ARB
Functions
GDE_proto.h File Reference
#include <attributes.h>
#include "GDE_menu.h"
#include "GDE_extglob.h"
Include dependency graph for GDE_proto.h:
This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Functions

charGDE_makeawarname (GmenuItem *gmenuitem, long i)
 
charGDE_maketmpawarname (GmenuItem *gmenuitem, long i)
 
void GDE_load_menu (AW_window *awm, AW_active dummy_1x, const char *menulabel)
 
GB_ERROR GDE_init (AW_root *aw_root, AW_default aw_def, GBDATA *gb_main, GDE_get_sequences_cb get_sequences, GDE_format_alignment_cb format_ali, gde_window_type window_type)
 
void LoadData (char *filen, NA_Alignment &dataset)
 
void AppendNA (NA_Base *buffer, int len, NA_Sequence *seq)
 
void Ascii2NA (char *buffer, int len, int matrix[16])
 
int WriteNA_Flat (NA_Alignment &aln, char *filename, int method)
 
void Warning (const char *s)
 
void InitNASeq (NA_Sequence *seq, int type)
 
GB_ERROR ReadGen (char *filename, NA_Alignment &dataset)
 
int WriteGen (NA_Alignment &aln, char *filename, int method)
 
void SetTime (void *b)
 
int WriteGDE (NA_Alignment &aln, char *filename, int method)
 
charuniqueID (void)
 
GB_ERROR LoadMenus (void)
 
bool Find (const char *target, const char *key)
 
int Find2 (const char *target, const char *key)
 
int Arbdb_get_curelem (NA_Alignment &dataset)
 
int ReadArbdb2 (NA_Alignment &dataset, AP_filter *filter, GapCompression compress, bool cutoff_stop_codon, TypeInfo typeinfo) __ATTR__USERESULT
 
int ReadArbdb (NA_Alignment &dataset, bool marked, AP_filter *filter, GapCompression compress, bool cutoff_stop_codon, TypeInfo typeinfo) __ATTR__USERESULT
 
int getelem (NA_Sequence *a, int b)
 
void putelem (NA_Sequence *a, int b, NA_Base c)
 
void GDE_startaction_cb (AW_window *aw, GmenuItem *gmenuitem)
 

Function Documentation

char* GDE_makeawarname ( GmenuItem gmenuitem,
long  i 
)

Definition at line 65 of file GDE.cxx.

References AWAR_PREFIX_GDE, and GDE_makeawarname_in().

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

char* GDE_maketmpawarname ( GmenuItem gmenuitem,
long  i 
)

Definition at line 66 of file GDE.cxx.

References AWAR_PREFIX_GDE_TEMP, and GDE_makeawarname_in().

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

void GDE_load_menu ( AW_window awm,
AW_active  dummy_1x,
const char menulabel 
)
GB_ERROR GDE_init ( AW_root aw_root,
AW_default  aw_def,
GBDATA gb_main,
GDE_get_sequences_cb  get_sequences,
GDE_format_alignment_cb  format_ali,
gde_window_type  window_type 
)
void LoadData ( char filen,
NA_Alignment dataset 
)
void AppendNA ( NA_Base buffer,
int  len,
NA_Sequence seq 
)
void Ascii2NA ( char buffer,
int  len,
int  matrix[16] 
)

Definition at line 259 of file GDE_FileIO.cxx.

Referenced by ReadGen(), and ReadNA_Flat().

int WriteNA_Flat ( NA_Alignment aln,
char filename,
int  method 
)
void Warning ( const char s)

Definition at line 334 of file GDE_FileIO.cxx.

References aw_message().

Referenced by putelem(), WriteGDE(), WriteGen(), and WriteNA_Flat().

void InitNASeq ( NA_Sequence seq,
int  type 
)
GB_ERROR ReadGen ( char filename,
NA_Alignment dataset 
)
int WriteGen ( NA_Alignment aln,
char filename,
int  method 
)
void SetTime ( void *  b)

Definition at line 287 of file GDE_Genbank.cxx.

References ARB_TIME::dd, ARB_TIME::hr, ARB_TIME::mm, ARB_TIME::mn, NULp, ARB_TIME::sc, and ARB_TIME::yy.

Referenced by AsciiTime(), and InitNASeq().

int WriteGDE ( NA_Alignment aln,
char filename,
int  method 
)
char* uniqueID ( void  )

Definition at line 129 of file GDE_HGLfile.cxx.

References ARB_calloc().

Referenced by InitNASeq().

GB_ERROR LoadMenus ( void  )

Load menu config files

loads all '*.menu' from "$ARBHOME/lib/gde" and "$ARB_PROP/gde"

Definition at line 506 of file GDE_ParseMenu.cxx.

References ARB_strdup(), error(), GB_create_directory(), GB_have_error(), GB_incur_error(), GB_is_directory(), GB_path_in_ARBLIB(), GB_path_in_arbprop(), GBS_global_string(), GBS_read_dir(), GBS_static_string(), gde_assert, NULp, and ParseMenus().

Referenced by GDE_init().

bool Find ( const char target,
const char key 
)

Definition at line 548 of file GDE_ParseMenu.cxx.

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

int Find2 ( const char target,
const char key 
)

Definition at line 553 of file GDE_ParseMenu.cxx.

Referenced by LoadData(), ReplaceArgs(), and ReplaceString().

int Arbdb_get_curelem ( NA_Alignment dataset)
int ReadArbdb2 ( NA_Alignment dataset,
AP_filter filter,
GapCompression  compress,
bool  cutoff_stop_codon,
TypeInfo  typeinfo 
)
int ReadArbdb ( NA_Alignment dataset,
bool  marked,
AP_filter filter,
GapCompression  compress,
bool  cutoff_stop_codon,
TypeInfo  typeinfo 
)
int getelem ( NA_Sequence a,
int  b 
)
void putelem ( NA_Sequence a,
int  b,
NA_Base  c 
)
void GDE_startaction_cb ( AW_window aw,
GmenuItem gmenuitem 
)