arb_primer.cxx File Reference

#include <arbdbt.h>
#include <arb_strarray.h>

Include dependency graph for arb_primer.cxx:

Go to the source code of this file.

Classes
struct	arb_prm_struct

Macros
#define	ADD_LEN   10
#define	PRM_BUFFERSIZE   256
#define	is_base(c)   (((c>='a') && (c<='z')) || ((c>='A')&&(c<='Z')))

Functions
int	getNumFromStdin ()
static GB_ERROR	arb_prm_menu ()
static GB_ERROR	arb_prm_read (int)
static void	arb_count_keys (const char *, long val, void *)
static void	arb_print_primer (const char *key, long val, void *)
static int	primer_print (char *dest, char *source, int size)
static long	arb_reduce_primer_len (const char *key, long val, void *cl_hash)
static void	arb_prm_primer (int)
int	ARB_main (int argc, char *argv[])

Variables
static arb_prm_struct	aprm

Macro Definition Documentation

#define ADD_LEN   10

Definition at line 14 of file arb_primer.cxx.

Referenced by arb_prm_menu(), and arb_prm_primer().

#define PRM_BUFFERSIZE   256

Definition at line 15 of file arb_primer.cxx.

Referenced by arb_prm_menu(), and getNumFromStdin().

#define is_base

(

c

)

(((c>='a') && (c<='z')) || ((c>='A')&&(c<='Z')))

Definition at line 209 of file arb_primer.cxx.

Referenced by primer_print().

Function Documentation

int getNumFromStdin ( )

inline

Definition at line 65 of file arb_primer.cxx.

References arb_prm_struct::buffer, and PRM_BUFFERSIZE.

Referenced by arb_prm_menu().

static GB_ERROR arb_prm_menu ( )

static

Definition at line 74 of file arb_primer.cxx.

References ADD_LEN, arb_prm_struct::alignment_names, ARB_strdup(), arb_prm_struct::buffer, error(), GBS_global_string(), getNumFromStdin(), arb_prm_struct::max_name, NULp, arb_prm_struct::outname, PRM_BUFFERSIZE, arb_prm_struct::prmanz, arb_prm_struct::prmlen, arb_prm_struct::prmsmin, and arb_prm_struct::source.

Referenced by ARB_main().

static GB_ERROR arb_prm_read ( int  )

static

Definition at line 130 of file arb_primer.cxx.

References arb_prm_struct::al_len, ARB_calloc(), arb_prm_struct::data, GB_brother(), GB_entry(), GB_find_string(), GB_IGNORE_CASE, arb_prm_struct::gb_main, GB_print_error(), GB_read_char_pntr(), GB_read_int(), GB_read_string_count(), GBT_count_marked_species(), GBT_first_marked_species(), GBT_get_presets(), GBT_next_marked_species(), NULp, SEARCH_GRANDCHILD, arb_prm_struct::source, and arb_prm_struct::sp_count.

Referenced by ARB_main().

static void arb_count_keys ( const char *  , long  val, void *    )

static

Definition at line 188 of file arb_primer.cxx.

References arb_prm_struct::key_cnt, and arb_prm_struct::one_key_cnt.

Referenced by arb_prm_primer().

static void arb_print_primer ( const char *  key, long  val, void *    )

static

Definition at line 197 of file arb_primer.cxx.

References arb_prm_struct::out.

Referenced by arb_prm_primer().

static int primer_print ( char *  dest, char *  source, int  size  )

static

Definition at line 211 of file arb_primer.cxx.

References is_base.

Referenced by arb_prm_primer().

static long arb_reduce_primer_len ( const char *  key, long  val, void *  cl_hash  )

static

Definition at line 231 of file arb_primer.cxx.

References arb_assert, buffer, GBS_read_hash(), GBS_write_hash(), and arb_prm_struct::reduce.

Referenced by arb_prm_primer().

static void arb_prm_primer ( int  )

static

Definition at line 250 of file arb_primer.cxx.

References ADD_LEN, arb_prm_struct::al_len, ARB_calloc(), arb_count_keys(), arb_print_primer(), arb_reduce_primer_len(), buffer, arb_prm_struct::data, GB_MIND_CASE, GBS_create_hash(), GBS_free_hash(), GBS_hash_do_const_loop(), GBS_hash_do_loop(), GBS_incr_hash(), arb_prm_struct::key_cnt, NULp, arb_prm_struct::one_key_cnt, arb_prm_struct::out, primer_print(), arb_prm_struct::prmanz, arb_prm_struct::prmlen, arb_prm_struct::prmsmin, arb_prm_struct::reduce, and arb_prm_struct::sp_count.

Referenced by ARB_main().

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

Definition at line 321 of file arb_primer.cxx.

References arb_prm_struct::alignment_names, arb_prm_menu(), arb_prm_primer(), arb_prm_read(), error(), EXIT_FAILURE, EXIT_SUCCESS, GB_abort_transaction(), GB_await_error(), GB_begin_transaction(), GB_close(), GB_commit_transaction(), GB_IO_error(), arb_prm_struct::gb_main, GB_open(), GBS_global_string(), GBT_get_alignment_names(), NULp, arb_prm_struct::out, arb_prm_struct::outname, and arb_prm_struct::prmanz.

Variable Documentation

arb_prm_struct aprm

static

Definition at line 63 of file arb_primer.cxx.