#include "ali_global.hxx"

Include dependency graph for ali_global.cxx:

Macros
#define	EXCLUSIVE_FLAG_DEFAULT 1

#define	MARK_FAMILY_FLAG_DEFAULT 0

#define	MARK_EXTENSION_FLAG_DEFAULT 0

#define	FIND_FAMILY_MODE_DEFAULT 1

#define	MAX_FAMILY_SIZE_DEFAULT 10

#define	MIN_FAMILY_SIZE_DEFAULT 5

#define	MIN_WEIGHT_DEFAULT 0.7

#define	EXT_MAX_WEIGHT_DEFAULT 0.2

#define	MULTI_GAP_FACTOR_DEFAULT 0.1

#define	INSERT_FACTOR_DEFAULT 2.0;

#define	MULTI_INSERT_FACTOR_DEFAULT 0.5;

#define	COST_LOW_DEFAULT 0.25

#define	COST_MIDDLE_DEFAULT 0.5

#define	COST_HIGH_DEFAULT 0.8

#define	MAX_COST_OF_SUB_PERCENT_DEFAULT 0.5

#define	MAX_COST_OF_HELIX 2.0

#define	ERROR_COUNT_DEFAULT 2

#define	MAX_NUMBER_OF_MAPS_DEFAULT 10

#define	MAX_NUMBER_OF_MAPS_ALIGNER_DEFAULT 2

#define	INTERVAL_BORDER_DEFAULT 5

#define	INTERVAL_CENTER_DEFAULT 5

#define	MATCHES_MIN_DEFAULT 1000

#define	PERCENT_MIN_DEFAULT 0.75

#define	FAM_LIST_MAX_DEFAULT 5

#define	EXT_LIST_MAX_DEFAULT 10

#define	USE_SPECIFIED_FAMILY_DEFAULT NULp

Variables
static double	default_substitute_matrix [5][5]

static double	default_binding_matrix [5][5]

Macro Definition Documentation

#define EXCLUSIVE_FLAG_DEFAULT 1

Definition at line 13 of file ali_global.cxx.

Referenced by ALI_GLOBAL::init().

#define MARK_FAMILY_FLAG_DEFAULT 0

Definition at line 14 of file ali_global.cxx.

Referenced by ALI_GLOBAL::init().

#define MARK_EXTENSION_FLAG_DEFAULT 0

Definition at line 15 of file ali_global.cxx.

Referenced by ALI_GLOBAL::init().

#define FIND_FAMILY_MODE_DEFAULT 1

Definition at line 16 of file ali_global.cxx.

Referenced by ALI_GLOBAL::init().

#define MAX_FAMILY_SIZE_DEFAULT 10

Definition at line 17 of file ali_global.cxx.

Referenced by ALI_GLOBAL::init().

#define MIN_FAMILY_SIZE_DEFAULT 5

Definition at line 18 of file ali_global.cxx.

Referenced by ALI_GLOBAL::init().

#define MIN_WEIGHT_DEFAULT 0.7

Definition at line 19 of file ali_global.cxx.

Referenced by ALI_GLOBAL::init().

#define EXT_MAX_WEIGHT_DEFAULT 0.2

Definition at line 20 of file ali_global.cxx.

Referenced by ALI_GLOBAL::init().

#define MULTI_GAP_FACTOR_DEFAULT 0.1

Definition at line 21 of file ali_global.cxx.

Referenced by ALI_GLOBAL::init().

#define INSERT_FACTOR_DEFAULT 2.0;

Definition at line 22 of file ali_global.cxx.

Referenced by ALI_GLOBAL::init().

#define MULTI_INSERT_FACTOR_DEFAULT 0.5;

Definition at line 23 of file ali_global.cxx.

Referenced by ALI_GLOBAL::init().

#define COST_LOW_DEFAULT 0.25

Definition at line 24 of file ali_global.cxx.

Referenced by ALI_GLOBAL::init().

#define COST_MIDDLE_DEFAULT 0.5

Definition at line 25 of file ali_global.cxx.

Referenced by ALI_GLOBAL::init().

#define COST_HIGH_DEFAULT 0.8

Definition at line 26 of file ali_global.cxx.

Referenced by ALI_GLOBAL::init().

#define MAX_COST_OF_SUB_PERCENT_DEFAULT 0.5

Definition at line 27 of file ali_global.cxx.

Referenced by ALI_GLOBAL::init().

#define MAX_COST_OF_HELIX 2.0

Definition at line 28 of file ali_global.cxx.

Referenced by ALI_GLOBAL::init().

#define ERROR_COUNT_DEFAULT 2

Definition at line 29 of file ali_global.cxx.

Referenced by ALI_GLOBAL::init().

#define MAX_NUMBER_OF_MAPS_DEFAULT 10

Definition at line 30 of file ali_global.cxx.

Referenced by ALI_GLOBAL::init().

#define MAX_NUMBER_OF_MAPS_ALIGNER_DEFAULT 2

Definition at line 31 of file ali_global.cxx.

Referenced by ALI_GLOBAL::init().

#define INTERVAL_BORDER_DEFAULT 5

Definition at line 32 of file ali_global.cxx.

Referenced by ALI_GLOBAL::init().

#define INTERVAL_CENTER_DEFAULT 5

Definition at line 33 of file ali_global.cxx.

Referenced by ALI_GLOBAL::init().

#define MATCHES_MIN_DEFAULT 1000

Definition at line 36 of file ali_global.cxx.

Referenced by ALI_GLOBAL::init().

#define PERCENT_MIN_DEFAULT 0.75

Definition at line 37 of file ali_global.cxx.

Referenced by ALI_GLOBAL::init().

#define FAM_LIST_MAX_DEFAULT 5

Definition at line 38 of file ali_global.cxx.

Referenced by ALI_GLOBAL::init().

#define EXT_LIST_MAX_DEFAULT 10

Definition at line 39 of file ali_global.cxx.

Referenced by ALI_GLOBAL::init().

#define USE_SPECIFIED_FAMILY_DEFAULT NULp

Definition at line 40 of file ali_global.cxx.

Referenced by ALI_GLOBAL::init().

Variable Documentation

double default_substitute_matrix[5][5]

static

Initial value:

= {
    
    { 0.0, 3.0, 1.0, 3.0, 5.0 }, 
    { 3.0, 0.0, 3.0, 1.0, 5.0 }, 
    { 1.0, 3.0, 0.0, 3.0, 5.0 }, 
    { 3.0, 1.0, 3.0, 0.0, 5.0 }, 
    { 5.0, 5.0, 5.0, 5.0, 0.0 } 
}

Definition at line 43 of file ali_global.cxx.

Referenced by ALI_GLOBAL::init().

double default_binding_matrix[5][5]

static

Initial value:

= {
    
    { 9.9, 9.9, 2.0, 0.9, 9.9 }, 
    { 9.9, 9.9, 0.6, 9.9, 9.9 }, 
    { 2.0, 0.6, 5.0, 1.1, 9.9 }, 
    { 0.9, 9.9, 1.1, 9.9, 9.9 }, 
    { 9.9, 9.9, 9.9, 9.9, 0.0 } 
}

Definition at line 52 of file ali_global.cxx.

Referenced by ALI_GLOBAL::init().

Macros

Variables

Macro Definition Documentation

Variable Documentation