NCBI C Toolkit Cross Reference

C/algo/blast/api/blast_seq.h

  1 /* $Id: blast_seq.h,v 1.29 2006/11/21 17:21:20 papadopo Exp $
  2 * ===========================================================================
  3 *
  4 *                            PUBLIC DOMAIN NOTICE
  5 *               National Center for Biotechnology Information
  6 *
  7 *  This software/database is a "United States Government Work" under the
  8 *  terms of the United States Copyright Act.  It was written as part of
  9 *  the author's offical duties as a United States Government employee and
 10 *  thus cannot be copyrighted.  This software/database is freely available
 11 *  to the public for use. The National Library of Medicine and the U.S.
 12 *  Government have not placed any restriction on its use or reproduction.
 13 *
 14 *  Although all reasonable efforts have been taken to ensure the accuracy
 15 *  and reliability of the software and data, the NLM and the U.S.
 16 *  Government do not and cannot warrant the performance or results that
 17 *  may be obtained by using this software or data. The NLM and the U.S.
 18 *  Government disclaim all warranties, express or implied, including
 19 *  warranties of performance, merchantability or fitness for any particular
 20 *  purpose.
 21 *
 22 *  Please cite the author in any work or product based on this material.
 23 *
 24 *  Author: Ilya Dondoshansky
 25 * ===========================================================================*/
 26 
 27 /** @file blast_seq.h
 28  * Functions converting from SeqLocs to structures used in BLAST and back.
 29  */
 30 
 31 #ifndef __BLAST_SEQ__
 32 #define __BLAST_SEQ__
 33 
 34 #ifdef __cplusplus
 35 extern "C" {
 36 #endif
 37 
 38 #ifndef NCBI_C_TOOLKIT
 39 #define NCBI_C_TOOLKIT
 40 #endif
 41 
 42 #include <objseq.h>
 43 #include <algo/blast/core/blast_def.h>
 44 #include <algo/blast/core/blast_query_info.h>
 45 #include <algo/blast/core/blast_options.h>
 46 
 47 /** @addtogroup CToolkitAlgoBlast
 48  *
 49  * @{
 50  */
 51 
 52 /** Detect duplicate IDs within a list of query sequences
 53  * @param query_seqlocs The list of query sequences [in]
 54  * @return TRUE if two or more sequences have duplicate IDs,
 55  *          FALSE if all IDs are unique
 56  */
 57 Boolean
 58 BlastSeqlocsHaveDuplicateIDs(SeqLoc* query_seqlocs);
 59 
 60 /** Convert a BlastMaskLoc list to a list of SeqLocs, used for formatting 
 61  * BLAST results.
 62  * @param program_number identifies blastn, blastp, etc. [in]
 63  * @param mask_loc internal mask structure [in]
 64  * @param query_loc SeqLoc of query [in]
 65  * @return Pointer to SeqLoc
 66  */
 67 SeqLocPtr 
 68 BlastMaskLocToSeqLoc(EBlastProgramType program_number, 
 69                      const BlastMaskLoc* mask_loc, 
 70                      SeqLoc* query_loc);
 71 /** Convert a list of mask locations in a form of SeqLoc into a BlastMaskLoc
 72  * structure. In case of multiple queries, it is not required to create a mask 
 73  * SeqLoc for every query.
 74  * @param program_number identifies blastn, blastp, etc. [in]
 75  * @param mask_locs Masking locations [in]
 76  * @param seq_locs Sequence locations [in]
 77  * @return Allocated and populated BlastMaskLoc structure.
 78  */
 79 BlastMaskLoc* 
 80 BlastMaskLocFromSeqLoc(SeqLoc* mask_locs, SeqLoc* seq_locs,
 81                        EBlastProgramType program_number);
 82 
 83 /** Frees a special type of SeqLoc list, used in BLAST for masking locations.
 84  * @param mask_loc Input list of mask SeqLocs [in]
 85  * @return NULL
 86  */
 87 SeqLoc*
 88 Blast_ValNodeMaskListFree(SeqLoc* mask_loc);
 89 
 90 /** Given a list of query SeqLoc's, create the sequence block and the query
 91  * info structure. This is the last time SeqLoc is needed before formatting.
 92  * @param query_slp List of query SeqLoc's [in]
 93  * @param query_options Query setup options, containing genetic code for
 94  *                      translation [in]
 95  * @param program_number Type of BLAST program [in]
 96  * @param masking_locs Masking locations, e.g. from lower case of repeats
 97  *                     filtering. [in]
 98  * @param query_info Query information structure, containing offsets into 
 99  *                   the concatenated sequence [out]
100  * @param query_blk Query block, containing (concatenated) sequence [out]
101  */
102 Int2 BLAST_SetUpQuery(EBlastProgramType program_number, SeqLocPtr query_slp, 
103         const QuerySetUpOptions* query_options, SeqLoc* masking_locs,
104         BlastQueryInfo** query_info, BLAST_SequenceBlk* *query_blk);
105 
106 /** Set up the subject sequence block in case of two sequences BLAST.
107  * @param program_number Type of BLAST program [in]
108  * @param subject_slp SeqLoc for the subject sequence [in]
109  * @param subject Subject sequence block [out]
110  */
111 Int2 BLAST_SetUpSubject(EBlastProgramType program_number, 
112         SeqLocPtr subject_slp, BLAST_SequenceBlk** subject);
113 
114 /** Find a genetic code string in ncbistdaa encoding, given an integer
115  *  genetic code value.
116  * @param gc genetic code value [in]
117  * @param genetic_code genetic code string [out]
118  */
119 Int2 BLAST_GeneticCodeFind(Int4 gc, Uint1** genetic_code);
120 
121 /* @} */
122 
123 #ifdef __cplusplus
124 }
125 #endif
126 
127 #endif /* !__BLAST_SEQ__ */
128
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