1 #ifndef DYNAMITEcdnawise10HEADERFILE
2 #define DYNAMITEcdnawise10HEADERFILE
3 #ifdef _cplusplus
4 extern "C" {
5 #endif
6 #include "dyna.h"
7 #include "geneparser4.h"
8 
9 
10 struct Wise2_CdnaWise10 {
11     int dynamite_hard_link;
12 #ifdef PTHREAD
13     pthread_mutex_t dynamite_mutex;
14 #endif
15     BaseMatrix * basematrix;
16     ShatterMatrix * shatter;
17     int leni;
18     int lenj;
19     ComplexSequence* query;
20     ComplexSequence* target;
21     GeneParser4Score * gp;
22     CodonMatrixScore * sc;
23     RandomCodonScore * rndcodon;
24     DnaMatrix* utr;
25     Score gap_open;
26     Score gap_ext;
27     Score utr_gap;
28     Score intron_gap;
29     } ;
30 /* CdnaWise10 defined */
31 #ifndef DYNAMITE_DEFINED_CdnaWise10
32 typedef struct Wise2_CdnaWise10 Wise2_CdnaWise10;
33 #define CdnaWise10 Wise2_CdnaWise10
34 #define DYNAMITE_DEFINED_CdnaWise10
35 #endif
36 
37 
38 #ifdef PTHREAD
39 struct thread_pool_holder_CdnaWise10 {
40     ComplexSequence* query; /* Query object placeholder */
41     cDNADB* querydb;/* Query database object */
42     boolean query_init;
43     ComplexSequence* target;/* Target object placeholder */
44     GenomicDB* targetdb;/* Target database object */
45     boolean target_init;
46     GeneParser4Score * gp;
47     CodonMatrixScore * sc;
48     RandomCodonScore * rndcodon;
49     DnaMatrix* utr;
50     Score gap_open;
51     Score gap_ext;
52     Score utr_gap;
53     Score intron_gap;
54     pthread_mutex_t input_lock;
55     pthread_mutex_t output_lock;
56     Hscore * out;
57     pthread_t * pool;
58     int number_of_threads;
59     boolean search_has_ended;
60     DBSearchImpl * dbsi;
61     } ;
62 #endif /* PTHREAD */
63 struct Wise2_CdnaWise10_access_func_holder {
64     int dynamite_hard_link;
65 #ifdef PTHREAD
66     pthread_mutex_t dynamite_mutex;
67 #endif
68     int (*access_main)(CdnaWise10*,int,int,int);
69     int (*access_special)(CdnaWise10*,int,int,int);
70     } ;
71 /* CdnaWise10_access_func_holder defined */
72 #ifndef DYNAMITE_DEFINED_CdnaWise10_access_func_holder
73 typedef struct Wise2_CdnaWise10_access_func_holder Wise2_CdnaWise10_access_func_holder;
74 #define CdnaWise10_access_func_holder Wise2_CdnaWise10_access_func_holder
75 #define DYNAMITE_DEFINED_CdnaWise10_access_func_holder
76 #endif
77 
78 
79 
80 
81     /***************************************************/
82     /* Callable functions                              */
83     /* These are the functions you are expected to use */
84     /***************************************************/
85 
86 
87 
88 /* Function:  PackAln_read_Shatter_CdnaWise10(mat)
89  *
90  * Descrip:    Reads off PackAln from shatter matrix structure
91  *
92  *
93  * Arg:        mat [UNKN ] Undocumented argument [CdnaWise10 *]
94  *
95  * Return [UNKN ]  Undocumented return value [PackAln *]
96  *
97  */
98 PackAln * Wise2_PackAln_read_Shatter_CdnaWise10(CdnaWise10 * mat);
99 #define PackAln_read_Shatter_CdnaWise10 Wise2_PackAln_read_Shatter_CdnaWise10
100 
101 
102 /* Function:  calculate_shatter_CdnaWise10(mat,dpenv)
103  *
104  * Descrip:    This function calculates the CdnaWise10 matrix when in shatter mode
105  *
106  *
107  * Arg:          mat [UNKN ] (null) [CdnaWise10 *]
108  * Arg:        dpenv [UNKN ] Undocumented argument [DPEnvelope *]
109  *
110  * Return [UNKN ]  Undocumented return value [boolean]
111  *
112  */
113 boolean Wise2_calculate_shatter_CdnaWise10(CdnaWise10 * mat,DPEnvelope * dpenv);
114 #define calculate_shatter_CdnaWise10 Wise2_calculate_shatter_CdnaWise10
115 
116 
