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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blast__options_8c_source.html below:

NCBI C++ ToolKit: src/algo/blast/core/blast_options.c Source File

(dust_options ==

)

(seg_options ==

)

(winmask_options) {

(*winmask_options ==

)

(*winmask_options)->taxid = 0;

(*winmask_options)->database =

;

(winmask_options);

(repeat_options);

(repeat_options ==

)

(*repeat_options ==

)

(*repeat_options ==

)

((*repeat_options)->database);

(*repeat_options)->database =

(db);

(*winmask_options ==

)

((*winmask_options)->database);

(*winmask_options)->database =

(db);

(read_quality_options) {

(read_quality_options);

(!read_quality_options) {

(!*read_quality_options) {

(*read_quality_options)->frac_ambig = 0.5;

(*read_quality_options)->entropy = 16;

(filter_options);

(*filter_options)->mask_at_hash =

;

(!opt1 && opt2)

(!opt1 && opt2)

(!opt1 && opt2)

(! (have1 || have2))

(have1 && ! have2) {

}

(! have1 && have2) {

(filter_options ==

)

(filter_options ==

)

(filter_options ==

)

);

);

);

);

);

(options ==

)

(*options ==

)

(options ==

)

(*options ==

)

(*options)->program_number = program;

);

);

xdrop_ungapped)

(xdrop_ungapped != 0)

(*options ==

)

(*options)->gap_x_dropoff_final =

(*options)->max_mismatches = 5;

(*options)->mismatch_window = 10;

(*options)->program_number = program;

x_dropoff_final)

(x_dropoff_final) {

(options ==

)

);

);

(options ==

)

(*options ==

)

(*options)->is_ooframe =

;

(*options)->gapped_calculation =

;

(*options)->program_number = program_number;

(*options)->complexity_adjusted_scoring =

;

*matrix,

gap_open,

gap_extend)

options->

= reward;

(greedy_extension) {

(options ==

)

);

);

);

);

(status == 2)

);

(old_opt ==

|| new_opt ==

)

(*new_opt ==

)

* matrix_name)

(

=0;

<strlen(opts->

); ++

)

(options ==

)

(options ==

) {

(*options ==

)

num_searchsp *

(

));

(options ==

)

(*options ==

)

(program_number) {

(*options)->program_number = program_number;

(*options)->stride = 0;

threshold,

word_size)

kB62_threshold = 11;

(matrixName ==

)

(

(matrixName,

) == 0)

*threshold = kB62_threshold;

(

(matrixName,

) == 0)

(

(matrixName,

) == 0)

(

(matrixName,

) == 0)

(

(matrixName,

) == 0)

(

(matrixName,

) == 0)

(

(matrixName,

) == 0)

*threshold = kB62_threshold;

kB62_windowsize = 40;

(matrixName ==

)

(

(matrixName,

) == 0)

(

(matrixName,

) == 0)

(

(matrixName,

) == 0)

(

(matrixName,

) == 0)

(

(matrixName,

) == 0)

template_type,

(template_length == 0)

(word_size != 11 && word_size != 12) {

);

(template_length != 16 && template_length != 18 &&

template_length != 21) {

);

(template_type > 2) {

);

(options ==

)

);

);

);

);

);

);

);

);

);

);

);

);

);

(*options ==

)

(*options)->program_number = program_number;

(*options)->mask_level = 101;

(*options)->do_sum_stats =

;

}

(!gapped_calculation ||

(*options)->do_sum_stats =

;

(*options)->do_sum_stats =

;

(*options)->hsp_filt_opt =

;

(*options)->max_edit_distance =

;

evalue,

hitlist_size,

min_diag_separation)

(min_diag_separation)

(options ==

)

);

);

);

);

);

*psi_options = options;

( !psi_options ) {

);

);

(psi_options);

( !db_options ) {

*db_options = options;

(db_options ==

)

(*score_options)->gapped_calculation)))

(*score_options)->gapped_calculation)))

(ext_options ==

|| score_options ==

)

);

);

);

);

lookup_options, blast_msg)) != 0)

word_options, blast_msg)) != 0)

score_options, blast_msg)) != 0)

(lookup_options->

> 5 && is_identity) {

);

);

(culling_opts);

( filt_opts ==

|| best_hit ==

|| *best_hit ==

) {

( filt_opts ==

|| culling ==

|| *culling ==

) {

writer_found =

;

(!subject_besthit_opts)

(subject_besthit_opts);

( filt_opts ==

|| subject_besthit ==

|| *subject_besthit ==

) {

*subject_besthit =

;

#define sfree(x)

Safe free a pointer: belongs to a higher level header.

const double kSegLocut

Locut parameter for SEG.

const int kSegWindow

Window that SEG examines at once.

const double kSegHicut

Hicut parameter for SEG.

