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#ifndef DYNAMITEdnamatcherHEADERFILE
#define DYNAMITEdnamatcherHEADERFILE
#ifdef _cplusplus
extern "C" {
#endif
#include "dnaalign.h"
#include "hitlist.h"
struct Wise2_DnaMatchPara {
int dynamite_hard_link;
#ifdef PTHREAD
pthread_mutex_t dynamite_mutex;
#endif
DPRunImpl * dpri;
DnaMatrix * mat;
DnaStartEnd * dse;
int gap;
int ext;
} ;
/* DnaMatchPara defined */
#ifndef DYNAMITE_DEFINED_DnaMatchPara
typedef struct Wise2_DnaMatchPara Wise2_DnaMatchPara;
#define DnaMatchPara Wise2_DnaMatchPara
#define DYNAMITE_DEFINED_DnaMatchPara
#endif
/***************************************************/
/* Callable functions */
/* These are the functions you are expected to use */
/***************************************************/
/* Function: hard_link_DnaMatchPara(obj)
*
* Descrip: Bumps up the reference count of the object
* Meaning that multiple pointers can 'own' it
*
*
* Arg: obj [UNKN ] Object to be hard linked [DnaMatchPara *]
*
* Return [UNKN ] Undocumented return value [DnaMatchPara *]
*
*/
DnaMatchPara * Wise2_hard_link_DnaMatchPara(DnaMatchPara * obj);
#define hard_link_DnaMatchPara Wise2_hard_link_DnaMatchPara
/* Function: DnaMatchPara_alloc(void)
*
* Descrip: Allocates structure: assigns defaults if given
*
*
*
* Return [UNKN ] Undocumented return value [DnaMatchPara *]
*
*/
DnaMatchPara * Wise2_DnaMatchPara_alloc(void);
#define DnaMatchPara_alloc Wise2_DnaMatchPara_alloc
/* Function: free_DnaMatchPara(obj)
*
* Descrip: Free Function: removes the memory held by obj
* Will chain up to owned members and clear all lists
*
*
* Arg: obj [UNKN ] Object that is free'd [DnaMatchPara *]
*
* Return [UNKN ] Undocumented return value [DnaMatchPara *]
*
*/
DnaMatchPara * Wise2_free_DnaMatchPara(DnaMatchPara * obj);
#define free_DnaMatchPara Wise2_free_DnaMatchPara
/* Unplaced functions */
/* There has been no indication of the use of these functions */
void Wise2_show_help_DnaMatchPara(FILE * ofp);
#define show_help_DnaMatchPara Wise2_show_help_DnaMatchPara
DnaMatchPara * Wise2_new_DnaMatchPara_from_argv(int * argc,char ** argv);
#define new_DnaMatchPara_from_argv Wise2_new_DnaMatchPara_from_argv
HitList * Wise2_HitList_from_Sequence_SequenceSet_DNA(Sequence * query,SequenceSet * set,DnaMatchPara * p);
#define HitList_from_Sequence_SequenceSet_DNA Wise2_HitList_from_Sequence_SequenceSet_DNA
/***************************************************/
/* Internal functions */
/* you are not expected to have to call these */
/***************************************************/
#ifdef _cplusplus
}
#endif
#endif
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