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

Files

file  aa_ungapped.c [code]
 Functions to iterate over seed hits and perform ungapped extensions.
 
file  blast_aalookup.c [code]
 Functions interacting with the protein BLAST lookup table.
 
file  blast_aascan.c [code]
 Functions for accessing hits in the protein BLAST lookup table.
 
file  blast_diagnostics.c [code]
 Manipulating diagnostics data returned from BLAST.
 
file  blast_dynarray.c [code]
 Definitions for various dynamic array types.
 
file  blast_dynarray.h [code]
 Declarations for various dynamic array types.
 
file  blast_encoding.c [code]
 Definitions of static arrays defined in blast_encoding.h.
 
file  blast_engine.c [code]
 Function calls to actually perform a BLAST search (high level).
 
file  blast_extend.c [code]
 Functions to initialize structures used for BLAST extension.
 
file  blast_filter.c [code]
 All code related to query sequence masking/filtering for BLAST.
 
file  blast_gapalign.c [code]
 Functions to perform gapped alignment.
 
file  blast_gapalign_priv.h [code]
 Private interface for blast_gapalign.c.
 
file  blast_hits.c [code]
 BLAST functions for saving hits after the (preliminary) gapped alignment.
 
file  blast_hits_priv.h [code]
 Utilities for dealing with BLAST HSPs in the core of BLAST.
 
file  blast_hspstream.c [code]
 BlastHSPStream is used to save hits from preliminary stage and pass on to the traceback stage.
 
file  blast_hspstream_mt_utils.c [code]
 Private interfaces to support the multi-threaded traceback in conjunction with the BlastHSPStream.
 
file  blast_hspstream_mt_utils.h [code]
 Private interfaces to support the multi-threaded traceback in conjunction with the BlastHSPStream.
 
file  blast_itree.c [code]
 Functions that implement an interval tree for fast HSP containment tests.
 
file  blast_itree.h [code]
 Interface for an interval tree, used for fast HSP containment tests.
 
file  blast_kappa.c [code]
 Utilities for doing Smith-Waterman alignments and adjusting the scoring system for each match in blastpgp.
 
file  blast_lookup.c [code]
 Functions that provide generic services for BLAST lookup tables.
 
file  blast_message.c [code]
 These functions provide access to Blast_Message objects, used by the BLAST code as a wrapper for error and warning messages.
 
file  blast_nalookup.c [code]
 Functions for constructing nucleotide blast lookup tables.
 
file  blast_nascan.c [code]
 Functions for scanning nucleotide BLAST lookup tables.
 
file  blast_options.c [code]
 The structures and functions in blast_options.
 
file  blast_parameters.c [code]
 Definitions for functions dealing with BLAST CORE parameter structures.
 
file  blast_posit.c [code]
 Port of posit.c/posit2.c to implement composition based statistics for PSI-BLAST.
 
file  blast_posit.h [code]
 Port of posit.h structures and impalaScaling for implementing composition based statistics for PSI-BLAST.
 
file  blast_program.c [code]
 Implementation auxiliary functions to determine traits of the various BLAST programs supported by core BLAST.
 
file  blast_psi.c [code]
 Implementation of the high level functions of PSI-BLAST's PSSM engine.
 
file  blast_psi_priv.c [code]
 Defintions for functions in private interface for Position Iterated BLAST API.
 
file  blast_psi_priv.h [code]
 Private interface for Position Iterated BLAST API, contains the PSSM generation engine.
 
file  blast_query_info.c [code]
 Functions to manipulate the BlastQueryInfo structure.
 
file  blast_seg.c [code]
 A utility to find low complexity AA regions.
 
file  blast_seqsrc.c [code]
 Definition of ADT to retrieve sequences for the BLAST engine and low level details of the implementation of the BlastSeqSrc framework.
 
file  blast_setup.c [code]
 Utilities initialize/setup BLAST.
 
file  blast_stat.c [code]
 Functions to calculate BLAST probabilities etc.
 
file  blast_sw.c [code]
 Smith-Waterman gapped alignment, for use with infrastructure of BLAST.
 
file  blast_traceback.c [code]
 Functions responsible for the traceback stage of the BLAST algorithm.
 
file  blast_traceback_mt_priv.c [code]
 Private interface to support the multi-threaded traceback.
 
file  blast_traceback_mt_priv.h [code]
 Private interface to support the multi-threaded traceback.
 
file  blast_tune.c [code]
 Routines that compute a blastn word size appropriate for finding, with high probability, alignments with specified length and percent identity.
 
file  blast_util.c [code]
 Various BLAST utilities.
 
file  boost_erf.c [code]
 
file  boost_erf.h [code]
 
file  gapinfo.c [code]
 Initialization and freeing of structures containing traceback information.
 
file  gencode_singleton.c [code]
 Implementation of the genetic code singleton.
 
file  greedy_align.c [code]
 Functions to perform greedy affine and non-affine gapped alignment.
 
file  hspfilter_besthit.c [code]
 Implementation of the BlastHSPWriter interface to save only best hits from a BLAST search, and subsequently return them in sorted order.
 
file  hspfilter_collector.c [code]
 Default implementation of the BlastHSPWriter interface to save hits from a BLAST search, and subsequently return them in sorted order.
 
file  hspfilter_culling.c [code]
 Implementation of the BlastHSPWriter interface to perform culling.
 
file  hspfilter_mapper.c [code]
 Implementation of the BlastHSPWriter interface to save only the best scoring * chains of HSPs for aligning RNA-Seq sequences to a genome.
 
file  index_ungapped.c [code]
 Definitions of functions needed to implement diagonal hash to support ungapped extensions for indexed version of megablast.
 
file  index_ungapped.h [code]
 Declarations of structures needed to implement diagonal hash to support ungapped extensions for indexed version of megablast.
 
file  jumper.c [code]
 
file  jumper.h [code]
 
 
file  lookup_util.c [code]
 Utility functions for lookup table generation.
 
file  lookup_wrap.c [code]
 Wrapper for different flavors of lookup tables allowing a uniform interface in the code.
 
file  masksubj.inl [code]
 
file  matrix_freq_ratios.c [code]
 Definitions for various scoring matrices' frequency ratios.
 
file  matrix_freq_ratios.h [code]
 Interface to retrieve the frequency ratios for various scoring matrices.
 
file  na_ungapped.c [code]
 Nucleotide ungapped extension routines.
 
file  ncbi_erf.c [code]
 
file  ncbi_math.c [code]
 Definitions for portable math library.
 
file  ncbi_std.c [code]
 A few utilities needed by code in algo/blast/core but not provided elsewhere.
 
file  pattern.c [code]
 Functions for finding pattern matches in sequence.
 
file  pattern_priv.h [code]
 Auxiliary functions for finding pattern matches in sequence (PHI-BLAST), that are used in multiple source files.
 
file  phi_extend.c [code]
 Word finder functions for PHI-BLAST.
 
file  phi_gapalign.c [code]
 Functions to perform gapped alignment in PHI BLAST.
 
file  phi_lookup.c [code]
 Functions for accessing the lookup table for PHI-BLAST.
 
file  spliced_hits.c [code]
 
file  split_query.c [code]
 
Modified on Mon Apr 22 04:04:23 2024 by modify_doxy.py rev. 669887