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 // SAMReadPairFragment.java
20 // Since: 2010/12/02
21 //
22 //--------------------------------------
23 package org.utgenome.gwt.utgb.client.bio;
24
25 /**
26 * Paired-end reads without the other mate data
27 *
28 * @author leo
29 *
30 */
31 public class SAMReadPairFragment extends Interval {
32 /**
33 *
34 */
35 private static final long serialVersionUID = 1L;
36
37 public SAMReadLight oneEnd;
38 public int mateStart;
39
40 public SAMReadPairFragment() {
41 }
42
43 public SAMReadPairFragment(SAMReadLight oneEnd, int mateStart) {
44 super(Math.min(oneEnd.unclippedStart, mateStart), Math.max(oneEnd.unclippedEnd, mateStart));
45 this.oneEnd = oneEnd;
46 this.mateStart = mateStart;
47 }
48
49 @Override
50 public String getName() {
51 return oneEnd.getName();
52 }
53
54 public Gap getGap() {
55 if (mateStart > oneEnd.unclippedEnd) {
56 return new Gap(oneEnd.unclippedEnd, mateStart);
57 }
58 else if (mateStart < oneEnd.unclippedStart) {
59 return new Gap(mateStart, oneEnd.unclippedStart);
60 }
61 else
62 return new Gap(-1, -1);
63 }
64
65 @Override
66 public void accept(OnGenomeDataVisitor visitor) {
67 visitor.visitSAMReadPairFragment(this);
68 }
69 }