NCBI C++ ToolKit
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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  CBlastAppDiagHandler
 Class to capture message from diag handler. 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  CBlastOptionsBuilder::SOptional< T >
 Optional-value idiom. 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  CCddInputData::CHitSegment
 Represents one alignment segment of a RPS-BLAST hit. More...
 
class  CCddInputData::CHit
 Single RPS-BLAST hit. More...
 
class  CCddInputData::compare_hitseg_range
 Class used for sorting hit segments by range. More...
 
class  CCddInputData::compare_range
 Class used for sorting ranges. More...
 
class  CCddInputData::compare_hits_by_seqid_eval
 Class used for sorting hits by subject seq-id and e-value. 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  ScorePositionSort
 
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...
 
struct  CIndexedDb_New::SVolumeDescriptor
 Information about one leaf index volume. More...
 
struct  CIndexedDb_New::SVolResults
 Reference count for the volume results. 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 CSeqLocInfo::ETranslationFrame CFrameFinder::ETranslationFrame
 Convenience typedef. More...
 
typedef const CRef< CSeqLocInfoCFrameFinder::argument_type
 
typedef bool CFrameFinder::result_type
 
typedef objects::CBlast4_parameters::Tdata CBlastOptionsBuilder::TValueList
 List of name/value pairs. More...
 
typedef list< CRef< objects::CBlast4_mask > > CBlastOptionsBuilder::TMaskList
 List of Blast4 masks. More...
 
typedef CBlastOptions::EAPILocality CBlastOptionsFactory::EAPILocality
 Convenience define. More...
 
typedef CBlastOptions::EAPILocality CBlastOptionsHandle::EAPILocality
 Convenience define. More...
 
typedef CRef< CSearchResultsCSearchResultSet::value_type
 data type contained by this container More...
 
typedef vector< CConstRef< objects::CSeq_id > > CSearchResultSet::TQueryIdVector
 List of query ids. More...
 
typedef vector< value_type >::size_type CSearchResultSet::size_type
 size_type type definition More...
 
typedef vector< CRef< CBlastAncillaryData > > CSearchResultSet::TAncillaryVector
 typedef for a vector of CRef<CBlastAncillaryData> More...
 
typedef vector< value_type >::const_iterator CSearchResultSet::const_iterator
 const_iterator type definition More...
 
typedef vector< value_type >::iterator CSearchResultSet::iterator
 iterator type definition More...
 
typedef Uint4 CCddInputData::TFreqs
 Type used for residue frequencies stored in CDD. More...
 
typedef Uint4 CCddInputData::TObsr
 Type used for number of independent observations stored in CDD. More...
 
typedef CRange< intCCddInputData::TRange
 
typedef int CMagicBlastResults::TResultsInfo
 
typedef CRef< CMagicBlastResultsCMagicBlastResultSet::value_type
 data type contained by this container More...
 
typedef vector< value_type >::size_type CMagicBlastResultSet::size_type
 size_type type definition More...
 
typedef vector< value_type >::const_iterator CMagicBlastResultSet::const_iterator
 const_iterator type definition More...
 
typedef vector< value_type >::iterator CMagicBlastResultSet::iterator
 iterator type definition More...
 
typedef set< objects::CSeq_id_Handle > CPsiBlastIterationState::TSeqIds
 List of CSeq_ids. More...
 
typedef list< CRef< objects::CSeq_loc > > IRemoteQueryData::TSeqLocs
 Type definition for CSeq_loc set used as queries in the BLAST remote search class. More...
 
typedef list< CRef< objects::CSeq_loc > > CRemoteBlast::TSeqLocList
 Typedef for a list of Seq-locs. More...
 
typedef list< CRef< objects::CBlast4_ka_block > > CRemoteBlast::TKarlinAltschulBlocks
 Convenience typedef for a list of CRef<CBlast4_ka_block> More...
 
typedef vector< CRef< objects::CSeq_interval > > CRemoteBlast::TSeqIntervalVector
 Defines a std::vector of CRef<CSeq_interval> More...
 
typedef vector< CRef< objects::CSeq_data > > CRemoteBlast::TSeqDataVector
 Defines a std::vector of CRef<CSeq_data> More...
 
typedef list< CRef< objects::CBlast4_parameter > > CRemoteBlast::TValueList
 Value list. More...
 
typedef objects::CBlast4_get_search_results_reply CRemoteBlast::TGSRR
 An alias for the most commonly used part of the Blast4 search results. More...
 
typedef vector< CConstRef< CSeq_loc > > CSeedTop::TSeedTopResults
 
typedef TData *() CStructWrapper< TData >::TDelete(TData *)
 type definition for a function that deallocated memory associated with an object. More...
 
typedef CStructWrapper< BlastScoreBlkTBlastScoreBlk
 
typedef CStructWrapper< LookupTableWrapTLookupTableWrap
 
typedef CStructWrapper< BlastDiagnosticsTBlastDiagnostics
 
typedef CStructWrapper< BlastHSPStreamTBlastHSPStream
 
typedef CStructWrapper< BlastSeqSrcTBlastSeqSrc
 
typedef CStructWrapper< SPHIPatternSearchBlkTSPHIPatternSearchBlk
 
typedef vector< TGiCSearchDatabase::TGiList
 Define a list of gis. More...
 
typedef vector< CRef< objects::CSeq_id > > CBlastServices::TSeqIdVector
 Defines a std::vector of CRef<CSeq_id> More...
 
typedef vector< CRef< objects::CBioseq > > CBlastServices::TBioseqVector
 Defines a std::vector of CRef<CBioseq> More...
 
typedef vector< CRef< objects::CSeq_interval > > CBlastServices::TSeqIntervalVector
 Defines a std::vector of CRef<CSeq_interval> More...
 
typedef vector< CRef< objects::CSeq_data > > CBlastServices::TSeqDataVector
 Defines a std::vector of CRef<CSeq_data> More...
 
typedef vector< CConstRef< CDbIndex::CSearchResults > > CIndexedDb_Old::TResultSet
 Type used to represent collections of search result sets. More...
 
typedef vector< CDbIndex::TSeqNumCIndexedDb_Old::TSeqMap
 Type used to map loaded indices to subject ids. More...
 
typedef std::vector< std::stringCIndexedDb_New::TStrVec
 Alias for a vector os strings. More...
 
typedef std::vector< SVolumeDescriptorCIndexedDb_New::TVolList
 List of leaf index volumes. More...
 
typedef CConstRef< CDbIndex::CSearchResultsCIndexedDb_New::TVolResults
 This type captures the seeds found by search of an index volume. More...
 
typedef std::vector< SVolResultsCIndexedDb_New::TResultsHolder
 List of reference counted result holders. More...
 
typedef ncbi::objects::CBlast4_parameters CBlastOptionsRemote::TBlast4Opts
 
typedef vector< CConstRef< objects::CSeq_loc > > CBlastOptionsRemote::TSeqLocVector
 
typedef CSeqLocInfo::ETranslationFrame CBlastQueryFilteredFrames::ETranslationFrame
 Data type for frame value, however inputs to methods use "int" instead of this type for readability and brevity. More...
 
typedef map< ETranslationFrame, BlastSeqLoc * > CBlastQueryFilteredFrames::TFrameSet
 Frame and BlastSeqLoc* info type. More...
 
typedef CPsiBlastIterationState::TSeqIds CPsiBlastAlignmentProcessor::THitIdentifiers
 Container of Seq-ids for the subject sequences (hits) aligned with the query. More...
 
typedef list< CRef< objects::CBlast4_error > > TErrorList
 Error value type used by Blast4 ASN.1 objects. More...
 
typedef SSeqDB_SeqSrc_Data TSeqDBData
 
typedef vector< CRef< objects::CScope > > CQuerySplitter::TScopeVector
 Defines a vector of CScope objects. More...
 
typedef vector< CRef< CBlastQueryVector > > CQuerySplitter::TSplitQueryVector
 Definition of a vector of CBlastQueryVectors, each element corresponds to a query chunk. More...
 
typedef COpenRange< TSeqPosTChunkRange
 Range describing a query chunk. More...
 
typedef blast::SDataLoaderConfig::EConfigOpts CAutoNcbiConfigFile::EConfigOpts
 

Enumerations

enum  CBlastSystemException::EErrCode { CBlastSystemException::eOutOfMemory , CBlastSystemException::eNetworkError }
 Error types that BLAST can generate. More...
 
enum  CBlastException::EErrCode {
  CBlastException::eCoreBlastError , CBlastException::eInvalidOptions , CBlastException::eInvalidArgument , CBlastException::eNotSupported ,
  CBlastException::eInvalidCharacter , CBlastException::eSeqSrcInit , CBlastException::eRpsInit , CBlastException::eSetup
}
 Error types that BLAST can generate. More...
 
enum  CBlastOptionsFactory::ETaskSets { CBlastOptionsFactory::eNuclNucl , CBlastOptionsFactory::eProtProt , CBlastOptionsFactory::eMapping , CBlastOptionsFactory::eAll }
 Sets of tasks for the command line BLAST binaries. More...
 
enum  CCddInputData::CHit::EApplyTo { CCddInputData::CHit::eQuery = 0 , CCddInputData::CHit::eSubject }
 Master selection for operations involving ranges. More...
 
enum  CMagicBlastResults::EResultsInfo { CMagicBlastResults::fUnaligned = 1 , CMagicBlastResults::fFiltered = 1 << 1 }
 Information flags about mapping results. More...
 
enum  CMagicBlastResults::EOrdering { CMagicBlastResults::eFwRevFirst = 0 , CMagicBlastResults::eRevFwFirst }
 Ordering of alignments. More...
 
enum  CPssmEngineException::EErrCode { CPssmEngineException::eNullInputData , CPssmEngineException::eInvalidInputData }
 Types of exceptions generated by the CPssmEngine class. More...
 
enum  CRemoteBlastException::EErrCode { CRemoteBlastException::eServiceNotAvailable , CRemoteBlastException::eIncompleteConfig }
 Types of exceptions generated by the CRemoteBlast class. More...
 
enum  CRemoteBlast::ESearchStatus { CRemoteBlast::eStatus_Unknown , CRemoteBlast::eStatus_Done , CRemoteBlast::eStatus_Pending , CRemoteBlast::eStatus_Failed }
 Represents the status of previously submitted search/RID. More...
 
enum  CRemoteBlast::EDebugMode { CRemoteBlast::eDebug = 0 , CRemoteBlast::eSilent }
 Debugging support can be turned on with eDebug or off with eSilent. More...
 
enum  CRemoteBlast::EState { CRemoteBlast::eStart = 0 , CRemoteBlast::eFailed , CRemoteBlast::eWait , CRemoteBlast::eDone }
 Various states the search can be in. More...
 
enum  CRemoteBlast::EImmediacy { CRemoteBlast::ePollAsync = 0 , CRemoteBlast::ePollImmed }
 Indicates whether to use async mode. More...
 
enum  CRemoteBlast::ENeedConfig {
  CRemoteBlast::eNoConfig = 0x0 , CRemoteBlast::eProgram = 0x1 , CRemoteBlast::eService = 0x2 , CRemoteBlast::eQueries = 0x4 ,
  CRemoteBlast::eSubject = 0x8 , CRemoteBlast::eNeedAll = 0xF
}
 This class attempts to verify whether all necessary configuration is complete before attempting to submit the search. More...
 
enum  CBlastRPSInfo::EOpenFlags {
  CBlastRPSInfo::fLookupTableFile = 1 , CBlastRPSInfo::fPssmFile = 2 , CBlastRPSInfo::fAuxInfoFile = 4 , CBlastRPSInfo::fFrequenciesFile = 8 ,
  CBlastRPSInfo::fObservationsFile = 16 , CBlastRPSInfo::fFreqRatiosFile = 32 , CBlastRPSInfo::fRpsBlast = fLookupTableFile | fPssmFile | fAuxInfoFile , CBlastRPSInfo::fDeltaBlast = fFrequenciesFile | fObservationsFile ,
  CBlastRPSInfo::fRpsBlastWithCBS = fRpsBlast | fFreqRatiosFile
}
 Flags for opening database files. More...
 
enum  { CThreadable::kMinNumThreads = 1 }
 Never have less than 1 thread. More...
 
enum  CSearchException::EErrCode { CSearchException::eConfigErr , CSearchException::eMemErr , CSearchException::eInternal }
 Errors are classified into one of two types. More...
 
enum  CSearchDatabase::EMoleculeType { CSearchDatabase::eBlastDbIsProtein , CSearchDatabase::eBlastDbIsNucleotide }
 Molecule of the BLAST database. More...
 
enum  CReference::EPublication {
  CReference::eGappedBlast = 0 , CReference::ePhiBlast , CReference::eMegaBlast , CReference::eCompBasedStats ,
  CReference::eCompAdjustedMatrices , CReference::eIndexedMegablast , CReference::eDeltaBlast , CReference::eMaxPublications
}
 Enumerates the various BLAST publications. More...
 
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  CBlastServicesException::EErrCode { CBlastServicesException::eArgErr , CBlastServicesException::eFileErr , CBlastServicesException::eRequestErr , CBlastServicesException::eMemErr }
 Errors are classified into one of two types. More...
 
enum  ESentinelType { eSentinels , eNoSentinels }
 Allows specification of whether sentinel bytes should be used or not. More...
 
enum  CPsiBlastValidate::EQueryFactoryType { CPsiBlastValidate::eQFT_Query , CPsiBlastValidate::eQFT_Subject }
 Enumeration to specify the different uses of the query factory. More...
 
enum  { CQueryDataPerChunk::kUninitialized = -1 }
 Initial value of all entries in the above cache. More...
 

Functions

 CBl2Seq::CBl2Seq (const SSeqLoc &query, const SSeqLoc &subject, EProgram p)
 Constructor to compare 2 sequences with default 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 TSeqLocVector &queries, const TSeqLocVector &subjects, EProgram p, bool dbscan_mode=false)
 Constructor to allow query concatenation with default options. 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, 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, CBlastOptionsHandle &opts, bool dbscan_mode=false)
 Constructor to allow query concatenation with specified options. More...
 
virtual CBl2Seq::~CBl2Seq ()
 Destructor. 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...
 
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...
 
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...
 
BlastDiagnosticsCBl2Seq::GetDiagnostics () const
 Retrieves the diagnostics information returned from the engine. More...
 
void CBl2Seq::GetAncillaryResults (CSearchResultSet::TAncillaryVector &retval) const
 Get the ancillary results for a BLAST search (to be used with the Run() method) 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...
 
static TSeqAlignVector CBl2Seq::CSearchResultSet2TSeqAlignVector (CRef< CSearchResultSet > res)
 Converts m_Results data member to a TSeqAlignVector. More...
 
void CBl2Seq::x_BuildAncillaryData ()
 Populate the internal m_AncillaryData member. More...
 
void CBl2Seq::x_Init (const TSeqLocVector &queries, const TSeqLocVector &subjs)
 Common initialization code for all c-tors. More...
 
void CBl2Seq::x_InitCLocalBlast ()
 Common initialization of the CLocalBlast object. More...
 
 CBl2Seq::CBl2Seq (const CBl2Seq &rhs)
 Prohibit copy constructor. More...
 
