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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: 2010/05/20
21  //
22  // $URL$ 
23  // $Author$
24  //--------------------------------------
25  package org.utgenome.gwt.utgb.client.ribbon;
26  
27  import java.util.ArrayList;
28  import java.util.List;
29  
30  /**
31   * Ribbon is a coordinate for representing insertions to reference and deletions to reference,
32   * 
33   * <pre>
34   * xOffset:            1 2 3 4 5 6 7 8 9
35   * normal coordinate:  1 2 3 4 5 6 7 8 9  
36   *                     - - - - - - - - - 
37   * -cigar: 9M                    
38   *                     
39   * [insertion]
40   * xOffset:            1 2 3 4 5 6 7 8 9 10 11
41   * ribbon coordinate:  1 2 3 - - - - - 4  5  6
42   *                          /         \
43   *                     - - -           -  -  -  
44   * -insertion(pos:4, length:5)
45   * -cigar: 3M5I3M
46   * 
47   * 
48   * 
49   * [deletion] 
50   * xOffset:            1 2 3 4 5 6  7  8  9 10 11
51   * ribbon coordinate:  1 2 3 7 8 9 10 11 12 13 14
52   *                     - - - - - -  -  -  -  -  -
53   *                         / \
54   *                         ---
55   *                     3.1 3.2 3.3
56   * -deletion(pos:4, length:3)
57   * -cigar: 3M3D7M
58   * </pre>
59   * 
60   * @author leo
61   * 
62   */
63  public class Ribbon {
64  
65  	public static enum CreaseType {
66  		INSERTION, DELETION
67  	}
68  
69  	/**
70  	 * A crease is a point where insertion or deletion occurs.
71  	 * 
72  	 * @author leo
73  	 * 
74  	 */
75  	public static class Crease {
76  		public int x;
77  		public int length;
78  		public CreaseType type;
79  
80  		private Crease(int x, int length, CreaseType type) {
81  			this.x = x;
82  			this.length = length;
83  			this.type = type;
84  		}
85  
86  		public boolean overlap(int start, int length) {
87  
88  			return false;
89  		}
90  
91  		public static Crease newInsertion(int x, int length) {
92  			return new Crease(x, length, CreaseType.INSERTION);
93  		}
94  
95  		public static Crease newDeletion(int x, int length) {
96  			return new Crease(x, length, CreaseType.DELETION);
97  		}
98  	}
99  
100 	private List<Crease> crease = new ArrayList<Crease>();
101 
102 	public Ribbon() {
103 
104 	}
105 
106 	public List<Crease> getCreaseInRange(int start, int end) {
107 		ArrayList<Crease> result = new ArrayList<Crease>();
108 		for (Crease each : crease) {
109 
110 		}
111 		return result;
112 	}
113 
114 }