433 lines
11 KiB
C
433 lines
11 KiB
C
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/*
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* Copyright 2018, Chanhee Park <parkchanhee@gmail.com> and Daehwan Kim <infphilo@gmail.com>
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*
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* This file is part of HISAT 2.
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*
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* HISAT 2 is free software: you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* HISAT 2 is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with HISAT 2. If not, see <http://www.gnu.org/licenses/>.
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*/
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#include <jni.h>
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#include <stdio.h>
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#include "ht2.h"
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#include "HT2Module.h"
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#define CLASSPATH_INTEGER "java/lang/Integer"
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#define CLASSPATH_HASHMAP "java/util/HashMap"
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#define CLASSPATH_ARRAYLIST "java/util/ArrayList"
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#define CLASSPATH_HT2POSITION "HT2Module$HT2Position"
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#ifdef DEBUG
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#define DEBUGLOG(fmt, ...) do { fprintf(stderr, "%s:%d:%s(): " fmt, __FILE__, __LINE__, __func__, ##__VA_ARGS__); } while(0)
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#else
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#define DEBUGLOG(fmt, ...)
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#endif
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static jint JNI_VERSION = JNI_VERSION_1_2;
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static jclass classInteger;
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static jclass classHashMap;
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static jclass classArrayList;
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static jclass classHT2Position;
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static jmethodID mthIntegerInit;
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static jmethodID mthIntegerIntValue;
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static jmethodID mthHashMapInit;
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static jmethodID mthHashMapPut;
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static jmethodID mthHashMapGet;
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static jmethodID mthArrayListInit;
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static jmethodID mthArrayListEnsureCapacity;
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static jmethodID mthArrayListAdd;
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static jmethodID mthHT2PositionInit;
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static jobject NewHashMap(JNIEnv *env)
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{
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jobject obj = (*env)->NewObject(env, classHashMap, mthHashMapInit);
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return obj;
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}
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static jobject NewInteger(JNIEnv *env, int value)
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{
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jobject obj = (*env)->NewObject(env, classInteger, mthIntegerInit, value);
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return obj;
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}
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static jobject NewArrayList(JNIEnv *env)
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{
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jobject obj = (*env)->NewObject(env, classArrayList, mthArrayListInit);
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return obj;
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}
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static jobject NewHT2Position(JNIEnv *env, struct ht2_position *htpos)
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{
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jobject obj = (*env)->NewObject(env, classHT2Position, mthHT2PositionInit,
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htpos->chr_id, htpos->direction, htpos->pos);
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return obj;
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}
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static int GetInteger(JNIEnv *env, jobject jobjInt, int *val)
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{
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int value = (*env)->CallIntMethod(env, jobjInt, mthIntegerIntValue);
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*val = value;
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return 0;
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}
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static void hashmap_put(JNIEnv *env, jobject jobjMap,
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const char *key_str, const int val)
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{
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jstring keyObj;
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jobject valueObj;
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keyObj = (*env)->NewStringUTF(env, key_str);
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valueObj = NewInteger(env, val);
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(*env)->CallObjectMethod(env, jobjMap, mthHashMapPut, keyObj, valueObj);
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(*env)->DeleteLocalRef(env, keyObj);
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(*env)->DeleteLocalRef(env, valueObj);
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}
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static int hashmap_get(JNIEnv *env, jobject jobjMap,
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const char *key_str, int *val)