117 /* Function:  search_CdnaWise10(dbsi,out,querydb,targetdb,gp,sc,rndcodon,utr,gap_open,gap_ext,utr_gap,intron_gap)
118  *
119  * Descrip:    This function makes a database search of CdnaWise10
120  *             It uses the dbsi structure to choose which implementation
121  *             to use of the database searching. This way at run time you
122  *             can switch between single threaded/multi-threaded or hardware
123  *
124  *
125  * Arg:              dbsi [UNKN ] Undocumented argument [DBSearchImpl *]
126  * Arg:               out [UNKN ] Undocumented argument [Hscore *]
127  * Arg:           querydb [UNKN ] Undocumented argument [cDNADB*]
128  * Arg:          targetdb [UNKN ] Undocumented argument [GenomicDB*]
129  * Arg:                gp [UNKN ] Undocumented argument [GeneParser4Score *]
130  * Arg:                sc [UNKN ] Undocumented argument [CodonMatrixScore *]
131  * Arg:          rndcodon [UNKN ] Undocumented argument [RandomCodonScore *]
132  * Arg:               utr [UNKN ] Undocumented argument [DnaMatrix*]
133  * Arg:          gap_open [UNKN ] Undocumented argument [Score]
134  * Arg:           gap_ext [UNKN ] Undocumented argument [Score]
135  * Arg:           utr_gap [UNKN ] Undocumented argument [Score]
136  * Arg:        intron_gap [UNKN ] Undocumented argument [Score]
137  *
138  * Return [UNKN ]  Undocumented return value [Search_Return_Type]
139  *
140  */
141 Search_Return_Type Wise2_search_CdnaWise10(DBSearchImpl * dbsi,Hscore * out,cDNADB* querydb,GenomicDB* targetdb ,GeneParser4Score * gp,CodonMatrixScore * sc,RandomCodonScore * rndcodon,DnaMatrix* utr,Score gap_open,Score gap_ext,Score utr_gap,Score intron_gap);
142 #define search_CdnaWise10 Wise2_search_CdnaWise10
143 
144 
145 /* Function:  serial_search_CdnaWise10(out,querydb,targetdb,gp,sc,rndcodon,utr,gap_open,gap_ext,utr_gap,intron_gap)
146  *
147  * Descrip:    This function makes a database search of CdnaWise10
148  *             It is a single processor implementation
149  *
150  *
151  * Arg:               out [UNKN ] Undocumented argument [Hscore *]
152  * Arg:           querydb [UNKN ] Undocumented argument [cDNADB*]
153  * Arg:          targetdb [UNKN ] Undocumented argument [GenomicDB*]
154  * Arg:                gp [UNKN ] Undocumented argument [GeneParser4Score *]
155  * Arg:                sc [UNKN ] Undocumented argument [CodonMatrixScore *]
156  * Arg:          rndcodon [UNKN ] Undocumented argument [RandomCodonScore *]
157  * Arg:               utr [UNKN ] Undocumented argument [DnaMatrix*]
158  * Arg:          gap_open [UNKN ] Undocumented argument [Score]
159  * Arg:           gap_ext [UNKN ] Undocumented argument [Score]
160  * Arg:           utr_gap [UNKN ] Undocumented argument [Score]
161  * Arg:        intron_gap [UNKN ] Undocumented argument [Score]
162  *
163  * Return [UNKN ]  Undocumented return value [Search_Return_Type]
164  *
165  */
166 Search_Return_Type Wise2_serial_search_CdnaWise10(Hscore * out,cDNADB* querydb,GenomicDB* targetdb ,GeneParser4Score * gp,CodonMatrixScore * sc,RandomCodonScore * rndcodon,DnaMatrix* utr,Score gap_open,Score gap_ext,Score utr_gap,Score intron_gap);
167 #define serial_search_CdnaWise10 Wise2_serial_search_CdnaWise10
168 
169 
170 /* Function:  PackAln_bestmemory_CdnaWise10(query,target,gp,sc,rndcodon,utr,gap_open,gap_ext,utr_gap,intron_gap,dpenv,dpri)
171  *
172  * Descrip:    This function chooses the best memory set-up for the alignment
173  *             using calls to basematrix, and then implements either a large
174  *             or small memory model.
