/*Copyright (c) 2012 The Broad Institute

*Permission is hereby granted, free of charge, to any person
*obtaining a copy of this software and associated documentation
*files (the "Software"), to deal in the Software without
*restriction, including without limitation the rights to use,
*copy, modify, merge, publish, distribute, sublicense, and/or sell
*copies of the Software, and to permit persons to whom the
*Software is furnished to do so, subject to the following
*conditions:

*The above copyright notice and this permission notice shall be
*included in all copies or substantial portions of the Software.

*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/


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

#ifndef _Included_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM
#define _Included_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM
#ifdef __cplusplus
extern "C" {
#endif
#undef org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_TRISTATE_CORRECTION
#define org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_TRISTATE_CORRECTION 3.0
#undef org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_sse41Mask
#define org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_sse41Mask 1LL
#undef org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_sse42Mask
#define org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_sse42Mask 2LL
#undef org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_avxMask
#define org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_avxMask 4LL
#undef org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_enableAll
#define org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_enableAll -1LL
/*
 * Class:     org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM
 * Method:    jniGetMachineType
 * Signature: ()J
 */
JNIEXPORT jlong JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniGetMachineType
  (JNIEnv *, jobject);

/*
 * Class:     org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM
 * Method:    jniInitializeClassFieldsAndMachineMask
 * Signature: (Ljava/lang/Class;Ljava/lang/Class;J)V
 */
JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniInitializeClassFieldsAndMachineMask
  (JNIEnv *, jobject, jclass, jclass, jlong);

/*
 * Class:     org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM
 * Method:    jniInitializeHaplotypes
 * Signature: (I[Lorg/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM/JNIHaplotypeDataHolderClass;)V
 */
JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniInitializeHaplotypes
  (JNIEnv *, jobject, jint, jobjectArray);

/*
 * Class:     org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM
 * Method:    jniFinalizeRegion
 * Signature: ()V
 */
JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniFinalizeRegion
  (JNIEnv *, jobject);

/*
 * Class:     org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM
 * Method:    jniComputeLikelihoods
 * Signature: (II[Lorg/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM/JNIReadDataHolderClass;[Lorg/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM/JNIHaplotypeDataHolderClass;[DI)V
 */
JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniComputeLikelihoods
  (JNIEnv *, jobject, jint, jint, jobjectArray, jobjectArray, jdoubleArray, jint);

/*
 * Class:     org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM
 * Method:    jniClose
 * Signature: ()V
 */
JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniClose
  (JNIEnv *, jobject);

#ifdef __cplusplus
}
#endif
#endif
