GDE_proto.h File Reference

#include <attributes.h>
#include "GDE_menu.h"
#include "GDE_extglob.h"

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Functions
char *	GDE_makeawarname (GmenuItem *gmenuitem, long i)
char *	GDE_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)
char *	uniqueID (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
	)

Definition at line 436 of file GDE.cxx.

References GmenuItem::active_mask, ARB_strBeginsWith(), AW_window::close_sub_menu(), db_access, gde_database_access::gb_main, gde_assert, GDE_menuitem_cb(), GmenuItem::help, AW_window::insert_menu_topic(), AW_window::insert_sub_menu(), Gmenu::item, GmenuItem::label, Gmenu::label, AW_window::makeWindowPopper(), GmenuItem::meta, Gmenu::meta, num_menus, Gmenu::numitems, and GmenuItem::popup.

Referenced by ED4_root::generate_window(), and popup_new_main_window().

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
	)

Definition at line 489 of file GDE.cxx.

References AWAR_DEFAULT_ALIGNMENT, AWAR_GDE_ALIGNMENT, AWAR_GDE_COMPRESSION, AWAR_GDE_CUTOFF_STOPCODON, AWAR_GDE_FILTER_NAME, AWAR_GDE_SPECIES, AW_root::awar_int(), AW_root::awar_string(), awt_create_filter_awars(), COMPRESS_NONINFO_COLUMNS, gde_database_access::format_ali, gb_main, gde_database_access::gb_main, GDE_WINDOWTYPE_DEFAULT, GDE_WINDOWTYPE_EDIT4, gde_database_access::get_sequences, LoadMenus(), AW_awar::map(), and gde_database_access::window_type.

Referenced by ed4_create_all_awars(), and nt_create_all_awars().

void LoadData	(	char *	filen,
		NA_Alignment &	dataset
	)

Definition at line 211 of file GDE_FileIO.cxx.

References aw_message(), DataType, error(), FileFormat, FileName, Find2(), FindType(), GBS_global_string(), LoadFile(), and NASEQ_ALIGN.

Referenced by GDE_startaction_cb().

void AppendNA	(	NA_Base *	buffer,
		int	len,
		NA_Sequence *	seq
	)

Definition at line 244 of file GDE_FileIO.cxx.

References ARB_realloc(), GBUFSIZ, NA_Sequence::offset, putelem(), NA_Sequence::seqlen, NA_Sequence::seqmaxlen, and NA_Sequence::sequence.

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

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
	)

Definition at line 268 of file GDE_FileIO.cxx.

References ALL, DNA, NA_Alignment::element, fputs(), getelem(), MASK, NA_Alignment::numelements, offset, NA_Sequence::offset, PROTEIN, NA_Alignment::rel_offset, RNA, NA_Sequence::seqlen, TEXT, and Warning().

Referenced by GDE_startaction_cb().

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
	)

Definition at line 339 of file GDE_FileIO.cxx.

References NA_Sequence::attr, NA_Sequence::authority, NA_Sequence::baggage, NA_Sequence::baggage_len, NA_Sequence::baggage_maxlen, NA_Sequence::barcode, NA_Sequence::col_lut, NA_Sequence::comments, NA_Sequence::comments_len, NA_Sequence::comments_maxlen, NA_Sequence::contig, Default_DNA_Trans, Default_NA_RTrans, Default_NAColor_LKUP, Default_PROColor_LKUP, Default_RNA_Trans, NA_Sequence::description, DNA, NA_Sequence::elementtype, NA_Sequence::groupb, NA_Sequence::groupf, NA_Sequence::groupid, NA_Sequence::id, IS_5_TO_3, IS_PRIMARY, MASK, NA_Sequence::membrane, TimeStamp::modify, NULp, NA_Sequence::offset, TimeStamp::origin, PROTEIN, NA_Sequence::rmatrix, RNA, NA_Sequence::seq_name, NA_Sequence::seqlen, NA_Sequence::seqmaxlen, NA_Sequence::sequence, SetTime(), NA_Sequence::short_name, SIZE_ID, strcpy_truncate(), NA_Sequence::t_stamp, TEXT, NA_Sequence::tmatrix, type, and uniqueID().

