1 #ifndef DYNAMITEcodonmatrixHEADERFILE
2 #define DYNAMITEcodonmatrixHEADERFILE
3 #ifdef _cplusplus
4 extern "C" {
5 #endif
6 #include "dyna.h"
7 
8 
9 struct Wise2_CodonMatrix {
10     int dynamite_hard_link;
11 #ifdef PTHREAD
12     pthread_mutex_t dynamite_mutex;
13 #endif
14     Probability prob[125][125];
15     } ;
16 /* CodonMatrix defined */
17 #ifndef DYNAMITE_DEFINED_CodonMatrix
18 typedef struct Wise2_CodonMatrix Wise2_CodonMatrix;
19 #define CodonMatrix Wise2_CodonMatrix
20 #define DYNAMITE_DEFINED_CodonMatrix
21 #endif
22 
23 
24 struct Wise2_CodonMatrixScore {
25     int dynamite_hard_link;
26 #ifdef PTHREAD
27     pthread_mutex_t dynamite_mutex;
28 #endif
29     Score score[125][125];
30     } ;
31 /* CodonMatrixScore defined */
32 #ifndef DYNAMITE_DEFINED_CodonMatrixScore
33 typedef struct Wise2_CodonMatrixScore Wise2_CodonMatrixScore;
34 #define CodonMatrixScore Wise2_CodonMatrixScore
35 #define DYNAMITE_DEFINED_CodonMatrixScore
36 #endif
37 
38 
39 
40 
41     /***************************************************/
42     /* Callable functions                              */
43     /* These are the functions you are expected to use */
44     /***************************************************/
45 
46 
47 
48 /* Function:  naive_CodonMatrixScore_from_prob(ct,cm)
49  *
50  * Descrip:    Combines CodonMatrixScore_from_CodonMatrix and naive_CodonMatrix
51  *
52  *
53  * Arg:        ct [UNKN ] Undocumented argument [CodonTable *]
54  * Arg:        cm [UNKN ] Undocumented argument [CompProb *]
55  *
56  * Return [UNKN ]  Undocumented return value [CodonMatrixScore *]
57  *
58  */
59 CodonMatrixScore * Wise2_naive_CodonMatrixScore_from_prob(CodonTable * ct,CompProb * cm);
60 #define naive_CodonMatrixScore_from_prob Wise2_naive_CodonMatrixScore_from_prob
61 
62 
63 /* Function:  CodonMatrixScore_from_CodonMatrix(cm)
64  *
65  * Descrip:    Makes a CodonMatrixScore from a CodonMatrix
66  *
67  *
68  * Arg:        cm [UNKN ] Undocumented argument [CodonMatrix *]
69  *
70  * Return [UNKN ]  Undocumented return value [CodonMatrixScore *]
71  *
72  */
73 CodonMatrixScore * Wise2_CodonMatrixScore_from_CodonMatrix(CodonMatrix * cm);
74 #define CodonMatrixScore_from_CodonMatrix Wise2_CodonMatrixScore_from_CodonMatrix
75 
76 
77 /* Function:  naive_CodonMatrix(ct,comp)
78  *
79  * Descrip:    Builds a probability matrix
80  *               No codon bias
81  *               No errors
82  *             N codons score 1.0, stop codons probability 0.00001
83  *
84  *
85  * Arg:          ct [UNKN ] Undocumented argument [CodonTable *]
86  * Arg:        comp [UNKN ] Undocumented argument [CompProb *]
87  *
88  * Return [UNKN ]  Undocumented return value [CodonMatrix *]
89  *
90  */
91 CodonMatrix * Wise2_naive_CodonMatrix(CodonTable * ct,CompProb * comp);
92 #define naive_CodonMatrix Wise2_naive_CodonMatrix
93 
94 
95 /* Function:  naive_CodonMatrixScore(ct,comp)
96  *
97  * Descrip:    Builds a codon matrix from CompMat which assummes:
98  *               No codon Bias
99  *               No errors
100  *             N codons score 0, stop codons score ??
