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cif2cbf.c

/**********************************************************************
 *          cif2cbf -- convert a cif to a cbf file                    *
 *                                                                    *
 * Version 0.7.7 19 February 2007                                     *
 *                                                                    *
 *                          Paul Ellis and                            *
 *         Herbert J. Bernstein (yaya@bernstein-plus-sons.com)        *
 *                                                                    *
 * (C) Copyright 2006, 2007 Herbert J. Bernstein                      *
 *                                                                    *
 **********************************************************************/

/**********************************************************************
 *                                                                    *
 * YOU MAY REDISTRIBUTE THE CBFLIB PACKAGE UNDER THE TERMS OF THE GPL *
 * WHILE YOU MAY ALTERNATIVE DISTRIBUTE THE API UNDER THE LGPL        *
 * YOU MAY ***NOT*** DISTRBUTE THIS PROGRAM UNDER THE LGPL            *
 *                                                                    *                                                                    *
 **********************************************************************/

/*************************** GPL NOTICES ******************************
 *                                                                    *
 * This program is free software; you can redistribute it and/or      *
 * modify it under the terms of the GNU General Public License as     *
 * published by the Free Software Foundation; either version 2 of     *
 * (the License, or (at your option) any later version.               *
 *                                                                    *
 * This program is distributed in the hope that it will be useful,    *
 * but WITHOUT ANY WARRANTY; without even the implied warranty of     *
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the      *
 * GNU General Public License for more details.                       *
 *                                                                    *
 * You should have received a copy of the GNU General Public License  *
 * along with this program; if not, write to the Free Software        *
 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA           *
 * 02111-1307  USA                                                    *
 *                                                                    *
 **********************************************************************/

/**********************************************************************
 *                                SYNOPSIS                            *
 *                                                                    *
 *  cif2cbf [-i input_cif] [-o output_cbf] \                          *
 *    [-c {p[acked]|c[annonical]|{b[yte_offset]}|\                    *
 *        {v[2packed]}|{f[latpacked]}[n[one]}] \                      *
 *    [-m {h[eaders]|n[oheaders]}] [-d {d[igest]|n[odigest]}] \       *
 *    [-e {b[ase64]|k|q[uoted-printable]| \                           *
 *                  d[ecimal]|h[exadecimal]|o[ctal]|n[one]}] \        *
 *    [-b {f[orward]|b[ackwards]}] \                                  *
 *    [-p {0|1|2|4}] \                                                *
 *    [-v dictionary]* [-w] \                                         *
 *    [input_cif] [output_cbf]                                        *
 *                                                                    *
 *  the options are:                                                  *
 *                                                                    *
 *  -i input_cif (default: stdin)                                     *
 *    the input  file in CIF or CBF  format.  If input_cif is not     *
 *    specified or is given as "-", it is copied from stdin to a      *
 *    temporary file.                                                 *
 *                                                                    *
 *  -o output_cbf (default: stdout)                                   *
 *    the output cif (if base64 or quoted-printable encoding is used) *
 *    or cbf (if no encoding is used).  if no output_cif is specified *
 *    or is given as "-", the output is written to stdout             *
 *    if the output_cbf is /dev/null, no output is written.           *
 *                                                                    *
 *  The remaining options specify the characteristics of the          *
 *  output cbf.  The characteristics of the input cif are derived     *
 *  from context.                                                     *
 *                                                                    *
 *  -c compression_scheme (packed, canonical, byte_offset,            *
 *    v2packed, flatpacked or none,                                   *
 *    default packed)                                                 *
 *                                                                    *
 *  -m [no]headers (default headers for cifs, noheaders for cbfs)     *
 *    selects MIME (N. Freed, N. Borenstein, RFC 2045, November 1996) *
 *    headers within binary data value text fields.                   *
 *                                                                    *
 *  -d [no]digest  (default md5 digest [R. Rivest, RFC 1321, April    *
 *    1992 using"RSA Data Security, Inc. MD5 Message-Digest           *
 *    Algorithm"] when MIME headers are selected)                     *
 *                                                                    *
 *  -e encoding (base64, quoted-printable or none, default base64)    *
 *    specifies one of the standard MIME encodings for an ascii cif   *
 *    or "none" for a binary cbf                                      *
 *                                                                    *
 *  -b byte_order (forward or backwards, default forward (1234) on    *
 *    little-endian machines, backwards (4321) on big-endian machines *
 *                                                                    *
 *  -p K_of_padding (0, 1, 2, 4) for no padding after binary data     *
 *    1023, 2047 or 4095 bytes of padding after binary data           *
 *                                                                    *
 *  -v dictionary specifies a dictionary to be used to validate       *
 *    the input cif and to apply aliases to the output cif.           *
 *    This option may be specified multiple times, with dictionaries  *
 *    layered in the order given.                                     *
 *                                                                    *
 *  -w process wide (2048 character) lines                            *
 *                                                                    *
 *                                                                    *
 **********************************************************************/

