::SetMBIndexLoaded (bool index_loaded=true)
 
bool CBlastOptionsLocal::GetIsOldStyleMBIndex () const
 
void CBlastOptionsLocal::SetUseIndex (bool use_index=true, const string &index_name="", bool force_index=false, bool old_style_index=false)
 
 CBlastProteinOptionsHandle::CBlastProteinOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
 Creates object with default options set. More...
 
virtual void CBlastProteinOptionsHandle::SetLookupTableDefaults ()
 Overrides LookupTableDefaults for protein options. More...
 
virtual void CBlastProteinOptionsHandle::SetQueryOptionDefaults ()
 Overrides QueryOptionDefaults for protein options. More...
 
virtual void CBlastProteinOptionsHandle::SetInitialWordOptionsDefaults ()
 Overrides InitialWordOptionsDefaults for protein options. More...
 
virtual void CBlastProteinOptionsHandle::SetGappedExtensionDefaults ()
 Overrides GappedExtensionDefaults for protein options. More...
 
virtual void CBlastProteinOptionsHandle::SetScoringOptionsDefaults ()
 Overrides ScoringOptionsDefaults for protein options. More...
 
virtual void CBlastProteinOptionsHandle::SetHitSavingOptionsDefaults ()
 Overrides HitSavingOptionsDefaults for protein options. More...
 
virtual void CBlastProteinOptionsHandle::SetEffectiveLengthsOptionsDefaults ()
 Overrides EffectiveLengthsOptionsDefaults for protein options. More...
 
virtual void CBlastProteinOptionsHandle::SetSubjectSequenceOptionsDefaults ()
 Overrides SubjectSequenceOptionsDefaults for protein options. More...
 
 CBlastAncillaryData::CBlastAncillaryData (EBlastProgramType program_type, int query_number, const BlastScoreBlk *sbp, const BlastQueryInfo *query_info)
 constructor More...
 
 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. More...
 
 CBlastAncillaryData::CBlastAncillaryData (const CBlastAncillaryData &rhs)
 Copy-constructor. More...
 
CBlastAncillaryDataCBlastAncillaryData::operator= (const CBlastAncillaryData &rhs)
 Assignment operator. More...
 
 CBlastAncillaryData::~CBlastAncillaryData ()
 Destructor. More...
 
void CBlastAncillaryData::do_copy (const CBlastAncillaryData &other)
 Workhorse for copy constructor and assignment operator. More...
 
 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. More...
 
 CSearchResults::~CSearchResults ()
 Our destructor. More...
 
void CSearchResults::GetMaskedQueryRegions (TMaskedQueryRegions &flt_query_regions) const
 Retrieve the query regions which were masked by BLAST. More...
 
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. More...
 
TQueryMessages CSearchResults::GetErrors (int min_severity=eBlastSevError) const
 Accessor for the error/warning messsages for this query. More...
 
string CSearchResults::GetErrorStrings () const
 Retrieve a string with the query identifier followed by the errors produced, returns a empty string if HasErrors() returns false. More...
 
string CSearchResults::GetWarningStrings () const
 Retrieve a string with the query identifier followed by the warnings produced, returns a empty string if HasWarnings() returns false. More...
 
bool CSearchResults::HasErrors () const
 Returns true if there are errors among the results for this object. More...
 
bool CSearchResults::HasWarnings () const
 Returns true if there are warnings among the results for this object. More...
 
bool CSearchResults::HasAlignments () const
 Return true if there are any alignments for this query. More...
 
CConstRef< objects::CSeq_id > CSearchResults::GetSeqId () const
 Accessor for the query's sequence identifier. More...
 
void CSearchResults::GetSubjectMasks (TSeqLocInfoVector &subj_masks) const
 Retrieve the masked locations for the subject sequences in the contained alignment. More...
 
void CSearchResults::SetSubjectMasks (const TSeqLocInfoVector &subj_masks)
 Set the masked locations for the subject sequences in the contained alignment. More...
 
void CSearchResults::TrimSeqAlign (objects::CSeq_align_set::Tdata::size_type max_size)
 Trim align_set size @parm size max num of alignments to keep (0 will erase all) More...
 
CSearchResultsCSearchResultSet::GetResults (size_type qi, size_type si)
 Retrieve results for a query-subject pair contained by this object. More...
 
const CSearchResultsCSearchResultSet::GetResults (size_type qi, size_type si) const
 Retrieve results for a query-subject pair. More...
 
CConstRef< CSearchResultsCSearchResultSet::operator[] (const objects::CSeq_id &ident) const
 Allow array-like access with CSeq_id indices to const CSearchResults contained by this object. More...
 
