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 // ReadCoverage.java
20 // Since: 2010/05/25
21 //
22 // $URL$
23 // $Author$
24 //--------------------------------------
25 package org.utgenome.gwt.utgb.client.bio;
26
27 /**
28 * Read coverage histogram
29 *
30 * @author leo
31 *
32 */
33 public class ReadCoverage extends Interval {
34
35 /**
36 *
37 */
38 private static final long serialVersionUID = 1L;
39
40 private String name = "read coverage";
41 /**
42 * Coverage of each pixel position
43 */
44 public int[] coverage;
45 public int pixelWidth;
46
47 public int maxHeight = 0;
48 public int minHeight = 0;
49
50 public ReadCoverage() {
51 }
52
53 public ReadCoverage(int start, int end, int pixelWidth, int[] coverage) {
54 super(start, end);
55 this.pixelWidth = pixelWidth;
56 this.coverage = coverage;
57
58 for (int each : coverage) {
59 if (maxHeight < each)
60 maxHeight = each;
61 if (minHeight > each)
62 minHeight = each;
63 }
64 }
65
66 @Override
67 public void accept(OnGenomeDataVisitor visitor) {
68 visitor.visitReadCoverage(this);
69 }
70
71 public void setName(String name) {
72 this.name = name;
73 }
74
75 @Override
76 public String getName() {
77 return name;
78 }
79 }