/**********************************************************************
 *                                CREDITS                             *
 *                                                                    *
 *  This program is a Crystallographic Information File (CIF)         *
 *  application.  Please see the IUCR Policy below.   See the IUCR    *
 *  web page (http://www.iucr.org) or its mirrors for background      *
 *  and references on CIF.                                            *
 *                                                                    *
 *  This program is a Crystallographic Binary File (CBF) application. *
 *  Please see the ImgCIF/CBF web page at                             *
 *                                                                    *
 *            http://ndbserver.rutgers.edu/mmcif/cbf                  *
 *                                                                    *
 *  for background and references.  The CBF definition is available   *
 *  on the web page created by Andy Hammersley at                     *
 *                                                                    *
 *     http://www.ersf.fr/computing/Forum/imgCIF/cbf_definition.html  *
 *                                                                    *
 *  This program is a CBFlib application.  See "CBFLIB, An ANSI-C     *
 *  API for Crystallographic Binary Files", Version 0.1, April 1998   *
 *  by Paul J. Ellis, Stanford Synchrotron Radiation Laboratory,      *
 *  ellis@ssrl.slac.stanford.edu                                      *
 *                                                                    *
 *  This program uses routines derived from mpack/munpack version     *
 *  1.5, ftp://ftp.andrew.cmu.edu/pub/mpack by John G. Myers,         *
 *  jgm+@cmu.edu.  "Mpack and munpack are utilties for encoding and   *
 *  decoding ... binary files in MIME ... format."  Please see the    *
 *  copyright notices and disclaimers in the mpack/munpack routines   *
 *                                                                    *
 *  This program uses routines derived from the "RSA Data Security,   *
 *  Inc. MD5 Message-Digest Algorithm."  Please see the copyright     *
 *  notice and disclaimer in md5c.c                                   *
 **********************************************************************/


/**********************************************************************
 *                                                                    *
 *                    Stanford University Notices                     *
 *  for the CBFlib software package that incorporates SLAC software   *
 *                 on which copyright is disclaimed                   *
 *                                                                    *
 * This software                                                      *
 * -------------                                                      *
 * The term 'this software', as used in these Notices, refers to      *
 * those portions of the software package CBFlib that were created by *
 * employees of the Stanford Linear Accelerator Center, Stanford      *
 * University.                                                        *
 *                                                                    *
 * Stanford disclaimer of copyright                                   *
 * --------------------------------                                   *
 * Stanford University, owner of the copyright, hereby disclaims its  *
 * copyright and all other rights in this software.  Hence, anyone    *
 * may freely use it for any purpose without restriction.             *
 *                                                                    *
 * Acknowledgement of sponsorship                                     *
 * ------------------------------                                     *
 * This software was produced by the Stanford Linear Accelerator      *
 * Center, Stanford University, under Contract DE-AC03-76SFO0515 with *
 * the Department of Energy.                                          *
 *                                                                    *
 * Government disclaimer of liability                                 *
 * ----------------------------------                                 *
 * Neither the United States nor the United States Department of      *
 * Energy, nor any of their employees, makes any warranty, express or *
 * implied, or assumes any legal liability or responsibility for the  *
 * accuracy, completeness, or usefulness of any data, apparatus,      *
 * product, or process disclosed, or represents that its use would    *
 * not infringe privately owned rights.                               *
 *                                                                    *
 * Stanford disclaimer of liability                                   *
 * --------------------------------                                   *
 * Stanford University makes no representations or warranties,        *
 * express or implied, nor assumes any liability for the use of this  *
 * software.                                                          *
 *                                                                    *
 * Maintenance of notices                                             *
 * ----------------------                                             *
 * In the interest of clarity regarding the origin and status of this *
 * software, this and all the preceding Stanford University notices   *
 * are to remain affixed to any copy or derivative of this software   *
 * made or distributed by the recipient and are to be affixed to any  *
 * copy of software made or distributed by the recipient that         *
 * contains a copy or derivative of this software.                    *
 *                                                                    *
 * Based on SLAC Software Notices, Set 4                              *
 * OTT.002a, 2004 FEB 03                                              *
 **********************************************************************/


/**********************************************************************
 *                                 NOTICE                             *
 * Creative endeavors depend on the lively exchange of ideas. There   *
 * are laws and customs which establish rights and responsibilities   *
 * for authors and the users of what authors create.  This notice     *
 * is not intended to prevent you from using the software and         *
 * documents in this package, but to ensure that there are no         *
 * misunderstandings about terms and conditions of such use.          *
 *                                                                    *
 * Please read the following notice carefully.  If you do not         *
 * understand any portion of this notice, please seek appropriate     *
 * professional legal advice before making use of the software and    *
 * documents included in this software package.  In addition to       *
 * whatever other steps you may be obliged to take to respect the     *
 * intellectual property rights of the various parties involved, if   *
 * you do make use of the software and documents in this package,     *
 * please give credit where credit is due by citing this package,     *
 * its authors and the URL or other source from which you obtained    *
 * it, or equivalent primary references in the literature with the    *
 * same authors.                                                      *
 *                                                                    *
 * Some of the software and documents included within this software   *
 * package are the intellectual property of various parties, and      *
 * placement in this package does not in any way imply that any       *
 * such rights have in any way been waived or diminished.             *
 *                                                                    *
 * With respect to any software or documents for which a copyright    *
 * exists, ALL RIGHTS ARE RESERVED TO THE OWNERS OF SUCH COPYRIGHT.   *
 *                                                                    *
 * Even though the authors of the various documents and software      *
 * found here have made a good faith effort to ensure that the        *
 * documents are correct and that the software performs according     *
 * to its documentation, and we would greatly appreciate hearing of   *
 * any problems you may encounter, the programs and documents any     *
 * files created by the programs are provided **AS IS** without any   *
 * warranty as to correctness, merchantability or fitness for any     *
 * particular or general use.                                         *
 *                                                                    *
 * THE RESPONSIBILITY FOR ANY ADVERSE CONSEQUENCES FROM THE USE OF    *
 * PROGRAMS OR DOCUMENTS OR ANY FILE OR FILES CREATED BY USE OF THE   *
 * PROGRAMS OR DOCUMENTS LIES SOLELY WITH THE USERS OF THE PROGRAMS   *
 * OR DOCUMENTS OR FILE OR FILES AND NOT WITH AUTHORS OF THE          *
 * PROGRAMS OR DOCUMENTS.                                             *
 **********************************************************************/

