107 lines
3.7 KiB
C++
107 lines
3.7 KiB
C++
/*Copyright (c) 2012 The Broad Institute
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*Permission is hereby granted, free of charge, to any person
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*obtaining a copy of this software and associated documentation
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*files (the "Software"), to deal in the Software without
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*restriction, including without limitation the rights to use,
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*copy, modify, merge, publish, distribute, sublicense, and/or sell
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*copies of the Software, and to permit persons to whom the
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*Software is furnished to do so, subject to the following
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*conditions:
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*The above copyright notice and this permission notice shall be
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*included in all copies or substantial portions of the Software.
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*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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#include "Sandbox.h"
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#include "org_broadinstitute_gatk_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_gatk_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_gatk_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_gatk_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_gatk_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_gatk_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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