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#ifndef DYNAMITEmotifmatrixdpHEADERFILE
#define DYNAMITEmotifmatrixdpHEADERFILE
#ifdef _cplusplus
extern "C" {
#endif
#include "motifmatrix.h"
#define MOTIF_MATRIX_IN(motif,i,j,score) (motif->mat[i][j] == 0 ? 0 : (score))
struct Wise2_LocalMotifMatrix {
int dynamite_hard_link;
#ifdef PTHREAD
pthread_mutex_t dynamite_mutex;
#endif
BaseMatrix * basematrix;
ShatterMatrix * shatter;
int leni;
int lenj;
ComplexSequence* query;
ComplexSequence* target;
MotifConsMatrix* motif;
MotifMatrixScore* ms;
} ;
/* LocalMotifMatrix defined */
#ifndef DYNAMITE_DEFINED_LocalMotifMatrix
typedef struct Wise2_LocalMotifMatrix Wise2_LocalMotifMatrix;
#define LocalMotifMatrix Wise2_LocalMotifMatrix
#define DYNAMITE_DEFINED_LocalMotifMatrix
#endif
struct Wise2_LocalMotifMatrix_access_func_holder {
int dynamite_hard_link;
#ifdef PTHREAD
pthread_mutex_t dynamite_mutex;
#endif
int (*access_main)(LocalMotifMatrix*,int,int,int);
int (*access_special)(LocalMotifMatrix*,int,int,int);
} ;
/* LocalMotifMatrix_access_func_holder defined */
#ifndef DYNAMITE_DEFINED_LocalMotifMatrix_access_func_holder
typedef struct Wise2_LocalMotifMatrix_access_func_holder Wise2_LocalMotifMatrix_access_func_holder;
#define LocalMotifMatrix_access_func_holder Wise2_LocalMotifMatrix_access_func_holder
#define DYNAMITE_DEFINED_LocalMotifMatrix_access_func_holder
#endif
/***************************************************/
/* Callable functions */
/* These are the functions you are expected to use */
/***************************************************/
/* Function: PackAln_read_Shatter_LocalMotifMatrix(mat)
*
* Descrip: Reads off PackAln from shatter matrix structure
*
*
* Arg: mat [UNKN ] Undocumented argument [LocalMotifMatrix *]
*
* Return [UNKN ] Undocumented return value [PackAln *]
*
*/
PackAln * Wise2_PackAln_read_Shatter_LocalMotifMatrix(LocalMotifMatrix * mat);
#define PackAln_read_Shatter_LocalMotifMatrix Wise2_PackAln_read_Shatter_LocalMotifMatrix
/* Function: calculate_shatter_LocalMotifMatrix(mat,dpenv)
*
* Descrip: This function calculates the LocalMotifMatrix matrix when in shatter mode
*
*
* Arg: mat [UNKN ] (null) [LocalMotifMatrix *]
* Arg: dpenv [UNKN ] Undocumented argument [DPEnvelope *]
*
* Return [UNKN ] Undocumented return value [boolean]
*
*/
boolean Wise2_calculate_shatter_LocalMotifMatrix(LocalMotifMatrix * mat,DPEnvelope * dpenv);
#define calculate_shatter_LocalMotifMatrix Wise2_calculate_shatter_LocalMotifMatrix
/* Function: search_LocalMotifMatrix(dbsi,out,query,target,motif,ms)
*
* Descrip: This function makes a database search of LocalMotifMatrix
* It uses the dbsi structure to choose which implementation
* to use of the database searching. This way at run time you
* can switch between single threaded/multi-threaded or hardware
*
*
* Arg: dbsi [UNKN ] Undocumented argument [DBSearchImpl *]
* Arg: out [UNKN ] Undocumented argument [Hscore *]
* Arg: query [UNKN ] Undocumented argument [ComplexSequence*]
* Arg: target [UNKN ] Undocumented argument [ComplexSequence*]
* Arg: motif [UNKN ] Undocumented argument [MotifConsMatrix*]
