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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  // DASResult.java
20  // Since: May 25, 2010
21  //
22  // $URL$ 
23  // $Author$
24  //--------------------------------------
25  package org.utgenome.gwt.utgb.client.bio;
26  
27  import java.io.Serializable;
28  import java.util.List;
29  
30  /**
31   * DAS Result
32   * 
33   * @author leo
34   * 
35   */
36  public class DASResult implements Serializable {
37  	/**
38  	 * 
39  	 */
40  	private static final long serialVersionUID = 1L;
41  
42  	public static class DASGFF implements Serializable {
43  		/**
44  		 * 
45  		 */
46  		private static final long serialVersionUID = 1L;
47  		public String version;
48  		public String href;
49  	}
50  
51  	public static class Segment implements Serializable {
52  		/**
53  		 * 
54  		 */
55  		private static final long serialVersionUID = 1L;
56  
57  		public String id;
58  		public long start;
59  		public long stop;
60  		public List<DASFeature> feature;
61  
62  	}
63  
64  	public static class DASFeature extends Read {
65  		private static final long serialVersionUID = 1L;
66  
67  		public String id;
68  
69  		public String label;
70  		public String score;
71  		public String orientation;
72  		public String phase;
73  
74  		public Method method;
75  		public FeatureType type;
76  		public Group group;
77  		public Target target;
78  
79  		public void setId(String id) {
80  			setName(id);
81  		}
82  
83  		public static class Target implements Serializable {
84  			/**
85  			 * 
86  			 */
87  			private static final long serialVersionUID = 1L;
88  			public String id;
89  			public long start;
90  			public long stop;
91  			public String value;
92  		}
93  
94  		public static class FeatureType implements Serializable {
95  			/**
96  			 * 
97  			 */
98  			private static final long serialVersionUID = 1L;
99  			public String id;
100 			public String category;
101 			public String reference;
102 			public String value;
103 		}
104 
105 		public static class Group implements Serializable {
106 			/**
107 			 * 
108 			 */
109 			private static final long serialVersionUID = 1L;
110 			public String id;
111 			public String type;
112 			public String label;
113 			public Link link;
114 			public Target target;
115 
116 			public static class Link implements Serializable {
117 				/**
118 				 * 
119 				 */
120 				private static final long serialVersionUID = 1L;
121 				public String href;
122 				public String value;
123 			}
124 		}
125 
126 		public static class Method implements Serializable {
127 			/**
128 			 * 
129 			 */
130 			private static final long serialVersionUID = 1L;
131 			public String id;
132 			public String value;
133 		}
134 	}
135 
136 	public DASGFF gff;
137 	public Segment segment;
138 
139 }