NCBI C++ ToolKit
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Search Toolkit Book for BlastMBLookupTable
The lookup table structure used for Mega BLAST. More...
#include <algo/blast/core/blast_nalookup.h>
Public Attributes | |
Int4 | word_length |
number of exact letter matches that will trigger an ungapped extension More... | |
Int4 | lut_word_length |
number of letters in a lookup table word More... | |
Int8 | hashsize |
= 4^(lut_word_length) More... | |
Boolean | discontiguous |
Are discontiguous words used? More... | |
Int4 | template_length |
Length of the discontiguous word template. More... | |
EDiscTemplateType | template_type |
Type of the discontiguous word template. More... | |
Boolean | two_templates |
Use two templates simultaneously. More... | |
EDiscTemplateType | second_template_type |
Type of the second discontiguous word template. More... | |
Boolean | stride |
is lookup table created with a stride More... | |
Int4 | scan_step |
Step size for scanning the database. More... | |
Int4 * | hashtable |
Array of positions. More... | |
Int4 * | hashtable2 |
Array of positions for second template. More... | |
Int4 * | next_pos |
Extra positions stored here. More... | |
Int4 * | next_pos2 |
Extra positions for the second template. More... | |
PV_ARRAY_TYPE * | pv_array |
Presence vector, used for quick presence check. More... | |
Int4 | pv_array_bts |
The exponent of 2 by which pv_array is smaller than the backbone. More... | |
Int4 | longest_chain |
Largest number of query positions for a given word. More... | |
void * | scansub_callback |
function for scanning subject sequences More... | |
void * | extend_callback |
function for extending hits More... | |
Int4 | num_unique_pos_added |
Number of positions added to the l.t. More... | |
Int4 | num_words_added |
Number of words added to the l.t. More... | |
BlastSeqLoc * | masked_locations |
masked locations, only non-NULL for soft-masking. More... | |
The lookup table structure used for Mega BLAST.
Definition at line 238 of file blast_nalookup.h.
Boolean BlastMBLookupTable::discontiguous |
Are discontiguous words used?
Definition at line 243 of file blast_nalookup.h.
Referenced by BlastChooseNaExtend(), s_BlastNaExtendDirect(), s_FillDiscMBTable(), s_MBChooseScanSubject(), TestFixture::ScanCheckHitsCore(), TestFixture::ScanMaxHitsTestCore(), TestFixture::ScanOffsetTestCore(), and NuclWordFinderTextFixture::setupLookupTable().
void* BlastMBLookupTable::extend_callback |
function for extending hits
Definition at line 264 of file blast_nalookup.h.
Referenced by BlastChooseNaExtend(), and NuclWordFinderTextFixture::setupAll().
Int8 BlastMBLookupTable::hashsize |
= 4^(lut_word_length)
Definition at line 242 of file blast_nalookup.h.
Referenced by BlastMBLookupTableNew(), s_FillContigMBTable(), s_FillDiscMBTable(), s_FillPV(), s_MBCountWordsInSubject_16_1(), s_MBLookup(), and s_MBScanSubject_Any().
Int4* BlastMBLookupTable::hashtable |
Array of positions.
Definition at line 253 of file blast_nalookup.h.
Referenced by BlastMBLookupTableDestruct(), BlastMBLookupTableNew(), s_FillContigMBTable(), s_FillDiscMBTable(), s_MBLookup(), and s_RemovePolyAWords().
Int4* BlastMBLookupTable::hashtable2 |
Array of positions for second template.
Definition at line 254 of file blast_nalookup.h.
Referenced by BlastMBLookupTableDestruct(), and s_FillDiscMBTable().
Int4 BlastMBLookupTable::longest_chain |
Largest number of query positions for a given word.
Definition at line 261 of file blast_nalookup.h.
Referenced by BlastMBLookupTableNew(), s_FillContigMBTable(), s_FillDiscMBTable(), s_MB_DiscWordScanSubject_1(), s_MB_DiscWordScanSubject_11_18_1(), s_MB_DiscWordScanSubject_11_21_1(), s_MB_DiscWordScanSubject_TwoTemplates_1(), s_MBScanSubject_10_1(), s_MBScanSubject_10_2(), s_MBScanSubject_10_3(), s_MBScanSubject_11_1Mod4(), s_MBScanSubject_11_2Mod4(), s_MBScanSubject_11_3Mod4(), s_MBScanSubject_9_1(), s_MBScanSubject_9_2(), s_MBScanSubject_Any(), and TestFixture::ScanMaxHitsTestCore().
Int4 BlastMBLookupTable::lut_word_length |
number of letters in a lookup table word
Definition at line 241 of file blast_nalookup.h.
Referenced by BlastChooseNaExtend(), BlastMBLookupTableNew(), BlastNaExtendJumper(), s_BlastNaExtend(), s_BlastNaExtendAligned(), s_BlastNaExtendDirect(), s_FillContigMBTable(), s_FillPV(), s_MB_DiscWordScanSubject_11_18_1(), s_MB_DiscWordScanSubject_11_21_1(), s_MBChooseScanSubject(), s_MBCountWordsInSubject_16_1(), s_MBScanSubject_10_1(), s_MBScanSubject_10_2(), s_MBScanSubject_10_3(), s_MBScanSubject_11_1Mod4(), s_MBScanSubject_11_2Mod4(), s_MBScanSubject_11_3Mod4(), s_MBScanSubject_9_1(), s_MBScanSubject_9_2(), s_MBScanSubject_Any(), s_RemovePolyAWords(), TestFixture::ScanCheckHitsCore(), TestFixture::ScanMaxHitsTestCore(), TestFixture::ScanOffsetTestCore(), and NuclWordFinderTextFixture::setupLookupTable().