CBl2SeqCBl2Seq::operator= (const CBl2Seq &rhs)
 Prohibit assignment operator. More...
 
void CBl2Seq::x_ResetInternalDs ()
 Clean up structures and results from any previous search. More...
 
 CBlastAdvancedProteinOptionsHandle::CBlastAdvancedProteinOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
 Creates object with default options set. More...
 
 CBlastAdvancedProteinOptionsHandle::CBlastAdvancedProteinOptionsHandle (CRef< CBlastOptions > opt)
 
ECompoAdjustModes CBlastAdvancedProteinOptionsHandle::GetCompositionBasedStats () const
 Returns this mode, which mostly specifies whether composition of db sequence is taken into account when calculating expect values. More...
 
void CBlastAdvancedProteinOptionsHandle::SetCompositionBasedStats (ECompoAdjustModes mode)
 Sets this mode, which mostly specifies whether composition of db sequence is taken into account when calculating expect values. More...
 
bool CBlastAdvancedProteinOptionsHandle::GetSmithWatermanMode () const
 Returns this mode, specifying that smith waterman rather than the normal blast heuristic should be used for final extensions. More...
 
void CBlastAdvancedProteinOptionsHandle::SetSmithWatermanMode (bool m=false)
 Sets this mode, specifying that smith waterman rather than the normal blast heuristic should be used for final extensions. 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...
 
 CBlastAdvancedProteinOptionsHandle::CBlastAdvancedProteinOptionsHandle (const CBlastAdvancedProteinOptionsHandle &rhs)
 Disallow copy constructor. More...
 
CBlastAdvancedProteinOptionsHandleCBlastAdvancedProteinOptionsHandle::operator= (const CBlastAdvancedProteinOptionsHandle &rhs)
 Disallow assignment operator. More...
 
static void Deleter< BlastHSPStream >::Delete (BlastHSPStream *p)
 
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...
 
 CFrameFinder::CFrameFinder (ETranslationFrame frame)
 ctor More...
 
result_type CFrameFinder::operator() (argument_type &seqlocinfo) const
 Returns true if its argument's frame corresponds to the one used to create this object. 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...
 
bool CConstRefCSeqId_LessThan::operator() (const CConstRef< objects::CSeq_id > &a, const CConstRef< objects::CSeq_id > &b) const
 
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...
 
 CAutomaticGenCodeSingleton::CAutomaticGenCodeSingleton (int genetic_code=0)
 Default constructor. More...
 
void CAutomaticGenCodeSingleton::AddGeneticCode (int genetic_code)
 Add the genetic code to the genetic code singleton. More...
 
 CAutomaticGenCodeSingleton::~CAutomaticGenCodeSingleton ()
 destructor More...
 
 CAutomaticGenCodeSingleton::DECLARE_CLASS_STATIC_FAST_MUTEX (sm_Mutex)
 Reference counter for this object so that the genetic code singleton is. More...
 
 CBlastAppDiagHandler::CBlastAppDiagHandler ()
 Constructor. More...
 
 CBlastAppDiagHandler::~CBlastAppDiagHandler ()
 Destructor. More...
 
virtual void CBlastAppDiagHandler::Post (const SDiagMessage &mess)
 Save and post diag message. More...
 
void CBlastAppDiagHandler::ResetMessages (void)
 Reset messgae buffer, erase all saved message. More...
 
void CBlastAppDiagHandler::DoNotSaveMessages (void)
 Call to turn off saving diag message, discard all saved message. More...
 
list< CRef< objects::CBlast4_error > > & CBlastAppDiagHandler::GetMessages (void)
 Return list of saved diag messages. More...
 
 CBLAST_SequenceBlk::CBLAST_SequenceBlk ()
 
 CBLAST_SequenceBlk::CBLAST_SequenceBlk (BLAST_SequenceBlk *p)
 
virtual CBLAST_SequenceBlk::~CBLAST_SequenceBlk ()
 
void CBLAST_SequenceBlk::Reset (BLAST_SequenceBlk *p=NULL)
 
BLAST_SequenceBlkCBLAST_SequenceBlk::Release ()
 
BLAST_SequenceBlkCBLAST_SequenceBlk::Get () const
 
 CBLAST_SequenceBlk::operator BLAST_SequenceBlk * ()
 
 CBLAST_SequenceBlk::operator BLAST_SequenceBlk * () const
 
BLAST_SequenceBlkCBLAST_SequenceBlk::operator-> ()
 
BLAST_SequenceBlkCBLAST_SequenceBlk::operator-> () const
 
BLAST_SequenceBlk ** CBLAST_SequenceBlk::operator& ()
 
virtual void CBLAST_SequenceBlk::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CBlastQueryInfo::CBlastQueryInfo ()
 
 CBlastQueryInfo::CBlastQueryInfo (BlastQueryInfo *p)
 
virtual CBlastQueryInfo::~CBlastQueryInfo ()
 
void CBlastQueryInfo::Reset (BlastQueryInfo *p=NULL)
 
BlastQueryInfoCBlastQueryInfo::Release ()
 
BlastQueryInfoCBlastQueryInfo::Get () const
 
 CBlastQueryInfo::operator BlastQueryInfo * ()
 
 CBlastQueryInfo::operator BlastQueryInfo * () const
 
BlastQueryInfoCBlastQueryInfo::operator-> ()
 
BlastQueryInfoCBlastQueryInfo::operator-> () const
 
BlastQueryInfo ** CBlastQueryInfo::operator& ()
 
virtual void CBlastQueryInfo::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CQuerySetUpOptions::CQuerySetUpOptions ()
 
 CQuerySetUpOptions::CQuerySetUpOptions (QuerySetUpOptions *p)
 
virtual CQuerySetUpOptions::~CQuerySetUpOptions ()
 
void CQuerySetUpOptions::Reset (QuerySetUpOptions *p=NULL)
 
QuerySetUpOptionsCQuerySetUpOptions::Release ()
 
QuerySetUpOptionsCQuerySetUpOptions::Get () const
 
 CQuerySetUpOptions::operator QuerySetUpOptions * ()
 
 CQuerySetUpOptions::operator QuerySetUpOptions * () const
 
QuerySetUpOptionsCQuerySetUpOptions::operator-> ()
 
QuerySetUpOptionsCQuerySetUpOptions::operator-> () const
 
QuerySetUpOptions ** CQuerySetUpOptions::operator& ()
 
virtual void CQuerySetUpOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CLookupTableOptions::CLookupTableOptions ()
 
 CLookupTableOptions::CLookupTableOptions (LookupTableOptions *p)
 
virtual CLookupTableOptions::~CLookupTableOptions ()
 
void CLookupTableOptions::Reset (LookupTableOptions *p=NULL)
 
LookupTableOptionsCLookupTableOptions::Release ()
 
LookupTableOptionsCLookupTableOptions::Get () const
 
 CLookupTableOptions::operator LookupTableOptions * ()
 
 CLookupTableOptions::operator LookupTableOptions * () const
 
LookupTableOptionsCLookupTableOptions::operator-> ()
 
LookupTableOptionsCLookupTableOptions::operator-> () const
 
LookupTableOptions ** CLookupTableOptions::operator& ()
 
virtual void CLookupTableOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CLookupTableWrap::CLookupTableWrap ()
 
 CLookupTableWrap::CLookupTableWrap (LookupTableWrap *p)
 
virtual CLookupTableWrap::~CLookupTableWrap ()
 
void CLookupTableWrap::Reset (LookupTableWrap *p=NULL)
 
LookupTableWrapCLookupTableWrap::Release ()
 
LookupTableWrapCLookupTableWrap::Get () const
 
 CLookupTableWrap::operator LookupTableWrap * ()
 
 CLookupTableWrap::operator LookupTableWrap * () const
 
LookupTableWrapCLookupTableWrap::operator-> ()
 
LookupTableWrapCLookupTableWrap::operator-> () const
 
LookupTableWrap ** CLookupTableWrap::operator& ()
 
virtual void CLookupTableWrap::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CBlastInitialWordOptions::CBlastInitialWordOptions ()
 
 CBlastInitialWordOptions::CBlastInitialWordOptions (BlastInitialWordOptions *p)
 
virtual CBlastInitialWordOptions::~CBlastInitialWordOptions ()
 
void CBlastInitialWordOptions::Reset (BlastInitialWordOptions *p=NULL)
 
BlastInitialWordOptionsCBlastInitialWordOptions::Release ()
 
BlastInitialWordOptionsCBlastInitialWordOptions::Get () const
 
 CBlastInitialWordOptions::operator BlastInitialWordOptions * ()
 
 CBlastInitialWordOptions::operator BlastInitialWordOptions * () const
 
BlastInitialWordOptionsCBlastInitialWordOptions::operator-> ()
 
BlastInitialWordOptionsCBlastInitialWordOptions::operator-> () const
 
BlastInitialWordOptions ** CBlastInitialWordOptions::operator& ()
 
virtual void CBlastInitialWordOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CBlastInitialWordParameters::CBlastInitialWordParameters ()
 
 CBlastInitialWordParameters::CBlastInitialWordParameters (BlastInitialWordParameters *p)
 
virtual CBlastInitialWordParameters::~CBlastInitialWordParameters ()
 
void CBlastInitialWordParameters::Reset (BlastInitialWordParameters *p=NULL)
 
BlastInitialWordParametersCBlastInitialWordParameters::Release ()
 
BlastInitialWordParametersCBlastInitialWordParameters::Get () const
 
 CBlastInitialWordParameters::operator BlastInitialWordParameters * ()
 
 CBlastInitialWordParameters::operator BlastInitialWordParameters * () const
 
BlastInitialWordParametersCBlastInitialWordParameters::operator-> ()
 
BlastInitialWordParametersCBlastInitialWordParameters::operator-> () const
 
BlastInitialWordParameters ** CBlastInitialWordParameters::operator& ()
 
virtual void CBlastInitialWordParameters::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CBlast_ExtendWord::CBlast_ExtendWord ()
 
 CBlast_ExtendWord::CBlast_ExtendWord (Blast_ExtendWord *p)
 
virtual CBlast_ExtendWord::~CBlast_ExtendWord ()
 
void CBlast_ExtendWord::Reset (Blast_ExtendWord *p=NULL)
 
Blast_ExtendWordCBlast_ExtendWord::Release ()
 
Blast_ExtendWordCBlast_ExtendWord::Get () const
 
 CBlast_ExtendWord::operator Blast_ExtendWord * ()
 
 CBlast_ExtendWord::operator Blast_ExtendWord * () const
 
Blast_ExtendWordCBlast_ExtendWord::operator-> ()
 
Blast_ExtendWordCBlast_ExtendWord::operator-> () const
 
Blast_ExtendWord ** CBlast_ExtendWord::operator& ()
 
virtual void CBlast_ExtendWord::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CBlastExtensionOptions::CBlastExtensionOptions ()
 
 CBlastExtensionOptions::CBlastExtensionOptions (BlastExtensionOptions *p)
 
virtual CBlastExtensionOptions::~CBlastExtensionOptions ()
 
void CBlastExtensionOptions::Reset (BlastExtensionOptions *p=NULL)
 
BlastExtensionOptionsCBlastExtensionOptions::Release ()
 
BlastExtensionOptionsCBlastExtensionOptions::Get () const
 
 CBlastExtensionOptions::operator BlastExtensionOptions * ()
 
 CBlastExtensionOptions::operator BlastExtensionOptions * () const
 
BlastExtensionOptionsCBlastExtensionOptions::operator-> ()
 
BlastExtensionOptionsCBlastExtensionOptions::operator-> () const
 
BlastExtensionOptions ** CBlastExtensionOptions::operator& ()
 
virtual void CBlastExtensionOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CBlastExtensionParameters::CBlastExtensionParameters ()
 
 CBlastExtensionParameters::CBlastExtensionParameters (BlastExtensionParameters *p)
 
virtual CBlastExtensionParameters::~CBlastExtensionParameters ()
 
void CBlastExtensionParameters::Reset (BlastExtensionParameters *p=NULL)
 
BlastExtensionParametersCBlastExtensionParameters::Release ()
 
BlastExtensionParametersCBlastExtensionParameters::Get () const
 
 CBlastExtensionParameters::operator BlastExtensionParameters * ()
 
 CBlastExtensionParameters::operator BlastExtensionParameters * () const
 
BlastExtensionParametersCBlastExtensionParameters::operator-> ()
 
BlastExtensionParametersCBlastExtensionParameters::operator-> () const
 
BlastExtensionParameters ** CBlastExtensionParameters::operator& ()
 
virtual void CBlastExtensionParameters::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CBlastHitSavingOptions::CBlastHitSavingOptions ()
 
 CBlastHitSavingOptions::CBlastHitSavingOptions (BlastHitSavingOptions *p)
 
virtual CBlastHitSavingOptions::~CBlastHitSavingOptions ()
 
void CBlastHitSavingOptions::Reset (BlastHitSavingOptions *p=NULL)
 
BlastHitSavingOptionsCBlastHitSavingOptions::Release ()
 
BlastHitSavingOptionsCBlastHitSavingOptions::Get () const
 
 CBlastHitSavingOptions::operator BlastHitSavingOptions * ()
 
 CBlastHitSavingOptions::operator BlastHitSavingOptions * () const
 
BlastHitSavingOptionsCBlastHitSavingOptions::operator-> ()
 
BlastHitSavingOptionsCBlastHitSavingOptions::operator-> () const
 
BlastHitSavingOptions ** CBlastHitSavingOptions::operator& ()
 
virtual void CBlastHitSavingOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CBlastHitSavingParameters::CBlastHitSavingParameters ()
 
 CBlastHitSavingParameters::CBlastHitSavingParameters (BlastHitSavingParameters *p)
 
virtual CBlastHitSavingParameters::~CBlastHitSavingParameters ()
 
void CBlastHitSavingParameters::Reset (BlastHitSavingParameters *p=NULL)
 
BlastHitSavingParametersCBlastHitSavingParameters::Release ()
 
BlastHitSavingParametersCBlastHitSavingParameters::Get () const
 
 CBlastHitSavingParameters::operator BlastHitSavingParameters * ()
 
 CBlastHitSavingParameters::operator BlastHitSavingParameters * () const
 
BlastHitSavingParametersCBlastHitSavingParameters::operator-> ()
 
BlastHitSavingParametersCBlastHitSavingParameters::operator-> () const
 
BlastHitSavingParameters ** CBlastHitSavingParameters::operator& ()
 
virtual void CBlastHitSavingParameters::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CPSIBlastOptions::CPSIBlastOptions ()
 
 CPSIBlastOptions::CPSIBlastOptions (PSIBlastOptions *p)
 
virtual CPSIBlastOptions::~CPSIBlastOptions ()
 
void CPSIBlastOptions::Reset (PSIBlastOptions *p=NULL)
 
PSIBlastOptionsCPSIBlastOptions::Release ()
 
PSIBlastOptionsCPSIBlastOptions::Get () const
 
 CPSIBlastOptions::operator PSIBlastOptions * ()
 
 CPSIBlastOptions::operator PSIBlastOptions * () const
 
PSIBlastOptionsCPSIBlastOptions::operator-> ()
 
