libbpp-raa-dev 2.4.0-2 / usr / include / Bpp / Raa / RAA_acnuc.h

#ifndef RAA_ACNUC_H
#define RAA_ACNUC_H

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#if defined(WIN32)
#define SOCKBUFS 8192
#endif
#ifdef __alpha
typedef long raa_long;
#define RAA_LONG_FORMAT "%lu"
#else
typedef long long raa_long;
#define RAA_LONG_FORMAT "%llu"
#endif

#ifndef TRUE
#define FALSE 0
#define TRUE (!FALSE)
#endif
#ifndef ERREUR
#define ERREUR 1
#endif

struct rlng       /* LONGL series of linked records containing lists of SUBSEQ ranks */
{int next; /* to LONGL for next element of the long list, or 0 when list is finished */
 int sub[1]; /* array (length given by global SUBINLNG) of ranks of SUBSEQ records or of 0s */
};

#define RAA_GFRAG_BSIZE 10000
struct gfrag_aux
{
  char buffer[RAA_GFRAG_BSIZE + 1];
  int lbuf, nseq_buf, first_buf, l_nseq_buf;
};

struct readsub_aux
{
  char* name;
  int lname, previous, length, type, toext, lkey, locus, frame, gencode, div;
  raa_long addr;
};

#define ANNOTCOUNT 40
struct annot_aux
{
  char* annotline[ANNOTCOUNT + 1];
  int annotcurrent, annotcount, annotdiv;
  raa_long annotaddr, annotaddrfirst, annotaddrlast;
  char annotsbuffer[ 300 ];
};

struct readsp_kw_aux
{
  char name[150], libel[200];
  int lsub, desc, syno, host, previous;
};

#define BLOCK_ELTS_IN_LIST 500
struct nextelt_aux
{
  int current_rank, previous, total;
  int tabnum[BLOCK_ELTS_IN_LIST];
  char* tabname[BLOCK_ELTS_IN_LIST];
  int tablength[BLOCK_ELTS_IN_LIST];
  raa_long taboffset[BLOCK_ELTS_IN_LIST];
  int tabdiv[BLOCK_ELTS_IN_LIST];
};

#define S_BUF_SHRT 5000 /* number of memorized SHORTL records */
struct readshrt_aux
{
  unsigned shrt_buffer[S_BUF_SHRT][3]; /* [0]=SHORTL_rank [1]=val [2]=next */
  int shrt_max, shrt_begin, total;
};

typedef struct shrt2_list
{
  int length;
  int size;
  unsigned point;
  unsigned next;
  unsigned vals[1];
} shrt2_list;

struct readsmj_aux
{
  int lastrec;
  char** names, ** libels;
  unsigned* plongs;
};

typedef struct raa_node
{
  char* name;
  char* libel;
  char* libel_upcase;
  int rank;
  int tid;
  int count;
  struct raa_node* parent;
  struct raa_pair* list_desc;
  struct raa_node* syno;
} raa_node;
struct raa_pair
{
  raa_node* value;
  struct raa_pair* next;
};

#define WIDTH_MAX 150

typedef enum { raa_sub_of_bib = 0, raa_spec_of_loc, raa_bib_of_loc, raa_aut_of_bib, raa_bib_of_aut,
               raa_sub_of_acc, raa_key_of_sub, raa_acc_of_loc } raa_shortl2_kind;

typedef struct _raa_db_access
{
  char* dbname;
  FILE* raa_sockfdr, * raa_sockfdw;
  int genbank, embl, swissprot, nbrf;
  int nseq, longa, maxa;
  int L_MNEMO, WIDTH_SP, WIDTH_KW, WIDTH_SMJ, WIDTH_AUT, WIDTH_BIB, ACC_LENGTH, SUBINLNG, lrtxt, VALINSHRT2;
  raa_node** sp_tree; /* NULL or the full taxonomy tree */
  int max_tid; /* largest correct taxon ID value */
  int* tid_to_rank; /* NULL or tid-to-rank table */
  struct rlng* rlng_buffer;
  struct gfrag_aux gfrag_data;
  struct readsub_aux readsub_data;
  int first_recs[20];
  struct annot_aux annot_data;
  struct readsp_kw_aux readspec_data, readkey_data;
  struct nextelt_aux nextelt_data;
  struct readshrt_aux readshrt_data;
  struct shrt2_list* readshrt2_data[raa_acc_of_loc + 1];
  struct readsmj_aux readsmj_data;
  void* matchkey_data;
  /* mostly for raa_query/raa_query_win usage */
  int tot_key_annots;
  char** key_annots, ** key_annots_min;
  unsigned char* want_key_annots;
#ifdef WIN32
  char sock_input[SOCKBUFS]; /* WIN32 socket input buffer */
  char* sock_input_pos, * sock_input_end;
  char sock_output[SOCKBUFS]; /* WIN32 socket output buffer */
  unsigned sock_output_lbuf;
#endif
  char buffer[5000];
  char remote_file[300];
  char* full_line;
  int max_full_line;
  int was_here;
  char* namestr;
  char residuecount[30];
  char* help;
  int lhelp;
  int tmp_total;
  int tmp_current;
  int* tmp_prelist;
  char* translate_buffer;
  int num_5_partial;
  char mnemo[WIDTH_MAX];
  char species[WIDTH_MAX];
  char access[WIDTH_MAX];
  char descript[WIDTH_MAX];
  char date[12];
} raa_db_access;


