NCBI C Toolkit Cross Reference

   /*   asn2idx.c
   * ===========================================================================
   *
   *                            PUBLIC DOMAIN NOTICE
   *            National Center for Biotechnology Information (NCBI)
   *
   *  This software/database is a "United States Government Work" under the
   *  terms of the United States Copyright Act.  It was written as part of
   *  the author's official duties as a United States Government employee and
  *  thus cannot be copyrighted.  This software/database is freely available
  *  to the public for use. The National Library of Medicine and the U.S.
  *  Government do not place any restriction on its use or reproduction.
  *  We would, however, appreciate having the NCBI and the author cited in
  *  any work or product based on this material
  *
  *  Although all reasonable efforts have been taken to ensure the accuracy
  *  and reliability of the software and data, the NLM and the U.S.
  *  Government do not and cannot warrant the performance or results that
  *  may be obtained by using this software or data. The NLM and the U.S.
  *  Government disclaim all warranties, express or implied, including
  *  warranties of performance, merchantability or fitness for any particular
  *  purpose.
  *
  * ===========================================================================
  *
  * File Name:  asn2idx.c
  *
  * Author:  Jonathan Kans
  *
  * Version Creation Date:   8/2/04
  *
  * $Revision: 1.5 $
  *
  * File Description:
  *
  *   Generates accession/file offset indices for Bioseq-set release files
  *
  * Modifications:  
  * --------------------------------------------------------------------------
  * Date     Name        Description of modification
  * -------  ----------  -----------------------------------------------------
  *
  *
  * ==========================================================================
  */
  
  #include <ncbi.h>
  #include <objall.h>
  #include <objsset.h>
  #include <objsub.h>
  #include <objfdef.h>
  #include <sqnutils.h>
  #include <lsqfetch.h>
  
  static Boolean NotInFilter (
    CharPtr filename,
    ValNodePtr exclude
  )
  
  {
    CharPtr     str;
    ValNodePtr  vnp;
  
    for (vnp = exclude; vnp != NULL; vnp = vnp->next) {
      str = (CharPtr) vnp->data.ptrvalue;
      if (StringHasNoText (str)) continue;
      if (StringStr (filename, str) != NULL) return FALSE;
    }
    return TRUE;
  }
  
  static void FileRecurse (
    CharPtr directory,
    CharPtr results,
    CharPtr subdir,
    CharPtr subfile,
    ValNodePtr exclude,
    Boolean binary,
    Boolean dorecurse
  )
  
  {
    Char        path [PATH_MAX];
    CharPtr     str;
    ValNodePtr  head, vnp;
  
    /* get list of all files in source directory */
  
    head = DirCatalog (directory);
  
    for (vnp = head; vnp != NULL; vnp = vnp->next) {
      if (vnp->choice == 0) {
        if (StringHasNoText (subdir) || StringStr (directory, subdir) != NULL) {
          str = (CharPtr) vnp->data.ptrvalue;
          if (! StringHasNoText (str)) {
  
            /* does filename have desired substring? */
  
            if (StringHasNoText (subfile) || StringStr (str, subfile) != NULL) {
 
             if (NotInFilter (str, exclude)) {
 
               /* process file that has desired suffix (usually .aso) */
 
               StringNCpy_0 (path, directory, sizeof (path));
               FileBuildPath (path, NULL, str);
 
               CreateAsnIndex (path, results, binary);
             }
           }
         }
       }
     } else if (vnp->choice == 1 && dorecurse) {
       StringNCpy_0 (path, directory, sizeof (path));
       str = (CharPtr) vnp->data.ptrvalue;
       FileBuildPath (path, str, NULL);
       FileRecurse (path, results, subdir, subfile, exclude, binary, dorecurse);
     }
   }
 
   /* clean up file list */
 
   ValNodeFreeData (head);
 }
 
 static ValNodePtr ParseStringByCommas (
   CharPtr str
 )
 