PSIBlastOptionsCPSIBlastOptions::operator-> () const
 
PSIBlastOptions ** CPSIBlastOptions::operator& ()
 
virtual void CPSIBlastOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CBlastDatabaseOptions::CBlastDatabaseOptions ()
 
 CBlastDatabaseOptions::CBlastDatabaseOptions (BlastDatabaseOptions *p)
 
virtual CBlastDatabaseOptions::~CBlastDatabaseOptions ()
 
void CBlastDatabaseOptions::Reset (BlastDatabaseOptions *p=NULL)
 
BlastDatabaseOptionsCBlastDatabaseOptions::Release ()
 
BlastDatabaseOptionsCBlastDatabaseOptions::Get () const
 
 CBlastDatabaseOptions::operator BlastDatabaseOptions * ()
 
 CBlastDatabaseOptions::operator BlastDatabaseOptions * () const
 
BlastDatabaseOptionsCBlastDatabaseOptions::operator-> ()
 
BlastDatabaseOptionsCBlastDatabaseOptions::operator-> () const
 
BlastDatabaseOptions ** CBlastDatabaseOptions::operator& ()
 
virtual void CBlastDatabaseOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CBlastScoreBlk::CBlastScoreBlk ()
 
 CBlastScoreBlk::CBlastScoreBlk (BlastScoreBlk *p)
 
virtual CBlastScoreBlk::~CBlastScoreBlk ()
 
void CBlastScoreBlk::Reset (BlastScoreBlk *p=NULL)
 
BlastScoreBlkCBlastScoreBlk::Release ()
 
BlastScoreBlkCBlastScoreBlk::Get () const
 
 CBlastScoreBlk::operator BlastScoreBlk * ()
 
 CBlastScoreBlk::operator BlastScoreBlk * () const
 
BlastScoreBlkCBlastScoreBlk::operator-> ()
 
BlastScoreBlkCBlastScoreBlk::operator-> () const
 
BlastScoreBlk ** CBlastScoreBlk::operator& ()
 
virtual void CBlastScoreBlk::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CBlastScoringOptions::CBlastScoringOptions ()
 
 CBlastScoringOptions::CBlastScoringOptions (BlastScoringOptions *p)
 
virtual CBlastScoringOptions::~CBlastScoringOptions ()
 
void CBlastScoringOptions::Reset (BlastScoringOptions *p=NULL)
 
BlastScoringOptionsCBlastScoringOptions::Release ()
 
BlastScoringOptionsCBlastScoringOptions::Get () const
 
 CBlastScoringOptions::operator BlastScoringOptions * ()
 
 CBlastScoringOptions::operator BlastScoringOptions * () const
 
BlastScoringOptionsCBlastScoringOptions::operator-> ()
 
BlastScoringOptionsCBlastScoringOptions::operator-> () const
 
BlastScoringOptions ** CBlastScoringOptions::operator& ()
 
virtual void CBlastScoringOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CBlastScoringParameters::CBlastScoringParameters ()
 
 CBlastScoringParameters::CBlastScoringParameters (BlastScoringParameters *p)
 
virtual CBlastScoringParameters::~CBlastScoringParameters ()
 
void CBlastScoringParameters::Reset (BlastScoringParameters *p=NULL)
 
BlastScoringParametersCBlastScoringParameters::Release ()
 
BlastScoringParametersCBlastScoringParameters::Get () const
 
 CBlastScoringParameters::operator BlastScoringParameters * ()
 
 CBlastScoringParameters::operator BlastScoringParameters * () const
 
BlastScoringParametersCBlastScoringParameters::operator-> ()
 
BlastScoringParametersCBlastScoringParameters::operator-> () const
 
BlastScoringParameters ** CBlastScoringParameters::operator& ()
 
virtual void CBlastScoringParameters::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CBlastEffectiveLengthsOptions::CBlastEffectiveLengthsOptions ()
 
 CBlastEffectiveLengthsOptions::CBlastEffectiveLengthsOptions (BlastEffectiveLengthsOptions *p)
 
virtual CBlastEffectiveLengthsOptions::~CBlastEffectiveLengthsOptions ()
 
void CBlastEffectiveLengthsOptions::Reset (BlastEffectiveLengthsOptions *p=NULL)
 
BlastEffectiveLengthsOptionsCBlastEffectiveLengthsOptions::Release ()
 
BlastEffectiveLengthsOptionsCBlastEffectiveLengthsOptions::Get () const
 
 CBlastEffectiveLengthsOptions::operator BlastEffectiveLengthsOptions * ()
 
 CBlastEffectiveLengthsOptions::operator BlastEffectiveLengthsOptions * () const
 
BlastEffectiveLengthsOptionsCBlastEffectiveLengthsOptions::operator-> ()
 
BlastEffectiveLengthsOptionsCBlastEffectiveLengthsOptions::operator-> () const
 
BlastEffectiveLengthsOptions ** CBlastEffectiveLengthsOptions::operator& ()
 
virtual void CBlastEffectiveLengthsOptions::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CBlastEffectiveLengthsParameters::CBlastEffectiveLengthsParameters ()
 
 CBlastEffectiveLengthsParameters::CBlastEffectiveLengthsParameters (BlastEffectiveLengthsParameters *p)
 
virtual CBlastEffectiveLengthsParameters::~CBlastEffectiveLengthsParameters ()
 
void CBlastEffectiveLengthsParameters::Reset (BlastEffectiveLengthsParameters *p=NULL)
 
BlastEffectiveLengthsParametersCBlastEffectiveLengthsParameters::Release ()
 
BlastEffectiveLengthsParametersCBlastEffectiveLengthsParameters::Get () const
 
 CBlastEffectiveLengthsParameters::operator BlastEffectiveLengthsParameters * ()
 
 CBlastEffectiveLengthsParameters::operator BlastEffectiveLengthsParameters * () const
 
BlastEffectiveLengthsParametersCBlastEffectiveLengthsParameters::operator-> ()
 
BlastEffectiveLengthsParametersCBlastEffectiveLengthsParameters::operator-> () const
 
BlastEffectiveLengthsParameters ** CBlastEffectiveLengthsParameters::operator& ()
 
virtual void CBlastEffectiveLengthsParameters::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CBlastGapAlignStruct::CBlastGapAlignStruct ()
 
 CBlastGapAlignStruct::CBlastGapAlignStruct (BlastGapAlignStruct *p)
 
virtual CBlastGapAlignStruct::~CBlastGapAlignStruct ()
 
void CBlastGapAlignStruct::Reset (BlastGapAlignStruct *p=NULL)
 
BlastGapAlignStructCBlastGapAlignStruct::Release ()
 
BlastGapAlignStructCBlastGapAlignStruct::Get () const
 
 CBlastGapAlignStruct::operator BlastGapAlignStruct * ()
 
 CBlastGapAlignStruct::operator BlastGapAlignStruct * () const
 
BlastGapAlignStructCBlastGapAlignStruct::operator-> ()
 
BlastGapAlignStructCBlastGapAlignStruct::operator-> () const
 
BlastGapAlignStruct ** CBlastGapAlignStruct::operator& ()
 
virtual void CBlastGapAlignStruct::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CBlastHSPResults::CBlastHSPResults ()
 
 CBlastHSPResults::CBlastHSPResults (BlastHSPResults *p)
 
virtual CBlastHSPResults::~CBlastHSPResults ()
 
void CBlastHSPResults::Reset (BlastHSPResults *p=NULL)
 
BlastHSPResultsCBlastHSPResults::Release ()
 
BlastHSPResultsCBlastHSPResults::Get () const
 
 CBlastHSPResults::operator BlastHSPResults * ()
 
 CBlastHSPResults::operator BlastHSPResults * () const
 
BlastHSPResultsCBlastHSPResults::operator-> ()
 
BlastHSPResultsCBlastHSPResults::operator-> () const
 
BlastHSPResults ** CBlastHSPResults::operator& ()
 
virtual void CBlastHSPResults::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CPSIMsa::CPSIMsa ()
 
 CPSIMsa::CPSIMsa (PSIMsa *p)
 
virtual CPSIMsa::~CPSIMsa ()
 
void CPSIMsa::Reset (PSIMsa *p=NULL)
 
PSIMsaCPSIMsa::Release ()
 
PSIMsaCPSIMsa::Get () const
 
 CPSIMsa::operator PSIMsa * ()
 
 CPSIMsa::operator PSIMsa * () const
 
PSIMsaCPSIMsa::operator-> ()
 
PSIMsaCPSIMsa::operator-> () const
 
PSIMsa ** CPSIMsa::operator& ()
 
virtual void CPSIMsa::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CPSIMatrix::CPSIMatrix ()
 
 CPSIMatrix::CPSIMatrix (PSIMatrix *p)
 
virtual CPSIMatrix::~CPSIMatrix ()
 
void CPSIMatrix::Reset (PSIMatrix *p=NULL)
 
PSIMatrixCPSIMatrix::Release ()
 
PSIMatrixCPSIMatrix::Get () const
 
 CPSIMatrix::operator PSIMatrix * ()
 
 CPSIMatrix::operator PSIMatrix * () const
 
PSIMatrixCPSIMatrix::operator-> ()
 
PSIMatrixCPSIMatrix::operator-> () const
 
PSIMatrix ** CPSIMatrix::operator& ()
 
virtual void CPSIMatrix::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CPSIDiagnosticsRequest::CPSIDiagnosticsRequest ()
 
 CPSIDiagnosticsRequest::CPSIDiagnosticsRequest (PSIDiagnosticsRequest *p)
 
virtual CPSIDiagnosticsRequest::~CPSIDiagnosticsRequest ()
 
void CPSIDiagnosticsRequest::Reset (PSIDiagnosticsRequest *p=NULL)
 
PSIDiagnosticsRequestCPSIDiagnosticsRequest::Release ()
 
PSIDiagnosticsRequestCPSIDiagnosticsRequest::Get () const
 
 CPSIDiagnosticsRequest::operator PSIDiagnosticsRequest * ()
 
 CPSIDiagnosticsRequest::operator PSIDiagnosticsRequest * () const
 
PSIDiagnosticsRequestCPSIDiagnosticsRequest::operator-> ()
 
PSIDiagnosticsRequestCPSIDiagnosticsRequest::operator-> () const
 
PSIDiagnosticsRequest ** CPSIDiagnosticsRequest::operator& ()
 
virtual void CPSIDiagnosticsRequest::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CPSIDiagnosticsResponse::CPSIDiagnosticsResponse ()
 
 CPSIDiagnosticsResponse::CPSIDiagnosticsResponse (PSIDiagnosticsResponse *p)
 
virtual CPSIDiagnosticsResponse::~CPSIDiagnosticsResponse ()
 
void CPSIDiagnosticsResponse::Reset (PSIDiagnosticsResponse *p=NULL)
 
PSIDiagnosticsResponseCPSIDiagnosticsResponse::Release ()
 
PSIDiagnosticsResponseCPSIDiagnosticsResponse::Get () const
 
 CPSIDiagnosticsResponse::operator PSIDiagnosticsResponse * ()
 
 CPSIDiagnosticsResponse::operator PSIDiagnosticsResponse * () const
 
PSIDiagnosticsResponseCPSIDiagnosticsResponse::operator-> ()
 
PSIDiagnosticsResponseCPSIDiagnosticsResponse::operator-> () const
 
PSIDiagnosticsResponse ** CPSIDiagnosticsResponse::operator& ()
 
virtual void CPSIDiagnosticsResponse::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CBlastSeqSrc::CBlastSeqSrc ()
 
 CBlastSeqSrc::CBlastSeqSrc (BlastSeqSrc *p)
 
virtual CBlastSeqSrc::~CBlastSeqSrc ()
 
void CBlastSeqSrc::Reset (BlastSeqSrc *p=NULL)
 
BlastSeqSrcCBlastSeqSrc::Release ()
 
BlastSeqSrcCBlastSeqSrc::Get () const
 
 CBlastSeqSrc::operator BlastSeqSrc * ()
 
 CBlastSeqSrc::operator BlastSeqSrc * () const
 
BlastSeqSrcCBlastSeqSrc::operator-> ()
 
BlastSeqSrcCBlastSeqSrc::operator-> () const
 
BlastSeqSrc ** CBlastSeqSrc::operator& ()
 
virtual void CBlastSeqSrc::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CBlastSeqSrcIterator::CBlastSeqSrcIterator ()
 
 CBlastSeqSrcIterator::CBlastSeqSrcIterator (BlastSeqSrcIterator *p)
 
virtual CBlastSeqSrcIterator::~CBlastSeqSrcIterator ()
 
void CBlastSeqSrcIterator::Reset (BlastSeqSrcIterator *p=NULL)
 
BlastSeqSrcIteratorCBlastSeqSrcIterator::Release ()
 
BlastSeqSrcIteratorCBlastSeqSrcIterator::Get () const
 
 CBlastSeqSrcIterator::operator BlastSeqSrcIterator * ()
 
 CBlastSeqSrcIterator::operator BlastSeqSrcIterator * () const
 
BlastSeqSrcIteratorCBlastSeqSrcIterator::operator-> ()
 
BlastSeqSrcIteratorCBlastSeqSrcIterator::operator-> () const
 
BlastSeqSrcIterator ** CBlastSeqSrcIterator::operator& ()
 
virtual void CBlastSeqSrcIterator::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CBlast_Message::CBlast_Message ()
 
 CBlast_Message::CBlast_Message (Blast_Message *p)
 
virtual CBlast_Message::~CBlast_Message ()
 
void CBlast_Message::Reset (Blast_Message *p=NULL)
 
Blast_MessageCBlast_Message::Release ()
 
Blast_MessageCBlast_Message::Get () const
 
 CBlast_Message::operator Blast_Message * ()
 
 CBlast_Message::operator Blast_Message * () const
 
Blast_MessageCBlast_Message::operator-> ()
 
Blast_MessageCBlast_Message::operator-> () const
 
Blast_Message ** CBlast_Message::operator& ()
 
virtual void CBlast_Message::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CBlastMaskLoc::CBlastMaskLoc ()
 
 CBlastMaskLoc::CBlastMaskLoc (BlastMaskLoc *p)
 
virtual CBlastMaskLoc::~CBlastMaskLoc ()
 
void CBlastMaskLoc::Reset (BlastMaskLoc *p=NULL)
 
BlastMaskLocCBlastMaskLoc::Release ()
 
BlastMaskLocCBlastMaskLoc::Get () const
 
 CBlastMaskLoc::operator BlastMaskLoc * ()
 
 CBlastMaskLoc::operator BlastMaskLoc * () const
 
BlastMaskLocCBlastMaskLoc::operator-> ()
 
BlastMaskLocCBlastMaskLoc::operator-> () const
 
BlastMaskLoc ** CBlastMaskLoc::operator& ()
 
virtual void CBlastMaskLoc::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CBlastSeqLoc::CBlastSeqLoc ()
 
 CBlastSeqLoc::CBlastSeqLoc (BlastSeqLoc *p)
 
virtual CBlastSeqLoc::~CBlastSeqLoc ()
 
void CBlastSeqLoc::Reset (BlastSeqLoc *p=NULL)
 
BlastSeqLocCBlastSeqLoc::Release ()
 
BlastSeqLocCBlastSeqLoc::Get () const
 
 CBlastSeqLoc::operator BlastSeqLoc * ()
 
 CBlastSeqLoc::operator BlastSeqLoc * () const
 
BlastSeqLocCBlastSeqLoc::operator-> ()
 
BlastSeqLocCBlastSeqLoc::operator-> () const
 
BlastSeqLoc ** CBlastSeqLoc::operator& ()
 
virtual void CBlastSeqLoc::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
 CSBlastProgress::CSBlastProgress ()
 
 CSBlastProgress::CSBlastProgress (SBlastProgress *p)
 
virtual CSBlastProgress::~CSBlastProgress ()
 
void CSBlastProgress::Reset (SBlastProgress *p=NULL)
 
SBlastProgressCSBlastProgress::Release ()
 
SBlastProgressCSBlastProgress::Get () const
 
 CSBlastProgress::operator SBlastProgress * ()
 
 CSBlastProgress::operator SBlastProgress * () const
 
SBlastProgressCSBlastProgress::operator-> ()
 
SBlastProgressCSBlastProgress::operator-> () const
 
SBlastProgress ** CSBlastProgress::operator& ()
 
virtual void CSBlastProgress::DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
virtual const char * CBlastSystemException::GetErrCodeString (void) const override
 Translate from the error code value to its string representation. More...
 