/**********************************************************************
 *                                                                    *
 *                           The IUCr Policy                          *
 *      for the Protection and the Promotion of the STAR File and     *
 *     CIF Standards for Exchanging and Archiving Electronic Data     *
 *                                                                    *
 * Overview                                                           *
 *                                                                    *
 * The Crystallographic Information File (CIF)[1] is a standard for   *
 * information interchange promulgated by the International Union of  *
 * Crystallography (IUCr). CIF (Hall, Allen & Brown, 1991) is the     *
 * recommended method for submitting publications to Acta             *
 * Crystallographica Section C and reports of crystal structure       *
 * determinations to other sections of Acta Crystallographica         *
 * and many other journals. The syntax of a CIF is a subset of the    *
 * more general STAR File[2] format. The CIF and STAR File approaches *
 * are used increasingly in the structural sciences for data exchange *
 * and archiving, and are having a significant influence on these     *
 * activities in other fields.                                        *
 *                                                                    *
 * Statement of intent                                                *
 *                                                                    *
 * The IUCr's interest in the STAR File is as a general data          *
 * interchange standard for science, and its interest in the CIF,     *
 * a conformant derivative of the STAR File, is as a concise data     *
 * exchange and archival standard for crystallography and structural  *
 * science.                                                           *
 *                                                                    *
 * Protection of the standards                                        *
 *                                                                    *
 * To protect the STAR File and the CIF as standards for              *
 * interchanging and archiving electronic data, the IUCr, on behalf   *
 * of the scientific community,                                       *
 *                                                                    *
 * * holds the copyrights on the standards themselves,                *
 *                                                                    *
 * * owns the associated trademarks and service marks, and            *
 *                                                                    *
 * * holds a patent on the STAR File.                                 *
 *                                                                    *
 * These intellectual property rights relate solely to the            *
 * interchange formats, not to the data contained therein, nor to     *
 * the software used in the generation, access or manipulation of     *
 * the data.                                                          *
 *                                                                    *
 * Promotion of the standards                                         *
 *                                                                    *
 * The sole requirement that the IUCr, in its protective role,        *
 * imposes on software purporting to process STAR File or CIF data    *
 * is that the following conditions be met prior to sale or           *
 * distribution.                                                      *
 *                                                                    *
 * * Software claiming to read files written to either the STAR       *
 * File or the CIF standard must be able to extract the pertinent     *
 * data from a file conformant to the STAR File syntax, or the CIF    *
 * syntax, respectively.                                              *
 *                                                                    *
 * * Software claiming to write files in either the STAR File, or     *
 * the CIF, standard must produce files that are conformant to the    *
 * STAR File syntax, or the CIF syntax, respectively.                 *
 *                                                                    *
 * * Software claiming to read definitions from a specific data       *
 * dictionary approved by the IUCr must be able to extract any        *
 * pertinent definition which is conformant to the dictionary         *
 * definition language (DDL)[3] associated with that dictionary.      *
 *                                                                    *
 * The IUCr, through its Committee on CIF Standards, will assist      *
 * any developer to verify that software meets these conformance      *
 * conditions.                                                        *
 *                                                                    *
 * Glossary of terms                                                  *
 *                                                                    *
 * [1] CIF:  is a data file conformant to the file syntax defined     *
 * at http://www.iucr.org/iucr-top/cif/spec/index.html                *
 *                                                                    *
 * [2] STAR File:  is a data file conformant to the file syntax       *
 * defined at http://www.iucr.org/iucr-top/cif/spec/star/index.html   *
 *                                                                    *
 * [3] DDL:  is a language used in a data dictionary to define data   *
 * items in terms of "attributes". Dictionaries currently approved    *
 * by the IUCr, and the DDL versions used to construct these          *
 * dictionaries, are listed at                                        *
 * http://www.iucr.org/iucr-top/cif/spec/ddl/index.html               *
 *                                                                    *
 * Last modified: 30 September 2000                                   *
 *                                                                    *
 * IUCr Policy Copyright (C) 2000 International Union of              *
 * Crystallography                                                    *
 **********************************************************************/

#include "cbf.h"
#include "img.h"
#include "cbf_string.h"

#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <ctype.h>
#include <time.h>
#include <errno.h>
#ifdef GNUGETOPT
#include "getopt.h"
#endif
#include <unistd.h>

