_PSIAlignmentTraits Struct Reference

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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 972 of file blast_psi_priv.c.

Public Attributes

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

Member Data Documentation

Uint4 _PSIAlignmentTraits::effective_length
 

length of alignment not including Xs

Definition at line 974 of file blast_psi_priv.c.

Referenced by _handleEitherAlignedNeitherX(), and _handleNeitherAligned().

Uint4 _PSIAlignmentTraits::n_identical
 

number of identical residues in alignment

Definition at line 976 of file blast_psi_priv.c.

Referenced by _handleBothAlignedSameResidueNoX(), and _handleNeitherAligned().

Uint4 _PSIAlignmentTraits::n_x_residues
 

number of X residues in alignment

Definition at line 975 of file blast_psi_priv.c.

Referenced by _handleEitherAlignedEitherX(), and _handleNeitherAligned().

Uint4 _PSIAlignmentTraits::start
 

starting offset of alignment w.r.t.

query

Definition at line 973 of file blast_psi_priv.c.

Referenced by _handleNeitherAligned().

The documentation for this struct was generated from the following file:
Generated on Mon Dec 7 09:48:28 2009 for NCBI C++ ToolKit by  doxygen 1.4.6
Modified on Mon Dec 07 16:22:18 2009 by modify_doxy.py rev. 173732