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/* $Id: blast_format.h,v 1.22 2004/06/07 18:40:48 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_format.h
Author: Ilya Dondoshansky
Contents: Functions needed for formatting of BLAST results
******************************************************************************
* $Revision: 1.22 $
* */
#ifndef __BLAST_FORMAT__
#define __BLAST_FORMAT__
#ifdef __cplusplus
extern "C" {
#endif
#ifndef NCBI_C_TOOLKIT
#define NCBI_C_TOOLKIT
#endif
#include <ncbi.h>
#include <asn.h>
#include <bxmlobj.h>
#include <algo/blast/core/blast_options.h>
#include <algo/blast/core/blast_hits.h>
#include <algo/blast/core/blast_seqsrc.h>
#include <algo/blast/core/blast_diagnostics.h>
#include <algo/blast/api/twoseq_api.h>
/** Options for formatting BLAST results
*/
typedef struct BlastFormattingOptions {
Uint1 align_view;
Uint4 align_options;
Uint4 print_options;
Boolean believe_query;
Boolean html;
void* outfp; /**< Output file: either FILE* or AsnIoPtr */
Int4 number_of_descriptions;
Int4 number_of_alignments;
Boolean ungapped; /**< Should this be here????? */
} BlastFormattingOptions;
/** Initialize the formatting options structure.
* @param program Number of the BLAST program [in]
* @param file_out Name of the file where output is printed [in]
* @param num_descriptions Number of definition lines to report per query [in]
* @param num_alignments Number of alignments to show per query [in]
* @param align_view What kind of formatted output to show? [in]
* @param format_options_ptr The initialized structure [out]
*/
Int2 BlastFormattingOptionsNew(Uint1 program, char* file_out,
Int4 num_descriptions, Int4 num_alignments, Int4 align_view,
BlastFormattingOptions** format_options_ptr);
/** Deallocate memory for formatting options. In particular,
* close the output file.
* @param format_options Structure to free [in]
*/
BlastFormattingOptions*
BlastFormattingOptionsFree(BlastFormattingOptions* format_options);
/** Used for pruning SeqALigns that are too big. */
typedef struct BlastPruneSapStruct {
SeqAlignPtr sap;
Int4 original_number; /**< how may unique hits were there originally. */
Int4 number; /**< How many hits on SeqALignPtr above. */
Boolean allocated; /**< If FALSE, SeqAlignPtr above does NOT belong to this
struc.*/
} BlastPruneSapStruct;
typedef struct MBXml {
BlastOutputPtr boutp;
AsnIoPtr aip;
AsnTypePtr atp;
AsnTypePtr BlastOutput;
AsnTypePtr BlastOutput_iterations;
AsnTypePtr BlastOutput_mbstat;
} MBXml;
/** Print formatted output.
* @param head Results in the SeqAlign form (freed after use) [in]
* @param blast_database BLAST database name [in]
* @param blast_program BLAST program name [in]
* @param num_queries Number of query sequences [in]
* @param query_slp Linked list of query SeqLocs [in]
* @param mask_loc Masking locations for all queries (freed after use) [in]
* @param format_options Formatting options [in]
* @param is_ooframe Are frame shifts allowed in alignments? [in]
*/
Int2 BLAST_FormatResults(SeqAlignPtr head, char* blast_database,
char* blast_program, Int4 num_queries,
SeqLocPtr query_slp, BlastMaskLoc* mask_loc,
const BlastFormattingOptions* format_options, Boolean is_ooframe);
/** Print the summary at the end of the BLAST report.
* @param program_number Type of BLAST program [in]
* @param format_options Formatting options [in]
* @param score_options Scoring options [in]
* @param sbp Statistical information [in]
* @param lookup_options Lookup table options [in]
* @param word_options Word finding options and parameters [in]
* @param ext_options Extension options and parameters [in]
* @param hit_options Hit saving options [in]
* @param eff_len_options Effective lengths options, containing user-specified
* values for database length or eff. search space [in]
* @param query_info Query information [in]
* @param seq_src Source of subject sequences [in]
* @param diagnostics Data about this run [in]
*/
Int2 PrintOutputFooter(Uint1 program_number,
const BlastFormattingOptions* format_options,
const BlastScoringOptions* score_options,
const BlastScoreBlk* sbp,
const LookupTableOptions* lookup_options,
const BlastInitialWordOptions* word_options,
const BlastExtensionOptions* ext_options,
const BlastHitSavingOptions* hit_options,
const BlastEffectiveLengthsOptions* eff_len_options,
const BlastQueryInfo* query_info, const BlastSeqSrc* seq_src,
const BlastDiagnostics* diagnostics);
/** Prints the top part of the traditional BLAST output, including version,
* reference(s) and database information.
* @param format_options Formatting options [in]
* @param is_megablast Is this a megablast search (i.e. greedy gapped
* extension used)? [in]
* @param dbname BLAST database name [in]
* @param is_protein Is the database protein or nucleotide? [in]
*/
Int2 BLAST_PrintOutputHeader(const BlastFormattingOptions* format_options,
Boolean is_megablast, char* dbname, Boolean is_protein);
void BLAST_PrintIntermediateResults(BlastHSPResults* results,
BlastQueryInfo* query_info, SeqLocPtr query_slp,
BlastSeqSrc* seq_src, BlastScoreBlk* sbp,
char* filename);
void
Blast_SeqIdGetDefLine(SeqIdPtr sip, char* descr, char** buffer_ptr,
Boolean ncbi_gi, Boolean accession_only,
Boolean seqid_only, Boolean believe_local_id);
#ifdef __cplusplus
}
#endif
#endif /* !__BLAST_FORMAT__ */
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