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 // GenomeKeywordEntry.java
20 // Since: 2010/05/19
21 //
22 // $URL$
23 // $Author$
24 //--------------------------------------
25 package org.utgenome.format.keyword;
26
27 /**
28 * Keyword associated to a genome region
29 *
30 * @author leo
31 *
32 */
33 public class GenomeKeywordEntry {
34
35 public String ref; // reference sequence ID (e.g. hg19, ut-medaka-1.0)
36 public String chr; // chromosome/contig/scaffold name
37 public String text; // text containing keywords
38 public int start; // start position
39 public int end; // end position
40
41 public GenomeKeywordEntry(String ref, String chr, String text, int start, int end) {
42 this.ref = ref;
43 this.chr = chr;
44 this.text = text;
45
46 if (end <= start) {
47 int tmp = start;
48 start = end;
49 end = tmp;
50 }
51
52 this.start = start;
53 this.end = end;
54 }
55
56 /**
57 * Alias is a keyword
58 *
59 * @author leo
60 *
61 */
62 public static class KeywordAlias {
63 public String keyword; // the keyword to redirect
64 public String alias; // aliases
65
66 public KeywordAlias(String keyword, String alias) {
67 this.keyword = keyword;
68 this.alias = alias;
69 }
70
71 }
72
73 }