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