amns_jni_call.c File Reference

#include "amns_interface.h"
#include <stdbool.h>
#include <math.h>
#include <assert.h>
#include <stdio.h>
#include "amns_jni_call.h"
#include <jni.h>

Include dependency graph for amns_jni_call.c:

Go to the source code of this file.

Functions
void	copyCError2JavaError (amns_c_error_type *error_stat, JNIEnv *env, jobject error_structure)
JNIEXPORT jlong JNICALL	Java_amns_Amns_ItmAmnsCcSetupReactants (JNIEnv *env, jobject obj, jint idx)
JNIEXPORT jlong JNICALL	Java_amns_Amns_ItmAmnsCcSetupReactantsNumber (JNIEnv *env, jobject obj, jint idx, jint number)
JNIEXPORT void JNICALL	Java_amns_Amns_ItmAmnsCCSetReactant (JNIEnv *env, jobject obj, jlong ptr, jobject acrt)
JNIEXPORT void JNICALL	Java_amns_Amns_ItmAmnsCCSetReactantIdx (JNIEnv *env, jobject obj, jlong ptr, jint idx, jobject acrt)
JNIEXPORT void JNICALL	Java_amns_Amns_ItmAmnsCCGetReactant (JNIEnv *env, jobject obj, jlong ptr, jobject jSpecies)
JNIEXPORT long JNICALL	Java_amns_Amns_ItmAmnsCCSetup (JNIEnv *env, jobject obj, jobject error_structure)
JNIEXPORT jlong JNICALL	Java_amns_Amns_ItmAmnsCCSetupTable (JNIEnv *env, jobject obj, jlong ptr_amns_handle, jobject j_reaction_type, jlong ptr_reactants_handle, jobject j_error_state)
JNIEXPORT jdouble JNICALL	Java_amns_Amns_ItmAmnsCCRX0B (JNIEnv *env, jobject obj, jlong ptrHandleRx, double j_arg1, double j_arg2, jobject j_error_state)
JNIEXPORT long JNICALL	Java_amns_Amns_ItmAmnsCCFinishTable (JNIEnv *env, jobject obj, jlong ptrHandleRX, jobject j_error_state)
JNIEXPORT jlong JNICALL	Java_amns_Amns_ItmAmnsCCFinishReactants (JNIEnv *env, jobject obj, jlong ptr_reactants_handle)
JNIEXPORT jlong JNICALL	Java_amns_Amns_ItmAmnsCCFinish (JNIEnv *env, jobject obj, jlong ptr_amns_handle, jobject j_error_state)
JNIEXPORT void JNICALL	Java_amns_Amns_ItmAmnsCCSet (JNIEnv *env, jobject obj, jlong ptrAmnsHandle, jobject j_amns_set_type, jobject j_error_state)
JNIEXPORT void JNICALL	Java_amns_Amns_ItmAmnsCCQuery (JNIEnv *env, jobject obj, jlong ptrAmnsHandle, jobject j_amns_query, jobject j_amns_answer, jobject j_error_state)
JNIEXPORT void JNICALL	Java_amns_Amns_ItmAmnsCCQueryTable (JNIEnv *env, jobject obj, jlong ptrTableHandle, jobject j_amns_query, jobject j_amns_answer, jobject j_error_state)
JNIEXPORT jdoubleArray JNICALL	Java_amns_Amns_ItmAmnsCCRX1A (JNIEnv *env, jobject obj, jlong ptrHandleRx, jint nx, jdoubleArray j_arg1, jobject j_error_state)
JNIEXPORT jdoubleArray JNICALL	Java_amns_Amns_ItmAmnsCCRX1B (JNIEnv *env, jobject obj, jlong ptrHandleRx, jint nx, jdoubleArray j_arg1, jdoubleArray j_arg2, jobject j_error_state)
JNIEXPORT jdoubleArray JNICALL	Java_amns_Amns_ItmAmnsCCRX1C (JNIEnv *env, jobject obj, jlong ptrHandleRx, jint nx, jdoubleArray j_arg1, jdoubleArray j_arg2, jdoubleArray j_arg3, jobject j_error_state)
JNIEXPORT void JNICALL	Java_amns_Amns_ItmAmnsCCSetTable (JNIEnv *env, jobject obj, jlong ptrAmnsCxHandle, jobject j_amns_set_type, jobject j_error_state)

Function Documentation

void copyCError2JavaError	(	amns_c_error_type *	error_stat,
		JNIEnv *	env,
		jobject	error_structure
	)

Definition at line 9 of file amns_jni_call.c.