EBlastStage

Enumeration for the stages in the BLAST search.

@ ePrelimSearch

Preliminary stage.

BLAST filtering functions.

Int2 BlastFilteringOptionsFromString(EBlastProgramType program_number, const char *instructions, SBlastFilterOptions **filtering_options, Blast_Message **blast_message)

Produces SBlastFilterOptions from a string that has been traditionally supported in blast.

#define DBSEQ_CHUNK_OVERLAP

By how much should the chunks of a subject sequence overlap if it is too long and has to be split.

#define BLASTERR_OPTION_PROGRAM_INVALID

The option is not supported with the specified program.

#define BLASTERR_OPTION_VALUE_INVALID

The value of the option is not supported (e.g., word size too small)

Int2 Blast_MessageWrite(Blast_Message **blast_msg, EBlastSeverity severity, int context, const char *message)

Writes a message to a structure.

const int kBlastMessageNoContext

Declared in blast_message.h as extern const.

#define BLASTERR_MEMORY

System error: out of memory condition.

#define BLASTERR_INVALIDPARAM

Invalid parameter: possible programmer error or pre-condition not met.

PSIBlastOptions * PSIBlastOptionsFree(PSIBlastOptions *psi_options)

Deallocate PSI BLAST options.

Int2 BLAST_FillQuerySetUpOptions(QuerySetUpOptions *options, EBlastProgramType program, const char *filter_string, Uint1 strand_option)

Fill non-default contents of the QuerySetUpOptions.

BlastHSPCullingOptions * BlastHSPCullingOptionsNew(int max)

Allocate a new object for culling options.

Int2 BlastDatabaseOptionsNew(BlastDatabaseOptions **db_options)

Allocates the BlastDatabase options structure and sets the default database genetic code value (BLAST...

Int2 SWindowMaskerOptionsResetDB(SWindowMaskerOptions **winmask_options, const char *db)

Resets name of db for window masker filtering.

Int2 SRepeatFilterOptionsNew(SRepeatFilterOptions **repeat_options)

Allocates memory for SRepeatFilterOptions, fills in defaults.

Int2 PSIBlastOptionsValidate(const PSIBlastOptions *psi_options, Blast_Message **blast_msg)

Validates the PSI BLAST options so that they have sane values.

Int2 BlastHSPBestHitOptionsValidate(const BlastHSPFilteringOptions *opts)

Validate the best hit algorithm parameters (if any) in the.

Int2 BLAST_ValidateOptions(EBlastProgramType program_number, const BlastExtensionOptions *ext_options, const BlastScoringOptions *score_options, const LookupTableOptions *lookup_options, const BlastInitialWordOptions *word_options, const BlastHitSavingOptions *hit_options, Blast_Message **blast_msg)

Validate all options.

Int2 BlastHSPFilteringOptions_AddCulling(BlastHSPFilteringOptions *filt_opts, BlastHSPCullingOptions **culling, EBlastStage stage)

Validates the BlastHSPFilteringOptions structure.

BlastHitSavingOptions * BlastHitSavingOptionsFree(BlastHitSavingOptions *options)

Deallocate memory for BlastHitSavingOptions.

Int2 BlastScoringOptionsValidate(EBlastProgramType program_number, const BlastScoringOptions *options, Blast_Message **blast_msg)

Validate contents of BlastScoringOptions.

Int2 BlastQuerySetUpOptionsNew(QuerySetUpOptions **options)

Allocate memory for QuerySetUpOptions and fill with default values.

Int2 BLAST_GetSuggestedThreshold(EBlastProgramType program_number, const char *matrixName, double *threshold)

Get thresholds for word-finding suggested by Stephen Altschul.

SDustOptions * SDustOptionsFree(SDustOptions *dust_options)

Frees SDustOptions.

Int2 BLAST_FillScoringOptions(BlastScoringOptions *options, EBlastProgramType program_number, Boolean greedy_extension, Int4 penalty, Int4 reward, const char *matrix, Int4 gap_open, Int4 gap_extend)

Fill non-default values in the BlastScoringOptions structure.