101  *
102  *
103  * Arg:          ct [UNKN ] CodonTable for codon->aa mapping [CodonTable *]
104  * Arg:        comp [UNKN ] Comparison matrix for the score of the individual access [CompMat *]
105  *
106  * Return [UNKN ]  Undocumented return value [CodonMatrixScore *]
107  *
108  */
109 CodonMatrixScore * Wise2_naive_CodonMatrixScore(CodonTable * ct,CompMat * comp);
110 #define naive_CodonMatrixScore Wise2_naive_CodonMatrixScore
111 
112 
113 /* Function:  show_CodonMatrixScore(cms,ct,ofp)
114  *
115  * Descrip:    Shows a codonmatrix
116  *
117  *
118  * Arg:        cms [UNKN ] Undocumented argument [CodonMatrixScore *]
119  * Arg:         ct [UNKN ] Undocumented argument [CodonTable *]
120  * Arg:        ofp [UNKN ] Undocumented argument [FILE *]
121  *
122  */
123 void Wise2_show_CodonMatrixScore(CodonMatrixScore * cms,CodonTable * ct,FILE * ofp);
124 #define show_CodonMatrixScore Wise2_show_CodonMatrixScore
125 
126 
127 /* Function:  hard_link_CodonMatrix(obj)
128  *
129  * Descrip:    Bumps up the reference count of the object
130  *             Meaning that multiple pointers can 'own' it
131  *
132  *
133  * Arg:        obj [UNKN ] Object to be hard linked [CodonMatrix *]
134  *
135  * Return [UNKN ]  Undocumented return value [CodonMatrix *]
136  *
137  */
138 CodonMatrix * Wise2_hard_link_CodonMatrix(CodonMatrix * obj);
139 #define hard_link_CodonMatrix Wise2_hard_link_CodonMatrix
140 
141 
142 /* Function:  CodonMatrix_alloc(void)
143  *
144  * Descrip:    Allocates structure: assigns defaults if given
145  *
146  *
147  *
148  * Return [UNKN ]  Undocumented return value [CodonMatrix *]
149  *
150  */
151 CodonMatrix * Wise2_CodonMatrix_alloc(void);
152 #define CodonMatrix_alloc Wise2_CodonMatrix_alloc
153 
154 
155 /* Function:  free_CodonMatrix(obj)
156  *
157  * Descrip:    Free Function: removes the memory held by obj
158  *             Will chain up to owned members and clear all lists
159  *
160  *
161  * Arg:        obj [UNKN ] Object that is free'd [CodonMatrix *]
162  *
163  * Return [UNKN ]  Undocumented return value [CodonMatrix *]
164  *
165  */
166 CodonMatrix * Wise2_free_CodonMatrix(CodonMatrix * obj);
167 #define free_CodonMatrix Wise2_free_CodonMatrix
168 
169 
170 /* Function:  hard_link_CodonMatrixScore(obj)
171  *
172  * Descrip:    Bumps up the reference count of the object
173  *             Meaning that multiple pointers can 'own' it
174  *
175  *
176  * Arg:        obj [UNKN ] Object to be hard linked [CodonMatrixScore *]
177  *
178  * Return [UNKN ]  Undocumented return value [CodonMatrixScore *]
179  *
180  */
181 CodonMatrixScore * Wise2_hard_link_CodonMatrixScore(CodonMatrixScore * obj);
182 #define hard_link_CodonMatrixScore Wise2_hard_link_CodonMatrixScore
183 
184 
185 /* Function:  CodonMatrixScore_alloc(void)
186  *
187  * Descrip:    Allocates structure: assigns defaults if given
188  *
189  *
190  *
191  * Return [UNKN ]  Undocumented return value [CodonMatrixScore *]
192  *
193  */
194 CodonMatrixScore * Wise2_CodonMatrixScore_alloc(void);
195 #define CodonMatrixScore_alloc Wise2_CodonMatrixScore_alloc
196 
197 
198 /* Function:  free_CodonMatrixScore(obj)
199  *
200  * Descrip:    Free Function: removes the memory held by obj
201  *             Will chain up to owned members and clear all lists
202  *
203  *
204  * Arg:        obj [UNKN ] Object that is free'd [CodonMatrixScore *]
205  *
206  * Return [UNKN ]  Undocumented return value [CodonMatrixScore *]
207  *
208  */
209 CodonMatrixScore * Wise2_free_CodonMatrixScore(CodonMatrixScore * obj);
210 #define free_CodonMatrixScore Wise2_free_CodonMatrixScore
211 
212 
213   /* Unplaced functions */
214   /* There has been no indication of the use of these functions */
215 
216 
217     /***************************************************/
218     /* Internal functions                              */
219     /* you are not expected to have to call these      */
220     /***************************************************/
221 
222 #ifdef _cplusplus
223 }
224 #endif
225 
226 #endif
227