* Arg: ms [UNKN ] Undocumented argument [MotifMatrixScore*]
*
* Return [UNKN ] Undocumented return value [Search_Return_Type]
*
*/
Search_Return_Type Wise2_search_LocalMotifMatrix(DBSearchImpl * dbsi,Hscore * out,ComplexSequence* query,ComplexSequence* target ,MotifConsMatrix* motif,MotifMatrixScore* ms);
#define search_LocalMotifMatrix Wise2_search_LocalMotifMatrix
/* Function: serial_search_LocalMotifMatrix(out,query,target,motif,ms)
*
* Descrip: This function makes a database search of LocalMotifMatrix
* It is a single processor implementation
*
*
* Arg: out [UNKN ] Undocumented argument [Hscore *]
* Arg: query [UNKN ] Undocumented argument [ComplexSequence*]
* Arg: target [UNKN ] Undocumented argument [ComplexSequence*]
* Arg: motif [UNKN ] Undocumented argument [MotifConsMatrix*]
* Arg: ms [UNKN ] Undocumented argument [MotifMatrixScore*]
*
* Return [UNKN ] Undocumented return value [Search_Return_Type]
*
*/
Search_Return_Type Wise2_serial_search_LocalMotifMatrix(Hscore * out,ComplexSequence* query,ComplexSequence* target ,MotifConsMatrix* motif,MotifMatrixScore* ms);
#define serial_search_LocalMotifMatrix Wise2_serial_search_LocalMotifMatrix
/* Function: PackAln_bestmemory_LocalMotifMatrix(query,target,motif,ms,dpenv,dpri)
*
* Descrip: This function chooses the best memory set-up for the alignment
* using calls to basematrix, and then implements either a large
* or small memory model.
*
* It is the best function to use if you just want an alignment
*
* If you want a label alignment, you will need
* /convert_PackAln_to_AlnBlock_LocalMotifMatrix
*
*
* Arg: query [UNKN ] query data structure [ComplexSequence*]
* Arg: target [UNKN ] target data structure [ComplexSequence*]
* Arg: motif [UNKN ] Resource [MotifConsMatrix*]
* Arg: ms [UNKN ] Resource [MotifMatrixScore*]
* Arg: dpenv [UNKN ] Undocumented argument [DPEnvelope *]
* Arg: dpri [UNKN ] Undocumented argument [DPRunImpl *]
*
* Return [UNKN ] Undocumented return value [PackAln *]
*
*/
PackAln * Wise2_PackAln_bestmemory_LocalMotifMatrix(ComplexSequence* query,ComplexSequence* target ,MotifConsMatrix* motif,MotifMatrixScore* ms,DPEnvelope * dpenv,DPRunImpl * dpri);
#define PackAln_bestmemory_LocalMotifMatrix Wise2_PackAln_bestmemory_LocalMotifMatrix
/* Function: allocate_Expl_LocalMotifMatrix(query,target,motif,ms,dpri)
*
* Descrip: This function allocates the LocalMotifMatrix structure
* and the basematrix area for explicit memory implementations
* It calls /allocate_LocalMotifMatrix_only
*
*
* Arg: query [UNKN ] query data structure [ComplexSequence*]
* Arg: target [UNKN ] target data structure [ComplexSequence*]
* Arg: motif [UNKN ] Resource [MotifConsMatrix*]
* Arg: ms [UNKN ] Resource [MotifMatrixScore*]
* Arg: dpri [UNKN ] Undocumented argument [DPRunImpl *]
*
* Return [UNKN ] Undocumented return value [LocalMotifMatrix *]
*
*/
LocalMotifMatrix * Wise2_allocate_Expl_LocalMotifMatrix(ComplexSequence* query,ComplexSequence* target ,MotifConsMatrix* motif,MotifMatrixScore* ms,DPRunImpl * dpri);
#define allocate_Expl_LocalMotifMatrix Wise2_allocate_Expl_LocalMotifMatrix
/* Function: recalculate_PackAln_LocalMotifMatrix(pal,mat)
*
