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  • 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

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demo/blastpgp.c
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static char const rcsid[] = "$Id: blastpgp.c,v 6.133 2005/08/31 20:34:02 coulouri Exp $";
 
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static char const rcsid[] = "$Id: blastpgp.c,v 6.135 2006/05/03 14:40:49 madden Exp $";
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/* $Id: blastpgp.c,v 6.133 2005/08/31 20:34:02 coulouri Exp $ */
 
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/* $Id: blastpgp.c,v 6.135 2006/05/03 14:40:49 madden Exp $ */
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/**************************************************************************
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*                                                                         *
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*                             COPYRIGHT NOTICE                            *
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* appreciated.                                                            *
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*                                                                         *
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**************************************************************************
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 * $Revision: 6.133 $ 
 
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 * $Revision: 6.135 $ 
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 * $Log: blastpgp.c,v $
 
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 * Revision 6.135  2006/05/03 14:40:49  madden
 
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 * Changed usage of -t flag to also include specification of whether
 
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 * unified p-values should be used to calculate the significance of
 
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 * alignments when composition-based statistics is used. (from Mike Gertz)
 
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 *
 
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 * Revision 6.134  2006/01/24 18:33:51  papadopo
 
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 * from Mike Gertz: Use enumerated values, rather than #define'd constants, to specify the composition adjustment method
 
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 *
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 * Revision 6.133  2005/08/31 20:34:02  coulouri
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 *     In PGPReadBlastOptions:
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 *       - set the value of options->kappa_expect_value.
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#include <ddvcreate.h>
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#include <blfmtutl.h>
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#include <objscoremat.h>
 
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#include <algo/blast/composition_adjustment/composition_constants.h>
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/* Used by the callback function. */
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FILE *global_fp=NULL;
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    {"Use lower case filtering of FASTA sequence",                     /* ARG_LCASE */
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     "F", NULL,NULL,TRUE,'U',ARG_BOOLEAN, 0.0,0,NULL},
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    { "Use composition based statistics\n"                             /* ARG_COMP_BASED_STATS */
 
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      "As first character:\n"
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      "0 or F or f: no composition-based statistics\n"
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      "1 or T or t: Composition-based statistics as in NAR  29:2994--3005, 2001\n"
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      "2: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties in round 1\n"
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      "3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally in round 1\n",
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      "3: Composition-based score adjustment as in Bioinformatics 21:902-911, "
 
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      "2005, unconditionally in round 1\n"
 
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      "As second character, if first character is equivalent to 1, 2, or 3:\n"
 
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      "U or u: unified p-value combining alignment p-value and "
 
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      "compositional p-value in round 1 only\n",
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      "1", NULL, NULL, FALSE, 't', ARG_STRING, 0.0, 0, NULL},
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    { "ASN.1 Scoremat input of checkpoint data:\n"
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      "0: no scoremat input\n"
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    case 'F':
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    case 'f':
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    case '0':
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        options->tweak_parameters = NO_COMP_ADJUSTMENT;
 
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        options->tweak_parameters = eNoCompositionBasedStats;
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        break;
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    case 'T':
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    case 't':
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    case '1':
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        options->tweak_parameters = COMP_BASED_STATISTICS;
 
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        options->tweak_parameters = eCompositionBasedStats;
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        break;
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    case '2':
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        ErrPostEx(SEV_WARNING, 1, 0, "the -t 2 argument "
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                  "is currently experimental\n");
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        options->tweak_parameters = COMP_MATRIX_ADJUSTMENT;
 
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        options->tweak_parameters = eCompositionMatrixAdjust;
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        break;
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    case '3':
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        ErrPostEx(SEV_WARNING, 1, 0, "the -t 3 argument "
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                  "is currently experimental\n");
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        options->tweak_parameters = COMP_BASED_STATISTICS |
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                                    COMP_MATRIX_ADJUSTMENT;
 
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        options->tweak_parameters = eCompoForceFullMatrixAdjust;
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        break;
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    default:
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        ErrPostEx(SEV_FATAL, 1, 0, "invalid argument for composition-"
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                  "based statistics; see -t options\n");
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        break;
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    }
 
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    options->unified_p = 0;
 
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    if (options->tweak_parameters > eNoCompositionBasedStats) {
 
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        switch (myargs[ARG_COMP_BASED_STATS].strvalue[1]) {
 
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        case 'U':
 
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        case 'u':
 
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            options->unified_p = 1;
 
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            ErrPostEx(SEV_WARNING, 1, 0, "unified p-values "
 
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                      "are currently experimental\n");
 
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            break;
 
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        case '\0':
 
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            break;
 
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        default:
 
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            ErrPostEx(SEV_WARNING, 1, 0, "unrecognized second character"
 
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                      "in value of -t, ignoring it\n");
 
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            break;
 
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        }
 
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    }
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    if ((options->tweak_parameters > 1) &&
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        ((NULL != myargs[ARG_CHECKPOINT_INPUT].strvalue) ||
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         (NULL != myargs[ARG_ALIGNMENT_IN].strvalue))) {