 CBlastSystemException::NCBI_EXCEPTION_DEFAULT (CBlastSystemException, CException)
 
virtual const char * CBlastException::GetErrCodeString (void) const override
 Translate from the error code value to its string representation. More...
 
 CBlastException::NCBI_EXCEPTION_DEFAULT (CBlastException, CException)
 
MT_LOCK Blast_CMT_LOCKInit (void)
 Initialize a mutex locking mechanism for BLAST. 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...
 
ELookupTableType CBlastNucleotideOptionsHandle::GetLookupTableType () const
 Returns LookupTableType. More...
 
void CBlastNucleotideOptionsHandle::SetLookupTableType (ELookupTableType type)
 Sets LookupTableType. More...
 
int CBlastNucleotideOptionsHandle::GetWordSize () const
 Returns WordSize. More...
 
void CBlastNucleotideOptionsHandle::SetWordSize (int ws)
 Sets WordSize. More...
 
objects::ENa_strand CBlastNucleotideOptionsHandle::GetStrandOption () const
 Returns StrandOption. More...
 
void CBlastNucleotideOptionsHandle::SetStrandOption (objects::ENa_strand strand)
 Sets StrandOption. More...
 
bool CBlastNucleotideOptionsHandle::GetDustFiltering () const
 Is dust filtering enabled? More...
 
void CBlastNucleotideOptionsHandle::SetDustFiltering (bool val)
 Enable dust filtering. More...
 
int CBlastNucleotideOptionsHandle::GetDustFilteringLevel () const
 Get level parameter for dust. More...
 
void CBlastNucleotideOptionsHandle::SetDustFilteringLevel (int level)
 Set level parameter for dust. More...
 
int CBlastNucleotideOptionsHandle::GetDustFilteringWindow () const
 Get window parameter for dust. More...
 
void CBlastNucleotideOptionsHandle::SetDustFilteringWindow (int window)
 Set window parameter for dust. More...
 
int CBlastNucleotideOptionsHandle::GetDustFilteringLinker () const
 Get linker parameter for dust. More...
 
void CBlastNucleotideOptionsHandle::SetDustFilteringLinker (int linker)
 Set linker parameter for dust. More...
 
bool CBlastNucleotideOptionsHandle::GetRepeatFiltering () const
 Is repeat filtering enabled? More...
 
void CBlastNucleotideOptionsHandle::SetRepeatFiltering (bool val)
 Enable repeat filtering. More...
 
const char * CBlastNucleotideOptionsHandle::GetRepeatFilteringDB () const
 Get the repeat filtering database. More...
 
void CBlastNucleotideOptionsHandle::SetRepeatFilteringDB (const char *db)
 Enable repeat filtering. More...
 
int CBlastNucleotideOptionsHandle::GetWindowMaskerTaxId () const
 Get the window masker taxid (or 0 if not set). More...
 
void CBlastNucleotideOptionsHandle::SetWindowMaskerTaxId (int taxid)
 Enable window masker and select a taxid (or 0 to disable). More...
 
const char * CBlastNucleotideOptionsHandle::GetWindowMaskerDatabase () const
 Get the window masker database name (or NULL if not set). More...
 
void CBlastNucleotideOptionsHandle::SetWindowMaskerDatabase (const char *db)
 Enable window masker and select a database (or NULL to disable). More...
 
double CBlastNucleotideOptionsHandle::GetXDropoff () const
 Returns XDropoff. More...
 
void CBlastNucleotideOptionsHandle::SetXDropoff (double x)
 Sets XDropoff. More...
 
EBlastPrelimGapExt CBlastNucleotideOptionsHandle::GetGapExtnAlgorithm () const
 Returns GapExtnAlgorithm. More...
 
void CBlastNucleotideOptionsHandle::SetGapExtnAlgorithm (EBlastPrelimGapExt algo)
 Sets GapExtnAlgorithm. More...
 
EBlastTbackExt CBlastNucleotideOptionsHandle::GetGapTracebackAlgorithm () const
 Returns GapTracebackAlgorithm. More...
 
void CBlastNucleotideOptionsHandle::SetGapTracebackAlgorithm (EBlastTbackExt algo)
 Sets GapTracebackAlgorithm. More...
 
int CBlastNucleotideOptionsHandle::GetMatchReward () const
 Returns MatchReward. More...
 
void CBlastNucleotideOptionsHandle::SetMatchReward (int r)
 Sets MatchReward. More...
 
int CBlastNucleotideOptionsHandle::GetMismatchPenalty () const
 Returns MismatchPenalty. More...
 
void CBlastNucleotideOptionsHandle::SetMismatchPenalty (int p)
 Sets MismatchPenalty. More...
 
const char * CBlastNucleotideOptionsHandle::GetMatrixName () const
 Returns MatrixName. More...
 
void CBlastNucleotideOptionsHandle::SetMatrixName (const char *matrix)
 Sets MatrixName. More...
 
int CBlastNucleotideOptionsHandle::GetGapOpeningCost () const
 Returns GapOpeningCost. More...
 
void CBlastNucleotideOptionsHandle::SetGapOpeningCost (int g)
 Sets GapOpeningCost. More...
 
int CBlastNucleotideOptionsHandle::GetGapExtensionCost () const
 Returns GapExtensionCost. More...
 
void CBlastNucleotideOptionsHandle::SetGapExtensionCost (int e)
 Sets GapExtensionCost. More...
 
void CBlastNucleotideOptionsHandle::SetTraditionalBlastnDefaults ()
 Sets TraditionalBlastnDefaults. More...
 
void CBlastNucleotideOptionsHandle::SetTraditionalMegablastDefaults ()
 Sets TraditionalMegablastDefaults. More...
 
void CBlastNucleotideOptionsHandle::SetVecScreenDefaults ()
 Sets default options for VecScreen. More...
 
virtual void CBlastNucleotideOptionsHandle::SetRemoteProgramAndService_Blast3 ()
 Set the program and service name for remote blast. 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...
 
 CBlastNucleotideOptionsHandle::CBlastNucleotideOptionsHandle (const CBlastNucleotideOptionsHandle &rhs)
 Disallow copy constructor. More...
 
CBlastNucleotideOptionsHandleCBlastNucleotideOptionsHandle::operator= (const CBlastNucleotideOptionsHandle &rhs)
 Disallow assignment operator. More...
 
 CBlastOptionsBuilder::CBlastOptionsBuilder (const string &program, const string &service, CBlastOptions::EAPILocality locality=CBlastOptions::eLocal, bool ignore_unsupported_options=false)
 Constructor. 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::HaveNegativeGiList ()
 Check whether a negative GI list is specified. More...
 
list< TGiCBlastOptionsBuilder::GetNegativeGiList ()
 Get the negative GI list. More...
 
bool CBlastOptionsBuilder::HaveTaxidList ()
 
list< TTaxIdCBlastOptionsBuilder::GetTaxidList ()
 Get the Tax list. More...
 
bool CBlastOptionsBuilder::HaveNegativeTaxidList ()
 Check whether a negative tax id list is specified. More...
 
list< TTaxIdCBlastOptionsBuilder::GetNegativeTaxidList ()
 Get the negative tax id 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::HaveQueryMasks ()
 Check whether query masks are specified. More...
 
TMaskList CBlastOptionsBuilder::GetQueryMasks ()
 Get the query masks. More...
 
TSeqRange CBlastOptionsBuilder::GetRestrictedQueryRange ()
 Return the range that was used to restrict the query sequence(s) (returns TSeqRange::GetEmpty() if not applicable) More...
 
void CBlastOptionsBuilder::SetIgnoreUnsupportedOptions (bool ignore)
 Set the 'ignore unsupported options' flag. More...
 
static EProgram CBlastOptionsBuilder::ComputeProgram (const string &program, const string &service)
 Compute the EProgram value to use for this search. More...
 
static EProgram CBlastOptionsBuilder::AdjustProgram (const TValueList *L, EProgram program, const string &program_string)
 Adjust the EProgram based on option values. More...
 
 CBlastOptionsBuilder::SOptional< T >::SOptional ()
 Constructor. More...
 
bool CBlastOptionsBuilder::SOptional< T >::Have ()
 Check whether the value has been set. More...
 
T CBlastOptionsBuilder::SOptional< T >::Get ()
 Get the value. More...
 
TCBlastOptionsBuilder::SOptional< T >::GetRef ()
 Get the reference to the stored value. More...
 
SOptional< T > & CBlastOptionsBuilder::SOptional< T >::operator= (const T &x)
 Assign the field from another optional field. More...
 
void CBlastOptionsBuilder::x_ApplyInteractions (CBlastOptionsHandle &boh)
 Apply values directly to BlastOptions object. 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...
 
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 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...
 
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...
 
 CBlastOptionsFactory::CBlastOptionsFactory ()
 Private c-tor. More...
 
 CBlastOptionsHandle::CBlastOptionsHandle (EAPILocality locality)
 Default c-tor. More...
 
bool CBlastOptionsHandle::Validate () const
 Validate the options contained in this object. More...
 
const CBlastOptionsCBlastOptionsHandle::GetOptions () const
 Return the object which this object is a handle for. More...
 
CBlastOptionsCBlastOptionsHandle::SetOptions ()
 Returns a reference to the internal options class which this object is a handle for. More...
 
virtual void CBlastOptionsHandle::SetDefaults ()
 Resets the state of the object to all default values. More...
 
void CBlastOptionsHandle::DoneDefaults ()
 Returns true if this object needs default values set. More...
 
int CBlastOptionsHandle::GetWindowSize () const
 Returns WindowSize. More...
 
void CBlastOptionsHandle::SetWindowSize (int ws)
 Sets WindowSize. More...
 
int CBlastOptionsHandle::GetOffDiagonalRange () const
 
void CBlastOptionsHandle::SetOffDiagonalRange (int r)
 
void CBlastOptionsHandle::ClearFilterOptions ()
 Clears the filtering options. More...
 
char * CBlastOptionsHandle::GetFilterString () const
 Returns FilterString. More...
 
void CBlastOptionsHandle::SetFilterString (const char *f, bool clear=true)
 Sets FilterString. More...
 
bool CBlastOptionsHandle::GetMaskAtHash () const
 Returns whether masking should only be done for lookup table creation. More...
 
void CBlastOptionsHandle::SetMaskAtHash (bool m=true)
 Sets MaskAtHash. More...
 
double CBlastOptionsHandle::GetGapXDropoff () const
 Returns GapXDropoff. More...
 
void CBlastOptionsHandle::SetGapXDropoff (double x)
 Sets GapXDropoff. More...
 
double CBlastOptionsHandle::GetGapTrigger () const
 Returns GapTrigger. More...
 
void CBlastOptionsHandle::SetGapTrigger (double g)
 Sets GapTrigger. More...
 
double CBlastOptionsHandle::GetGapXDropoffFinal () const
 Returns GapXDropoffFinal. More...
 
void CBlastOptionsHandle::SetGapXDropoffFinal (double x)
 Sets GapXDropoffFinal. More...
 
int CBlastOptionsHandle::GetHitlistSize () const
 Returns HitlistSize. More...
 
void CBlastOptionsHandle::SetHitlistSize (int s)
 Sets HitlistSize. More...
 
int CBlastOptionsHandle::GetMaxNumHspPerSequence () const
 Returns MaxNumHspPerSequence. More...
 
void CBlastOptionsHandle::SetMaxNumHspPerSequence (int m)
 Sets MaxNumHspPerSequence. More...
 
int CBlastOptionsHandle::GetMaxHspsPerSubject () const
 Returns MaxHspsPerSubjectQueryPair. More...
 
void CBlastOptionsHandle::SetMaxHspsPerSubject (int m)
 Sets MaxHspPerSubjectQueryPair. More...
 
double CBlastOptionsHandle::GetEvalueThreshold () const
 Returns EvalueThreshold. More...
 
void CBlastOptionsHandle::SetEvalueThreshold (double eval)
 Sets EvalueThreshold. More...
 
int CBlastOptionsHandle::GetCutoffScore () const
 Returns CutoffScore. More...
 
void CBlastOptionsHandle::SetCutoffScore (int s)
 Sets CutoffScore. More...
 
double CBlastOptionsHandle::GetPercentIdentity () const
 Returns PercentIdentity. More...
 
void CBlastOptionsHandle::SetPercentIdentity (double p)
 Sets PercentIdentity. More...
 
double CBlastOptionsHandle::GetQueryCovHspPerc () const
 Returns QueryCovHspPerc. More...
 
void CBlastOptionsHandle::SetQueryCovHspPerc (double p)
 Sets QueryCovHspPerc. More...
 
int CBlastOptionsHandle::GetMinDiagSeparation () const
 Returns MinDiagSeparation. More...
 
void CBlastOptionsHandle::SetMinDiagSeparation (int d)
 Sets MinDiagSeparation. More...
 
bool CBlastOptionsHandle::GetGappedMode () const
 Returns GappedMode. More...
 
void CBlastOptionsHandle::SetGappedMode (bool m=true)
 Sets GappedMode. More...
 
int CBlastOptionsHandle::GetCullingLimit () const
 Returns Culling limit. More...
 
void CBlastOptionsHandle::SetCullingLimit (int s)
 Sets Culling limit. More...
 
int CBlastOptionsHandle::GetMaskLevel () const
 Returns MaskLevel -RMH-. More...
 
void CBlastOptionsHandle::SetMaskLevel (int ml)
 Sets MaskLevel -RMH-. More...
 
bool CBlastOptionsHandle::GetComplexityAdjMode () const
 Returns Complexity Adjustment Mode -RMH-. More...
 
void CBlastOptionsHandle::SetComplexityAdjMode (bool m=true)
 Sets ComplexityAdjMode -RMH-. More...
 
double CBlastOptionsHandle::GetLowScorePerc () const
 Returns low score percentage for ungapped alignments. More...
 
void CBlastOptionsHandle::SetLowScorePerc (double p)
 Sets low score percentage for ungapped alignments. More...
 