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{
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jstring keyObj;
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jobject valueObj;
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keyObj = (*env)->NewStringUTF(env, key_str);
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valueObj = (*env)->CallObjectMethod(env, jobjMap, mthHashMapGet, keyObj);
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if(valueObj == NULL) {
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DEBUGLOG("Can't find key: %s\n", key_str);
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(*env)->DeleteLocalRef(env, keyObj);
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return -1;
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}
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// Integer -> int
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int value = 0;
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if(GetInteger(env, valueObj, &value) < 0) {
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DEBUGLOG("Can't get Integer\n");
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(*env)->DeleteLocalRef(env, keyObj);
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(*env)->DeleteLocalRef(env, valueObj);
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return -1;
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}
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(*env)->DeleteLocalRef(env, keyObj);
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(*env)->DeleteLocalRef(env, valueObj);
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*val = value;
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return 0;
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}
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static jobject conv_ht2option(JNIEnv *env, ht2_option_t *opts)
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{
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jobject hashMap = NewHashMap(env);
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#define HT2_OPT_BUILD(_name) \
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hashmap_put(env, hashMap, #_name , opts->_name)
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HT2_OPT_BUILD(offRate);
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HT2_OPT_BUILD(useMm);
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HT2_OPT_BUILD(useShmem);
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HT2_OPT_BUILD(mmSweep);
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HT2_OPT_BUILD(noRefNames);
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HT2_OPT_BUILD(noSplicedAlignment);
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HT2_OPT_BUILD(gVerbose);
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HT2_OPT_BUILD(startVerbose);
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HT2_OPT_BUILD(sanityCheck);
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HT2_OPT_BUILD(useHaplotype);
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return hashMap;
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}
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static void update_ht2option(JNIEnv *env, ht2_option_t *opts, jobject jmapObject)
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{
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#define HT2_OPT_UPDATE(_name) \
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do { \
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int value = 0; \
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if(hashmap_get(env, jmapObject, #_name, &value) == 0) { \
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DEBUGLOG("Using %s, %d\n", #_name, value); \
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opts->_name = value; \
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} else { \
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DEBUGLOG("Using default %s, %d\n", #_name, opts->_name); \
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}\
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} while(0)
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HT2_OPT_UPDATE(offRate);
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HT2_OPT_UPDATE(useMm);
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HT2_OPT_UPDATE(useShmem);
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HT2_OPT_UPDATE(mmSweep);
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HT2_OPT_UPDATE(noRefNames);
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HT2_OPT_UPDATE(noSplicedAlignment);
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HT2_OPT_UPDATE(gVerbose);
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HT2_OPT_UPDATE(startVerbose);
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HT2_OPT_UPDATE(sanityCheck);
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HT2_OPT_UPDATE(useHaplotype);
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}
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static void conv_refnames_result(JNIEnv *env,
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struct ht2_index_getrefnames_result *result, jobject jobjList)
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{
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size_t i;
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// Resize
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DEBUGLOG("count: %d\n", result->count);
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(*env)->CallVoidMethod(env, jobjList, mthArrayListEnsureCapacity, result->count);
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for(i = 0; i < result->count; i++) {
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DEBUGLOG("names[%d] %s\n", i, result->names[i]);
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jobject elem = (*env)->NewStringUTF(env, result->names[i]);
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(*env)->CallObjectMethod(env, jobjList, mthArrayListAdd, elem);
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(*env)->DeleteLocalRef(env, elem);
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}
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}
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static void conv_repeat_expand_result(JNIEnv *env,
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struct ht2_repeat_expand_result *result,
