diff options
Diffstat (limited to 'algo/blast/core/gapinfo.h')
| -rw-r--r-- | algo/blast/core/gapinfo.h | 92 |
1 files changed, 49 insertions, 43 deletions
diff --git a/algo/blast/core/gapinfo.h b/algo/blast/core/gapinfo.h index 3e241ea8..f985c0e2 100644 --- a/algo/blast/core/gapinfo.h +++ b/algo/blast/core/gapinfo.h @@ -1,57 +1,63 @@ -/* $Id: gapinfo.h,v 1.5 2003/08/11 14:57:16 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. -* -* ===========================================================================*/ +/* $Id: gapinfo.h,v 1.12 2004/06/16 14:53:03 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. + * + * =========================================================================== + * + * Author: Ilya Dondoshansky + * + */ -/***************************************************************************** - -File name: gapinfo.h - -Author: Ilya Dondoshansky - -Contents: Structures definitions from gapxdrop.h in ncbitools - -****************************************************************************** - * $Revision: 1.5 $ - * */ +/** @file gapinfo.h + * Structures definitions from gapxdrop.h in ncbitools + * @todo FIXME: doxygen comments + */ #ifndef __GAPINFO__ #define __GAPINFO__ +#include <algo/blast/core/blast_def.h> + #ifdef __cplusplus extern "C" { #endif -#include <algo/blast/core/blast_def.h> -#define GAPALIGN_SUB ((Uint1)0) /*op types within the edit script*/ -#define GAPALIGN_INS ((Uint1)1) -#define GAPALIGN_DEL ((Uint1)2) -#define GAPALIGN_DECLINE ((Uint1)3) +/** Operation types within the edit script*/ +typedef enum EGapAlignOpType { + eGapAlignDel = 0, /**< Deletion: a gap in query */ + eGapAlignDel2 = 1,/**< Frame shift deletion of two nucleotides */ + eGapAlignDel1 = 2,/**< Frame shift deletion of one nucleotide */ + eGapAlignSub = 3, /**< Substitution */ + eGapAlignIns1 = 4,/**< Frame shift insertion of one nucleotide */ + eGapAlignIns2 = 5,/**< Frame shift insertion of two nucleotides */ + eGapAlignIns = 6, /**< Insertion: a gap in subject */ + eGapAlignDecline = 7 /**< Non-aligned region */ +} EGapAlignOpType; +/** Edit script: linked list of correspondencies between two sequences */ typedef struct GapEditScript { - Uint1 op_type; /* GAPALIGN_SUB, GAPALIGN_INS, or GAPALIGN_DEL */ - Int4 num; /* Number of operations */ - struct GapEditScript* next; + EGapAlignOpType op_type; /**< Type of operation */ + Int4 num; /**< Number of operations */ + struct GapEditScript* next; /**< Pointer to next link */ } GapEditScript; typedef struct GapEditBlock { |