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  • Committer: Bazaar Package Importer
  • Author(s): Aaron M. Ucko
  • Date: 2005-03-27 12:00:15 UTC
  • mfrom: (2.1.2 hoary)
  • Revision ID: james.westby@ubuntu.com-20050327120015-embhesp32nj73p9r
Tags: 6.1.20041020-3
http://bugs.debian.org/295110
* Fix FTBFS under GCC 4.0 caused by inconsistent use of "static" on
  functions.  (Closes: #295110.)
* Add a watch file, now that we can.  (Upstream's layout needs version=3.)

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biostruc/cdd/cddposutil.c
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/* $Id: cddposutil.c,v 1.15 2001/12/31 13:47:06 bauer Exp $
 
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/* $Id: cddposutil.c,v 1.18 2004/03/31 17:58:51 papadopo Exp $
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*===========================================================================
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*
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*                            PUBLIC DOMAIN NOTICE
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*
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* Initial Version Creation Date: 12/21/1999
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*
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* $Revision: 1.15 $
 
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* $Revision: 1.18 $
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*
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* File Description: CDD utilities involving position-specific scoring 
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*                   matrices (PSSMs)
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* Modifications:
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* --------------------------------------------------------------------------
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* $Log: cddposutil.c,v $
 
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* Revision 1.18  2004/03/31 17:58:51  papadopo
 
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* Mike Gertz' changes for length adjustment calculations
 
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*
 
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* Revision 1.17  2004/01/22 15:43:57  bauer
 
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* call BlastCalculateEffectiveLengths in CddSetUpSearchInternalByLoc
 
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*
 
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* Revision 1.16  2003/05/29 13:17:56  thiessen
 
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* fix memory leak in CddposFreeMemory()
 
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*
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* Revision 1.15  2001/12/31 13:47:06  bauer
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* made block_width a local variable in CddSetUpSearchInternalByLoc to deal with changes in blast data structures
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*
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  MemFree(posSearch->posRowSigma);
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  MemFree(posSearch->posInformation);
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  MemFree(posSearch->posUseSequences);
 
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  MemFree(posSearch->posGaplessColumnWeights);
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}
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        */
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        if (retval)
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                return retval;
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        if (search->pbp->gapped_calculation &&
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                StringCmp(search->prog_name, "blastn") != 0)
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                min_query_length = 1/(search->sbp->kbp_gap_std[search->first_context]->K);
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        else
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                min_query_length = 1/(search->sbp->kbp[search->first_context]->K);
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        last_length_adjustment = 0;
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        for (index=0; index<5; index++)
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        {
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                length_adjustment = ((search->sbp->kbp[search->first_context]->logK)+log((Nlm_FloatHi)(length-last_length_adjustment)*(Nlm_FloatHi)(MAX(1, (search->dblen)-(search->dbseq_num*last_length_adjustment)))))/(search->sbp->kbp[search->first_context]->H);
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                if (length_adjustment >= length-min_query_length)
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                {
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                        length_adjustment = length-min_query_length;
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                        break;
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                }
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                if (ABS(last_length_adjustment-length_adjustment) <= 1)
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                        break;
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                last_length_adjustment = length_adjustment;
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        }
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        search->length_adjustment = MAX(length_adjustment, 0);
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        search->dblen_eff = MAX(1, search->dblen - search->dbseq_num*search->length_adjustment);
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        effective_query_length = MAX(length - search->length_adjustment, min_query_length);
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        for (index=search->first_context; index<=search->last_context; index++)
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        {
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                search->context[index].query->effective_length = effective_query_length;
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        }
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        if (search->searchsp_eff == 0)
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                search->searchsp_eff = ((Nlm_FloatHi) search->dblen_eff)*((Nlm_FloatHi) effective_query_length);
 
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        if( 0 != BlastComputeLengthAdjustment(1/min_query_length,
 
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                                         search->sbp->
 
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                                         kbp[search->first_context]->logK,
 
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                                         1/search->sbp->
 
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                                         kbp[search->first_context]->H,
 
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                                         0.0, 
 
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                                         length,
 
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                                         search->dblen, search->dbseq_num,
 
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                                         &length_adjustment) ) {
 
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            ErrPostEx(SEV_WARNING, 0, 0,
 
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                      "BlastComputeLengthAdjustment failed!");
 
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        }
 
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        search->length_adjustment = length_adjustment;
 
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        search->dblen_eff =
 
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            search->dblen - search->dbseq_num*search->length_adjustment;
 
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        effective_query_length    = length - length_adjustment;
 
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        for (index=search->first_context; index<=search->last_context; index++)
 
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        {
 
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            search->context[index].query->effective_length =
 
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                effective_query_length;
 
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        }
 
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        if (search->searchsp_eff == 0)
 
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            search->searchsp_eff =
 
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                ((Nlm_FloatHi) search->dblen_eff)*
 
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                ((Nlm_FloatHi) effective_query_length);
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        /* The default is that cutoff_s was not set and is zero. */
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        if (options->cutoff_s == 0)