5 #ifndef _Included_beagle_BeagleJNIWrapper
6 #define _Included_beagle_BeagleJNIWrapper
15 JNIEXPORT jobjectArray JNICALL Java_beagle_BeagleJNIWrapper_getResourceList
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);
31 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_finalize
32 (JNIEnv *, jobject, jint);
39 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setPatternWeights
40 (JNIEnv *, jobject, jint, jdoubleArray);
47 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setTipStates
48 (JNIEnv *, jobject, jint, jint, jintArray);
55 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_getTipStates
56 (JNIEnv *, jobject, jint, jint, jintArray);
64 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setTipPartials
65 (JNIEnv *, jobject, jint, jint, jdoubleArray);
72 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setPartials
73 (JNIEnv *, jobject, jint, jint, jdoubleArray);
80 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_getPartials
81 (JNIEnv *, jobject, jint, jint, jint, jdoubleArray);
88 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setEigenDecomposition
89 (JNIEnv *, jobject, jint, jint, jdoubleArray, jdoubleArray, jdoubleArray);
96 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setStateFrequencies
97 (JNIEnv *, jobject, jint, jint, jdoubleArray);
104 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setCategoryWeights
105 (JNIEnv *, jobject, jint, jint, jdoubleArray);
112 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setCategoryRates
113 (JNIEnv *, jobject, jint, jdoubleArray);
120 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setTransitionMatrix
121 (JNIEnv *, jobject, jint, jint, jdoubleArray, jdouble);
128 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_getTransitionMatrix
129 (JNIEnv *, jobject, jint, jint, jdoubleArray);
136 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_updateTransitionMatrices
137 (JNIEnv *, jobject, jint, jint, jintArray, jintArray, jintArray, jdoubleArray, jint);
144 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_updatePartials
145 (JNIEnv *, jobject, jint, jintArray, jint, jint);
152 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_waitForPartials
153 (JNIEnv *, jobject, jint, jintArray, jint);
160 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_accumulateScaleFactors
161 (JNIEnv *, jobject, jint, jintArray, jint, jint);
168 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_removeScaleFactors
169 (JNIEnv *, jobject, jint, jintArray, jint, jint);
176 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_resetScaleFactors
177 (JNIEnv *, jobject, jint, jint);
184 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_copyScaleFactors
185 (JNIEnv *, jobject, jint, jint, jint);
192 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_calculateRootLogLikelihoods
193 (JNIEnv *, jobject, jint, jintArray, jintArray, jintArray, jintArray, jint, jdoubleArray);
200 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_calculateEdgeLogLikelihoods
201 (JNIEnv *, jobject, jint, jintArray, jintArray, jintArray, jintArray, jintArray, jintArray, jintArray, jintArray, jint, jdoubleArray, jdoubleArray, jdoubleArray);
208 JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_getSiteLogLikelihoods
209 (JNIEnv *, jobject, jint, jdoubleArray);