_PSIMsa Struct Reference

Search Toolkit Book for _PSIMsa

#include <blast_psi_priv.h>

Collaboration diagram for _PSIMsa:

[legend]List of all members.

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Detailed Description

Internal multiple alignment data structure used by the PSSM engine.

Definition at line 203 of file blast_psi_priv.h.

Public Attributes
PSIMsaDimensions *	dimensions
	dimensions of field below
_PSIMsaCell **	cell
	multiple sequence alignment matrix (dimensions: query_length x num_seqs + 1)
Uint1 *	query
	query sequence (length: query_length)
Uint4 **	residue_counts
	matrix to keep track of the raw residue counts at each position of the multiple sequence alignment (dimensions: query_length x alphabet_size)
Uint4	alphabet_size
	number of elements in alphabet
Uint4 *	num_matching_seqs
	number of sequences aligned at a given position in the multiple sequence alignment (length: query_length).

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Member Data Documentation

Uint4 _PSIMsa::alphabet_size

number of elements in alphabet Definition at line 215 of file blast_psi_priv.h. Referenced by _PSIComputeFreqRatios(), _PSIMsaNew(), and _PSIUpdatePositionCounts().

_PSIMsaCell** _PSIMsa::cell

multiple sequence alignment matrix (dimensions: query_length x num_seqs + 1) Definition at line 205 of file blast_psi_priv.h. Referenced by _PSICalculateMatchWeights(), _PSICalculateNormalizedSequenceWeights(), _PSICheckSequenceWeights(), _PSIComputeFreqRatios(), _PSIComputePositionExtents(), _PSIGetAlignedSequencesForPosition(), _PSIGetLeftExtents(), _PSIGetRightExtents(), _PSIMsaFree(), _PSIMsaNew(), _PSISpreadGapWeights(), _PSIStructureGroupCustomization(), s_PSIValidateAlignedColumns(), s_PSIValidateNoFlankingGaps(), and s_PSIValidateNoGapsInQuery().

PSIMsaDimensions* _PSIMsa::dimensions

dimensions of field below Definition at line 204 of file blast_psi_priv.h. Referenced by _PSICheckSequenceWeights(), _PSIComputeAlignedRegionLengths(), _PSIComputeAlignmentBlocks(), _PSIComputeFreqRatios(), _PSIComputePositionExtents(), _PSIComputeSequenceWeights(), _PSIGetAlignedSequencesForPosition(), _PSIGetLeftExtents(), _PSIGetRightExtents(), _PSIMsaFree(), _PSIMsaNew(), _PSISaveDiagnostics(), _PSISpreadGapWeights(), _PSIStructureGroupCustomization(), _PSIUpdatePositionCounts(), PSICreatePssmWithDiagnostics(), s_PSIValidateAlignedColumns(), s_PSIValidateNoFlankingGaps(), s_PSIValidateNoGapsInQuery(), and s_PSIValidateParticipatingSequences().

Uint4* _PSIMsa::num_matching_seqs

number of sequences aligned at a given position in the multiple sequence alignment (length: query_length). Corresponds to posit.h:posSearch->posCount Definition at line 217 of file blast_psi_priv.h. Referenced by _PSICheckSequenceWeights(), _PSIComputeSequenceWeights(), _PSIMsaFree(), _PSISpreadGapWeights(), and _PSIUpdatePositionCounts().

Uint1* _PSIMsa::query

query sequence (length: query_length) Definition at line 208 of file blast_psi_priv.h. Referenced by _PSIMsaFree(), PSICreatePssmWithDiagnostics(), and s_PSIValidateNoGapsInQuery().

Uint4** _PSIMsa::residue_counts

matrix to keep track of the raw residue counts at each position of the multiple sequence alignment (dimensions: query_length x alphabet_size) Definition at line 210 of file blast_psi_priv.h. Referenced by _PSIMsaFree(), and _PSIUpdatePositionCounts().

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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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