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 // OnGenome.java
20 // Since: May 16, 2010
21 //
22 // $URL$
23 // $Author$
24 //--------------------------------------
25 package org.utgenome.gwt.utgb.client.bio;
26
27 import java.io.Serializable;
28
29 /**
30 * A common interface for data mapped onto a genome sequence (e.g., Read, Gene, SAMRead, WigGraphData, etc.)
31 *
32 * @author leo
33 *
34 */
35 public interface OnGenome extends Serializable {
36
37 /**
38 * return 1-based start position of the data. The interval represents [start, end). ([inclusive, exclusive))
39 *
40 * @return
41 */
42 public int getStart();
43
44 /**
45 * return 1-based end position of the data. The interval represents [start, end). ([inclusive, exclusive))
46 *
47 * @return
48 */
49 public int getEnd();
50
51 /**
52 * return the length of the data
53 *
54 * @return
55 */
56 public int length();
57
58 public String getName();
59
60 public void accept(OnGenomeDataVisitor visitor);
61 }