+++ /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.
- *****************************************************************/
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <sys/stat.h>
-#include <sys/types.h>
-#include <unistd.h>
-#include "squid.h"
-#include "ssi.h"
-#ifdef CLUSTALO
-#include <limits.h>
-#endif
-
-static sqd_uint32 v20magic = 0xf3f3e9b1; /* SSI 1.0: "ssi1" + 0x80808080 */
-static sqd_uint32 v20swap = 0xb1e9f3f3; /* byteswapped */
-
-static int read_i16(FILE *fp, sqd_uint16 *ret_result);
-static int read_i32(FILE *fp, sqd_uint32 *ret_result);
-static int read_i64(FILE *fp, sqd_uint64 *ret_result);
-static int read_offset(FILE *fp, char mode, SSIOFFSET *ret_offset);
-static int write_i16(FILE *fp, sqd_uint16 n);
-static int write_i32(FILE *fp, sqd_uint32 n);
-static int write_i64(FILE *fp, sqd_uint64 n);
-static int write_offset(FILE *fp, SSIOFFSET *offset);
-static int binary_search(SSIFILE *sfp, char *key, int klen, SSIOFFSET *base,
- sqd_uint32 recsize, sqd_uint32 maxidx);
-static int indexfile_position(SSIFILE *sfp, SSIOFFSET *base, sqd_uint32 len,
- sqd_uint32 n);
-static void clear_ssifile(SSIFILE *sfp);
-static sqd_uint64 current_index_size(SSIINDEX *g);
-static int activate_external_sort(SSIINDEX *g);
-static int load_indexfile(SSIFILE *sfp);
-static int parse_pkey_info(char *buf, char mode, struct ssipkey_s *pkey);
-static int parse_skey_info(char *buf, struct ssiskey_s *skey);
-
-/* Function: SSIOpen()
- * Date: SRE, Sun Dec 31 12:40:03 2000 [St. Louis]
- *
- * Purpose: Opens the SSI index file {filename} and returns
- * a SSIFILE * stream thru {ret_sfp}.
- * The caller must eventually close this stream using
- * SSIClose(). More than one index file can be open
- * at once.
- *
- * Args: filename - full path to a SSI index file
- *
- * Returns: Returns 0 on success, nonzero on failure.
- */
-int
-SSIOpen(char *filename, SSIFILE **ret_sfp)
-{
- SSIFILE *sfp = NULL;
- int status;
- if ((sfp = malloc(sizeof(SSIFILE))) == NULL) return SSI_ERR_MALLOC;
- if ((sfp->fp = fopen(filename, "rb")) == NULL) {
- free(sfp);
- return SSI_ERR_NOFILE;
- }
- status = load_indexfile(sfp);
- *ret_sfp = sfp;
- return status;
-}
-/* load_indexfile(): given a SSIFILE structure with an open and positioned
- * stream (fp) -- but no other data loaded -- read the next SSIFILE
- * in from disk. We use this routine without its SSIOpen() wrapper
- * as part of the external mergesort when creating large indices.
- */
-static int
-load_indexfile(SSIFILE *sfp)
-{
- sqd_uint32 magic;
- sqd_uint16 i; /* counter over files */
- int status; /* overall return status if an error is thrown */
-
- status = SSI_ERR_BADFORMAT; /* default: almost every kind of error is a bad format error */
-
- sfp->filename = NULL;
- sfp->fileformat = NULL;
- sfp->fileflags = NULL;
- sfp->bpl = NULL;
- sfp->rpl = NULL;
- sfp->nfiles = 0;
- if (! read_i32(sfp->fp, &magic)) {status = SSI_ERR_BADMAGIC; goto FAILURE; }
- if (magic != v20magic && magic != v20swap) {status = SSI_ERR_BADMAGIC; goto FAILURE; }
- if (! read_i32(sfp->fp, &(sfp->flags))) goto FAILURE;
-
- /* If we have 64-bit offsets, make sure we can deal with them.
- */
-#ifndef HAS_64BIT_FILE_OFFSETS
- if ((sfp->flags & SSI_USE64_INDEX) ||
- (sfp->flags & SSI_USE64))
- { status = SSI_ERR_NO64BIT; goto FAILURE; }
-#endif
-
- sfp->imode = (sfp->flags & SSI_USE64_INDEX) ? SSI_OFFSET_I64 : SSI_OFFSET_I32;
- sfp->smode = (sfp->flags & SSI_USE64) ? SSI_OFFSET_I64 : SSI_OFFSET_I32;
-
- if (! read_i16(sfp->fp, &(sfp->nfiles))) goto FAILURE;
- if (! read_i32(sfp->fp, &(sfp->nprimary))) goto FAILURE;
- if (! read_i32(sfp->fp, &(sfp->nsecondary))) goto FAILURE;
- if (! read_i32(sfp->fp, &(sfp->flen))) goto FAILURE;
- if (! read_i32(sfp->fp, &(sfp->plen))) goto FAILURE;
- if (! read_i32(sfp->fp, &(sfp->slen))) goto FAILURE;
- if (! read_i32(sfp->fp, &(sfp->frecsize))) goto FAILURE;
- if (! read_i32(sfp->fp, &(sfp->precsize))) goto FAILURE;
- if (! read_i32(sfp->fp, &(sfp->srecsize))) goto FAILURE;
-
- if (! read_offset(sfp->fp, sfp->imode, &(sfp->foffset))) goto FAILURE;
- if (! read_offset(sfp->fp, sfp->imode, &(sfp->poffset))) goto FAILURE;
- if (! read_offset(sfp->fp, sfp->imode, &(sfp->soffset))) goto FAILURE;
-
- /* Read the file information and keep it.
- * We expect the number of files to be small, so reading it
- * once should be advantageous overall. If SSI ever had to
- * deal with large numbers of files, you'd probably want to
- * read file information on demand.
- */
- if (sfp->nfiles == 0) goto FAILURE;
- if ((sfp->filename=malloc(sizeof(char *) *sfp->nfiles)) == NULL) {status = SSI_ERR_MALLOC; goto FAILURE; }
- for (i = 0; i < sfp->nfiles; i++) sfp->filename[i] = NULL;
- if ((sfp->fileformat=malloc(sizeof(sqd_uint32)*sfp->nfiles)) == NULL) {status = SSI_ERR_MALLOC; goto FAILURE; }
- if ((sfp->fileflags =malloc(sizeof(sqd_uint32)*sfp->nfiles)) == NULL) {status = SSI_ERR_MALLOC; goto FAILURE; }
- if ((sfp->bpl =malloc(sizeof(sqd_uint32)*sfp->nfiles)) == NULL) {status = SSI_ERR_MALLOC; goto FAILURE; }
- if ((sfp->rpl =malloc(sizeof(sqd_uint32)*sfp->nfiles)) == NULL) {status = SSI_ERR_MALLOC; goto FAILURE; }
-
- for (i = 0; i < sfp->nfiles; i++)
- {
- /* We have to explicitly position, because header and file
- * records may expand in the future; frecsize and foffset
- * give us forwards compatibility.
- */
- if (indexfile_position(sfp, &(sfp->foffset), sfp->frecsize, i) !=0) goto FAILURE;
- if ((sfp->filename[i] =malloc(sizeof(char)*sfp->flen)) == NULL) {status = SSI_ERR_MALLOC; goto FAILURE; }
- if (fread(sfp->filename[i],sizeof(char),sfp->flen, sfp->fp)!=sfp->flen) goto FAILURE;
- if (! read_i32(sfp->fp, &(sfp->fileformat[i]))) goto FAILURE;
- if (! read_i32(sfp->fp, &(sfp->fileflags[i]))) goto FAILURE;
- if (! read_i32(sfp->fp, &(sfp->bpl[i]))) goto FAILURE;
- if (! read_i32(sfp->fp, &(sfp->rpl[i]))) goto FAILURE;
- }
-
- /* Success. Return 0.
- */
- return 0;
-
- FAILURE:
- /* Failure: free the damaged structure, return status code.
- */
- SSIClose(sfp);
- return status;
-}
-
-
-
-/* Function: SSIGetOffsetByName()
- * Date: SRE, Sun Dec 31 13:55:31 2000 [St. Louis]
- *
- * Purpose: Looks up the string {key} in the open index {sfp}.
- * {key} can be either a primary or secondary key. If {key}
- * is found, {*ret_fh} contains a unique handle on
- * the file that contains {key} (suitable for an SSIFileInfo()
- * call, or for comparison to the handle of the last file
- * that was opened for retrieval), and {offset} is filled
- * in with the offset in that file.