* Descrip: This function recalculates the PackAln structure produced by LocalMotifMatrix
* For example, in linear space methods this is used to score them
*
*
* Arg: pal [UNKN ] Undocumented argument [PackAln *]
* Arg: mat [UNKN ] Undocumented argument [LocalMotifMatrix *]
*
*/
void Wise2_recalculate_PackAln_LocalMotifMatrix(PackAln * pal,LocalMotifMatrix * mat);
#define recalculate_PackAln_LocalMotifMatrix Wise2_recalculate_PackAln_LocalMotifMatrix
/* Function: allocate_Small_LocalMotifMatrix(query,target,motif,ms)
*
* Descrip: This function allocates the LocalMotifMatrix structure
* and the basematrix area for a small memory implementations
* It calls /allocate_LocalMotifMatrix_only
*
*
* Arg: query [UNKN ] query data structure [ComplexSequence*]
* Arg: target [UNKN ] target data structure [ComplexSequence*]
* Arg: motif [UNKN ] Resource [MotifConsMatrix*]
* Arg: ms [UNKN ] Resource [MotifMatrixScore*]
*
* Return [UNKN ] Undocumented return value [LocalMotifMatrix *]
*
*/
LocalMotifMatrix * Wise2_allocate_Small_LocalMotifMatrix(ComplexSequence* query,ComplexSequence* target ,MotifConsMatrix* motif,MotifMatrixScore* ms);
#define allocate_Small_LocalMotifMatrix Wise2_allocate_Small_LocalMotifMatrix
/* Function: PackAln_calculate_Small_LocalMotifMatrix(mat,dpenv)
*
* Descrip: This function calculates an alignment for LocalMotifMatrix structure in linear space
* If you want only the start/end points
* use /AlnRangeSet_calculate_Small_LocalMotifMatrix
*
* The function basically
* finds start/end points
* foreach start/end point
* calls /full_dc_LocalMotifMatrix
*
*
* Arg: mat [UNKN ] Undocumented argument [LocalMotifMatrix *]
* Arg: dpenv [UNKN ] Undocumented argument [DPEnvelope *]
*
* Return [UNKN ] Undocumented return value [PackAln *]
*
*/
PackAln * Wise2_PackAln_calculate_Small_LocalMotifMatrix(LocalMotifMatrix * mat,DPEnvelope * dpenv);
#define PackAln_calculate_Small_LocalMotifMatrix Wise2_PackAln_calculate_Small_LocalMotifMatrix
/* Function: AlnRangeSet_calculate_Small_LocalMotifMatrix(mat)
*
* Descrip: This function calculates an alignment for LocalMotifMatrix structure in linear space
* If you want the full alignment, use /PackAln_calculate_Small_LocalMotifMatrix
* If you have already got the full alignment, but want the range set, use /AlnRangeSet_from_PackAln_LocalMotifMatrix
* If you have got the small matrix but not the alignment, use /AlnRangeSet_from_LocalMotifMatrix
*
*
* Arg: mat [UNKN ] Undocumented argument [LocalMotifMatrix *]
*
* Return [UNKN ] Undocumented return value [AlnRangeSet *]
*
*/
AlnRangeSet * Wise2_AlnRangeSet_calculate_Small_LocalMotifMatrix(LocalMotifMatrix * mat);
#define AlnRangeSet_calculate_Small_LocalMotifMatrix Wise2_AlnRangeSet_calculate_Small_LocalMotifMatrix
/* Function: AlnRangeSet_from_LocalMotifMatrix(mat)
*
* Descrip: This function reads off a start/end structure
* for LocalMotifMatrix structure in linear space
* If you want the full alignment use
* /PackAln_calculate_Small_LocalMotifMatrix
* If you have not calculated the matrix use
* /AlnRange_calculate_Small_LocalMotifMatrix
*
*
* Arg: mat [UNKN ] Undocumented argument [LocalMotifMatrix *]
