Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / clustalo / src / squid / gsi64.h

diff --git a/website/archive/binaries/mac/src/clustalo/src/squid/gsi64.h b/website/archive/binaries/mac/src/clustalo/src/squid/gsi64.h
deleted file mode 100644 (file)
index b451c1b..0000000
--- a/website/archive/binaries/mac/src/clustalo/src/squid/gsi64.h
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-/*****************************************************************
- * @LICENSE@
- *****************************************************************/
-
-#ifndef GSI64H_INCLUDED
-#define GSI64H_INCLUDED
-#ifdef USE_GSI64
-
-/* gsi64.h
- * Database indexing (GSI64 format support)
- * CVS $Id: gsi64.h,v 1.2 2000/12/21 23:42:59 eddy Exp)
- *
- * A GSI64 (generic sequence index, 64 bit hack) file is composed of
- * recnum + nfiles + 1 records. Each record contains
- * three fields; key, file number, and disk offset.
- * Record 0 contains:
- *   [ "GSI64" ]  [ 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 64 bit integers.
- * 
- * A short test program that verifies the sizes of these
- * data types would be a good idea...
- * 
- * Because we use 64-bit offsets, ftell64(), and fseek64(),
- * we rely on the OS actually providing these. This is
- * a temporary hack for human genome analysis.
- */
-typedef unsigned long long  sqd_uint64; /* 64 bit integer. */
-
-#define GSI64_KEYSIZE    32         /* keys are 32 bytes long */  
-#define GSI64_RECSIZE    42        /* 32 + 2 + 8 bytes       */
-#define SQD_UINT16_MAX 65535       /* 2^16-1 */
-#define SQD_UINT64_MAX 18446744073709551615LU /* 2^64-1 */
-
-struct gsi64_s {
-  FILE        *gsifp;          /* open GSI index file            */
-  sqd_uint16   nfiles;         /* number of files = 16 bit int   */
-  sqd_uint64   recnum;         /* number of records = 64 bit int */
-};
-typedef struct gsi64_s GSI64FILE;
-
-struct gsi64key_s {
-  char       key[GSI64_KEYSIZE];
-  sqd_uint16 filenum;
-  sqd_uint64 offset;
-};
-struct gsi64index_s {
-  char           **filenames;
-  int             *fmt;
-  sqd_uint16       nfiles;
-
-  struct gsi64key_s *elems;
-  sqd_uint64         nkeys;
-};  
-
-
-
-/* if ntohl() and friends are not available, you
- * can slip replacements in by providing sre_ntohl()
- * functions. (i.e., there is a possible portability problem here.)
- */
-#if 0
-#define sre_ntohl(x)  ntohl(x); 
-#define sre_ntohs(x)  ntohs(x);
-#define sre_htonl(x)  htonl(x); 
-#define sre_htons(x)  htons(x);
-#endif
-
-/* from gsi64.c
- */
-extern GSI64FILE *GSI64Open(char *gsifile);
-extern int        GSI64GetRecord(GSI64FILE *gsi, char *f1, sqd_uint16 *f2, sqd_uint64 *f3);
-extern int        GSI64GetOffset(GSI64FILE *gsi, char *key, char *sqfile, 
-                                int *fmt, long long *ret_offset);
-extern void     GSI64Close(GSI64FILE *gsi);
-extern struct gsi64index_s *GSI64AllocIndex(void);
-extern void     GSI64FreeIndex(struct gsi64index_s *g);
-extern void     GSI64AddFileToIndex(struct gsi64index_s *g, char *filename, int fmt);
-extern void     GSI64AddKeyToIndex(struct gsi64index_s *g, char *key, int filenum, long long offset);
-extern void     GSI64SortIndex(struct gsi64index_s *g);
-extern void     GSI64WriteIndex(FILE *fp, struct gsi64index_s *g);
-extern void     GSI64WriteHeader(FILE *fp, int nfiles, long long nkeys);
-extern int      GSI64WriteFileRecord(FILE *fp, char *fname, int idx, int fmt);
-extern int      GSI64WriteKeyRecord(FILE *fp, char *key, int fileidx, long long offset);
-
-#endif /* USE_GSI64 */
-#endif /*GSIH_INCLUDED*/