BlastHSPFilteringOptions * BlastHSPFilteringOptionsFree(BlastHSPFilteringOptions *opts)

Deallocate a BlastHSPFilteringOptions structure.

Int2 SRepeatFilterOptionsResetDB(SRepeatFilterOptions **repeat_options, const char *db)

Resets name of db for repeat filtering.

Int2 BlastScoringOptionsNew(EBlastProgramType program_number, BlastScoringOptions **options)

Allocate memory for BlastScoringOptions and fill with default values.

Int2 BlastEffectiveLengthsOptionsNew(BlastEffectiveLengthsOptions **options)

Allocate memory for BlastEffectiveLengthsOptions* and fill with default values.

SReadQualityOptions * SReadQualityOptionsFree(SReadQualityOptions *read_quality_options)

Frees memory for SReadQualityOptions.

Boolean SBlastFilterOptionsMaskAtHash(const SBlastFilterOptions *filter_options)

Queries whether masking should be done only for the lookup table or for the entire search.

Boolean SBlastFilterOptionsNoFiltering(const SBlastFilterOptions *filter_options)

Queries whether no masking is required.

Int2 BLAST_GetSuggestedWindowSize(EBlastProgramType program_number, const char *matrixName, Int4 *window_size)

Get window sizes for two hit algorithm suggested by Stephen Altschul.

Int2 SBlastFilterOptionsValidate(EBlastProgramType program_number, const SBlastFilterOptions *filter_options, Blast_Message **blast_message)

Validates filter options to ensure that program and options are consistent and that options have vali...

const int kDustLinker

Parameter used by dust to link together close low-complexity segments.

BlastHSPSubjectBestHitOptions * BlastHSPSubjectBestHitOptionsFree(BlastHSPSubjectBestHitOptions *subject_besthit_opts)

Deallocates subject besthit structure.

Int2 BLAST_InitDefaultOptions(EBlastProgramType program_number, LookupTableOptions **lookup_options, QuerySetUpOptions **query_setup_options, BlastInitialWordOptions **word_options, BlastExtensionOptions **ext_options, BlastHitSavingOptions **hit_options, BlastScoringOptions **score_options, BlastEffectiveLengthsOptions **eff_len_options, PSIBlastOptions **psi_options, BlastDatabaseOptions **db_options)

Initialize all the BLAST search options structures with the default values.

SRepeatFilterOptions * SRepeatFilterOptionsFree(SRepeatFilterOptions *repeat_options)

Frees SRepeatFilterOptions.

BlastInitialWordOptions * BlastInitialWordOptionsFree(BlastInitialWordOptions *options)

Deallocate memory for BlastInitialWordOptions.

Int2 BlastHitSavingOptionsNew(EBlastProgramType program_number, BlastHitSavingOptions **options, Boolean gapped_calculation)

Allocate memory for BlastHitSavingOptions.

Int2 BLAST_FillEffectiveLengthsOptions(BlastEffectiveLengthsOptions *options, Int4 dbseq_num, Int8 db_length, Int8 *searchsp_eff, Int4 num_searchsp)

Fill the non-default values in the BlastEffectiveLengthsOptions structure.

Int2 SSegOptionsNew(SSegOptions **seg_options)

Allocates memory for SSegOptions, fills in defaults.

SWindowMaskerOptions * SWindowMaskerOptionsFree(SWindowMaskerOptions *winmask_options)

Frees SWindowMaskerOptions.

BlastEffectiveLengthsOptions * BlastEffectiveLengthsOptionsFree(BlastEffectiveLengthsOptions *options)

Deallocate memory for BlastEffectiveLengthsOptions*.

SBlastFilterOptions * SBlastFilterOptionsFree(SBlastFilterOptions *filter_options)

Frees SBlastFilterOptions and all subservient structures.

Int2 SWindowMaskerOptionsNew(SWindowMaskerOptions **winmask_options)

Allocates memory for SWindowMaskerOptions, fills in defaults.

Int2 BlastScoringOptionsSetMatrix(BlastScoringOptions *opts, const char *matrix_name)

Resets matrix name option.

static SDustOptions * s_MergeDustOptions(const SDustOptions *opt1, const SDustOptions *opt2)

Merges together two sets of dust options, choosing the most non-default one.