#define C2CBUFSIZ 8192
#define NUMDICTS 50

#ifdef __MINGW32__
#define NOMKSTEMP
#define NOTMPDIR
#endif



int local_exit (int status);
int outerror(int err);

int outerror(int err) 
{
      
  if ((err&CBF_FORMAT)==CBF_FORMAT)
    fprintf(stderr, " cif2cbf: The file format is invalid.\n");
  if ((err&CBF_ALLOC)==CBF_ALLOC)
    fprintf(stderr, " cif2cbf Memory allocation failed.\n");
  if ((err&CBF_ARGUMENT)==CBF_ARGUMENT)
    fprintf(stderr, " cif2cbf: Invalid function argument.\n");
  if ((err&CBF_ASCII)==CBF_ASCII)
    fprintf(stderr, " cif2cbf: The value is ASCII (not binary).\n");
  if ((err&CBF_BINARY)==CBF_BINARY)
    fprintf(stderr, " cif2cbf: The value is binary (not ASCII).\n");
  if ((err&CBF_BITCOUNT)==CBF_BITCOUNT)
    fprintf(stderr, " cif2cbf: The expected number of bits does" 
      " not match the actual number written.\n");
  if ((err&CBF_ENDOFDATA)==CBF_ENDOFDATA)
    fprintf(stderr, " cif2cbf: The end of the data was reached"
     " before the end of the array.\n");
  if ((err&CBF_FILECLOSE)==CBF_FILECLOSE)
    fprintf(stderr, " cif2cbf: File close error.\n");
  if ((err&CBF_FILEOPEN)==CBF_FILEOPEN)
    fprintf(stderr, " cif2cbf: File open error.\n");
  if ((err&CBF_FILEREAD)==CBF_FILEREAD)
    fprintf(stderr, " cif2cbf: File read error.\n");
  if ((err&CBF_FILESEEK)==CBF_FILESEEK)
    fprintf(stderr, " cif2cbf: File seek error.\n");
  if ((err&CBF_FILETELL)==CBF_FILETELL)
    fprintf(stderr, " cif2cbf: File tell error.\n");
  if ((err&CBF_FILEWRITE)==CBF_FILEWRITE)
    fprintf(stderr, " cif2cbf: File write error.\n");
  if ((err&CBF_IDENTICAL)==CBF_IDENTICAL)
    fprintf(stderr, " cif2cbf: A data block with the new name already exists.\n");
  if ((err&CBF_NOTFOUND)==CBF_NOTFOUND)
    fprintf(stderr, " cif2cbf: The data block, category, column or"
      " row does not exist.\n");
  if ((err&CBF_OVERFLOW)==CBF_OVERFLOW)
    fprintf(stderr, " cif2cbf: The number read cannot fit into the "
      "destination argument.\n        The destination has been set to the nearest value.\n");
  if ((err& CBF_UNDEFINED)==CBF_UNDEFINED)
    fprintf(stderr, " cif2cbf: The requested number is not defined (e.g. 0/0).\n");
  if ((err&CBF_NOTIMPLEMENTED)==CBF_NOTIMPLEMENTED)
    fprintf(stderr, " cif2cbf: The requested functionality is not yet implemented.\n");
  return 0;

}

#undef cbf_failnez
#define cbf_failnez(x) \
 {int err; \
  err = (x); \
  if (err) { \
    fprintf(stderr,"CBFlib fatal error %d\n",err); \
    outerror(err); \
    local_exit (-1); \
  } \
 }

void set_MP_terms(int crterm, int nlterm);

int main (int argc, char *argv [])
{
  FILE *in, *out=NULL, *file, *dict;
  clock_t a,b;
  cbf_handle cif;
  cbf_handle cbf;
  cbf_handle dic;
  cbf_handle odic;
  int devnull = 0;
  int c;
  int errflg = 0;
  char *cifin, *cbfout;
  char *dictionary[NUMDICTS];
  char *ciftmp=NULL;
#ifndef NOMKSTEMP
  int ciftmpfd;
#endif
  int ciftmpused;
  int padflag;
  int nbytes;
  int ndict = 0;
  int kd;
  int wide = 0;
  char buf[C2CBUFSIZ];
  unsigned int blocks, categories, blocknum, catnum, blockitems, itemnum;
  CBF_NODETYPE itemtype;
  const char *datablock_name;
  const char *saveframe_name;
  const char *category_name;
  const char *column_name;
  const char *value;
  unsigned int colnum, rownum;
  unsigned int columns;
  unsigned int rows;

  int mime, digest, encoding, compression, bytedir, cbforcif, term;


     /* Extract options */

/**********************************************************************
 *  cif2cbf [-i input_cif] [-o output_cbf] \                          *
 *    [-c {p[acked]|c[annonical]|{b[yte_offset]}|\                    *
 *        {v[2packed]}|{f[latpacked]}[n[one]}] \                      *
 *    [-m {h[eaders]|n[oheaders]}] [-d {d[igest]|n[odigest]}]  \      *
 *    [-e {b[ase64]|k|q[uoted-printable]| \                           *
 *                  d[ecimal]|h[exadecimal]|o[ctal]|n[one]}] \        *
 *    [-b {f[orward]|b[ackwards]}] \                                  *
 *    [-p {0|1|2|4}] \                                                *
 *    [-v dictionary]* [-w]\                                          *
 *    [input_cif] [output_cbf]                                        *
 *                                                                    *
 **********************************************************************/

   mime = 0;
   digest = 0;
   encoding = 0;
   compression = 0;
   bytedir = 0;
   ndict = 0;
   padflag = 0;

   cifin = NULL;
   cbfout = NULL;
   ciftmpused = 0;
   
