core Directory Reference

Directory dependency graph for core:

Files
file	aa_ungapped.h [code]
	Protein ungapped extension code.
file	blast_aalookup.h [code]
	Routines for creating protein BLAST lookup tables.
file	blast_aascan.h [code]
	Routines for creating protein BLAST lookup tables.
file	blast_def.h [code]
	Definitions used throughout BLAST.
file	blast_diagnostics.h [code]
	Various diagnostics (hit counts, etc.) returned from the BLAST engine.
file	blast_encoding.h [code]
	Declarations of static arrays used to define some NCBI encodings to be used in a toolkit independent manner by the BLAST engine.
file	blast_engine.h [code]
	Function calls to actually perform a BLAST search (high level).
file	blast_export.h [code]
	Defines to provide correct exporting from BLAST DLL in Windows.
file	blast_extend.h [code]
	Ungapped extension structures that are common to nucleotide and protein extension routines.
file	blast_filter.h [code]
	BLAST filtering functions.
file	blast_gapalign.h [code]
	Structures and functions prototypes used for BLAST gapped extension.
file	blast_hits.h [code]
	Structures and API used for saving BLAST hits.
file	blast_hspfilter.h [code]
	Declaration of ADT to filter and/or process HSPs in the BLAST engine.
file	blast_hspstream.h [code]
	Declaration of ADT to save and retrieve lists of HSPs in the BLAST engine.
file	blast_kappa.h [code]
	Header file for composition-based statistics.
file	blast_lookup.h [code]
	Common definitions for protein and nucleotide lookup tables.
file	blast_message.h [code]
	Structures for BLAST messages.
file	blast_nalookup.h [code]
	Routines for creating nucleotide BLAST lookup tables.
file	blast_nascan.h [code]
	Routines for scanning nucleotide BLAST lookup tables.
file	blast_options.h [code]
	The structures and functions in blast_options.
file	blast_parameters.h [code]
	Structure and function definitions for BLAST parameter structures, which are internal to the CORE of BLAST.
file	blast_program.h [code]
	Definitions for various programs supported by core BLAST.
file	blast_psi.h [code]
	High level definitions and declarations for the PSSM engine of PSI-BLAST.
file	blast_query_info.h [code]
	Definitions and functions associated with the BlastQueryInfo structure.
file	blast_rps.h [code]
	RPS BLAST structure definitions.
file	blast_seg.h [code]
	SEG filtering functions.
file	blast_seqsrc.h [code]
	Declaration of ADT to retrieve sequences for the BLAST engine.
file	blast_seqsrc_impl.h [code]
	Definitions needed for implementing the BlastSeqSrc interface and low level details of the implementation of the BlastSeqSrc framework.
file	blast_setup.h [code]
	Utilities initialize/setup BLAST.
file	blast_stat.h [code]
	Definitions and prototypes used by blast_stat.c to calculate BLAST statistics.
file	blast_sw.h [code]
	Smith-Waterman alignment for use within the infrastructure of BLAST.
file	blast_toolkit.h [code]
	Choose C++ basic defines.
file	blast_traceback.h [code]
	Functions to do gapped alignment with traceback.
file	blast_tune.h [code]
	Compute a blastn word size appropriate for finding, with high probability, alignments with specified length and percent identity.
file	blast_util.h [code]
	Various auxiliary BLAST utility functions.
file	gapinfo.h [code]
	Definitions of structures used for saving traceback information.
file	gencode_singleton.h [code]
	Defines the interface to interact with the genetic code singleton object.
file	greedy_align.h [code]
	Prototypes and structures for greedy gapped alignment.
file	hspfilter_besthit.h [code]
	Implementation of a number of BlastHSPWriters to save hits from a BLAST search, and subsequently return them in sorted order.
file	hspfilter_collector.h [code]
	Implementation of a number of BlastHSPWriters to save hits from a BLAST search, and subsequently return them in sorted order.
file	hspfilter_culling.h [code]
	Implementation of the BlastHSPWriter interface to perform culling.
file	hspfilter_mapper.h [code]
	Implementation of a number of BlastHSPWriters to save the best chain of RNA-Seq hits to a genome.
file	link_hsps.h [code]
	Functions to link HSPs using sum statistics.
file	lookup_util.h [code]
	Utility functions for lookup table generation.
file	lookup_wrap.h [code]
	Wrapper for all lookup tables used in BLAST.
file	mb_indexed_lookup.h [code]
	Declarations for functions that extract hits from indexed blast databases (specialized for megablast)
file	na_ungapped.h [code]
	Nucleotide ungapped extension code.
file	ncbi_math.h [code]
	Prototypes for portable math library (ported from C Toolkit)
file	ncbi_std.h [code]
	Type and macro definitions from C toolkit that are not defined in C++ toolkit.
file	pattern.h [code]
	Functions for finding pattern matches in sequence (PHI-BLAST).
file	phi_extend.h [code]
	Word finder for PHI-BLAST.
file	phi_gapalign.h [code]
	Function prototypes used for PHI BLAST gapped extension and gapped extension with traceback.
file	phi_lookup.h [code]
	Pseudo lookup table structure and database scanning functions used in PHI-BLAST.
file	spliced_hits.h [code]
file	split_query.h [code]