NCBI C++ ToolKit
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BlastInitialWordParameters Struct Reference

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Parameter block that contains a pointer to BlastInitialWordOptions and the values derived from it. More...

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

+ Collaboration diagram for BlastInitialWordParameters:

Public Attributes

BlastInitialWordOptionsoptions
 The original (unparsed) options. More...
 
Int4 x_dropoff_max
 largest X-drop cutoff across all contexts More...
 
Int4 cutoff_score_min
 smallest cutoff score across all contexts More...
 
BlastUngappedCutoffscutoffs
 cutoff values (one per context) More...
 
ESeedContainerType container_type
 How to store offset pairs for initial seeds? More...
 
Int4 nucl_score_table [256]
 the combined score of all match/mismatch combinations for aligning four bases More...
 
Boolean matrix_only_scoring
 Use the scoring matrix ( not table ) to score ungapped and gapped alignments -RMH-. More...
 
Boolean ungapped_extension
 Should an ungapped extension be performed? More...
 

Detailed Description

Parameter block that contains a pointer to BlastInitialWordOptions and the values derived from it.

Definition at line 108 of file blast_parameters.h.

Member Data Documentation

◆ container_type

ESeedContainerType BlastInitialWordParameters::container_type

◆ cutoff_score_min

Int4 BlastInitialWordParameters::cutoff_score_min

◆ cutoffs

BlastUngappedCutoffs* BlastInitialWordParameters::cutoffs

◆ matrix_only_scoring

Boolean BlastInitialWordParameters::matrix_only_scoring

Use the scoring matrix ( not table ) to score ungapped and gapped alignments -RMH-.

Definition at line 118 of file blast_parameters.h.

Referenced by BlastInitialWordParametersNew(), s_BlastnDiagHashExtendInitialHit(), and s_BlastnDiagTableExtendInitialHit().

◆ nucl_score_table

Int4 BlastInitialWordParameters::nucl_score_table[256]

the combined score of all match/mismatch combinations for aligning four bases

Definition at line 116 of file blast_parameters.h.

Referenced by BlastInitialWordParametersNew(), MB_IndexedWordFinder(), s_BlastnDiagHashExtendInitialHit(), s_BlastnDiagTableExtendInitialHit(), and NuclWordFinderTextFixture::setupExtendWord().

◆ options

BlastInitialWordOptions* BlastInitialWordParameters::options

◆ ungapped_extension

Boolean BlastInitialWordParameters::ungapped_extension

◆ x_dropoff_max

Int4 BlastInitialWordParameters::x_dropoff_max

The documentation for this struct was generated from the following file:
Modified on Mon Apr 22 04:01:27 2024 by modify_doxy.py rev. 669887