Int2 SBlastFilterOptionsMerge(SBlastFilterOptions **combined, const SBlastFilterOptions *opt1, const SBlastFilterOptions *opt2)

Merges two sets of options together, taking the non-default one as preferred.

BlastExtensionOptions * BlastExtensionOptionsFree(BlastExtensionOptions *options)

Deallocate memory for BlastExtensionOptions.

Int2 BLAST_FillInitialWordOptions(BlastInitialWordOptions *options, EBlastProgramType program, Int4 window_size, double xdrop_ungapped)

Fill non-default values in the BlastInitialWordOptions structure.

Int2 SDustOptionsNew(SDustOptions **dust_options)

Allocates memory for SDustOptions, fills in defaults.

Int2 BlastInitialWordOptionsValidate(EBlastProgramType program_number, const BlastInitialWordOptions *options, Blast_Message **blast_msg)

Validate correctness of the initial word options.

Int2 BLAST_FillExtensionOptions(BlastExtensionOptions *options, EBlastProgramType program, Int4 greedy, double x_dropoff, double x_dropoff_final)

Fill non-default values in the BlastExtensionOptions structure.

Int2 LookupTableOptionsValidate(EBlastProgramType program_number, const LookupTableOptions *options, Blast_Message **blast_msg)

Validate LookupTableOptions.

Int2 BlastHitSavingOptionsValidate(EBlastProgramType program_number, const BlastHitSavingOptions *options, Blast_Message **blast_msg)

Validate BlastHitSavingOptions.

const double kPSSM_NoImpalaScaling

Value used to indicate that no IMPALA-style scaling should be performed when scaling a PSSM.

BlastHSPCullingOptions * BlastHSPCullingOptionsFree(BlastHSPCullingOptions *culling_opts)

Deallocates culling options structure.

Int2 BLAST_FillHitSavingOptions(BlastHitSavingOptions *options, double evalue, Int4 hitlist_size, Boolean is_gapped, Int4 culling_limit, Int4 min_diag_separation)

Allocate memory for BlastHitSavingOptions.

SSegOptions * SSegOptionsFree(SSegOptions *seg_options)

Frees SSegOptions.

Int2 BlastHSPCullingOptionsValidate(const BlastHSPFilteringOptions *opts)

Validate culling options.

Int2 BlastHSPSubjectBestHitOptionsValidate(const BlastHSPFilteringOptions *opts)

Validate subject besthit options.

static Boolean s_DiscWordOptionsValidate(Int4 word_size, Uint1 template_length, Uint1 template_type, Blast_Message **blast_msg)

Validate options for the discontiguous word megablast Word size must be 11 or 12; template length 16,...

BlastHSPFilteringOptions * BlastHSPFilteringOptionsNew()

Allocate and initialize a BlastHSPFilteringOptions structure.

Int2 LookupTableOptionsNew(EBlastProgramType program_number, LookupTableOptions **options)

Allocate memory for lookup table options and fill with default values.

BlastDatabaseOptions * BlastDatabaseOptionsFree(BlastDatabaseOptions *db_options)

Deallocate database options.

const int kDustLevel

Declared in blast_def.h as extern const.

BlastHSPSubjectBestHitOptions * BlastHSPSubjectBestHitOptionsNew(Boolean isProtein)

Allocate a new object for subject besthit options.

const int kDustWindow

Window parameter used by dust.

Int2 BLAST_FillLookupTableOptions(LookupTableOptions *options, EBlastProgramType program_number, Boolean is_megablast, double threshold, Int4 word_size)

Allocate memory for lookup table options and fill with default values.

Int2 SReadQualityOptionsNew(SReadQualityOptions **read_quality_options)

Allocates memory for SReadQualityOptions, fills in defaults.

Int2 BlastHSPFilteringOptions_AddSubjectBestHit(BlastHSPFilteringOptions *filt_opts, BlastHSPSubjectBestHitOptions **subject_besthit)

static SWindowMaskerOptions * s_MergeWindowMaskerOptions(const SWindowMaskerOptions *opt1, const SWindowMaskerOptions *opt2)

Merges together two sets of window masker options, choosing the most non-default one.

BlastHSPBestHitOptions * BlastHSPBestHitOptionsNew(double overhang, double score_edge)

Allocate and initialize a BlastHSPBestHitOptions structure.

