--- /dev/null
+/*****************************************************************
+ * 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 SSIH_INCLUDED
+#define SSIH_INCLUDED
+
+/* ssi.h
+ * Database indexing (SSI format support)
+ * CVS $Id: ssi.h,v 1.7 2002/02/24 19:39:27 eddy Exp)
+ *
+ * See: ssi_format.tex in Docs/
+ */
+
+#include <stdio.h>
+#include "squid.h"
+
+/* Limits
+ */
+#define SSI_MAXFILES 32767 /* 2^15-1 */
+#define SSI_MAXKEYS 2147483647L /* 2^31-1 */
+#define SSI_MAXRAM 200 /* allow 200MB indexes before external sort mode */
+
+/* typedef: SSIOFFSET
+ * Use the union to save space, since the two offset types are
+ * mutually exclusive, controlled by "mode"
+ */
+struct ssioffset_s {
+ char mode; /* GSI_OFFSET_I32, for example */
+ union {
+ sqd_uint32 i32; /* an offset that fseek() can use */
+ sqd_uint64 i64; /* an offset that e.g. fseeko64() can use */
+ } off;
+};
+typedef struct ssioffset_s SSIOFFSET;
+#define SSI_OFFSET_I32 0
+#define SSI_OFFSET_I64 1
+
+/* Structure: SSIFILE
+ * xref: SSI API documentation in ssi-format.tex
+ */
+struct ssifile_s {
+ FILE *fp; /* open SSI index file */
+ sqd_uint32 flags; /* optional behavior flags */
+ sqd_uint16 nfiles; /* number of files = 16 bit int */
+ sqd_uint32 nprimary; /* number of primary keys */
+ sqd_uint32 nsecondary; /* number of secondary keys */
+ sqd_uint32 flen; /* length of filenames (inc '\0') */
+ sqd_uint32 plen; /* length of primary keys (inc '\0') */
+ sqd_uint32 slen; /* length of secondary keys (inc '\0') */
+ sqd_uint32 frecsize; /* # bytes in a file record */
+ sqd_uint32 precsize; /* # bytes in a primary key record */
+ sqd_uint32 srecsize; /* # bytes in a secondary key record */
+ SSIOFFSET foffset; /* disk offset, start of file records */
+ SSIOFFSET poffset; /* disk offset, start of pri key recs */
+ SSIOFFSET soffset; /* disk offset, start of sec key recs */
+
+ char imode; /* mode for index file offsets, 32 v. 64 bit */
+ char smode; /* mode for sequence file offsets, 32 v. 64 bit */
+
+ /* File information:
+ */
+ char **filename; /* list of file names [0..nfiles-1] */
+ sqd_uint32 *fileformat; /* file formats */
+ sqd_uint32 *fileflags; /* optional per-file behavior flags */
+ sqd_uint32 *bpl; /* bytes per line in file */
+ sqd_uint32 *rpl; /* residues per line in file */
+};
+typedef struct ssifile_s SSIFILE;
+
+/* optional per-index behavior flags in SSIFILE structure's flags:
+ */
+#define SSI_USE64 1<<0 /* seq offsets are 64-bit */
+#define SSI_USE64_INDEX 1<<1 /* index file offsets are 64-bit */
+
+/* optional per-file behavior flags in fileflags
+ */
+#define SSI_FAST_SUBSEQ 1<<0 /* can do subseq lookup in this file */
+
+/* Structure: SSIINDEX
+ *
+ * Used when building up an index and writing it to disk
+ */
+struct ssipkey_s { /* Primary key data: */
+ char *key; /* key name */
+ sqd_uint16 fnum; /* file number */
+ SSIOFFSET r_off; /* record offset */
+ SSIOFFSET d_off; /* data offset */
+ sqd_uint32 len; /* sequence length */
+};
+struct ssiskey_s { /* Secondary key data: */
+ char *key; /* secondary key name */
+ char *pkey; /* primary key name */
+};
+struct ssiindex_s {
+ int smode; /* sequence mode: SSI_OFFSET_I32 or _I64 */
+ int imode; /* index mode: SSI_OFFSET_I32 or _I64 */
+ int external; /* TRUE if pkeys and skeys are on disk */
+ int max_ram; /* maximum RAM in MB before switching to external */
+
+ char **filenames;
+ sqd_uint32 *fileformat;
+ sqd_uint32 *bpl;
+ sqd_uint32 *rpl;
+ sqd_uint32 flen; /* length of longest filename, inc '\0' */
+ sqd_uint16 nfiles;
+
+ struct ssipkey_s *pkeys;
+ sqd_uint32 plen; /* length of longest pkey, including '\0' */
+ sqd_uint32 nprimary;
+ char *ptmpfile; /* name of tmp file, for external sort mode */
+ FILE *ptmp; /* handle on open ptmpfile */
+
+ struct ssiskey_s *skeys;
+ sqd_uint32 slen; /* length of longest skey, including '\0' */
+ sqd_uint32 nsecondary;
+ char *stmpfile; /* name of tmp file, for external sort mode */
+ FILE *stmp; /* handle on open ptmpfile */
+};
+typedef struct ssiindex_s SSIINDEX;
+
+/* These control malloc and realloc chunk sizes in the index
+ * construction code.