*
* Return [UNKN ] Undocumented return value [AlnRangeSet *]
*
*/
AlnRangeSet * Wise2_AlnRangeSet_from_LocalMotifMatrix(LocalMotifMatrix * mat);
#define AlnRangeSet_from_LocalMotifMatrix Wise2_AlnRangeSet_from_LocalMotifMatrix
/* Function: convert_PackAln_to_AlnBlock_LocalMotifMatrix(pal)
*
* Descrip: Converts a path alignment to a label alignment
* The label alignment is probably much more useful than the path
*
*
* Arg: pal [UNKN ] Undocumented argument [PackAln *]
*
* Return [UNKN ] Undocumented return value [AlnBlock *]
*
*/
AlnBlock * Wise2_convert_PackAln_to_AlnBlock_LocalMotifMatrix(PackAln * pal);
#define convert_PackAln_to_AlnBlock_LocalMotifMatrix Wise2_convert_PackAln_to_AlnBlock_LocalMotifMatrix
/* Function: PackAln_read_Expl_LocalMotifMatrix(mat)
*
* Descrip: Reads off PackAln from explicit matrix structure
*
*
* Arg: mat [UNKN ] Undocumented argument [LocalMotifMatrix *]
*
* Return [UNKN ] Undocumented return value [PackAln *]
*
*/
PackAln * Wise2_PackAln_read_Expl_LocalMotifMatrix(LocalMotifMatrix * mat);
#define PackAln_read_Expl_LocalMotifMatrix Wise2_PackAln_read_Expl_LocalMotifMatrix
/* Function: PackAln_read_generic_LocalMotifMatrix(mat,h)
*
* Descrip: Reads off PackAln from explicit matrix structure
*
*
* Arg: mat [UNKN ] Undocumented argument [LocalMotifMatrix *]
* Arg: h [UNKN ] Undocumented argument [LocalMotifMatrix_access_func_holder]
*
* Return [UNKN ] Undocumented return value [PackAln *]
*
*/
PackAln * Wise2_PackAln_read_generic_LocalMotifMatrix(LocalMotifMatrix * mat,LocalMotifMatrix_access_func_holder h);
#define PackAln_read_generic_LocalMotifMatrix Wise2_PackAln_read_generic_LocalMotifMatrix
/* Function: calculate_LocalMotifMatrix(mat)
*
* Descrip: This function calculates the LocalMotifMatrix matrix when in explicit mode
* To allocate the matrix use /allocate_Expl_LocalMotifMatrix
*
*
* Arg: mat [UNKN ] LocalMotifMatrix which contains explicit basematrix memory [LocalMotifMatrix *]
*
* Return [UNKN ] Undocumented return value [boolean]
*
*/
boolean Wise2_calculate_LocalMotifMatrix(LocalMotifMatrix * mat);
#define calculate_LocalMotifMatrix Wise2_calculate_LocalMotifMatrix
/* Function: calculate_dpenv_LocalMotifMatrix(mat,dpenv)
*
* Descrip: This function calculates the LocalMotifMatrix matrix when in explicit mode, subject to the envelope
*
*
* Arg: mat [UNKN ] LocalMotifMatrix which contains explicit basematrix memory [LocalMotifMatrix *]
* Arg: dpenv [UNKN ] Undocumented argument [DPEnvelope *]
*
* Return [UNKN ] Undocumented return value [boolean]
*
*/
boolean Wise2_calculate_dpenv_LocalMotifMatrix(LocalMotifMatrix * mat,DPEnvelope * dpenv);
#define calculate_dpenv_LocalMotifMatrix Wise2_calculate_dpenv_LocalMotifMatrix
/* Function: LocalMotifMatrix_alloc(void)
*
* Descrip: Allocates structure: assigns defaults if given
*
*
*
* Return [UNKN ] Undocumented return value [LocalMotifMatrix *]
*
*/
LocalMotifMatrix * Wise2_LocalMotifMatrix_alloc(void);
#define LocalMotifMatrix_alloc Wise2_LocalMotifMatrix_alloc
/* Function: free_LocalMotifMatrix(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 [LocalMotifMatrix *]
*
