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Viewing changes to algo/blast/api/blast_tabular.c

  • Committer: Bazaar Package Importer
  • Author(s): Barry deFreese
  • Date: 2006-07-19 23:28:07 UTC
  • mfrom: (1.1.5 upstream)
  • Revision ID: james.westby@ubuntu.com-20060719232807-et3cdmcjgmnyleyx
Tags: 6.1.20060507-3ubuntu1
Re-merge with Debian

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algo/blast/api/blast_tabular.c
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/* $Id: blast_tabular.c,v 1.30 2005/11/22 13:30:34 madden Exp $
 
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/* $Id: blast_tabular.c,v 1.32 2006/04/25 17:59:02 papadopo Exp $
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* ===========================================================================
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*
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*                            PUBLIC DOMAIN NOTICE
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 * On-the-fly tabular formatting of BLAST results
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 */
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static char const rcsid[] = "$Id: blast_tabular.c,v 1.30 2005/11/22 13:30:34 madden Exp $";
 
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static char const rcsid[] = "$Id: blast_tabular.c,v 1.32 2006/04/25 17:59:02 papadopo Exp $";
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#include <algo/blast/api/blast_tabular.h>
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#include <algo/blast/core/blast_util.h>
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BlastTabularFormatData*
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BlastTabularFormatDataNew(FILE* outfp, SeqLoc* query_seqloc,
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                          EBlastTabularFormatOptions format_option)
 
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                          EBlastTabularFormatOptions format_option,
 
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                          Boolean believe_query)
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{
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   BlastTabularFormatData* tf_data = 
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      (BlastTabularFormatData*) calloc(1, sizeof(BlastTabularFormatData));
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   tf_data->outfp = outfp;
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   tf_data->query_slp = query_seqloc;
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   tf_data->format_options = format_option;
 
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   tf_data->believe_query = believe_query;
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   return tf_data;
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}
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   Int4* starts;
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   Int4* lengths;
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   Int4 offset;
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   GapEditScript* esp;
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   Int4 start1, start2;
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   char* buffer;
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   Boolean reverse;
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   reverse = (hsp->query.frame != hsp->subject.frame);
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   /* Calculate number of segments. */
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   esp = hsp->gap_info;
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   for (numseg = 0; esp; esp = esp->next, ++numseg);
 
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   numseg = hsp->gap_info->size;
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   /* Find the starts and lengths of each segment. */
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   start1 = hsp->query.offset;
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   start2 = hsp->subject.offset;
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   GapCollectDataForSeqalign(hsp, hsp->gap_info, numseg, query_length,
 
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   GapCollectDataForSeqalign(hsp, hsp->gap_info, 0, numseg, query_length,
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                             subject_length, translate1, translate2,
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                             &starts, &lengths, NULL, &start1, &start2);
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            description. */
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         if (tf_data->show_gi || tf_data->show_accession) {
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            Blast_SeqIdGetDefLine(subject_id, &subject_buffer, 
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                                  tf_data->show_gi, tf_data->show_accession); 
 
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                                  tf_data->show_gi, tf_data->show_accession,
 
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                                  TRUE); 
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         } else {
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            if ( !(subject_buffer = (char*) malloc(sizeof(char)*SEQIDLEN_MAX)))
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               return NULL;
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         query_index = 
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            Blast_GetQueryIndexFromContext(hsp->context, program);
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         Blast_SeqIdGetDefLine(query_id_array[query_index], &query_buffer, 
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                               tf_data->show_gi, tf_data->show_accession);
 
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                               tf_data->show_gi, tf_data->show_accession,
 
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                               tf_data->believe_query);
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         eval_buff_ptr = eval_buff;
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         ScoreAndEvalueToBuffers(hsp->bit_score, hsp->evalue,