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 // Reference.java
20 // Since: Apr 10, 2009
21 //
22 // $URL$
23 // $Author$
24 //--------------------------------------
25 package org.utgenome.format.silk.read;
26
27 /**
28 * Reference Sequence
29 *
30 * @author leo
31 *
32 */
33 public class Reference
34 {
35 public String name;
36 public long start;
37 public String strand;
38 public int tag;
39 public long s2st;
40 public long s2ed;
41 public String s2strand;
42 public int score;
43
44 public void addRead(Read read)
45 {
46
47 }
48
49 public void appendSequence(String sequence)
50 {
51 // incrementally process long sequence data
52
53 }
54
55 }