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

  • Committer: Package Import Robot
  • Author(s): Aaron M. Ucko
  • Date: 2011-09-05 18:55:02 UTC
  • mfrom: (1.1.11 upstream)
  • Revision ID: package-import@ubuntu.com-20110905185502-iuvmoe65ytljhckn
Tags: 6.1.20110713-1
* New upstream release.
* debian/*.symbols: update accordingly.
* make/makeshlb.unx: link libcn3dOGL.so against -lm for sqrt.
* doc/man/*.1: update for new release.
* debian/rules:
  - (VIB): add asnmacro, as upstream takes care to publish binaries thereof.
  - Retire obsolete multiarch-unaware checks for libpthread.
  - Fully modernize Debhelper usage; in particular, transition to overrides.
* debian/compat: advance to 9 per rules modernization.
* debian/ncbi-tools-bin.install: add asnmacro.
* make/makenet.unx: link asnmacro only against libraries it directly needs.
* doc/man/asnmacro.1: give asnmacro a man page.
* doc/man/Psequin.1: list it in SEE ALSO.
* network/id1arch/idfetch.c: revert redundant change (from #295110).
* Convert to multiarch.
  - debian/rules: Install libraries (and ncbithr.o) to multiarch directories.
  - debian/lib*.install: match multiarch library paths.
  - debian/control:
    + Build-Depends: debhelper (>= 8.1.3~), implying a recent dpkg-dev.
    + Set Multi-Arch: as appropriate across the board, and specify
      Pre-Depends: ${misc:Pre-Depends} for runtime libraries.
* debian/*.lintian-overrides: drop leading slashes for Lintian 2.5.x.
* debian/control: Standards-Version: 3.9.2 (already compliant).

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algo/blast/core/blast_kappa.c
1
 
/* $Id: blast_kappa.c,v 1.100 2010/07/30 17:44:35 kazimird Exp $
 
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/* $Id: blast_kappa.c,v 1.110 2011/05/31 16:09:30 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_kappa.c,v 1.100 2010/07/30 17:44:35 kazimird Exp $";
 
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"$Id: blast_kappa.c,v 1.110 2011/05/31 16:09:30 kazimird Exp $";
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#endif /* SKIP_DOXYGEN_PROCESSING */
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#include <float.h>
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                                hitParams->link_hsp_params, TRUE);
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    } else {
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        status =
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            Blast_HSPListGetEvalues(queryInfo, hsp_list, TRUE, sbp,
 
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            Blast_HSPListGetEvalues(queryInfo, subject_length, hsp_list, TRUE, FALSE, sbp,
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                                    0.0, /* use a non-zero gap decay
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                                            only when linking HSPs */
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                                    1.0); /* Use scaling factor equal to
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    } else {
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        /* We must recompute the start for the gapped alignment, as the
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           one in the HSP was unacceptable.*/
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        q_start =
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            BlastGetStartForGappedAlignment(query_data->data,
 
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        Boolean retval =
 
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            BlastGetOffsetsForGappedAlignment(query_data->data,
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                                            subject_data->data, sbp,
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                                            hsp->query.offset,
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                                            hsp->query.end -
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                                            hsp->query.offset,
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                                            hsp->subject.offset,
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                                            hsp->subject.end -
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                                            hsp->subject.offset);
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        s_start =
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            (hsp->subject.offset - hsp->query.offset) + q_start;
 
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                                            hsp,
 
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                                            &q_start, 
 
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                                            &s_start);
 
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        /* ASSERT(retval == TRUE); */
 
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        if (retval == FALSE)
 
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           return NULL;
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    }
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    /* Undo the shift so there is no side effect on the incoming HSP
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       list. */
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       p-value is desired; value needs to be passed in eventually*/
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    int compositionTestIndex = extendParams->options->unifiedP;
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    Uint1* genetic_code_string = GenCodeSingletonFind(default_db_genetic_code);
 
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    Boolean perform_partial_fetch = BlastSeqSrcGetSupportsPartialFetching(seqSrc);
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    ASSERT(program_number == eBlastTypeBlastp ||
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           program_number == eBlastTypeTblastn ||
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        }
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        if (BlastCompo_EarlyTermination(thisMatch->best_evalue,
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                                        redoneMatches, numQueries)) {
 
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            Blast_HSPListFree(thisMatch);
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            break;
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        }
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        /* Get the sequence for this match */
 
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        if (perform_partial_fetch) {
 
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            Int4 oid = thisMatch->oid;
 
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            Int4 i;
 
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            BlastHSPRangeList *range_list = NULL;
 
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            BlastSeqSrcSetRangesArg *arg = NULL;
 
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            ASSERT(Blast_SubjectIsTranslated(program_number));
 
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            for (i=0; i<thisMatch->hspcnt; i++) {
 
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                BlastHSP *hsp = thisMatch->hsp_array[i];
 
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                Int4 begin = (hsp->subject.offset - 2) * CODON_LENGTH;
 
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                Int4 end = (hsp->subject.end + 2) * CODON_LENGTH;
 
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                if (hsp->subject.frame < 0) {
 
2213
                    Int4 len = BlastSeqSrcGetSeqLen(seqSrc, &oid);
 
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                    Int4 begin_new = len - end;
 
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                    end = len - begin;
 
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                    begin = begin_new;
 
2217
                }
 
2218
                range_list = BlastHSPRangeListAddRange(range_list, begin, end);
 
2219
            }
 
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            arg = BlastSeqSrcSetRangesArgNew(thisMatch->hspcnt);
 
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            arg->oid = oid;
 
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2223
            BlastHSPRangeBuildSetRangesArg(range_list, arg);
 
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            BlastSeqSrcSetSeqRanges(seqSrc, arg);
 
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            BlastHSPRangeListFree(range_list);
 
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            BlastSeqSrcSetRangesArgFree(arg);
 
2227
        }
 
2228
 
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        status_code =
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            s_MatchingSequenceInitialize(&matchingSeq, program_number,
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                                         seqSrc, default_db_genetic_code,