   while ((c = getopt(argc, argv, "i:o:c:m:d:e:b:p:v:w")) != EOF) {
     switch (c) {
       case 'i':
         if (cifin) errflg++;
         else cifin = optarg;
         break;
       case 'o':
         if (cbfout) errflg++;
         else cbfout = optarg;
         break;
       case 'c':
         if (compression) errflg++;
         if (optarg[0] == 'p' || optarg[0] == 'P') {
           compression = CBF_PACKED;
         } else {
           if (optarg[0] == 'c' || optarg[0] == 'C') {
             compression = CBF_CANONICAL;
           } else {
             if (optarg[0] == 'b' || optarg[0] == 'B') {
               compression = CBF_BYTE_OFFSET;
             } else {
               if (optarg[0] == 'n' || optarg[0] == 'N') {
                 compression = CBF_NONE;
               } else {
                 if (optarg[0] == 'v' || optarg[0] == 'V') {
                   compression = CBF_PACKED_V2;
                 } else {
                   if (optarg[0] == 'f' || optarg[0] == 'F') {
                   compression = CBF_PACKED|CBF_FLAT_IMAGE;
                   } else {             
                     errflg++;
                   }
                 }
               }
             }
           }
         }
         break;
       case 'm':
         if (mime) errflg++;
         if (optarg[0] == 'h' || optarg[0] == 'H' ) {
           mime = MIME_HEADERS;
         } else {
           if (optarg[0] == 'n' || optarg[0] == 'N' ) {
           mime = PLAIN_HEADERS;
           } else {
             errflg++;
           }
         }
         break;
       case 'd':
         if (digest) errflg++;
         if (optarg[0] == 'd' || optarg[0] == 'H' ) {
           digest = MSG_DIGEST;
         } else {
           if (optarg[0] == 'n' || optarg[0] == 'N' ) {
           digest = MSG_NODIGEST;
           } else {
             errflg++;
           }
         }
         break;
       case 'b':
         if (bytedir) errflg++;
         if (optarg[0] == 'f' || optarg[0] == 'F') {
           bytedir = ENC_FORWARD;
         } else {
           if (optarg[0] == 'b' || optarg[0] == 'B' ) {
             bytedir = ENC_BACKWARD;
           } else {
             errflg++;
           }
         }
         break;
       case 'p':
         if (padflag) errflg++;
         if (optarg[0] == '1') {
           padflag = PAD_1K;
         } else if (optarg[0] == '2'){
           padflag = PAD_2K;
         } else if (optarg[0] == '4'){
           padflag = PAD_4K;
         } else errflg++;
         break;
       case 'e':
         if (encoding) errflg++;
         if (optarg[0] == 'b' || optarg[0] == 'B' ) {
           encoding = ENC_BASE64;
         } else {
           if (optarg[0] == 'k' || optarg[0] == 'K' ) {
             encoding = ENC_BASE32K;
           } else {
             if (optarg[0] == 'q' || optarg[0] == 'Q' ) {
             encoding = ENC_QP;
             } else {
               if (optarg[0] == 'd' || optarg[0] == 'D' ) {
                 encoding = ENC_BASE10;
               } else {
                 if (optarg[0] == 'h' || optarg[0] == 'H' ) {
                   encoding = ENC_BASE16;
                 } else {
                   if (optarg[0] == 'o' || optarg[0] == 'O' ) {
                     encoding = ENC_BASE8;
                   } else {
                     if (optarg[0] == 'n' || optarg[0] == 'N' ) {
                       encoding = ENC_NONE;
                     } else {
                       errflg++;
                     }
                   }
                 }
               }
             }
           }
         }
         break;
       case 'v':
         if (ndict < NUMDICTS)
           dictionary[ndict++] = optarg;
         else if (ndict == NUMDICTS) {
           errflg++;
           ndict++;
           fprintf(stderr, " Too many dictionaries, increase NUMDICTS");
         }
         break;
      case 'w':
        if (wide) errflg++;
        else wide = 1;
        break;
       default:
         errflg++;
         break;
      }
    }
   for (; optind < argc; optind++) {
     if (!cifin) {
        cifin = argv[optind];
     } else {
       if (!cbfout) {
         cbfout = argv[optind];
       } else {
         errflg++;
       }
     }
   }
   if (errflg) {
     fprintf(stderr,"cif2cbf:  Usage: \n");
     fprintf(stderr,
       "  cif2cbf [-i input_cif] [-o output_cbf] \\\n");
     fprintf(stderr,
       "    [-c {p[acked]|c[annonical]|{b[yte_offset]}|\\\n");
     fprintf(stderr,
       "        {v[2packed}|{f[latpacked}[n[one]}] \\\n"); 
     fprintf(stderr,
       "    [-m {h[eaders]|n[oheaders]}] [-d {d[igest]|n[odigest]}] \\\n");
     fprintf(stderr,
       "    [-e {b[ase64]|q[uoted-printable]|\\\n");
     fprintf(stderr,
       "                  d[ecimal]|h[examdecimal|o[ctal]|n[one]}] \\\n");
     fprintf(stderr,
       "                  [-b {f[orward]|b[ackwards]}\\\n");
     fprintf(stderr,
       "                  [-p {1|2|4}\\\n");
     fprintf(stderr,
       "    [-v dictionary]* [-w] \\\n");
     fprintf(stderr,
       "    [input_cif] [output_cbf] \n\n");
     exit(2);
   }


     /* Set up for CIF of CBF output */

   if (!encoding) {
     encoding = ENC_BASE64;
   }
   cbforcif = CBF;
   term = ENC_CRTERM | ENC_LFTERM;
   if (encoding == ENC_BASE64 || \
       encoding == ENC_BASE32K || \
       encoding == ENC_QP || \
       encoding == ENC_BASE10 || \
       encoding == ENC_BASE16 || \
       encoding == ENC_BASE8) {
     cbforcif = CIF;
     term = ENC_LFTERM;
   }

