annotate clustalomega/clustal-omega-1.0.2/src/squid/gsi.c @ 1:bc707542e5de

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/*****************************************************************
 * 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;
}