GDE_def.h File Reference

#include <arbdbt.h>

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Classes
struct	TimeStamp
struct	NA_Sequence
struct	NA_Alignment

Macros
#define	gde_assert(bed)   arb_assert(bed)
#define	GBUFSIZ   4096
#define	TEXTFIELDWIDTH   15
#define	TEXTFIELD   0x1
#define	SLIDER   0x2
#define	CHOOSER   0x3
#define	CHOICE_MENU   0x4
#define	CHOICE_LIST   0x5
#define	CHOICE_TREE   0x6
#define	CHOICE_SAI   0x7
#define	CHOICE_WEIGHTS   0x8
#define	FILE_SELECTOR   0x9
#define	GDE   0x100
#define	GENBANK   0x101
#define	NA_FLAT   0x102
#define	NONE   0x0
#define	ALL   0x10
#define	NASEQ_ALIGN   0x201
#define	DNA   0x300
#define	RNA   0x301
#define	TEXT   0x302
#define	MASK   0x303
#define	PROTEIN   0x304
#define	IS_5_TO_3   0x01
#define	IS_3_TO_5   0x02
#define	IS_CIRCULAR   0x04
#define	IS_PRIMARY   0x10
#define	IS_SECONDARY   0x20
#define	IS_ORIG_PRIMARY   0x80
#define	IS_ORIG_SECONDARY   0x100
#define	IS_ORIG_5_TO_3   0x200
#define	IS_ORIG_3_TO_5   0x400
#define	DEFAULT_X_ATTR   IS_5_TO_3+IS_PRIMARY;
#define	SIZE_FIELD_GENBANK   80
#define	SIZE_ID   SIZE_FIELD_GENBANK
#define	SIZE_SEQ_NAME   SIZE_FIELD_GENBANK
#define	SIZE_SHORT_NAME   32
#define	SIZE_DESCRIPTION   SIZE_FIELD_GENBANK
#define	SIZE_AUTHORITY   SIZE_FIELD_GENBANK

Typedefs
typedef unsigned char	NA_Base

Functions
void	strcpy_truncate (char *dest, const char *source, size_t dest_size)

Macro Definition Documentation

#define gde_assert

(

bed

)

arb_assert(bed)

Definition at line 12 of file GDE_def.h.

Referenced by export_to_DB(), GDE_load_menu(), GDE_menuitem_cb(), GDE_startaction_cb(), InsertDatainGDE(), LoadFile(), LoadMenus(), NormalizeOffset(), ParseMenus(), ReadArbdb(), ReadArbdb2(), setup_gde_config_def(), and write_sequence_autoinc_alisize().

#define GBUFSIZ   4096

Definition at line 14 of file GDE_def.h.

Referenced by AppendNA(), AsciiTime(), FindType(), GDE_startaction_cb(), ParseMenus(), ReadGen(), and ReadNA_Flat().

#define TEXTFIELDWIDTH   15

Definition at line 15 of file GDE_def.h.

Referenced by ParseMenus().

#define TEXTFIELD   0x1

Definition at line 18 of file GDE_def.h.

Referenced by GDE_menuitem_cb(), ParseMenus(), and ReplaceArgs().

#define SLIDER   0x2

Definition at line 19 of file GDE_def.h.

Referenced by GDE_menuitem_cb(), ParseMenus(), and ReplaceArgs().

#define CHOOSER   0x3

Definition at line 20 of file GDE_def.h.

Referenced by GDE_menuitem_cb(), ParseMenus(), and ReplaceArgs().

#define CHOICE_MENU   0x4

Definition at line 21 of file GDE_def.h.

Referenced by GDE_menuitem_cb(), ParseMenus(), and ReplaceArgs().

#define CHOICE_LIST   0x5

Definition at line 22 of file GDE_def.h.

Referenced by ParseMenus(), and ReplaceArgs().

#define CHOICE_TREE   0x6

Definition at line 23 of file GDE_def.h.

Referenced by GDE_menuitem_cb(), ParseMenus(), and ReplaceArgs().

#define CHOICE_SAI   0x7

Definition at line 24 of file GDE_def.h.

Referenced by GDE_menuitem_cb(), ParseMenus(), and ReplaceArgs().

#define CHOICE_WEIGHTS   0x8

Definition at line 25 of file GDE_def.h.

Referenced by GDE_menuitem_cb(), ParseMenus(), and ReplaceArgs().

#define FILE_SELECTOR   0x9

Definition at line 26 of file GDE_def.h.

Referenced by GDE_menuitem_cb(), ParseMenus(), ReplaceArgs(), and shall_store_in_config().

#define GDE   0x100

Definition at line 29 of file GDE_def.h.

Referenced by FindType(), GDE_startaction_cb(), LoadFile(), and ParseMenus().

#define GENBANK   0x101

Definition at line 30 of file GDE_def.h.

