+++ /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.
- *****************************************************************/
-
-/* gsi.c
- * Interfaces for GSI "generic sequence index" files.
- * broken away from sqio.c and extended: SRE, Wed Aug 5 10:32:53 1998
- *
- *
- * GSI definition:
- * 1 + <nfiles> + <nkeys> total records.
- * Each record = 38 bytes.
- *
- * one header record : <"GSI" (32)> <nfiles (2)> <nkeys (4)>
- * <nfiles> file records : <filename (32)> <fileno (2)> <fmt (4)>
- * <nkeys> key records : <key (32)> <fileno (2)> <offset(4)>
- *
- * Matches up with my Perl scripts that create GSI files.
- *
- * RCS $Id: gsi.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: gsi.c,v 1.5 2001/08/04 20:15:42 eddy Exp)
- */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#ifndef SEEK_SET
-#include <unistd.h> /* needed for poor crippled SunOS */
-#endif
-
-#include "squid.h"
-#include "gsi.h"
-
-
-/*****************************************************************
- * GSI index file access routines
- *****************************************************************/
-
-/* Function: GSIOpen()
- *
- * Purpose: Open a GSI file. Returns the number of records in
- * the file and a file pointer. Returns NULL on failure.
- * The file pointer should be fclose()'d normally.
- */
-GSIFILE *
-GSIOpen(char *gsifile)
-{
- GSIFILE *gsi;
- char magic[GSI_KEYSIZE];
-
- gsi = (GSIFILE *) MallocOrDie (sizeof(GSIFILE));
- if ((gsi->gsifp = fopen(gsifile, "r")) == NULL)
- { free(gsi); squid_errno = SQERR_NOFILE; return NULL; }
-
- if (! fread(magic, sizeof(char), GSI_KEYSIZE, gsi->gsifp))
- { free(gsi); squid_errno = SQERR_NODATA; return NULL; }
- if (strcmp(magic, "GSI") != 0)
- { free(gsi); squid_errno = SQERR_FORMAT; return NULL; }
-
- if (! fread(&(gsi->nfiles), sizeof(sqd_uint16), 1, gsi->gsifp))
- { free(gsi); squid_errno = SQERR_NODATA; return NULL; }
- if (! fread(&(gsi->recnum), sizeof(sqd_uint32), 1, gsi->gsifp))
- { free(gsi); squid_errno = SQERR_NODATA; return NULL; }
-
- gsi->nfiles = sre_ntoh16(gsi->nfiles); /* convert from network short */
- gsi->recnum = sre_ntoh32(gsi->recnum); /* convert from network long */
-
- return gsi;
-}
-
-/* Function: GSIGetRecord()
- *
- * Purpose: Each non-header record of a GSI index files consists
- * of 38 bytes: 32 bytes of character string, a 2 byte
- * short, and a 4 byte long. This function returns the
- * three values.
- *
- * Args: gsi - open GSI index file, correctly positioned at a record
- * f1 - char[32], allocated by caller (or NULL if unwanted)
- * f2 - pointer to short (or NULL if unwanted)
- * f3 - pointer to long (or NULL if unwanted)
- *
- * Return: 0 on failure and sets squid_errno.
- */
-int
-GSIGetRecord(GSIFILE *gsi, char *f1, sqd_uint16 *f2, sqd_uint32 *f3)
-{
- if (f1 == NULL) fseek(gsi->gsifp, GSI_KEYSIZE, SEEK_CUR);
- else if (! fread(f1, GSI_KEYSIZE, 1, gsi->gsifp))
- { squid_errno = SQERR_NODATA; return 0; }
-
- if (f2 == NULL) fseek(gsi->gsifp, sizeof(sqd_uint16), SEEK_CUR);
- else if (! fread(f2, sizeof(sqd_uint16), 1, gsi->gsifp))
- { squid_errno = SQERR_NODATA; return 0; }
-
- if (f3 == NULL) fseek(gsi->gsifp, sizeof(sqd_uint32), SEEK_CUR);
- else if (! fread(f3, sizeof(sqd_uint32), 1, gsi->gsifp))
- { squid_errno = SQERR_NODATA; return 0; }
-
- if (f2 != NULL) *f2 = sre_ntoh16(*f2);
- if (f3 != NULL) *f3 = sre_ntoh32(*f3);
-
- return 1;
-}
-
-
-/* Function: GSIGetOffset()
- *
- * Purpose: From a key (sequence name), find a disk offset
- * in an open general sequence index file by binary
- * search. Presumably GSI indexing could be even faster
- * if we used hashing.
- *
- * Args: gsi - GSI index file, opened by GSIOpen()
- * key - name of key to retrieve indices for
- * ret_seqfile - pre-alloced char[32] array for seqfile name
- * ret_fmt - format of seqfile
- * ret_offset - return: disk offset in seqfile.