CRef< CSearchResultsCSearchResultSet::operator[] (const objects::CSeq_id &ident)
 Allow array-like access with CSeq_id indices to CSearchResults contained by this object. More...
 
 CSearchResultSet::CSearchResultSet (EResultType res_type=eDatabaseSearch)
 Simplest constructor. More...
 
 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. More...
 
 CSearchResultSet::CSearchResultSet (TSeqAlignVector aligns, TSearchMessages msg_vec, EResultType res_type=eDatabaseSearch)
 Parametrized constructor. More...
 
TSeqLocInfoVector CSearchResultSet::GetFilteredQueryRegions () const
 Retrieves the filtered query regions. More...
 
void CSearchResultSet::SetFilteredQueryRegions (const TSeqLocInfoVector &masks)
 Sets the filtered query regions. More...
 
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. More...
 
void CSearchResultSet::push_back (value_type &element)
 Add a value to the back of this container. More...
 
void CSearchResultSet::SetRID (const string &rid)
 Sets the RID for these results. More...
 
 CBlastRPSOptionsHandle::CBlastRPSOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
 Creates object with default options set. More...
 
 CBlastRPSOptionsHandle::CBlastRPSOptionsHandle (CRef< CBlastOptions > opt)
 Create Options Handle from Existing CBlastOptions Object. More...
 
virtual void CBlastRPSOptionsHandle::SetLookupTableDefaults ()
 Overrides LookupTableDefaults for RPS-BLAST options. More...
 
virtual void CBlastRPSOptionsHandle::SetQueryOptionDefaults ()
 Overrides QueryOptionDefaults for RPS-BLAST options. More...
 
virtual void CBlastRPSOptionsHandle::SetInitialWordOptionsDefaults ()
 Overrides InitialWordOptionsDefaults for RPS-BLAST options. More...
 
virtual void CBlastRPSOptionsHandle::SetGappedExtensionDefaults ()
 Overrides GappedExtensionDefaults for RPS-BLAST options. More...
 
virtual void CBlastRPSOptionsHandle::SetScoringOptionsDefaults ()
 Overrides ScoringOptionsDefaults for RPS-BLAST options. More...
 
virtual void CBlastRPSOptionsHandle::SetHitSavingOptionsDefaults ()
 Overrides HitSavingOptionsDefaults for RPS-BLAST options. More...
 
virtual void CBlastRPSOptionsHandle::SetEffectiveLengthsOptionsDefaults ()
 Overrides EffectiveLengthsOptionsDefaults for RPS-BLAST options. More...
 
virtual void CBlastRPSOptionsHandle::SetSubjectSequenceOptionsDefaults ()
 Overrides SubjectSequenceOptionsDefaults for RPS-BLAST options. More...
 
bool CBlastQueryFilteredFrames::x_NeedsTrans ()
 Returns true if this program needs coordinate translation. More...
 
 CBlastQueryFilteredFrames::CBlastQueryFilteredFrames (EBlastProgramType program)
 Construct container for frame values and BlastSeqLocs for the specified search program. More...
 
 CBlastQueryFilteredFrames::CBlastQueryFilteredFrames (EBlastProgramType program, const TMaskedQueryRegions &mqr)
 Construct container for frame values and BlastSeqLocs from a TMaskedQueryRegions vector. More...
 
 CBlastQueryFilteredFrames::~CBlastQueryFilteredFrames ()
 Destructor; frees any BlastSeqLoc lists not released by the caller. More...
 
void CBlastQueryFilteredFrames::Release (int frame)
 Release the BlastSeqLocs for a given frame. More...
 
void CBlastQueryFilteredFrames::UseProteinCoords (TSeqPos dna_length)
 Adjusts all stored masks from nucleotide to protein offsets. More...
 
const set< ETranslationFrame > & CBlastQueryFilteredFrames::ListFrames ()
 Returns the list of frame values for which this object contains masking information. More...
 
bool CBlastQueryFilteredFrames::Empty ()
 Returns true if this object contains any masking information. More...
 
void CBlastQueryFilteredFrames::x_VerifyFrame (int frame)
 Verify the specified frame value. More...
 
bool CBlastQueryFilteredFrames::QueryHasMultipleFrames () const
 Check whether the query is multiframe for this type of search. More...
 
void CBlastQueryFilteredFrames::AddSeqLoc (const objects::CSeq_interval &intv, int frame)
 Add a masked interval to the specified frame. More...
 
BlastSeqLoc ** CBlastQueryFilteredFrames::operator[] (int frame)
 Access the BlastSeqLocs for a given frame. More...
 
 CBlastpKmerOptionsHandle::CBlastpKmerOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
 Creates object with default options set. More...
 