175  *
176  *             It is the best function to use if you just want an alignment
177  *
178  *             If you want a label alignment, you will need
179  *             /convert_PackAln_to_AlnBlock_CdnaWise10
180  *
181  *
182  * Arg:             query [UNKN ] query data structure [ComplexSequence*]
183  * Arg:            target [UNKN ] target data structure [ComplexSequence*]
184  * Arg:                gp [UNKN ] Resource [GeneParser4Score *]
185  * Arg:                sc [UNKN ] Resource [CodonMatrixScore *]
186  * Arg:          rndcodon [UNKN ] Resource [RandomCodonScore *]
187  * Arg:               utr [UNKN ] Resource [DnaMatrix*]
188  * Arg:          gap_open [UNKN ] Resource [Score]
189  * Arg:           gap_ext [UNKN ] Resource [Score]
190  * Arg:           utr_gap [UNKN ] Resource [Score]
191  * Arg:        intron_gap [UNKN ] Resource [Score]
192  * Arg:             dpenv [UNKN ] Undocumented argument [DPEnvelope *]
193  * Arg:              dpri [UNKN ] Undocumented argument [DPRunImpl *]
194  *
195  * Return [UNKN ]  Undocumented return value [PackAln *]
196  *
197  */
198 PackAln * Wise2_PackAln_bestmemory_CdnaWise10(ComplexSequence* query,ComplexSequence* target ,GeneParser4Score * gp,CodonMatrixScore * sc,RandomCodonScore * rndcodon,DnaMatrix* utr,Score gap_open,Score gap_ext,Score utr_gap,Score intron_gap,DPEnvelope * dpenv,DPRunImpl * dpri);
199 #define PackAln_bestmemory_CdnaWise10 Wise2_PackAln_bestmemory_CdnaWise10
200 
201 
202 /* Function:  allocate_Expl_CdnaWise10(query,target,gp,sc,rndcodon,utr,gap_open,gap_ext,utr_gap,intron_gap,dpri)
203  *
204  * Descrip:    This function allocates the CdnaWise10 structure
205  *             and the basematrix area for explicit memory implementations
206  *             It calls /allocate_CdnaWise10_only
207  *
208  *
209  * Arg:             query [UNKN ] query data structure [ComplexSequence*]
210  * Arg:            target [UNKN ] target data structure [ComplexSequence*]
211  * Arg:                gp [UNKN ] Resource [GeneParser4Score *]
212  * Arg:                sc [UNKN ] Resource [CodonMatrixScore *]
213  * Arg:          rndcodon [UNKN ] Resource [RandomCodonScore *]
214  * Arg:               utr [UNKN ] Resource [DnaMatrix*]
215  * Arg:          gap_open [UNKN ] Resource [Score]
216  * Arg:           gap_ext [UNKN ] Resource [Score]
217  * Arg:           utr_gap [UNKN ] Resource [Score]
218  * Arg:        intron_gap [UNKN ] Resource [Score]
219  * Arg:              dpri [UNKN ] Undocumented argument [DPRunImpl *]
220  *
221  * Return [UNKN ]  Undocumented return value [CdnaWise10 *]
222  *
223  */
224 CdnaWise10 * Wise2_allocate_Expl_CdnaWise10(ComplexSequence* query,ComplexSequence* target ,GeneParser4Score * gp,CodonMatrixScore * sc,RandomCodonScore * rndcodon,DnaMatrix* utr,Score gap_open,Score gap_ext,Score utr_gap,Score intron_gap,DPRunImpl * dpri);
225 #define allocate_Expl_CdnaWise10 Wise2_allocate_Expl_CdnaWise10
226 
227 
228 /* Function:  recalculate_PackAln_CdnaWise10(pal,mat)
229  *
230  * Descrip:    This function recalculates the PackAln structure produced by CdnaWise10
231  *             For example, in linear space methods this is used to score them
232  *
233  *
234  * Arg:        pal [UNKN ] Undocumented argument [PackAln *]
235  * Arg:        mat [UNKN ] Undocumented argument [CdnaWise10 *]
236  *
237  */
238 void Wise2_recalculate_PackAln_CdnaWise10(PackAln * pal,CdnaWise10 * mat);