#define NA_FLAT   0x102

Definition at line 31 of file GDE_def.h.

Referenced by FindType(), GDE_startaction_cb(), LoadFile(), and ParseMenus().

#define NONE   0x0

Definition at line 34 of file GDE_def.h.

Referenced by DI_MATRIX::calculate_pro(), di_protdist::di_protdist(), GDE_startaction_cb(), di_protdist::makedists(), sq_calc_seq_quality_cb(), and SQ_check_tree_structure().

#define ALL   0x10

Definition at line 35 of file GDE_def.h.

#define NASEQ_ALIGN   0x201

Definition at line 38 of file GDE_def.h.

Referenced by FindType(), and LoadData().

#define DNA   0x300

Definition at line 41 of file GDE_def.h.

Referenced by export_to_DB(), getelem(), InitNASeq(), InsertDatainGDE(), putelem(), ReadGen(), ReadNA_Flat(), WriteGDE(), WriteGen(), and WriteNA_Flat().

#define RNA   0x301

Definition at line 42 of file GDE_def.h.

Referenced by export_to_DB(), getelem(), InitNASeq(), InsertDatainGDE(), putelem(), ReadGen(), WriteGDE(), WriteGen(), and WriteNA_Flat().

#define TEXT   0x302

Definition at line 43 of file GDE_def.h.

Referenced by getelem(), InitNASeq(), InsertDatainGDE(), ParseMenus(), putelem(), ReadGen(), ReadNA_Flat(), WriteGDE(), and WriteNA_Flat().

#define MASK   0x303

Definition at line 44 of file GDE_def.h.

Referenced by getelem(), InitNASeq(), putelem(), ReadGen(), ReadNA_Flat(), WriteGDE(), WriteGen(), and WriteNA_Flat().

#define PROTEIN   0x304

Definition at line 45 of file GDE_def.h.

Referenced by export_to_DB(), getelem(), InitNASeq(), InsertDatainGDE(), putelem(), ReadGen(), ReadNA_Flat(), WriteGDE(), WriteGen(), and WriteNA_Flat().

#define IS_5_TO_3   0x01

Definition at line 48 of file GDE_def.h.

Referenced by InitNASeq(), and WriteGDE().

#define IS_3_TO_5   0x02

Definition at line 49 of file GDE_def.h.

Referenced by WriteGDE().

#define IS_CIRCULAR   0x04

Definition at line 50 of file GDE_def.h.

Referenced by ReadGen(), WriteGDE(), and WriteGen().

#define IS_PRIMARY   0x10

Definition at line 51 of file GDE_def.h.

Referenced by InitNASeq(), and WriteGDE().

#define IS_SECONDARY   0x20

Definition at line 52 of file GDE_def.h.

Referenced by WriteGDE().

#define IS_ORIG_PRIMARY   0x80

Definition at line 53 of file GDE_def.h.

Referenced by WriteGDE().

#define IS_ORIG_SECONDARY   0x100

Definition at line 54 of file GDE_def.h.

Referenced by WriteGDE().

#define IS_ORIG_5_TO_3   0x200

Definition at line 55 of file GDE_def.h.

Referenced by WriteGDE().

#define IS_ORIG_3_TO_5   0x400

Definition at line 56 of file GDE_def.h.

Referenced by WriteGDE().

#define DEFAULT_X_ATTR   IS_5_TO_3+IS_PRIMARY;

Definition at line 58 of file GDE_def.h.

Referenced by ReadGen(), and set_constant_fields().

#define SIZE_FIELD_GENBANK   80

Definition at line 76 of file GDE_def.h.

#define SIZE_ID   SIZE_FIELD_GENBANK

Definition at line 77 of file GDE_def.h.

Referenced by InitNASeq(), InsertDatainGDE(), and ReadGen().

#define SIZE_SEQ_NAME   SIZE_FIELD_GENBANK

Definition at line 78 of file GDE_def.h.

Referenced by InsertDatainGDE(), and ReadGen().

#define SIZE_SHORT_NAME   32

Definition at line 79 of file GDE_def.h.

Referenced by InsertDatainGDE(), ReadGen(), and ReadNA_Flat().

#define SIZE_DESCRIPTION   SIZE_FIELD_GENBANK

Definition at line 80 of file GDE_def.h.

Referenced by ReadGen().

#define SIZE_AUTHORITY   SIZE_FIELD_GENBANK

Definition at line 81 of file GDE_def.h.

Referenced by InsertDatainGDE(), and ReadGen().

Typedef Documentation

typedef unsigned char NA_Base

Definition at line 73 of file GDE_def.h.

Function Documentation

void strcpy_truncate ( char *  dest, const char *  source, size_t  dest_size  )

inline

Definition at line 137 of file GDE_def.h.

References arb_assert.

Referenced by InitNASeq(), InsertDatainGDE(), ReadArbdb(), ReadGen(), ReadNA_Flat(), and truncate_4000().