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/* $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.
*
* ===========================================================================*/
/*****************************************************************************
File name: gapinfo.h
Author: Ilya Dondoshansky
Contents: Structures definitions from gapxdrop.h in ncbitools
******************************************************************************
* $Revision: 1.5 $
* */
#ifndef __GAPINFO__
#define __GAPINFO__
#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)
typedef struct GapEditScript {
Uint1 op_type; /* GAPALIGN_SUB, GAPALIGN_INS, or GAPALIGN_DEL */
Int4 num; /* Number of operations */
struct GapEditScript* next;
} GapEditScript;
typedef struct GapEditBlock {
Int4 start1, start2, /* starts of alignments. */
length1, length2, /* total lengths of the sequences. */
original_length1, /* Untranslated lengths of the sequences. */
original_length2;
Int2 frame1, frame2; /* frames of the sequences. */
Boolean translate1, translate2; /* are either of these be translated. */
Boolean reverse; /* reverse sequence 1 and 2 when producing SeqALign? */
Boolean is_ooframe; /* Is this out_of_frame edit block? */
Boolean discontinuous; /* Is this OK to produce discontinuous SeqAlign? */
GapEditScript* esp;
} GapEditBlock;
/*
Structure to keep memory for state structure.
*/
typedef struct GapStateArrayStruct {
Int4 length, /* length of the state_array. */
used; /* how much of length is used. */
Uint1* state_array; /* array to be used. */
struct GapStateArrayStruct* next;
} GapStateArrayStruct;
GapEditScript*
GapEditScriptNew (GapEditScript* old);
GapEditScript* GapEditScriptDelete (GapEditScript* esp);
GapEditBlock* GapEditBlockNew (Int4 start1, Int4 start2);
GapEditBlock* GapEditBlockDelete (GapEditBlock* edit_block);
GapStateArrayStruct*
GapStateFree(GapStateArrayStruct* state_struct);
#ifdef __cplusplus
}
#endif
#endif /* !__GAPINFO__ */
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