composition_constants.h File Reference

Constants used in compositional score matrix adjustment. More...

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

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Macros
#define	COMPO_SCORE_MIN   INT2_MIN
	Minimum score in a matrix. More...
#define	COMPO_NUM_TRUE_AA   20
	Number of standard amino acids. More...
#define	COMPO_LARGEST_ALPHABET   28
	The largest alphabet supported by this code (the code supports 26 or 28 character amino acid alphabets). More...

Typedefs
typedef enum ECompoAdjustModes	ECompoAdjustModes
	An collection of constants that specify all permissible modes of composition adjustment. More...
typedef enum EMatrixAdjustRule	EMatrixAdjustRule
	An collection of constants that specify all rules that may be used to generate a compositionally adjusted matrix. More...

Enumerations
enum	ECompoAdjustModes {   eNoCompositionBasedStats = 0 , eCompositionBasedStats = 1 , eCompositionMatrixAdjust = 2 , eCompoForceFullMatrixAdjust = 3 ,   eNumCompoAdjustModes }
	An collection of constants that specify all permissible modes of composition adjustment. More...
enum	EMatrixAdjustRule {   eDontAdjustMatrix = (-1) , eCompoScaleOldMatrix = 0 , eUnconstrainedRelEntropy = 1 , eRelEntropyOldMatrixNewContext = 2 ,   eRelEntropyOldMatrixOldContext = 3 , eUserSpecifiedRelEntropy = 4 }
	An collection of constants that specify all rules that may be used to generate a compositionally adjusted matrix. More...

Detailed Description

Constants used in compositional score matrix adjustment.

Author

E. Michael Gertz, Alejandro Schaffer, Yi-Kuo Yu

Definition in file composition_constants.h.

Macro Definition Documentation

COMPO_LARGEST_ALPHABET

#define COMPO_LARGEST_ALPHABET   28

The largest alphabet supported by this code (the code supports 26 or 28 character amino acid alphabets).

Used to specify the size of structures that are statically allocated.

Definition at line 51 of file composition_constants.h.

COMPO_NUM_TRUE_AA

#define COMPO_NUM_TRUE_AA   20

Number of standard amino acids.

Definition at line 46 of file composition_constants.h.

COMPO_SCORE_MIN

#define COMPO_SCORE_MIN   INT2_MIN

Minimum score in a matrix.

Definition at line 43 of file composition_constants.h.

Typedef Documentation

ECompoAdjustModes

typedef enum ECompoAdjustModes ECompoAdjustModes

An collection of constants that specify all permissible modes of composition adjustment.

EMatrixAdjustRule

typedef enum EMatrixAdjustRule EMatrixAdjustRule

An collection of constants that specify all rules that may be used to generate a compositionally adjusted matrix.

Enumeration Type Documentation

ECompoAdjustModes

enum ECompoAdjustModes

An collection of constants that specify all permissible modes of composition adjustment.

Enumerator
eNoCompositionBasedStats	Don't use composition based statistics.
eCompositionBasedStats	Composition-based statistics as in NAR 29:2994-3005, 2001.
eCompositionMatrixAdjust	Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties. Cannot be applied to PSSMs.
eCompoForceFullMatrixAdjust	Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally. Cannot be applied to PSSMs.
eNumCompoAdjustModes

Definition at line 59 of file composition_constants.h.

EMatrixAdjustRule

enum EMatrixAdjustRule

An collection of constants that specify all rules that may be used to generate a compositionally adjusted matrix.

Enumerator
eDontAdjustMatrix
eCompoScaleOldMatrix
eUnconstrainedRelEntropy
eRelEntropyOldMatrixNewContext
eRelEntropyOldMatrixOldContext
eUserSpecifiedRelEntropy

Definition at line 76 of file composition_constants.h.