239 #define recalculate_PackAln_CdnaWise10 Wise2_recalculate_PackAln_CdnaWise10
240 
241 
242 /* Function:  allocate_Small_CdnaWise10(query,target,gp,sc,rndcodon,utr,gap_open,gap_ext,utr_gap,intron_gap)
243  *
244  * Descrip:    This function allocates the CdnaWise10 structure
245  *             and the basematrix area for a small memory implementations
246  *             It calls /allocate_CdnaWise10_only
247  *
248  *
249  * Arg:             query [UNKN ] query data structure [ComplexSequence*]
250  * Arg:            target [UNKN ] target data structure [ComplexSequence*]
251  * Arg:                gp [UNKN ] Resource [GeneParser4Score *]
252  * Arg:                sc [UNKN ] Resource [CodonMatrixScore *]
253  * Arg:          rndcodon [UNKN ] Resource [RandomCodonScore *]
254  * Arg:               utr [UNKN ] Resource [DnaMatrix*]
255  * Arg:          gap_open [UNKN ] Resource [Score]
256  * Arg:           gap_ext [UNKN ] Resource [Score]
257  * Arg:           utr_gap [UNKN ] Resource [Score]
258  * Arg:        intron_gap [UNKN ] Resource [Score]
259  *
260  * Return [UNKN ]  Undocumented return value [CdnaWise10 *]
261  *
262  */
263 CdnaWise10 * Wise2_allocate_Small_CdnaWise10(ComplexSequence* query,ComplexSequence* target ,GeneParser4Score * gp,CodonMatrixScore * sc,RandomCodonScore * rndcodon,DnaMatrix* utr,Score gap_open,Score gap_ext,Score utr_gap,Score intron_gap);
264 #define allocate_Small_CdnaWise10 Wise2_allocate_Small_CdnaWise10
265 
266 
267 /* Function:  PackAln_calculate_Small_CdnaWise10(mat,dpenv)
268  *
269  * Descrip:    This function calculates an alignment for CdnaWise10 structure in linear space
270  *             If you want only the start/end points
271  *             use /AlnRangeSet_calculate_Small_CdnaWise10
272  *
273  *             The function basically
274  *               finds start/end points
275  *               foreach start/end point
276  *                 calls /full_dc_CdnaWise10
277  *
278  *
279  * Arg:          mat [UNKN ] Undocumented argument [CdnaWise10 *]
280  * Arg:        dpenv [UNKN ] Undocumented argument [DPEnvelope *]
281  *
282  * Return [UNKN ]  Undocumented return value [PackAln *]
283  *
284  */
285 PackAln * Wise2_PackAln_calculate_Small_CdnaWise10(CdnaWise10 * mat,DPEnvelope * dpenv);
286 #define PackAln_calculate_Small_CdnaWise10 Wise2_PackAln_calculate_Small_CdnaWise10
287 
288 
289 /* Function:  AlnRangeSet_calculate_Small_CdnaWise10(mat)
290  *
291  * Descrip:    This function calculates an alignment for CdnaWise10 structure in linear space
292  *             If you want the full alignment, use /PackAln_calculate_Small_CdnaWise10
293  *             If you have already got the full alignment, but want the range set, use /AlnRangeSet_from_PackAln_CdnaWise10
294  *             If you have got the small matrix but not the alignment, use /AlnRangeSet_from_CdnaWise10
295  *
296  *
297  * Arg:        mat [UNKN ] Undocumented argument [CdnaWise10 *]
298  *
299  * Return [UNKN ]  Undocumented return value [AlnRangeSet *]
300  *
301  */
302 AlnRangeSet * Wise2_AlnRangeSet_calculate_Small_CdnaWise10(CdnaWise10 * mat);
303 #define AlnRangeSet_calculate_Small_CdnaWise10 Wise2_AlnRangeSet_calculate_Small_CdnaWise10
304 
305 
306 /* Function:  AlnRangeSet_from_CdnaWise10(mat)
307  *
308  * Descrip:    This function reads off a start/end structure
