BlastUngappedCutoffs Struct Reference

Search Toolkit Book for BlastUngappedCutoffs

All the ungapped cutoff values that can change from context to context. More...

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

Public Attributes
Int4	x_dropoff_init
	Raw X-dropoff value specified by the bit score in BlastInitialWordOptions. More...
Int4	x_dropoff
	Raw X-dropoff value used in the ungapped extension. More...
Int4	cutoff_score
	Cutoff score for saving ungapped hits. More...
Int4	reduced_nucl_cutoff_score
	for blastn, a reduced cutoff score for use with approximate ungapped alignments More...

Detailed Description

All the ungapped cutoff values that can change from context to context.

Definition at line 95 of file blast_parameters.h.

Member Data Documentation

cutoff_score

Int4 BlastUngappedCutoffs::cutoff_score

Cutoff score for saving ungapped hits.

Definition at line 99 of file blast_parameters.h.

Referenced by Blast_HSPReevaluateWithAmbiguitiesUngapped(), BlastInitialWordParametersUpdate(), BlastRPSWordFinder(), MB_IndexedWordFinder(), printBlastInitialWordParamters(), s_BlastAaWordFinder_OneHit(), s_BlastAaWordFinder_TwoHit(), s_BlastnDiagHashExtendInitialHit(), s_BlastnDiagTableExtendInitialHit(), s_ChainingAlignment(), and NuclWordFinderTextFixture::setupExtendWord().

reduced_nucl_cutoff_score

Int4 BlastUngappedCutoffs::reduced_nucl_cutoff_score

for blastn, a reduced cutoff score for use with approximate ungapped alignments

Definition at line 100 of file blast_parameters.h.

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

x_dropoff

Int4 BlastUngappedCutoffs::x_dropoff

Raw X-dropoff value used in the ungapped extension.

Definition at line 98 of file blast_parameters.h.

Referenced by BlastInitialWordParametersUpdate(), BlastRPSWordFinder(), MB_IndexedWordFinder(), printBlastInitialWordParamters(), s_BlastAaWordFinder_OneHit(), s_BlastAaWordFinder_TwoHit(), s_BlastnDiagHashExtendInitialHit(), s_BlastnDiagTableExtendInitialHit(), and NuclWordFinderTextFixture::setupExtendWord().

x_dropoff_init

Int4 BlastUngappedCutoffs::x_dropoff_init

Raw X-dropoff value specified by the bit score in BlastInitialWordOptions.

Definition at line 96 of file blast_parameters.h.

Referenced by BlastInitialWordParametersNew(), BlastInitialWordParametersUpdate(), and printBlastInitialWordParamters().

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

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