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jobject jobjList)
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{
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size_t i;
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// Resize
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DEBUGLOG("count: %d\n", result->count);
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(*env)->CallVoidMethod(env, jobjList, mthArrayListEnsureCapacity, result->count);
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// Add Items
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for(i = 0; i < result->count; i++) {
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struct ht2_position *htpos = &result->positions[i];
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DEBUGLOG("position[%d]: %u, %d, %lu\n", i, htpos->chr_id, htpos->direction, htpos->pos);
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jobject elem = NewHT2Position(env, htpos);
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(*env)->CallObjectMethod(env, jobjList, mthArrayListAdd, elem);
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(*env)->DeleteLocalRef(env, elem);
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}
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}
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JNIEXPORT jlong JNICALL Java_HT2Module_init(JNIEnv *env,
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jobject thisObj, jstring indexNameObj, jobject optionMap)
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{
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DEBUGLOG("Init\n");
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const char *index_path = (*env)->GetStringUTFChars(env, indexNameObj, NULL);
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if(index_path == NULL) {
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DEBUGLOG("Can't get string\n");
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return 0;
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}
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DEBUGLOG("Index Path: %s\n", index_path);
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ht2_option_t ht2opt;
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ht2_init_options(&ht2opt);
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if(optionMap != NULL) {
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// update options
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update_ht2option(env, &ht2opt, optionMap);
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}
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ht2_handle_t handle = ht2_init(index_path, &ht2opt);
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DEBUGLOG("Initailzed %p\n", handle);
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(*env)->ReleaseStringUTFChars(env, indexNameObj, index_path);
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return (jlong)handle;
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}
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JNIEXPORT void JNICALL Java_HT2Module_close(JNIEnv *env,
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jobject thisObj, jlong handlePtr)
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{
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DEBUGLOG("Closing\n");
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ht2_handle_t handle = (ht2_handle_t)handlePtr;
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DEBUGLOG("Received handle: %p\n", handle);
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ht2_close(handle);
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}
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JNIEXPORT jobject JNICALL Java_HT2Module_get_1options(JNIEnv *env,
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jobject thisObj)
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{
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DEBUGLOG("get_option\n");
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// Get Default options
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ht2_option_t ht2opt;
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ht2_init_options(&ht2opt);
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// convert ht2opt to java hashmap
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jobject hashobj = conv_ht2option(env, &ht2opt);
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return hashobj;
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}
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JNIEXPORT jstring JNICALL Java_HT2Module_index_1getrefnamebyid(JNIEnv *env,
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jobject thisObj, jlong handlePtr, jint chr_id)
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{
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DEBUGLOG("index_getrefnamebyid\n");
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ht2_handle_t handle = (ht2_handle_t)handlePtr;
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if(handle == NULL) {
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DEBUGLOG("Invalid handle\n");
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return NULL;
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}
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const char *refname = ht2_index_getrefnamebyid(handle, chr_id);
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if(refname == NULL) {
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DEBUGLOG("Can't get refname(%d)\n", chr_id);
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return NULL;
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}
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return (*env)->NewStringUTF(env, refname);
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}
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JNIEXPORT jobject JNICALL Java_HT2Module_index_1getrefnames(JNIEnv *env,
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jobject thisObj, jlong handlePtr)
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{
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DEBUGLOG("index_getrefnames\n");
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ht2_handle_t handle = (ht2_handle_t)handlePtr;
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if(handle == NULL) {