* Return [UNKN ] Undocumented return value [LocalMotifMatrix *]
*
*/
LocalMotifMatrix * Wise2_free_LocalMotifMatrix(LocalMotifMatrix * obj);
#define free_LocalMotifMatrix Wise2_free_LocalMotifMatrix
/* Unplaced functions */
/* There has been no indication of the use of these functions */
/***************************************************/
/* Internal functions */
/* you are not expected to have to call these */
/***************************************************/
int Wise2_LocalMotifMatrix_shatter_access_main(LocalMotifMatrix * mat,int i,int j,int state);
#define LocalMotifMatrix_shatter_access_main Wise2_LocalMotifMatrix_shatter_access_main
int Wise2_LocalMotifMatrix_shatter_access_special(LocalMotifMatrix * mat,int i,int j,int state);
#define LocalMotifMatrix_shatter_access_special Wise2_LocalMotifMatrix_shatter_access_special
int Wise2_score_only_LocalMotifMatrix(ComplexSequence* query,ComplexSequence* target ,MotifConsMatrix* motif,MotifMatrixScore* ms);
#define score_only_LocalMotifMatrix Wise2_score_only_LocalMotifMatrix
LocalMotifMatrix * Wise2_allocate_LocalMotifMatrix_only(ComplexSequence* query,ComplexSequence* target ,MotifConsMatrix* motif,MotifMatrixScore* ms);
#define allocate_LocalMotifMatrix_only Wise2_allocate_LocalMotifMatrix_only
void Wise2_init_LocalMotifMatrix(LocalMotifMatrix * mat);
#define init_LocalMotifMatrix Wise2_init_LocalMotifMatrix
AlnRange * Wise2_AlnRange_build_LocalMotifMatrix(LocalMotifMatrix * mat,int stopj,int stopspecstate,int * startj,int * startspecstate);
#define AlnRange_build_LocalMotifMatrix Wise2_AlnRange_build_LocalMotifMatrix
boolean Wise2_read_hidden_LocalMotifMatrix(LocalMotifMatrix * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,PackAln * out);
#define read_hidden_LocalMotifMatrix Wise2_read_hidden_LocalMotifMatrix
int Wise2_max_hidden_LocalMotifMatrix(LocalMotifMatrix * mat,int hiddenj,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore);
#define max_hidden_LocalMotifMatrix Wise2_max_hidden_LocalMotifMatrix
boolean Wise2_read_special_strip_LocalMotifMatrix(LocalMotifMatrix * mat,int stopi,int stopj,int stopstate,int * startj,int * startstate,PackAln * out);
#define read_special_strip_LocalMotifMatrix Wise2_read_special_strip_LocalMotifMatrix
int Wise2_max_special_strip_LocalMotifMatrix(LocalMotifMatrix * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore);
#define max_special_strip_LocalMotifMatrix Wise2_max_special_strip_LocalMotifMatrix
int Wise2_max_matrix_to_special_LocalMotifMatrix(LocalMotifMatrix * mat,int i,int j,int state,int cscore,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore);
#define max_matrix_to_special_LocalMotifMatrix Wise2_max_matrix_to_special_LocalMotifMatrix
void Wise2_calculate_hidden_LocalMotifMatrix(LocalMotifMatrix * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv);
#define calculate_hidden_LocalMotifMatrix Wise2_calculate_hidden_LocalMotifMatrix
void Wise2_init_hidden_LocalMotifMatrix(LocalMotifMatrix * mat,int starti,int startj,int stopi,int stopj);
#define init_hidden_LocalMotifMatrix Wise2_init_hidden_LocalMotifMatrix
