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BlastLinkHSPParameters Struct Reference

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Parameter block for linking HSPs with sum statistics. More...

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

Public Attributes

double gap_prob
 Probability of decay for linking HSPs. More...
 
Int4 gap_size
 Small gap size for linking HSPs. More...
 
Int4 overlap_size
 Maximal overlap allowed in successive linked HSPs. More...
 
double gap_decay_rate
 Decay rate for linking HSPs and calculating cutoff scores. More...
 
Int4 cutoff_small_gap
 Cutoff sum score for linked HSPs with small gaps. More...
 
Int4 cutoff_big_gap
 Cutoff sum score for linked HSPs with big gaps. More...
 
Int4 longest_intron
 Length of a longest intron for uneven gap linking of HSPs. More...
 

Detailed Description

Parameter block for linking HSPs with sum statistics.

Definition at line 137 of file blast_parameters.h.

Member Data Documentation

◆ cutoff_big_gap

Int4 BlastLinkHSPParameters::cutoff_big_gap

◆ cutoff_small_gap

Int4 BlastLinkHSPParameters::cutoff_small_gap

Cutoff sum score for linked HSPs with small gaps.

Small gap calculations are ignored if this value is set to 0.

Definition at line 144 of file blast_parameters.h.

Referenced by BlastLinkHSPParametersUpdate(), BOOST_AUTO_TEST_CASE(), CalculateLinkHSPCutoffs(), s_BlastEvenGapLinkHSPs(), LinkHspTestFixture::setupCutoffScores(), and LinkHspTestFixture::setupHitParams().

◆ gap_decay_rate

double BlastLinkHSPParameters::gap_decay_rate

◆ gap_prob

double BlastLinkHSPParameters::gap_prob

Probability of decay for linking HSPs.

Definition at line 138 of file blast_parameters.h.

Referenced by BlastLinkHSPParametersNew(), BOOST_AUTO_TEST_CASE(), CalculateLinkHSPCutoffs(), and s_BlastEvenGapLinkHSPs().

◆ gap_size

Int4 BlastLinkHSPParameters::gap_size

◆ longest_intron

Int4 BlastLinkHSPParameters::longest_intron

Length of a longest intron for uneven gap linking of HSPs.

Definition at line 148 of file blast_parameters.h.

Referenced by BLAST_LinkHsps(), BlastHitSavingParametersNew(), s_BlastUnevenGapLinkHSPs(), s_LinkedHSPSetsAdmissible(), s_SumHSPEvalue(), and LinkHspTestFixture::setupHitParams().

◆ overlap_size

Int4 BlastLinkHSPParameters::overlap_size

Maximal overlap allowed in successive linked HSPs.

Definition at line 140 of file blast_parameters.h.

Referenced by BlastLinkHSPParametersNew(), CalculateLinkHSPCutoffs(), s_BlastEvenGapLinkHSPs(), s_LinkedHSPSetsAdmissible(), and s_SumHSPEvalue().


The documentation for this struct was generated from the following file:
Modified on Fri Sep 20 14:57:20 2024 by modify_doxy.py rev. 669887