← Back to branch summary

~ubuntu-branches/ubuntu/edgy/ncbi-tools6/edgy

« back to all changes in this revision

Viewing changes to algo/blast/core/phi_lookup.c

  • Committer: Bazaar Package Importer
  • Author(s): Barry deFreese
  • Date: 2006-07-19 23:28:07 UTC
  • mfrom: (1.1.5 upstream)
  • Revision ID: james.westby@ubuntu.com-20060719232807-et3cdmcjgmnyleyx
Tags: 6.1.20060507-3ubuntu1
Re-merge with Debian

Show diffs side-by-side

added added

removed removed

Lines of Context:
algo/blast/core/phi_lookup.c
1
 
/* $Id: phi_lookup.c,v 1.30 2005/11/16 14:27:04 madden Exp $
 
1
/* $Id: phi_lookup.c,v 1.31 2006/04/20 19:28:30 madden Exp $
2
2
 * ===========================================================================
3
3
 *
4
4
 *                            PUBLIC DOMAIN NOTICE
34
34
 
35
35
#ifndef SKIP_DOXYGEN_PROCESSING
36
36
static char const rcsid[] = 
37
 
    "$Id: phi_lookup.c,v 1.30 2005/11/16 14:27:04 madden Exp $";
 
37
    "$Id: phi_lookup.c,v 1.31 2006/04/20 19:28:30 madden Exp $";
38
38
#endif /* SKIP_DOXYGEN_PROCESSING */
39
39
 
40
40
#include <algo/blast/core/blast_def.h>
456
456
                                kMaskAaAlphabetBits; 
457
457
                            if (posIndex >= PHI_MAX_PATTERN_LENGTH) {
458
458
                                Blast_MessageWrite(error_msg, eBlastSevWarning,
459
 
                                                   2, 1, "Pattern too long");
 
459
                                                   kBlastMessageNoContext, "Pattern too long");
460
460
                                return(-1);
461
461
                            }
462
462
                        }
506
506
                  add its probability to positionProbability*/
507
507
                while ((next_char=pattern[++charIndex]) != ']') { /*end of set*/
508
508
                    if ((next_char < 'A') || (next_char > 'Z') || (next_char == '\0')) {
509
 
                        Blast_MessageWrite(error_msg, eBlastSevWarning, 2, 1, 
 
509
                        Blast_MessageWrite(error_msg, eBlastSevWarning, kBlastMessageNoContext, 
510
510
                            "pattern description has a non-alphabetic"
511
511
                            "character inside a bracket");
512
512
                        
558
558
            pattern_blk->patternProbability *= positionProbability;
559
559
        }
560
560
        if (posIndex >= PHI_MAX_PATTERN_LENGTH) {
561
 
            Blast_MessageWrite(error_msg, eBlastSevWarning, 2, 1, 
 
561
            Blast_MessageWrite(error_msg, eBlastSevWarning, kBlastMessageNoContext, 
562
562
                               "Pattern is too long");
563
563
        }
564
564
    }
633
633
        s_InitDNAPattern(pattern_blk);
634
634
 
635
635
    if (wildcardProduct > kWildcardThreshold) {
636
 
        Blast_MessageWrite(error_msg, eBlastSevWarning, 2, 1, 
 
636
        Blast_MessageWrite(error_msg, eBlastSevWarning, kBlastMessageNoContext, 
637
637
                           "Due to variable wildcards pattern is likely to "
638
638
                           "occur too many times in a single sequence\n");
639
639
    }