                                                                                                {

  // we have to return values into Java
  // note that we are playing here with pointers - they should be preserved accross calls
  // but will not be garbage collected from java

  jclass cls = (*env)->GetObjectClass(env, error_structure);
  jfieldID paramFlag = (*env)->GetFieldID(env, cls, "flag", "Z");
  jfieldID paramString = (*env)->GetFieldID(env, cls, "string", "Ljava/lang/String;");

  jstring ret_message;

  if(error_stat->string != NULL) {
    ret_message = (*env)->NewStringUTF(env,error_stat->string);
  } else {
    ret_message = (*env)->NewStringUTF(env,"");
  }
  if(ret_message == NULL) {
    (*env)->SetObjectField(env, error_structure, paramString, "");
  } else {
    (*env)->SetObjectField(env, error_structure, paramString, ret_message);
  }

  jboolean ret_flag = error_stat->flag;
  (*env)->SetBooleanField(env, error_structure, paramFlag, ret_flag);
}

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JNIEXPORT jlong JNICALL Java_amns_Amns_ItmAmnsCCFinish	(	JNIEnv *	env,
		jobject	obj,
		jlong	ptr_amns_handle,
		jobject	j_error_state
	)

Definition at line 284 of file amns_jni_call.c.

                                                                                {

  amns_c_error_type error_stat = DEFAULT_AMNS_C_ERROR_TYPE;     
  void* amns_handle = (void*) ptr_amns_handle;

  // DEBUG printf("[JNI] Before calling ITM_AMNS_CC_FINISH\n");
  // DEBUG printf("[JNI] amns_handle: %lu\n", (long)ptr_amns_handle);
  ITM_AMNS_CC_FINISH(&amns_handle, &error_stat);
  // DEBUG printf("[JNI] After calling ITM_AMNS_CC_FINISH\n");
  
  // we have to make sure that error_stat is passed back inside object

  copyCError2JavaError( &error_stat, env, j_error_state);

  return (long) amns_handle;

}

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JNIEXPORT jlong JNICALL Java_amns_Amns_ItmAmnsCCFinishReactants	(	JNIEnv *	env,
		jobject	obj,
		jlong	ptr_reactants_handle
	)

Definition at line 268 of file amns_jni_call.c.

                                                                                              {

  void* reactants_handle = (void *) ptr_reactants_handle;

  // DEBUG printf("[JNI] Before calling ITM_AMNS_CC_FINISH_REACTANTS\n");
  // DEBUG printf("[JNI] reactants_handle: %lu\n", (long)ptr_reactants_handle);
  ITM_AMNS_CC_FINISH_REACTANTS(&reactants_handle);
  // DEBUG printf("[JNI] After calling ITM_AMNS_CC_FINISH_REACTANTS\n");        

  return (long) reactants_handle;
}

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JNIEXPORT long JNICALL Java_amns_Amns_ItmAmnsCCFinishTable	(	JNIEnv *	env,
		jobject	obj,
		jlong	ptrHandleRX,
		jobject	j_error_state
	)

Definition at line 246 of file amns_jni_call.c.

                                                                                    {
  
  amns_c_error_type error_stat = DEFAULT_AMNS_C_ERROR_TYPE;
  void* amns_cx_handle = (void *) ptrHandleRX;

  // DEBUG printf("[JNI] Before calling ITM_AMNS_CC_FINISH_TABLE\n");
  // DEBUG printf("[JNI] cx_handle: %lu\n", (long)ptrHandleRX);
  ITM_AMNS_CC_FINISH_TABLE(&amns_cx_handle, &error_stat);
  // DEBUG printf("[JNI] After calling ITM_AMNS_CC_FINISH_TABLE\n");

  // we have to make sure that error_stat is passed back inside object

  copyCError2JavaError( &error_stat, env, j_error_state );

  return (jlong) amns_cx_handle;
        
}

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JNIEXPORT void JNICALL Java_amns_Amns_ItmAmnsCCGetReactant	(	JNIEnv *	env,
		jobject	obj,
		jlong	ptr,
		jobject	jSpecies
	)

Definition at line 116 of file amns_jni_call.c.

