123 lines
3.1 KiB
Java
123 lines
3.1 KiB
Java
/*
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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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import java.util.Map;
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import java.util.HashMap;
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import java.util.List;
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import java.util.ArrayList;
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public class HT2Module {
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static {
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System.loadLibrary("ht2jni");
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}
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public static class HT2Position {
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int chr_id;
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int direction;
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long position;
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HT2Position(int id, int dir, int pos) {
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this.chr_id = id;
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this.direction = dir;
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this.position = pos;
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}
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@Override
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public String toString()
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{
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return getClass().getSimpleName()
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+ "[chr_id=" + chr_id
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+ ", direction=" + direction
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+ ", position=" + position + "]";
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}
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}
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private native long init(String indexName, Map<String, Integer> options);
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private native void close(long handle);
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private native Map<String, Integer> get_options();
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private native String index_getrefnamebyid(long handle, int id);
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private native List<String> index_getrefnames(long handle);
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private native List<HT2Position> repeat_expand(long handle, String name, long rpos, long rlen);
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private long handle;
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HT2Module() {
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handle = 0;
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}
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public void initLibrary(String indexName) {
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initLibrary(indexName, null);
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}
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public void initLibrary(String indexName, Map<String, Integer> options)
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{
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if(handle == 0) {
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handle = init(indexName, options);
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}
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}
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public Map<String, Integer> initOption()
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{
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return get_options();
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}
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public String getRefNameById(int chr_id)
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{
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if(handle == 0) {
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// TODO: Exception
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return "";
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}
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// TODO: Exception(OutOfIndex)
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return index_getrefnamebyid(handle, chr_id);
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}
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public List<String> getRefNames()
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{
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if(handle == 0) {
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// TODO: Exception
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return new ArrayList<>();
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}
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return index_getrefnames(handle);
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}
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public List<HT2Position> repeatExpand(String name, long position, long length)
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{
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if(handle == 0) {
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// TODO: Exception
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return new ArrayList<>();
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}
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return repeat_expand(handle, name, position, length);
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}
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public void cleanup()
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{
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if(handle != 0) {
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close(handle);
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handle = 0;
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}
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}
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public void finalize() {
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cleanup();
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}
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}
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