typedef enum { raa_sub = 0, raa_loc, raa_key, raa_spec, raa_shrt, raa_lng, raa_ext, raa_smj,
               raa_aut, raa_bib, raa_txt, raa_acc } raa_file;
typedef void (*raa_char_void_function)(raa_db_access*, char*);

/* global variables */
extern raa_char_void_function raa_error_mess_proc; /*this function sd call raa_acnucclose*/


extern int raa_acnucopen (const char* clientid, raa_db_access** psock);
extern int raa_decode_address(char* url, char** p_ip_name, int* socket, char** p_remote_db);
extern int raa_acnucopen_alt (const char* serveurName, int port, const char* db_name, const char* clientid, raa_db_access** psock);
extern int raa_open_socket(const char* serveurName, int port, const char* clientid, raa_db_access** psock);
extern int raa_opendb(raa_db_access* raa_current_db, const char* db_name);
int raa_opendb_pw(raa_db_access* raa_current_db, const char* db_name, void* ptr, char*(*getpasswordf)(void*) );
extern int raa_gfrag(raa_db_access* raa_current_db, int nsub, int first, int lfrag, char* dseq);
extern void raa_acnucclose(raa_db_access* raa_current_db);
extern int raa_prep_acnuc_query(raa_db_access* raa_current_db);
extern int raa_proc_query(raa_db_access* raa_current_db, char* query, char** message, char* nomliste, int* numlist,
                          int* count, int* locus, int* type);
int raa_nexteltinlist(raa_db_access* raa_current_db, int first, int lrank, char** pname, int* plength);
int raa_nexteltinlist_annots(raa_db_access* raa_current_db, int first, int lrank, char** pname, int* plength,
                             raa_long* paddr, int* pdiv);
raa_long scan_raa_long(char* txt);
int raa_seq_to_annots(raa_db_access* raa_current_db, int numseq, raa_long* faddr, int* div);
char* print_raa_long(raa_long val, char* buffer);
char* raa_read_annots(raa_db_access* raa_current_db, raa_long faddr, int div);
char* raa_next_annots(raa_db_access* raa_current_db, raa_long* faddr);
char* raa_translate_cds(raa_db_access* raa_current_db, int seqnum);
char raa_translate_init_codon(raa_db_access* raa_current_db, int numseq);
int raa_iknum(raa_db_access* raa_current_db, char* name, raa_file cas);
int raa_isenum(raa_db_access* raa_current_db, char* name);
int raa_bcount(raa_db_access* raa_current_db, int lrank);
void raa_bit1(raa_db_access* raa_current_db, int lrank, int num);
void raa_bit0(raa_db_access* raa_current_db, int lrank, int num);
int raa_btest(raa_db_access* raa_current_db, int lrank, int num);
void raa_copylist(raa_db_access* raa_current_db, int from, int to);
void raa_zerolist(raa_db_access* raa_current_db, int rank);
void raa_setliststate(raa_db_access* raa_current_db, int lrank, int locus, int type);
char* raa_getliststate(raa_db_access* raa_current_db, int lrank, int* locus, int* type, int* count);
char* raa_residuecount(raa_db_access* raa_current_db, int lrank);
int raa_getemptylist(raa_db_access* raa_current_db, char* name);
int raa_setlistname(raa_db_access* raa_current_db, int lrank, char* name);
int raa_getlistrank(raa_db_access* raa_current_db, char* name);
int raa_releaselist(raa_db_access* raa_current_db, int lrank);
int raa_countfilles(raa_db_access* raa_current_db, int lrank);
int raa_alllistranks(raa_db_access* raa_current_db, int** pranks);
int raa_fcode(raa_db_access* raa_current_db, raa_file cas, char* name);
int raa_read_first_rec(raa_db_access* raa_current_db, raa_file cas);
char* raa_readsub(raa_db_access* raa_current_db, int num, int* plength, int* ptype, int* pext, int* plkey, int* plocus,
                  int* pframe, int* pgencode);