                                                                                                                  {

  void *reactant_handle = (void*) ptr;

  amns_c_reactant_type species  = DEFAULT_AMNS_C_REACTANT_TYPE;

  // at first, get all elements of the species
  jclass cls = (*env)->GetObjectClass(env, jSpecies);
  jfieldID paramZN = (*env)->GetFieldID(env, cls, "ZN", "D");
  jfieldID paramZA = (*env)->GetFieldID(env, cls, "ZA", "D");
  jfieldID paramMI = (*env)->GetFieldID(env, cls, "MI", "D");
  jfieldID paramLR = (*env)->GetFieldID(env, cls, "LR", "I");
  jfieldID paramRealSpecifier = (*env)->GetFieldID(env, cls, "real_specifier", "D");
  jfieldID paramIntSpecifier = (*env)->GetFieldID(env, cls, "int_specifier", "I");

  // retrieve data into C structure
  ITM_AMNS_CC_GET_REACTANT(reactant_handle, 1, &species);
  // DEBUG printf("[JNI] After calling ITM_AMNS_CC_GET_REACTANTS\n");

  // copy data back to Java
  (*env)->SetDoubleField(env, jSpecies, paramZN, (jdouble)species.ZN );
  (*env)->SetDoubleField(env, jSpecies, paramZA, species.ZA );
  (*env)->SetDoubleField(env, jSpecies, paramMI, species.MI );
  (*env)->SetIntField(env, jSpecies, paramLR, species.LR );
  (*env)->SetDoubleField(env, jSpecies, paramRealSpecifier, species.real_specifier);
  (*env)->SetIntField(env, jSpecies, paramIntSpecifier, species.int_specifier); 
}

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JNIEXPORT void JNICALL Java_amns_Amns_ItmAmnsCCQuery	(	JNIEnv *	env,
		jobject	obj,
		jlong	ptrAmnsHandle,
		jobject	j_amns_query,
		jobject	j_amns_answer,
		jobject	j_error_state
	)

Definition at line 337 of file amns_jni_call.c.

                                                                              {

  amns_c_error_type error_stat = DEFAULT_AMNS_C_ERROR_TYPE;
  amns_c_query_type query = DEFAULT_AMNS_C_QUERY_TYPE;
  amns_c_answer_type answer = DEFAULT_AMNS_C_ANSWER_TYPE;
  void *amns_handler = (void *) ptrAmnsHandle;

  // we have to retrieve the query and pass it to function

  jclass cls = (*env)->GetObjectClass(env, j_amns_query);
  jfieldID paramString = (*env)->GetFieldID(env, cls, "string", "Ljava/lang/String;");

  jstring j_query_string = (*env)->GetObjectField(env, j_amns_query, paramString);

  char *query_string = (char*)(*env)->GetStringUTFChars(env, j_query_string, NULL);

  query.string = query_string;

  // DEBUG printf("[JNI] Before calling ITM_AMNS_CC_QUERY\n");
  // DEBUG printf("[JNI] amns_handle: %lu\n", (long)ptrAmnsHandle);
  ITM_AMNS_CC_QUERY(amns_handler, &query, &answer, &error_stat);
  // DEBUG printf("[JNI] After calling ITM_AMNS_CC_QUERY\n");   

  // copy error to Java
  copyCError2JavaError( &error_stat, env, j_error_state);

  // copy answer to Java
        
  jclass cls_answer = (*env)->GetObjectClass(env, j_amns_answer);
  jfieldID answerNumber = (*env)->GetFieldID(env, cls_answer, "number", "I");
  jfieldID answerString = (*env)->GetFieldID(env, cls_answer, "string", "Ljava/lang/String;");

  jstring answer_value;

  if(answer.string != NULL) {
    answer_value = (*env)->NewStringUTF(env,answer.string);
  } else {
    answer_value = (*env)->NewStringUTF(env,"");
  }
  if(answer_value == NULL) {
    (*env)->SetObjectField(env, j_amns_answer, answerString, "");
  } else {
    (*env)->SetObjectField(env, j_amns_answer, answerString, answer_value);
  }

  jint answer_number = answer.number;
  (*env)->SetIntField(env, j_amns_answer, answerNumber, answer_number);
}

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JNIEXPORT void JNICALL Java_amns_Amns_ItmAmnsCCQueryTable	(	JNIEnv *	env,
		jobject	obj,
		jlong	ptrTableHandle,
		jobject	j_amns_query,
		jobject	j_amns_answer,
		jobject	j_error_state
	)

Definition at line 392 of file amns_jni_call.c.

