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+/* $Id: blast_tabular.h,v 1.2 2004/06/14 20:43:30 dondosha Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's offical duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+* ===========================================================================*/
+
+/*****************************************************************************
+
+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__ */
+