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

  • Committer: Bazaar Package Importer
  • Author(s): Aaron M. Ucko
  • Date: 2008-03-19 19:42:00 UTC
  • mfrom: (1.1.8 upstream)
  • Revision ID: james.westby@ubuntu.com-20080319194200-7t0o0fgni3pijh1x
Tags: 6.1.20080302-1
* New upstream release
* debian/lib{ncbi6,vibrant6a}.symbols: update and clean up.
* debian/lib{ncbi,vibrant}6-dev.install: ship new headers.
* debian/ncbi-tools-bin.docs, doc/man/tbl2asn.1: belatedly ship
  tbl2asn.txt, and restore tbl2asn.1's reference thereto.
* doc/man/*.1: correct usage of ' and -.
* doc/man/{blast,cleanasn,nps2gps,tbl2asn}.1: resync with help output.
* debian/control: tighten dependencies between binary packages.
* debian/{control,rules}: require cdbs 0.4.51; drop workaround for #462130.
* debian/{control,rules,*.override}: rename Lintian overrides to
  $pkg.lintian-overrides and employ dh_lintian from debhelper (>= 6.0.7)
  in lieu of custom logic.
* debian/*.doc-base*: modernize (and correct) section assignments per
  doc-base 0.8.10: science -> Science/Biology, net -> System/Administration.
* debian/makemenu: drop obsolete Encoding key from generated .desktop files.

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algo/blast/core/blast_options.c
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/* $Id: blast_options.c,v 1.205 2007/05/22 20:55:36 kazimird Exp $
 
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/* $Id: blast_options.c,v 1.207 2007/10/25 15:55:36 kazimird Exp $
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 * ===========================================================================
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 *
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 *                            PUBLIC DOMAIN NOTICE
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#ifndef SKIP_DOXYGEN_PROCESSING
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static char const rcsid[] = 
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    "$Id: blast_options.c,v 1.205 2007/05/22 20:55:36 kazimird Exp $";
 
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    "$Id: blast_options.c,v 1.207 2007/10/25 15:55:36 kazimird Exp $";
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#endif /* SKIP_DOXYGEN_PROCESSING */
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#include <algo/blast/core/blast_options.h>
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      (*options)->gap_trigger = BLAST_GAP_TRIGGER_NUCL;
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      (*options)->x_dropoff = BLAST_UNGAPPED_X_DROPOFF_NUCL;
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   }
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   (*options)->ungapped_extension = TRUE;
 
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   (*options)->program_number = program;
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   return 0;
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   ASSERT(options);
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   /* For some blastn variants (i.e., megablast), and for PHI BLAST there is no
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    * ungapped extension. */
 
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   /* PHI-BLAST has no ungapped extension phase.  Megablast may not have it,
 
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    but generally does now. */
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   if (program_number != eBlastTypeBlastn  &&
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       (!Blast_ProgramIsPhiBlast(program_number)) &&
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       options->x_dropoff <= 0.0)
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}
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Int2
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BlastExtensionOptionsNew(EBlastProgramType program, BlastExtensionOptions* *options)
 
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BlastExtensionOptionsNew(EBlastProgramType program, BlastExtensionOptions* *options, Boolean gapped)
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{
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        *options = (BlastExtensionOptions*) 
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    /** @todo how to determine this for PSI-BLAST bootstrap run (i.e. when
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     * program is blastp? */
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    if (Blast_QueryIsPssm(program) && ! Blast_SubjectIsTranslated(program)) {
 
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    if (gapped && (Blast_QueryIsPssm(program) && ! Blast_SubjectIsTranslated(program))) {
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        (*options)->compositionBasedStats = eCompositionBasedStats;
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    }
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   if (word_size)
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      options->word_size = word_size;
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   if ((program_number == eBlastTypeTblastn ||
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        program_number == eBlastTypeBlastp) && 
 
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        program_number == eBlastTypeBlastp ||
 
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        program_number == eBlastTypeBlastx) && 
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       word_size > 5)
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       options->lut_type = eCompressedAaLookupTable;
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    } else if (program_number != eBlastTypeBlastn && options->word_size > 5)
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    {
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        if (program_number == eBlastTypeBlastp ||
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            program_number == eBlastTypeTblastn)
 
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            program_number == eBlastTypeTblastn ||
 
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            program_number == eBlastTypeBlastx)
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        {
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            if (options->word_size > 7) {
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                Blast_MessageWrite(blast_msg, eBlastSevError, 
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                                   kBlastMessageNoContext,
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                                   "Word-size must be less than "
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                                   "8 for a tblastn search");
 
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                                   "8 for a tblastn, blastp or blastx search");
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                return BLASTERR_OPTION_VALUE_INVALID;
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            }
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        }
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    }
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    if (program_number == eBlastTypeBlastp ||
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        program_number == eBlastTypeTblastn)
 
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        program_number == eBlastTypeTblastn ||
 
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        program_number == eBlastTypeBlastx)
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    {
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        if (options->word_size > 5 &&
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            options->lut_type != eCompressedAaLookupTable) {
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           Blast_MessageWrite(blast_msg, eBlastSevError, kBlastMessageNoContext,
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                         "Blastp or Tblastn with word size > 5 requires a "
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                         "compressed alphabet lookup table");
 
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           Blast_MessageWrite(blast_msg, eBlastSevError,
 
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                              kBlastMessageNoContext,
 
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                              "Blastp, Blastx or Tblastn with word size"
 
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                              " > 5 requires a "
 
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                              "compressed alphabet lookup table");
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           return BLASTERR_OPTION_VALUE_INVALID;
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        }
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        else if (options->lut_type == eCompressedAaLookupTable &&
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   if ((status=BlastInitialWordOptionsNew(program_number, word_options)))
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      return status;
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   if ((status = BlastExtensionOptionsNew(program_number, ext_options)))
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      return status;
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   if ((status=BlastScoringOptionsNew(program_number, score_options)))
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      return status;
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   if ((status = BlastExtensionOptionsNew(program_number, ext_options,
 
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                                       (*score_options)->gapped_calculation)))
 
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      return status;
 
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   if ((status=BlastHitSavingOptionsNew(program_number, hit_options,
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                                        (*score_options)->gapped_calculation)))
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      return status;
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        }
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    }
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    if (ext_options->compositionBasedStats != eNoCompositionBasedStats)
 
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    {
 
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            if (!Blast_QueryIsPssm(program_number) && program_number != eBlastTypeTblastn && 
 
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                 program_number != eBlastTypeBlastp) {
 
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                        Blast_MessageWrite(blast_msg, eBlastSevWarning, kBlastMessageNoContext,
 
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                            "Compositional adjustments are only supported with blastp or tblastn");
 
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                        return BLASTERR_OPTION_VALUE_INVALID;
 
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            }
 
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            if (!score_options->gapped_calculation) {
 
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                        Blast_MessageWrite(blast_msg, eBlastSevWarning, kBlastMessageNoContext,
 
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                            "Compositional adjustments are only supported for gapped searches");
 
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                        return BLASTERR_OPTION_VALUE_INVALID;
 
1485
            }
 
1486
            
 
1487
    }
 
1488
 
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    return 0;
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}
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