Wrapper for Clustal Omega.

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

diff --git a/binaries/src/clustalo/src/squid/gsi.h b/binaries/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*/