Mercurial > repos > timpalpant > java_genomics_toolkit

comparison src/edu/unc/genomics/nucleosomes/NucleosomeCall.java @ 2:e16016635b2a

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author timpalpant
date Mon, 13 Feb 2012 22:12:06 -0500
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1:a54db233ee3d 2:e16016635b2a
1 package edu.unc.genomics.nucleosomes;
2
3 import java.util.Comparator;
4
5 import edu.unc.genomics.ValuedInterval;
6 import edu.unc.genomics.io.IntervalFileFormatException;
7
8 /**
9 * @author timpalpant
10 *
11 */
12 public class NucleosomeCall extends ValuedInterval implements Comparable<NucleosomeCall> {
13
14 private static final long serialVersionUID = 6522702303121259979L;
15
16 private int dyad;
17 private double dyadStdev;
18 private double dyadMean;
19 private double conditionalPosition;
20 private int length;
21 private double lengthStdev;
22
23 /**
24 * @param chr
25 * @param start
26 * @param stop
27 */
28 public NucleosomeCall(String chr, int start, int stop) {
29 super(chr, start, stop);
30 }
31
32 public static NucleosomeCall parse(String line) {
33 if (line.startsWith("#")) return null;
34
35 String[] entry = line.split("\t");
36 if (entry.length < 10) {
37 throw new IntervalFileFormatException("Invalid nucleosome call has < 10 columns");
38 }
39
40 String chr = entry[0];
41 int start = Integer.parseInt(entry[1]);
42 int stop = Integer.parseInt(entry[2]);
43
44 NucleosomeCall call = new NucleosomeCall(chr, start, stop);
45 call.setLength(Integer.parseInt(entry[3]));
46 call.setLengthStdev(Double.parseDouble(entry[4]));
47 call.setDyad(Integer.parseInt(entry[5]));
48 call.setDyadStdev(Double.parseDouble(entry[6]));
49 call.setConditionalPosition(Double.parseDouble(entry[7]));
50 call.setDyadMean(Double.parseDouble(entry[8]));
51 call.setValue(Double.parseDouble(entry[9]));
52
53 return call;
54 }
55
56 @Override
57 public String toString() {
58 return chr+"\t"+start+"\t"+stop+"\t"+length()+"\t"+lengthStdev+"\t"+dyad+"\t"+dyadStdev+"\t"+conditionalPosition+"\t"+dyadMean+"\t"+occupancy();
59 }
60
61 /**
62 * @return the dyad
63 */
64 public int getDyad() {
65 return dyad;
66 }
67
68 /**
69 * @param dyad the dyad to set
70 */
71 public void setDyad(int dyad) {
72 this.dyad = dyad;
73 }
74
75 /**
76 * @return the dyadStdev
77 */
78 public double getDyadStdev() {
79 return dyadStdev;
80 }
81
82 /**
83 * @param dyadStdev the dyadStdev to set
84 */
85 public void setDyadStdev(double dyadStdev) {
86 this.dyadStdev = dyadStdev;
87 }
88
89 /**
90 * @return the dyadMean
91 */
92 public double getDyadMean() {
93 return dyadMean;
94 }
95
96 /**
97 * @param dyadMean the dyadMean to set
98 */
99 public void setDyadMean(double dyadMean) {
100 this.dyadMean = dyadMean;
101 }
102
103 /**
104 * @return the conditionalPosition
105 */
106 public double getConditionalPosition() {
107 return conditionalPosition;
108 }
109
110 /**
111 * @param conditionalPosition the conditionalPosition to set
112 */
113 public void setConditionalPosition(double conditionalPosition) {
114 this.conditionalPosition = conditionalPosition;
115 }
116
117 /**
118 * @return the length
119 */
120 public int getLength() {
121 return length;
122 }
123
124 /**
125 * @param length the length to set
126 */
127 public void setLength(int length) {
128 this.length = length;
129 }
130
131 /**
132 * @return the lengthStdev
133 */
134 public double getLengthStdev() {
135 return lengthStdev;
136 }
137
138 /**
139 * @param lengthStdev the lengthStdev to set
140 */
141 public void setLengthStdev(double lengthStdev) {
142 this.lengthStdev = lengthStdev;
143 }
144
145 public double occupancy() {
146 return value;
147 }
148
149 public void setOccupancy(double value) {
150 this.value = value;
151 }
152
153 @Override
154 public int compareTo(NucleosomeCall o) {
155 DyadComparator comparator = new DyadComparator();
156 return comparator.compare(this, o);
157 }
158
159 public static class DyadComparator implements Comparator<NucleosomeCall> {
160
161 @Override
162 public int compare(NucleosomeCall o1, NucleosomeCall o2) {
163 if (o1.getDyad() == o2.getDyad()) {
164 return 0;
165 } else if (o1.getDyad() < o2.getDyad()) {
166 return -1;
167 } else {
168 return 1;
169 }
170 }
171
172 }
173
174 }