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/*
* Copyright 2018, Chanhee Park <parkchanhee@gmail.com> and Daehwan Kim <infphilo@gmail.com>
*
* This file is part of HISAT 2.
*
* HISAT 2 is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* HISAT 2 is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with HISAT 2. If not, see <http://www.gnu.org/licenses/>.
*/
import java.util.Map;
import java.util.HashMap;
import java.util.List;
import java.util.ArrayList;
public class HT2Module {
static {
System.loadLibrary("ht2jni");
}
public static class HT2Position {
int chr_id;
int direction;
long position;
HT2Position(int id, int dir, int pos) {
this.chr_id = id;
this.direction = dir;
this.position = pos;
}
@Override
public String toString()
{
return getClass().getSimpleName()
+ "[chr_id=" + chr_id
+ ", direction=" + direction
+ ", position=" + position + "]";
}
}
private native long init(String indexName, Map<String, Integer> options);
private native void close(long handle);
private native Map<String, Integer> get_options();
private native String index_getrefnamebyid(long handle, int id);
private native List<String> index_getrefnames(long handle);
private native List<HT2Position> repeat_expand(long handle, String name, long rpos, long rlen);
private long handle;
HT2Module() {
handle = 0;
}
public void initLibrary(String indexName) {
initLibrary(indexName, null);
}
public void initLibrary(String indexName, Map<String, Integer> options)
{
if(handle == 0) {
handle = init(indexName, options);
}
}
public Map<String, Integer> initOption()
{
return get_options();
}
public String getRefNameById(int chr_id)
{
if(handle == 0) {
// TODO: Exception
return "";
}
// TODO: Exception(OutOfIndex)
return index_getrefnamebyid(handle, chr_id);
}
public List<String> getRefNames()
{
if(handle == 0) {
// TODO: Exception
return new ArrayList<>();
}
return index_getrefnames(handle);
}
public List<HT2Position> repeatExpand(String name, long position, long length)
{
if(handle == 0) {
// TODO: Exception
return new ArrayList<>();
}
return repeat_expand(handle, name, position, length);
}
public void cleanup()
{
if(handle != 0) {
close(handle);
handle = 0;
}
}
public void finalize() {
cleanup();
}
}
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