- *
- * Args: sfp - open index file
- * key - string to search for
- * ret_fh - RETURN: handle on file that key is in
- * ret_offset - RETURN: offset of the start of that key's record
- *
- * Returns: 0 on success.
- * non-zero on error.
- */
-int
-SSIGetOffsetByName(SSIFILE *sfp, char *key, int *ret_fh,
- SSIOFFSET *ret_offset)
-{
- int status;
- sqd_uint16 fnum;
-
- /* Look in the primary keys.
- */
- status = binary_search(sfp, key, sfp->plen, &(sfp->poffset), sfp->precsize,
- sfp->nprimary);
- if (status == 0) {
- /* We found it as a primary key; get our data & return.
- */
- if (! read_i16(sfp->fp, &fnum)) return SSI_ERR_NODATA;
- *ret_fh = (int) fnum;
- if (! read_offset(sfp->fp, sfp->smode, ret_offset)) return SSI_ERR_NODATA;
-
- return 0; /* success! (we don't need the other key data) */
- } else if (status == SSI_ERR_NO_SUCH_KEY) {
- /* Not in the primary keys? OK, try the secondary keys.
- */
- if (sfp->nsecondary > 0) {
- char *pkey;
- status = binary_search(sfp, key, sfp->slen, &(sfp->soffset), sfp->srecsize,
- sfp->nsecondary);
- if (status != 0) return status;
- if ((pkey = malloc(sizeof(char) * sfp->plen)) == NULL) return SSI_ERR_MALLOC;
- if (fread(pkey, sizeof(char), sfp->plen, sfp->fp) != sfp->plen) return SSI_ERR_NODATA;
-
- status = SSIGetOffsetByName(sfp, pkey, ret_fh, ret_offset);
- free(pkey);
- }
- return status;
-
- } else return status;
- /*NOTREACHED*/
-}
-
-/* Function: SSIGetOffsetByNumber()
- * Date: SRE, Mon Jan 1 19:42:42 2001 [St. Louis]
- *
- * Purpose: Looks up primary key #{n} in the open index {sfp}.
- * {n} ranges from 0..nprimary-1. When key #{n}
- * is found, {*ret_fh} contains a unique
- * handle on the file that contains {key} (suitable
- * for an SSIFileInfo() call, or for comparison to
- * the handle of the last file that was opened for retrieval),
- * and {offset} is filled in with the offset in that file.
- *
- * Args: sfp - open index file
- * n - primary key number to retrieve.
- * ret_fh - RETURN: handle on file that key is in
- * ret_offset - RETURN: offset of the start of that key's record
- *
- * Returns: 0 on success.
- * non-zero on error.
- */
-int
-SSIGetOffsetByNumber(SSIFILE *sfp, int n, int *ret_fh, SSIOFFSET *ret_offset)
-{
- sqd_uint16 fnum;
- char *pkey;
-
- if (n >= sfp->nprimary) return SSI_ERR_NO_SUCH_KEY;
- if (indexfile_position(sfp, &(sfp->poffset), sfp->precsize, n) != 0)
- return SSI_ERR_SEEK_FAILED;
-
- if ((pkey = malloc(sizeof(char) * sfp->plen)) == NULL) return SSI_ERR_MALLOC;
- if (fread(pkey, sizeof(char), sfp->plen, sfp->fp) != sfp->plen) return SSI_ERR_NODATA;
- if (! read_i16(sfp->fp, &fnum)) return SSI_ERR_NODATA;
- if (! read_offset(sfp->fp, sfp->smode, ret_offset)) return SSI_ERR_NODATA;
- *ret_fh = fnum;
- free(pkey);
- return 0;
-}
-
-/* Function: SSIGetSubseqOffset()
- * Date: SRE, Mon Jan 1 19:49:31 2001 [St. Louis]
- *
- * Purpose: Implements SSI_FAST_SUBSEQ.
- *
- * Looks up a primary or secondary {key} in the open
- * index {sfp}. Asks for the nearest offset to a
- * subsequence starting at position {requested_start}
- * in the sequence (numbering the sequence 1..L).
- * If {key} is found, on return, {ret_fh}
- * contains a unique handle on the file that contains
- * {key} (suitable for an SSIFileInfo() call, or for
- * comparison to the handle of the last file that was
- * opened for retrieval); {record_offset} contains the
- * disk offset to the start of the record; {data_offset}
- * contains the disk offset either exactly at the requested
- * residue, or at the start of the line containing the
- * requested residue; {ret_actual_start} contains the
- * coordinate (1..L) of the first valid residue at or
- * after {data_offset}. {ret_actual_start} is <=
- * {requested_start}.
- *
- * Args: sfp - open index file
- * key - primary or secondary key to find
- * requested_start - residue we'd like to start at (1..L)
- * ret_fh - RETURN: handle for file the key is in
- * record_offset - RETURN: offset of entire record
- * data_offset - RETURN: offset of subseq (see above)
- * ret_actual_start- RETURN: coord (1..L) of residue at data_offset
- *
- * Returns: 0 on success, non-zero on failure.
- */
-int
-SSIGetSubseqOffset(SSIFILE *sfp, char *key, int requested_start,
- int *ret_fh, SSIOFFSET *record_offset,
- SSIOFFSET *data_offset, int *ret_actual_start)
-{
- int status;
- sqd_uint32 len;
- int r, b, i, l; /* tmp variables for "clarity", to match docs */
-
- /* Look up the key. Rely on the fact that SSIGetOffsetByName()
- * leaves the index file positioned at the rest of the data for this key.
- */
- status = SSIGetOffsetByName(sfp, key, ret_fh, record_offset);
- if (status != 0) return status;
-
- /* Check that we're allowed to do subseq lookup on that file.
- */
- if (! (sfp->fileflags[*ret_fh] & SSI_FAST_SUBSEQ))
- return SSI_ERR_NO_SUBSEQS;
-
- /* Read the data we need for subseq lookup
- */
- if (! read_offset(sfp->fp, sfp->smode, data_offset)) return SSI_ERR_NODATA;
- if (! read_i32(sfp->fp, &len)) return SSI_ERR_NODATA;
-
- /* Set up tmp variables for clarity of equations below,
- * and to make them match documentation (ssi-format.tex).
- */
- r = sfp->rpl[*ret_fh]; /* residues per line */
- b = sfp->bpl[*ret_fh]; /* bytes per line */
- i = requested_start; /* start position 1..L */
- l = (i-1)/r; /* data line # (0..) that the residue is on */
- if (r == 0 || b == 0) return SSI_ERR_NO_SUBSEQS;
- if (i < 0 || i > len) return SSI_ERR_RANGE;
-
- /* When b = r+1, there's nothing but sequence on each data line (and the \0),
- * and we can find each residue precisely.
- */
- if (b == r+1) {
- if (sfp->smode == SSI_OFFSET_I32) {
- data_offset->mode = SSI_OFFSET_I32;
- data_offset->off.i32 = data_offset->off.i32 + l*b + (i-1)%r;
- } else if (sfp->smode == SSI_OFFSET_I64) {
- data_offset->mode = SSI_OFFSET_I64;
- data_offset->off.i64 = data_offset->off.i64 + l*b + (i-1)%r;
- }
- *ret_actual_start = requested_start;
- } else {
- /* else, there's other stuff on seq lines, so the best
- * we can do easily is to position at start of relevant line.
- */
- if (sfp->smode == SSI_OFFSET_I32) {
- data_offset->mode = SSI_OFFSET_I32;
- data_offset->off.i32 = data_offset->off.i32 + l*b;
- } else if (sfp->smode == SSI_OFFSET_I64) {
- data_offset->mode = SSI_OFFSET_I64;
- data_offset->off.i64 = data_offset->off.i64 + l*b;
- }
- /* yes, the eq below is = 1 + (i-1)/r*r but it's not = i. that's an integer /. */
- *ret_actual_start = 1 + l*r;
- }
- return 0;
-}
-
-/* Function: SSISetFilePosition()
- * Date: SRE, Tue Jan 2 09:13:46 2001 [St. Louis]
- *
- * Purpose: Uses {offset} to sets the file position for {fp}, usually an
- * open sequence file, relative to the start of the file.
- * Hides the details of system-dependent shenanigans necessary for
- * file positioning in large (>2 GB) files.
- *
- * Behaves just like fseek(fp, offset, SEEK_SET) for 32 bit
- * offsets and <2 GB files.
