_PSISequenceWeights Struct Reference

Search Toolkit Book for _PSISequenceWeights

#include <blast_psi_priv.h>

List of all members.

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Detailed Description

Internal data structure to keep computed sequence weights.

Definition at line 304 of file blast_psi_priv.h.

Public Attributes
double **	match_weights
	weighted observed residue frequencies (f_i in 2001 paper).
Uint4	match_weights_size
	kept for help deallocate the field above
double *	norm_seq_weights
	Stores the normalized sequence weights (length: num_seqs + 1).
double *	row_sigma
	array of length num_seqs + 1
double *	sigma
	array of length query_length
double *	std_prob
	standard amino acid probabilities
double *	gapless_column_weights
	FIXME.
int **	posDistinctDistrib
	For position i, how many positions in its block have j distinct letters.
Uint4	posDistinctDistrib_size
	Kept to deallocate field above.
int *	posNumParticipating
	number of sequences at each position.

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Member Data Documentation

double* _PSISequenceWeights::gapless_column_weights

FIXME. Definition at line 330 of file blast_psi_priv.h. Referenced by _PSICalculateMatchWeights(), _PSISequenceWeightsFree(), and _PSISequenceWeightsNew().

double** _PSISequenceWeights::match_weights

weighted observed residue frequencies (f_i in 2001 paper). (dimensions: query_length x BlastScoreBlk's alphabet_size) Definition at line 314 of file blast_psi_priv.h. Referenced by _PSICalculateMatchWeights(), _PSISequenceWeightsFree(), _PSISequenceWeightsNew(), and s_fillColumnProbabilities().

Uint4 _PSISequenceWeights::match_weights_size

kept for help deallocate the field above Definition at line 317 of file blast_psi_priv.h. Referenced by _PSISequenceWeightsFree(), and _PSISequenceWeightsNew().

double* _PSISequenceWeights::norm_seq_weights

Stores the normalized sequence weights (length: num_seqs + 1). Definition at line 319 of file blast_psi_priv.h. Referenced by _PSICalculateMatchWeights(), _PSISequenceWeightsFree(), and _PSISequenceWeightsNew().

int** _PSISequenceWeights::posDistinctDistrib

For position i, how many positions in its block have j distinct letters. Copied from posit.h:posSearchItems.posDistinctDistrib Definition at line 331 of file blast_psi_priv.h. Referenced by _PSISequenceWeightsFree(), _PSISequenceWeightsNew(), and s_effectiveObservations().

Uint4 _PSISequenceWeights::posDistinctDistrib_size

Kept to deallocate field above. Definition at line 334 of file blast_psi_priv.h. Referenced by _PSISequenceWeightsFree(), and _PSISequenceWeightsNew().

int* _PSISequenceWeights::posNumParticipating

number of sequences at each position. Copied from posit.h:posSearchItems.posNumParticipating Definition at line 335 of file blast_psi_priv.h. Referenced by _PSISequenceWeightsFree(), _PSISequenceWeightsNew(), and s_effectiveObservations().

double* _PSISequenceWeights::row_sigma

array of length num_seqs + 1 Definition at line 321 of file blast_psi_priv.h. Referenced by _PSISequenceWeightsFree(), and _PSISequenceWeightsNew().

double* _PSISequenceWeights::sigma

array of length query_length Definition at line 324 of file blast_psi_priv.h. Referenced by _PSISequenceWeightsFree(), and _PSISequenceWeightsNew().

double* _PSISequenceWeights::std_prob

standard amino acid probabilities Definition at line 326 of file blast_psi_priv.h. Referenced by _PSISaveDiagnostics(), _PSISequenceWeightsFree(), _PSISequenceWeightsNew(), and PSICreatePssmWithDiagnostics().

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The documentation for this struct was generated from the following file:

• src/algo/blast/core/blast_psi_priv.h

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