     /* Set up for headers */

   if (!mime) {
     mime = MIME_HEADERS;
   }
   if (!digest) {
     if (mime == MIME_HEADERS) {
       digest = MSG_DIGEST;
     } else {
       digest = MSG_NODIGEST;
     }
   }

     /* Set up for decimal, hexadecimal or octal output */
  if (!bytedir)
     bytedir = ENC_BACKWARD;

     /* Set up for Compression */

   if (!compression)
     compression = CBF_PACKED;


    /* Read the cif */

   if (!cifin || strcmp(cifin?cifin:"","-") == 0) {
     ciftmp = (char *)malloc(strlen("/tmp/cif2cbfXXXXXX")+1);
#ifdef NOTMPDIR
     strcpy(ciftmp, "cif2cbfXXXXXX");
#else
     strcpy(ciftmp, "/tmp/cif2cbfXXXXXX");
#endif
#ifdef NOMKSTEMP
     if ((ciftmp = mktemp(ciftmp)) == NULL ) {
       fprintf(stderr,"\n cif2cbf: Can't create temporary file name %s.\n", ciftmp);
       fprintf(stderr,"%s\n",strerror(errno));
       exit(1);
     }
     if ( (file = fopen(ciftmp,"wb+")) == NULL) {
       fprintf(stderr,"Can't open temporary file %s.\n", ciftmp);
       fprintf(stderr,"%s\n",strerror(errno));
       exit(1);         
     }
#else
     if ((ciftmpfd = mkstemp(ciftmp)) == -1 ) {
       fprintf(stderr,"\n cif2cbf: Can't create temporary file %s.\n", ciftmp);
       fprintf(stderr,"%s\n",strerror(errno));
       exit(1);
     }
     if ( (file = fdopen(ciftmpfd, "w+")) == NULL) {
       fprintf(stderr,"Can't open temporary file %s.\n", ciftmp);
       fprintf(stderr,"%s\n",strerror(errno));
       exit(1);
     }
#endif
     while ((nbytes = fread(buf, 1, C2CBUFSIZ, stdin))) {
       if(nbytes != fwrite(buf, 1, nbytes, file)) {
         fprintf(stderr,"Failed to write %s.\n", ciftmp);
         exit(1);
       }
     }
     fclose(file);
     cifin = ciftmp;
     ciftmpused = 1;
   }
   if ( cbf_make_handle (&cif) ) {
     fprintf(stderr,"Failed to create handle for input_cif\n");
     exit(1);
   }
   
   if ( cbf_make_handle (&dic) ) {
     fprintf(stderr,"Failed to create handle for dictionary\n");
     exit(1);
   }


   if ( cbf_make_handle (&cbf) ) {
     fprintf(stderr,"Failed to create handle for output_cbf\n");
     exit(1);
   }

   for (kd=0; kd< ndict; kd++) {
   
     if (!(dict = fopen (dictionary[kd], "rb")))  {
      fprintf (stderr,"Couldn't open the dictionary %s\n", dictionary[kd]);
        exit (1);
     }
     cbf_failnez(cbf_read_widefile(dic, dict, MSG_DIGEST))
     cbf_failnez(cbf_convert_dictionary(cif,dic))
     cbf_failnez(cbf_get_dictionary(cif,&odic))
     cbf_failnez(cbf_set_dictionary(cbf,odic))
      
   }
   
   a = clock ();

   /* Read the file */
   if (!(in = fopen (cifin, "rb"))) {
     fprintf (stderr,"Couldn't open the input CIF file %s\n", cifin);
     exit (1);
   }

   if (ciftmpused) {
     if (unlink(ciftmp) != 0 ) {
       fprintf(stderr,"cif2cif:  Can't unlink temporary file %s.\n", ciftmp);
       fprintf(stderr,"%s\n",strerror(errno));
       exit(1);
     }
   }

   if (!wide) {
       cbf_failnez (cbf_read_file (cif, in, MSG_DIGEST))
   } else {
       cbf_failnez (cbf_read_widefile (cif, in, MSG_DIGEST))
   }

   cbf_failnez (cbf_rewind_datablock(cif))

   cbf_failnez (cbf_count_datablocks(cif, &blocks))

   for (blocknum = 0; blocknum < blocks;  blocknum++ )
   { /* start of copy loop */


     cbf_failnez (cbf_select_datablock(cif, blocknum))
     cbf_failnez (cbf_datablock_name(cif, &datablock_name))
     cbf_failnez (cbf_force_new_datablock(cbf, datablock_name))

     if ( !cbf_rewind_blockitem(cif, &itemtype) ) {
     cbf_failnez (cbf_count_blockitems(cif, &blockitems))

     for (itemnum = 0; itemnum < blockitems;  itemnum++) {
       cbf_select_blockitem(cif, itemnum, &itemtype);
       if (itemtype == CBF_CATEGORY) {
         cbf_category_name(cif,&category_name);
         cbf_force_new_category(cbf, category_name);
         cbf_count_rows(cif,&rows);
         cbf_count_columns(cif,&columns);