boolean Wise2_full_dc_LocalMotifMatrix(LocalMotifMatrix * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,PackAln * out,int * donej,int totalj,DPEnvelope * dpenv);
#define full_dc_LocalMotifMatrix Wise2_full_dc_LocalMotifMatrix
boolean Wise2_do_dc_single_pass_LocalMotifMatrix(LocalMotifMatrix * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv,int perc_done);
#define do_dc_single_pass_LocalMotifMatrix Wise2_do_dc_single_pass_LocalMotifMatrix
void Wise2_push_dc_at_merge_LocalMotifMatrix(LocalMotifMatrix * mat,int starti,int stopi,int startj,int * stopj,DPEnvelope * dpenv);
#define push_dc_at_merge_LocalMotifMatrix Wise2_push_dc_at_merge_LocalMotifMatrix
void Wise2_follow_on_dc_LocalMotifMatrix(LocalMotifMatrix * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_done);
#define follow_on_dc_LocalMotifMatrix Wise2_follow_on_dc_LocalMotifMatrix
void Wise2_run_up_dc_LocalMotifMatrix(LocalMotifMatrix * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_done);
#define run_up_dc_LocalMotifMatrix Wise2_run_up_dc_LocalMotifMatrix
void Wise2_init_dc_LocalMotifMatrix(LocalMotifMatrix * mat);
#define init_dc_LocalMotifMatrix Wise2_init_dc_LocalMotifMatrix
int Wise2_start_end_find_end_LocalMotifMatrix(LocalMotifMatrix * mat,int * endj);
#define start_end_find_end_LocalMotifMatrix Wise2_start_end_find_end_LocalMotifMatrix
boolean Wise2_dc_optimised_start_end_calc_LocalMotifMatrix(LocalMotifMatrix *mat,DPEnvelope * dpenv);
#define dc_optimised_start_end_calc_LocalMotifMatrix Wise2_dc_optimised_start_end_calc_LocalMotifMatrix
void Wise2_init_start_end_linear_LocalMotifMatrix(LocalMotifMatrix * mat);
#define init_start_end_linear_LocalMotifMatrix Wise2_init_start_end_linear_LocalMotifMatrix
AlnConvertSet * Wise2_AlnConvertSet_LocalMotifMatrix(void);
#define AlnConvertSet_LocalMotifMatrix Wise2_AlnConvertSet_LocalMotifMatrix
int Wise2_LocalMotifMatrix_explicit_access_main(LocalMotifMatrix * mat,int i,int j,int state);
#define LocalMotifMatrix_explicit_access_main Wise2_LocalMotifMatrix_explicit_access_main
int Wise2_LocalMotifMatrix_explicit_access_special(LocalMotifMatrix * mat,int i,int j,int state);
#define LocalMotifMatrix_explicit_access_special Wise2_LocalMotifMatrix_explicit_access_special
int Wise2_find_end_LocalMotifMatrix(LocalMotifMatrix * mat,int * ri,int * rj,int * state,boolean * isspecial,LocalMotifMatrix_access_func_holder h);
#define find_end_LocalMotifMatrix Wise2_find_end_LocalMotifMatrix
void Wise2_LocalMotifMatrix_debug_show_matrix(LocalMotifMatrix * mat,int starti,int stopi,int startj,int stopj,FILE * ofp);
#define LocalMotifMatrix_debug_show_matrix Wise2_LocalMotifMatrix_debug_show_matrix
int Wise2_max_calc_LocalMotifMatrix(LocalMotifMatrix * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore,LocalMotifMatrix_access_func_holder h);
#define max_calc_LocalMotifMatrix Wise2_max_calc_LocalMotifMatrix
int Wise2_max_calc_special_LocalMotifMatrix(LocalMotifMatrix * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore,LocalMotifMatrix_access_func_holder h);
#define max_calc_special_LocalMotifMatrix Wise2_max_calc_special_LocalMotifMatrix
#ifdef _cplusplus
}
#endif
#endif
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