ARB
Macros | Variables
ali_global.cxx File Reference
#include "ali_global.hxx"
Include dependency graph for ali_global.cxx:

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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().