 CBlastxOptionsHandle::CBlastxOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
 Creates object with default options set. More...
 
void CBlastxOptionsHandle::SetLookupTableDefaults ()
 Overrides LookupTableDefaults for blastx options. More...
 
void CBlastxOptionsHandle::SetQueryOptionDefaults ()
 Overrides QueryOptionDefaults for blastx options. More...
 
void CBlastxOptionsHandle::SetGappedExtensionDefaults ()
 Overrides SetGappedExtensionDefaults for blastx option. More...
 
void CBlastxOptionsHandle::SetScoringOptionsDefaults ()
 Overrides ScoringOptionsDefaults for blastx options. More...
 
void CBlastxOptionsHandle::SetHitSavingOptionsDefaults ()
 Overrides HitSavingOptionsDefaults for blastx options. More...
 
 CCddInputData::CCddInputData (const Uint1 *query, unsigned int query_length, CConstRef< objects::CSeq_align_set > seqaligns, const PSIBlastOptions &opts, const string &dbname, const string &matrix_name="BLOSUM62", int gap_existence=0, int gap_extension=0, PSIDiagnosticsRequest *diags=NULL, const string &query_title="")
 Constructor. More...
 
virtual CCddInputData::~CCddInputData ()
 Virtual destructor. More...
 
void CCddInputData::Process (void)
 Pre-process CD matches to query. More...
 
void CCddInputData::x_ProcessAlignments (double min_evalue, double max_evalue)
 Process RPS-BLAST hits. More...
 
void CCddInputData::x_RemoveMultipleCdHits (void)
 Remove multiple hits to the same CD. More...
 
void CCddInputData::x_FillHitsData (void)
 Read data needed for PSSM computation from CDD and populate arrays. More...
 
void CCddInputData::x_CreateMsa (void)
 Create multiple alignment of CDs. More...
 
bool CCddInputData::x_ValidateMsa (void) const
 Validate multiple alignment of CDs. More...
 
 CCddInputData::CHit::CHit (const CHit &hit)
 Copy constructor. More...
 
 CCddInputData::CHit::~CHit ()
 Destructor. More...
 
int CCddInputData::CHit::GetLength (void) const
 Get hit length in residues, counts number of matching residues, gaps are not counted. More...
 
void CCddInputData::CHit::FillData (const CSeqDB &seqdb, const CBlastRPSInfo &profile_data)
 Allocate and populate arrays of data for PSSM computation. More...
 
bool CCddInputData::x_ValidateHits (void) const
 Validate internal representation of RPS-BLAST hits. More...
 
void CCddInputData::x_ExtractQueryForPssm (void)
 Create query as Bioseq. More...
 
bool CCddInputData::CHit::Validate (void) const
 Validate hit. More...
 
bool CCddInputData::CHit::IsEmpty (void) const
 Is hit empty. More...
 
void CCddInputData::CHit::IntersectWith (const vector< TRange > &segments, EApplyTo app)
 Intersect hit segments with list of ranges and store result in hit segments. More...
 
void CCddInputData::CHit::IntersectWith (const CHit &hit, EApplyTo app)
 Intersect hit with another hit and store result. More...
 
void CCddInputData::CHit::Subtract (const CHit &hit)
 Subtract from another hit from this hit using query ranges. More...
 
void CCddInputData::CHitSegment::FillData (int db_oid, const CBlastRPSInfo &profile_data)
 Allocate and populate arrays for MSA data (weighted residue counts and effective observations used for PSSM computation) More...
 
bool CCddInputData::CHitSegment::Validate (void) const
 Validate hit segment. More...
 
void CCddInputData::CHitSegment::AdjustRanges (int d_from, int d_to)
 Change ranges on query and subject by given values. More...
 
bool CCddInputData::CHitSegment::IsEmpty (void) const
 Does the hit segment represent an empty range. More...
 
void CCddInputData::CHitSegment::x_FillResidueCounts (int db_oid, const CBlastRPSInfo &profile_data)
 Populate arrays of weighted residue counts. More...
 
void CCddInputData::CHitSegment::x_FillObservations (int db_oid, const CBlastRPSInfo &profile_data)
 Populate arrays of effective numbers of observations. More...
 
 CDeltaBlast::CDeltaBlast (CRef< IQueryFactory > query_factory, CRef< CLocalDbAdapter > blastdb, CRef< CLocalDbAdapter > domaindb, CConstRef< CDeltaBlastOptionsHandle > options)
 Constructor to compare a single sequence against a database of protein sequences, and use RPS-BLAST to search CDD. More...
 
