Search Toolkit Book for BlastLinkHSPParameters

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 sum score for linked HSPs with big gaps.

Definition at line 147 of file blast_parameters.h.

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

◆ 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

Decay rate for linking HSPs and calculating cutoff scores.

Definition at line 142 of file blast_parameters.h.

Referenced by BLAST_LinkHsps(), BlastHitSavingParametersUpdate(), BlastInitialWordParametersUpdate(), BlastLinkHSPParametersNew(), BOOST_AUTO_TEST_CASE(), CalculateLinkHSPCutoffs(), s_BlastEvenGapLinkHSPs(), and s_SumHSPEvalue().

◆ 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

Small gap size for linking HSPs.

Definition at line 139 of file blast_parameters.h.

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

◆ 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:

include/algo/blast/core/blast_parameters.h

Public Attributes