- */
-int
-GSIGetOffset(GSIFILE *gsi, char *key, char *ret_seqfile,
- int *ret_format, long *ret_offset)
-{
- sqd_uint32 left, right, mid;
- int cmp;
- char name[GSI_KEYSIZE + 1];
- sqd_uint32 offset;
- sqd_uint16 filenum;
- sqd_uint32 fmt;
-
- name[GSI_KEYSIZE] = '\0';
-
- left = gsi->nfiles + 1;
- right = gsi->nfiles + gsi->recnum;
- mid = (left + right) / 2;
- fseek(gsi->gsifp, mid * GSI_RECSIZE, SEEK_SET);
-
- while (GSIGetRecord(gsi, name, &filenum, &offset))
- {
- cmp = strcmp(name, key);
- if (cmp == 0) break; /* found it! */
- else if (left >= right) return 0; /* oops, missed it; fail. */
- else if (cmp < 0) left = mid + 1; /* it's right of mid */
- else if (cmp > 0) right = mid - 1; /* it's left of mid */
- mid = (left + right) / 2;
- fseek(gsi->gsifp, mid * GSI_RECSIZE, SEEK_SET);
- }
-
- /* Using file number, look up the sequence file and format.
- */
- fseek(gsi->gsifp, filenum * GSI_RECSIZE, SEEK_SET);
- GSIGetRecord(gsi, ret_seqfile, NULL, &fmt);
- *ret_format = (int) fmt;
- *ret_offset = (long) offset;
-
- return 1;
-}
-
-/* Function: GSIClose()
- *
- * Purpose: Close an open GSI sequence index file.
- */
-void
-GSIClose(GSIFILE *gsi)
-{
- fclose(gsi->gsifp);
- free(gsi);
-}
-
-
-/*****************************************************************
- * GSI index construction routines
- * SRE, Wed Nov 10 11:49:14 1999 [St. Louis]
- *
- * API:
- * g = GSIAllocIndex();
- *
- * [foreach filename, <32 char, no directory path]
- * GSIAddFileToIndex(g, filename);
- * filenum++;
- * [foreach key, <32 char, w/ filenum 1..nfiles, w/ 32bit offset]
- * GSIAddKeyToIndex(g, key, filenum, offset);
- *
- * GSISortIndex(g);
- * GSIWriteIndex(fp, g);
- * GSIFreeIndex(g);
- *****************************************************************/
-struct gsiindex_s *
-GSIAllocIndex(void)
-{
- struct gsiindex_s *g;
-
- g = MallocOrDie(sizeof(struct gsiindex_s));
- g->filenames = MallocOrDie(sizeof(char *) * 10);
- g->fmt = MallocOrDie(sizeof(int) * 10);
- g->elems = MallocOrDie(sizeof(struct gsikey_s) * 100);
- g->nfiles = 0;
- g->nkeys = 0;
- return g;
-}
-void
-GSIFreeIndex(struct gsiindex_s *g)
-{
- int i;
- for (i = 0; i < g->nfiles; i++) free(g->filenames[i]);
- free(g->filenames);
- free(g->fmt);
- free(g->elems);
- free(g);
-}
-void
-GSIAddFileToIndex(struct gsiindex_s *g, char *filename, int fmt)
-{
- int len;
-
- len = strlen(filename);
- if (len >= GSI_KEYSIZE) Die("File name too long to be indexed.");
- g->filenames[g->nfiles] = sre_strdup(filename, len);
- g->fmt[g->nfiles] = fmt;
- g->nfiles++;
- if (g->nfiles % 10 == 0) {
- g->filenames = ReallocOrDie(g->filenames, sizeof(char *) * (g->nfiles + 10));
- g->fmt = ReallocOrDie(g->fmt, sizeof(int) * (g->nfiles + 10));
- }
-}
-void
-GSIAddKeyToIndex(struct gsiindex_s *g, char *key, int filenum, long offset)
-{
- if (strlen(key) >= GSI_KEYSIZE) Die("key too long in GSI index");
- if (filenum > SQD_UINT16_MAX) Die("too many files in GSI index");
- if (offset > SQD_UINT32_MAX) Die("offset too big in GSI index");
-
- strncpy(g->elems[g->nkeys].key, key, GSI_KEYSIZE-1);
- g->elems[g->nkeys].key[GSI_KEYSIZE-1] = '\0';
- g->elems[g->nkeys].filenum = (sqd_uint16) filenum;
- g->elems[g->nkeys].offset = (sqd_uint32) offset;
- g->nkeys++;
-
- if (g->nkeys % 100 == 0)
- g->elems = ReallocOrDie(g->elems, sizeof(struct gsikey_s) * (g->nkeys + 100));
-}
-static int
-gsi_keysorter(const void *k1, const void *k2)
-{
- struct gsikey_s *key1;
- struct gsikey_s *key2;
- key1 = (struct gsikey_s *) k1;
- key2 = (struct gsikey_s *) k2;
- return strcmp(key1->key, key2->key);
-}
-void
-GSISortIndex(struct gsiindex_s *g)
-{
- qsort((void *) g->elems, g->nkeys, sizeof(struct gsikey_s), gsi_keysorter);
-}
-void
-GSIWriteIndex(FILE *fp, struct gsiindex_s *g)
-{
- sqd_uint32 i;
-
- /* Range checking.