Int2 SBlastFilterOptionsNew(SBlastFilterOptions **filter_options, EFilterOptions type)

Allocates memory for SBlastFilterOptions and.

static Int2 s_BlastExtensionScoringOptionsValidate(EBlastProgramType program_number, const BlastExtensionOptions *ext_options, const BlastScoringOptions *score_options, Blast_Message **blast_msg)

Checks that the extension and scoring options are consistent with each other.

Boolean BlastEffectiveLengthsOptions_IsSearchSpaceSet(const BlastEffectiveLengthsOptions *options)

Return true if the search spaces is set for any of the queries in the search.

Int2 PSIBlastOptionsNew(PSIBlastOptions **psi_options)

Initialize default options for PSI BLAST.

static SSegOptions * s_MergeSegOptions(const SSegOptions *opt1, const SSegOptions *opt2)

Merges together two sets of SEG options, choosing the most non-default one.

Int2 BlastHSPFilteringOptions_AddBestHit(BlastHSPFilteringOptions *filt_opts, BlastHSPBestHitOptions **best_hit, EBlastStage stage)

Add the best hit options.

static SRepeatFilterOptions * s_MergeRepeatOptions(const SRepeatFilterOptions *opt1, const SRepeatFilterOptions *opt2)

Merges together two sets of repeat filter options, choosing the most non-default one.

Int2 BlastInitialWordOptionsNew(EBlastProgramType program, BlastInitialWordOptions **options)

Allocate memory for BlastInitialWordOptions and fill with default values.

BlastScoringOptions * BlastScoringOptionsFree(BlastScoringOptions *options)

Deallocate memory for BlastScoringOptions.

Int2 BlastExtensionOptionsValidate(EBlastProgramType program_number, const BlastExtensionOptions *options, Blast_Message **blast_msg)

Validate contents of BlastExtensionOptions.

BlastHSPBestHitOptions * BlastHSPBestHitOptionsFree(BlastHSPBestHitOptions *opt)

Deallocate a BlastHSPBestHitOptions structure.

LookupTableOptions * LookupTableOptionsFree(LookupTableOptions *options)

Deallocates memory for LookupTableOptions*.

Int2 BlastScoringOptionsDup(BlastScoringOptions **new_opt, const BlastScoringOptions *old_opt)

Produces copy of "old" options, with new memory allocated.

QuerySetUpOptions * BlastQuerySetUpOptionsFree(QuerySetUpOptions *options)

Deallocate memory for QuerySetUpOptions.

Int2 BlastHSPFilteringOptionsValidate(const BlastHSPFilteringOptions *opts)

Validates the BlastHSPFilteringOptions structure.

Int2 BlastExtensionOptionsNew(EBlastProgramType program, BlastExtensionOptions **options, Boolean gapped)

Allocate memory for BlastExtensionOptions and fill with default values.

The structures and functions in blast_options.

#define PSI_INCLUSION_ETHRESH

Defaults for PSI-BLAST and DELTA-BLAST options.

#define BLAST_GAP_X_DROPOFF_NUCL

default dropoff for non-greedy nucleotide gapped extensions

#define BLAST_HITLIST_SIZE

Number of database sequences to save hits for.

#define BLAST_GAP_OPEN_MEGABLAST

default gap open penalty (megablast with greedy gapped alignment)

#define BLAST_UNGAPPED_X_DROPOFF_NUCL

ungapped dropoff score for blastn (and megablast)

#define BLAST_WORD_THRESHOLD_BLASTX

default threshold (blastx)

#define BLAST_UNGAPPED_X_DROPOFF_PROT

default dropoff for ungapped extension; ungapped extensions will stop when the score for the extensio...

#define BLAST_WORDSIZE_MAPPER

default word size for mapping rna-seq to a genome

#define BLAST_GAP_EXTN_MEGABLAST

default gap open penalty (megablast) with greedy gapped alignment)

#define DEFAULT_SUBJECT_BESTHIT_PROT_MAX_RANGE_DIFF

@ eJumperWithTraceback

Jumper extension (mapping)

@ eDynProgScoreOnly

standard affine gapping

@ eGreedyScoreOnly

Greedy extension (megaBlast)

@ eSmithWatermanScoreOnly

Score-only smith-waterman.

#define BLAST_GAP_OPEN_PROT

Protein gap costs are the defaults for the BLOSUM62 scoring matrix.