 CDeltaBlast::CDeltaBlast (CRef< IQueryFactory > query_factory, CRef< CLocalDbAdapter > blastdb, CRef< CLocalDbAdapter > domaindb, CConstRef< CDeltaBlastOptionsHandle > options, CRef< CBlastRPSOptionsHandle > rps_options)
 Constructor to compare a single sequence against a database of protein sequences, and use RPS-BLAST to search CDD. More...
 
CRef< CSearchResultSetCDeltaBlast::Run ()
 Run the DELTA-BLAST engine with one iteration. More...
 
CConstRef< objects::CPssmWithParameters > CDeltaBlast::GetPssm (int index=0) const
 Accessor for PSSM computd from CDD hits and used in protein search. More...
 
CRef< objects::CPssmWithParameters > CDeltaBlast::GetPssm (int index=0)
 Accessor for PSSM computd from CDD hits and used in protein search. More...
 
CRef< CSearchResultSetCDeltaBlast::x_FindDomainHits (void)
 Search domain database. More...
 
void CDeltaBlast::x_Validate (void)
 Perform sanity checks on input parameters. More...
 
 CDeltaBlastOptionsHandle::CDeltaBlastOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
 Creates object with default options set. More...
 
virtual void CDeltaBlastOptionsHandle::SetQueryOptionDefaults ()
 Override the parent class' default for filtering query sequence (i.e. More...
 
void CDeltaBlastOptionsHandle::SetDeltaBlastDefaults ()
 Sets Delta Blast defaults. More...
 
virtual void CDeltaBlastOptionsHandle::SetGappedExtensionDefaults ()
 Override the parent class' defaults for gapped extension (i.e. More...
 
 CDiscNucleotideOptionsHandle::CDiscNucleotideOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
 Creates object with default options set. More...
 
void CDiscNucleotideOptionsHandle::SetMBLookupTableDefaults ()
 Sets MBLookupTableDefaults. More...
 
void CDiscNucleotideOptionsHandle::SetMBInitialWordOptionsDefaults ()
 Sets MBInitialWordOptionsDefaults. More...
 
void CDiscNucleotideOptionsHandle::SetMBGappedExtensionDefaults ()
 Sets MBGappedExtensionDefaults. More...
 
void CDiscNucleotideOptionsHandle::SetMBScoringOptionsDefaults ()
 Sets MBScoringOptionsDefaults. More...
 
void CDiscNucleotideOptionsHandle::SetTraditionalBlastnDefaults ()
 NOTE: Unavailable for discontiguous megablast. More...
 
 CEffectiveSearchSpaceCalculator::CEffectiveSearchSpaceCalculator (CRef< IQueryFactory > query_factory, const CBlastOptions &options, Int4 db_num_seqs, Int8 db_num_bases, BlastScoreBlk *sbp=NULL)
 Constructor. More...
 
Int8 CEffectiveSearchSpaceCalculator::GetEffSearchSpace (size_t query_index=0) const
 Retrieve the effective search space calculated for a given query. More...
 
Int8 CEffectiveSearchSpaceCalculator::GetEffSearchSpaceForContext (size_t ctx_index) const
 Retrieve the effective search space calculated for a given query context. More...
 
BlastQueryInfoCEffectiveSearchSpaceCalculator::GetQueryInfo () const
 Retrieve the BlastQueryInfo structure that stores the effective search spaces for all queries. More...
 
 CLocalBlast::CLocalBlast (CRef< IQueryFactory > query_factory, CRef< CBlastOptionsHandle > opts_handle, const CSearchDatabase &dbinfo)
 Constructor with database description. More...
 
 CLocalBlast::CLocalBlast (CRef< IQueryFactory > query_factory, CRef< CBlastOptionsHandle > opts_handle, CRef< CLocalDbAdapter > db)
 Constructor with subject adapter (. More...
 
 CLocalBlast::CLocalBlast (CRef< IQueryFactory > query_factory, CRef< CBlastOptionsHandle > opts_handle, BlastSeqSrc *seqsrc, CRef< IBlastSeqInfoSrc > seqInfoSrc)
 Constructor with database description. More...
 
CRef< CSearchResultSetCLocalBlast::Run ()
 Executes the search. More...
 
Int4 CLocalBlast::GetNumExtensions ()
 Retrieve the number of extensions performed during the search. More...
 
BlastDiagnosticsCLocalBlast::GetDiagnostics ()
 Get the diagnostics structure (deep copy, needs to be deleted by caller) More...
 
 CLocalDbAdapter::CLocalDbAdapter (const CSearchDatabase &dbinfo)
 Constructor. More...
 
 CLocalDbAdapter::CLocalDbAdapter (CRef< IQueryFactory > subject_sequences, CConstRef< CBlastOptionsHandle > opts_handle, bool dbscan_mode=false)
 Constructor. More...
 
