NCBI C++ ToolKit
api Directory Reference
+ Directory dependency graph for api:

Files

file  bioseq_extract_data_priv.cpp [code]
 Implementations of CBlastQuerySourceBioseqSet and CBlastSeqVectorFromCSeq_data classes.
 
file  bioseq_extract_data_priv.hpp [code]
 Internal auxiliary setup classes/functions for extracting sequence data from Bioseqs.
 
file  bl2seq.cpp [code]
 Implementation of CBl2Seq class.
 
file  blast_advprot_options.cpp [code]
 Implements the CBlastAdvancedProteinOptionsHandle class.
 
file  blast_aux.cpp [code]
 Implements C++ wrapper classes for structures in algo/blast/core as well as some auxiliary functions to convert CSeq_loc to/from BlastMask structures.
 
file  blast_aux_priv.cpp [code]
 Implements various auxiliary (private) functions for BLAST.
 
file  blast_aux_priv.hpp [code]
 Auxiliary functions for BLAST.
 
file  blast_dbindex.cpp [code]
 Functionality for indexed databases.
 
file  blast_memento_priv.hpp [code]
 Classes that capture the state of the BLAST options (or subsets of options) and restore them later (usually upon destruction) using the RAII idiom.
 
file  blast_mtlock.cpp [code]
 Initialization for the mutex locking interface.
 
file  blast_node.cpp [code]
 BLAST node api.
 
file  blast_nucl_options.cpp [code]
 Implements the CBlastNucleotideOptionsHandle class.
 
file  blast_objmgr_priv.hpp [code]
 Definitions which are dependant on the NCBI C++ Object Manager.
 
file  blast_objmgr_tools.cpp [code]
 Functions in xblast API code that interact with object manager.
 
file  blast_options_builder.cpp [code]
 Defines the CBlastOptionsBuilder class.
 
file  blast_options_cxx.cpp [code]
 Implements the CBlastOptions class, which encapsulates options structures from algo/blast/core.
 
file  blast_options_handle.cpp [code]
 Implementation for the CBlastOptionsHandle and the CBlastOptionsFactory classes.
 
file  blast_options_local_priv.cpp [code]
 Definition of local representation of BLAST options.
 
file  blast_options_local_priv.hpp [code]
 Private header for local representation of BLAST options.
 
file  blast_prot_options.cpp [code]
 Implements the CBlastProteinOptionsHandle class.
 
file  blast_results.cpp [code]
 Implementation of classes which constitute the results of running a BLAST search.
 
file  blast_rps_options.cpp [code]
 Implements the CBlastRPSOptionsHandle class.
 
file  blast_seqalign.cpp [code]
 Utility function to convert internal BLAST result structures into CSeq_align_set objects.
 
file  blast_seqalign.hpp [code]
 Utility function to convert internal BLAST result structures into objects::CSeq_align_set objects.
 
file  blast_seqinfosrc_aux.cpp [code]
 Implementation of auxiliary functions using IBlastSeqInfoSrc to retrieve ids and related sequence information.
 
file  blast_setup.hpp [code]
 Internal auxiliary setup classes/functions for C++ BLAST APIs.
 
file  blast_setup_cxx.cpp [code]
 Auxiliary setup functions for Blast objects interface.
 
file  blast_usage_report.cpp [code]
 BLAST usage report api.
 
file  blastp_kmer_options.cpp [code]
 Implements the CBlastpKmerOptionsHandle class.
 
file  blastx_options.cpp [code]
 Implements the CBlastxOptionsHandle class.
 
file  cdd_pssm_input.cpp [code]
 
file  deltablast.cpp [code]
 Implementation of CDeltaBlast.
 
file  deltablast_options.cpp [code]
 Implements the CDeltaBlastOptionsHandle class.
 
file  disc_nucl_options.cpp [code]
 Implements the CDiscNucleotideOptionsHandle class.
 
file  dust_filter.cpp [code]
 Calls sym dust lib in algo/dustmask and returns CSeq_locs for use by BLAST.
 
file  dust_filter.hpp [code]
 Calls sym dust lib in algo/dustmask and returns CSeq_locs for use by BLAST.
 
file  effsearchspace_calc.cpp [code]
 Defines auxiliary class to calculate the effective search space.
 
file  local_blast.cpp [code]
 NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on them until this notice is removed.
 
file  local_db_adapter.cpp [code]
 Defines class which provides internal BLAST database representations to the internal BLAST APIs.
 
file  local_search.cpp [code]
 This file implements the Uniform Blast Search Interface in terms of the local BLAST database search class NOTE: This is OBJECT MANAGER DEPENDANT because of its use of CDbBlast!
 
file  magicblast.cpp [code]
 Implementation of CMagicBlast.
 
file  magicblast_options.cpp [code]
 
file  msa_pssm_input.cpp [code]
 Implementation of the concrete strategy to obtain PSSM input data for PSI-BLAST from a multiple sequence alignment.
 
file  objmgr_query_data.cpp [code]
 NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on them until this notice is removed.
 
file  objmgrfree_query_data.cpp [code]
 NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on them until this notice is removed.
 
file  phiblast_nucl_options.cpp [code]
 Implements the CPHIBlastNuclOptionsHandle class.
 
