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[jabaws.git] / website / archive / binaries / mac / src / clustalo / src / squid / gsi.h

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