 CLocalDbAdapter::CLocalDbAdapter (BlastSeqSrc *seqSrc, CRef< IBlastSeqInfoSrc > seqInfoSrc)
 Constructor taking custom BlastSeqSrc and IBlastSeqInfoSrc objects. More...
 
virtual CLocalDbAdapter::~CLocalDbAdapter ()
 Destructor. More...
 
void CLocalDbAdapter::ResetBlastSeqSrcIteration ()
 This method should be called so that if the implementation has an internal "bookmark" of the chunks of the database it has assigned to different threads, this can be reset at the start of a PSI-BLAST iteration (or when reusing the same object to iterate over the database/subjects when the query is split). More...
 
BlastSeqSrcCLocalDbAdapter::MakeSeqSrc ()
 Retrieves or constructs the BlastSeqSrc. More...
 
IBlastSeqInfoSrcCLocalDbAdapter::MakeSeqInfoSrc ()
 Retrieves or constructs the IBlastSeqInfoSrc. More...
 
bool CLocalDbAdapter::IsProtein () const
 Returns true if this object represents protein or nucleotide sequences. More...
 
string CLocalDbAdapter::GetFilteringAlgorithmKey ()
 Retrieve the database filtering id from key. More...
 
virtual CRef< ISeqSearchCLocalSearchFactory::GetSeqSearch ()
 Get an object to manage a local sequence search. More...
 
virtual CRef< IPssmSearchCLocalSearchFactory::GetPssmSearch ()
 Get an object to manage a remote PSSM search. More...
 
virtual CRef< CBlastOptionsHandleCLocalSearchFactory::GetOptions (EProgram)
 Get an options handle for a search of the specified type. More...
 
virtual CRef< CSearchResultSetCLocalSeqSearch::Run ()
 Run the search. More...
 
virtual void CLocalSeqSearch::SetOptions (CRef< CBlastOptionsHandle > options)
 Configure the search. More...
 
virtual void CLocalSeqSearch::SetSubject (CConstRef< CSearchDatabase > subject)
 Set the databases to search. More...
 
virtual void CLocalSeqSearch::SetQueryFactory (CRef< IQueryFactory > query_factory)
 Set the factory which will return the queries to search for. More...
 
virtual void CLocalPssmSearch::SetOptions (CRef< CBlastOptionsHandle > options)
 Configure this search. More...
 
virtual void CLocalPssmSearch::SetSubject (CConstRef< CSearchDatabase > subject)
 Set the databases to search. More...
 
virtual void CLocalPssmSearch::SetQuery (CRef< objects::CPssmWithParameters > pssm)
 Set the PSSM with which to search the database. More...
 
virtual CRef< CSearchResultSetCLocalPssmSearch::Run ()
 Run a single iteration of the search. More...
 
 CMagicBlast::CMagicBlast (CRef< IQueryFactory > query_factory, CRef< CLocalDbAdapter > blastdb, CRef< CMagicBlastOptionsHandle > options)
 Constructor to map short reads as queries to a genome as BLAST database. More...
 
CRef< CSeq_align_setCMagicBlast::Run (void)
 Run the RNA-Seq mapping. More...
 
CRef< CMagicBlastResultSetCMagicBlast::RunEx (void)
 
int CMagicBlast::x_Run (void)
 
void CMagicBlast::x_Validate (void)
 Perform sanity checks on input arguments. More...
 
static CRef< CSeq_align_setCMagicBlast::x_CreateSeqAlignSet (const HSPChain *results, CRef< ILocalQueryData > qdata, CRef< IBlastSeqInfoSrc > seqinfo_src, const BlastQueryInfo *query_info)
 Create results. More...
 
CRef< CSeq_align_setCMagicBlast::x_BuildSeqAlignSet (const BlastMappingResults *results)
 
CRef< CMagicBlastResultSetCMagicBlast::x_BuildResultSet (const BlastMappingResults *results)
 
 CMagicBlastResults::CMagicBlastResults (CConstRef< CSeq_id > query_id, CConstRef< CSeq_id > mate_id, CRef< CSeq_align_set > aligns, const TMaskedQueryRegions *query_mask=NULL, const TMaskedQueryRegions *mate_mask=NULL, int query_length=0, int mate_length=0)
 Constructor for a pair. More...
 
