/* $Id: blast_tabular.h,v 1.2 2004/06/14 20:43:30 dondosha Exp $
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/*****************************************************************************

File name: blast_tabular.h

Author: Ilya Dondoshansky

Contents: Functions needed for formatting of BLAST results

******************************************************************************
 * $Revision: 1.2 $
 * */
#ifndef __BLAST_TABULAR__
#define __BLAST_TABULAR__

#ifdef __cplusplus
extern "C" {
#endif

#ifndef NCBI_C_TOOLKIT
#define NCBI_C_TOOLKIT
#endif

#include <ncbi.h>
#include <asn.h>
#include <algo/blast/core/blast_hits.h>
#include <algo/blast/core/lookup_wrap.h>
#include <algo/blast/core/blast_seqsrc.h>
#include <algo/blast/core/blast_hspstream.h>
#include <algo/blast/core/blast_gapalign.h>
#include <objloc.h>

/** Data structure containing all information necessary for production of the
 * tabular output.
 */
typedef struct BlastTabularFormatData {
   Uint1 program; /**< Type of BLAST program */
   BlastHSPStream* hsp_stream; /**< Source of the BLAST results */
   BlastSeqSrc* seq_src; /**< Source of the subject sequences */
   BLAST_SequenceBlk* query; /**< Query sequence */
   BlastQueryInfo* query_info; /**< Query information, including context
                                  offsets and effective lengths. */
   BlastScoringParameters* score_params;
   BlastExtensionParameters* ext_params;
   BlastHitSavingParameters* hit_params;
   BlastEffectiveLengthsParameters* eff_len_params;
   Uint1* gen_code_string;
   BlastGapAlignStruct* gap_align;
   SeqLoc* query_slp; /**< Source of query sequences identifiers */
   FILE* outfp; /**< Output stream */
   Boolean perform_traceback; /**< Must gapped extension with traceback be
                                 performed before formatting? */
} BlastTabularFormatData;

/** Function initializing the BlastTabularFormatData data structure fields. */
BlastTabularFormatData* 
Blast_TabularFormatDataInit(Uint1 program, BlastHSPStream* hsp_stream,
   BlastSeqSrc* seq_src, BLAST_SequenceBlk* query, BlastQueryInfo* query_info,
   const BlastScoringOptions* scoring_options, BlastScoreBlk* sbp,
   const BlastEffectiveLengthsOptions* eff_len_options,
   const BlastExtensionOptions* ext_options,
   const BlastHitSavingOptions* hit_options,
   const BlastDatabaseOptions* db_options, SeqLoc* query_slp, FILE* outfp);

/** Free the tabular formatting data structure and all its internally 
 * allocated substructures. 
 */
void BlastTabularFormatDataFree(BlastTabularFormatData* tf_data);

/** Driver for the thread producing tabular output. */
void* Blast_TabularFormatThread(void* data);

#ifdef __cplusplus
}
#endif
#endif /* !__BLAST_TABULAR__ */