Int8 CBlastOptionsHandle::GetDbLength () const
 Returns DbLength. More...
 
void CBlastOptionsHandle::SetDbLength (Int8 len)
 Sets DbLength. More...
 
unsigned int CBlastOptionsHandle::GetDbSeqNum () const
 Returns DbSeqNum. More...
 
void CBlastOptionsHandle::SetDbSeqNum (unsigned int num)
 Sets DbSeqNum. More...
 
Int8 CBlastOptionsHandle::GetEffectiveSearchSpace () const
 Returns EffectiveSearchSpace. More...
 
void CBlastOptionsHandle::SetEffectiveSearchSpace (Int8 eff)
 Sets EffectiveSearchSpace. More...
 
 CBlastOptionsHandle::CBlastOptionsHandle (CRef< CBlastOptions > opt)
 Create Options Handle from Existing CBlastOptions Object. More...
 
virtual void CBlastOptionsHandle::SetRemoteProgramAndService_Blast3 ()=0
 Set the program and service name for remote blast. More...
 
virtual void CBlastOptionsHandle::SetLookupTableDefaults ()=0
 Sets LookupTableDefaults. More...
 
virtual void CBlastOptionsHandle::SetQueryOptionDefaults ()=0
 Sets QueryOptionDefaults. More...
 
virtual void CBlastOptionsHandle::SetInitialWordOptionsDefaults ()=0
 Sets InitialWordOptionsDefaults. More...
 
virtual void CBlastOptionsHandle::SetGappedExtensionDefaults ()=0
 Sets GappedExtensionDefaults. More...
 
virtual void CBlastOptionsHandle::SetScoringOptionsDefaults ()=0
 Sets ScoringOptionsDefaults. More...
 
virtual void CBlastOptionsHandle::SetHitSavingOptionsDefaults ()=0
 Sets HitSavingOptionsDefaults. More...
 
virtual void CBlastOptionsHandle::SetEffectiveLengthsOptionsDefaults ()=0
 Sets EffectiveLengthsOptionsDefaults. More...
 
virtual void CBlastOptionsHandle::SetSubjectSequenceOptionsDefaults ()=0
 Sets SubjectSequenceOptionsDefaults. More...
 
 CBlastProteinOptionsHandle::CBlastProteinOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
 Creates object with default options set. More...
 
 CBlastProteinOptionsHandle::CBlastProteinOptionsHandle (CRef< CBlastOptions > opt)
 Create Options Handle from Existing CBlastOptions Object. More...
 
double CBlastProteinOptionsHandle::GetWordThreshold () const
 Returns WordThreshold. More...
 
void CBlastProteinOptionsHandle::SetWordThreshold (double wt)
 Sets WordThreshold. More...
 
int CBlastProteinOptionsHandle::GetWordSize () const
 Returns WordSize. More...
 
void CBlastProteinOptionsHandle::SetWordSize (int ws)
 Sets WordSize. More...
 
double CBlastProteinOptionsHandle::GetXDropoff () const
 Returns XDropoff. More...
 
void CBlastProteinOptionsHandle::SetXDropoff (double x)
 Sets XDropoff. More...
 
bool CBlastProteinOptionsHandle::GetSegFiltering () const
 Is SEG filtering enabled? More...
 
void CBlastProteinOptionsHandle::SetSegFiltering (bool val)
 Enable SEG filtering. More...
 
int CBlastProteinOptionsHandle::GetSegFilteringWindow () const
 Get window parameter for seg. More...
 
void CBlastProteinOptionsHandle::SetSegFilteringWindow (int window)
 Set window parameter for seg. More...
 
double CBlastProteinOptionsHandle::GetSegFilteringLocut () const
 Get locut parameter for seg. More...
 
void CBlastProteinOptionsHandle::SetSegFilteringLocut (double locut)
 Set locut parameter for seg. More...
 
double CBlastProteinOptionsHandle::GetSegFilteringHicut () const
 Get hicut parameter for seg. More...
 
void CBlastProteinOptionsHandle::SetSegFilteringHicut (double hicut)
 Set hicut parameter for seg. More...
 
const char * CBlastProteinOptionsHandle::GetMatrixName () const
 Returns MatrixName. More...
 
void CBlastProteinOptionsHandle::SetMatrixName (const char *matrix)
 Sets MatrixName. More...
 
int CBlastProteinOptionsHandle::GetGapOpeningCost () const
 Returns GapOpeningCost. More...
 
void CBlastProteinOptionsHandle::SetGapOpeningCost (int g)
 Sets GapOpeningCost. More...
 
int CBlastProteinOptionsHandle::GetGapExtensionCost () const
 Returns GapExtensionCost. More...
 
void CBlastProteinOptionsHandle::SetGapExtensionCost (int e)
 Sets GapExtensionCost. More...
 
virtual void CBlastProteinOptionsHandle::SetRemoteProgramAndService_Blast3 ()
 Set the program and service name for remote blast. 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...
 
 CBlastProteinOptionsHandle::CBlastProteinOptionsHandle (const CBlastProteinOptionsHandle &rhs)
 Disallow copy constructor. More...
 
CBlastProteinOptionsHandleCBlastProteinOptionsHandle::operator= (const CBlastProteinOptionsHandle &rhs)
 Disallow assignment operator. 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 ()
 Destructor. More...
 
 CBlastAncillaryData::CBlastAncillaryData (const CBlastAncillaryData &rhs)
 Copy-constructor. More...
 
CBlastAncillaryDataCBlastAncillaryData::operator= (const CBlastAncillaryData &rhs)
 Assignment operator. More...
 
const Blast_GumbelBlkCBlastAncillaryData::GetGumbelBlk () const
 Retrieve gumbel parameters. More...
 
const Blast_KarlinBlkCBlastAncillaryData::GetUngappedKarlinBlk () const
 Retrieve ungapped Karlin parameters. More...
 
const Blast_KarlinBlkCBlastAncillaryData::GetGappedKarlinBlk () const
 Retrieve gapped Karlin parameters. More...
 
const Blast_KarlinBlkCBlastAncillaryData::GetPsiUngappedKarlinBlk () const
 Retrieve PSI-BLAST ungapped Karlin parameters. More...
 
const Blast_KarlinBlkCBlastAncillaryData::GetPsiGappedKarlinBlk () const
 Retrieve PSI-BLAST gapped Karlin parameters. More...
 
Int8 CBlastAncillaryData::GetSearchSpace () const
 Retrieve the search space for this query sequence. More...
 
Int8 CBlastAncillaryData::GetLengthAdjustment () const
 Retrieve the length adjustment for boundary conditions. More...
 
void CBlastAncillaryData::SetLengthAdjustment (int len_adj)
 Set the length adjustment for boundary conditions. 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::SetRID (const string &rid)
 Sets the RID for these results. More...
 
string CSearchResults::GetRID () const
 Returns the RID for these results (if applicable), otherwise returns an empty string. More...
 
CConstRef< objects::CSeq_align_set > CSearchResults::GetSeqAlign () const
 Accessor for the Seq-align results. More...
 
CRef< objects::CSeq_align_set > CSearchResults::SetSeqAlign ()
 Only intended to be used if you need to edit the seqlign. 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...
 
CRef< CBlastAncillaryDataCSearchResults::GetAncillaryData () const
 Accessor for the query's search ancillary. More...
 
TQueryMessages CSearchResults::GetErrors (int min_severity=eBlastSevError) const
 Accessor for the error/warning messsages for this query. 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...
 
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...
 
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...
 
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...
 
const SPHIQueryInfoCSearchResults::GetPhiQueryInfo () const
 Retrieves PHI-BLAST information about pattern on query. 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...
 
 CSearchResults::CSearchResults (const CSearchResults &rhs)
 Prohibit copy constructor. More...
 
CSearchResultsCSearchResults::operator= (const CSearchResults &rhs)
 Prohibit assignment operator. More...
 
 CSearchResultSet::CSearchResultSet (EResultType res_type=eDatabaseSearch)
 Simplest constructor. More...
 
 CSearchResultSet::CSearchResultSet (TSeqAlignVector aligns, TSearchMessages msg_vec, EResultType res_type=eDatabaseSearch)
 Parametrized 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...
 
CSearchResultsCSearchResultSet::operator[] (size_type i)
 Allow array-like access with integer indices to CSearchResults contained by this object. More...
 
const CSearchResultsCSearchResultSet::operator[] (size_type i) const
 Allow array-like access with integer indices to const CSearchResults contained by this object. 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...
 
CRef< CSearchResultsCSearchResultSet::operator[] (const objects::CSeq_id &ident)
 Allow array-like access with CSeq_id indices to CSearchResults contained by this object. 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...
 
size_type CSearchResultSet::GetNumResults () const
 Return the number of results contained by this object. More...
 
size_type CSearchResultSet::GetNumQueries () const
 Return the number of unique query ID's represented by this object. More...
 
void CSearchResultSet::SetFilteredQueryRegions (const TSeqLocInfoVector &masks)
 Sets the filtered query regions. More...
 
TSeqLocInfoVector CSearchResultSet::GetFilteredQueryRegions () const
 Retrieves the filtered query regions. More...
 
size_type CSearchResultSet::size () const
 Identical to GetNumResults, provided to facilitate STL-style iteration. More...
 
bool CSearchResultSet::empty () const
 Returns whether this container is empty or not. More...
 
const_iterator CSearchResultSet::begin () const
 Returns const_iterator to beginning of container, provided to facilitate STL-style iteration. More...
 
const_iterator CSearchResultSet::end () const
 Returns const_iterator to end of container, provided to facilitate STL-style iteration. More...
 
iterator CSearchResultSet::begin ()
 Returns iterator to beginning of container, provided to facilitate STL-style iteration. More...
 
iterator CSearchResultSet::end ()
 Returns iterator to end of container, provided to facilitate STL-style iteration. More...
 
void CSearchResultSet::clear ()
 Clears the contents of this object. More...
 
void CSearchResultSet::push_back (value_type &element)
 Add a value to the back of this container. More...
 
EResultType CSearchResultSet::GetResultType () const
 Get the type of results contained in this object. More...
 
void CSearchResultSet::SetRID (const string &rid)
 Sets the RID for these results. 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...
 
 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...
 
double CBlastRPSOptionsHandle::GetWordThreshold () const
 Returns WordThreshold. More...
 
int CBlastRPSOptionsHandle::GetWordSize () const
 Returns WordSize. More...
 
double CBlastRPSOptionsHandle::GetXDropoff () const
 Returns XDropoff. More...
 
void CBlastRPSOptionsHandle::SetXDropoff (double x)
 Sets XDropoff. More...
 
bool CBlastRPSOptionsHandle::GetSegFiltering () const
 Is SEG filtering enabled? More...
 
void CBlastRPSOptionsHandle::SetSegFiltering (bool val)
 Enable SEG filtering. More...
 
int CBlastRPSOptionsHandle::GetSegFilteringWindow () const
 Get window parameter for seg. More...
 
void CBlastRPSOptionsHandle::SetSegFilteringWindow (int window)
 Set window parameter for seg. More...
 
double CBlastRPSOptionsHandle::GetSegFilteringLocut () const
 Get locut parameter for seg. More...
 
void CBlastRPSOptionsHandle::SetSegFilteringLocut (double locut)
 Set locut parameter for seg. More...
 
double CBlastRPSOptionsHandle::GetSegFilteringHicut () const
 Get hicut parameter for seg. More...
 
void CBlastRPSOptionsHandle::SetSegFilteringHicut (double hicut)
 Set hicut parameter for seg. More...
 
bool CBlastRPSOptionsHandle::GetCompositionBasedStats (void) const
 Get composition based statistics mode. More...
 
void CBlastRPSOptionsHandle::SetCompositionBasedStats (bool mode)
 Set composition based statistics mode. More...
 
int CBlastRPSOptionsHandle::GetGapOpeningCost () const
 Returns GapOpeningCost. More...
 
int CBlastRPSOptionsHandle::GetGapExtensionCost () const
 Returns GapExtensionCost. More...
 
virtual void CBlastRPSOptionsHandle::SetRemoteProgramAndService_Blast3 ()
 Set the program and service name for remote blast. 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...
 
 CBlastRPSOptionsHandle::CBlastRPSOptionsHandle (const CBlastRPSOptionsHandle &rhs)
 Disallow copy constructor. More...
 
CBlastRPSOptionsHandleCBlastRPSOptionsHandle::operator= (const CBlastRPSOptionsHandle &rhs)
 Disallow assignment operator. More...
 
virtual IBlastSeqInfoSrc::~IBlastSeqInfoSrc ()
 
virtual list< CRef< objects::CSeq_id > > IBlastSeqInfoSrc::GetId (Uint4 index) const =0
 Method to retrieve a sequence identifier given its ordinal number. More...
 
virtual CConstRef< objects::CSeq_loc > IBlastSeqInfoSrc::GetSeqLoc (Uint4 index) const =0
 Method to retrieve the sequence location given its ordinal number. More...
 
virtual Uint4 IBlastSeqInfoSrc::GetLength (Uint4 index) const =0
 Method to retrieve a sequence length given its ordinal number. More...
 
virtual size_t IBlastSeqInfoSrc::Size () const =0
 Returns the size of the underlying container of sequences. More...
 
virtual bool IBlastSeqInfoSrc::HasGiList () const =0
 Returns true if the subject is restricted by a GI list. More...
 
virtual bool IBlastSeqInfoSrc::GetMasks (Uint4 index, const TSeqRange &target_range, TMaskedSubjRegions &retval) const =0
 Retrieves the subject masks for the corresponding index. More...
 
virtual bool IBlastSeqInfoSrc::GetMasks (Uint4 index, const vector< TSeqRange > &target_ranges, TMaskedSubjRegions &retval) const =0
 Retrieves the subject masks for the corresponding index. More...
 
virtual bool IBlastSeqInfoSrc::CanReturnPartialSequence () const =0
 Return true if the implementation can return anything besides a seq-loc for the entire sequence. 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 GetSequenceLengthAndId (const IBlastSeqInfoSrc *seqinfo_src, int oid, int(*rank_func)(const CRef< objects::CSeq_id > &), CRef< objects::CSeq_id > &seqid, TSeqPos *length)
 Retrieves subject sequence Seq-id and length, using the provided sequence id ranking function. 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...
 
 CBlastpKmerOptionsHandle::CBlastpKmerOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
 Creates object with default options set. More...
 
 CBlastpKmerOptionsHandle::CBlastpKmerOptionsHandle (CRef< CBlastOptions > opt)
 
 CBlastpKmerOptionsHandle::~CBlastpKmerOptionsHandle ()
 
double CBlastpKmerOptionsHandle::GetThresh () const
 Returns threshold for Jaccard distance (range: 0-1) More...
 
void CBlastpKmerOptionsHandle::SetThresh (double thresh=0.1)
 Sets Threshold for Jaccard distance. More...
 
int CBlastpKmerOptionsHandle::GetMinHits () const
 Returns the number of hits to initiate calculation of Jaccard distance. More...
 
void CBlastpKmerOptionsHandle::SetMinHits (int minhits=1)
 Sets the number of hits ot initiate calculation of Jaccard distance. More...
 
int CBlastpKmerOptionsHandle::GetCandidateSeqs () const
 Gets the max number of candidate matches to process with BLAST. More...
 
void CBlastpKmerOptionsHandle::SetCandidateSeqs (int candidates=1000)
 Sets the max number of candidate matches to process with BLAST @candidates max number of target sequences to process with BLAST [in]. More...
 
virtual void CBlastpKmerOptionsHandle::SetRemoteProgramAndService_Blast3 ()
 Set the program and service name for remote blast. More...
 