 CMagicBlastResults::CMagicBlastResults (CConstRef< CSeq_id > query_id, CRef< CSeq_align_set > aligns, const TMaskedQueryRegions *query_mask=NULL, int query_length=0)
 Constructor for a single read. More...
 
void CMagicBlastResults::SortAlignments (EOrdering order)
 Sort alignments by selected criteria (pair configuration) More...
 
void CMagicBlastResults::x_SetInfo (int first_length, const TMaskedQueryRegions *first_masks, int last_length=0, const TMaskedQueryRegions *last_masks=NULL)
 
CRef< CSeq_align_setCMagicBlastResultSet::GetFlatResults (bool no_discordant=false)
 Get all results as a single Seq-align-set object. More...
 
 CMagicBlastOptionsHandle::CMagicBlastOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
 Creates object with default options set. More...
 
 CMagicBlastOptionsHandle::CMagicBlastOptionsHandle (CRef< CBlastOptions > opt)
 Create Options Handle from Existing CBlastOptions Object. More...
 
virtual void CMagicBlastOptionsHandle::SetDefaults ()
 Sets Defaults. More...
 
virtual void CMagicBlastOptionsHandle::SetRNAToGenomeDefaults ()
 
virtual void CMagicBlastOptionsHandle::SetRNAToRNADefaults ()
 
virtual void CMagicBlastOptionsHandle::SetGenomeToGenomeDefaults ()
 
virtual void CMagicBlastOptionsHandle::SetLookupTableDefaults ()
 Overrides LookupTableDefaults for nucleotide options. More...
 
virtual void CMagicBlastOptionsHandle::SetQueryOptionDefaults ()
 Overrides QueryOptionDefaults for nucleotide options. More...
 
virtual void CMagicBlastOptionsHandle::SetInitialWordOptionsDefaults ()
 Overrides InitialWordOptionsDefaults for nucleotide options. More...
 
virtual void CMagicBlastOptionsHandle::SetGappedExtensionDefaults ()
 Overrides GappedExtensionDefaults for nucleotide options. More...
 
virtual void CMagicBlastOptionsHandle::SetScoringOptionsDefaults ()
 Overrides ScoringOptionsDefaults for nucleotide options. More...
 
virtual void CMagicBlastOptionsHandle::SetHitSavingOptionsDefaults ()
 Overrides HitSavingOptionsDefaults for nucleotide options. More...
 
virtual void CMagicBlastOptionsHandle::SetEffectiveLengthsOptionsDefaults ()
 Overrides EffectiveLengthsOptionsDefaults for nucleotide options. More...
 
virtual void CMagicBlastOptionsHandle::SetSubjectSequenceOptionsDefaults ()
 Overrides SubjectSequenceOptionsDefaults for nucleotide options. More...
 
 CPsiBlastInputClustalW::CPsiBlastInputClustalW (CNcbiIstream &input_file, const PSIBlastOptions &opts, const char *matrix_name=NULL, const PSIDiagnosticsRequest *diags=NULL, const unsigned char *query=NULL, unsigned int query_length=0, int gap_existence=0, int gap_opening=0, unsigned int msa_master_idx=0)
 Construct a concrete strategy, used to configure the CPssmEngine object. More...
 
virtual CPsiBlastInputClustalW::~CPsiBlastInputClustalW ()
 virtual destructor More...
 
void CPsiBlastInputClustalW::x_ReadAsciiMsa (CNcbiIstream &input_file)
 Reads the multiple sequence alignment from the input file. More...
 
void CPsiBlastInputClustalW::x_ExtractQueryForPssm ()
 Extracts the query bioseq from m_SeqEntry. More...
 
void CPsiBlastInputClustalW::Process ()
 The work to process the alignment is done here. More...
 
void CPsiBlastInputClustalW::x_ValidateQueryInMsa ()
 Searches the query sequence (m_Query) in the aligned sequences (m_AsciiMsa) and moves the first instance it finds to the front of this data structure. More...
 
void CPsiBlastInputClustalW::x_ExtractQueryFromMsa (unsigned int msa_master_idx=0)
 Extracts the query sequence from the multiple sequence alignment, assuming it's the first one, into m_Query. More...
 
void CPsiBlastInputClustalW::x_CopyQueryToMsa ()
 Copies query sequence data to multiple alignment data structure. More...
 
void CPsiBlastInputClustalW::x_ExtractAlignmentData ()
 Populates the multiple alignment data structure. More...
 
 CObjMgr_LocalQueryData::CObjMgr_LocalQueryData (TSeqLocVector *queries, const CBlastOptions *options)
 Ctor that takes a vector of SSeqLocs. More...
 
