_PSIAlignmentTraits Struct Reference

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Auxiliary structure to maintain information about two aligned regions between the query and a subject sequence. More...

Public Attributes
Uint4	start
	starting offset of alignment w.r.t. More...
Uint4	effective_length
	length of alignment not including Xs More...
Uint4	n_x_residues
	number of X residues in alignment More...
Uint4	n_identical
	number of identical residues in alignment More...

Detailed Description

Auxiliary structure to maintain information about two aligned regions between the query and a subject sequence.

It is used to store the data manipulated by the finite state machine used in s_PSIPurgeSimilarAlignments.

Definition at line 1040 of file blast_psi_priv.c.

Member Data Documentation

effective_length

Uint4 _PSIAlignmentTraits::effective_length

length of alignment not including Xs

Definition at line 1042 of file blast_psi_priv.c.

Referenced by _handleEitherAlignedNeitherX(), and _handleNeitherAligned().

n_identical

Uint4 _PSIAlignmentTraits::n_identical

number of identical residues in alignment

Definition at line 1044 of file blast_psi_priv.c.

Referenced by _handleBothAlignedSameResidueNoX(), and _handleNeitherAligned().

n_x_residues

Uint4 _PSIAlignmentTraits::n_x_residues

number of X residues in alignment

Definition at line 1043 of file blast_psi_priv.c.

Referenced by _handleEitherAlignedEitherX(), and _handleNeitherAligned().

start

Uint4 _PSIAlignmentTraits::start

starting offset of alignment w.r.t.

query

Definition at line 1041 of file blast_psi_priv.c.

Referenced by _handleNeitherAligned(), and _PSIResetAlignmentTraits().

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

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