- *
- * Warning: if all else fails, in desperation, it will try to
- * use fsetpos(). This requires making assumptions about fpos_t
- * that may be unwarranted... assumptions that ANSI C prohibits
- * me from making... though I believe the ./configure
- * script robustly tests whether I can play with fpos_t like this.
- *
- * Args: fp - file to position.
- * offset - SSI offset relative to file start.
- *
- * Returns: 0 on success, nonzero on error.
- */
-int
-SSISetFilePosition(FILE *fp, SSIOFFSET *offset)
-{
- if (offset->mode == SSI_OFFSET_I32) {
- if (fseek(fp, offset->off.i32, SEEK_SET) != 0) return SSI_ERR_SEEK_FAILED;
- }
-#ifndef HAS_64BIT_FILE_OFFSETS
- else return SSI_ERR_NO64BIT;
-#elif defined HAVE_FSEEKO && SIZEOF_OFF_T == 8
- else if (fseeko(fp, offset->off.i64, SEEK_SET) != 0) return SSI_ERR_SEEK_FAILED;
-#elif defined HAVE_FSEEKO64 && SIZEOF_OFF64_T == 8
- else if (fseeko64(fp, offset->off.i64, SEEK_SET) != 0) return SSI_ERR_SEEK_FAILED;
-#elif defined HAVE_FSEEK64
- else if (fseek64(fp, offset->off.i64, SEEK_SET) != 0) return SSI_ERR_SEEK_FAILED;
-#elif defined ARITHMETIC_FPOS_T && SIZEOF_FPOS_T == 8
- else if (fsetpos(fp, &(offset->off.i64)) != 0) return SSI_ERR_SEEK_FAILED;
-#endif
- return 0;
-}
-
-
-/* Function: SSIFileInfo()
- * Date: SRE, Tue Jan 2 10:31:01 2001 [St. Louis]
- *
- * Purpose: Given a file number {fh} in an open index file
- * {sfp}, retrieve file name {ret_filename} and
- * the file format {ret_format}.
- *
- * {ret_filename} is a pointer to a string maintained
- * internally by {sfp}. It should not be free'd;
- * SSIClose(sfp) takes care of it.
- *
- * Args: sfp - open index file
- * fh - handle on file to look up
- * ret_filename - RETURN: name of file n
- * ret_format - RETURN: format of file n
- *
- * Returns: 0 on success, nonzero on failure.
- */
-int
-SSIFileInfo(SSIFILE *sfp, int fh, char **ret_filename, int *ret_format)
-{
- if (fh < 0 || fh >= sfp->nfiles) return SSI_ERR_BADARG;
- *ret_filename = sfp->filename[fh];
- *ret_format = sfp->fileformat[fh];
- return 0;
-}
-
-/* Function: SSIClose()
- * Date: SRE, Sun Dec 31 14:56:37 2000 [St. Louis]
- *
- * Purpose: Close an open {SSIFILE *}.
- *
- * Args: sfp - index file to close.
- *
- * Returns: (void)
- */
-void
-SSIClose(SSIFILE *sfp)
-{
- if (sfp != NULL) {
- clear_ssifile(sfp);
- if (sfp->fp != NULL) fclose(sfp->fp);
- free(sfp);
- }
-}
-/* clear_ssifile(): free the innards of SSIFILE, without
- * destroying the structure or closing the stream.
- */
-static void
-clear_ssifile(SSIFILE *sfp)
-{
- int i;
-
- if (sfp->filename != NULL) {
- for (i = 0; i < sfp->nfiles; i++)
- if (sfp->filename[i] != NULL) free(sfp->filename[i]);
- free(sfp->filename);
- }
- if (sfp->fileformat != NULL) free(sfp->fileformat);
- if (sfp->fileflags != NULL) free(sfp->fileflags);
- if (sfp->bpl != NULL) free(sfp->bpl);
- if (sfp->rpl != NULL) free(sfp->rpl);
-}
-
-
-/* Function: SSIRecommendMode()
- * Date: SRE, Fri Feb 16 08:23:47 2001 [St. Louis]
- *
- * Purpose: Examines the file and determines whether it should be
- * indexed with large file support or not; returns
- * SSI_OFFSET_I32 for most files, SSI_OFFSET_I64 for large
- * files, or -1 on failure.
- *
- * Args: file - name of file to check for size
- *
- * Returns: -1 on failure (including case where file is too big)
- * SSI_OFFSET_I32 for most files (<= 2^31-1 bytes)
- * SSI_OFFSET_I64 for large files (> 2^31-1 bytes)
- */
-int
-SSIRecommendMode(char *file)
-{
-#if HAVE_STAT64
- struct stat64 s1;
- if (stat64(file, &s1) == 0) {
- if (s1.st_size <= 2146483647L) return SSI_OFFSET_I32;
- else return SSI_OFFSET_I64;
- }
-#else
- struct stat s2;
- if (stat(file, &s2) == 0) {
- if (s2.st_size <= 2146483647L) return SSI_OFFSET_I32;
- else return SSI_OFFSET_I64;
- }
-#endif
- return -1;
-}
-
-
-/* Function: SSICreateIndex()
- * Date: SRE, Tue Jan 2 11:23:25 2001 [St. Louis]
- *
- * Purpose: Creates and initializes a SSI index structure.
- * Sequence file offset type is specified by {mode}.
- *
- * Args: mode - SSI_OFFSET_I32 or SSI_OFFSET_I64, sequence file index mode.
- *
- * Returns: ptr to new index structure, or NULL on failure.
- * Caller is responsible for free'ing the returned
- * structure with SSIFreeIndex().
- */
-SSIINDEX *
-SSICreateIndex(int mode)
-{
- SSIINDEX *g;
-
- g = NULL;
- if ((g = malloc(sizeof(SSIINDEX))) == NULL) goto FAILURE;
- g->smode = mode;
- g->imode = SSI_OFFSET_I32; /* index always starts as 32-bit; may get upgraded later */
- g->external = FALSE;
- g->max_ram = SSI_MAXRAM;
-
-#ifndef HAS_64BIT_FILE_OFFSETS
- if (mode == SSI_OFFSET_I64)
- Die("\
-Can't create a 64-bit SSI index on this system, sorry;\n\
-I don't have 64-bit file offset functions available.\n");
-#endif
-
- g->filenames = NULL;
- g->fileformat = NULL;
- g->bpl = NULL;
- g->rpl = NULL;
- g->flen = 0;
- g->nfiles = 0;
-
- g->pkeys = NULL;
- g->plen = 0;
- g->nprimary = 0;
- g->ptmpfile = "tmp.ssi.1"; /* hardcoded, for now. */
- g->ptmp = NULL;
-
- g->skeys = NULL;
- g->slen = 0;
- g->nsecondary = 0;
- g->stmpfile = "tmp.ssi.2"; /* hardcoded, for now. */
- g->stmp = NULL;
-
- /* All mallocs must go after NULL initializations, because of the cleanup strategy;
- * we'll try to free anything non-NULL if a malloc fails.
- */
- if ((g->filenames = malloc(sizeof(char *) * SSI_FILE_BLOCK)) == NULL) goto FAILURE;
- if ((g->fileformat= malloc(sizeof(sqd_uint32) * SSI_FILE_BLOCK)) == NULL) goto FAILURE;
- if ((g->bpl = malloc(sizeof(sqd_uint32) * SSI_FILE_BLOCK)) == NULL) goto FAILURE;
- if ((g->rpl = malloc(sizeof(sqd_uint32) * SSI_FILE_BLOCK)) == NULL) goto FAILURE;
-
- if ((g->pkeys = malloc(sizeof(struct ssipkey_s)* SSI_KEY_BLOCK))== NULL) goto FAILURE;
- if ((g->skeys = malloc(sizeof(struct ssipkey_s)* SSI_KEY_BLOCK))== NULL) goto FAILURE;
-
- return g;
-
- FAILURE:
- SSIFreeIndex(g); /* free the damaged structure */
- return NULL;
-}
-
-/* Function: SSIGetFilePosition()
- * Date: SRE, Tue Jan 2 09:59:26 2001 [St. Louis]
- *
- * Purpose: Fills {ret_offset} with the current disk
- * offset of {fp}, relative to the start of the file.
- * {mode} is set to either SSI_OFFSET_I32 or
- * SSI_OFFSET_I64. If {mode} is _I32 (32 bit), just wraps
- * a call to ftell(); otherwise deals with system-dependent
- * details of 64-bit file offsets.
