Wrapper for Clustal Omega.

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

diff --git a/binaries/src/clustalo/src/squid/gsi64.h b/binaries/src/clustalo/src/squid/gsi64.h
new file mode 100644 (file)
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+++ b/binaries/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*/