                                                                                   {

  amns_c_error_type error_stat = DEFAULT_AMNS_C_ERROR_TYPE;
  amns_c_query_type query = DEFAULT_AMNS_C_QUERY_TYPE;
  amns_c_answer_type answer = DEFAULT_AMNS_C_ANSWER_TYPE;
  void *table_handler = (void *) ptrTableHandle;

  // we have to retrieve the query and pass it to function

  jclass cls = (*env)->GetObjectClass(env, j_amns_query);
  jfieldID paramString = (*env)->GetFieldID(env, cls, "string", "Ljava/lang/String;");

  jstring j_query_string = (*env)->GetObjectField(env, j_amns_query, paramString);

  char *query_string = (char*)(*env)->GetStringUTFChars(env, j_query_string, NULL);

  query.string = query_string;

  // DEBUG printf("[JNI] Before calling ITM_AMNS_CC_QUERY_TABLE\n");
  // DEBUG printf("[JNI] table_handle: %lu\n", (long)ptrTableHandle);
  ITM_AMNS_CC_QUERY_TABLE(table_handler, &query, &answer, &error_stat);
  // DEBUG printf("[JNI] After calling ITM_AMNS_CC_QUERY_TABLE\n");     

  // copy error to Java
  copyCError2JavaError( &error_stat, env, j_error_state);

  // copy answer to Java
        
  jclass cls_answer = (*env)->GetObjectClass(env, j_amns_answer);
  jfieldID answerNumber = (*env)->GetFieldID(env, cls_answer, "number", "I");
  jfieldID answerString = (*env)->GetFieldID(env, cls_answer, "string", "Ljava/lang/String;");

  jstring answer_value;

  if(answer.string != NULL) {
    answer_value = (*env)->NewStringUTF(env,answer.string);
  } else {
    answer_value = (*env)->NewStringUTF(env,"");
  }
  if(answer_value == NULL) {
    (*env)->SetObjectField(env, j_amns_answer, answerString, "");
  } else {
    (*env)->SetObjectField(env, j_amns_answer, answerString, answer_value);
  }

  jint answer_number = answer.number;
  (*env)->SetIntField(env, j_amns_answer, answerNumber, answer_number);
}

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JNIEXPORT jdouble JNICALL Java_amns_Amns_ItmAmnsCCRX0B	(	JNIEnv *	env,
		jobject	obj,
		jlong	ptrHandleRx,
		double	j_arg1,
		double	j_arg2,
		jobject	j_error_state
	)

Definition at line 218 of file amns_jni_call.c.

                                                                                 {

  amns_c_error_type error_stat = DEFAULT_AMNS_C_ERROR_TYPE;
  void* amns_cx_handle = (void *) ptrHandleRx;
  double arg1 = (double) j_arg1;
  double arg2 = (double) j_arg2;
  double rate;

  // DEBUG printf("[JNI] Before calling ITM_AMNS_CC_RX_0_B\n");
  // DEBUG printf("[JNI] cx_handle: %x, arg1: %e, arg2: %e\n", ptrHandleRx, arg1, arg2);
  ITM_AMNS_CC_RX_0_B(amns_cx_handle, &rate, arg1, arg2, &error_stat);
  // DEBUG printf("[JNI] After calling ITM_AMNS_CC_RX_0_B\n");
  // DEBUG printf("[JNI] rate: %e\n", rate);

  // we have to make sure that error_stat is passed back inside object

  copyCError2JavaError( &error_stat, env, j_error_state);

  return (jdouble) rate;

}

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JNIEXPORT jdoubleArray JNICALL Java_amns_Amns_ItmAmnsCCRX1A	(	JNIEnv *	env,
		jobject	obj,
		jlong	ptrHandleRx,
		jint	nx,
		jdoubleArray	j_arg1,
		jobject	j_error_state
	)

Definition at line 447 of file amns_jni_call.c.