- *
- * Args: fp - open stream
- * mode - SSI_OFFSET_I32 or SSI_OFFSET_I64
- * ret_offset - RETURN: file position
- *
- * Returns: 0 on success. nonzero on error.
- */
-int
-SSIGetFilePosition(FILE *fp, int mode, SSIOFFSET *ret_offset)
-{
- if (mode == SSI_OFFSET_I32)
- {
- ret_offset->mode = SSI_OFFSET_I32;
- ret_offset->off.i32 = ftell(fp);
- if (ret_offset->off.i32 == -1) return SSI_ERR_TELL_FAILED;
- }
- else if (mode != SSI_OFFSET_I64) abort(); /* only happens on a coding error */
- else {
- ret_offset->mode = SSI_OFFSET_I64;
-#ifndef HAS_64BIT_FILE_OFFSETS
- return SSI_ERR_NO64BIT;
-#elif defined HAVE_FTELLO && SIZEOF_OFF_T == 8
- if ((ret_offset->off.i64 = ftello(fp)) == -1) return SSI_ERR_TELL_FAILED;
-#elif defined HAVE_FTELLO64 && SIZEOF_OFF64_T == 8
- if ((ret_offset->off.i64 = ftello64(fp)) == -1) return SSI_ERR_TELL_FAILED;
-#elif defined HAVE_FTELL64
- if ((ret_offset->off.i64 = ftell64(fp)) == -1) return SSI_ERR_TELL_FAILED;
-#elif defined ARITHMETIC_FPOS_T && SIZEOF_FPOS_T == 8
- if (fgetpos(fp, &(ret_offset->off.i64)) != 0) return SSI_ERR_TELL_FAILED;
-#endif
- }
- return 0;
-}
-
-/* Function: SSIAddFileToIndex()
- * Date: SRE, Tue Jan 2 12:54:36 2001 [St. Louis]
- *
- * Purpose: Adds the sequence file {filename}, which is known to
- * be in format {fmt}, to the index {g}. Creates and returns
- * a unique filehandle {fh} for then associating primary keys
- * with this file using SSIAddPrimaryKeyToIndex().
- *
- * Args: g - active index
- * filename - file to add
- * fmt - format code for this file (e.g. SQFILE_FASTA)
- * ret_fh - RETURN: unique handle for this file
- *
- * Returns: 0 on success; nonzero on error.
- */
-int
-SSIAddFileToIndex(SSIINDEX *g, char *filename, int fmt, int *ret_fh)
-{
- int n;
-
- if (g->nfiles >= SSI_MAXFILES) return SSI_ERR_TOOMANY_FILES;
-
- n = strlen(filename);
- if ((n+1) > g->flen) g->flen = n+1;
-
- g->filenames[g->nfiles] = FileTail(filename, FALSE);
- g->fileformat[g->nfiles] = fmt;
- g->bpl[g->nfiles] = 0;
- g->rpl[g->nfiles] = 0;
- *ret_fh = g->nfiles; /* handle is simply = file number */
- g->nfiles++;
-
- if (g->nfiles % SSI_FILE_BLOCK == 0) {
- g->filenames = realloc(g->filenames, sizeof(char *) * (g->nfiles+SSI_FILE_BLOCK));
- if (g->filenames == NULL) return SSI_ERR_MALLOC;
- g->fileformat= realloc(g->fileformat, sizeof(sqd_uint32) * (g->nfiles+SSI_FILE_BLOCK));
- if (g->fileformat == NULL) return SSI_ERR_MALLOC;
- g->bpl = realloc(g->bpl, sizeof(sqd_uint32) * (g->nfiles+SSI_FILE_BLOCK));
- if (g->bpl == NULL) return SSI_ERR_MALLOC;
- g->rpl = realloc(g->rpl, sizeof(sqd_uint32) * (g->nfiles+SSI_FILE_BLOCK));
- if (g->rpl == NULL) return SSI_ERR_MALLOC;
- }
- return 0;
-}
-
-
-/* Function: SSISetFileForSubseq()
- * Date: SRE, Tue Jan 9 10:02:05 2001 [St. Louis]
- *
- * Purpose: Set SSI_FAST_SUBSEQ for the file indicated by
- * filehandle {fh} in the index {g}, setting
- * parameters {bpl} and {rpl} to the values given.
- * {bpl} is the number of bytes per sequence data line.
- * {rpl} is the number of residues per sequence data line.
- * Caller must be sure that {bpl} and {rpl} do not change
- * on any line of any sequence record in the file
- * (except for the last data line of each record). If
- * this is not the case in this file, SSI_FAST_SUBSEQ
- * will not work, and this routine should not be
- * called.
- *
- * Args: g - the active index
- * fh - handle for file to set SSI_FAST_SUBSEQ on
- * bpl - bytes per data line
- * rpl - residues per data line
- *
- * Returns: 0 on success; 1 on error.
- */
-int
-SSISetFileForSubseq(SSIINDEX *g, int fh, int bpl, int rpl)
-{
- if (fh < 0 || fh >= g->nfiles) return SSI_ERR_BADARG;
- if (bpl <= 0 || rpl <= 0) return SSI_ERR_BADARG;
- g->bpl[fh] = bpl;
- g->rpl[fh] = rpl;
- return 0;
-}
-
-
-/* Function: SSIAddPrimaryKeyToIndex()
- * Date: SRE, Tue Jan 2 11:50:54 2001 [St. Louis]
- *
- * Purpose: Put primary key {key} in the index {g}, while telling
- * the index this primary key is in the file associated
- * with filehandle {fh} (returned by a previous call
- * to SSIAddFileToIndex()), and its record starts at
- * position {r_off} in the file.
- *
- * {d_off} and {L} are optional; they may be left unset
- * by passing NULL and 0, respectively. (If one is
- * provided, both must be provided.) If they are provided,
- * {d_off} gives the position of the first line of sequence
- * data in the record, and {L} gives the length of
- * the sequence in residues. They are used when
- * SSI_FAST_SUBSEQ is set for this file. If SSI_FAST_SUBSEQ
- * is not set for the file, {d_off} and {L} will be
- * ignored by the index reading API even if they are stored
- * by the index writing API, so it doesn't hurt for the
- * indexing program to provide them; typically they
- * won't know whether it's safe to set SSI_FAST_SUBSEQ
- * for the whole file until the whole file has been
- * read and every key has already been added to the index.
- *
- * Args: g - active index
- * key - primary key to add
- * fh - handle on file that this key's in
- * r_off - offset to start of record
- * d_off - offset to start of sequence data
- * L - length of sequence, or 0
- *
- * Returns: 0 on success, nonzero on error.
- */
-int
-SSIAddPrimaryKeyToIndex(SSIINDEX *g, char *key, int fh,
- SSIOFFSET *r_off, SSIOFFSET *d_off, int L)
-{
- int n; /* a string length */
-
- if (fh >= SSI_MAXFILES) return SSI_ERR_TOOMANY_FILES;
- if (g->nprimary >= SSI_MAXKEYS) return SSI_ERR_TOOMANY_KEYS;
- if (L > 0 && d_off == NULL) abort(); /* need both. */
-
- /* Before adding the key: check how big our index is.
- * If it's getting too large, switch to external mode.
- */
- if (!g->external && current_index_size(g) >= g->max_ram)
- if (activate_external_sort(g) != 0) return SSI_ERR_NOFILE;
-
- /* Update maximum pkey length, if needed.
- */
- n = strlen(key);
- if ((n+1) > g->plen) g->plen = n+1;
-
- /* External mode? Simply append to disk...
- */
- if (g->external) {
- if (g->smode == SSI_OFFSET_I32) {
- fprintf(g->ptmp, "%s\t%d\t%lu\t%lu\t%lu\n",
- key, fh, (unsigned long) r_off->off.i32,
- (unsigned long) (d_off == NULL? 0 : d_off->off.i32),
- (unsigned long) L);
- } else {
-#ifdef CLUSTALO
- fprintf(g->ptmp, "%s\t%d\t%llu\t%llu\t%lu\n",
- key, fh, (unsigned long long)r_off->off.i64,
- d_off == NULL? 0 : (unsigned long long) d_off->off.i64,
- (unsigned long) L);
-#else
- fprintf(g->ptmp, "%s\t%d\t%llu\t%llu\t%lu\n",
- key, fh, r_off->off.i64,
- d_off == NULL? 0 : d_off->off.i64,
- (unsigned long) L);
-#endif
- }
- g->nprimary++;
- return 0;
- }
-
- /* Else: internal mode, keep keys in memory...
