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/* $Id: blast_filter.h,v 1.17 2004/04/29 15:09:27 madden 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_filter.h
Author: Ilya Dondoshansky
Contents: BLAST filtering functions.
Detailed Contents:
******************************************************************************
* $Revision: 1.17 $
* */
#ifndef __BLAST_FILTER__
#define __BLAST_FILTER__
#ifdef __cplusplus
extern "C" {
#endif
#include <algo/blast/core/blast_def.h>
#include <algo/blast/core/blast_message.h>
/** Create and initialize a new sequence interval.
* @param from Start of the interval [in]
* @param to End of the interval [in]
* @return Pointer to the allocated BlastSeqLoc structure.
*/
BlastSeqLoc* BlastSeqLocNew(Int4 from, Int4 to);
/** Deallocate a BlastSeqLoc structure */
BlastSeqLoc* BlastSeqLocFree(BlastSeqLoc* loc);
/** Deallocate memory for a list of BlastMaskLoc structures */
BlastMaskLoc* BlastMaskLocFree(BlastMaskLoc* mask_loc);
/** Allocate memory for a BlastMaskLoc.
* @param index which context (i.e., strand) [in]
* @param loc_list List of locations on that strand [in]
* @return Pointer to the allocated BlastMaskLoc structure.
*/
BlastMaskLoc* BlastMaskLocNew(Int4 index, BlastSeqLoc *loc_list);
/** Go through all mask locations in one sequence,
* combine any that overlap. Deallocate the memory for the locations that
* were on the list, produce a new (merged) list of locations.
* @param mask_loc The list of masks to be merged [in]
* @param mask_loc_out The new (merged) list of masks. [out]
* @param link_value Largest gap size between locations fow which they
* should be linked together [in]
*/
Int2
CombineMaskLocations(BlastSeqLoc* mask_loc, BlastSeqLoc* *mask_loc_out,
Int4 link_value);
/** This function takes the list of mask locations (i.e., regions that
* should not be searched or not added to lookup table) and makes up a set
* of SSeqRange*'s that should be searched (that is, takes the
* complement). If the entire sequence is filtered, then a SSeqRange is
* created and both of its elements (left and right) are set to -1 to indicate
* this.
* If any of the mask_loc's is NULL, a SSeqRange for full span of the
* respective query sequence is created.
* @param program_number Type of BLAST program [in]
* @param query_info The query information structure [in]
* @param mask_loc All mask locations [in]
* @param complement_mask Linked list of SSeqRange*s with offsets. [out]
*/
Int2
BLAST_ComplementMaskLocations(Uint1 program_number,
BlastQueryInfo* query_info, BlastMaskLoc* mask_loc,
BlastSeqLoc* *complement_mask);
/** Runs filtering functions, according to the string "instructions", on the
* SeqLocPtr. Should combine all SeqLocs so they are non-redundant.
* @param program_number Type of BLAST program [in]
* @param sequence The sequence or part of the sequence to be filtered [in]
* @param length Length of the (sub)sequence [in]
* @param offset Offset into the full sequence [in]
* @param instructions String of instructions to filtering functions. [in]
* @param mask_at_hash If TRUE masking is done while making the lookup table
* only. [out]
* @param seqloc_retval Resulting locations for filtered region. [out]
*/
Int2
BlastSetUp_Filter(Uint1 program_number, Uint1* sequence, Int4 length,
Int4 offset, const char* instructions, Boolean *mask_at_hash, BlastSeqLoc* *seqloc_retval);
/** Does preparation for filtering and then calls BlastSetUp_Filter
* @param query_blk sequence to be filtered [in]
* @param query_info info on sequence to be filtered [in]
* @param program_number one of blastn,blastp,blastx,etc. [in]
* @param filter_string instructions for filtering [in]
* @param filter_out Resulting locations for filtered region. [out]
* @param mask_at_hash If TRUE masking is done while making the lookup table
* only. [out]
* @param blast_message message that needs to be sent back to user.
*/
Int2
BlastSetUp_GetFilteringLocations(BLAST_SequenceBlk* query_blk, BlastQueryInfo* query_info,
Uint1 program_number, const char* filter_string, BlastMaskLoc* *filter_out, Boolean* mask_at_hash,
Blast_Message* *blast_message);
/** Masks the letters in buffer.
* This is a low-level routine and takes a raw buffer which it assumes
* to be in ncbistdaa (protein) or blastna (nucleotide).
* @param buffer the sequence to be masked (will be modified). [out]
* @param length length of the sequence to be masked . [in]
* @param is_na nucleotide if TRUE [in]
* @param mask_loc the SeqLoc to use for masking [in]
* @param reverse minus strand if TRUE [in]
* @param offset how far along sequence is 1st residuse in buffer [in]
*
*/
Int2
Blast_MaskTheResidues(Uint1 * buffer, Int4 length, Boolean is_na,
ListNode * mask_loc, Boolean reverse, Int4 offset);
/** Masks the sequence given a BlastMaskLoc
* @param query_blk sequence to be filtered [in]
* @param query_info info on sequence to be filtered [in]
* @param filter_maskloc Locations to filter [in]
* @param program_number one of blastn,blastp,blastx,etc. [in]
*/
Int2
BlastSetUp_MaskQuery(BLAST_SequenceBlk* query_blk, BlastQueryInfo* query_info,
BlastMaskLoc *filter_maskloc, Uint1 program_number);
#ifdef __cplusplus
}
#endif
#endif /* !__BLAST_FILTER__ */
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