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

GB_ERROR ReadGen	(	char *	filename,
		NA_Alignment &	dataset
	)

Definition at line 64 of file GDE_Genbank.cxx.

References AppendNA(), ARB_calloc(), ARB_realloc(), ARB_recalloc(), ARB_strdup(), Arbdb_get_curelem(), Ascii2NA(), AsciiTime(), NA_Sequence::attr, NA_Sequence::authority, buffer, CheckType(), NA_Sequence::col_lut, NA_Sequence::comments, NA_Sequence::comments_len, NA_Sequence::comments_maxlen, Default_PROColor_LKUP, DEFAULT_X_ATTR, NA_Sequence::description, DNA, NA_Alignment::element, NA_Sequence::elementtype, error(), Find(), GB_IO_error(), GBUFSIZ, NA_Sequence::id, InitNASeq(), IS_CIRCULAR, MASK, max, NA_Alignment::maxlen, NULp, NA_Alignment::numelements, NA_Sequence::offset, TimeStamp::origin, PROTEIN, NA_Sequence::rmatrix, RNA, NA_Sequence::seq_name, NA_Sequence::seqlen, NA_Sequence::sequence, NA_Sequence::short_name, SIZE_AUTHORITY, SIZE_DESCRIPTION, SIZE_ID, SIZE_SEQ_NAME, SIZE_SHORT_NAME, strcpy_truncate(), NA_Sequence::t_stamp, TEXT, and NA_Sequence::tmatrix.

Referenced by LoadFile().

int WriteGen	(	NA_Alignment &	aln,
		char *	filename,
		int	method
	)

Definition at line 227 of file GDE_Genbank.cxx.

References ALL, NA_Sequence::attr, NA_Sequence::authority, NA_Sequence::comments, TimeStamp::dd, NA_Sequence::description, DNA, NA_Alignment::element, NA_Sequence::elementtype, GDEmonth, getelem(), NA_Sequence::id, IS_CIRCULAR, MASK, TimeStamp::mm, NA_Alignment::numelements, NA_Sequence::offset, TimeStamp::origin, PROTEIN, RNA, NA_Sequence::seq_name, NA_Sequence::seqlen, NA_Sequence::short_name, NA_Sequence::t_stamp, NA_Sequence::tmatrix, Warning(), and TimeStamp::yy.

Referenced by GDE_startaction_cb().

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
	)

Definition at line 33 of file GDE_HGLfile.cxx.

References ALL, NA_Sequence::attr, NA_Sequence::authority, NA_Sequence::baggage, NA_Sequence::barcode, NA_Sequence::comments, NA_Sequence::contig, TimeStamp::dd, NA_Sequence::description, DNA, NA_Alignment::element, NA_Sequence::elementtype, getelem(), NA_Sequence::groupid, TimeStamp::hr, NA_Sequence::id, IS_3_TO_5, IS_5_TO_3, IS_CIRCULAR, IS_ORIG_3_TO_5, IS_ORIG_5_TO_3, IS_ORIG_PRIMARY, IS_ORIG_SECONDARY, IS_PRIMARY, IS_SECONDARY, MASK, NA_Sequence::membrane, TimeStamp::mm, TimeStamp::mn, NA_Alignment::numelements, NA_Sequence::offset, TimeStamp::origin, PROTEIN, NA_Alignment::rel_offset, RemoveQuotes(), RNA, TimeStamp::sc, NA_Sequence::seq_name, NA_Sequence::short_name, StripSpecial(), NA_Sequence::t_stamp, TEXT, NA_Sequence::tmatrix, Warning(), and TimeStamp::yy.

Referenced by GDE_startaction_cb().

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 508 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 550 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 555 of file GDE_ParseMenu.cxx.