- */
- if ((g->pkeys[g->nprimary].key = sre_strdup(key, n)) == NULL) return SSI_ERR_MALLOC;
- g->pkeys[g->nprimary].fnum = (sqd_uint16) fh;
- g->pkeys[g->nprimary].r_off = *r_off;
- if (d_off != NULL && L > 0) {
- g->pkeys[g->nprimary].d_off = *d_off;
- g->pkeys[g->nprimary].len = L;
- } else {
- /* yeah, this looks stupid, but look: we have to give a valid
- looking, non-NULL d_off of some sort, or writes will fail.
- It's going to be unused anyway. */
- g->pkeys[g->nprimary].d_off = *r_off;
- g->pkeys[g->nprimary].len = 0;
- }
- g->nprimary++;
-
- if (g->nprimary % SSI_KEY_BLOCK == 0) {
- g->pkeys = realloc(g->pkeys, sizeof(struct ssipkey_s) * (g->nprimary+SSI_KEY_BLOCK));
- if (g->pkeys == NULL) return SSI_ERR_MALLOC;
- }
- return 0;
-}
-
-
-/* Function: SSIAddSecondaryKeyToIndex()
- * Date: SRE, Tue Jan 2 12:44:40 2001 [St. Louis]
- *
- * Purpose: Puts secondary key {key} in the index {g}, associating
- * it with primary key {pkey} that was previously
- * registered by SSIAddPrimaryKeyToIndex().
- *
- * Args: g - active index
- * key - secondary key to add
- * pkey - primary key to associate this key with
- *
- * Returns: 0 on success, nonzero on failure.
- */
-int
-SSIAddSecondaryKeyToIndex(SSIINDEX *g, char *key, char *pkey)
-{
- int n; /* a string length */
-
- if (g->nsecondary >= SSI_MAXKEYS) return SSI_ERR_TOOMANY_KEYS;
-
- /* Before adding the key: check how big our index is.
- * If it's getting too large, switch to external mode.
- */
- if (!g->external && current_index_size(g) >= g->max_ram)
- if (activate_external_sort(g) != 0) return SSI_ERR_NOFILE;
-
- /* Update maximum secondary key length, if necessary.
- */
- n = strlen(key);
- if ((n+1) > g->slen) g->slen = n+1;
-
- /* if external mode: write info to disk.
- */
- if (g->external) {
- fprintf(g->stmp, "%s\t%s\n", key, pkey);
- g->nsecondary++;
- return 0;
- }
-
- /* else, internal mode... store info in memory.
- */
- if ((g->skeys[g->nsecondary].key = sre_strdup(key, n)) == NULL) return SSI_ERR_MALLOC;
- if ((g->skeys[g->nsecondary].pkey = sre_strdup(pkey, -1)) == NULL) return SSI_ERR_MALLOC;
- g->nsecondary++;
-
- if (g->nsecondary % SSI_KEY_BLOCK == 0) {
- g->skeys = realloc(g->skeys, sizeof(struct ssiskey_s) * (g->nsecondary+SSI_KEY_BLOCK));
- if (g->skeys == NULL) return SSI_ERR_MALLOC;
- }
- return 0;
-}
-
-
-
-
-/* Function: SSIWriteIndex()
- * Date: SRE, Tue Jan 2 13:55:56 2001 [St. Louis]
- *
- * Purpose: Writes complete index {g} in SSI format to a
- * binary file {file}. Does all
- * the overhead of sorting the primary and secondary keys,
- * and maintaining the association of secondary keys
- * with primary keys during and after the sort.
- *
- * Args: file - file to write to
- * g - index to sort & write out.
- *
- * Returns: 0 on success, nonzero on error.
- */
-/* needed for qsort() */
-static int
-pkeysort(const void *k1, const void *k2)
-{
- struct ssipkey_s *key1;
- struct ssipkey_s *key2;
- key1 = (struct ssipkey_s *) k1;
- key2 = (struct ssipkey_s *) k2;
- return strcmp(key1->key, key2->key);
-}
-static int
-skeysort(const void *k1, const void *k2)
-{
- struct ssiskey_s *key1;
- struct ssiskey_s *key2;
- key1 = (struct ssiskey_s *) k1;
- key2 = (struct ssiskey_s *) k2;
- return strcmp(key1->key, key2->key);
-}
-int
-SSIWriteIndex(char *file, SSIINDEX *g)
-{
- FILE *fp;
- int status;
- int i;
- sqd_uint32 header_flags, file_flags;
- sqd_uint32 frecsize, precsize, srecsize;
- sqd_uint64 foffset, poffset, soffset;
- char *s, *s2;
-
- if ((fp = fopen(file,"wb")) == NULL) return SSI_ERR_NOFILE;
- status = 0;
-
- /* How big is the index? If it's going to be > 2GB, we need
- * to flip to 64-bit index mode. 2047 (instead of 2048) gives us
- * some slop room.
- * die'ing here is pretty brutal - if we flip to 64-bit index
- * mode, we hve 100's of millions of keys, so we've processed
- * a long time before reaching this point. Ah well.
- */
- if (current_index_size(g) >= 2047) {
- g->imode = SSI_OFFSET_I64;
-#ifndef HAS_64BIT_FILE_OFFSETS
- Die("\
-Can't switch to 64-bit SSI index mode on this system, sorry;\n\
-I don't have 64-bit file offset functions available.\n");
-#endif
- }
-
- /* Magic-looking numbers come from adding up sizes
- * of things in bytes
- */
- frecsize = 16 + g->flen;
- precsize = (g->smode == SSI_OFFSET_I64) ? 22+g->plen : 14+g->plen;
- srecsize = g->slen + g->plen;
-
- header_flags = 0;
- if (g->smode == SSI_OFFSET_I64) header_flags |= SSI_USE64;
- if (g->imode == SSI_OFFSET_I64) header_flags |= SSI_USE64_INDEX;
-
- /* Magic-looking numbers again come from adding up sizes
- * of things in bytes
- */
- foffset = (header_flags & SSI_USE64_INDEX) ? 66 : 54;
- poffset = foffset + frecsize*g->nfiles;
- soffset = poffset + precsize*g->nprimary;
-
- /* Sort the keys
- * If external mode, make system calls to UNIX/POSIX "sort" in place, then
- * open new sorted files for reading thru ptmp and stmp handles.
- * If internal mode, call qsort.
- *
- * Note that you'd better force a POSIX locale for the sort; else,
- * some silly distro (e.g. Mandrake Linux >=8.1) may have specified
- * LC_COLLATE=en_US, and this'll give a sort "bug" in which it doesn't
- * sort by byte order.
