1 /*--------------------------------------------------------------------------
2 * Copyright 2008 utgenome.org
3 *
4 * Licensed under the Apache License, Version 2.0 (the "License");
5 * you may not use this file except in compliance with the License.
6 * You may obtain a copy of the License at
7 *
8 * http://www.apache.org/licenses/LICENSE-2.0
9 *
10 * Unless required by applicable law or agreed to in writing, software
11 * distributed under the License is distributed on an "AS IS" BASIS,
12 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
13 * See the License for the specific language governing permissions and
14 * limitations under the License.
15 *--------------------------------------------------------------------------*/
16 //--------------------------------------
17 // utgb-shell Project
18 //
19 // Read.java
20 // Since: Apr 10, 2009
21 //
22 // $URL$
23 // $Author$
24 //--------------------------------------
25 package org.utgenome.format.silk.read;
26
27 import java.util.ArrayList;
28 import java.util.Properties;
29
30 public class Read
31 {
32 // -read(name, view_start, view_end, start, end, strand, sequence, QV*, _[json])|
33 public String name;
34 public long viewstart;
35 public long viewend;
36 public long start;
37 public long end;
38 public String strand;
39 public String sequence;
40 public ArrayList<Integer> qv = new ArrayList<Integer>();
41 private Properties prop = new Properties();
42
43 @Override
44 public String toString()
45 {
46 return String.format("name:%s, start:%s, end:%s, strand:%s, sequence:%s", name, start, end, strand, sequence);
47 }
48
49 public void put(String key, String value)
50 {
51 prop.put(key, value);
52 }
53 }