ARB
Functions | Variables
GDE_event.cxx File Reference
#include "GDE_extglob.h"
#include "GDE_awars.h"
#include <awt_filter.hxx>
#include <aw_window.hxx>
#include <aw_root.hxx>
#include <aw_question.hxx>
#include <aw_awar.hxx>
#include <aw_msg.hxx>
#include <aw_file.hxx>
#include <AP_filter.hxx>
#include <arb_progress.h>
#include <arb_strbuf.h>
#include <arb_global_defs.h>
#include <set>
#include <string>
#include <unistd.h>
Include dependency graph for GDE_event.cxx:

Go to the source code of this file.

Functions

static charReplaceArgs (AW_root *awr, char *Action, GmenuItem *gmenuitem, int number)
 
static void ReplaceString (char *&Action, const char *olds, const char *news)
 
static void ReplaceFile (char *&Action, GfileFormat file)
 
static void GDE_freesequ (NA_Sequence *sequ)
 
static GB_ERROR write_sequence_autoinc_alisize (GBDATA *gb_data, long &ali_len, const char *sequence, int seq_len)
 
bool isgap (char c)
 
bool isTU (char c)
 
char eatgaps (const char *seq, int &index)
 
static charfix_aligned_data (const char *old_seq, const char *new_seq, GB_alignment_type ali_type)
 
static void export_to_DB (NA_Alignment &dataset, size_t oldnumelements, bool aligned_data)
 
static charpreCreateTempfile (const char *name)
 
void GDE_startaction_cb (AW_window *aw, GmenuItem *gmenuitem)
 

Variables

adfiltercbstructagde_filter
 

Function Documentation

static char* ReplaceArgs ( AW_root awr,
char Action,
GmenuItem gmenuitem,
int  number 
)
static
static void ReplaceString ( char *&  Action,
const char olds,
const char news 
)
static
static void ReplaceFile ( char *&  Action,
GfileFormat  file 
)
static

Definition at line 191 of file GDE_event.cxx.

References GfileFormat::name, ReplaceString(), and GfileFormat::symbol.

Referenced by GDE_startaction_cb().

static void GDE_freesequ ( NA_Sequence sequ)
static
static GB_ERROR write_sequence_autoinc_alisize ( GBDATA gb_data,
long ali_len,
const char sequence,
int  seq_len 
)
static
bool isgap ( char  c)
inline

Definition at line 277 of file GDE_event.cxx.

References GAP::is_std_gap().

Referenced by eatgaps().

bool isTU ( char  c)
inline

Definition at line 278 of file GDE_event.cxx.

Referenced by fix_aligned_data().

char eatgaps ( const char seq,
int index 
)
inline

increments index forward to next base (or EOS)

Returns
first gap char seen or 0

Definition at line 280 of file GDE_event.cxx.

References isgap().

Referenced by fix_aligned_data().

static char* fix_aligned_data ( const char old_seq,
const char new_seq,
GB_alignment_type  ali_type 
)
static

Definition at line 292 of file GDE_event.cxx.

References ARB_strdup(), eatgaps(), GB_AT_DNA, GB_AT_RNA, and isTU().

Referenced by export_to_DB().

static void export_to_DB ( NA_Alignment dataset,
size_t  oldnumelements,
bool  aligned_data 
)
static
static char* preCreateTempfile ( const char name)
static

Definition at line 566 of file GDE_event.cxx.

References aw_message(), GB_await_error(), GB_create_tempfile(), and GBS_global_string().

Referenced by GDE_startaction_cb().

void GDE_startaction_cb ( AW_window aw,
GmenuItem gmenuitem 
)

Variable Documentation

adfiltercbstruct* agde_filter

Definition at line 23 of file GDE.cxx.