                                                                                   {
  
  amns_c_error_type error_stat = DEFAULT_AMNS_C_ERROR_TYPE;
  void *handle_rx_in = (void *) ptrHandleRx;

  jsize len_arr1 = (*env)->GetArrayLength(env, j_arg1);
  jdouble *arg1 = (*env)->GetDoubleArrayElements(env, j_arg1, 0);

  double *outputArray = (double *) malloc(nx * sizeof(double));

  // DEBUG printf("[JNI] Before calling ITM_AMNS_CC_RX_1_A\n");
  // DEBUG printf("[JNI] table_handle: %lu\n", (long)handle_rx_in);
  ITM_AMNS_CC_RX_1_A(handle_rx_in, nx, outputArray, arg1, &error_stat);
  // DEBUG printf("[JNI] After calling ITM_AMNS_CC_RX_1_A\n");

  // copy error to Java
  copyCError2JavaError( &error_stat, env, j_error_state);

  jdoubleArray outJNIArray = (*env)->NewDoubleArray(env, nx);
  if (NULL == outJNIArray) {
    return NULL;
  }
  (*env)->SetDoubleArrayRegion(env, outJNIArray, 0 , nx, outputArray);

  return outJNIArray;   
}

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JNIEXPORT jdoubleArray JNICALL Java_amns_Amns_ItmAmnsCCRX1B	(	JNIEnv *	env,
		jobject	obj,
		jlong	ptrHandleRx,
		jint	nx,
		jdoubleArray	j_arg1,
		jdoubleArray	j_arg2,
		jobject	j_error_state
	)

Definition at line 480 of file amns_jni_call.c.

                                                                                   {
  
  amns_c_error_type error_stat = DEFAULT_AMNS_C_ERROR_TYPE;
  void *handle_rx_in = (void *) ptrHandleRx;

  jsize len_arr1 = (*env)->GetArrayLength(env, j_arg1);
  jdouble *arg1 = (*env)->GetDoubleArrayElements(env, j_arg1, 0);

  jsize len_arr2 = (*env)->GetArrayLength(env, j_arg2);
  jdouble *arg2 = (*env)->GetDoubleArrayElements(env, j_arg2, 0);       

  double *outputArray = (double *) malloc(nx * sizeof(double));

  // DEBUG printf("[JNI] Before calling ITM_AMNS_CC_RX_1_B\n");
  // DEBUG printf("[JNI] table_handle: %lu\n", (long)handle_rx_in);

  /*printf("--- JNI CODE - arg1 - start ---\n");
    int ii=0;
    for(ii=0; ii<nx; ii++ ) {
    printf("%1.6f ", arg1[ii]);
    }
    printf("\n");
    printf("--- JNI CODE - end ---\n");
    fflush(stdout);
    printf("--- JNI CODE - arg2 - start ---\n");
    for(ii=0; ii<nx; ii++ ) {
    printf("%1.6f ", arg2[ii]);
    }
    printf("\n");
    printf("--- JNI CODE - end ---\n");
    fflush(stdout);*/

  ITM_AMNS_CC_RX_1_B(handle_rx_in, nx, outputArray, arg1, arg2, &error_stat);
  // DEBUG printf("[JNI] After calling ITM_AMNS_CC_RX_1_B\n");

  // copy error to Java
  copyCError2JavaError( &error_stat, env, j_error_state);

  jdoubleArray outJNIArray = (*env)->NewDoubleArray(env, nx);
  if (NULL == outJNIArray) {
    return NULL;
  }
  (*env)->SetDoubleArrayRegion(env, outJNIArray, 0 , nx, outputArray);

  return outJNIArray;   

}

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JNIEXPORT jdoubleArray JNICALL Java_amns_Amns_ItmAmnsCCRX1C	(	JNIEnv *	env,
		jobject	obj,
		jlong	ptrHandleRx,
		jint	nx,
		jdoubleArray	j_arg1,
		jdoubleArray	j_arg2,
		jdoubleArray	j_arg3,
		jobject	j_error_state
	)

Definition at line 535 of file amns_jni_call.c.

                                                                                   {

  amns_c_error_type error_stat = DEFAULT_AMNS_C_ERROR_TYPE;
  void *handle_rx_in = (void *) ptrHandleRx;


  jsize len_arr1 = (*env)->GetArrayLength(env, j_arg1);
  jdouble *arg1 = (*env)->GetDoubleArrayElements(env, j_arg1, 0);

  jsize len_arr2 = (*env)->GetArrayLength(env, j_arg2);
  jdouble *arg2 = (*env)->GetDoubleArrayElements(env, j_arg2, 0);

  jsize len_arr3 = (*env)->GetArrayLength(env, j_arg3);
  jdouble *arg3 = (*env)->GetDoubleArrayElements(env, j_arg3, 0);

  double *outputArray = (double *) malloc(nx * sizeof(double));

