/***************************************************************** * 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 #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*/