         /*  Transfer the columns names from cif to cbf */
         if ( ! cbf_rewind_column(cif) ) {
           do {
             cbf_failnez(cbf_column_name(cif, &column_name))
             cbf_failnez(cbf_new_column(cbf, column_name))
           } while ( ! cbf_next_column(cif) );
           cbf_rewind_column(cif);
           cbf_rewind_row(cif);
         }
         /* Transfer the rows from cif to cbf */
         for (rownum = 0; rownum < rows; rownum++ ) {
           cbf_failnez (cbf_select_row(cif, rownum))
           cbf_failnez (cbf_new_row(cbf))
           cbf_rewind_column(cif);
           for (colnum = 0; colnum < columns; colnum++ ) {
             const char *typeofvalue;

             cbf_failnez (cbf_select_column(cif, colnum))
             cbf_failnez (cbf_column_name(cif, &column_name))

             if ( ! cbf_get_value(cif, &value) ) {
               if (compression && value && column_name && !cbf_cistrcmp("compression_type",column_name)) {
                 cbf_failnez (cbf_select_column(cbf, colnum))
                 switch (compression&CBF_COMPRESSION_MASK) {
                   case (CBF_NONE):
                     cbf_failnez (cbf_set_value      (cbf,"none"))
                     cbf_failnez (cbf_set_typeofvalue(cbf,"word"))
                     break;
                   case (CBF_CANONICAL):
                     cbf_failnez (cbf_set_value      (cbf,"canonical"))
                     cbf_failnez (cbf_set_typeofvalue(cbf,"word"))
                     break;
                   case (CBF_PACKED):
                     cbf_failnez (cbf_set_value      (cbf,"packed"))
                     cbf_failnez (cbf_set_typeofvalue(cbf,"word"))
                     break;
                   case (CBF_PACKED_V2):
                     cbf_failnez (cbf_set_value      (cbf,"packed_v2"))
                     cbf_failnez (cbf_set_typeofvalue(cbf,"word"))
                     break;
                   case (CBF_BYTE_OFFSET):
                     cbf_failnez (cbf_set_value      (cbf,"byte_offsets"))
                     cbf_failnez (cbf_set_typeofvalue(cbf,"word"))
                     break;
                   case (CBF_PREDICTOR):
                     cbf_failnez (cbf_set_value      (cbf,"predictor"))
                     cbf_failnez (cbf_set_typeofvalue(cbf,"word"))
                     break;
                   default:
                     cbf_failnez (cbf_set_value      (cbf,"."))
                     cbf_failnez (cbf_set_typeofvalue(cbf,"null"))
                     break;
                 }
                 if (compression&CBF_FLAG_MASK) {
                   if (compression&CBF_UNCORRELATED_SECTIONS) {
                     cbf_failnez (cbf_require_column   (cbf, "compression_type_flag"))
                     cbf_failnez (cbf_set_value        (cbf, "uncorrelated_sections"))
                     cbf_failnez (cbf_set_typeofvalue  (cbf, "word"))
                   } else if (compression&CBF_FLAT_IMAGE)  {
                     cbf_failnez (cbf_require_column   (cbf, "compression_type_flag"))
                     cbf_failnez (cbf_set_value        (cbf, "flat"))
                     cbf_failnez (cbf_set_typeofvalue  (cbf, "word"))
                   }
                 } else {
                   if (!cbf_find_column(cbf, "compression_type_flag")) {
                     cbf_failnez (cbf_set_value      (cbf,"."))
                     cbf_failnez (cbf_set_typeofvalue(cbf,"null"))
                   }
                 }
               } else  if (compression && value && column_name && !cbf_cistrcmp("compression_type_flag",column_name)) {
                 if (compression&CBF_FLAG_MASK) {
                   if (compression&CBF_UNCORRELATED_SECTIONS) {
                     cbf_failnez (cbf_require_column   (cbf, "compression_type_flag"))
                     cbf_failnez (cbf_set_value        (cbf, "uncorrelated_sections"))
                     cbf_failnez (cbf_set_typeofvalue  (cbf, "word"))
                   } else if (compression&CBF_FLAT_IMAGE)  {
                     cbf_failnez (cbf_require_column   (cbf, "compression_type_flag"))
                     cbf_failnez (cbf_set_value        (cbf, "flat"))
                     cbf_failnez (cbf_set_typeofvalue  (cbf, "word"))
                   }
                 } else {
                   if (!cbf_find_column(cbf, "compression_type_flag")) {
                     cbf_failnez (cbf_set_value      (cbf,"."))
                     cbf_failnez (cbf_set_typeofvalue(cbf,"null"))
                   }
                 }                  
               } else {
                 cbf_failnez (cbf_get_typeofvalue(cif, &typeofvalue))
                 cbf_failnez (cbf_select_column(cbf, colnum))
                 cbf_failnez (cbf_set_value(cbf, value))
                 cbf_failnez (cbf_set_typeofvalue(cbf, typeofvalue))
               }
             } else {

               void * array;
               int binary_id, elsigned, elunsigned;
               size_t elements,elements_read, elsize;
                int minelement, maxelement;
               unsigned int cifcompression;
               int realarray;
               const char *byteorder;
               size_t dim1, dim2, dim3, padding;

               cbf_failnez(cbf_get_arrayparameters_wdims(
                 cif, &cifcompression,
                 &binary_id, &elsize, &elsigned, &elunsigned,
                 &elements, &minelement, &maxelement, &realarray,
                 &byteorder, &dim1, &dim2, &dim3, &padding))
               if ((array=malloc(elsize*elements))) {
                 cbf_failnez (cbf_select_column(cbf,colnum))
                 if (!realarray)  {
                   cbf_failnez (cbf_get_integerarray(
                     cif, &binary_id, array, elsize, elsigned,
                     elements, &elements_read))
                   cbf_failnez(cbf_set_integerarray_wdims(
                     cbf, compression,
                     binary_id, array, elsize, elsigned, elements,
                     "little_endian", dim1, dim2, dim3, 0))
                 } else {
                   cbf_failnez (cbf_get_realarray(
                     cif, &binary_id, array, elsize,
                     elements, &elements_read))
                   cbf_failnez(cbf_set_realarray_wdims(
                     cbf, compression,
                     binary_id, array, elsize, elements,
                     "little_endian", dim1, dim2, dim3, 0))                   
                 }
                 free(array);
               } else {
                 fprintf(stderr,
                   "\nFailed to allocate memory %ld bytes",
                   (long) elsize*elements);
                 exit(1);
               }
             }
           }
         }
       } else {
         cbf_saveframe_name(cif,&saveframe_name);
         cbf_force_new_saveframe(cbf, saveframe_name);