file  phiblast_prot_options.cpp [code]
 Implements the CPHIBlastProtOptionsHandle class.
 
file  prelim_search_runner.hpp [code]
 Defines internal auxiliary functor object to run the preliminary stage of the BLAST search.
 
file  prelim_stage.cpp [code]
 NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on them until this notice is removed.
 
file  psi_pssm_input.cpp [code]
 Implementation of the concrete strategy to obtain PSSM input data for PSI-BLAST.
 
file  psibl2seq.cpp [code]
 Implementation of CPsiBl2Seq.
 
file  psiblast.cpp [code]
 Implementation of CPsiBlast.
 
file  psiblast_aux_priv.cpp [code]
 Definitions of auxiliary functions/classes for PSI-BLAST.
 
file  psiblast_aux_priv.hpp [code]
 Declarations of auxiliary functions/classes for PSI-BLAST.
 
file  psiblast_impl.cpp [code]
 Implements implementation class for PSI-BLAST and PSI-BLAST 2 Sequences.
 
file  psiblast_impl.hpp [code]
 Defines implementation class for PSI-BLAST and PSI-BLAST 2 Sequences.
 
file  psiblast_iteration.cpp [code]
 Defines class which represents the iteration state in PSI-BLAST.
 
file  psiblast_options.cpp [code]
 Implements the CPSIBlastOptionsHandle class.
 
file  pssm_engine.cpp [code]
 Implementation of the C++ API for the PSI-BLAST PSSM generation engine.
 
file  query_data.cpp [code]
 NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on them until this notice is removed.
 
file  remote_blast.cpp [code]
 Queueing and Polling code for Remote Blast API.
 
file  remote_search.cpp [code]
 This file implements the uniform Blast search interface in terms of the blast4 network API via the CRemoteBlast library.
 
file  repeats_filter_cxx.cpp [code]
 C++ version of repeats filtering.
 
file  rps_aux.cpp [code]
 Implements auxiliary classes to manage RPS-BLAST related C-structures.
 
file  rpsblast_local.cpp [code]
 
file  rpstblastn_options.cpp [code]
 Implements the CRPSTBlastnOptionsHandle class.
 
file  search_strategy.cpp [code]
 Imports and exports search strategies.
 
file  seedtop.cpp [code]
 Implements the CSeedTop class.
 
file  seqinfosrc_bioseq.cpp [code]
 Implementation of the concrete strategy for an IBlastSeqInfoSrc interface to retrieve sequence identifiers and lengths from a IQueryFactory object.
 
file  seqinfosrc_bioseq.hpp [code]
 Defines a concrete strategy for the IBlastSeqInfoSrc interface for sequence identifiers retrieval from a CBioseq/CBioseq_set object.
 
file  seqinfosrc_seqdb.cpp [code]
 Implementation of the concrete strategy for an IBlastSeqInfoSrc interface to retrieve sequence identifiers and lengths from a BLAST database.
 
file  seqinfosrc_seqvec.cpp [code]
 Implementation of the concrete strategy for an IBlastSeqInfoSrc interface to retrieve sequence identifiers and lengths from a vector of Seq-locs.
 
file  seqsrc_multiseq.cpp [code]
 Implementation of the BlastSeqSrc interface for a vector of sequence locations.
 
file  seqsrc_query_factory.cpp [code]
 Implementation of the BlastSeqSrc interface for a query factory.
 
file  seqsrc_query_factory.hpp [code]
 Implementation of the BlastSeqSrc interface for a query factory.
 
file  seqsrc_seqdb.cpp [code]
 Implementation of the BlastSeqSrc interface for a C++ BLAST databases API.
 
file  setup_factory.cpp [code]
 NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on them until this notice is removed.
 
file  split_query.hpp [code]
 Declares CQuerySplitter, a class to split the query sequence(s)
 
file  split_query_aux_priv.cpp [code]
 Auxiliary functions and classes to assist in query splitting.
 
file  split_query_aux_priv.hpp [code]
 Auxiliary functions and classes to assist in query splitting.
 
file  split_query_blk.cpp [code]
 Implementation of C++ wrapper for SSplitQueryBlk.
 
file  split_query_blk.hpp [code]
 Definition of C++ wrapper for SSplitQueryBlk.
 
file  split_query_cxx.cpp [code]
 Defines CQuerySplitter, a class to split the query sequence(s)
 
file  subj_ranges_set.cpp [code]
 Defines classes to maintain lists of subject offset ranges in sequence data for targetted retrieval during the traceback stage.
 
file  tblastn_options.cpp [code]
 Implements the CTBlastnOptionsHandle class.
 
file  tblastx_options.cpp [code]
 Implements the CTBlastxOptionsHandle class.
 
file  traceback_stage.cpp [code]
 NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on them until this notice is removed.
 
file  uniform_search.cpp [code]
 Implementation of the uniform BLAST search interface auxiliary classes.
 
file  version.cpp [code]
 Implementation of the BLAST engine's version and reference classes.
 
file  winmask_filter.cpp [code]
 Blast wrappers for WindowMasker filtering.
 
file  winmask_filter.hpp [code]
 Blast wrappers for WindowMasker filtering.
 
Modified on Sun Feb 25 03:09:26 2024 by modify_doxy.py rev. 669887