File: motifmatrixdp.h

package info (click to toggle)
wise 2.4.1-21
  • links: PTS, VCS
  • area: main
  • in suites: buster
  • size: 27,140 kB
  • sloc: ansic: 276,365; makefile: 1,003; perl: 886; lex: 93; yacc: 81; sh: 24
file content (437 lines) | stat: -rw-r--r-- 20,552 bytes parent folder | download | duplicates (8)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
#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