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1   /*--------------------------------------------------------------------------
2    *  Copyright 2010 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  // SAMReadPair.java
20  // Since: Aug 2, 2010
21  //
22  //--------------------------------------
23  package org.utgenome.gwt.utgb.client.bio;
24  
25  /**
26   * Mate pair (paired end) of SAMReads
27   * 
28   * @author leo
29   * 
30   */
31  public class SAMReadPair extends Interval {
32  
33  	private static final long serialVersionUID = 1L;
34  
35  	private SAMReadLight first;
36  	private SAMReadLight second;
37  
38  	public SAMReadPair() {
39  	}
40  
41  	public SAMReadPair(SAMReadLight first, SAMReadLight second) {
42  		super(Math.min(first.unclippedStart, second.unclippedStart), Math.max(first.unclippedEnd, second.unclippedEnd));
43  		if (!(first.isFirstRead() && second.isSecondRead())) {
44  			throw new IllegalArgumentException("invalid sam read pair:\n" + first + "\n" + second);
45  		}
46  
47  		this.first = first;
48  		this.second = second;
49  	}
50  
51  	public SAMReadLight getFirst() {
52  		return first;
53  	}
54  
55  	public SAMReadLight getSecond() {
56  		return second;
57  	}
58  
59  	public Gap getGap() {
60  		return new Gap(first.getEnd(), second.getStart());
61  	}
62  
63  	@Override
64  	public String getName() {
65  		return first.getName();
66  	}
67  
68  	@Override
69  	public void accept(OnGenomeDataVisitor visitor) {
70  		visitor.visitSAMReadPair(this);
71  	}
72  }