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DEBUGLOG("Invalid handle\n");
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return NULL;
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}
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struct ht2_index_getrefnames_result *result = NULL;
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ht2_error_t ret = ht2_index_getrefnames(handle, &result);
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jobject refnames = NewArrayList(env);
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if(ret == HT2_OK) {
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DEBUGLOG("refnames size: %d\n", result->count);
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conv_refnames_result(env, result, refnames);
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free(result);
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} else {
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DEBUGLOG("Can't get refnames\n");
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}
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return refnames;
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}
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JNIEXPORT jobject JNICALL Java_HT2Module_repeat_1expand(JNIEnv *env,
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jobject thisObj, jlong handlePtr, jstring nameObj, jlong rpos, jlong rlen)
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{
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DEBUGLOG("repeat_expand\n");
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ht2_handle_t handle = (ht2_handle_t)handlePtr;
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if(handle == NULL) {
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DEBUGLOG("Invalid handle\n");
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return NULL;
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}
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const char *name = (*env)->GetStringUTFChars(env, nameObj, NULL);
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if(name == NULL) {
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DEBUGLOG("Can't get string\n");
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return NULL;
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}
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DEBUGLOG("Repeat Expand: %s, %lu, %lu\n", name, rpos, rlen);
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struct ht2_repeat_expand_result *result = NULL;
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ht2_error_t ret = ht2_repeat_expand(handle, name, rpos, rlen, &result);
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jobject positions = NewArrayList(env);
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if(ret == HT2_OK) {
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DEBUGLOG("expand position size: %d\n", result->count);
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conv_repeat_expand_result(env, result, positions);
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free(result);
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} else {
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DEBUGLOG("Can't expand repeat\n");
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}
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(*env)->ReleaseStringUTFChars(env, nameObj, name);
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return positions;
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}
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jint JNI_OnLoad(JavaVM *vm, void *reserved)
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{
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DEBUGLOG("JNI Loaded\n");
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JNIEnv *env;
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if((*vm)->GetEnv(vm, (void **)&env, JNI_VERSION) != JNI_OK) {
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return JNI_ERR;
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}
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// Load Class
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#define LOAD_CLASS(_globalRef, _clazz) \
|
||
|
|
do { \
|
||
|
|
jclass tmpClassRef = (*env)->FindClass(env, _clazz); \
|
||
|
|
if(tmpClassRef == NULL) { \
|
||
|
|
DEBUGLOG("Can't find class %s\n", _clazz); \
|
||
|
|
return JNI_ERR; \
|
||
|
|
} \
|
||
|
|
_globalRef = (jclass)(*env)->NewGlobalRef(env, tmpClassRef); \
|
||
|
|
(*env)->DeleteLocalRef(env, tmpClassRef); \
|
||
|
|
} while(0)
|
||
|
|
|
||
|
|
LOAD_CLASS(classInteger, CLASSPATH_INTEGER);
|
||
|
|
LOAD_CLASS(classHashMap, CLASSPATH_HASHMAP);
|
||
|
|
LOAD_CLASS(classArrayList, CLASSPATH_ARRAYLIST);
|
||
|
|
LOAD_CLASS(classHT2Position, CLASSPATH_HT2POSITION);
|
||
|
|
|
||
|
|
|
||
|
|
// Load Method
|
||
|
|
|
||
|
|
// Integer
|
||
|
|
mthIntegerInit = (*env)->GetMethodID(env, classInteger, "<init>", "(I)V");
|
||
|
|
mthIntegerIntValue = (*env)->GetMethodID(env, classInteger, "intValue", "()I");
|
||
|
|
|
||
|
|
// HashMap
|
||
|
|
mthHashMapInit = (*env)->GetMethodID(env, classHashMap, "<init>", "()V");
|
||
|
|
mthHashMapPut = (*env)->GetMethodID(env, classHashMap, "put",
|
||
|
|
"(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;");
|
||
|
|
mthHashMapGet = (*env)->GetMethodID(env, classHashMap, "get",
|
||
|
|
"(Ljava/lang/Object;)Ljava/lang/Object;");
|
||
|
|
|
||
|
|
// ArrayList
|
||
|
|
mthArrayListInit = (*env)->GetMethodID(env, classArrayList, "<init>", "()V");
|
||
|
|
mthArrayListEnsureCapacity = (*env)->GetMethodID(env, classArrayList, "ensureCapacity", "(I)V");
|
||
|
|
mthArrayListAdd = (*env)->GetMethodID(env, classArrayList, "add",
|
||
|
|
"(Ljava/lang/Object;)Z");
|
||
|
|
|
||
|
|
// HT2Position
|
||
|
|
mthHT2PositionInit = (*env)->GetMethodID(env, classHT2Position, "<init>", "(III)V");
|
||
|
|
|
||
|
|
return JNI_VERSION;
|
||
|
|
}
|
||
|
|
|
||
|
|
|
||
|
|
void JNI_OnUnload(JavaVM *vm, void *reserved)
|
||
|
|
{
|
||
|
|
DEBUGLOG("JNI Unload\n");
|
||
|
|
JNIEnv *env;
|
||
|
|
|
||
|
|
(*vm)->GetEnv(vm, (void **)&env, JNI_VERSION);
|
||
|
|
|
||
|
|
(*env)->DeleteGlobalRef(env, classInteger);
|
||
|
|
(*env)->DeleteGlobalRef(env, classHashMap);
|
||
|
|
(*env)->DeleteGlobalRef(env, classArrayList);
|
||
|
|
(*env)->DeleteGlobalRef(env, classHT2Position);
|
||
|
|
|
||
|
|
}
|
||
|
|
|