NCBI C++ ToolKit
Public Attributes | List of all members
BlastHitSavingOptions Struct Reference

Search Toolkit Book for BlastHitSavingOptions

Options used when evaluating and saving hits These include: a. More...

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

+ Collaboration diagram for BlastHitSavingOptions:

Public Attributes

double expect_value
 The expect value cut-off threshold for an HSP, or a combined hit if sum statistics is used. More...
 
Int4 cutoff_score
 The (raw) score cut-off threshold. More...
 
double percent_identity
 The percent identity cut-off threshold. More...
 
Int4 hitlist_size
 Maximal number of database sequences to return results for. More...
 
Int4 hsp_num_max
 Maximal number of HSPs to save for one database sequence. More...
 
Int4 total_hsp_limit
 Maximal total number of HSPs to keep. More...
 
Int4 culling_limit
 If the query range of an HSP is contained in at least this many higher-scoring HSPs, throw away the HSP as redundant (turned off if zero) More...
 
Int4 mask_level
 Only keep the highest scoring HSP when more than one HSP overlaps the same region of the query by more than or equal to mask_level %. More...
 
Boolean do_sum_stats
 Force sum statistics to be used to combine HSPs, TRUE by default for all ungapped searches and translated gapped searches (except RPS-BLAST) More...
 
Int4 longest_intron
 The longest distance between HSPs allowed for combining via sum statistics with uneven gaps. More...
 
Int4 min_hit_length
 optional minimum alignment length; alignments not at least this long are discarded More...
 
Int4 min_diag_separation
 How many diagonals separate a hit from a substantial alignment before it's not blocked out. More...
 
EBlastProgramType program_number
 indicates blastn, blastp, etc. More...
 
BlastHSPFilteringOptionshsp_filt_opt
 Contains options to configure the HSP filtering/writering structures If not set, the default HSP filtering strategy is used. More...
 
double low_score_perc
 Low-score option. More...
 
double query_cov_hsp_perc
 Min query coverage hsp percentage. More...
 
Int4 max_hsps_per_subject
 Queries are paired reads, for mapping. More...
 
Boolean paired
 Splice HSPs for each query (for mapping RNA-Seq to a genome) More...
 
Boolean splice
 

Detailed Description

Options used when evaluating and saving hits These include: a.

Restrictions on the number of hits to be saved; b. Restrictions on the quality and positions of hits to be saved; c. Parameters used to evaluate the quality of hits.

Definition at line 392 of file blast_options.h.

Member Data Documentation

Int4 BlastHitSavingOptions::culling_limit

If the query range of an HSP is contained in at least this many higher-scoring HSPs, throw away the HSP as redundant (turned off if zero)

Definition at line 403 of file blast_options.h.

Referenced by BLAST_FillHitSavingOptions(), BlastHitSavingOptionsValidate(), CBlastHitSavingOptions::DebugDump(), CBlastOptionsLocal::GetCullingLimit(), and CBlastOptionsLocal::SetCullingLimit().

Int4 BlastHitSavingOptions::cutoff_score
Boolean BlastHitSavingOptions::do_sum_stats

Force sum statistics to be used to combine HSPs, TRUE by default for all ungapped searches and translated gapped searches (except RPS-BLAST)

Definition at line 412 of file blast_options.h.

Referenced by BlastHitSavingParametersNew(), BOOST_AUTO_TEST_CASE(), CBlastHitSavingOptions::DebugDump(), CBlastOptionsLocal::GetSumStatisticsMode(), and CBlastOptionsLocal::SetSumStatisticsMode().

double BlastHitSavingOptions::expect_value
Int4 BlastHitSavingOptions::hitlist_size
BlastHSPFilteringOptions* BlastHitSavingOptions::hsp_filt_opt
Int4 BlastHitSavingOptions::hsp_num_max

Maximal number of HSPs to save for one database sequence.

Definition at line 400 of file blast_options.h.

Referenced by BlastHspNumMax(), CBlastHitSavingOptions::DebugDump(), CBlastOptionsLocal::GetMaxNumHspPerSequence(), and CBlastOptionsLocal::SetMaxNumHspPerSequence().

Int4 BlastHitSavingOptions::longest_intron
double BlastHitSavingOptions::low_score_perc

Low-score option.

Do not pass ungapped alignments on for later processing if the hitlist is already full of other alignments unless the ungapped aligment is above the fraction X of the least significant database match. zero should turn this off.

Definition at line 435 of file blast_options.h.

Referenced by BLAST_PreliminarySearchEngine(), BlastHitSavingParametersNew(), CBlastOptionsLocal::GetLowScorePerc(), and CBlastOptionsLocal::SetLowScorePerc().

Int4 BlastHitSavingOptions::mask_level

Only keep the highest scoring HSP when more than one HSP overlaps the same region of the query by more than or equal to mask_level %.

-RMH-

Definition at line 406 of file blast_options.h.

Referenced by BlastHitSavingParametersUpdate(), CBlastOptionsLocal::GetMaskLevel(), and CBlastOptionsLocal::SetMaskLevel().

Int4 BlastHitSavingOptions::max_hsps_per_subject
Int4 BlastHitSavingOptions::min_diag_separation

How many diagonals separate a hit from a substantial alignment before it's not blocked out.

Must be > 0 to be used.

Definition at line 421 of file blast_options.h.

Referenced by BLAST_FillHitSavingOptions(), BLAST_GetGappedScore(), Blast_TracebackFromHSPList(), CBlastHitSavingOptions::DebugDump(), CBlastOptionsLocal::GetMinDiagSeparation(), and CBlastOptionsLocal::SetMinDiagSeparation().

Int4 BlastHitSavingOptions::min_hit_length

optional minimum alignment length; alignments not at least this long are discarded

Definition at line 419 of file blast_options.h.

Referenced by BOOST_AUTO_TEST_CASE(), and CBlastHitSavingOptions::DebugDump().

Boolean BlastHitSavingOptions::paired

Splice HSPs for each query (for mapping RNA-Seq to a genome)

Definition at line 446 of file blast_options.h.

Referenced by BlastHSPMapperParamsNew(), CBlastOptionsLocal::GetPaired(), and CBlastOptionsLocal::SetPaired().

double BlastHitSavingOptions::percent_identity
EBlastProgramType BlastHitSavingOptions::program_number

indicates blastn, blastp, etc.

Definition at line 423 of file blast_options.h.

Referenced by BlastHSPBestHitParamsNew(), BlastHSPCollectorParamsNew(), BlastHSPMapperParamsNew(), and CBlastOptionsLocal::SetProgram().

double BlastHitSavingOptions::query_cov_hsp_perc
Boolean BlastHitSavingOptions::splice
Int4 BlastHitSavingOptions::total_hsp_limit

Maximal total number of HSPs to keep.

Definition at line 402 of file blast_options.h.

Referenced by CBlastHitSavingOptions::DebugDump().


The documentation for this struct was generated from the following file:
Modified on Sat May 27 15:28:38 2017 by modify_doxy.py rev. 533848