<commit_before>/* DO NOT EDIT THIS FILE - it is machine generated */
#include <jni.h>
/* Header for class beagle_BeagleJNIWrapper */

#ifndef _Included_beagle_BeagleJNIWrapper
#define _Included_beagle_BeagleJNIWrapper
#ifdef __cplusplus
extern "C" {
#endif
/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    getResourceList
 * Signature: ()[Lbeagle/ResourceDetails;
 */
JNIEXPORT jobjectArray JNICALL Java_beagle_BeagleJNIWrapper_getResourceList
  (JNIEnv *, jobject);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    createInstance
 * Signature: (IIIIIIIII[IIJJLbeagle/InstanceDetails;)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_createInstance
  (JNIEnv *, jobject, jint, jint, jint, jint, jint, jint, jint, jint, jint, jintArray, jint, jlong, jlong, jobject);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    finalize
 * Signature: (I)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_finalize
  (JNIEnv *, jobject, jint);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    setPatternWeights
 * Signature: (I[D)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setPatternWeights
  (JNIEnv *, jobject, jint, jdoubleArray);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    setTipStates
 * Signature: (II[I)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setTipStates
  (JNIEnv *, jobject, jint, jint, jintArray);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    getTipStates
 * Signature: (II[I)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_getTipStates
  (JNIEnv *, jobject, jint, jint, jintArray);


/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    setTipPartials
 * Signature: (II[D)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setTipPartials
  (JNIEnv *, jobject, jint, jint, jdoubleArray);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    setPartials
 * Signature: (II[D)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setPartials
  (JNIEnv *, jobject, jint, jint, jdoubleArray);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    getPartials
 * Signature: (III[D)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_getPartials
  (JNIEnv *, jobject, jint, jint, jint, jdoubleArray);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    setEigenDecomposition
 * Signature: (II[D[D[D)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setEigenDecomposition
  (JNIEnv *, jobject, jint, jint, jdoubleArray, jdoubleArray, jdoubleArray);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    setStateFrequencies
 * Signature: (II[D)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setStateFrequencies
  (JNIEnv *, jobject, jint, jint, jdoubleArray);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    setCategoryWeights
 * Signature: (II[D)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setCategoryWeights
  (JNIEnv *, jobject, jint, jint, jdoubleArray);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    setCategoryRates
 * Signature: (I[D)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setCategoryRates
  (JNIEnv *, jobject, jint, jdoubleArray);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    setTransitionMatrix
 * Signature: (II[DD)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setTransitionMatrix
  (JNIEnv *, jobject, jint, jint, jdoubleArray, jdouble);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    getTransitionMatrix
 * Signature: (II[D)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_getTransitionMatrix
  (JNIEnv *, jobject, jint, jint, jdoubleArray);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    updateTransitionMatrices
 * Signature: (II[I[I[I[DI)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_updateTransitionMatrices
  (JNIEnv *, jobject, jint, jint, jintArray, jintArray, jintArray, jdoubleArray, jint);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    updatePartials
 * Signature: (I[III)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_updatePartials
  (JNIEnv *, jobject, jint, jintArray, jint, jint);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    waitForPartials
 * Signature: (I[II)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_waitForPartials
  (JNIEnv *, jobject, jint, jintArray, jint);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    accumulateScaleFactors
 * Signature: (I[III)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_accumulateScaleFactors<commit_msg>JNI wrappers for convolution<commit_after>/* DO NOT EDIT THIS FILE - it is machine generated */
#include <jni.h>
/* Header for class beagle_BeagleJNIWrapper */

#ifndef _Included_beagle_BeagleJNIWrapper
#define _Included_beagle_BeagleJNIWrapper
#ifdef __cplusplus
extern "C" {
#endif
/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    getResourceList
 * Signature: ()[Lbeagle/ResourceDetails;
 */
JNIEXPORT jobjectArray JNICALL Java_beagle_BeagleJNIWrapper_getResourceList
  (JNIEnv *, jobject);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    createInstance
 * Signature: (IIIIIIIII[IIJJLbeagle/InstanceDetails;)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_createInstance
  (JNIEnv *, jobject, jint, jint, jint, jint, jint, jint, jint, jint, jint, jintArray, jint, jlong, jlong, jobject);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    finalize
 * Signature: (I)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_finalize
  (JNIEnv *, jobject, jint);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    setPatternWeights
 * Signature: (I[D)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setPatternWeights
  (JNIEnv *, jobject, jint, jdoubleArray);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    setTipStates
 * Signature: (II[I)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setTipStates
  (JNIEnv *, jobject, jint, jint, jintArray);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    getTipStates
 * Signature: (II[I)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_getTipStates
  (JNIEnv *, jobject, jint, jint, jintArray);


/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    setTipPartials
 * Signature: (II[D)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setTipPartials
  (JNIEnv *, jobject, jint, jint, jdoubleArray);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    setPartials
 * Signature: (II[D)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setPartials
  (JNIEnv *, jobject, jint, jint, jdoubleArray);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    getPartials
 * Signature: (III[D)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_getPartials
  (JNIEnv *, jobject, jint, jint, jint, jdoubleArray);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    setEigenDecomposition
 * Signature: (II[D[D[D)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setEigenDecomposition
  (JNIEnv *, jobject, jint, jint, jdoubleArray, jdoubleArray, jdoubleArray);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    setStateFrequencies
 * Signature: (II[D)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setStateFrequencies
  (JNIEnv *, jobject, jint, jint, jdoubleArray);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    setCategoryWeights
 * Signature: (II[D)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setCategoryWeights
  (JNIEnv *, jobject, jint, jint, jdoubleArray);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    setCategoryRates
 * Signature: (I[D)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setCategoryRates
  (JNIEnv *, jobject, jint, jdoubleArray);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    setTransitionMatrix
 * Signature: (II[DD)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_setTransitionMatrix
  (JNIEnv *, jobject, jint, jint, jdoubleArray, jdouble);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    getTransitionMatrix
 * Signature: (II[D)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_getTransitionMatrix
  (JNIEnv *, jobject, jint, jint, jdoubleArray);


/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    convolveTransitionMatrices
 * Signature: (I[D)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_convolveTransitionMatrices
   (JNIEnv *env, jobject obj, jint instance, jintArray inFirstIndices, jintArray inSecondIndices, jintArray inResultIndices, jint matrixCount);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    updateTransitionMatrices
 * Signature: (II[I[I[I[DI)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_updateTransitionMatrices
  (JNIEnv *, jobject, jint, jint, jintArray, jintArray, jintArray, jdoubleArray, jint);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    updatePartials
 * Signature: (I[III)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_updatePartials
  (JNIEnv *, jobject, jint, jintArray, jint, jint);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    waitForPartials
 * Signature: (I[II)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_waitForPartials
  (JNIEnv *, jobject, jint, jintArray, jint);

/*
 * Class:     beagle_BeagleJNIWrapper
 * Method:    accumulateScaleFactors
 * Signature: (I[III)I
 */
JNIEXPORT jint JNICALL Java_beagle_BeagleJNIWrapper_accumulateScaleFactors
{'fraction_non_alphanumeric': 0.09566148901981789, 'fraction_numerical': 0.0, 'mean_word_length': 5.050550874918989, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 2, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
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