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  • Committer: Bazaar Package Importer
  • Author(s): Barry deFreese
  • Date: 2005-09-27 15:38:20 UTC
  • mfrom: (1.1.3 upstream) (2.1.1 sarge)
  • Revision ID: james.westby@ubuntu.com-20050927153820-1t1sta0qirjpxaar
Tags: 6.1.20050429-1ubuntu1
GL/GLU Transition

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tools/blastconcat.c
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static char const rcsid[] = "$Id: blastconcat.c,v 1.9 2004/04/21 19:25:04 coulouri Exp $";
 
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static char const rcsid[] = "$Id: blastconcat.c,v 1.10 2005/01/10 18:52:29 coulouri Exp $";
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/* ===========================================================================
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*
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          functionality.
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******************************************************************************/
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/* $Revision: 1.9 $ 
 
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/* $Revision: 1.10 $ 
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*  $Log: blastconcat.c,v $
 
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*  Revision 1.10  2005/01/10 18:52:29  coulouri
 
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*  fixes from morgulis to allow concatenation of >255 queries in [t]blastn
 
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*
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*  Revision 1.9  2004/04/21 19:25:04  coulouri
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*  do not cast lvalues
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*
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          Uint4 i = 0;
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          DenseSegPtr dsp = (DenseSegPtr)(sap->segs);
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          for( ; i < dsp->numseg; ++i )
 
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          for( ; i < (dsp->dim)*(dsp->numseg); i += dsp->dim )
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          {
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            start = dsp->starts[i];
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            query = mult_queries->WhichQuery[start + 1] - 1;
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            start = start - mult_queries->QueryStarts[query];
 
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            if( start != -1 )
 
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              start = start - mult_queries->QueryStarts[query];
 
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            dsp->starts[i] = start;
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          }
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   AM: Changes to align on the byte boundaries.
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*/
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BioseqPtr LIBCALL 
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BlastMakeFakeBspConcat PROTO((BspArray bsp_arr, Uint1 num_bsps, Boolean is_na, Uint4 num_spacers)){
 
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BlastMakeFakeBspConcat PROTO((BspArray bsp_arr, Uint4 num_bsps, Boolean is_na, Uint4 num_spacers)){
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        BioseqPtr tot;
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        Int4 bsp_iter, letter_iter;
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                /* "compact" len refers to #bytes to store the seq, not to #of letters */
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         based on numbering beginning with 1, not 0 for queries and positions
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*/
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QueriesPtr LIBCALL 
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BlastMakeMultQueries PROTO((BspArray bsp_arr, Uint1 num_queries, Boolean is_na, Uint1 spacer_len,
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                            SeqLocPtr PNTR lcase_mask_arr)) {
 
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BlastMakeMultQueries PROTO((BspArray bsp_arr, Uint4 num_queries, Boolean is_na, Uint4 num_spacers, SeqLocPtr PNTR lcase_mask_arr))
 
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{
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        QueriesPtr queries;
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        Int4 bsp_iter, pos_iter;
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        BioseqPtr curr_bsp;
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                starts[bsp_iter] = curr_index;
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                curr_index += curr_length;
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                ends[bsp_iter] = curr_index - 1;
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                curr_index += spacer_len;
 
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                curr_index += num_spacers;
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                if( is_na && bsp_iter != num_queries - 1 && curr_length%2 ) ++curr_index;
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        }
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        curr_index -= spacer_len;
 
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        curr_index -= num_spacers;
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        /* now curr_index = total number of letters in concat. query */
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        queries->QueryStarts = starts;
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        queries->QueryEnds = ends;