- */
- /* AW: gcc says: comparison always false die to limited range of data type */
-#ifndef CLUSTALO
- if (g->nfiles > SQD_UINT16_MAX) Die("Too many files in GSI index.");
-#endif
- if (g->nkeys > SQD_UINT32_MAX) Die("Too many keys in GSI index.");
-
- GSIWriteHeader(fp, g->nfiles, g->nkeys);
- for (i = 0; i < g->nfiles; i++)
- GSIWriteFileRecord(fp, g->filenames[i], i+1, g->fmt[i]);
- for (i = 0; i < g->nkeys; i++)
- GSIWriteKeyRecord(fp, g->elems[i].key, g->elems[i].filenum, g->elems[i].offset);
-}
-
-
-
-
-
-/* Function: GSIWriteHeader()
- * Date: SRE, Wed Aug 5 10:36:02 1998 [St. Louis]
- *
- * Purpose: Write the first record to an open GSI file:
- * "GSI" <nfiles> <nkeys>
- *
- * Args: fp - open file to write to.
- * nfiles - number of files indexed
- * nkeys - number of keys indexed
- *
- * Returns: void
- */
-void
-GSIWriteHeader(FILE *fp, int nfiles, long nkeys)
-{
- char key[GSI_KEYSIZE];
- sqd_uint16 f1;
- sqd_uint32 f2;
-
- /* beware potential range errors!
- */
- if (nfiles > SQD_UINT16_MAX) Die("GSI: nfiles out of range");
- if (nkeys > SQD_UINT32_MAX) Die("GSI: nkeys out of range");
-
- f1 = (sqd_uint16) nfiles;
- f2 = (sqd_uint32) nkeys;
- f1 = sre_hton16(f1);
- f2 = sre_hton32(f2);
- strcpy(key, "GSI");
-
- if (fwrite(key, 1, GSI_KEYSIZE, fp) < GSI_KEYSIZE) PANIC;
- if (fwrite(&f1, 2, 1, fp) < 1) PANIC;
- if (fwrite(&f2, 4, 1, fp) < 1) PANIC;
-}
-
-
-/* Function: GSIWriteFileRecord()
- * Date: SRE, Wed Aug 5 10:45:51 1998 [St. Louis]
- *
- * Purpose: Write a file record to an open GSI file.
- *
- * Args: fp - open GSI file
- * fname - file name (max 31 characters)
- * idx - file number
- * fmt - file format (e.g. kPearson, etc.)
- *
- * Returns: 0 on failure. 1 on success.
- */
-int
-GSIWriteFileRecord(FILE *fp, char *fname, int idx, int fmt)
-{
- sqd_uint16 f1;
- sqd_uint32 f2;
-
- if (strlen(fname) >= GSI_KEYSIZE) return 0;
- if (idx > SQD_UINT16_MAX) Die("GSI: file index out of range");
- if (fmt > SQD_UINT32_MAX) Die("GSI: format index out of range");
-
- f1 = (sqd_uint16) idx;
- f2 = (sqd_uint32) fmt;
- f1 = sre_hton16(f1);
- f2 = sre_hton32(f2);
-
- if (fwrite(fname, 1, GSI_KEYSIZE, fp) < GSI_KEYSIZE) PANIC;
- if (fwrite(&f1, 2, 1, fp) < 1) PANIC;
- if (fwrite(&f2, 4, 1, fp) < 1) PANIC;
- return 1;
-}
-
-
-/* Function: GSIWriteKeyRecord()
- * Date: SRE, Wed Aug 5 10:52:30 1998 [St. Louis]
- *
- * Purpose: Write a key record to a GSI file.
- *
- * Args: fp - open GSI file for writing
- * key - key (max 31 char + \0)
- * fileidx - which file number to find this key in
- * offset - offset for this key
- *
- * Returns: 1 on success, else 0.
- * will fail if key >= 32 chars, for instance.
- */
-int
-GSIWriteKeyRecord(FILE *fp, char *key, int fileidx, long offset)
-{
- sqd_uint16 f1;
- sqd_uint32 f2;
-
- if (strlen(key) >= GSI_KEYSIZE) return 0;
- if (fileidx > SQD_UINT16_MAX) Die("GSI: file index out of range");
- if (offset > SQD_UINT32_MAX) Die("GSI: offset out of range");
-
- f1 = (sqd_uint16) fileidx;
- f2 = (sqd_uint32) offset;
- f1 = sre_hton16(f1);
- f2 = sre_hton32(f2);
-
- if (fwrite(key, 1, GSI_KEYSIZE, fp) < GSI_KEYSIZE) PANIC;
- if (fwrite(&f1, 2, 1, fp) < 1) PANIC;
- if (fwrite(&f2, 4, 1, fp) < 1) PANIC;
- return 1;
-}
-
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