#define BLAST_WORDSIZE_MEGABLAST

default word size (contiguous megablast; for discontig megablast the word size is explicitly overridd...

#define DEFAULT_SUBJECT_BESTHIT_NUCL_MAX_RANGE_DIFF

#define BLAST_GAP_OPEN_NUCL

default gap open penalty (blastn)

#define BLAST_GAP_TRIGGER_NUCL

default bit score that will trigger a gapped extension for blastn

#define BLAST_GAP_EXTN_PROT

cost to extend a gap.

#define BLAST_GAP_X_DROPOFF_FINAL_NUCL

default dropoff for nucleotide gapped extensions)

#define MAX_DB_WORD_COUNT_MAPPER

Default max frequency for a database word.

#define BLAST_DEFAULT_MATRIX

Default matrix name: BLOSUM62.

#define BLAST_EXPECT_VALUE

Default parameters for saving hits.

#define BLAST_SCAN_RANGE_NUCL

default scan range (blastn)

#define BLAST_WINDOW_SIZE_NUCL

default window size (blastn)

#define BLAST_GAP_X_DROPOFF_GREEDY

default dropoff for greedy nucleotide gapped extensions

#define BLAST_WORD_THRESHOLD_TBLASTX

default threshold (tblastx)

#define BLAST_WORD_THRESHOLD_BLASTP

neighboring word score thresholds; a threshold of zero means that only query and subject words that m...

#define BLAST_GAP_EXTN_NUCL

default gap open penalty (blastn)

#define BLAST_GAP_TRIGGER_PROT

default bit score that will trigger gapped extension

#define BLAST_GAP_X_DROPOFF_PROT

default dropoff for preliminary gapped extensions

#define PSI_PSEUDO_COUNT_CONST

Pseudo-count constant for PSI-BLAST.

#define BLAST_REWARD

default nucleotide match score

@ eGreedyTbck

Greedy extension (megaBlast)

@ eDynProgTbck

standard affine gapping

@ eSmithWatermanTbckFull

Smith-waterman to find all alignments.

#define BLAST_PENALTY

default reward and penalty (only applies to blastn/megablast)

#define BLAST_WINDOW_SIZE_PROT

Some default values (used when creating blast options block and for command-line program defaults.

EFilterOptions

Types of filtering options.

@ eDustRepeats

Repeat and dust filtering for nucleotides.

@ eRepeats

Repeat filtering for nucleotides.

@ eDust

low-complexity for nucleotides.

@ eEmpty

no filtering at all.

@ eSeg

low-complexity for proteins.

#define BLAST_GAP_X_DROPOFF_FINAL_PROT

default dropoff for the final gapped extension with traceback

#define BLAST_GENETIC_CODE

Default genetic code for query and/or database.

#define BLAST_WORD_THRESHOLD_TBLASTN

default neighboring threshold (tblastn/rpstblastn)

#define BLAST_WORDSIZE_PROT

length of word to trigger an extension.

#define BLAST_WORDSIZE_NUCL

default word size (blastn)

#define kDefaultRepeatFilterDb

Default value for repeats database filtering.

@ eNaLookupTable

blastn lookup table

@ eMBLookupTable

megablast lookup table (includes both contiguous and discontiguous megablast)

@ ePhiNaLookupTable

nucleotide lookup table for phi-blast

@ eAaLookupTable

standard protein (blastp) lookup table

@ eCompressedAaLookupTable

compressed alphabet (blastp) lookup table

@ ePhiLookupTable

protein lookup table specialized for phi-blast

@ eRPSLookupTable

RPS lookup table (rpsblast and rpstblastn)

@ eNaHashLookupTable

used for 16-base words

Boolean Blast_ProgramIsMapping(EBlastProgramType p)

Boolean Blast_QueryIsPssm(EBlastProgramType p)

Returns true if the query is PSSM.

Boolean Blast_ProgramIsPhiBlast(EBlastProgramType p)

Returns true if program is PHI-BLAST (i.e.

Boolean Blast_QueryIsTranslated(EBlastProgramType p)

Returns true if the query is translated.

Boolean Blast_ProgramIsNucleotide(EBlastProgramType p)

Boolean Blast_QueryIsPattern(EBlastProgramType p)

Boolean Blast_ProgramIsRpsBlast(EBlastProgramType p)

Returns true if program is RPS-BLAST (i.e.

