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/*****************************************************************
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* SQUID - a library of functions for biological sequence analysis
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* Copyright (C) 1992-2002 Washington University School of Medicine
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* This source code is freely distributed under the terms of the
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* GNU General Public License. See the files COPYRIGHT and LICENSE
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*****************************************************************/
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* Database indexing (SSI format support)
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* CVS $Id: ssi.h,v 1.7 2002/02/24 19:39:27 eddy Exp)
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* See: ssi_format.tex in Docs/
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#define SSI_MAXFILES 32767 /* 2^15-1 */
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#define SSI_MAXKEYS 2147483647L /* 2^31-1 */
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#define SSI_MAXRAM 200 /* allow 200MB indexes before external sort mode */
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* Use the union to save space, since the two offset types are
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* mutually exclusive, controlled by "mode"
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char mode; /* GSI_OFFSET_I32, for example */
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sqd_uint32 i32; /* an offset that fseek() can use */
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sqd_uint64 i64; /* an offset that e.g. fseeko64() can use */
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typedef struct ssioffset_s SSIOFFSET;
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#define SSI_OFFSET_I32 0
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#define SSI_OFFSET_I64 1
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* xref: SSI API documentation in ssi-format.tex
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FILE *fp; /* open SSI index file */
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sqd_uint32 flags; /* optional behavior flags */
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sqd_uint16 nfiles; /* number of files = 16 bit int */
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sqd_uint32 nprimary; /* number of primary keys */
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sqd_uint32 nsecondary; /* number of secondary keys */
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sqd_uint32 flen; /* length of filenames (inc '\0') */
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sqd_uint32 plen; /* length of primary keys (inc '\0') */
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sqd_uint32 slen; /* length of secondary keys (inc '\0') */
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sqd_uint32 frecsize; /* # bytes in a file record */
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sqd_uint32 precsize; /* # bytes in a primary key record */
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sqd_uint32 srecsize; /* # bytes in a secondary key record */
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SSIOFFSET foffset; /* disk offset, start of file records */
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SSIOFFSET poffset; /* disk offset, start of pri key recs */
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SSIOFFSET soffset; /* disk offset, start of sec key recs */
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char imode; /* mode for index file offsets, 32 v. 64 bit */
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char smode; /* mode for sequence file offsets, 32 v. 64 bit */
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char **filename; /* list of file names [0..nfiles-1] */
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sqd_uint32 *fileformat; /* file formats */
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sqd_uint32 *fileflags; /* optional per-file behavior flags */
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sqd_uint32 *bpl; /* bytes per line in file */
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sqd_uint32 *rpl; /* residues per line in file */
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typedef struct ssifile_s SSIFILE;
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/* optional per-index behavior flags in SSIFILE structure's flags:
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#define SSI_USE64 1<<0 /* seq offsets are 64-bit */
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#define SSI_USE64_INDEX 1<<1 /* index file offsets are 64-bit */
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/* optional per-file behavior flags in fileflags
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#define SSI_FAST_SUBSEQ 1<<0 /* can do subseq lookup in this file */
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/* Structure: SSIINDEX
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* Used when building up an index and writing it to disk
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struct ssipkey_s { /* Primary key data: */
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char *key; /* key name */
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sqd_uint16 fnum; /* file number */
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SSIOFFSET r_off; /* record offset */
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SSIOFFSET d_off; /* data offset */
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sqd_uint32 len; /* sequence length */
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struct ssiskey_s { /* Secondary key data: */
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char *key; /* secondary key name */
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char *pkey; /* primary key name */
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int smode; /* sequence mode: SSI_OFFSET_I32 or _I64 */
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int imode; /* index mode: SSI_OFFSET_I32 or _I64 */
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int external; /* TRUE if pkeys and skeys are on disk */
