src/ClustalOmega/src/squid/ssi.c
dafeef0b
 /*****************************************************************
  * 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>
b5f31f05
 #include <inttypes.h>
dafeef0b
 #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
b5f31f05
         fprintf(g->ptmp, "%s\t%d\t%" PRIu64 "\t%" PRIu64 "\t%lu\n",
dafeef0b
                 key, fh, (unsigned long long)r_off->off.i64, 
b5f31f05
                 d_off == NULL ? 0 : (unsigned long long) d_off->off.i64,
dafeef0b
 	      (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 {
b5f31f05
       fprintf(g->ptmp, "%s\t%u\t%" PRIu64 "\t%" PRIu64 "\t%lu\n",
dafeef0b
 	      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.
    */
   throw(ClustalOmegaException, "0");
 }
 
 
 #endif /* test driving code */