NCBI C++ ToolKit
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BlastScoreBlk Struct Reference

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Structure used for scoring calculations. More...

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

+ Collaboration diagram for BlastScoreBlk:

Public Attributes

Boolean protein_alphabet
 TRUE if alphabet_code is for a protein alphabet (e.g., ncbistdaa etc.), FALSE for nt. More...
 
Uint1 alphabet_code
 NCBI alphabet code. More...
 
Int2 alphabet_size
 size of alphabet. More...
 
Int2 alphabet_start
 numerical value of 1st letter. More...
 
char * name
 name of scoring matrix. More...
 
ListNodecomments
 Comments about scoring matrix. More...
 
SBlastScoreMatrixmatrix
 scoring matrix data More...
 
SPsiBlastScoreMatrixpsi_matrix
 PSSM and associated data. More...
 
Boolean matrix_only_scoring
 Score ungapped/gapped alignment only using the matrix parameters and with raw scores. More...
 
Boolean complexity_adjusted_scoring
 Use cross_match-like complexity adjustment on raw scores. More...
 
Int4 loscore
 Min. More...
 
Int4 hiscore
 Max. More...
 
Int4 penalty
 penalty for mismatch in blastn. More...
 
Int4 reward
 reward for match in blastn. More...
 
double scale_factor
 multiplier for all cutoff and dropoff scores More...
 
Boolean read_in_matrix
 If TRUE, matrix is read in, otherwise produce one from penalty and reward above. More...
 
Blast_ScoreFreq ** sfp
 score frequencies for scoring matrix. More...
 
Blast_KarlinBlk ** kbp
 Karlin-Altschul parameters. More...
 
Blast_KarlinBlk ** kbp_gap
 K-A parameters for gapped alignments. More...
 
Blast_GumbelBlkgbp
 Gumbel parameters for FSC. More...
 
Blast_KarlinBlk ** kbp_std
 K-A parameters for ungapped alignments. More...
 
Blast_KarlinBlk ** kbp_psi
 K-A parameters for position-based alignments. More...
 
Blast_KarlinBlk ** kbp_gap_std
 K-A parameters for std (not position-based) alignments. More...
 
Blast_KarlinBlk ** kbp_gap_psi
 K-A parameters for psi alignments. More...
 
Blast_KarlinBlkkbp_ideal
 Ideal values (for query with average database composition). More...
 
Int4 number_of_contexts
 Used by sfp and kbp, how large are these. More...
 
Uint1ambiguous_res
 Array of ambiguous res. More...
 
Int2 ambig_size
 size of array above. More...
 
Int2 ambig_occupy
 How many occupied? More...
 
Boolean round_down
 Score must be rounded down to nearest even score if odd. More...
 

Detailed Description

Structure used for scoring calculations.

Definition at line 177 of file blast_stat.h.

Member Data Documentation

Uint1 BlastScoreBlk::alphabet_code
Int2 BlastScoreBlk::alphabet_size
Int2 BlastScoreBlk::alphabet_start
Int2 BlastScoreBlk::ambig_occupy

How many occupied?

Definition at line 219 of file blast_stat.h.

Referenced by BLAST_ScoreSetAmbigRes(), BlastResCompStr(), CBlastScoreBlk::DebugDump(), and s_BlastScoreBlk_Copy().

Int2 BlastScoreBlk::ambig_size

size of array above.

FIXME: not needed here?

Definition at line 219 of file blast_stat.h.

Referenced by BLAST_ScoreSetAmbigRes(), CBlastScoreBlk::DebugDump(), and s_BlastScoreBlk_Copy().

Uint1* BlastScoreBlk::ambiguous_res

Array of ambiguous res.

(e.g, 'X', 'N')

Definition at line 218 of file blast_stat.h.

Referenced by BLAST_ScoreSetAmbigRes(), BlastResCompStr(), BlastScoreBlkFree(), and s_BlastScoreBlk_Copy().

ListNode* BlastScoreBlk::comments

Comments about scoring matrix.

Definition at line 184 of file blast_stat.h.

Referenced by BlastScoreBlkFree(), BlastScoreBlkNucleotideMatrixRead(), BlastScoreBlkProteinMatrixRead(), and s_BlastScoreBlk_Copy().

Boolean BlastScoreBlk::complexity_adjusted_scoring

Use cross_match-like complexity adjustment on raw scores.

-RMH-

Definition at line 195 of file blast_stat.h.

Referenced by Blast_TracebackFromHSPList(), BlastSetup_ScoreBlkInit(), and s_BlastScoreBlk_Copy().

Blast_GumbelBlk* BlastScoreBlk::gbp
Int4 BlastScoreBlk::hiscore
Blast_KarlinBlk** BlastScoreBlk::kbp
Blast_KarlinBlk** BlastScoreBlk::kbp_gap
Blast_KarlinBlk ** BlastScoreBlk::kbp_gap_psi
Blast_KarlinBlk ** BlastScoreBlk::kbp_gap_std
Blast_KarlinBlk* BlastScoreBlk::kbp_ideal
Blast_KarlinBlk ** BlastScoreBlk::kbp_psi
Blast_KarlinBlk** BlastScoreBlk::kbp_std
Int4 BlastScoreBlk::loscore
SBlastScoreMatrix* BlastScoreBlk::matrix
Boolean BlastScoreBlk::matrix_only_scoring

Score ungapped/gapped alignment only using the matrix parameters and with raw scores.

Ignore penalty/reward and do not report Karlin-Altschul stats. This is used by the rmblastn program. -RMH-

Definition at line 189 of file blast_stat.h.

Referenced by BLAST_PreliminarySearchEngine(), Blast_ScoreBlkMatrixInit(), BlastExtensionParametersNew(), BlastHitSavingParametersUpdate(), BlastInitialWordParametersNew(), BlastInitialWordParametersUpdate(), BOOST_AUTO_TEST_CASE(), s_BlastScoreBlk_Copy(), and s_BlastSearchEngineCore().

char* BlastScoreBlk::name
Int4 BlastScoreBlk::number_of_contexts
Int4 BlastScoreBlk::penalty
Boolean BlastScoreBlk::protein_alphabet
SPsiBlastScoreMatrix* BlastScoreBlk::psi_matrix
Boolean BlastScoreBlk::read_in_matrix

If TRUE, matrix is read in, otherwise produce one from penalty and reward above.

Definition at line 202 of file blast_stat.h.

Referenced by Blast_ScoreBlkMatrixFill(), Blast_ScoreBlkMatrixInit(), CBlastScoreBlk::DebugDump(), s_BlastScoreBlk_Copy(), and s_PHIScoreBlkFill().

Int4 BlastScoreBlk::reward
Boolean BlastScoreBlk::round_down
double BlastScoreBlk::scale_factor
Blast_ScoreFreq** BlastScoreBlk::sfp

The documentation for this struct was generated from the following file:
Modified on Wed Aug 16 05:49:42 2017 by modify_doxy.py rev. 533848