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int max_ram; /* maximum RAM in MB before switching to external */
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sqd_uint32 *fileformat;
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sqd_uint32 flen; /* length of longest filename, inc '\0' */
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struct ssipkey_s *pkeys;
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sqd_uint32 plen; /* length of longest pkey, including '\0' */
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char *ptmpfile; /* name of tmp file, for external sort mode */
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FILE *ptmp; /* handle on open ptmpfile */
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struct ssiskey_s *skeys;
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sqd_uint32 slen; /* length of longest skey, including '\0' */
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sqd_uint32 nsecondary;
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char *stmpfile; /* name of tmp file, for external sort mode */
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FILE *stmp; /* handle on open ptmpfile */
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typedef struct ssiindex_s SSIINDEX;
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/* These control malloc and realloc chunk sizes in the index
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#define SSI_FILE_BLOCK 10
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#define SSI_KEY_BLOCK 100
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/* Error codes set by the API
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#define SSI_ERR_NODATA 1 /* no data? an fread() failed */
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#define SSI_ERR_NO_SUCH_KEY 2 /* that key's not in the index */
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#define SSI_ERR_MALLOC 3
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#define SSI_ERR_NOFILE 4 /* no such file? an fopen() failed */
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#define SSI_ERR_BADMAGIC 5 /* magic number mismatch in GSIOpen() */
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#define SSI_ERR_BADFORMAT 6 /* didn't read what I expected to fread() */
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#define SSI_ERR_NO64BIT 7 /* needed 64-bit support and didn't have it */
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#define SSI_ERR_SEEK_FAILED 8 /* an fseek() (or similar) failed */
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#define SSI_ERR_TELL_FAILED 9 /* an ftell() (or similar) failed */
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#define SSI_ERR_NO_SUBSEQS 10 /* fast subseq is disallowed */
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#define SSI_ERR_RANGE 11 /* subseq requested is out of range */
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#define SSI_ERR_BADARG 12 /* something wrong with a function argument */
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#define SSI_ERR_TOOMANY_FILES 13 /* ran out of range for files in an index */
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#define SSI_ERR_TOOMANY_KEYS 14 /* ran out of range for keys in an index */
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#define SSI_ERR_FWRITE 15
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#define SSI_ERR_EXTERNAL_SORT 16 /* external sort failed */
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/* The SSI file reading API:
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extern int SSIOpen(char *filename, SSIFILE **ret_sfp);
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extern int SSIGetOffsetByName(SSIFILE *sfp, char *key, int *ret_fh,
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SSIOFFSET *ret_offset);
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extern int SSIGetOffsetByNumber(SSIFILE *sfp, int n, int *ret_fh,
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SSIOFFSET *ret_offset);
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extern int SSIGetSubseqOffset(SSIFILE *sfp, char *key, int requested_start,
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int *ret_fh, SSIOFFSET *record_offset,
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SSIOFFSET *data_offset, int *ret_actual_start);
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extern int SSISetFilePosition(FILE *fp, SSIOFFSET *offset);
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extern int SSIFileInfo(SSIFILE *sfp, int fh, char **ret_filename, int *ret_format);
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extern void SSIClose(SSIFILE *sfp);
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/* The SSI index file writing API:
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extern int SSIRecommendMode(char *file);
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extern SSIINDEX *SSICreateIndex(int mode);
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extern int SSIGetFilePosition(FILE *fp, int mode, SSIOFFSET *ret_offset);
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extern int SSIAddFileToIndex(SSIINDEX *g, char *filename, int fmt, int *ret_fh);
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extern int SSISetFileForSubseq(SSIINDEX *g, int fh, int bpl, int rpl);
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extern int SSIAddPrimaryKeyToIndex(SSIINDEX *g, char *key, int fh,
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SSIOFFSET *r_off, SSIOFFSET *d_off,
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extern int SSIAddSecondaryKeyToIndex(SSIINDEX *g, char *key, char *pkey);
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extern int SSIWriteIndex(char *file, SSIINDEX *g);
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extern void SSIFreeIndex(SSIINDEX *g);
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/* The SSI misc. functions API:
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extern char *SSIErrorString(int n);
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/* The SSI debugging API:
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extern void SSIForceExternalSort(SSIINDEX *g);
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#endif /*SSIH_INCLUDED*/
added
removed
src/squid/ssi.h