         if ( !cbf_rewind_category(cif) ) {
           cbf_failnez (cbf_count_categories(cif, &categories))

           for (catnum = 0; catnum < categories;  catnum++) {
             cbf_select_category(cif, catnum);
             cbf_category_name(cif,&category_name);
             cbf_force_new_category(cbf, category_name);
             cbf_count_rows(cif,&rows);
             cbf_count_columns(cif,&columns);

           /*  Transfer the columns names from cif to cbf */
           if ( ! cbf_rewind_column(cif) ) {
             do {
               cbf_failnez(cbf_column_name(cif, &column_name))
               cbf_failnez(cbf_new_column(cbf, column_name))
             } while ( ! cbf_next_column(cif) );
             cbf_rewind_column(cif);
             cbf_rewind_row(cif);
           }
           /* Transfer the rows from cif to cbf */
           for (rownum = 0; rownum < rows; rownum++ ) {
             cbf_failnez (cbf_select_row(cif, rownum))
             cbf_failnez (cbf_new_row(cbf))
             cbf_rewind_column(cif);
             for (colnum = 0; colnum < columns; colnum++ ) {
               const char *typeofvalue;

               cbf_failnez (cbf_select_column(cif, colnum))

               if ( ! cbf_get_value(cif, &value) ) {
                 cbf_failnez (cbf_get_typeofvalue(cif, &typeofvalue))
                 cbf_failnez (cbf_select_column(cbf, colnum))
                 cbf_failnez (cbf_set_value(cbf, value))
                 cbf_failnez (cbf_set_typeofvalue(cbf, typeofvalue))
               } else {

                 void * array;
                 int binary_id, elsigned, elunsigned;
                 size_t elements,elements_read, elsize;
                 int minelement, maxelement;
                 unsigned int cifcompression;
                 int realarray;
                 const char * byteorder;
                 size_t dim1, dim2, dim3, padding;

                 cbf_failnez(cbf_get_arrayparameters_wdims(
                   cif, &cifcompression,
                   &binary_id, &elsize, &elsigned, &elunsigned,
                   &elements, &minelement, &maxelement, &realarray,
                   &byteorder, &dim1, &dim2, &dim3, &padding))
                 if ((array=malloc(elsize*elements))) {
                   cbf_failnez (cbf_select_column(cbf,colnum))
                   if (!realarray) {
                   cbf_failnez (cbf_get_integerarray(
                   cif, &binary_id, array, elsize, elsigned,
                   elements, &elements_read))
                   cbf_failnez(cbf_set_integerarray_wdims(
                     cbf, compression,
                     binary_id, array, elsize, elsigned, elements,
                     byteorder, dim1, dim2, dim3, padding))
                   } else  {
                     cbf_failnez (cbf_get_realarray(
                       cif, &binary_id, array, elsize,
                       elements, &elements_read))
                     cbf_failnez(cbf_set_realarray_wdims(
                     cbf, compression,
                     binary_id, array, elsize, elements,
                     byteorder, dim1, dim2, dim3, padding))
                   }
                   free(array);
                 } else {
                   fprintf(stderr,
                     "\nFailed to allocate memory %ld bytes",
                     (long) elsize*elements);
                   exit(1);
                 }
               }
             }
           }
         }
       }
     }
   }

   }

   }

   b = clock ();
   fprintf (stderr,
     " Time to read input_cif: %.3fs\n",
       ((b - a) * 1.0) / CLOCKS_PER_SEC);
   a = clock ();

   out = NULL;
   if ( ! cbfout || strcmp(cbfout?cbfout:"","-") == 0 ) {
      out = stdout;
   } else if ( strcmp(cbfout?cbfout:"","/dev/null") ==0 ){
         devnull=1;
   } else {
     out = fopen (cbfout, "w+b");
   }
   if ( ( devnull == 0 ) &&  ! out ) {
     if (encoding == ENC_NONE) {
       printf (" Couldn't open the CBF file %s\n", cbfout);
     } else {
       printf (" Couldn't open the CIF file %s\n", cbfout);
     }
     exit (1);
   }

   if ( ! devnull ){
   cbf_failnez (cbf_write_file (cbf, out, 1, cbforcif, mime | digest | padflag,
                                         encoding | bytedir | term))
   }
   cbf_failnez (cbf_free_handle (cbf))
   b = clock ();
   if (encoding == ENC_NONE) {
     fprintf (stderr, " Time to write the CBF image: %.3fs\n",
       ((b - a) * 1.0) / CLOCKS_PER_SEC);
   } else {
         if ( ! devnull )
     fprintf (stderr, " Time to write the CIF image: %.3fs\n",
       ((b - a) * 1.0) / CLOCKS_PER_SEC);
   }

   exit(0);

}

int local_exit (int status)
{
  exit(status);
  return 1; /* avoid warnings */
}

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