#include <arbdbt.h>
#include <adGene.h>
#include <map>
#include <list>
#include <set>
#include <string>
#include <unistd.h>
#include <sys/types.h>

Include dependency graph for arb_gene_probe.cxx:

Go to the source code of this file.

Classes
struct	nameOrder

struct	PositionPair

struct	ltNonOverlap

class	GenePositionMap

Macros
#define	gp_assert(cond) arb_assert(cond)

#define	CHECK_SEMI_ESCAPED(s)

Typedefs
typedef map< const char *, string, nameOrder >	FullNameMap

typedef list< PositionPair >	PositionPairList

Functions
static GB_ERROR	create_data_entry (GBDATA gb_species2, const char sequence, int seqlen)

static GBDATA *	create_gene_species (GBDATA gb_species_data2, const char internal_name, const char long_name, int abspos, const char sequence, int length)

static GB_ERROR	create_genelike_entry (const char internal_name, GBDATA gb_species_data2, int start_pos, int end_pos, const char ali_genome, const char long_name)

static GB_ERROR	create_intergene (GBDATA gb_species_data2, int start_pos, int end_pos, const char ali_genome, const char *long_gene_name)

static GB_ERROR	create_gene (GBDATA gb_species_data2, int start_pos, int end_pos, const char ali_genome, const char *long_gene_name)

static GB_ERROR	create_split_gene (GBDATA gb_species_data2, PositionPairList &part_list, const char ali_genome, const char *long_gene_name)

static GB_ERROR	scan_gene_positions (GBDATA *gb_gene, PositionPairList &part_list)

static GB_ERROR	insert_genes_of_organism (GBDATA gb_organism, GBDATA gb_species_data2)

int	ARB_main (int argc, char *argv[])

Variables
static int	gene_counter = 0

static int	split_gene_counter = 0

static int	intergene_counter = 0

static FullNameMap	names

Macro Definition Documentation

#define gp_assert ( cond ) arb_assert(cond)

Definition at line 22 of file arb_gene_probe.cxx.

Referenced by GenePositionMap::announceGene(), ARB_main(), create_gene_species(), create_split_gene(), and insert_genes_of_organism().

#define CHECK_SEMI_ESCAPED ( s )

Definition at line 227 of file arb_gene_probe.cxx.

Referenced by create_gene_species().

Typedef Documentation

typedef map<const char *, string, nameOrder> FullNameMap

Definition at line 50 of file arb_gene_probe.cxx.

typedef list<PositionPair> PositionPairList

Definition at line 95 of file arb_gene_probe.cxx.

Function Documentation

static GB_ERROR create_data_entry	(	GBDATA *	gb_species2,
		const char *	sequence,
		int	seqlen
	)

static

Definition at line 202 of file arb_gene_probe.cxx.

References error(), GB_await_error(), GB_create_container(), GBT_write_string(), and NULp.

Referenced by create_gene_species().

static GBDATA* create_gene_species	(	GBDATA *	gb_species_data2,
		const char *	internal_name,
		const char *	long_name,
		int	abspos,
		const char *	sequence,
		int	length
	)

static

Definition at line 231 of file arb_gene_probe.cxx.

References CHECK_SEMI_ESCAPED, create_data_entry(), error(), GB_await_error(), GB_create(), GB_create_container(), GB_end_transaction(), GB_export_error(), GB_push_transaction(), GB_read_char_pntr(), GB_STRING, GB_write_string(), GBS_global_string(), GBT_write_int(), gp_assert, names, and NULp.

Referenced by create_genelike_entry(), and create_split_gene().

static GB_ERROR create_genelike_entry	(	const char *	internal_name,
		GBDATA *	gb_species_data2,
		int	start_pos,
		int	end_pos,
		const char *	ali_genome,
		const char *	long_name
	)