HMSBEAGLE  1.0.0
beagle_BeagleJNIWrapper.h
1 /* DO NOT EDIT THIS FILE - it is machine generated */
2 #include <jni.h>
3 /* Header for class beagle_BeagleJNIWrapper */
4 
5 #ifndef _Included_beagle_BeagleJNIWrapper
6 #define _Included_beagle_BeagleJNIWrapper
7 #ifdef __cplusplus
8 extern "C" {
9 #endif
10 /*
11  * Class: beagle_BeagleJNIWrapper
12  * Method: getResourceList
13  * Signature: ()[Lbeagle/ResourceDetails;
14  */
15 JNIEXPORT jobjectArray JNICALL Java_beagle_BeagleJNIWrapper_getResourceList
16  (JNIEnv *, jobject);
17 
18 /*
19  * Class: beagle_BeagleJNIWrapper
20  * Method: createInstance
21  * Signature: (IIIIIIIII[IIJJLbeagle/InstanceDetails;)I
22  */
23 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_createInstance
24  (JNIEnv *, jobject, jint, jint, jint, jint, jint, jint, jint, jint, jint, jintArray, jint, jlong, jlong, jobject);
25 
26 /*
27  * Class: beagle_BeagleJNIWrapper
28  * Method: finalize
29  * Signature: (I)I
30  */
31 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_finalize
32  (JNIEnv *, jobject, jint);
33 
34 /*
35  * Class: beagle_BeagleJNIWrapper
36  * Method: setPatternWeights
37  * Signature: (I[D)I
38  */
39 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setPatternWeights
40  (JNIEnv *, jobject, jint, jdoubleArray);
41 
42 /*
43  * Class: beagle_BeagleJNIWrapper
44  * Method: setTipStates
45  * Signature: (II[I)I
46  */
47 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setTipStates
48  (JNIEnv *, jobject, jint, jint, jintArray);
49 
50 /*
51  * Class: beagle_BeagleJNIWrapper
52  * Method: getTipStates
53  * Signature: (II[I)I
54  */
55 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_getTipStates
56  (JNIEnv *, jobject, jint, jint, jintArray);
57 
58 
59 /*
60  * Class: beagle_BeagleJNIWrapper
61  * Method: setTipPartials
62  * Signature: (II[D)I
63  */
64 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setTipPartials
65  (JNIEnv *, jobject, jint, jint, jdoubleArray);
66 
67 /*
68  * Class: beagle_BeagleJNIWrapper
69  * Method: setPartials
70  * Signature: (II[D)I
71  */
72 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setPartials
73  (JNIEnv *, jobject, jint, jint, jdoubleArray);
74 
75 /*
76  * Class: beagle_BeagleJNIWrapper
77  * Method: getPartials
78  * Signature: (III[D)I
79  */
80 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_getPartials
81  (JNIEnv *, jobject, jint, jint, jint, jdoubleArray);
82 
83 /*
84  * Class: beagle_BeagleJNIWrapper
85  * Method: setEigenDecomposition
86  * Signature: (II[D[D[D)I
87  */
88 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setEigenDecomposition
89  (JNIEnv *, jobject, jint, jint, jdoubleArray, jdoubleArray, jdoubleArray);
90 
91 /*
92  * Class: beagle_BeagleJNIWrapper
93  * Method: setStateFrequencies
94  * Signature: (II[D)I
95  */
96 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setStateFrequencies
97  (JNIEnv *, jobject, jint, jint, jdoubleArray);
98 
99 /*
100  * Class: beagle_BeagleJNIWrapper
101  * Method: setCategoryWeights
102  * Signature: (II[D)I
103  */
104 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setCategoryWeights
105  (JNIEnv *, jobject, jint, jint, jdoubleArray);
106 
107 /*
108  * Class: beagle_BeagleJNIWrapper
109  * Method: setCategoryRates
110  * Signature: (I[D)I
111  */
112 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setCategoryRates
113  (JNIEnv *, jobject, jint, jdoubleArray);
114 
115 /*
116  * Class: beagle_BeagleJNIWrapper
117  * Method: setTransitionMatrix
118  * Signature: (II[DD)I
119  */
120 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setTransitionMatrix
121  (JNIEnv *, jobject, jint, jint, jdoubleArray, jdouble);
122 
123 /*
124  * Class: beagle_BeagleJNIWrapper
125  * Method: getTransitionMatrix
126  * Signature: (II[D)I
127  */
128 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_getTransitionMatrix
129  (JNIEnv *, jobject, jint, jint, jdoubleArray);
130 
131 /*
132  * Class: beagle_BeagleJNIWrapper
133  * Method: updateTransitionMatrices
134  * Signature: (II[I[I[I[DI)I
135  */
136 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_updateTransitionMatrices
137  (JNIEnv *, jobject, jint, jint, jintArray, jintArray, jintArray, jdoubleArray, jint);
138 
139 /*
140  * Class: beagle_BeagleJNIWrapper
141  * Method: updatePartials
142  * Signature: (I[III)I
143  */
144 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_updatePartials
145  (JNIEnv *, jobject, jint, jintArray, jint, jint);
146 
147 /*
148  * Class: beagle_BeagleJNIWrapper
149  * Method: waitForPartials
150  * Signature: (I[II)I
151  */
152 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_waitForPartials
153  (JNIEnv *, jobject, jint, jintArray, jint);
154 
155 /*
156  * Class: beagle_BeagleJNIWrapper
157  * Method: accumulateScaleFactors
158  * Signature: (I[III)I
159  */
160 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_accumulateScaleFactors
161  (JNIEnv *, jobject, jint, jintArray, jint, jint);
162 
163 /*
164  * Class: beagle_BeagleJNIWrapper
165  * Method: removeScaleFactors
166  * Signature: (I[III)I
167  */
168 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_removeScaleFactors
169  (JNIEnv *, jobject, jint, jintArray, jint, jint);
170 
171 /*
172  * Class: beagle_BeagleJNIWrapper
173  * Method: resetScaleFactors
174  * Signature: (II)I
175  */
176 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_resetScaleFactors
177  (JNIEnv *, jobject, jint, jint);
178 
179 /*
180  * Class: beagle_BeagleJNIWrapper
181  * Method: copyScaleFactors
182  * Signature: (II)II
183  */
184 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_copyScaleFactors
185  (JNIEnv *, jobject, jint, jint, jint);
186 
187 /*
188  * Class: beagle_BeagleJNIWrapper
189  * Method: calculateRootLogLikelihoods
190  * Signature: (I[I[I[I[II[D)I
191  */
192 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_calculateRootLogLikelihoods
193  (JNIEnv *, jobject, jint, jintArray, jintArray, jintArray, jintArray, jint, jdoubleArray);
194 
195 /*
196  * Class: beagle_BeagleJNIWrapper
197  * Method: calculateEdgeLogLikelihoods
198  * Signature: (I[I[I[I[I[I[I[I[II[D[D[D)I
199  */
200 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_calculateEdgeLogLikelihoods
201  (JNIEnv *, jobject, jint, jintArray, jintArray, jintArray, jintArray, jintArray, jintArray, jintArray, jintArray, jint, jdoubleArray, jdoubleArray, jdoubleArray);
202 
203 /*
204  * Class: beagle_BeagleJNIWrapper
205  * Method: getSiteLogLikelihoods
206  * Signature: (I[D)I
207  */
208 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_getSiteLogLikelihoods
209  (JNIEnv *, jobject, jint, jdoubleArray);
210 
211 #ifdef __cplusplus
212 }
213 #endif
214 #endif