LookupTableOptions Struct Reference

Search Toolkit Book for LookupTableOptions

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

#include <algo/blast/core/blast_options.h>

Public Attributes
double	threshold
	Score threshold for putting words in a lookup table (fractional values are allowed, and could be important if there is scaling involved) More...
ELookupTableType	lut_type
	What kind of lookup table to construct? More...
Int4	word_size
	Determines the size of the lookup table. More...
Int4	mb_template_length
	Length of the discontiguous words. More...
Int4	mb_template_type
	Type of a discontiguous word template. More...
char *	phi_pattern
	PHI-BLAST pattern. More...
EBlastProgramType	program_number
	indicates blastn, blastp, etc. More...
Uint4	stride
	number of words to skip after collecting each word More...
Boolean	db_filter
	scan the database and include only words that appear in the database between 1 and 9 times (currently implemented only for MB lookuptable and lookup table word size 16) More...
Uint1	max_db_word_count
	words with larger frequency in the database will be masked in the lookup table, if the db_filter optoion is on More...

Detailed Description

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

Definition at line 206 of file blast_options.h.

Member Data Documentation

db_filter

Boolean LookupTableOptions::db_filter

scan the database and include only words that appear in the database between 1 and 9 times (currently implemented only for MB lookuptable and lookup table word size 16)

Definition at line 217 of file blast_options.h.

Referenced by BlastChooseNaLookupTable(), BlastMBLookupTableNew(), BlastNaHashLookupTableNew(), BOOST_AUTO_TEST_CASE(), CBlastOptionsLocal::GetLookupDbFilter(), LookupTableOptionsValidate(), s_FillContigMBTable(), and CBlastOptionsLocal::SetLookupDbFilter().

lut_type

ELookupTableType LookupTableOptions::lut_type

What kind of lookup table to construct?

Definition at line 210 of file blast_options.h.

Referenced by BLAST_FillLookupTableOptions(), CLookupTableOptions::DebugDump(), CBlastOptionsLocal::GetLookupTableType(), LookupTableOptionsValidate(), LookupTableWrapInit_MT(), CBlastOptionsLocal::SetLookupTableType(), CBlastOptionsLocal::SetPHIPattern(), and CBlastOptionsLocal::SetWordSize().

max_db_word_count

Uint1 LookupTableOptions::max_db_word_count

words with larger frequency in the database will be masked in the lookup table, if the db_filter optoion is on

Definition at line 221 of file blast_options.h.

Referenced by BLAST_FillLookupTableOptions(), BlastMBLookupTableNew(), BlastNaHashLookupTableNew(), CBlastOptionsLocal::GetMaxDbWordCount(), s_FillContigMBTable(), and CBlastOptionsLocal::SetMaxDbWordCount().

mb_template_length

Int4 LookupTableOptions::mb_template_length

Length of the discontiguous words.

Definition at line 212 of file blast_options.h.

Referenced by BlastChooseNaLookupTable(), BlastMBLookupTableNew(), BOOST_AUTO_TEST_CASE(), CLookupTableOptions::DebugDump(), CBlastOptionsLocal::GetMBTemplateLength(), LookupTableOptionsValidate(), s_FillDiscMBTable(), CBlastOptionsLocal::SetMBTemplateLength(), and TestFixture::SetUpLookupTable().

mb_template_type

Int4 LookupTableOptions::mb_template_type

Type of a discontiguous word template.

Definition at line 213 of file blast_options.h.

Referenced by BOOST_AUTO_TEST_CASE(), CLookupTableOptions::DebugDump(), CBlastOptionsLocal::GetMBTemplateType(), LookupTableOptionsValidate(), s_FillDiscMBTable(), CBlastOptionsLocal::SetMBTemplateType(), and TestFixture::SetUpLookupTable().

phi_pattern

char* LookupTableOptions::phi_pattern

PHI-BLAST pattern.

Definition at line 214 of file blast_options.h.

Referenced by CBlastOptionsLocal::GetPHIPattern(), LookupTableOptionsFree(), LookupTableOptionsValidate(), LookupTableWrapInit_MT(), CBlastOptionsLocal::SetPHIPattern(), CPhiblastTestFixture::setUpLookupTable(), CBlastOptionsLocal::x_Copy_CLookupTableOptions(), and CSeedTop::x_MakeLookupTable().

program_number

EBlastProgramType LookupTableOptions::program_number

indicates blastn, blastp, etc.

Definition at line 215 of file blast_options.h.

Referenced by BlastChooseNaLookupTable(), s_FillContigMBTable(), and CBlastOptionsLocal::SetProgram().

stride

Uint4 LookupTableOptions::stride

number of words to skip after collecting each word

Definition at line 216 of file blast_options.h.

Referenced by BlastMBLookupTableNew(), CBlastOptionsLocal::GetLookupTableStride(), s_FillContigMBTable(), and CBlastOptionsLocal::SetLookupTableStride().

threshold

double LookupTableOptions::threshold

Score threshold for putting words in a lookup table (fractional values are allowed, and could be important if there is scaling involved)

Definition at line 207 of file blast_options.h.

Referenced by BLAST_FillLookupTableOptions(), BlastAaLookupTableNew(), BlastCompressedAaLookupTableNew(), CLookupTableOptions::DebugDump(), CBlastOptionsLocal::GetWordThreshold(), LookupTableOptionsValidate(), and CBlastOptionsLocal::SetWordThreshold().

word_size

Int4 LookupTableOptions::word_size

Determines the size of the lookup table.

Definition at line 211 of file blast_options.h.

Referenced by BLAST_FillLookupTableOptions(), BLAST_ValidateOptions(), BlastAaLookupTableNew(), BlastChooseNaLookupTable(), BlastCompressedAaLookupTableNew(), BlastMBLookupTableNew(), BlastNaHashLookupTableNew(), BlastNaLookupTableNew(), BlastSmallNaLookupTableNew(), BOOST_AUTO_TEST_CASE(), CLookupTableOptions::DebugDump(), CIndexedDb_New::DoPreSearch(), CBlastOptionsLocal::GetWordSize(), LookupTableOptionsValidate(), CIndexedDb_Old::PreSearch(), s_FillDiscMBTable(), CBlastOptionsLocal::SetLookupTableType(), CBlastOptionsLocal::SetWordSize(), and SubjectIndexNew().

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The documentation for this struct was generated from the following file:

• include/algo/blast/core/blast_options.h