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 // ChrLoc.java
20 // Since: 2009/10/02
21 //
22 // $URL$
23 // $Author$
24 //--------------------------------------
25 package org.utgenome.gwt.utgb.client.bio;
26
27 import java.io.Serializable;
28
29 public class ChrLoc implements Serializable {
30 /**
31 *
32 */
33 private static final long serialVersionUID = 1L;
34
35 public int start;
36 public int end;
37 public String chr;
38
39 public ChrLoc() {
40 }
41
42 public ChrLoc(String chr, int start, int end) {
43 this.chr = chr;
44 this.start = start;
45 this.end = end;
46 }
47
48 public ChrLoc getLocForPositiveStrand() {
49 if (start < end)
50 return new ChrLoc(chr, start, end);
51 else
52 return new ChrLoc(chr, end, start);
53 }
54
55 public int length() {
56 return viewEnd() - viewStart();
57 }
58
59 public int viewStart() {
60 if (isSense())
61 return start;
62 else
63 return end;
64 }
65
66 public int viewEnd() {
67 if (isSense())
68 return end;
69 else
70 return start;
71 }
72
73 public boolean isSense() {
74 return start <= end;
75 }
76
77 public boolean isAntiSense() {
78 return !isSense();
79 }
80
81 @Override
82 public String toString() {
83 return chr + ":" + start + "-" + end;
84 }
85 }