309  *             for CdnaWise10 structure in linear space
310  *             If you want the full alignment use
311  *             /PackAln_calculate_Small_CdnaWise10
312  *             If you have not calculated the matrix use
313  *             /AlnRange_calculate_Small_CdnaWise10
314  *
315  *
316  * Arg:        mat [UNKN ] Undocumented argument [CdnaWise10 *]
317  *
318  * Return [UNKN ]  Undocumented return value [AlnRangeSet *]
319  *
320  */
321 AlnRangeSet * Wise2_AlnRangeSet_from_CdnaWise10(CdnaWise10 * mat);
322 #define AlnRangeSet_from_CdnaWise10 Wise2_AlnRangeSet_from_CdnaWise10
323 
324 
325 /* Function:  convert_PackAln_to_AlnBlock_CdnaWise10(pal)
326  *
327  * Descrip:    Converts a path alignment to a label alignment
328  *             The label alignment is probably much more useful than the path
329  *
330  *
331  * Arg:        pal [UNKN ] Undocumented argument [PackAln *]
332  *
333  * Return [UNKN ]  Undocumented return value [AlnBlock *]
334  *
335  */
336 AlnBlock * Wise2_convert_PackAln_to_AlnBlock_CdnaWise10(PackAln * pal);
337 #define convert_PackAln_to_AlnBlock_CdnaWise10 Wise2_convert_PackAln_to_AlnBlock_CdnaWise10
338 
339 
340 /* Function:  PackAln_read_Expl_CdnaWise10(mat)
341  *
342  * Descrip:    Reads off PackAln from explicit matrix structure
343  *
344  *
345  * Arg:        mat [UNKN ] Undocumented argument [CdnaWise10 *]
346  *
347  * Return [UNKN ]  Undocumented return value [PackAln *]
348  *
349  */
350 PackAln * Wise2_PackAln_read_Expl_CdnaWise10(CdnaWise10 * mat);
351 #define PackAln_read_Expl_CdnaWise10 Wise2_PackAln_read_Expl_CdnaWise10
352 
353 
354 /* Function:  PackAln_read_generic_CdnaWise10(mat,h)
355  *
356  * Descrip:    Reads off PackAln from explicit matrix structure
357  *
358  *
359  * Arg:        mat [UNKN ] Undocumented argument [CdnaWise10 *]
360  * Arg:          h [UNKN ] Undocumented argument [CdnaWise10_access_func_holder]
361  *
362  * Return [UNKN ]  Undocumented return value [PackAln *]
363  *
364  */
365 PackAln * Wise2_PackAln_read_generic_CdnaWise10(CdnaWise10 * mat,CdnaWise10_access_func_holder h);
366 #define PackAln_read_generic_CdnaWise10 Wise2_PackAln_read_generic_CdnaWise10
367 
368 
369 /* Function:  calculate_CdnaWise10(mat)
370  *
371  * Descrip:    This function calculates the CdnaWise10 matrix when in explicit mode
372  *             To allocate the matrix use /allocate_Expl_CdnaWise10
373  *
374  *
375  * Arg:        mat [UNKN ] CdnaWise10 which contains explicit basematrix memory [CdnaWise10 *]
376  *
377  * Return [UNKN ]  Undocumented return value [boolean]
378  *
379  */
380 boolean Wise2_calculate_CdnaWise10(CdnaWise10 * mat);
381 #define calculate_CdnaWise10 Wise2_calculate_CdnaWise10
382 
383 
384 /* Function:  calculate_dpenv_CdnaWise10(mat,dpenv)
385  *
386  * Descrip:    This function calculates the CdnaWise10 matrix when in explicit mode, subject to the envelope
387  *
388  *
389  * Arg:          mat [UNKN ] CdnaWise10 which contains explicit basematrix memory [CdnaWise10 *]
390  * Arg:        dpenv [UNKN ] Undocumented argument [DPEnvelope *]
391  *
392  * Return [UNKN ]  Undocumented return value [boolean]
393  *
394  */
395 boolean Wise2_calculate_dpenv_CdnaWise10(CdnaWise10 * mat,DPEnvelope * dpenv);
396 #define calculate_dpenv_CdnaWise10 Wise2_calculate_dpenv_CdnaWise10
397 
398 
399 /* Function:  CdnaWise10_alloc(void)
400  *