  // DEBUG printf("[JNI] Before calling ITM_AMNS_CC_RX_1_C\n");
  // DEBUG printf("[JNI] table_handle: %lu\n", (long)handle_rx_in);
  ITM_AMNS_CC_RX_1_C(handle_rx_in, nx, outputArray, arg1, arg2, arg3, &error_stat);
  // DEBUG printf("[JNI] After calling ITM_AMNS_CC_RX_1_C\n");

  // copy error to Java
  copyCError2JavaError( &error_stat, env, j_error_state);

  jdoubleArray outJNIArray = (*env)->NewDoubleArray(env, nx);
  if (NULL == outJNIArray) {
    return NULL;
  }
  (*env)->SetDoubleArrayRegion(env, outJNIArray, 0 , nx, outputArray);

  return outJNIArray;

}

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JNIEXPORT void JNICALL Java_amns_Amns_ItmAmnsCCSet	(	JNIEnv *	env,
		jobject	obj,
		jlong	ptrAmnsHandle,
		jobject	j_amns_set_type,
		jobject	j_error_state
	)

Definition at line 306 of file amns_jni_call.c.

                                                                            {

  amns_c_set_type set = DEFAULT_AMNS_C_SET_TYPE;
  amns_c_error_type error_stat = DEFAULT_AMNS_C_ERROR_TYPE;
  void *amns_handler = (void *) ptrAmnsHandle;

  jclass cls = (*env)->GetObjectClass(env, j_amns_set_type);
  jfieldID paramString = (*env)->GetFieldID(env, cls, "string", "Ljava/lang/String;");

  jstring j_set_type_string = (*env)->GetObjectField(env, j_amns_set_type, paramString);

  char *set_type_string = (char*)(*env)->GetStringUTFChars(env, j_set_type_string, NULL);

  set.string = set_type_string;

  // DEBUG printf("[JNI] Before calling ITM_AMNS_CC_SET\n");
  // DEBUG printf("[JNI] amns_handle: %lu\n", (long)ptrAmnsHandle);
  ITM_AMNS_CC_SET(amns_handler, &set, &error_stat);
  // DEBUG printf("[JNI] After calling ITM_AMNS_CC_SET\n");     

  copyCError2JavaError( &error_stat, env, j_error_state);
        
  (*env)->ReleaseStringUTFChars(env, j_set_type_string, set_type_string);               

}

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JNIEXPORT void JNICALL Java_amns_Amns_ItmAmnsCCSetReactant	(	JNIEnv *	env,
		jobject	obj,
		jlong	ptr,
		jobject	acrt
	)

Definition at line 54 of file amns_jni_call.c.

                                                                                                              {
  
  void *reactant_handle = (void*) ptr;

  amns_c_reactant_type species  = DEFAULT_AMNS_C_REACTANT_TYPE;
        
  jclass cls = (*env)->GetObjectClass(env, acrt);
  jfieldID paramZN = (*env)->GetFieldID(env, cls, "ZN", "D");
  jfieldID paramZA = (*env)->GetFieldID(env, cls, "ZA", "D");
  jfieldID paramMI = (*env)->GetFieldID(env, cls, "MI", "D");
  jfieldID paramLR = (*env)->GetFieldID(env, cls, "LR", "I");
  jfieldID paramRealSpecifier = (*env)->GetFieldID(env, cls, "real_specifier", "D");
  jfieldID paramIntSpecifier = (*env)->GetFieldID(env, cls, "int_specifier", "I");

  jdouble zn = (*env)->GetDoubleField(env, acrt, paramZN);
  jdouble za = (*env)->GetDoubleField(env, acrt, paramZA);
  jdouble mi = (*env)->GetDoubleField(env, acrt, paramMI);
  jint lr = (*env)->GetIntField(env, acrt, paramLR);
  jdouble rs = (*env)->GetDoubleField(env, acrt, paramRealSpecifier);
  jint int_spec = (*env)->GetIntField(env, acrt, paramIntSpecifier);

  // DEBUG printf("[JNI] Values from Java: %f:%f:%f:%i:%f:%i\n", zn, za, mi, lr, rs, int_spec);

  species.ZN=zn; species.ZA=za; species.MI=mi; species.LR=lr; species.real_specifier=rs; species.int_specifier=int_spec;
  ITM_AMNS_CC_SET_REACTANT(reactant_handle, 1, &species);
  // DEBUG printf("[JNI] After calling ITM_AMNS_CC_SET_REACTANT\n");
}

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JNIEXPORT void JNICALL Java_amns_Amns_ItmAmnsCCSetReactantIdx	(	JNIEnv *	env,
		jobject	obj,
		jlong	ptr,
		jint	idx,
		jobject	acrt
	)

Definition at line 82 of file amns_jni_call.c.

