82 lines
2.7 KiB
C++
82 lines
2.7 KiB
C++
#include "Sandbox.h"
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#include "org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h"
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#include "utils.h"
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#include "jni_common.h"
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/*
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* Class: Sandbox
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* Method: jniGetMachineType
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* Signature: ()J
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*/
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JNIEXPORT jlong JNICALL Java_Sandbox_jniGetMachineType
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(JNIEnv * env, jobject thisObj)
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{
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return 0;
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}
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/*
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* Class: Sandbox
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* Method: jniInitializeClassFieldsAndMachineMask
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* Signature: (Ljava/lang/Class;Ljava/lang/Class;J)V
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*/
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JNIEXPORT void JNICALL Java_Sandbox_jniInitializeClassFieldsAndMachineMask
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(JNIEnv* env, jobject thisObject, jclass readDataHolderClass, jclass haplotypeDataHolderClass, jlong mask)
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{
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Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniInitializeClassFieldsAndMachineMask(env, thisObject, readDataHolderClass,
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haplotypeDataHolderClass, mask);
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}
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/*
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* Class: Sandbox
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* Method: jniInitializeHaplotypes
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* Signature: (I[LSandbox/JNIHaplotypeDataHolderClass;)V
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*/
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JNIEXPORT void JNICALL Java_Sandbox_jniInitializeHaplotypes
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(JNIEnv * env, jobject thisObject, jint numHaplotypes, jobjectArray haplotypeDataArray)
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{
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Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniInitializeHaplotypes(env, thisObject, numHaplotypes, haplotypeDataArray);
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}
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/*
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* Class: Sandbox
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* Method: jniFinalizeRegion
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* Signature: ()V
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*/
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JNIEXPORT void JNICALL Java_Sandbox_jniFinalizeRegion
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(JNIEnv * env, jobject thisObject)
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{
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Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniFinalizeRegion(env, thisObject);
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}
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/*
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* Class: Sandbox
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* Method: jniComputeLikelihoods
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* Signature: (II[LSandbox/JNIReadDataHolderClass;[LSandbox/JNIHaplotypeDataHolderClass;[DI)V
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*/
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JNIEXPORT void JNICALL Java_Sandbox_jniComputeLikelihoods
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(JNIEnv* env, jobject thisObject, jint numReads, jint numHaplotypes,
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jobjectArray readDataArray, jobjectArray haplotypeDataArray, jdoubleArray likelihoodArray, jint maxNumThreadsToUse)
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{
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Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniComputeLikelihoods(env, thisObject,
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numReads, numHaplotypes, readDataArray, haplotypeDataArray, likelihoodArray, maxNumThreadsToUse);
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}
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/*
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* Class: Sandbox
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* Method: jniClose
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* Signature: ()V
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*/
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JNIEXPORT void JNICALL Java_Sandbox_jniClose
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(JNIEnv* env, jobject thisObject)
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{ Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniClose(env, thisObject); }
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JNIEXPORT void JNICALL Java_Sandbox_doEverythingNative
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(JNIEnv* env, jobject thisObject, jstring fileNameString)
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{
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const char* fileName = env->GetStringUTFChars(fileNameString, 0);
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char local_array[800];
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strncpy(local_array, fileName, 200);
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env->ReleaseStringUTFChars(fileNameString, fileName);
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do_compute(local_array, true, 10000, false);
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}
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