 {
   Char        ch;
   ValNodePtr  head = NULL;
   CharPtr     last, ptr, tmp;
 
   if (StringHasNoText (str)) return NULL;
 
   tmp = StringSave (str);
   last = tmp;
   ptr = last;
   ch = *ptr;
   while (ch != '\0') {
     if (ch == ',') {
       *ptr = '\0';
       if (! StringHasNoText (last)) {
         TrimSpacesAroundString (last);
         ValNodeCopyStr (&head, 0, last);
       }
       ptr++;
       last = ptr;
       ch = *ptr;
     } else {
       ptr++;
       ch = *ptr;
     }
   }
   if (! StringHasNoText (last)) {
     TrimSpacesAroundString (last);
     ValNodeCopyStr (&head, 0, last);
   }
   MemFree (tmp);
 
   return head;
 }
 
 /* Args structure contains optional command-line arguments */
 
 #define p_argInputPath    0
 #define r_argOutputPath   1
 #define d_argSubDirName   2
 #define x_argFileSelect   3
 #define f_argFilter       4
 #define b_argBinary       5
 #define t_argRecurse      6
 
 Args myargs [] = {
   {"Path to Files", NULL, NULL, NULL,
     FALSE, 'p', ARG_STRING, 0.0, 0, NULL},
   {"Path for Results", NULL, NULL, NULL,
     TRUE, 'r', ARG_STRING, 0.0, 0, NULL},
   {"Required Subdirectory", NULL, NULL, NULL,
     TRUE, 'd', ARG_STRING, 0.0, 0, NULL},
   {"File Selection Substring", ".aso", NULL, NULL,
     TRUE, 'x', ARG_STRING, 0.0, 0, NULL},
   {"Filter", "gbcon,gbest,gbgss,gbhtg,gbsts", NULL, NULL,
     FALSE, 'f', ARG_STRING, 0.0, 0, NULL},
   {"Bioseq-sets are Binary", "F", NULL, NULL,
     TRUE, 'b', ARG_BOOLEAN, 0.0, 0, NULL},
   {"Recurse", "F", NULL, NULL,
     TRUE, 't', ARG_BOOLEAN, 0.0, 0, NULL},
 };
 
 Int2 Main (void)
 
 {
   Boolean     binary, dorecurse;
   CharPtr     directory, filter, results, subdir, subfile;
   ValNodePtr  exclude = NULL;
 
   /* standard setup */
 
   ErrSetFatalLevel (SEV_MAX);
   ErrClearOptFlags (EO_SHOW_USERSTR);
   UseLocalAsnloadDataAndErrMsg ();
   ErrPathReset ();
 
   if (! AllObjLoad ()) {
     Message (MSG_FATAL, "AllObjLoad failed");
     return 1;
   }
   if (! SubmitAsnLoad ()) {
     Message (MSG_FATAL, "SubmitAsnLoad failed");
     return 1;
   }
   if (! FeatDefSetLoad ()) {
     Message (MSG_FATAL, "FeatDefSetLoad failed");
     return 1;
   }
   if (! SeqCodeSetLoad ()) {
     Message (MSG_FATAL, "SeqCodeSetLoad failed");
     return 1;
   }
   if (! GeneticCodeTableLoad ()) {
     Message (MSG_FATAL, "GeneticCodeTableLoad failed");
     return 1;
   }
 
   /* process command line arguments */
 
   if (! GetArgs ("asn2idx", sizeof (myargs) / sizeof (Args), myargs)) {
     return 0;
   }
 
   /* additional setup modifications */
 
   directory = (CharPtr) myargs [p_argInputPath].strvalue;
   results = (CharPtr) myargs [r_argOutputPath].strvalue;
   if (StringHasNoText (results)) {
     results = NULL;
   }
   subdir = (CharPtr) myargs [d_argSubDirName].strvalue;
   subfile = (CharPtr) myargs [x_argFileSelect].strvalue;
   filter = (CharPtr) myargs [f_argFilter].strvalue;
   binary = (Boolean) myargs [b_argBinary].intvalue;
   dorecurse = (Boolean) myargs [t_argRecurse].intvalue;
 
   if (StringHasNoText (directory)) {
     Message (MSG_FATAL, "Required path to files not specified");
     return 1;
   }
 
   exclude = ParseStringByCommas (filter);
 
   /* index recursively within specified directory */
 
   FileRecurse (directory, results, subdir, subfile, exclude, binary, dorecurse);
 
   /* now create master index combining individual indices */
 
   CreateMasterAsnIndex (directory, results);
 
   ValNodeFreeData (exclude);
 
   return 0;
 }