- */
- if (g->external) {
- char cmd[1024];
-
- fclose(g->ptmp);
- g->ptmp = NULL;
- sprintf(cmd, "env LC_ALL=POSIX sort -o %s %s\n", g->ptmpfile, g->ptmpfile);
- if ((status = system(cmd)) != 0) return SSI_ERR_EXTERNAL_SORT;
- if ((g->ptmp = fopen(g->ptmpfile, "r")) == NULL) return SSI_ERR_EXTERNAL_SORT;
-
- fclose(g->stmp);
- g->stmp = NULL;
- sprintf(cmd, "env LC_ALL=POSIX sort -o %s %s\n", g->stmpfile, g->stmpfile);
- if ((status = system(cmd)) != 0) return SSI_ERR_EXTERNAL_SORT;
- if ((g->stmp = fopen(g->stmpfile, "r")) == NULL) return SSI_ERR_EXTERNAL_SORT;
- } else {
- qsort((void *) g->pkeys, g->nprimary, sizeof(struct ssipkey_s), pkeysort);
- qsort((void *) g->skeys, g->nsecondary, sizeof(struct ssiskey_s), skeysort);
- }
-
- /* Write the header
- */
- if (! write_i32(fp, v20magic)) return SSI_ERR_FWRITE;
- if (! write_i32(fp, header_flags)) return SSI_ERR_FWRITE;
- if (! write_i16(fp, g->nfiles)) return SSI_ERR_FWRITE;
- if (! write_i32(fp, g->nprimary)) return SSI_ERR_FWRITE;
- if (! write_i32(fp, g->nsecondary)) return SSI_ERR_FWRITE;
- if (! write_i32(fp, g->flen)) return SSI_ERR_FWRITE;
- if (! write_i32(fp, g->plen)) return SSI_ERR_FWRITE;
- if (! write_i32(fp, g->slen)) return SSI_ERR_FWRITE;
- if (! write_i32(fp, frecsize)) return SSI_ERR_FWRITE;
- if (! write_i32(fp, precsize)) return SSI_ERR_FWRITE;
- if (! write_i32(fp, srecsize)) return SSI_ERR_FWRITE;
- if (g->imode == SSI_OFFSET_I32) {
- if (! write_i32(fp, foffset)) return SSI_ERR_FWRITE;
- if (! write_i32(fp, poffset)) return SSI_ERR_FWRITE;
- if (! write_i32(fp, soffset)) return SSI_ERR_FWRITE;
- } else {
- if (! write_i64(fp, foffset)) return SSI_ERR_FWRITE;
- if (! write_i64(fp, poffset)) return SSI_ERR_FWRITE;
- if (! write_i64(fp, soffset)) return SSI_ERR_FWRITE;
- }
-
- /* The file section
- */
- if ((s = malloc(sizeof(char) * g->flen)) == NULL) return SSI_ERR_MALLOC;
- for (i = 0; i < g->nfiles; i++)
- {
- file_flags = 0;
- if (g->bpl[i] > 0 && g->rpl[i] > 0) file_flags |= SSI_FAST_SUBSEQ;
-
- strcpy(s, g->filenames[i]);
- if (fwrite(s, sizeof(char), g->flen, fp) != g->flen) return SSI_ERR_FWRITE;
- if (! write_i32(fp, g->fileformat[i])) return SSI_ERR_FWRITE;
- if (! write_i32(fp, file_flags)) return SSI_ERR_FWRITE;
- if (! write_i32(fp, g->bpl[i])) return SSI_ERR_FWRITE;
- if (! write_i32(fp, g->rpl[i])) return SSI_ERR_FWRITE;
- }
- free(s);
-
- /* The primary key section
- */
- if ((s = malloc(sizeof(char) * g->plen)) == NULL) return SSI_ERR_MALLOC;
- if (g->external) {
- char *buf = NULL;
- int buflen = 0;
- struct ssipkey_s pkey;
- for (i = 0; i < g->nprimary; i++)
- {
- if (sre_fgets(&buf, &buflen, g->ptmp) == NULL) return SSI_ERR_NODATA;
- if (parse_pkey_info(buf, g->smode, &pkey) != 0) return SSI_ERR_BADFORMAT;
- strcpy(s, pkey.key);
- if (fwrite(s, sizeof(char), g->plen, fp) != g->plen) return SSI_ERR_FWRITE;
- if (! write_i16( fp, pkey.fnum)) return SSI_ERR_FWRITE;
- if (! write_offset(fp, &(pkey.r_off))) return SSI_ERR_FWRITE;
- if (! write_offset(fp, &(pkey.d_off))) return SSI_ERR_FWRITE;
- if (! write_i32( fp, pkey.len)) return SSI_ERR_FWRITE;
- }
- free(buf);
- } else {
- for (i = 0; i < g->nprimary; i++)
- {
- strcpy(s, g->pkeys[i].key);
- if (fwrite(s, sizeof(char), g->plen, fp) != g->plen) return SSI_ERR_FWRITE;
- if (! write_i16( fp, g->pkeys[i].fnum)) return SSI_ERR_FWRITE;
- if (! write_offset(fp, &(g->pkeys[i].r_off))) return SSI_ERR_FWRITE;
- if (! write_offset(fp, &(g->pkeys[i].d_off))) return SSI_ERR_FWRITE;
- if (! write_i32( fp, g->pkeys[i].len)) return SSI_ERR_FWRITE;
- }
- }
-
- /* The secondary key section
- */
- if (g->nsecondary > 0) {
- if ((s2 = malloc(sizeof(char) * g->slen)) == NULL) return SSI_ERR_MALLOC;
-
- if (g->external) {
- struct ssiskey_s skey;
- char *buf = NULL;
- int n = 0;
-
- for (i = 0; i < g->nsecondary; i++)
- {
- if (sre_fgets(&buf, &n, g->stmp) == NULL) return SSI_ERR_NODATA;
- if (parse_skey_info(buf, &skey) != 0) return SSI_ERR_BADFORMAT;
- strcpy(s2, skey.key);
- strcpy(s, skey.pkey);
- if (fwrite(s2, sizeof(char), g->slen, fp) != g->slen) return SSI_ERR_FWRITE;
- if (fwrite(s, sizeof(char), g->plen, fp) != g->plen) return SSI_ERR_FWRITE;
- }
- free(buf);
- } else {
- for (i = 0; i < g->nsecondary; i++)
- {
- strcpy(s2, g->skeys[i].key);
- strcpy(s, g->skeys[i].pkey);
- if (fwrite(s2, sizeof(char), g->slen, fp) != g->slen) return SSI_ERR_FWRITE;
- if (fwrite(s, sizeof(char), g->plen, fp) != g->plen) return SSI_ERR_FWRITE;
- }
- }
- free(s2);
- }
-
- free(s);
- fclose(fp);
- return status;
-}
-
-
-/* Function: SSIFreeIndex()
- * Date: SRE, Tue Jan 2 11:44:08 2001 [St. Louis]
- *
- * Purpose: Free an index structure {g}.
- *
- * Args: g - ptr to an open index.
- *
- * Returns: (void)
- */
-void
-SSIFreeIndex(SSIINDEX *g)
-{
- int i;
- if (g != NULL)
- {
- if (g->external == FALSE) {
- for (i = 0; i < g->nprimary; i++) free(g->pkeys[i].key);
- for (i = 0; i < g->nsecondary; i++) free(g->skeys[i].key);
- for (i = 0; i < g->nsecondary; i++) free(g->skeys[i].pkey);
- if (g->pkeys != NULL) free(g->pkeys);
- if (g->skeys != NULL) free(g->skeys);
- } else {
- if (g->ptmp != NULL) fclose(g->ptmp);
- if (g->stmp != NULL) fclose(g->stmp);
-#if DEBUGLEVEL == 0
- remove(g->ptmpfile);
- remove(g->stmpfile);
-#endif
- }
- for (i = 0; i < g->nfiles; i++) free(g->filenames[i]);
- if (g->filenames != NULL) free(g->filenames);
- if (g->fileformat != NULL) free(g->fileformat);
- if (g->bpl != NULL) free(g->bpl);
- if (g->rpl != NULL) free(g->rpl);
- free(g);
- }
-}
-
-
-/* Function: SSIErrorString()
- * Date: SRE, Tue Jan 2 10:38:10 2001 [St. Louis]
- *
- * Purpose: Returns a ptr to an internal string corresponding
- * to error {n}, a code returned from any of the
- * functions in the API that return non-zero on error.
- *
- * Args: n - error code
- *
- * Returns: ptr to an internal string.
