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/* $Id: blast_filter.h,v 1.23 2004/09/13 12:40:35 madden Exp $
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* ===========================================================================
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* National Center for Biotechnology Information
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* This software/database is a "United States Government Work" under the
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* terms of the United States Copyright Act. It was written as part of
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* the author's official duties as a United States Government employee and
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* thus cannot be copyrighted. This software/database is freely available
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* to the public for use. The National Library of Medicine and the U.S.
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* Government have not placed any restriction on its use or reproduction.
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* Although all reasonable efforts have been taken to ensure the accuracy
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* and reliability of the software and data, the NLM and the U.S.
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* Government do not and cannot warrant the performance or results that
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* may be obtained by using this software or data. The NLM and the U.S.
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* Government disclaim all warranties, express or implied, including
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* warranties of performance, merchantability or fitness for any particular
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* Please cite the author in any work or product based on this material.
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* ===========================================================================
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* Author: Ilya Dondoshansky
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/** @file blast_filter.h
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* BLAST filtering functions. @todo FIXME: contains more than filtering
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* functions, combine with blast_dust.h?
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#ifndef __BLAST_FILTER__
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#define __BLAST_FILTER__
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#include <algo/blast/core/blast_def.h>
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#include <algo/blast/core/blast_message.h>
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/** Create and initialize a new sequence interval.
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* @param head existing BlastSeqLoc to add onto, if *head
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* is NULL then it will be set to new BlastSeqLoc, may be NULL [in|out]
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* @param from Start of the interval [in]
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* @param to End of the interval [in]
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* @return Pointer to the allocated BlastSeqLoc structure.
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BlastSeqLoc* BlastSeqLocNew(BlastSeqLoc** head, Int4 from, Int4 to);
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/** Deallocate all BlastSeqLoc objects in a chain.
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* @param loc object to be freed [in]
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* @return NULL pointer returned.
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BlastSeqLoc* BlastSeqLocFree(BlastSeqLoc* loc);
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/** Deallocate memory for a BlastMaskLoc structure
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* as well as the BlastSeqLoc's pointed to.
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* @param mask_loc the object to be deleted [in]
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* @return NULL pointer
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BlastMaskLoc* BlastMaskLocFree(BlastMaskLoc* mask_loc);
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/** Allocate memory for a BlastMaskLoc, also allocates array for BlastSeqLoc* of length total.
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* @param total which context (i.e., strand) [in]
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* @return Pointer to the allocated BlastMaskLoc structure.
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BlastMaskLoc* BlastMaskLocNew(Int4 total);
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/** Go through all mask locations in one sequence,
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* combine any that overlap. Deallocate the memory for the locations that
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* were on the list, produce a new (merged) list of locations.
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* @param mask_loc The list of masks to be merged [in]
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* @param mask_loc_out The new (merged) list of masks. [out]
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* @param link_value Largest gap size between locations fow which they
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* should be linked together [in]
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CombineMaskLocations(BlastSeqLoc* mask_loc, BlastSeqLoc* *mask_loc_out,
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/** This function takes the list of mask locations (i.e., regions that
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* should not be searched or not added to lookup table) and makes up a set
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* of SSeqRange*'s in the concatenated sequence built from a set of queries,
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* that should be searched (that is, takes the complement).
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* If all sequences in the query set are completely filtered, then an
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* SSeqRange is created and both of its elements (left and right) are set to
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* -1 to indicate this.
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* If any of the mask_loc's is NULL, an SSeqRange for the full span of the
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* respective query sequence is created.
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* @param program_number Type of BLAST program [in]
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* @param query_info The query information structure [in]
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* @param mask_loc All mask locations [in]
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* @param complement_mask Linked list of SSeqRange*s in the concatenated
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* sequence to be indexed in the lookup table . [out]
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BLAST_ComplementMaskLocations(EBlastProgramType program_number,
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BlastQueryInfo* query_info, BlastMaskLoc* mask_loc,
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BlastSeqLoc* *complement_mask);
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/** Runs filtering functions, according to the string "instructions", on the
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* SeqLocPtr. Should combine all SeqLocs so they are non-redundant.
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* @param program_number Type of BLAST program [in]
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* @param sequence The sequence or part of the sequence to be filtered [in]
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* @param length Length of the (sub)sequence [in]
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* @param offset Offset into the full sequence [in]
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* @param instructions String of instructions to filtering functions. [in]
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* @param mask_at_hash If TRUE masking is done while making the lookup table
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* @param seqloc_retval Resulting locations for filtered region. [out]
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BlastSetUp_Filter(EBlastProgramType program_number,
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const char* instructions,
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Boolean *mask_at_hash,
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BlastSeqLoc* *seqloc_retval);
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/** Does preparation for filtering and then calls BlastSetUp_Filter
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* @param query_blk sequence to be filtered [in]
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* @param query_info info on sequence to be filtered [in]
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* @param program_number one of blastn,blastp,blastx,etc. [in]
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* @param filter_string instructions for filtering [in]
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* @param filter_out resulting locations for filtered region. [out]
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* @param mask_at_hash If TRUE masking is done while making the lookup table
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* @param blast_message message that needs to be sent back to user.
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BlastSetUp_GetFilteringLocations(BLAST_SequenceBlk* query_blk, BlastQueryInfo* query_info,
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EBlastProgramType program_number, const char* filter_string, BlastMaskLoc** filter_out, Boolean* mask_at_hash,
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Blast_Message* *blast_message);
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/** Masks the letters in buffer.
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* This is a low-level routine and takes a raw buffer which it assumes
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* to be in ncbistdaa (protein) or blastna (nucleotide).
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* @param buffer the sequence to be masked (will be modified). [out]
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* @param length length of the sequence to be masked . [in]
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* @param is_na nucleotide if TRUE [in]
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* @param mask_loc the BlastSeqLoc to use for masking [in]
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* @param reverse minus strand if TRUE [in]
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* @param offset how far along sequence is 1st residuse in buffer [in]
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Blast_MaskTheResidues(Uint1 * buffer, Int4 length, Boolean is_na,
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BlastSeqLoc* mask_loc, Boolean reverse, Int4 offset);
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/** Masks the sequence given a BlastMaskLoc
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* @param query_blk sequence to be filtered [in]
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* @param query_info info on sequence to be filtered [in]
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* @param filter_maskloc Locations to filter [in]
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* @param program_number one of blastn,blastp,blastx,etc. [in]
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BlastSetUp_MaskQuery(BLAST_SequenceBlk* query_blk, BlastQueryInfo* query_info,
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BlastMaskLoc *filter_maskloc, EBlastProgramType program_number);
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#endif /* !__BLAST_FILTER__ */
added
removed
algo/blast/core/blast_filter.h