+ */
+#define SSI_FILE_BLOCK 10
+#define SSI_KEY_BLOCK 100
+
+/* Error codes set by the API
+ */
+#define SSI_ERR_OK 0
+#define SSI_ERR_NODATA 1 /* no data? an fread() failed */
+#define SSI_ERR_NO_SUCH_KEY 2 /* that key's not in the index */
+#define SSI_ERR_MALLOC 3
+#define SSI_ERR_NOFILE 4 /* no such file? an fopen() failed */
+#define SSI_ERR_BADMAGIC 5 /* magic number mismatch in GSIOpen() */
+#define SSI_ERR_BADFORMAT 6 /* didn't read what I expected to fread() */
+#define SSI_ERR_NO64BIT 7 /* needed 64-bit support and didn't have it */
+#define SSI_ERR_SEEK_FAILED 8 /* an fseek() (or similar) failed */
+#define SSI_ERR_TELL_FAILED 9 /* an ftell() (or similar) failed */
+#define SSI_ERR_NO_SUBSEQS 10 /* fast subseq is disallowed */
+#define SSI_ERR_RANGE 11 /* subseq requested is out of range */
+#define SSI_ERR_BADARG 12 /* something wrong with a function argument */
+#define SSI_ERR_TOOMANY_FILES 13 /* ran out of range for files in an index */
+#define SSI_ERR_TOOMANY_KEYS 14 /* ran out of range for keys in an index */
+#define SSI_ERR_FWRITE 15
+#define SSI_ERR_EXTERNAL_SORT 16 /* external sort failed */
+
+/* The SSI file reading API:
+ */
+extern int SSIOpen(char *filename, SSIFILE **ret_sfp);
+extern int SSIGetOffsetByName(SSIFILE *sfp, char *key, int *ret_fh,
+ SSIOFFSET *ret_offset);
+extern int SSIGetOffsetByNumber(SSIFILE *sfp, int n, int *ret_fh,
+ SSIOFFSET *ret_offset);
+extern int SSIGetSubseqOffset(SSIFILE *sfp, char *key, int requested_start,
+ int *ret_fh, SSIOFFSET *record_offset,
+ SSIOFFSET *data_offset, int *ret_actual_start);
+extern int SSISetFilePosition(FILE *fp, SSIOFFSET *offset);
+extern int SSIFileInfo(SSIFILE *sfp, int fh, char **ret_filename, int *ret_format);
+extern void SSIClose(SSIFILE *sfp);
+
+/* The SSI index file writing API:
+ */
+extern int SSIRecommendMode(char *file);
+extern SSIINDEX *SSICreateIndex(int mode);
+extern int SSIGetFilePosition(FILE *fp, int mode, SSIOFFSET *ret_offset);
+extern int SSIAddFileToIndex(SSIINDEX *g, char *filename, int fmt, int *ret_fh);
+extern int SSISetFileForSubseq(SSIINDEX *g, int fh, int bpl, int rpl);
+extern int SSIAddPrimaryKeyToIndex(SSIINDEX *g, char *key, int fh,
+ SSIOFFSET *r_off, SSIOFFSET *d_off,
+ int L);
+extern int SSIAddSecondaryKeyToIndex(SSIINDEX *g, char *key, char *pkey);
+extern int SSIWriteIndex(char *file, SSIINDEX *g);
+extern void SSIFreeIndex(SSIINDEX *g);
+
+/* The SSI misc. functions API:
+ */
+extern char *SSIErrorString(int n);
+
+/* The SSI debugging API:
+ */
+extern void SSIForceExternalSort(SSIINDEX *g);
+
+#endif /*SSIH_INCLUDED*/
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