diff options
Diffstat (limited to 'demo/blastpgp.c')
| -rw-r--r-- | demo/blastpgp.c | 33 |
1 files changed, 20 insertions, 13 deletions
diff --git a/demo/blastpgp.c b/demo/blastpgp.c index d2bfc9b7..31ac2210 100644 --- a/demo/blastpgp.c +++ b/demo/blastpgp.c @@ -1,6 +1,6 @@ -static char const rcsid[] = "$Id: blastpgp.c,v 6.137 2007/03/14 17:55:27 madden Exp $"; +static char const rcsid[] = "$Id: blastpgp.c,v 6.139 2008/01/02 20:16:11 madden Exp $"; -/* $Id: blastpgp.c,v 6.137 2007/03/14 17:55:27 madden Exp $ */ +/* $Id: blastpgp.c,v 6.139 2008/01/02 20:16:11 madden Exp $ */ /************************************************************************** * * * COPYRIGHT NOTICE * @@ -26,8 +26,14 @@ static char const rcsid[] = "$Id: blastpgp.c,v 6.137 2007/03/14 17:55:27 madden * appreciated. * * * ************************************************************************** - * $Revision: 6.137 $ + * $Revision: 6.139 $ * $Log: blastpgp.c,v $ + * Revision 6.139 2008/01/02 20:16:11 madden + * XML output respects -v and -b option, JIRA SB-30 + * + * Revision 6.138 2008/01/02 14:02:06 madden + * Make composition-based score adjustments the default for blastp and tblastn + * * Revision 6.137 2007/03/14 17:55:27 madden * - #include string.h to get a prototype for strcasecmp In * - In tick_callback, suppress unused parameter warnings in tick_callback @@ -712,17 +718,17 @@ static Args myargs[] = { NULL, NULL, NULL, TRUE, 'l', ARG_STRING, 0.0, 0, NULL}, {"Use lower case filtering of FASTA sequence", /* ARG_LCASE */ "F", NULL,NULL,TRUE,'U',ARG_BOOLEAN, 0.0,0,NULL}, - { "Use composition based statistics\n" /* ARG_COMP_BASED_STATS */ + { "Use composition based score adjustment\n" /* ARG_COMP_BASED_STATS */ "As first character:\n" "0 or F or f: no composition-based statistics\n" - "1 or T or t: Composition-based statistics as in NAR 29:2994--3005, 2001\n" - "2: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties in round 1\n" + "2 or T or t: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties in round 1\n" + "1: Composition-based statistics as in NAR 29:2994--3005, 2001\n" "3: Composition-based score adjustment as in Bioinformatics 21:902-911, " "2005, unconditionally in round 1\n" "As second character, if first character is equivalent to 1, 2, or 3:\n" "U or u: unified p-value combining alignment p-value and " "compositional p-value in round 1 only\n", - "1", NULL, NULL, FALSE, 't', ARG_STRING, 0.0, 0, NULL}, + "2", NULL, NULL, FALSE, 't', ARG_STRING, 0.0, 0, NULL}, { "ASN.1 Scoremat input of checkpoint data:\n" "0: no scoremat input\n" "1: Restart is from ASCII scoremat checkpoint file,\n" @@ -1126,14 +1132,12 @@ PGPBlastOptionsPtr PGPReadBlastOptions(void) break; case 'T': case 't': - case '1': - options->tweak_parameters = eCompositionBasedStats; - break; case '2': - ErrPostEx(SEV_WARNING, 1, 0, "the -t 2 argument " - "is currently experimental\n"); options->tweak_parameters = eCompositionMatrixAdjust; break; + case '1': + options->tweak_parameters = eCompositionBasedStats; + break; case '3': ErrPostEx(SEV_WARNING, 1, 0, "the -t 3 argument " "is currently experimental\n"); @@ -1919,11 +1923,14 @@ Int2 Main (void) !bop->options->gapped_calculation, thisPassNum, "No hits found", search->mask); } else { - iterp = BXMLBuildOneIteration(head, other_returns, + BlastPruneSapStructPtr prune = + BlastPruneHitsFromSeqAlign(head, bop->number_of_alignments, NULL); + iterp = BXMLBuildOneIteration(prune->sap, other_returns, bop->options->is_ooframe, !bop->options->gapped_calculation, thisPassNum, (search->posConverged ? "CONVERGED" : NULL), search->mask); + prune = BlastPruneSapStructDestruct(prune); } IterationAsnWrite(iterp, psixp->aip, psixp->atp); |