char* raa_readsub_pannots(raa_db_access* raa_current_db, int num, int* plength, int* ptype, int* pext, int* plkey, int* plocus,
                          int* pframe, int* pgencode, raa_long* paddr, int* pdiv);
char* raa_readloc(raa_db_access* raa_current_db, int num, int* sub, int* pnuc, int* spec, int* host, int* plref,
                  int* molec, int* placc, int* org);
char* raa_readspec(raa_db_access* raa_current_db, int num, char** plibel, int* plsub, int* desc, int* syno, int* plhost);
char* raa_readkey(raa_db_access* raa_current_db, int num, char** plibel, int* plsub, int* desc, int* syno);
char* raa_readsmj(raa_db_access* raa_current_db, int num, char** plibel, int* plong);
char* raa_readacc(raa_db_access* raa_current_db, int num, int* plsub);
int raa_readext(raa_db_access* raa_current_db, int num, int* mere, int* deb, int* fin);
int raa_readlng(raa_db_access* raa_current_db, int num);
unsigned raa_readshrt(raa_db_access* raa_current_db, unsigned point, int* val);
unsigned raa_followshrt2(raa_db_access* raa_current_db, int* p_point, int* p_rank, raa_shortl2_kind kind);
char* raa_ghelp(raa_db_access* raa_current_db, char* fname, char* topic);
int raa_nextmatchkey(raa_db_access* raa_current_db, int num, char* pattern, char** matching);
int raa_savelist(raa_db_access* raa_current_db, int lrank, FILE* out, int use_acc, char* prefix);
int raa_modifylist(raa_db_access* raa_current_db, int lrank, char* type /* "length" or "date" */, char* operation /* ">2000" */,
                   int* pnewlrank, int (* check_interrupt)(void), int* p_processed);
int raa_knowndbs(raa_db_access* raa_current_db, char*** pnames, char*** pdescriptions);
char* raa_short_descr(raa_db_access* raa_current_db, int seqnum, char* text, int maxlen, raa_long pinf, int div, char* name);
void* raa_prep_extract(raa_db_access* raa_current_db, char* format, FILE* outstream, char* choix,
                       char* feature_name, char* bornes, char* min_bornes, char** message, int lrank);
int raa_extract_1_seq(void* opaque);
int raa_extract_interrupt(raa_db_access* raa_current_db, void* opaque);
void* raa_prep_coordinates(raa_db_access* raa_current_db, int lrank, int seqnum,
                           char* operation, /* "simple","fragment","feature","region" */
                           char* feature_name, char* bounds, char* min_bounds);
int* raa_1_coordinate_set(void*);
int raa_loadtaxonomy(raa_db_access* raa_current_db, char* rootname,
                     int (* progress_function)(int, void*), void* progress_arg,
                     int (* need_interrupt_f)(void*), void* interrupt_arg);
char* raa_get_taxon_info(raa_db_access* raa_current_db, char* name, int rank, int tid, int* p_rank,
                         int* p_tid, int* p_parent, struct raa_pair** p_desc_list);
char* raa_getattributes(raa_db_access* raa_current_db, const char* id,
                        int* prank, int* plength, int* pframe, int* pgc, char** pacc, char** pdesc, char** pspecies, char** pseq);
char* raa_seqrank_attributes(raa_db_access* raa_current_db, int rank,
                             int* plength, int* pframe, int* pgc, char** pacc, char** pdesc, char** pspecies, char** pseq);

int sock_fputs(raa_db_access* raa_current_db, const char* line);
int sock_flush(raa_db_access* raa_current_db);
char* read_sock(raa_db_access* raa_current_db);


int trim_key(char* name); /* remove trailing spaces */
void majuscules(char* name);
int atoi_u(const char* p);
void compact(char* chaine);
int strcmptrail(char* s1, int l1, char* s2, int l2);


#endif/* RAA_ACNUC_H  */