 CBlastpKmerOptionsHandle::CBlastpKmerOptionsHandle (const CBlastpKmerOptionsHandle &rhs)
 Disallow copy constructor. More...
 
CBlastpKmerOptionsHandleCBlastpKmerOptionsHandle::operator= (const CBlastpKmerOptionsHandle &rhs)
 Disallow assignment operator. More...
 
 CBlastxOptionsHandle::CBlastxOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
 Creates object with default options set. More...
 
objects::ENa_strand CBlastxOptionsHandle::GetStrandOption () const
 Returns StrandOption. More...
 
void CBlastxOptionsHandle::SetStrandOption (objects::ENa_strand strand)
 Sets StrandOption. More...
 
int CBlastxOptionsHandle::GetQueryGeneticCode () const
 Returns QueryGeneticCode. More...
 
void CBlastxOptionsHandle::SetQueryGeneticCode (int gc)
 Sets QueryGeneticCode. More...
 
bool CBlastxOptionsHandle::GetOutOfFrameMode () const
 Returns OutOfFrameMode. More...
 
void CBlastxOptionsHandle::SetOutOfFrameMode (bool m=true)
 Sets OutOfFrameMode. More...
 
int CBlastxOptionsHandle::GetFrameShiftPenalty () const
 Returns FrameShiftPenalty. More...
 
void CBlastxOptionsHandle::SetFrameShiftPenalty (int p)
 Sets FrameShiftPenalty. More...
 
int CBlastxOptionsHandle::GetLongestIntronLength () const
 Returns LongestIntronLength. More...
 
void CBlastxOptionsHandle::SetLongestIntronLength (int l)
 Sets LongestIntronLength. More...
 
ECompoAdjustModes CBlastxOptionsHandle::GetCompositionBasedStats () const
 Returns this mode, which mostly specifies whether composition of db sequence is taken into account when calculating expect values. More...
 
void CBlastxOptionsHandle::SetCompositionBasedStats (ECompoAdjustModes mode)
 Sets this mode, which mostly specifies whether composition of db sequence is taken into account when calculating expect values. More...
 
bool CBlastxOptionsHandle::GetSmithWatermanMode () const
 Returns this mode, specifying that smith waterman rather than the normal blast heuristic should be used for final extensions. More...
 
void CBlastxOptionsHandle::SetSmithWatermanMode (bool m=false)
 Sets this mode, specifying that smith waterman rather than the normal blast heuristic should be used for final extensions. More...
 
virtual void CBlastxOptionsHandle::SetRemoteProgramAndService_Blast3 ()
 Set the program and service name for remote blast. More...
 
void CBlastxOptionsHandle::SetLookupTableDefaults ()
 Overrides LookupTableDefaults for blastx options. More...
 
void CBlastxOptionsHandle::SetQueryOptionDefaults ()
 Overrides QueryOptionDefaults for blastx options. More...
 
void CBlastxOptionsHandle::SetScoringOptionsDefaults ()
 Overrides ScoringOptionsDefaults for blastx options. More...
 
void CBlastxOptionsHandle::SetHitSavingOptionsDefaults ()
 Overrides HitSavingOptionsDefaults for blastx options. More...
 
void CBlastxOptionsHandle::SetGappedExtensionDefaults ()
 Overrides SetGappedExtensionDefaults for blastx option. More...
 
 CBlastxOptionsHandle::CBlastxOptionsHandle (const CBlastxOptionsHandle &rhs)
 Disallow copy constructor. More...
 
CBlastxOptionsHandleCBlastxOptionsHandle::operator= (const CBlastxOptionsHandle &rhs)
 Disallow assignment operator. More...
 
virtual IPssmInputCdd::~IPssmInputCdd ()
 
virtual PSICdMsaIPssmInputCdd::GetData (void)=0
 Get CD data for PSSM computation. More...
 
virtual const PSIBlastOptionsIPssmInputCdd::GetOptions (void)=0
 Get CDD-related PSI-BLAST options. More...
 
virtual const PSIDiagnosticsRequestIPssmInputCdd::GetDiagnosticsRequest (void)
 Get diagnostics options. More...
 
virtual void IPssmInputCdd::Process (void)=0
 Pre-process CDs used for PSSM computation. 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...
 
unsigned char * CCddInputData::GetQuery (void)
 Get query sequence. More...
 
unsigned int CCddInputData::GetQueryLength (void)
 Get query length. More...
 
const char * CCddInputData::GetMatrixName (void)
 Get scoring matrix name. More...
 
const PSIDiagnosticsRequestCCddInputData::GetDiagnosticsRequest (void)
 Get options for PSSM engine diagnostics. More...
 
PSICdMsaCCddInputData::GetData (void)
 Get data for PSSM computation. More...
 
const PSIBlastOptionsCCddInputData::GetOptions (void)
 Get CDD-related PSSM engine options. More...
 
void CCddInputData::Process (void)
 Pre-process CD matches to query. More...
 
void CCddInputData::SetMinCddEvalue (double val)
 Set minimum e-value threshold for inclusion of CDs in PSSM computation. More...
 
CRef< objects::CBioseq > CCddInputData::GetQueryForPssm (void)
 Get query as Bioseq. More...
 
int CCddInputData::GetGapExistence (void)
 Get gap existence to use when building PSSM. More...
 
int CCddInputData::GetGapExtension (void)
 Get gap extension to use when building PSSM. More...
 
 CCddInputData::CHitSegment::CHitSegment (TRange q, TRange s)
 Constructor. More...
 
 CCddInputData::CHitSegment::CHitSegment (const CHitSegment &seg)
 Copy constructor. 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...
 
bool CCddInputData::CHitSegment::IsEmpty (void) const
 Does the hit segment represent an empty range. More...
 
void CCddInputData::CHitSegment::AdjustRanges (int d_from, int d_to)
 Change ranges on query and subject by given values. More...
 
int CCddInputData::CHitSegment::GetLength (void) const
 Get length of the hit segment in residues. More...
 
CHitSegmentCCddInputData::CHitSegment::operator= (const CHitSegment &hit)
 Fobidding assignment operator. 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...
 
 CCddInputData::CHit::CHit (const objects::CDense_seg &denseg, double evalue)
 Constructor. More...
 
 CCddInputData::CHit::CHit (const CHit &hit)
 Copy constructor. More...
 
 CCddInputData::CHit::~CHit ()
 Destructor. More...
 
void CCddInputData::CHit::FillData (const CSeqDB &seqdb, const CBlastRPSInfo &profile_data)
 Allocate and populate arrays of data for PSSM computation. 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...
 
bool CCddInputData::CHit::Validate (void) const
 Validate hit. More...
 
bool CCddInputData::CHit::IsEmpty (void) const
 Is hit empty. More...
 
int CCddInputData::CHit::GetLength (void) const
 Get hit length in residues, counts number of matching residues, gaps are not counted. More...
 
vector< CHitSegment * > & CCddInputData::CHit::GetSegments (void)
 Get hit segments. More...
 
const vector< CHitSegment * > & CCddInputData::CHit::GetSegments (void) const
 Get hit segments. More...
 
bool CCddInputData::compare_hitseg_range::operator() (const CHitSegment *a, const CHitSegment *b) const
 
bool CCddInputData::compare_range::operator() (const TRange &a, const TRange &b) const
 
bool CCddInputData::compare_hits_by_seqid_eval::operator() (CHit *const &a, CHit *const &b)
 
void CCddInputData::x_ProcessAlignments (double min_evalue, double max_evalue)
 Process RPS-BLAST hits. 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...
 
void CCddInputData::x_RemoveMultipleCdHits (void)
 Remove multiple hits to the same CD. More...
 
bool CCddInputData::x_ValidateMsa (void) const
 Validate multiple alignment of CDs. 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...
 
 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...
 
 CDeltaBlast::~CDeltaBlast ()
 Destructor. 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::GetDomainResults ()
 Get results of conserved domain search (intermediate results) More...
 
CRef< CSearchResultSetCDeltaBlast::Run ()
 Run the DELTA-BLAST engine with one iteration. More...
 
 CDeltaBlast::CDeltaBlast (const CDeltaBlast &rhs)
 Prohibit copy constructor. More...
 
CDeltaBlastCDeltaBlast::operator= (const CDeltaBlast &rhs)
 Prohibit assignment operator. 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...
 
 CDeltaBlastOptionsHandle::~CDeltaBlastOptionsHandle ()
 Destructor. More...
 
double CDeltaBlastOptionsHandle::GetDomainInclusionThreshold (void) const
 Get e-value threshold for including domains in Pssm calculation. More...
 
void CDeltaBlastOptionsHandle::SetDomainInclusionThreshold (double th)
 Set e-value threshold for including domains in Pssm calculation. More...
 
double CDeltaBlastOptionsHandle::GetPSIInclusionThreshold (void) const
 Get e-value threshold for including sequences in Pssm calculation. More...
 
void CDeltaBlastOptionsHandle::SetPSIInclusionThreshold (double th)
 Set e-value threshold for including sequences in Pssm calculation. More...
 
virtual void CDeltaBlastOptionsHandle::SetRemoteProgramAndService_Blast3 ()
 Set the program and service name for remote blast. More...
 
virtual void CDeltaBlastOptionsHandle::SetQueryOptionDefaults ()
 Override the parent class' default for filtering query sequence (i.e. More...
 
virtual void CDeltaBlastOptionsHandle::SetGappedExtensionDefaults ()
 Override the parent class' defaults for gapped extension (i.e. More...
 
void CDeltaBlastOptionsHandle::SetDeltaBlastDefaults ()
 Sets Delta Blast defaults. More...
 
 CDeltaBlastOptionsHandle::CDeltaBlastOptionsHandle (const CDeltaBlastOptionsHandle &rhs)
 Disallow copy constructor. More...
 
CDeltaBlastOptionsHandleCDeltaBlastOptionsHandle::operator= (const CDeltaBlastOptionsHandle &rhs)
 Disallow assignment operator. More...
 
 CDiscNucleotideOptionsHandle::CDiscNucleotideOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
 Creates object with default options set. More...
 
unsigned char CDiscNucleotideOptionsHandle::GetTemplateLength () const
 Returns TemplateLength. More...
 
void CDiscNucleotideOptionsHandle::SetTemplateLength (unsigned char length)
 Sets TemplateLength. More...
 
unsigned char CDiscNucleotideOptionsHandle::GetTemplateType () const
 Returns TemplateType. More...
 
void CDiscNucleotideOptionsHandle::SetTemplateType (unsigned char type)
 Sets TemplateType. More...
 
void CDiscNucleotideOptionsHandle::SetWordSize (int ws)
 Sets WordSize. More...
 
void CDiscNucleotideOptionsHandle::SetTraditionalBlastnDefaults ()
 NOTE: Unavailable for discontiguous megablast. More...
 
virtual void CDiscNucleotideOptionsHandle::SetRemoteProgramAndService_Blast3 ()
 Set the program and service name for remote blast. 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...
 
 CDiscNucleotideOptionsHandle::CDiscNucleotideOptionsHandle (const CDiscNucleotideOptionsHandle &rhs)
 Disallow copy constructor. More...
 
CDiscNucleotideOptionsHandleCDiscNucleotideOptionsHandle::operator= (const CDiscNucleotideOptionsHandle &rhs)
 Disallow assignment operator. 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...
 
 CBlastHSPListQueueData::CBlastHSPListQueueData ()
 Constructor. More...
 
 CBlastHSPListQueueData::~CBlastHSPListQueueData ()
 Destructor. More...
 
int CBlastHSPListQueueData::Read (BlastHSPList **hsp_list)
 Read from the queue. More...
 
int CBlastHSPListQueueData::Write (BlastHSPList **hsp_list)
 Write to the queue. More...
 
void CBlastHSPListQueueData::Close ()
 Close the queue for writing. More...
 
bool CBlastHSPListQueueData::NeedWait ()
 Check if wait on semaphore is needed. 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...
 
 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...
 
TInterruptFnPtr CLocalBlast::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...
 
TSearchMessages CLocalBlast::GetSearchMessages () const
 Retrieve any error/warning messages that occurred during 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...
 
void CLocalBlast::SetBatchNumber (int batch_num)
 
 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...
 
int CLocalDbAdapter::GetFilteringAlgorithm ()
 Retrieve the database filtering algorithm. More...
 
string CLocalDbAdapter::GetFilteringAlgorithmKey ()
 Retrieve the database filtering id from key. More...
 
bool CLocalDbAdapter::IsProtein () const
 Returns true if this object represents protein or nucleotide sequences. More...
 
string CLocalDbAdapter::GetDatabaseName () const
 Returns the database name if appropriate, else kEmptyStr for subject sequences. More...
 
bool CLocalDbAdapter::IsBlastDb () const
 Returns true if this object represents a BLAST database. More...
 
bool CLocalDbAdapter::IsDbScanMode () const
 Returns true if this is not a database but is database scanning mode. More...
 
CRef< CSearchDatabaseCLocalDbAdapter::GetSearchDatabase ()
 
 CLocalDbAdapter::CLocalDbAdapter (const CLocalDbAdapter &)
 Prohibit copy-constructor. More...
 
CLocalDbAdapterCLocalDbAdapter::operator= (const CLocalDbAdapter &)
 Prohibit assignment operator. 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 CRef< CSearchResultSetCLocalSeqSearch::Run ()
 Run the search. 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...
 
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...
 
 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...
 
 CMagicBlast::~CMagicBlast ()
 Destructor. More...
 
CRef< CSeq_align_setCMagicBlast::Run (void)
 Run the RNA-Seq mapping. More...
 
CRef< CMagicBlastResultSetCMagicBlast::RunEx (void)
 
TSearchMessages CMagicBlast::GetSearchMessages (void) const
 
 CMagicBlast::CMagicBlast (const CMagicBlast &rhs)
 Prohibit copy constructor. More...
 
CMagicBlastCMagicBlast::operator= (const CMagicBlast &rhs)
 Prohibit assignment operator. More...
 
void CMagicBlast::x_Validate (void)
 Perform sanity checks on input arguments. More...
 
int CMagicBlast::x_Run (void)
 
CRef< CSeq_align_setCMagicBlast::x_BuildSeqAlignSet (const BlastMappingResults *results)
 
CRef< CMagicBlastResultSetCMagicBlast::x_BuildResultSet (const BlastMappingResults *results)
 
static CRef< CSeq_align_setCMagicBlast::x_CreateSeqAlignSet (const HSPChain *results, CRef< ILocalQueryData > qdata, CRef< IBlastSeqInfoSrc > seqinfo_src, const BlastQueryInfo *query_info, bool btop_splice_signals)
 Create results. More...
 
 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...
 
CConstRef< CSeq_align_setCMagicBlastResults::GetSeqAlign (void) const
 Get alignments. More...
 
