#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:

Functions
static char *	ReplaceArgs (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 char *	fix_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 char *	preCreateTempfile (const char *name)

static const char *	jobLabel (const char *itemLabel)

void	GDE_startaction_cb (AW_window aw, GmenuItem gmenuitem)

Variables
adfiltercbstruct *	agde_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

Definition at line 173 of file GDE_event.cxx.

References GBS_strstruct::cat(), Find2(), GBS_strstruct::get_position(), GBS_strstruct::ncat(), and GBS_strstruct::release().

Referenced by GDE_startaction_cb(), and ReplaceFile().

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

Definition at line 195 of file GDE_event.cxx.

References NA_Sequence::baggage, NA_Sequence::comments, and NA_Sequence::sequence.

Referenced by NA_Alignment::~NA_Alignment().

static GB_ERROR write_sequence_autoinc_alisize	(	GBDATA *	gb_data,
		long &	ali_len,
		const char *	sequence,
		int	seq_len
	)

static

Definition at line 233 of file GDE_event.cxx.

References ARB_strndup(), error(), GB_get_father(), GB_get_root(), gb_main, GB_read_key_pntr(), GB_write_string(), GBT_get_alignment_len(), GBT_set_alignment_len(), gde_assert, and NULp.

Referenced by export_to_DB().

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

(re-)import data into arb DB

Parameters

dataset	normally has been read from file (which was created by external tool)
oldnumelements	start index into dataset
aligned_data	if true => only import sequences; expect checksums did not change; repair some minor, unwanted changes (case, T<>U, gaptype)

Definition at line 326 of file GDE_event.cxx.

References NA_Alignment::alignment_name, NA_Alignment::alignment_type, aw_message(), db_access, DNA, arb_progress::done(), NA_Alignment::element, NA_Sequence::elementtype, error(), fix_aligned_data(), gde_database_access::format_ali, GB_AT_AA, GB_AT_DNA, GB_AT_RNA, GB_AT_UNKNOWN, GB_await_error(), GB_begin_transaction(), GB_delete(), GB_end_transaction_show_error(), gb_main, gde_database_access::gb_main, GB_read_char_pntr(), NA_Sequence::gb_species, gb_species_data, GB_STRING, GBS_checksum(), GBS_global_string(), GBS_global_string_copy(), GBS_string_2_key(), GBS_string_eval(), GBT_add_data(), GBT_find_or_create_SAI(), GBT_find_or_create_species_rel_species_data(), GBT_find_sequence(), GBT_find_species_rel_species_data(), GBT_get_alignment_len(), GBT_get_alignment_type(), GBT_get_species_data(), gde_assert, arb_progress::inc_and_check_user_abort(), NULp, NA_Alignment::numelements, PROTEIN, RNA, NA_Sequence::seqlen, NA_Sequence::sequence, NA_Sequence::short_name, NA_Sequence::tmatrix, and write_sequence_autoinc_alisize().