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_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 | link_hsps.c [code] |
| Functions to link with use of sum statistics. | |
| 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] |