                                                                            {

  void *reactant_handle = (void*) ptr;

  amns_c_reactant_type species  = DEFAULT_AMNS_C_REACTANT_TYPE;
        
  jclass cls = (*env)->GetObjectClass(env, acrt);
  jfieldID paramZN = (*env)->GetFieldID(env, cls, "ZN", "D");
  jfieldID paramZA = (*env)->GetFieldID(env, cls, "ZA", "D");
  jfieldID paramMI = (*env)->GetFieldID(env, cls, "MI", "D");
  jfieldID paramLR = (*env)->GetFieldID(env, cls, "LR", "I");
  jfieldID paramRealSpecifier = (*env)->GetFieldID(env, cls, "real_specifier", "D");
  jfieldID paramIntSpecifier = (*env)->GetFieldID(env, cls, "int_specifier", "I");

  jdouble zn = (*env)->GetDoubleField(env, acrt, paramZN);
  jdouble za = (*env)->GetDoubleField(env, acrt, paramZA);
  jdouble mi = (*env)->GetDoubleField(env, acrt, paramMI);
  jint lr = (*env)->GetIntField(env, acrt, paramLR);
  jdouble rs = (*env)->GetDoubleField(env, acrt, paramRealSpecifier);
  jint int_spec = (*env)->GetIntField(env, acrt, paramIntSpecifier);

  // DEBUG printf("[JNI] Values from Java: %f:%f:%f:%i:%f:%i\n", zn, za, mi, lr, rs, int_spec);

  species.ZN=zn; species.ZA=za; species.MI=mi; species.LR=lr; species.real_specifier=rs; species.int_specifier=int_spec;
  // DEBUG printf("[JNI] Calling ITM_AMNS_CC_SET_REACTANT with index: %d\n", idx);
  ITM_AMNS_CC_SET_REACTANT(reactant_handle, idx, &species);
  // DEBUG printf("[JNI] After calling ITM_AMNS_CC_SET_REACTANT\n");
}

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JNIEXPORT void JNICALL Java_amns_Amns_ItmAmnsCCSetTable	(	JNIEnv *	env,
		jobject	obj,
		jlong	ptrAmnsCxHandle,
		jobject	j_amns_set_type,
		jobject	j_error_state
	)

Definition at line 578 of file amns_jni_call.c.

                                                                               {
  amns_c_set_type set = DEFAULT_AMNS_C_SET_TYPE;
  amns_c_error_type error_stat = DEFAULT_AMNS_C_ERROR_TYPE;
  void *amns_cx_handler = (void *) ptrAmnsCxHandle;

  jclass cls = (*env)->GetObjectClass(env, j_amns_set_type);
  jfieldID paramString = (*env)->GetFieldID(env, cls, "string", "Ljava/lang/String;");

  jstring j_set_type_string = (*env)->GetObjectField(env, j_amns_set_type, paramString);

  char *set_type_string = (char*)(*env)->GetStringUTFChars(env, j_set_type_string, NULL);

  set.string = set_type_string;

  // DEBUG printf("[JNI] Before calling ITM_AMNS_CC_SET_TABLE\n");
  // DEBUG printf("[JNI] amns_cx_handle: %lu\n", (long)ptrAmnsCxHandle);
  ITM_AMNS_CC_SET_TABLE(amns_cx_handler, &set, &error_stat);
  // DEBUG printf("[JNI] After calling ITM_AMNS_CC_SET_TABLE\n");

  copyCError2JavaError( &error_stat, env, j_error_state);

  (*env)->ReleaseStringUTFChars(env, j_set_type_string, set_type_string);       
}

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JNIEXPORT long JNICALL Java_amns_Amns_ItmAmnsCCSetup	(	JNIEnv *	env,
		jobject	obj,
		jobject	error_structure
	)

Definition at line 152 of file amns_jni_call.c.