401  * Descrip:    Allocates structure: assigns defaults if given
402  *
403  *
404  *
405  * Return [UNKN ]  Undocumented return value [CdnaWise10 *]
406  *
407  */
408 CdnaWise10 * Wise2_CdnaWise10_alloc(void);
409 #define CdnaWise10_alloc Wise2_CdnaWise10_alloc
410 
411 
412 /* Function:  free_CdnaWise10(obj)
413  *
414  * Descrip:    Free Function: removes the memory held by obj
415  *             Will chain up to owned members and clear all lists
416  *
417  *
418  * Arg:        obj [UNKN ] Object that is free'd [CdnaWise10 *]
419  *
420  * Return [UNKN ]  Undocumented return value [CdnaWise10 *]
421  *
422  */
423 CdnaWise10 * Wise2_free_CdnaWise10(CdnaWise10 * obj);
424 #define free_CdnaWise10 Wise2_free_CdnaWise10
425 
426 
427   /* Unplaced functions */
428   /* There has been no indication of the use of these functions */
429 
430 
431     /***************************************************/
432     /* Internal functions                              */
433     /* you are not expected to have to call these      */
434     /***************************************************/
435 int Wise2_CdnaWise10_shatter_access_main(CdnaWise10 * mat,int i,int j,int state);
436 #define CdnaWise10_shatter_access_main Wise2_CdnaWise10_shatter_access_main
437 int Wise2_CdnaWise10_shatter_access_special(CdnaWise10 * mat,int i,int j,int state);
438 #define CdnaWise10_shatter_access_special Wise2_CdnaWise10_shatter_access_special
439 void * Wise2_thread_loop_CdnaWise10(void * ptr);
440 #define thread_loop_CdnaWise10 Wise2_thread_loop_CdnaWise10
441 int Wise2_score_only_CdnaWise10(ComplexSequence* query,ComplexSequence* target ,GeneParser4Score * gp,CodonMatrixScore * sc,RandomCodonScore * rndcodon,DnaMatrix* utr,Score gap_open,Score gap_ext,Score utr_gap,Score intron_gap);
442 #define score_only_CdnaWise10 Wise2_score_only_CdnaWise10
443 CdnaWise10 * Wise2_allocate_CdnaWise10_only(ComplexSequence* query,ComplexSequence* target ,GeneParser4Score * gp,CodonMatrixScore * sc,RandomCodonScore * rndcodon,DnaMatrix* utr,Score gap_open,Score gap_ext,Score utr_gap,Score intron_gap);
444 #define allocate_CdnaWise10_only Wise2_allocate_CdnaWise10_only
445 void Wise2_init_CdnaWise10(CdnaWise10 * mat);
446 #define init_CdnaWise10 Wise2_init_CdnaWise10
447 AlnRange * Wise2_AlnRange_build_CdnaWise10(CdnaWise10 * mat,int stopj,int stopspecstate,int * startj,int * startspecstate);
448 #define AlnRange_build_CdnaWise10 Wise2_AlnRange_build_CdnaWise10
449 boolean Wise2_read_hidden_CdnaWise10(CdnaWise10 * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,PackAln * out);
450 #define read_hidden_CdnaWise10 Wise2_read_hidden_CdnaWise10
451 int Wise2_max_hidden_CdnaWise10(CdnaWise10 * mat,int hiddenj,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore);
452 #define max_hidden_CdnaWise10 Wise2_max_hidden_CdnaWise10
453 boolean Wise2_read_special_strip_CdnaWise10(CdnaWise10 * mat,int stopi,int stopj,int stopstate,int * startj,int * startstate,PackAln * out);
454 #define read_special_strip_CdnaWise10 Wise2_read_special_strip_CdnaWise10
455 int Wise2_max_special_strip_CdnaWise10(CdnaWise10 * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore);
456 #define max_special_strip_CdnaWise10 Wise2_max_special_strip_CdnaWise10
457 int Wise2_max_matrix_to_special_CdnaWise10(CdnaWise10 * mat,int i,int j,int state,int cscore,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore);