BlastSeqLoc* BlastMBLookupTable::masked_locations |
masked locations, only non-NULL for soft-masking.
Definition at line 268 of file blast_nalookup.h.
Referenced by BlastMBLookupTableDestruct(), BlastMBLookupTableNew(), s_BlastNaExtend(), and s_BlastNaExtendAligned().
Int4* BlastMBLookupTable::next_pos |
Extra positions stored here.
Definition at line 255 of file blast_nalookup.h.
Referenced by BlastMBLookupTableDestruct(), s_FillContigMBTable(), s_FillDiscMBTable(), and s_MBLookup().
Int4* BlastMBLookupTable::next_pos2 |
Extra positions for the second template.
Definition at line 256 of file blast_nalookup.h.
Referenced by BlastMBLookupTableDestruct(), and s_FillDiscMBTable().
Int4 BlastMBLookupTable::num_unique_pos_added |
Number of positions added to the l.t.
Definition at line 266 of file blast_nalookup.h.
Referenced by BlastMBLookupTableNew(), s_FillContigMBTable(), and s_FillDiscMBTable().
Int4 BlastMBLookupTable::num_words_added |
Number of words added to the l.t.
Definition at line 267 of file blast_nalookup.h.
Referenced by BlastMBLookupTableNew(), s_FillContigMBTable(), and s_FillDiscMBTable().
PV_ARRAY_TYPE* BlastMBLookupTable::pv_array |
Presence vector, used for quick presence check.
Definition at line 257 of file blast_nalookup.h.
Referenced by BlastMBLookupTableDestruct(), BlastMBLookupTableNew(), s_FillContigMBTable(), s_FillDiscMBTable(), s_FillPV(), s_MBCountWordsInSubject_16_1(), s_MBLookup(), and s_ScanSubjectForWordCounts().
Int4 BlastMBLookupTable::pv_array_bts |
The exponent of 2 by which pv_array is smaller than the backbone.
Definition at line 259 of file blast_nalookup.h.
Referenced by BlastMBLookupTableNew(), s_FillContigMBTable(), s_FillDiscMBTable(), s_FillPV(), s_MBCountWordsInSubject_16_1(), and s_MBLookup().
Int4 BlastMBLookupTable::scan_step |
Step size for scanning the database.
Definition at line 252 of file blast_nalookup.h.
Referenced by BlastChooseNaExtend(), BlastMBLookupTableNew(), s_MBChooseScanSubject(), s_MBScanSubject_10_1(), s_MBScanSubject_10_2(), s_MBScanSubject_10_3(), s_MBScanSubject_11_1Mod4(), s_MBScanSubject_11_2Mod4(), s_MBScanSubject_11_3Mod4(), s_MBScanSubject_9_1(), s_MBScanSubject_9_2(), s_MBScanSubject_Any(), and NuclWordFinderTextFixture::setupLookupTable().
void* BlastMBLookupTable::scansub_callback |
function for scanning subject sequences
Definition at line 263 of file blast_nalookup.h.
Referenced by TestFixture::RunScanSubject(), and s_MBChooseScanSubject().
EDiscTemplateType BlastMBLookupTable::second_template_type |
Type of the second discontiguous word template.
Definition at line 248 of file blast_nalookup.h.
Referenced by s_FillDiscMBTable(), and s_MB_DiscWordScanSubject_TwoTemplates_1().
Boolean BlastMBLookupTable::stride |
is lookup table created with a stride
Definition at line 251 of file blast_nalookup.h.
Referenced by BlastMBLookupTableNew(), s_BlastNaExtend(), s_BlastNaExtendAligned(), and s_BlastNaExtendDirect().
Int4 BlastMBLookupTable::template_length |
Length of the discontiguous word template.
Definition at line 244 of file blast_nalookup.h.
Referenced by BOOST_AUTO_TEST_CASE(), s_BlastNaExtendDirect(), s_FillDiscMBTable(), s_MB_DiscWordScanSubject_1(), s_MB_DiscWordScanSubject_11_18_1(), s_MB_DiscWordScanSubject_11_21_1(), s_MB_DiscWordScanSubject_TwoTemplates_1(), TestFixture::ScanCheckHitsCore(), TestFixture::ScanMaxHitsTestCore(), TestFixture::ScanOffsetTestCore(), and NuclWordFinderTextFixture::setupLookupTable().
EDiscTemplateType BlastMBLookupTable::template_type |
Type of the discontiguous word template.
Definition at line 245 of file blast_nalookup.h.
Referenced by s_FillDiscMBTable(), s_MB_DiscWordScanSubject_1(), s_MB_DiscWordScanSubject_11_18_1(), s_MB_DiscWordScanSubject_11_21_1(), s_MB_DiscWordScanSubject_TwoTemplates_1(), s_MBChooseScanSubject(), and TestFixture::ScanCheckHitsCore().
Boolean BlastMBLookupTable::two_templates |
Use two templates simultaneously.
Definition at line 247 of file blast_nalookup.h.
Referenced by s_FillDiscMBTable(), and s_MBChooseScanSubject().
Int4 BlastMBLookupTable::word_length |
number of exact letter matches that will trigger an ungapped extension
Definition at line 239 of file blast_nalookup.h.
Referenced by BlastChooseNaExtend(), BlastMBLookupTableNew(), BlastNaExtendJumper(), s_BlastNaExtend(), s_BlastNaExtendAligned(), s_BlastNaExtendDirect(), s_FillContigMBTable(), s_FillPV(), and NuclWordFinderTextFixture::setupLookupTable().