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/*****************************************************************
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* SQUID - a library of functions for biological sequence analysis
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* Copyright (C) 1992-2002 Washington University School of Medicine
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* This source code is freely distributed under the terms of the
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* GNU General Public License. See the files COPYRIGHT and LICENSE
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*****************************************************************/
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* Database indexing (GSI format support)
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* 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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* A GSI (generic sequence index) file is composed of
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* recnum + nfiles + 1 records. Each record contains
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* three fields; key, file number, and disk offset.
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* [ "GSI" ] [ nfiles ] [ recnum ]
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* Records 1..nfiles map file names to file numbers, and contain:
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* [ filename ] [ file number, 1..nfiles ] [ 0 (unused) ]
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* Records nfiles+1 to recnum+nfiles+1 provide disk offset
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* and file number indices for every key:
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* [ key ] [ file number ] [ offset]
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* Because the file is binary, we take some (but not
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* complete) care to improve portability amongst platforms.
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* This means using network order integers (see ntohl())
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* and defining types for 16 and 32 bit integers.
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* Because we use 32-bit offsets, ftell(), and fseek(),
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* there is an implicit 2 Gb file size maximum.
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* AFAIK neither ANSI C nor POSIX provide a portable solution
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* to this problem. fsetpos(), fgetpos() use an
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* opaque fpos_t datatype that we can't write portably
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* to a disk file. Suggestions welcomed.
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#define GSI_KEYSIZE 32 /* keys are 32 bytes long */
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#define GSI_RECSIZE 38 /* 32 + 2 + 4 bytes */
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#define SQD_UINT16_MAX 65535 /* 2^16-1 */
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#define SQD_UINT32_MAX 4294967295U/* 2^32-1 */
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FILE *gsifp; /* open GSI index file */
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sqd_uint16 nfiles; /* number of files = 16 bit int */
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sqd_uint32 recnum; /* number of records = 32 bit int */
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typedef struct gsi_s GSIFILE;
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char key[GSI_KEYSIZE];
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struct gsikey_s *elems;
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extern GSIFILE *GSIOpen(char *gsifile);
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extern int GSIGetRecord(GSIFILE *gsi, char *f1, sqd_uint16 *f2, sqd_uint32 *f3);
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extern int GSIGetOffset(GSIFILE *gsi, char *key, char *sqfile,
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int *fmt, long *ret_offset);
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extern void GSIClose(GSIFILE *gsi);
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extern struct gsiindex_s *GSIAllocIndex(void);
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extern void GSIFreeIndex(struct gsiindex_s *g);
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extern void GSIAddFileToIndex(struct gsiindex_s *g, char *filename, int fmt);
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extern void GSIAddKeyToIndex(struct gsiindex_s *g, char *key, int filenum, long offset);
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extern void GSISortIndex(struct gsiindex_s *g);
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extern void GSIWriteIndex(FILE *fp, struct gsiindex_s *g);
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extern void GSIWriteHeader(FILE *fp, int nfiles, long nkeys);
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extern int GSIWriteFileRecord(FILE *fp, char *fname, int idx, int fmt);
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extern int GSIWriteKeyRecord(FILE *fp, char *key, int fileidx, long offset);
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#endif /*GSIH_INCLUDED*/
added
removed
src/squid/gsi.h
