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1 /*****************************************************************
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2 * SQUID - a library of functions for biological sequence analysis
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3 * Copyright (C) 1992-2002 Washington University School of Medicine
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4 *
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5 * This source code is freely distributed under the terms of the
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6 * GNU General Public License. See the files COPYRIGHT and LICENSE
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7 * for details.
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8 *****************************************************************/
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9
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10 #ifndef GSIH_INCLUDED
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11 #define GSIH_INCLUDED
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12
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13 /* gsi.h
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14 * Database indexing (GSI format support)
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15 * RCS $Id: gsi.h 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: gsi.h,v 1.3 2001/08/04 20:15:42 eddy Exp)
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16 *
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17 * A GSI (generic sequence index) file is composed of
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18 * recnum + nfiles + 1 records. Each record contains
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19 * three fields; key, file number, and disk offset.
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20 * Record 0 contains:
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21 * [ "GSI" ] [ nfiles ] [ recnum ]
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22 * Records 1..nfiles map file names to file numbers, and contain:
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23 * [ filename ] [ file number, 1..nfiles ] [ 0 (unused) ]
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24 * Records nfiles+1 to recnum+nfiles+1 provide disk offset
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25 * and file number indices for every key:
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26 * [ key ] [ file number ] [ offset]
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27 *
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28 * Because the file is binary, we take some (but not
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29 * complete) care to improve portability amongst platforms.
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30 * This means using network order integers (see ntohl())
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31 * and defining types for 16 and 32 bit integers.
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32 *
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33 * Because we use 32-bit offsets, ftell(), and fseek(),
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34 * there is an implicit 2 Gb file size maximum.
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35 * AFAIK neither ANSI C nor POSIX provide a portable solution
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36 * to this problem. fsetpos(), fgetpos() use an
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37 * opaque fpos_t datatype that we can't write portably
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38 * to a disk file. Suggestions welcomed.
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39 */
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40 #define GSI_KEYSIZE 32 /* keys are 32 bytes long */
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41 #define GSI_RECSIZE 38 /* 32 + 2 + 4 bytes */
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42 #define SQD_UINT16_MAX 65535 /* 2^16-1 */
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43 #define SQD_UINT32_MAX 4294967295U/* 2^32-1 */
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44
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45 struct gsi_s {
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46 FILE *gsifp; /* open GSI index file */
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47 sqd_uint16 nfiles; /* number of files = 16 bit int */
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48 sqd_uint32 recnum; /* number of records = 32 bit int */
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49 };
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50 typedef struct gsi_s GSIFILE;
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51
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52 struct gsikey_s {
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53 char key[GSI_KEYSIZE];
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54 sqd_uint16 filenum;
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55 sqd_uint32 offset;
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56 };
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57 struct gsiindex_s {
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58 char **filenames;
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59 int *fmt;
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60 sqd_uint16 nfiles;
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61
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62 struct gsikey_s *elems;
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63 int nkeys;
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64 };
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65
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66
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67 /* from gsi.c
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68 */
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69 extern GSIFILE *GSIOpen(char *gsifile);
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70 extern int GSIGetRecord(GSIFILE *gsi, char *f1, sqd_uint16 *f2, sqd_uint32 *f3);
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71 extern int GSIGetOffset(GSIFILE *gsi, char *key, char *sqfile,
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72 int *fmt, long *ret_offset);
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73 extern void GSIClose(GSIFILE *gsi);
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74 extern struct gsiindex_s *GSIAllocIndex(void);
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75 extern void GSIFreeIndex(struct gsiindex_s *g);
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76 extern void GSIAddFileToIndex(struct gsiindex_s *g, char *filename, int fmt);
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77 extern void GSIAddKeyToIndex(struct gsiindex_s *g, char *key, int filenum, long offset);
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78 extern void GSISortIndex(struct gsiindex_s *g);
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79 extern void GSIWriteIndex(FILE *fp, struct gsiindex_s *g);
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80 extern void GSIWriteHeader(FILE *fp, int nfiles, long nkeys);
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81 extern int GSIWriteFileRecord(FILE *fp, char *fname, int idx, int fmt);
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82 extern int GSIWriteKeyRecord(FILE *fp, char *key, int fileidx, long offset);
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83
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84 #endif /*GSIH_INCLUDED*/
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