 CObjMgr_LocalQueryData::CObjMgr_LocalQueryData (CBlastQueryVector &queries, const CBlastOptions *options)
 Ctor that takes a CBlastQueryVector (preferred over TSeqLocVector). More...
 
virtual BLAST_SequenceBlkCObjMgr_LocalQueryData::GetSequenceBlk ()
 Accessor for the BLAST_SequenceBlk structure. More...
 
virtual BlastQueryInfoCObjMgr_LocalQueryData::GetQueryInfo ()
 Accessor for the BlastQueryInfo structure. More...
 
virtual size_t CObjMgr_LocalQueryData::GetNumQueries ()
 Get the number of queries. More...
 
virtual CConstRef< CSeq_locCObjMgr_LocalQueryData::GetSeq_loc (size_t index)
 Get the Seq_loc for the sequence indicated by index. More...
 
virtual size_t CObjMgr_LocalQueryData::GetSeqLength (size_t index)
 Get the length of the sequence indicated by index. More...
 
 CObjMgr_RemoteQueryData::CObjMgr_RemoteQueryData (const TSeqLocVector *queries)
 Construct query data from a TSeqLocVector. More...
 
 CObjMgr_RemoteQueryData::CObjMgr_RemoteQueryData (CBlastQueryVector &queries)
 Construct query data from a CBlastQueryVector. More...
 
virtual CRef< objects::CBioseq_set > CObjMgr_RemoteQueryData::GetBioseqSet ()
 Accessor for the CBioseq_set. More...
 
virtual TSeqLocs CObjMgr_RemoteQueryData::GetSeqLocs ()
 Accessor for the TSeqLocs. More...
 
 CObjMgr_QueryFactory::CObjMgr_QueryFactory (TSeqLocVector &queries)
 ctor that takes a vector of SSeqLoc More...
 
 CObjMgr_QueryFactory::CObjMgr_QueryFactory (CBlastQueryVector &queries)
 ctor that takes a CBlastQueryVector (preferred) More...
 
vector< CRef< objects::CScope > > CObjMgr_QueryFactory::ExtractScopes ()
 Retrieve the CScope objects associated with the query sequences associated with this object. More...
 
TSeqLocVector CObjMgr_QueryFactory::GetTSeqLocVector ()
 Retrieves the TSeqLocVector used to construct this object or a conversion of the CBlastQueryVector provided. More...
 
TSeqLocInfoVector CObjMgr_QueryFactory::ExtractUserSpecifiedMasks ()
 Retrieve any user specified masking locations. More...
 
CRef< ILocalQueryDataCObjMgr_QueryFactory::x_MakeLocalQueryData (const CBlastOptions *opts)
 factory method to create an ILocalQueryData, only called if the data members above are not set More...
 
CRef< IRemoteQueryDataCObjMgr_QueryFactory::x_MakeRemoteQueryData ()
 factory method to create an IRemoteQueryData, only called if the data members above are not set More...
 
 CObjMgrFree_LocalQueryData::CObjMgrFree_LocalQueryData (CConstRef< CBioseq_set > bioseq_set, const CBlastOptions *options)
 
virtual BLAST_SequenceBlkCObjMgrFree_LocalQueryData::GetSequenceBlk ()
 Accessor for the BLAST_SequenceBlk structure. More...
 
virtual BlastQueryInfoCObjMgrFree_LocalQueryData::GetQueryInfo ()
 Accessor for the BlastQueryInfo structure. More...
 
virtual size_t CObjMgrFree_LocalQueryData::GetNumQueries ()
 Get the number of queries. More...
 
virtual CConstRef< CSeq_locCObjMgrFree_LocalQueryData::GetSeq_loc (size_t index)
 Get the Seq_loc for the sequence indicated by index. More...
 
virtual size_t CObjMgrFree_LocalQueryData::GetSeqLength (size_t index)
 Get the length of the sequence indicated by index. More...
 
 CObjMgrFree_RemoteQueryData::CObjMgrFree_RemoteQueryData (CConstRef< CBioseq_set > bioseq_set)
 Construct query data from a CBioseq_set. More...
 
virtual CRef< CBioseq_setCObjMgrFree_RemoteQueryData::GetBioseqSet ()
 Accessor for the CBioseq_set. More...
 
virtual TSeqLocs CObjMgrFree_RemoteQueryData::GetSeqLocs ()
 Accessor for the TSeqLocs. More...
 
 CObjMgrFree_QueryFactory::CObjMgrFree_QueryFactory (CConstRef< objects::CBioseq > bioseq)
 Parametrized constructor taking a single Bioseq. More...
 
 CObjMgrFree_QueryFactory::CObjMgrFree_QueryFactory (CConstRef< objects::CBioseq_set > bioseq_set)
 Parametrized constructor taking a Bioseq-set. More...
 
CRef< ILocalQueryDataCObjMgrFree_QueryFactory::x_MakeLocalQueryData (const CBlastOptions *opts)
 factory method to create an ILocalQueryData, only called if the data members above are not set More...
 