- */
-char *
-SSIErrorString(int n)
-{
- switch (n) {
- case SSI_ERR_OK: return "ok (no error)";
- case SSI_ERR_NODATA: return "no data, fread() failed";
- case SSI_ERR_NO_SUCH_KEY: return "no such key";
- case SSI_ERR_MALLOC: return "out of memory, malloc() failed";
- case SSI_ERR_NOFILE: return "file not found, fopen() failed";
- case SSI_ERR_BADMAGIC: return "not a SSI file? (bad magic)";
- case SSI_ERR_BADFORMAT: return "corrupt format? unexpected data";
- case SSI_ERR_NO64BIT: return "no large file support for this system";
- case SSI_ERR_SEEK_FAILED: return "failed to reposition on disk";
- case SSI_ERR_TELL_FAILED: return "failed to get file position on disk";
- case SSI_ERR_NO_SUBSEQS: return "no fast subseq support for this seqfile";
- case SSI_ERR_RANGE: return "subseq start is out of range";
- case SSI_ERR_BADARG: return "an argument is out of range";
- case SSI_ERR_TOOMANY_FILES: return "number of files exceeds limit";
- case SSI_ERR_TOOMANY_KEYS: return "number of keys exceeds limit";
- case SSI_ERR_FWRITE: return "an fwrite() failed";
- case SSI_ERR_EXTERNAL_SORT: return "some problem with external sorting";
- default: return "unrecognized code";
- }
- /*NOTREACHED*/
-}
-
-static int
-read_i16(FILE *fp, sqd_uint16 *ret_result)
-{
- sqd_uint16 result;
- if (fread(&result, sizeof(sqd_uint16), 1, fp) != 1) return 0;
- *ret_result = sre_ntoh16(result);
- return 1;
-}
-static int
-write_i16(FILE *fp, sqd_uint16 n)
-{
- n = sre_hton16(n);
- if (fwrite(&n, sizeof(sqd_uint16), 1, fp) != 1) return 0;
- return 1;
-}
-static int
-read_i32(FILE *fp, sqd_uint32 *ret_result)
-{
- sqd_uint32 result;
- if (fread(&result, sizeof(sqd_uint32), 1, fp) != 1) return 0;
- *ret_result = sre_ntoh32(result);
- return 1;
-}
-static int
-write_i32(FILE *fp, sqd_uint32 n)
-{
- n = sre_hton32(n);
- if (fwrite(&n, sizeof(sqd_uint32), 1, fp) != 1) return 0;
- return 1;
-}
-static int
-read_i64(FILE *fp, sqd_uint64 *ret_result)
-{
- sqd_uint64 result;
- if (fread(&result, sizeof(sqd_uint64), 1, fp) != 1) return 0;
- *ret_result = sre_ntoh64(result);
- return 1;
-}
-static int
-write_i64(FILE *fp, sqd_uint64 n)
-{
- n = sre_hton64(n);
- if (fwrite(&n, sizeof(sqd_uint64), 1, fp) != 1) return 0;
- return 1;
-}
-static int
-read_offset(FILE *fp, char mode, SSIOFFSET *ret_offset)
-{
- if (mode == SSI_OFFSET_I32) {
- ret_offset->mode = SSI_OFFSET_I32;
- if (! read_i32(fp, &(ret_offset->off.i32))) return 0;
- } else if (mode == SSI_OFFSET_I64) {
- ret_offset->mode = SSI_OFFSET_I64;
- if (! read_i64(fp, &(ret_offset->off.i64))) return 0;
- } else return 0;
-
- return 1;
-}
-static int
-write_offset(FILE *fp, SSIOFFSET *offset)
-{
- if (offset->mode == SSI_OFFSET_I32) return write_i32(fp, offset->off.i32);
- else if (offset->mode == SSI_OFFSET_I64) return write_i64(fp, offset->off.i64);
- else abort();
- /*UNREACHED*/
- return 1; /* silence bitchy compilers */
-}
-
-static int
-parse_pkey_info(char *buf, char mode, struct ssipkey_s *pkey)
-{
- char *s, *tok;
- int n;
-
- s = buf;
- if ((tok = sre_strtok(&s, "\t\n", &n)) == NULL) return SSI_ERR_BADFORMAT;
- pkey->key = tok;
- if ((tok = sre_strtok(&s, "\t\n", &n)) == NULL) return SSI_ERR_BADFORMAT;
- pkey->fnum = (sqd_uint16) atoi(tok);
-
- if (mode == SSI_OFFSET_I32) {
- if ((tok = sre_strtok(&s, "\t\n", &n)) == NULL) return SSI_ERR_BADFORMAT;
- pkey->r_off.mode = mode;
- pkey->r_off.off.i32 = (sqd_uint32) strtoul(tok, NULL, 10);
- if ((tok = sre_strtok(&s, "\t\n", &n)) == NULL) return SSI_ERR_BADFORMAT;
- pkey->d_off.mode = mode;
- pkey->d_off.off.i32 = (sqd_uint32) strtoul(tok, NULL, 10);
- }
-#ifdef HAS_64BIT_FILE_OFFSETS
- else {
- if ((tok = sre_strtok(&s, "\t\n", &n)) == NULL) return SSI_ERR_BADFORMAT;
- pkey->r_off.mode = mode;
- pkey->r_off.off.i64 = (sqd_uint64) strtoull(tok, NULL, 10);
- if ((tok = sre_strtok(&s, "\t\n", &n)) == NULL) return SSI_ERR_BADFORMAT;
- pkey->d_off.mode = mode;
- pkey->d_off.off.i64 = (sqd_uint64) strtoull(tok, NULL, 10);
- }
-#else
- else {
- return SSI_ERR_NO64BIT;
- }
-#endif
- if ((tok = sre_strtok(&s, "\t\n", &n)) == NULL) return SSI_ERR_BADFORMAT;
- pkey->len = (sqd_uint32) strtoul(tok, NULL, 10);
-
- return 0;
-}
-static int
-parse_skey_info(char *buf, struct ssiskey_s *skey)
-{
- char *s, *tok;
- int n;
-
- s = buf;
- if ((tok = sre_strtok(&s, "\t\n", &n)) == NULL) return SSI_ERR_BADFORMAT;
- skey->key = tok;
- if ((tok = sre_strtok(&s, "\t\n", &n)) == NULL) return SSI_ERR_BADFORMAT;
- skey->pkey = tok;
- return 0;
-}
-
-/* Function: binary_search()
- * Date: SRE, Sun Dec 31 16:05:03 2000 [St. Louis]
- *
- * Purpose: Find a key in a SSI index, by a binary search
- * in an alphabetically sorted list of keys. If successful,
- * return 0, and the index file is positioned to read
- * the rest of the data for that key. Else returns nonzero.
- *
- * Args: sfp - an open SSIFILE
- * key - key to find
- * klen - key length to allocate (plen or slen from sfp)
- * base - base offset (poffset or soffset)
- * recsize - size of each key record in bytes (precsize or srecsize)
- * maxidx - # of keys (nprimary or nsecondary)
- *
- * Returns: 0 on success, and leaves file positioned for reading remaining
- * data for the key.
- * Nonzero on failure:
- * SSI_ERR_NO_SUCH_KEY - that key's not in the index
- * SSI_ERR_MALLOC - a memory allocation failure
- * SSI_ERR_NODATA - an fread() failed
- */
-static int
-binary_search(SSIFILE *sfp, char *key, int klen, SSIOFFSET *base,
- sqd_uint32 recsize, sqd_uint32 maxidx)
-{
- char *name;
- sqd_uint32 left, right, mid;
- int cmp;
- int status;
-
- if (maxidx == 0) return SSI_ERR_NO_SUCH_KEY; /* special case: empty index */
- if ((name = malloc (sizeof(char)*klen)) == NULL) return SSI_ERR_MALLOC;
- left = 0;
- right = maxidx-1;
- while (1) { /* A binary search: */
- mid = (left+right) / 2; /* careful here. only works because
- we limit unsigned vars to signed ranges. */
- if ((status = indexfile_position(sfp, base, recsize, mid)) != 0)
- { free(name); return status; }
- if (fread(name, sizeof(char), klen, sfp->fp) != klen)
- { free(name); return SSI_ERR_NODATA; }
- cmp = strcmp(name, key);
- if (cmp == 0) break; /* found it! */
- else if (left >= right) /* oops, missed it; fail */
- { free(name); return SSI_ERR_NO_SUCH_KEY; }
- else if (cmp < 0) left = mid+1; /* it's right of mid */
- else if (cmp > 0) {
- if (mid == 0) { free(name); return SSI_ERR_NO_SUCH_KEY; } /* special case, beware */
- else right = mid-1; /* it's left of mid */
- }
- }
- free(name);
- return 0; /* and sfp->fp is positioned... */
-}
-
-/* Function: indexfile_position()
- * Date: SRE, Mon Jan 1 19:32:49 2001 [St. Louis]
- *
- * Purpose: Position the open index file {sfp} at the start
- * of record {n} in a list of records that starts at
- * base offset {base}, where each record takes up {l}
- * bytes. (e.g. the position is byte (base + n*l)).
- *
- * Args: sfp - open SSIFILE
- * base - offset of record 0 (e.g. sfp->foffset)
- * len - size of each record in bytes (e.g. sfp->frecsize)
- * n - which record to get (e.g. 0..sfp->nfiles)
- *
- * Returns: 0 on success, non-zero on failure.
- */
-static int
-indexfile_position(SSIFILE *sfp, SSIOFFSET *base, sqd_uint32 len, sqd_uint32 n)
-{
- SSIOFFSET pos;
- int status;
-
- if (base->mode == SSI_OFFSET_I32) {
- pos.mode = SSI_OFFSET_I32;
- pos.off.i32 = base->off.i32 + n*len;
- } else if (base->mode == SSI_OFFSET_I64) {
- pos.mode = SSI_OFFSET_I64;
- pos.off.i64 = base->off.i64 + n*len;
- } else return 0;
- if ((status = SSISetFilePosition(sfp->fp, &pos)) != 0) return status;
- return 0;
-}
-
-/* Function: current_index_size()
- * Date: SRE, Tue Feb 20 18:23:30 2001 [St. Louis]
- *
- * Purpose: Calculates the size of the current index,
- * in megabytes.
