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/* $Id: blast_input.h,v 1.10 2003/12/03 17:30:25 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 official 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_input.h
Author: Ilya Dondoshansky
Contents: Reading FASTA sequences for BLAST
$Revision: 1.10 $
******************************************************************************/
#ifndef __BLAST_INPUT__
#define __BLAST_INPUT__
#ifdef __cplusplus
extern "C" {
#endif
#ifndef NCBI_C_TOOLKIT
#define NCBI_C_TOOLKIT
#endif
#include <ncbi.h>
#include <algo/blast/core/blast_def.h>
/** Read the query sequences from a file, return a SeqLoc list.
* @param infp The input file [in]
* @param query_is_na Are sequences nucleotide (or protein)? [in]
* @param strand Which strands should SeqLocs contain (0 for protein,
* 1 for plus, 2 for minus, 3 for both)? [in]
* @param from Starting offset in query location [in]
* @param to Ending offset in query location (-1 for end of sequence) [in]
* @param lcase_mask The lower case masking locations (no lower case masking
* if NULL [out]
* @param query_slp List of query SeqLocs [out]
* @param ctr_start Number from which to start counting local ids [in]
* @param num_queries Number of sequences read [out]
* @return Have all sequences been read?
*/
Boolean
BLAST_GetQuerySeqLoc(FILE *infp, Boolean query_is_na, Uint1 strand,
Int4 from, Int4 to, BlastMaskLoc** lcase_mask, SeqLocPtr* query_slp, Int4 ctr_start,
Int4* num_queries);
/** Given a file containing sequence(s) in fasta format,
* read a sequence and fill out a BLAST_SequenceBlk structure.
*
* @param fasta_fp the file to read from, assumed to already be open
* @param seq pointer to the sequence block to fill out
* @return Zero if successful, one on any error.
*/
Int4 MakeBlastSequenceBlkFromFasta(FILE *fasta_fp, BLAST_SequenceBlk* seq);
#ifdef __cplusplus
}
#endif
#endif /* !__BLAST_INPUT__ */
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