EBlastProgramType

Defines the engine's notion of the different applications of the BLAST algorithm.

Boolean Blast_SubjectIsTranslated(EBlastProgramType p)

Returns true if the subject is translated.

Definitions and prototypes used by blast_stat.c to calculate BLAST statistics.

char * BLAST_PrintAllowedValues(const char *matrix, Int4 gap_open, Int4 gap_extend)

Prints a messages about the allowed open etc values for the given matrix, BlastKarlinBlkGappedFill sh...

Int2 Blast_KarlinBlkGappedLoadFromTables(Blast_KarlinBlk *kbp, Int4 gap_open, Int4 gap_extend, const char *matrix_name, Boolean standard_only)

Attempts to fill KarlinBlk for given gap opening, extensions etc.

char * BLAST_PrintMatrixMessage(const char *matrix, Boolean standard_only)

Prints a messages about the allowed matrices, BlastKarlinBlkGappedFill should return 1 before this is...

Boolean BLAST_CheckRewardPenaltyScores(Int4 reward, Int4 penalty)

Check the validity of the reward and penalty scores.

Various auxiliary BLAST utility functions.

char * BLAST_StrToUpper(const char *string)

Returns a copy of the input string with all its characters turned to uppercase.

Constants used in compositional score matrix adjustment.

@ eCompositionBasedStats

Composition-based statistics as in NAR 29:2994-3005, 2001.

@ eNoCompositionBasedStats

Don't use composition based statistics.

uint8_t Uint1

1-byte (8-bit) unsigned integer

int16_t Int2

2-byte (16-bit) signed integer

int32_t Int4

4-byte (32-bit) signed integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

int64_t Int8

8-byte (64-bit) signed integer

Implementation of a number of BlastHSPWriters to save hits from a BLAST search, and subsequently retu...

#define kBestHit_OverhangMax

Maximum value for overhang.

#define kBestHit_OverhangMin

Minimum value for overhang.

#define kBestHit_ScoreEdgeMin

Minimum value for score_edge.

#define kBestHit_ScoreEdgeMax

Maximum value for score_edge.

Implementation of a number of BlastHSPWriters to save hits from a BLAST search, and subsequently retu...

if(yy_accept[yy_current_state])

int strcmp(const char *str1, const char *str2)

#define DIM(A)

dimension of an array.

#define INT4_MAX

largest nubmer represented by signed int

void * BlastMemDup(const void *orig, size_t size)

Copies memory using memcpy and malloc.

Uint1 Boolean

bool replacment for C

#define TRUE

bool replacment for C indicating true.

#define FALSE

bool replacment for C indicating false.

#define INT2_MAX

largest number represented by signed (two byte) short

#define ASSERT

macro for assert.

#define MAX(a, b)

returns larger of a and b.

Options used to create the ReadDBFILE structure Include database name and various information for res...

Int4 genetic_code

Genetic code to use for translation, tblast[nx] only.

Options for setting up effective lengths and search spaces.

Int8 * searchsp_eff

Search space to be used for statistical calculations (one such per query context)

Int8 db_length

Database length to be used for statistical calculations.

Int4 dbseq_num

Number of database sequences to be used for statistical calculations.

Int4 num_searchspaces

Number of elements in searchsp_eff, this must be equal to the number of contexts in the search.

Options used for gapped extension These include: a.

EBlastTbackExt eTbackExt

type of traceback extension.

EBlastPrelimGapExt ePrelimGapExt

type of preliminary gapped extension (normally) for calculating score.

double gap_x_dropoff_final

X-dropoff value for the final gapped extension (in bits)

double gap_x_dropoff

X-dropoff value for gapped extension (in bits)

Int4 compositionBasedStats

mode of compositional adjustment to use; if zero then compositional adjustment is not used

Options for the Best Hit HSP collection algorithm.

Options for the HSP culling algorithm.

int max_hits

Maximum number of hits per area of query.

Structure containing the HSP filtering/writing options.

EBlastStage culling_stage

BlastHSPBestHitOptions * best_hit

Best Hit algorithm.

BlastHSPSubjectBestHitOptions * subject_besthit_opts

Subject Culling.

EBlastStage best_hit_stage

BlastHSPCullingOptions * culling_opts

culling algorithm

unsigned int max_range_diff

Options used when evaluating and saving hits These include: a.

Int4 culling_limit

If the query range of an HSP is contained in at least this many higher-scoring HSPs,...