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

int Arbdb_get_curelem

(

NA_Alignment &

dataset

)

Definition at line 18 of file GDE_arbdb_io.cxx.

References ARB_alloc(), ARB_realloc(), NA_Alignment::element, NA_Alignment::maxnumelements, and NA_Alignment::numelements.

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

int ReadArbdb2	(	NA_Alignment &	dataset,
		AP_filter *	filter,
		GapCompression	compress,
		bool	cutoff_stop_codon,
		TypeInfo	typeinfo
	)

Definition at line 325 of file GDE_arbdb_io.cxx.

References aw_message(), db_access, error(), gde_assert, gde_database_access::get_sequences, InsertDatainGDE(), and NULp.

Referenced by GDE_startaction_cb().

int ReadArbdb	(	NA_Alignment &	dataset,
		bool	marked,
		AP_filter *	filter,
		GapCompression	compress,
		bool	cutoff_stop_codon,
		TypeInfo	typeinfo
	)

Definition at line 354 of file GDE_arbdb_io.cxx.

References NA_Alignment::alignment_name, ARB_alloc(), ARB_calloc(), aw_message(), db_access, gde_database_access::gb_main, NA_Alignment::gb_main, GB_read_char_pntr(), gb_species_data, GBS_global_string(), GBT_find_sequence(), GBT_first_marked_species_rel_species_data(), GBT_first_species_rel_species_data(), GBT_get_alignment_len(), GBT_get_species_data(), GBT_next_marked_species(), GBT_next_species(), gde_assert, InsertDatainGDE(), NULp, and strcpy_truncate().

Referenced by GDE_startaction_cb().

int getelem	(	NA_Sequence *	a,
		int	b
	)

Definition at line 419 of file GDE_arbdb_io.cxx.

References DNA, NA_Sequence::elementtype, MASK, offset, NA_Sequence::offset, PROTEIN, RNA, NA_Sequence::seqlen, NA_Sequence::sequence, and TEXT.

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

void putelem	(	NA_Sequence *	a,
		int	b,
		NA_Base	c
	)

Definition at line 436 of file GDE_arbdb_io.cxx.

References DNA, NA_Sequence::elementtype, MASK, NA_Sequence::offset, PROTEIN, RNA, NA_Sequence::seqlen, NA_Sequence::seqmaxlen, NA_Sequence::sequence, TEXT, and Warning().

Referenced by AppendNA().

void GDE_startaction_cb	(	AW_window *	aw,
		GmenuItem *	gmenuitem
	)

Definition at line 584 of file GDE_event.cxx.

References GmenuItem::aligned, ALL, ARB_strdup(), aw_message(), aw_message_if(), AW_root::awar(), AWAR_GDE_COMPRESSION, AWAR_GDE_CUTOFF_STOPCODON, AWAR_GDE_SPECIES, AWAR_PREFIX_GDE_TEMP, AWT_get_combined_filter_name(), awt_get_filter(), awt_invalid_filter(), buffer, db_access, error(), export_to_DB(), Find(), GfileFormat::format, GB_have_error(), gde_database_access::gb_main, NA_Alignment::gb_main, GBK_system(), GBS_global_string_copy(), GBUFSIZ, GDE, gde_assert, GENBANK, AW_window::get_root(), gde_database_access::get_sequences, GmenuItem::input, jobLabel(), GmenuItem::label, LoadData(), GmenuItem::method, NA_FLAT, GfileFormat::name, NONE, GmenuItem::numargs, NA_Alignment::numelements, GmenuItem::numinputs, GmenuItem::numoutputs, GmenuItem::output, preCreateTempfile(), AW_awar::read_int(), ReadArbdb(), ReadArbdb2(), ReplaceArgs(), ReplaceFile(), ReplaceString(), GfileFormat::save, GmenuItem::seqtype, arb_progress::subtitle(), ta, GfileFormat::typeinfo, UNKNOWN_TYPEINFO, WriteGDE(), WriteGen(), and WriteNA_Flat().

Referenced by GDE_menuitem_cb().