1 /*--------------------------------------------------------------------------
2 * Copyright 2009 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-core Project
18 //
19 // ReferenceSequence.java
20 // Since: 2009/04/27
21 //
22 // $URL$
23 // $Author$
24 //--------------------------------------
25 package org.utgenome.gwt.utgb.client.bio;
26
27 /**
28 * reference genome sequence to which genome reads are aligned
29 *
30 * @author leo
31 *
32 */
33 public class ReferenceSequence implements OnGenome {
34
35 private static final long serialVersionUID = 1L;
36
37 public int start;
38 public String name;
39 public String sequence;
40
41 public ReferenceSequence() {
42 }
43
44 public void accept(OnGenomeDataVisitor visitor) {
45 visitor.visitSequence(this);
46 }
47
48 public int getStart() {
49 return start;
50 }
51
52 public int getEnd() {
53 if (sequence == null)
54 return start;
55 else
56 return start + sequence.length();
57 }
58
59 public String getName() {
60 return this.name;
61 }
62
63 public int length() {
64 return sequence != null ? sequence.length() : 0;
65 }
66 }