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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  // Ribbon.java
20  // Since: 2010/01/26
21  //
22  // $URL$ 
23  // $Author$
24  //--------------------------------------
25  package org.utgenome.gwt.ribbon.client.model;
26  
27  import java.io.Serializable;
28  import java.util.ArrayList;
29  
30  /**
31   * Ribbon for representing indels on a genome sequence
32   * 
33   * @author leo
34   * 
35   */
36  public class Ribbon implements Serializable {
37  
38  	private static final long serialVersionUID = 1L;
39  
40  	/**
41  	 * A segment of the ribbon
42  	 * 
43  	 * @author leo
44  	 * 
45  	 */
46  	public static class RibbonSegment {
47  
48  		public static enum SegmentType {
49  			GAP, FOLD, NORMAL
50  		}
51  
52  		/**
53  		 * start position on the reference genome
54  		 */
55  		public int start;
56  		/**
57  		 * end position on the reference genome
58  		 */
59  		public int end;
60  
61  		/**
62  		 * the length of this ribbon segment
63  		 */
64  		public int length;
65  
66  		/**
67  		 * GAP, FOLD, or NORMAL
68  		 */
69  		public SegmentType type;
70  		/**
71  		 * true if this segment is visible to the user, otherwise false
72  		 */
73  		public boolean isVisible = true;
74  
75  		public RibbonSegment(int start, int end, int length, SegmentType type) {
76  			this.start = start;
77  			this.end = end;
78  			this.type = type;
79  		}
80  	}
81  
82  	public ArrayList<RibbonSegment> segment = new ArrayList<RibbonSegment>();
83  
84  	public Ribbon() {
85  	}
86  
87  }