NCBI C++ ToolKit
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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... | |
Parameter block for linking HSPs with sum statistics.
Definition at line 137 of file blast_parameters.h.
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().
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().
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().
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().
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().
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().
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().