- */
-static sqd_uint64
-current_index_size(SSIINDEX *g)
-{
- sqd_uint64 frecsize, precsize, srecsize;
- sqd_uint64 total;
-
- /* Magic-looking numbers come from adding up sizes
- * of things in bytes
- */
- frecsize = 16 + g->flen;
- precsize = (g->smode == SSI_OFFSET_I64) ? 22+g->plen : 14+g->plen;
- srecsize = g->plen+g->slen;
- total = (66L + /* header size, if 64bit index offsets */
- frecsize * g->nfiles + /* file section size */
- precsize * g->nprimary + /* primary key section size */
- srecsize * g->nsecondary) / /* secondary key section size */
- 1048576L;
- return total;
-}
-/* Function: activate_external_sort()
- * Date: SRE, Mon Feb 4 09:08:08 2002 [St. Louis]
- *
- * Purpose: Switch to external sort mode.
- * Open file handles for external index files (ptmp, stmp).
- * Flush current index information to these files.
- * Free current memory, turn over control to the tmpfiles.
- *
- * Return: 0 on success; non-zero on failure.
- */
-static int
-activate_external_sort(SSIINDEX *g)
-{
- int i;
- /* it's a bit late to be checking this, but... */
- if (g->external) return 0; /* we already are external, fool */
- if (FileExists(g->ptmpfile)) return 1;
- if (FileExists(g->stmpfile)) return 1;
- if ((g->ptmp = fopen(g->ptmpfile, "w")) == NULL) return 1;
- if ((g->stmp = fopen(g->stmpfile, "w")) == NULL) return 1;
-
- /* Flush the current indices.
- */
- SQD_DPRINTF1(("Switching to external sort - flushing ssiindex to disk...\n"));
- for (i = 0; i < g->nprimary; i++) {
- if (g->smode == SSI_OFFSET_I32) {
- fprintf(g->ptmp, "%s\t%u\t%lu\t%lu\t%lu\n",
- g->pkeys[i].key, g->pkeys[i].fnum,
- (unsigned long) g->pkeys[i].r_off.off.i32,
- (unsigned long) g->pkeys[i].d_off.off.i32,
- (unsigned long) g->pkeys[i].len);
- } else {
- fprintf(g->ptmp, "%s\t%u\t%llu\t%llu\t%lu\n",
- g->pkeys[i].key, g->pkeys[i].fnum,
- (unsigned long long) g->pkeys[i].r_off.off.i64,
- (unsigned long long) g->pkeys[i].d_off.off.i64,
- (unsigned long) g->pkeys[i].len);
- }
- }
- for (i = 0; i < g->nsecondary; i++)
- fprintf(g->stmp, "%s\t%s\n", g->skeys[i].key, g->skeys[i].pkey);
-
- /* Free the memory now that we've flushed our lists to disk
- */
- for (i = 0; i < g->nprimary; i++) free(g->pkeys[i].key);
- for (i = 0; i < g->nsecondary; i++) free(g->skeys[i].key);
- for (i = 0; i < g->nsecondary; i++) free(g->skeys[i].pkey);
- if (g->pkeys != NULL) free(g->pkeys);
- if (g->skeys != NULL) free(g->skeys);
- g->pkeys = NULL;
- g->skeys = NULL;
-
- /* Turn control over to external accumulation mode.
- */
- g->external = TRUE;
- return 0;
-}
-
-
-/*****************************************************************
- * Debugging API
- *****************************************************************/
-void
-SSIForceExternalSort(SSIINDEX *g)
-{
- if (activate_external_sort(g) != 0)
- Die("failed to turn external sorting on.");
-}
-
-
-/*****************************************************************
- * Test driving mode
- *****************************************************************/
-#ifdef MUGGINS_LETS_ME_SLEEP
-/* Minimally:
- cc -g -Wall -o shiva -DDEBUGLEVEL=1 -DMUGGINS_LETS_ME_SLEEP ssi.c sqerror.c sre_string.c types.c sre_ctype.c sre_math.c file.c -lm
-*/
-
-int
-main(int argc, char **argv)
-{
- char name[32], accession[32];
- SSIINDEX *ssi;
- int mode;
- SSIOFFSET r_off, d_off;
- FILE *ofp;
- int i;
- int fh; /* a file handle */
- int status; /* return status from a SSI call */
-
- mode = SSI_OFFSET_I32;
- if ((ssi = SSICreateIndex(mode)) == NULL)
- Die("Failed to allocate SSI index");
-
- /* Generate two FASTA files, tmp.0 and tmp.1, and index them.
- */
- if ((ofp = fopen("tmp.0", "w")) == NULL)
- Die("failed to open tmp.0");
- if ((status = SSIAddFileToIndex(ssi, "tmp.0", SQFILE_FASTA, &fh)) != 0)
- Die("SSIAddFileToIndex() failed: %s", SSIErrorString(status));
- for (i = 0; i < 10; i++) {
- if ((status = SSIGetFilePosition(ofp, mode, &r_off)) != 0)
- Die("SSIGetFilePosition() failed: %s", SSIErrorString(status));
- sprintf(name, "seq%d", i);
- sprintf(accession, "ac%d", i);
- fprintf(ofp, ">%s [%s] Description? we don't need no steenking description.\n",
- name, accession);
- if ((status = SSIGetFilePosition(ofp, mode, &d_off)) != 0)
- Die("SSIGetFilePosition() failed: %s", SSIErrorString(status));
- fprintf(ofp, "AAAAAAAAAA\n");
- fprintf(ofp, "CCCCCCCCCC\n");
- fprintf(ofp, "GGGGGGGGGG\n");
- fprintf(ofp, "TTTTTTTTTT\n");
-
- if ((status = SSIAddPrimaryKeyToIndex(ssi, name, fh, &r_off, &d_off, 40)) != 0)
- Die("SSIAddPrimaryKeyToIndex() failed: %s", SSIErrorString(status));
- if ((status = SSIAddSecondaryKeyToIndex(ssi, accession, name)) != 0)
- Die("SSIAddSecondaryKeyToIndex() failed: %s", SSIErrorString(status));
- }
- SSISetFileForSubseq(ssi, fh, 11, 10);
- fclose(ofp);
-
- if ((ofp = fopen("tmp.1", "w")) == NULL)
- Die("failed to open tmp.1");
- if ((status = SSIAddFileToIndex(ssi, "tmp.1", SQFILE_FASTA, &fh)) != 0)
- Die("SSIAddFileToIndex() failed: %s", SSIErrorString(status));
- for (i = 10; i < 20; i++) {
- if ((status = SSIGetFilePosition(ofp, mode, &r_off)) != 0)
- Die("SSIGetFilePosition() failed: %s", SSIErrorString(status));
- sprintf(name, "seq%d", i);
- sprintf(accession, "ac%d", i);
- fprintf(ofp, ">%s [%s] i/o, i/o, it's off to disk we go.\n",
- name, accession);
- if ((status = SSIGetFilePosition(ofp, mode, &d_off)) != 0)
- Die("SSIGetFilePosition() failed: %s", SSIErrorString(status));
- fprintf(ofp, "AAAAAAAAAA 10\n");
- fprintf(ofp, "CCCCCCCCCC 20\n");
- fprintf(ofp, "GGGGGGGGGG 30\n");
- fprintf(ofp, "TTTTTTTTTT 40\n");
-
- if ((status = SSIAddPrimaryKeyToIndex(ssi, name, fh, &r_off, &d_off, 40)) != 0)
- Die("SSIAddPrimaryKeyToIndex() failed: %s", SSIErrorString(status));
- if ((status = SSIAddSecondaryKeyToIndex(ssi, accession, name)) != 0)
- Die("SSIAddSecondaryKeyToIndex() failed: %s", SSIErrorString(status));
- }
- SSISetFileForSubseq(ssi, fh, 14, 10);
- fclose(ofp);
-
- /* Write the index to tmp.ssi
- */
- if ((status = SSIWriteIndex("tmp.ssi", ssi)) != 0)
- Die("SSIWriteIndex() failed: %s", SSIErrorString(status));
- SSIFreeIndex(ssi);
-
- /* Now reopen the index and run some tests.
- */
- exit(0);
-}
-
-
-#endif /* test driving code */
-
-
-
git://source.jalview.org / jabaws.git / blobdiff