Int4 longest_intron

The longest distance between HSPs allowed for combining via sum statistics with uneven gaps.

double expect_value

The expect value cut-off threshold for an HSP, or a combined hit if sum statistics is used.

Int4 cutoff_score

The (raw) score cut-off threshold.

Int4 hitlist_size

Maximal number of database sequences to return results for.

Int4 min_diag_separation

How many diagonals separate a hit from a substantial alignment before it's not blocked out.

Int4 max_edit_distance

Maximum number of mismatches and gaps.

BlastHSPFilteringOptions * hsp_filt_opt

Contains options to configure the HSP filtering/writering structures If not set, the default HSP filt...

Options needed for initial word finding and processing.

double x_dropoff

X-dropoff value (in bits) for the ungapped extension.

Int4 window_size

Maximal allowed distance between 2 hits in case 2 hits are required to trigger the extension.

Int4 scan_range

Maximal number of gaps allowed between 2 hits.

Scoring options block Used to produce the BlastScoreBlk structure This structure may be needed for lo...

Int2 penalty

Penalty for a mismatch.

EBlastProgramType program_number

indicates blastn, blastp, etc.

Int4 gap_open

Extra penalty for starting a gap.

Int4 gap_extend

Penalty for each gap residue.

Int2 reward

Reward for a match.

Boolean gapped_calculation

gap-free search if FALSE

char * matrix_path

Directory path to where matrices are stored.

char * matrix

Name of the matrix containing all scores: needed for finding neighboring words.

Boolean is_ooframe

Should out-of-frame gapping be used in a translated search?

Structure to hold the a message from the core of the BLAST engine.

Options needed to construct a lookup table Also needed: query sequence and query length.

Int4 word_size

Determines the size of the lookup table.

char * phi_pattern

PHI-BLAST pattern.

Uint1 max_db_word_count

words with larger frequency in the database will be masked in the lookup table, if the db_filter opto...

Boolean db_filter

scan the database and include only words that appear in the database between 1 and 9 times (currently...

double threshold

Score threshold for putting words in a lookup table (fractional values are allowed,...

Int4 mb_template_type

Type of a discontiguous word template.

ELookupTableType lut_type

What kind of lookup table to construct?

Int4 mb_template_length

Length of the discontiguous words.

Options used in protein BLAST only (PSI, PHI, RPS and translated BLAST) Some of these possibly should...

Boolean nsg_compatibility_mode

Compatibility option for the NCBI's structure group (note nsg_ prefix, stands for NCBI's structure gr...

double impala_scaling_factor

Scaling factor as used in IMPALA to do the matrix rescaling.

double inclusion_ethresh

Minimum evalue for inclusion in PSSM calculation.

Boolean ignore_unaligned_positions

This turns off a validation for the multiple sequence alignment in the PSSM engine for unaligned posi...

Int4 pseudo_count

Pseudocount constant.

Boolean use_best_alignment

If set to TRUE, use the best alignment when multiple HSPs are found in a query-subject alignment (i....

Options required for setting up the query sequence.

Uint1 strand_option

In blastn: which strand to search: 1 = forward; 2 = reverse; 3 = both.

char * filter_string

DEPRECATED, filtering options above.

SBlastFilterOptions * filtering_options

structured options for all filtering offered from algo/blast/core for BLAST.

SRepeatFilterOptions * repeatFilterOptions

for organism specific repeat filtering.

SSegOptions * segOptions

low-complexity filtering for proteins sequences (includes translated nucleotides).

SReadQualityOptions * readQualityOptions

quality filtering for mapping next-generation sequences

Boolean mask_at_hash

mask query only for lookup table creation

SWindowMaskerOptions * windowMaskerOptions

organism specific filtering with window masker.

SDustOptions * dustOptions

low-complexity filtering for nucleotides.

Options for dust algorithm, applies only to nucl.

int linker

min distance to link segments.

Filtering options for mapping next-generation sequences.

Filtering options for organsim specific repeats filtering.

char * database

Nucleotide database for mini BLAST search.

Options for SEG algorithm, applies only to protein-protein comparisons.

int window

initial window to trigger further work.

Filtering options for organism-specific filtering with Window Masker.

const char * database

Use winmasker database at this location.

int taxid

Select masking database for this TaxID.

voidp calloc(uInt items, uInt size)

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