                                                                                                        {
  void* amns_handle = NULL;
  amns_c_error_type error_stat = DEFAULT_AMNS_C_ERROR_TYPE;

  // DEBUG printf("[JNI] Before calling ITM_AMNS_CC_SETUP\n");
  ITM_AMNS_CC_SETUP(&amns_handle, &error_stat);
  // DEBUG printf("[JNI] After calling ITM_AMNS_CC_SETUP\n");
  // DEBUG printf("[JNI] Pointer: %lu\n", (long)amns_handle);

  copyCError2JavaError( &error_stat, env, error_structure );

  return (long) amns_handle;
}

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JNIEXPORT jlong JNICALL Java_amns_Amns_ItmAmnsCcSetupReactants	(	JNIEnv *	env,
		jobject	obj,
		jint	idx
	)

Definition at line 36 of file amns_jni_call.c.

                                                                                                   {
  void *reactant_handle;
  ITM_AMNS_CC_SETUP_REACTANTS(&reactant_handle, "", idx, 1);
  // DEBUG printf("[JNI] After calling ITM_AMNS_CC_SETUP_REACTANTS\n");
  // DEBUG printf("[JNI] Pointer: %lu\n", (long)reactant_handle);
  return (long)reactant_handle;
}

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JNIEXPORT jlong JNICALL Java_amns_Amns_ItmAmnsCcSetupReactantsNumber	(	JNIEnv *	env,
		jobject	obj,
		jint	idx,
		jint	number
	)

Definition at line 44 of file amns_jni_call.c.

                                                                                                                      {
  void *reactant_handle;
  // DEBUG printf("[JNI] Calling ITM_AMNS_CC_SETUP_REACTANTS with number of reactions: %d\n", number);
  ITM_AMNS_CC_SETUP_REACTANTS(&reactant_handle, "", idx, number);
  // DEBUG printf("[JNI] After calling ITM_AMNS_CC_SETUP_REACTANTS\n");
  // DEBUG printf("[JNI] Pointer: %lu\n", (long)reactant_handle);
  return (long)reactant_handle;
}

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JNIEXPORT jlong JNICALL Java_amns_Amns_ItmAmnsCCSetupTable	(	JNIEnv *	env,
		jobject	obj,
		jlong	ptr_amns_handle,
		jobject	j_reaction_type,
		jlong	ptr_reactants_handle,
		jobject	j_error_state
	)

Definition at line 166 of file amns_jni_call.c.

                                                                                    {
  // declare structures used in call
  amns_c_error_type error_stat = DEFAULT_AMNS_C_ERROR_TYPE;
  void* amns_cx_handle;
  amns_c_reaction_type xx_rx;

  // get pointers
  void *amns_handle = (void*) ptr_amns_handle;
  void *reactants_handle = (void*) ptr_reactants_handle;

  // retrieve and copy values from reaction_type object
  jclass cls = (*env)->GetObjectClass(env, j_reaction_type);
  jfieldID paramString = (*env)->GetFieldID(env, cls, "string", "Ljava/lang/String;");
  jfieldID paramIsotope = (*env)->GetFieldID(env, cls, "isotopeResolved", "I");

  jstring j_reaction_string = (*env)->GetObjectField(env, j_reaction_type, paramString);
  jint j_reaction_isotope = (*env)->GetIntField(env, j_reaction_type, paramIsotope);

  char *reaction_string = (char*) (*env)->GetStringUTFChars(env, j_reaction_string, NULL);
  int reaction_isotope = (int) j_reaction_isotope;

  xx_rx.string = reaction_string;
  xx_rx.isotope_resolved = reaction_isotope;

  // DEBUG printf("[JNI] Reaction type = %s, %u\n", xx_rx.string, xx_rx.isotope_resolved);

  // we can now call C function
  // note that we will return amns_cx_handle as return value from function
  // DEBUG printf("[JNI] Before calling ITM_AMNS_CC_SETUP_TABLE\n");
  // DEBUG printf("[JNI] amns_handle pointer: %lu\n", (long)amns_handle);
  // DEBUG printf("[JNI] reactants_handle pointer: %lu\n", (long)reactants_handle);
  ITM_AMNS_CC_SETUP_TABLE(amns_handle, &xx_rx, reactants_handle, &amns_cx_handle, &error_stat);

  // DEBUG printf("[JNI] After calling ITM_AMNS_CC_SETUP_TABLE\n");
  // DEBUG printf("[JNI] reaction_handle pointer: %lu\n", (long)amns_cx_handle);

  // we have to make sure that error_stat is passed back inside object

  copyCError2JavaError( &error_stat, env, j_error_state);       

  // remember to release string
  (*env)->ReleaseStringUTFChars(env, j_reaction_string, reaction_string);

  return (long) amns_cx_handle;
}

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