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/* $Id: gapinfo.h,v 1.20 2005/04/27 19:49:49 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 gapinfo.h
* Definitions of structures used for saving traceback information.
*/
#ifndef __GAPINFO__
#define __GAPINFO__
#include <algo/blast/core/blast_def.h>
#ifdef __cplusplus
extern "C" {
#endif
/** 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 */
eGapAlignInvalid = 8 /**< Invalid operation */
} EGapAlignOpType;
/** Edit script: linked list of correspondencies between two sequences */
typedef struct GapEditScript {
EGapAlignOpType op_type; /**< Type of operation */
Int4 num; /**< Number of operations */
struct GapEditScript* next; /**< Pointer to next link */
} GapEditScript;
/** A version of GapEditScript used to store initial results
from the gapped alignment routines */
typedef struct GapPrelimEditScript {
EGapAlignOpType op_type; /**< Type of operation */
Int4 num; /**< Number of operations */
} GapPrelimEditScript;
/** Preliminary version of GapEditBlock, used directly by the low-
* level dynamic programming routines
*/
typedef struct GapPrelimEditBlock {
GapPrelimEditScript *edit_ops; /**< array of edit operations */
Int4 num_ops_allocated; /**< size of allocated array */
Int4 num_ops; /**< number of edit ops presently in use */
EGapAlignOpType last_op; /**< most recent operation added */
} GapPrelimEditBlock;
/** 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; /**< Next link in the list. */
} GapStateArrayStruct;
/** Initialize the edit script structure.
* @param old Pointer to existing edit script to which
* the new script will be appended
* @return Pointer to the new edit script
*/
GapEditScript*
GapEditScriptNew (GapEditScript* old);
/** Free all links of an edit script structure.
* @param esp Pointer to first link in the edit script [in]
* @return Always NULL
*/
GapEditScript*
GapEditScriptDelete (GapEditScript* esp);
/** Frees a preliminary edit block structure
* @param edit_block The edit block to free [in]
* @return Always NULL
*/
GapPrelimEditBlock *
GapPrelimEditBlockFree(GapPrelimEditBlock *edit_block);
/** Allocates a preliminary edit block structure
* @return Pointer to the allocated preliminary edit block
*/
GapPrelimEditBlock *
GapPrelimEditBlockNew(void);
/** Add a new operation to a preliminary edit block, possibly combining
* it with the last operation if the two operations are identical
*
* @param edit_block The script to update [in/modified]
* @param op_type The operation type to add [in]
* @param num_ops The number of the specified type of operation to add [in]
*/
void
GapPrelimEditBlockAdd(GapPrelimEditBlock *edit_block,
EGapAlignOpType op_type, Int4 num_ops);
/** Append one GapPrelimEditBlock to the end of the other.
* @param edit_block1 First traceback block [in]
* @param edit_block2 Second traceback block, to be appended at the end of
* the first.
*/
void
GapPrelimEditBlockAppend(GapPrelimEditBlock *edit_block1,
GapPrelimEditBlock *edit_block2);
/** Reset a preliminary edit block without freeing it
* @param edit_block The preliminary edit block to reset
*/
void
GapPrelimEditBlockReset(GapPrelimEditBlock *edit_block);
/** Free the gap state structure.
* @param state_struct The state structure to free
* @return Always NULL
*/
GapStateArrayStruct*
GapStateFree(GapStateArrayStruct* state_struct);
#ifdef __cplusplus
}
#endif
#endif /* !__GAPINFO__ */
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