458 #define max_matrix_to_special_CdnaWise10 Wise2_max_matrix_to_special_CdnaWise10
459 void Wise2_calculate_hidden_CdnaWise10(CdnaWise10 * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv);
460 #define calculate_hidden_CdnaWise10 Wise2_calculate_hidden_CdnaWise10
461 void Wise2_init_hidden_CdnaWise10(CdnaWise10 * mat,int starti,int startj,int stopi,int stopj);
462 #define init_hidden_CdnaWise10 Wise2_init_hidden_CdnaWise10
463 boolean Wise2_full_dc_CdnaWise10(CdnaWise10 * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,PackAln * out,int * donej,int totalj,DPEnvelope * dpenv);
464 #define full_dc_CdnaWise10 Wise2_full_dc_CdnaWise10
465 boolean Wise2_do_dc_single_pass_CdnaWise10(CdnaWise10 * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv,int perc_done);
466 #define do_dc_single_pass_CdnaWise10 Wise2_do_dc_single_pass_CdnaWise10
467 void Wise2_push_dc_at_merge_CdnaWise10(CdnaWise10 * mat,int starti,int stopi,int startj,int * stopj,DPEnvelope * dpenv);
468 #define push_dc_at_merge_CdnaWise10 Wise2_push_dc_at_merge_CdnaWise10
469 void Wise2_follow_on_dc_CdnaWise10(CdnaWise10 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_done);
470 #define follow_on_dc_CdnaWise10 Wise2_follow_on_dc_CdnaWise10
471 void Wise2_run_up_dc_CdnaWise10(CdnaWise10 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_done);
472 #define run_up_dc_CdnaWise10 Wise2_run_up_dc_CdnaWise10
473 void Wise2_init_dc_CdnaWise10(CdnaWise10 * mat);
474 #define init_dc_CdnaWise10 Wise2_init_dc_CdnaWise10
475 int Wise2_start_end_find_end_CdnaWise10(CdnaWise10 * mat,int * endj);
476 #define start_end_find_end_CdnaWise10 Wise2_start_end_find_end_CdnaWise10
477 boolean Wise2_dc_optimised_start_end_calc_CdnaWise10(CdnaWise10 *mat,DPEnvelope * dpenv);
478 #define dc_optimised_start_end_calc_CdnaWise10 Wise2_dc_optimised_start_end_calc_CdnaWise10
479 void Wise2_init_start_end_linear_CdnaWise10(CdnaWise10 * mat);
480 #define init_start_end_linear_CdnaWise10 Wise2_init_start_end_linear_CdnaWise10
481 AlnConvertSet * Wise2_AlnConvertSet_CdnaWise10(void);
482 #define AlnConvertSet_CdnaWise10 Wise2_AlnConvertSet_CdnaWise10
483 int Wise2_CdnaWise10_explicit_access_main(CdnaWise10 * mat,int i,int j,int state);
484 #define CdnaWise10_explicit_access_main Wise2_CdnaWise10_explicit_access_main
485 int Wise2_CdnaWise10_explicit_access_special(CdnaWise10 * mat,int i,int j,int state);
486 #define CdnaWise10_explicit_access_special Wise2_CdnaWise10_explicit_access_special
487 int Wise2_find_end_CdnaWise10(CdnaWise10 * mat,int * ri,int * rj,int * state,boolean * isspecial,CdnaWise10_access_func_holder h);
488 #define find_end_CdnaWise10 Wise2_find_end_CdnaWise10
489 void Wise2_CdnaWise10_debug_show_matrix(CdnaWise10 * mat,int starti,int stopi,int startj,int stopj,FILE * ofp);
490 #define CdnaWise10_debug_show_matrix Wise2_CdnaWise10_debug_show_matrix
491 int Wise2_max_calc_CdnaWise10(CdnaWise10 * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore,CdnaWise10_access_func_holder h);
492 #define max_calc_CdnaWise10 Wise2_max_calc_CdnaWise10
493 int Wise2_max_calc_special_CdnaWise10(CdnaWise10 * mat,int i,int j,int state,boolean isspecial,int * reti,int * retj,int * retstate,boolean * retspecial,int * cellscore,CdnaWise10_access_func_holder h);
494 #define max_calc_special_CdnaWise10 Wise2_max_calc_special_CdnaWise10
495 
496 #ifdef _cplusplus
497 }
498 #endif
499 
500 #endif
501