CRef< CSeq_align_setCMagicBlastResults::SetSeqAlign (void)
 Get non-const alignments. More...
 
bool CMagicBlastResults::IsPaired (void) const
 Are alignments computed for paired reads. More...
 
bool CMagicBlastResults::IsConcordant (void) const
 Are an aligned pair concordant? More...
 
TResultsInfo CMagicBlastResults::GetFirstInfo (void) const
 Get alignment flags for the query. More...
 
TResultsInfo CMagicBlastResults::GetLastInfo (void) const
 Get alignment flags for the mate. More...
 
const CSeq_idCMagicBlastResults::GetQueryId (void) const
 Get query sequence id. More...
 
const CSeq_idCMagicBlastResults::GetFirstId (void) const
 Get sequence id of the first segment of a paired read. More...
 
const CSeq_idCMagicBlastResults::GetLastId (void) const
 Get sequence id of the last sequence of a paired read. More...
 
bool CMagicBlastResults::FirstAligned (void) const
 Is the query aligned. More...
 
bool CMagicBlastResults::LastAligned (void) const
 Is the mate aligned. 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)
 
 CMagicBlastResultSet::CMagicBlastResultSet (void)
 Create an empty results set. More...
 
CRef< CSeq_align_setCMagicBlastResultSet::GetFlatResults (bool no_discordant=false)
 Get all results as a single Seq-align-set object. More...
 
size_type CMagicBlastResultSet::size () const
 Get number of results, provided to facilitate STL-style iteration. More...
 
bool CMagicBlastResultSet::empty () const
 Is the container empty. More...
 
const_iterator CMagicBlastResultSet::begin () const
 Returns const iteartor to the beginning of the container, provided to facilitate STL-style iteartion. More...
 
const_iterator CMagicBlastResultSet::end () const
 Returns const iterator to the end of the container. More...
 
iterator CMagicBlastResultSet::begin ()
 Returns iterator to the beginning of the container. More...
 
iterator CMagicBlastResultSet::end ()
 Returns iterator to the end of the container. More...
 
void CMagicBlastResultSet::clear ()
 Clear all results. More...
 
void CMagicBlastResultSet::reserve (size_t num)
 Reserve memory for a number of result elemetns. More...
 
void CMagicBlastResultSet::push_back (CMagicBlastResultSet::value_type &element)
 Add results to the end of the container. More...
 
 CMagicBlastResultSet::CMagicBlastResultSet (const CMagicBlastResultSet &)
 
CMagicBlastResultSetCMagicBlastResultSet::operator= (const CMagicBlastResultSet &)
 
 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 ()
 
bool CMagicBlastOptionsHandle::GetLookupDbFilter () const
 Return db filtering option for the lookup table. More...
 
void CMagicBlastOptionsHandle::SetLookupDbFilter (bool b)
 Set db filtering option for the lookup table. More...
 
Uint1 CMagicBlastOptionsHandle::GetMaxDbWordCount (void) const
 Get maximum word count for lookup table word masking by database frequency. More...
 
void CMagicBlastOptionsHandle::SetMaxDbWordCount (Uint1 num)
 Set maximum word count for lookup table word masking by database frequency. More...
 
int CMagicBlastOptionsHandle::GetLookupTableStride () const
 Return number of words skipped betweem collected ones when creating a lookup table. More...
 
void CMagicBlastOptionsHandle::SetLookupTableStride (int s)
 Set lookup table stride: number of words skipped between collected ones when creating a lookup table. More...
 
bool CMagicBlastOptionsHandle::GetReadQualityFiltering () const
 Return true if query quality filtering is on. More...
 
void CMagicBlastOptionsHandle::SetReadQualityFiltering (bool val=true)
 Turn on/off query quaility filtering with default parameters. More...
 
double CMagicBlastOptionsHandle::GetMaxFractionAmbiguous () const
 Get maximum fraction of ambiguous bases for query quality filtering. More...
 
void CMagicBlastOptionsHandle::SetMaxFractionAmbiguous (double val)
 Get maximum fraction of ambiguous bases for query quality filtering. More...
 
int CMagicBlastOptionsHandle::GetMinDimerEntropy () const
 Get mininum dimer entropy for query quality filtering. More...
 
void CMagicBlastOptionsHandle::SetMinDimerEntropy (int val)
 Set minimum dimer entropy for query quality filtering. More...
 
int CMagicBlastOptionsHandle::GetWordSize () const
 Return word size. More...
 
void CMagicBlastOptionsHandle::SetWordSize (int w)
 Set word size. More...
 
int CMagicBlastOptionsHandle::GetGapXDropoff () const
 Return x-dropoff parameter for gapped alignment. More...
 
void CMagicBlastOptionsHandle::SetGapXDropoff (int d)
 Set x-dropoff parameter for gapped alignment. More...
 
int CMagicBlastOptionsHandle::GetMismatchPenalty () const
 Returns mismatch penalty. More...
 
void CMagicBlastOptionsHandle::SetMismatchPenalty (int p)
 Sets mismatch penalty. More...
 
int CMagicBlastOptionsHandle::GetGapOpeningCost () const
 Return gap opening cost. More...
 
void CMagicBlastOptionsHandle::SetGapOpeningCost (int g)
 Set gap opening cost. More...
 
int CMagicBlastOptionsHandle::GetGapExtensionCost () const
 Return gap extension cost. More...
 
void CMagicBlastOptionsHandle::SetGapExtensionCost (int g)
 Sets gap extension cost. More...
 
int CMagicBlastOptionsHandle::GetCutoffScore () const
 Return a single alignment cutoff score. More...
 
void CMagicBlastOptionsHandle::SetCutoffScore (int s)
 Set a single alignment cutoff score. More...
 
vector< double > CMagicBlastOptionsHandle::GetCutoffScoreCoeffs ()
 Get coefficients for alignment cutoff score as a linear function of query length: x[0] + x[1] * length. More...
 
void CMagicBlastOptionsHandle::SetCutoffScoreCoeffs (const vector< double > &c)
 Set coefficients for alignment cutoff score as a linear function of query length: x[0] + x[1] * length. More...
 
int CMagicBlastOptionsHandle::GetMaxEditDistance () const
 
void CMagicBlastOptionsHandle::SetMaxEditDistance (int e)
 
bool CMagicBlastOptionsHandle::GetPaired () const
 Are the mapping reads assumed paired. More...
 
void CMagicBlastOptionsHandle::SetPaired (bool p)
 Set input reads as paired/not paired. More...
 
bool CMagicBlastOptionsHandle::GetSpliceAlignments () const
 Return the splice/unsplice alignments switch value. More...
 
void CMagicBlastOptionsHandle::SetSpliceAlignments (bool s)
 Set splicing alignments. More...
 
int CMagicBlastOptionsHandle::GetLongestIntronLength (void) const
 Get max intron length. More...
 
void CMagicBlastOptionsHandle::SetLongestIntronLength (int len)
 Set max intron length. More...
 
virtual void CMagicBlastOptionsHandle::SetRemoteProgramAndService_Blast3 ()
 Set the program and service name for remote blast. More...
 
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...
 
 CMagicBlastOptionsHandle::CMagicBlastOptionsHandle (const CMagicBlastOptionsHandle &rhs)
 Disallow copy constructor. More...
 
CMagicBlastOptionsHandleCMagicBlastOptionsHandle::operator= (const CMagicBlastOptionsHandle &rhs)
 Disallow assignment operator. 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::Process ()
 The work to process the alignment is done here. More...
 
unsigned char * CPsiBlastInputClustalW::GetQuery ()
 Get the query sequence used as master for the multiple sequence alignment in ncbistdaa encoding. More...
 
unsigned int CPsiBlastInputClustalW::GetQueryLength ()
 Get the query's length. More...
 
PSIMsaCPsiBlastInputClustalW::GetData ()
 Obtain the multiple sequence alignment structure. More...
 
const PSIBlastOptionsCPsiBlastInputClustalW::GetOptions ()
 Obtain the options for the PSSM engine. More...
 
const char * CPsiBlastInputClustalW::GetMatrixName ()
 Obtain the name of the underlying matrix to use when building the PSSM. More...
 
int CPsiBlastInputClustalW::GetGapExistence ()
 Obtain the gap existence value to use when building the PSSM. More...
 
int CPsiBlastInputClustalW::GetGapExtension ()
 Obtain the gap extension value to use when building the PSSM. More...
 
const PSIDiagnosticsRequestCPsiBlastInputClustalW::GetDiagnosticsRequest ()
 Obtain the diagnostics data that is requested from the PSSM engine. More...
 
CRef< objects::CBioseq > CPsiBlastInputClustalW::GetQueryForPssm ()
 @inheritDoc More...
 
void CPsiBlastInputClustalW::x_ReadAsciiMsa (CNcbiIstream &input_file)
 Reads the multiple sequence alignment from the input file. 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_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_CopyQueryToMsa ()
 Copies query sequence data to multiple alignment data structure. More...
 
void CPsiBlastInputClustalW::x_ExtractAlignmentData ()
 Populates the multiple alignment data structure. More...
 
void CPsiBlastInputClustalW::x_ExtractQueryForPssm ()
 Extracts the query bioseq from m_SeqEntry. More...
 
 CPsiBlastInputClustalW::CPsiBlastInputClustalW (const CPsiBlastInputClustalW &)
 prohibit copy constructor More...
 
CPsiBlastInputClustalWCPsiBlastInputClustalW::operator= (const CPsiBlastInputClustalW &)
 prohibit assignment operator 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...
 
TSeqLocInfoVector CObjMgr_QueryFactory::ExtractUserSpecifiedMasks ()
 Retrieve any user specified masking locations. More...
 
TSeqLocVector CObjMgr_QueryFactory::GetTSeqLocVector ()
 Retrieves the TSeqLocVector used to construct this object or a conversion of the CBlastQueryVector provided. 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_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...
 
 CPHIBlastNuclOptionsHandle::~CPHIBlastNuclOptionsHandle ()
 
const char * CPHIBlastNuclOptionsHandle::GetPHIPattern () const
 Retrieves the pattern string option. More...
 
void CPHIBlastNuclOptionsHandle::SetPHIPattern (const char *p)
 Sets the pattern string option. More...
 
 CPHIBlastNuclOptionsHandle::CPHIBlastNuclOptionsHandle (const CPHIBlastNuclOptionsHandle &rhs)
 Disallow copy constructor. More...
 
CPHIBlastNuclOptionsHandleCPHIBlastNuclOptionsHandle::operator= (const CPHIBlastNuclOptionsHandle &rhs)
 Disallow assignment operator. More...
 
 CPHIBlastProtOptionsHandle::CPHIBlastProtOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
 Creates object with default options set. More...
 
 CPHIBlastProtOptionsHandle::~CPHIBlastProtOptionsHandle ()
 
const char * CPHIBlastProtOptionsHandle::GetPHIPattern () const
 Retrieves the pattern string option. More...
 
void CPHIBlastProtOptionsHandle::SetPHIPattern (const char *p)
 Sets the pattern string option. More...
 
 CPHIBlastProtOptionsHandle::CPHIBlastProtOptionsHandle (const CPHIBlastProtOptionsHandle &rhs)
 Disallow copy constructor. More...
 
CPHIBlastProtOptionsHandleCPHIBlastProtOptionsHandle::operator= (const CPHIBlastProtOptionsHandle &rhs)
 Disallow assignment operator. 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...
 
CRef< SInternalDataCBlastPrelimSearch::Run ()
 Borrow the internal data and results results. More...
 
virtual void CBlastPrelimSearch::SetNumberOfThreads (size_t nthreads)
 @inheritDoc 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...
 
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...
 
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...
 
bool CBlastPrelimSearch::Run (vector< list< CRef< CStd_seg > > > &results)
 
const TSeqLocInfoVectorCBlastPrelimSearch::GetQueryMasks (void) const
 Return query masks. More...
 
 CBlastPrelimSearch::CBlastPrelimSearch (const CBlastPrelimSearch &rhs)
 Prohibit copy constructor. More...
 
CBlastPrelimSearchCBlastPrelimSearch::operator= (const CBlastPrelimSearch &rhs)
 Prohibit assignment operator. 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...
 
bool CBlastPrelimSearch::x_BuildStdSegList (vector< list< CRef< CStd_seg > > > &list)
 
 CPsiBlastInputFreqRatios::CPsiBlastInputFreqRatios (const unsigned char *query, unsigned int query_length, const CNcbiMatrix< double > &freq_ratios, const char *matrix_name=NULL, int gap_existence=0, int gap_extension=0, double impala_scale_factor=0)
 Constructor. More...
 
void CPsiBlastInputFreqRatios::Process ()
 No-op as we assume the data is passed in to the constructor. More...
 
unsigned char * CPsiBlastInputFreqRatios::GetQuery ()
 @inheritDoc More...
 
unsigned int CPsiBlastInputFreqRatios::GetQueryLength ()
 Get the query's length. More...
 
const char * CPsiBlastInputFreqRatios::GetMatrixName ()
 Obtain the name of the underlying matrix to use when building the PSSM. More...
 
int CPsiBlastInputFreqRatios::GetGapExistence ()
 Obtain the gap existence value to use when building the PSSM. More...
 
int CPsiBlastInputFreqRatios::GetGapExtension ()
 Obtain the gap extension value to use when building the PSSM. More...
 
double CPsiBlastInputFreqRatios::GetImpalaScaleFactor ()
 Obtain the IMPALA Scale Factor value to use when building the PSSM. More...
 
const CNcbiMatrix< double > & CPsiBlastInputFreqRatios::GetData ()
 Obtain a matrix of frequency ratios with this->GetQueryLength() columns and BLASTAA_SIZE rows. More...
 
 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...
 
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...
 
PSIMsaCPsiBlastInputData::GetData ()
 Obtain the multiple sequence alignment structure. 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...
 
int CPsiBlastInputData::GetGapExistence ()
 Obtain the gap existence value to use when building the PSSM. More...
 
int CPsiBlastInputData::GetGapExtension ()
 Obtain the gap extension value to use when building the PSSM. More...
 
const PSIDiagnosticsRequestCPsiBlastInputData::GetDiagnosticsRequest ()
 Obtain the diagnostics data that is requested from the PSSM engine. More...
 
CRef< objects::CBioseq > CPsiBlastInputData::GetQueryForPssm ()
 @inheritDoc More...
 
static void CPsiBlastInputData::x_GetSubjectSequence (const objects::CDense_seg &ds, objects::CScope &scope, string &sequence_data)
 Tries to fetch the sequence data for the subject for the segments specified in the Dense-seg. 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...
 
void CPsiBlastInputData::x_ExtractAlignmentData ()
 Populates the multiple alignment data structure. More...
 
void CPsiBlastInputData::x_CopyQueryToMsa ()
 Copies query sequence data to multiple alignment data structure. More...
 
unsigned int CPsiBlastInputData::GetNumAlignedSequences () const
 Returns the number of sequences that make up the multiple sequence alignment. More...
 
void CPsiBlastInputData::x_ProcessDenseg (const objects::CDense_seg &denseg, unsigned int msa_index, double evalue, double bit_score)
 Iterates over the Dense-seg passed in and extracts alignment information to multiple alignment data structure. More...
 
void CPsiBlastInputData::x_ExtractQueryForPssm ()
 Extracts the query bioseq from m_SeqAlignSet. More...
 
