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Viewing changes to algo/blast/core/na_ungapped.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/na_ungapped.c
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/* $Id: na_ungapped.c,v 1.39 2010/07/27 18:24:31 kazimird Exp $
 
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/* $Id: na_ungapped.c,v 1.43 2011/07/12 17:54:32 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: na_ungapped.c,v 1.39 2010/07/27 18:24:31 kazimird Exp $";
 
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    "$Id: na_ungapped.c,v 1.43 2011/07/12 17:54:32 kazimird Exp $";
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#endif                          /* SKIP_DOXYGEN_PROCESSING */
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#include <algo/blast/core/na_ungapped.h>
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            Int4 context = BSearchContextInfo(q_off, query_info);
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            cutoffs = word_params->cutoffs + context;
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            ungapped_data = &dummy_ungapped_data;
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            s_NuclUngappedExtend(query, subject, matrix, q_off, s_end, s_off,
 
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            /* 
 
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             * Skip use of the scoring table and go straight to the matrix
 
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             * based extension if matrix_only_scoring is set.  Used by
 
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             * app rmblastn.
 
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             * -RMH-
 
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             */
 
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            if ( word_params->options->program_number == eBlastTypeBlastn &&
 
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                 word_params->matrix_only_scoring )
 
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            {
 
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               s_NuclUngappedExtendExact(query, subject, matrix, q_off,
 
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                                  s_off, -(cutoffs->x_dropoff), ungapped_data);
 
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            }else {
 
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               s_NuclUngappedExtend(query, subject, matrix, q_off, s_end, s_off,
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                                 -(cutoffs->x_dropoff), ungapped_data,
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                                 word_params->nucl_score_table,
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                                 cutoffs->reduced_nucl_cutoff_score);
 
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            }
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            if (off_found || ungapped_data->score >= cutoffs->cutoff_score) {
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                BlastUngappedData *final_data =
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            Int4 context = BSearchContextInfo(q_off, query_info);
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            cutoffs = word_params->cutoffs + context;
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            ungapped_data = &dummy_ungapped_data;
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            s_NuclUngappedExtend(query, subject, matrix, q_off, s_end,
 
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            /* 
 
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             * Skip use of the scoring table and go straight to the matrix
 
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             * based extension if matrix_only_scoring is set.  Used by
 
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             * app rmblastn.
 
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             * -RMH-
 
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             */
 
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            if ( word_params->options->program_number == eBlastTypeBlastn &&                          word_params->matrix_only_scoring )
 
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            {
 
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                s_NuclUngappedExtendExact(query, subject, matrix, q_off,
 
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                                  s_off, -(cutoffs->x_dropoff), ungapped_data);
 
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            }else {
 
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                s_NuclUngappedExtend(query, subject, matrix, q_off, s_end,
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                                 s_off, -(cutoffs->x_dropoff),
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                                 ungapped_data,
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                                 word_params->nucl_score_table,
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                                 cutoffs->reduced_nucl_cutoff_score);
 
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            }
 
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            if (off_found || ungapped_data->score >= cutoffs->cutoff_score) {
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                BlastUngappedData *final_data =
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                    (BlastUngappedData *) malloc(sizeof(BlastUngappedData));
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           technically be negative, but the compressed version
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           of the query has extra pad bytes before q[0] */
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        if (s_offset > 0) {
 
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        if ( (s_offset > 0) && (q_offset > 0) ) {
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            Uint1 q_byte = q[q_offset - 4];
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            Uint1 s_byte = s[s_offset / COMPRESSION_RATIO - 1];
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            ext_left = s_ExactMatchExtendLeft[q_byte ^ s_byte];
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        /* look for up to 4 exact matches to the right of the seed */
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        if (ext_left < ext_to) {
 
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        if ((ext_left < ext_to) && ((q_offset + lut_word_length) < query->length)) {
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            Uint1 q_byte = q[q_offset + lut_word_length];
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            Uint1 s_byte = s[(s_offset + lut_word_length) / COMPRESSION_RATIO];
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            Int4 ext_right = s_ExactMatchExtendRight[q_byte ^ s_byte];
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    scan_range[2] = subject->length - lut_word_length; /*end pos (inclusive) of scan*/
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    /* if sequence is masked, fall back to generic scanner and extender */
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    if (subject->mask_type) {
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        scansub = (TNaScanSubjectFunction) 
 
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    if (subject->mask_type != eNoSubjMasking) {
 
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        if (lookup_wrap->lut_type == eMBLookupTable &&
 
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            ((BlastMBLookupTable *) lookup_wrap->lut)->discontiguous) {
 
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            /* discontiguous scan subs assumes any (non-aligned starting offset */
 
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        } else {
 
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            scansub = (TNaScanSubjectFunction) 
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                  BlastChooseNucleotideScanSubjectAny(lookup_wrap);
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        if (extend != (TNaExtendFunction)s_BlastNaExtendDirect) {
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             extend = (lookup_wrap->lut_type == eSmallNaLookupTable) 
 
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            if (extend != (TNaExtendFunction)s_BlastNaExtendDirect) {
 
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                 extend = (lookup_wrap->lut_type == eSmallNaLookupTable) 
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                    ? (TNaExtendFunction)s_BlastSmallNaExtend
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                    : (TNaExtendFunction)s_BlastNaExtend;
 
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            }
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        }
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        /* generic scanner permits any (non-aligned) starting offset */
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        scan_range[1] = subject->seq_ranges[0].left + word_length - lut_word_length;