CRef< IRemoteQueryDataCObjMgrFree_QueryFactory::x_MakeRemoteQueryData ()
 factory method to create an IRemoteQueryData, only called if the data members above are not set More...
 
 CPHIBlastNuclOptionsHandle::CPHIBlastNuclOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
 Creates object with default options set. More...
 
 CPHIBlastProtOptionsHandle::CPHIBlastProtOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
 Creates object with default options set. More...
 
 CBlastPrelimSearch::CBlastPrelimSearch (CRef< IQueryFactory > query_factory, CRef< CBlastOptions > options, const CSearchDatabase &dbinfo)
 Constructor which creates and manages a BLAST database handle for the caller. More...
 
 CBlastPrelimSearch::CBlastPrelimSearch (CRef< IQueryFactory > query_factory, CRef< CBlastOptions > options, CRef< CLocalDbAdapter > db, size_t num_threads=1)
 Constructor which creates BlastSeqSrc object from the already constructed BLAST database handle. More...
 
 CBlastPrelimSearch::CBlastPrelimSearch (CRef< IQueryFactory > query_factory, CRef< CBlastOptions > options, BlastSeqSrc *seqsrc, CConstRef< objects::CPssmWithParameters > pssm=null)
 Constructor which takes a PSSM and an already initialized BlastSeqSrc object. More...
 
virtual void CBlastPrelimSearch::SetNumberOfThreads (size_t nthreads)
 @inheritDoc More...
 
void CBlastPrelimSearch::x_Init (CRef< IQueryFactory > query_factory, CRef< CBlastOptions > options, CConstRef< objects::CPssmWithParameters > pssm, BlastSeqSrc *seqsrc, size_t num_threads=1)
 Internal initialization function Initializes internal data structures except the BlastSeqSrc. More...
 
int CBlastPrelimSearch::x_LaunchMultiThreadedSearch (SInternalData &internal_data)
 Runs the preliminary search in multi-threaded mode. More...
 
CRef< SInternalDataCBlastPrelimSearch::Run ()
 Borrow the internal data and results results. More...
 
int CBlastPrelimSearch::CheckInternalData ()
 Checks that internal data is valid. More...
 
BlastHSPResultsCBlastPrelimSearch::ComputeBlastHSPResults (BlastHSPStream *stream, Uint4 max_num_hsps=0, bool *rm_hsps=NULL, vector< bool > *rm_hsps_info=NULL) const
 Return HSPs in a structure other than the HSPStream? Provide conversion? How to combine this with CBlastTracebackStage? More...
 
bool CBlastPrelimSearch::Run (vector< list< CRef< CStd_seg > > > &results)
 
bool CBlastPrelimSearch::x_BuildStdSegList (vector< list< CRef< CStd_seg > > > &list)
 
 CPsiBlastInputData::CPsiBlastInputData (const unsigned char *query, unsigned int query_length, CConstRef< objects::CSeq_align_set > sset, CRef< objects::CScope > scope, const PSIBlastOptions &opts, const char *matrix_name=NULL, int gap_existence=0, int gap_opening=0, const PSIDiagnosticsRequest *diags=NULL, const string &query_title="")
 Construct a concrete strategy, used to configure the CPssmEngine object. More...
 
virtual CPsiBlastInputData::~CPsiBlastInputData ()
 virtual destructor More...
 
void CPsiBlastInputData::Process ()
 The work to process the alignment is done here. More...
 
void CPsiBlastInputData::x_ExtractQueryForPssm ()
 Extracts the query bioseq from m_SeqAlignSet. More...
 
unsigned int CPsiBlastInputData::x_CountAndSelectQualifyingAlignments ()
 Examines the sequence alignment and keeps track of those hits which have an HSP with an e-value below the inclusion threshold specified in the PSIBlastOptions structure. More...
 
unsigned int CPsiBlastInputData::GetNumAlignedSequences () const
 Returns the number of sequences that make up the multiple sequence alignment. More...
 
PSIMsaCPsiBlastInputData::GetData ()
 Obtain the multiple sequence alignment structure. More...
 
unsigned char * CPsiBlastInputData::GetQuery ()
 Get the query sequence used as master for the multiple sequence alignment in ncbistdaa encoding. More...
 
unsigned int CPsiBlastInputData::GetQueryLength ()
 Get the query's length. More...
 
const PSIBlastOptionsCPsiBlastInputData::GetOptions ()
 Obtain the options for the PSSM engine. More...
 
const char * CPsiBlastInputData::GetMatrixName ()
 Obtain the name of the underlying matrix to use when building the PSSM. More...