 CPsiBlastInputData::CPsiBlastInputData (const CPsiBlastInputData &)
 prohibit copy constructor More...
 
CPsiBlastInputDataCPsiBlastInputData::operator= (const CPsiBlastInputData &)
 prohibit assignment operator More...
 
 CPsiBl2Seq::CPsiBl2Seq (CRef< objects::CPssmWithParameters > pssm, CRef< IQueryFactory > subject, CConstRef< CPSIBlastOptionsHandle > options)
 Constructor to compare a PSSM against protein sequences. More...
 
 CPsiBl2Seq::CPsiBl2Seq (CRef< objects::CPssmWithParameters > pssm, CRef< CLocalDbAdapter > subject, CConstRef< CPSIBlastOptionsHandle > options)
 Constructor to compare a PSSM against protein sequences. More...
 
 CPsiBl2Seq::CPsiBl2Seq (CRef< IQueryFactory > query, CRef< IQueryFactory > subject, CConstRef< CBlastProteinOptionsHandle > options)
 Constructor to compare protein sequences in an object manager-free manner. More...
 
 CPsiBl2Seq::~CPsiBl2Seq ()
 Destructor. More...
 
CRef< CSearchResultSetCPsiBl2Seq::Run ()
 Run the PSI-BLAST 2 Sequences engine. More...
 
void CPsiBl2Seq::x_InitSubject (CRef< IQueryFactory > subject, const CBlastOptionsHandle *options)
 Auxiliary method to initialize the subject. More...
 
 CPsiBl2Seq::CPsiBl2Seq (const CPsiBl2Seq &rhs)
 Prohibit copy constructor. More...
 
CPsiBl2SeqCPsiBl2Seq::operator= (const CPsiBl2Seq &rhs)
 Prohibit assignment operator. More...
 
 CPsiBlast::CPsiBlast (CRef< IQueryFactory > query_factory, CRef< CLocalDbAdapter > blastdb, CConstRef< CPSIBlastOptionsHandle > options)
 Constructor to compare a single sequence against a database of protein sequences. More...
 
 CPsiBlast::CPsiBlast (CRef< objects::CPssmWithParameters > pssm, CRef< CLocalDbAdapter > blastdb, CConstRef< CPSIBlastOptionsHandle > options)
 Constructor to compare a PSSM against a database of protein sequences. More...
 
 CPsiBlast::~CPsiBlast ()
 Destructor. More...
 
void CPsiBlast::SetPssm (CConstRef< objects::CPssmWithParameters > pssm)
 This method allows the same object to be reused when performing multiple iterations. More...
 
CConstRef< objects::CPssmWithParameters > CPsiBlast::GetPssm () const
 Accessor for the most recently used PSSM. More...
 
CRef< CSearchResultSetCPsiBlast::Run ()
 Run the PSI-BLAST engine for one iteration. More...
 
 CPsiBlast::CPsiBlast (const CPsiBlast &rhs)
 Prohibit copy constructor. More...
 
CPsiBlastCPsiBlast::operator= (const CPsiBlast &rhs)
 Prohibit assignment operator. 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...
 
 CPsiBlastIterationState::CPsiBlastIterationState (unsigned int num_iterations=1)
 Constructor. More...
 
 CPsiBlastIterationState::~CPsiBlastIterationState ()
 Destructor. More...
 
 CPsiBlastIterationState::operator bool ()
 Allow implicit conversion to a boolean value, returning true if there are more iterations to perform or false if iterations are done. More...
 
bool CPsiBlastIterationState::HasConverged ()
 Determines if the PSI-BLAST search has converged (i.e. More...
 
bool CPsiBlastIterationState::HasMoreIterations () const
 Determines if more iterations are still needed. More...
 
TSeqIds CPsiBlastIterationState::GetPreviouslyFoundSeqIds () const
 Retrieve the set of Seq-id's found in the previous iteration. More...
 
void CPsiBlastIterationState::Advance (const TSeqIds &list)
 Advance the iterator by passing it the list of Seq-ids which passed the inclusion criteria for the current iteration. More...
 
static void CPsiBlastIterationState::GetSeqIds (CConstRef< objects::CSeq_align_set > seqalign, CConstRef< CPSIBlastOptionsHandle > opts, TSeqIds &retval)
 Extract the sequence ids from the sequence alignment which identify those sequences that will be used for PSSM construction. More...
 
unsigned int CPsiBlastIterationState::GetIterationNumber () const
 Return the number of the current iteration. More...
 
 CPsiBlastIterationState::CPsiBlastIterationState (const CPsiBlastIterationState &rhs)
 Prohibit copy constructor. More...
 
CPsiBlastIterationStateCPsiBlastIterationState::operator= (const CPsiBlastIterationState &rhs)
 Prohibit assignment operator. More...
 
void CPsiBlastIterationState::x_ThrowExceptionOnLogicError ()
 After the iteration state object has converged or exhausted its iterations, it shouldn't be modified, so it throws a CBlastException if this happens. More...
 
 CPSIBlastOptionsHandle::CPSIBlastOptionsHandle (EAPILocality locality=CBlastOptions::eLocal)
 Creates object with default options set. More...
 
 CPSIBlastOptionsHandle::CPSIBlastOptionsHandle (CRef< CBlastOptions > opt)
 
 CPSIBlastOptionsHandle::~CPSIBlastOptionsHandle ()
 Destructor. More...
 
double CPSIBlastOptionsHandle::GetInclusionThreshold () const
 Returns InclusionThreshold. More...
 
void CPSIBlastOptionsHandle::SetInclusionThreshold (double incthr)
 Sets InclusionThreshold. More...
 
int CPSIBlastOptionsHandle::GetPseudoCount () const
 Returns PseudoCount. More...
 
void CPSIBlastOptionsHandle::SetPseudoCount (int p)
 Sets PseudoCount. More...
 
void CPSIBlastOptionsHandle::SetPSITblastnDefaults ()
 Sets default options for psi tblastn search. More...
 
virtual void CPSIBlastOptionsHandle::SetRemoteProgramAndService_Blast3 ()
 Set the program and service name for remote blast. More...
 
virtual void CPSIBlastOptionsHandle::SetQueryOptionDefaults ()
 Override the parent class' default for filtering query sequence (i.e. More...
 
void CPSIBlastOptionsHandle::SetPSIBlastDefaults ()
 Sets PSIBlastDefaults. More...
 
 CPSIBlastOptionsHandle::CPSIBlastOptionsHandle (const CPSIBlastOptionsHandle &rhs)
 Disallow copy constructor. More...
 
CPSIBlastOptionsHandleCPSIBlastOptionsHandle::operator= (const CPSIBlastOptionsHandle &rhs)
 Disallow assignment operator. More...
 
virtual const char * CPssmEngineException::GetErrCodeString (void) const override
 Translate from the error code value to its string representation. More...
 
 CPssmEngineException::NCBI_EXCEPTION_DEFAULT (CPssmEngineException, CBlastException)
 
 CPssmEngine::CPssmEngine (IPssmInputData *input)
 Constructor to configure the PSSM engine with a PSSM input data strategy object Checks that no data returned by the IPssmInputData interface is NULL. More...
 
 CPssmEngine::CPssmEngine (IPssmInputFreqRatios *input)
 Constructor to perform the last 2 stages of the PSSM creation algorithm Checks that no data returned by the IPssmInputFreqRatios interface is NULL. More...
 
 CPssmEngine::CPssmEngine (IPssmInputCdd *input)
 Constructor to configure the PSSM engine with a PSSM input data strategy object for CDD-based PSSM computation. More...
 
 CPssmEngine::~CPssmEngine ()
 Destructor. More...
 
void CPssmEngine::SetUngappedStatisticalParams (CConstRef< CBlastAncillaryData > ancillary_data)
 Sets the Karlin & Altschul parameters in the BlastScoreBlk to be used in PSSM generation. More...
 
CRef< objects::CPssmWithParameters > CPssmEngine::Run ()
 Runs the PSSM engine to compute the PSSM. More...
 
static unsigned char * CPssmEngine::x_GuardProteinQuery (const unsigned char *query, unsigned int query_length)
 Copies query sequence and adds protein sentinel bytes at the beginning and at the end of the sequence. More...
 
BlastQueryInfoCPssmEngine::x_InitializeQueryInfo (unsigned int query_length)
 Initialiazes the core BlastQueryInfo structure for a single protein sequence. More...
 
void CPssmEngine::x_InitializeScoreBlock (const unsigned char *query, unsigned int query_length, const char *matrix_name, int gap_existence, int gap_extension)
 Initializes the BlastScoreBlk data member required to run the PSSM engine. More...
 
unsigned char * CPssmEngine::x_GetQuery () const
 Private interface to retrieve query sequence from its data source interface. More...
 
unsigned int CPssmEngine::x_GetQueryLength () const
 Private interface to retrieve query length from its data source interface. More...
 
const char * CPssmEngine::x_GetMatrixName () const
 Private interface to retrieve matrix name from its data source interface. More...
 
int CPssmEngine::x_GetGapExistence () const
 Private interface to retrieve gap existence cost from data source. More...
 
int CPssmEngine::x_GetGapExtension () const
 Private interface to retrieve gap extension cost from data source. More...
 
CRef< objects::CPssmWithParameters > CPssmEngine::x_CreatePssmFromMsa ()
 Using IPssmInputData as a delegate to provide input data in the form of a multiple sequence alignment, creates a PSSM using the CORE C PSSM engine API. More...
 
CRef< objects::CPssmWithParameters > CPssmEngine::x_CreatePssmFromFreqRatios ()
 Using IPssmInputFreqRatios as a delegate to provide the input PSSM's frequency ratios, creates a PSSM using the CORE C PSSM engine API. More...
 
CRef< objects::CPssmWithParameters > CPssmEngine::x_CreatePssmFromCDD ()
 Using IPssmInputCdd as a delegate to provide data in the form of multiple alignment of CDs, creates PSSM using the CORE C PSSM engine API. More...
 
static CRef< objects::CPssmWithParameters > CPssmEngine::x_PSIMatrix2Asn1 (const PSIMatrix *pssm, const char *matrix_name, const PSIBlastOptions *opts=NULL, const PSIDiagnosticsResponse *diagnostics=NULL)
 Converts the PSIMatrix structure into a ASN.1 CPssmWithParameters object. More...
 
static std::string CPssmEngine::x_ErrorCodeToString (int error_code)
 Convert a PSSM return status into a string. More...
 
 CPssmEngine::CPssmEngine ()
 Default constructor available for derived test classes. More...
 
 CPssmEngine::CPssmEngine (const CPssmEngine &rhs)
 Prohibit copy constructor. More...
 
CPssmEngineCPssmEngine::operator= (const CPssmEngine &rhs)
 Prohibit assignment operator. More...
 
static CNcbiMatrix< int > * CScorematPssmConverter::GetScores (const objects::CPssmWithParameters &pssm)
 Returns matrix of BLASTAA_SIZE by query size (dimensions are opposite of what is stored in the BlastScoreBlk) containing scores. More...
 
static CNcbiMatrix< double > * CScorematPssmConverter::GetFreqRatios (const objects::CPssmWithParameters &pssm)
 Returns matrix of BLASTAA_SIZE by query size (dimensions are opposite of what is stored in the BlastScoreBlk) containing frequency ratios. More...
 
static void CScorematPssmConverter::GetInformationContent (const objects::CPssmWithParameters &pssm, vector< double > &retval)
 Returns the information content per position of the PSSM. More...
 
static void CScorematPssmConverter::GetGaplessColumnWeights (const objects::CPssmWithParameters &pssm, vector< double > &retval)
 Returns the relative gapless PSSM column weights to pseudocounts for the provided PSSM. More...
 
static CNcbiMatrix< int > * CScorematPssmConverter::GetResidueFrequencies (const objects::CPssmWithParameters &pssm)
 Returns matrix of BLASTAA_SIZE by query size (dimensions are opposite of what is stored in the BlastScoreBlk) containing the residue frequencies per position of the PSSM. More...
 
static CNcbiMatrix< double > * CScorematPssmConverter::GetWeightedResidueFrequencies (const objects::CPssmWithParameters &pssm)
 Returns matrix of BLASTAA_SIZE by query size (dimensions are opposite of what is stored in the BlastScoreBlk) containing the weighted residue frequencies per position of the PSSM. More...
 
static void CScorematPssmConverter::GetSigma (const objects::CPssmWithParameters &pssm, vector< double > &retval)
 Data used in sequence weights computation. More...
 
static void CScorematPssmConverter::GetIntervalSizes (const objects::CPssmWithParameters &pssm, vector< int > &retval)
 Length of the aligned regions per position of the query sequence. More...
 
static void CScorematPssmConverter::GetNumMatchingSeqs (const objects::CPssmWithParameters &pssm, vector< int > &retval)
 Gets the number of matching sequences per position of the PSSM. More...
 
virtual IPssmInput_Base::~IPssmInput_Base ()
 virtual destructor More...
 
virtual unsigned char * IPssmInput_Base::GetQuery ()=0
 Get the query sequence used as master for the multiple sequence alignment in ncbistdaa encoding. More...
 
virtual unsigned int IPssmInput_Base::GetQueryLength ()=0
 Get the query's length. More...
 
virtual const char * IPssmInput_Base::GetMatrixName ()
 Obtain the name of the underlying matrix to use when building the PSSM. More...
 
virtual int IPssmInput_Base::GetGapExistence ()
 Obtain the gap existence value for the underlying matrix used to build the PSSM. More...
 
virtual int IPssmInput_Base::GetGapExtension ()
 Obtain the gap extension value for the underlying matrix used to build the PSSM. More...
 
virtual CRef< objects::CBioseq > IPssmInput_Base::GetQueryForPssm ()
 Get a CBioseq object for attachment into the CPssmWithParameters that CPssmEngine produces (only attached if it's not NULL). More...
 
virtual IPssmInputData::~IPssmInputData ()
 virtual destructor More...
 
virtual void IPssmInputData::Process ()=0
 Algorithm to produce multiple sequence alignment structure should be implemented in this method. More...
 
virtual PSIMsaIPssmInputData::GetData ()=0
 Obtain the multiple sequence alignment structure. More...
 
virtual const PSIBlastOptionsIPssmInputData::GetOptions ()=0
 Obtain the options for the PSSM engine. More...
 
virtual const PSIDiagnosticsRequestIPssmInputData::GetDiagnosticsRequest ()
 Obtain the diagnostics data that is requested from the PSSM engine Its results will be populated in the PssmWithParameters ASN.1 object. More...
 
virtual IPssmInputFreqRatios::~IPssmInputFreqRatios ()
 virtual destructor More...
 
virtual void IPssmInputFreqRatios::Process ()=0
 Algorithm to produce the PSSM's frequecy ratios should be implemented in this method. More...
 
virtual const CNcbiMatrix< double > & IPssmInputFreqRatios::GetData ()=0
 Obtain a matrix of frequency ratios with this->GetQueryLength() columns and BLASTAA_SIZE rows. More...
 
virtual double IPssmInputFreqRatios::GetImpalaScaleFactor ()
 
 ILocalQueryData::ILocalQueryData ()