1 package compbio.data.sequence;
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3 import java.io.BufferedWriter;
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4 import java.io.IOException;
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5 import java.io.OutputStream;
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6 import java.io.OutputStreamWriter;
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7 import java.text.NumberFormat;
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8 import java.util.ArrayList;
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9 import java.util.Locale;
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10 import java.util.Set;
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11 import java.util.TreeSet;
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13 import javax.xml.bind.annotation.XmlAccessType;
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14 import javax.xml.bind.annotation.XmlAccessorType;
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16 import compbio.util.annotation.Immutable;
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19 * A value class for AACon annotation results storage. The objects of this type
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25 @XmlAccessorType(XmlAccessType.FIELD)
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27 public class Score {
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29 static final NumberFormat NUMBER_FORMAT = NumberFormat
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30 .getNumberInstance(Locale.UK);
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32 NUMBER_FORMAT.setGroupingUsed(false);
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33 NUMBER_FORMAT.setMaximumFractionDigits(3);
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35 // This should be Enum<?> but JAXB cannot serialize it.
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36 private final String method;
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38 private TreeSet<Range> ranges = new TreeSet<Range>();
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40 private ArrayList<Float> scores = new ArrayList<Float>(0);
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43 // JaXB default constructor
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48 * Instantiate the Score
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51 * the ConservationMethod with which {@code scores} were
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54 * the actual conservation values for each column of the
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57 public Score(Enum<?> method, ArrayList<Float> scores) {
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58 this.method = method.toString();
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59 this.scores = new ArrayList<Float>(scores);
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64 * the ConservationMethod with which {@code scores} were
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67 * the actual conservation values for each column of the
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70 * The set of ranges i.e. parts of the sequence with specific
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71 * function, usually can be calculated based on scores
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73 public Score(Enum<?> method, ArrayList<Float> scores, TreeSet<Range> ranges) {
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74 this.method = method.toString();
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75 this.ranges = ranges;
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76 this.scores = scores;
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79 public Score(Enum<?> method, TreeSet<Range> ranges) {
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80 this.method = method.toString();
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81 this.ranges = ranges;
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84 public Score(Enum<?> method, float[] scores) {
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85 this.method = method.toString();
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86 this.scores = toList(scores);
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89 private ArrayList<Float> toList(float[] values) {
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90 ArrayList<Float> vlist = new ArrayList<Float>();
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91 for (float v : values) {
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92 vlist.add(new Float(v));
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97 * Returns the ConservationMethod
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99 * @return the ConservationMethod
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101 public String getMethod() {
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106 * The column scores for the alignment
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108 * @return the column scores for the alignment
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110 public ArrayList<Float> getScores() {
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115 * Return Ranges if any Collections.EMPTY_SET otherwise
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119 public TreeSet<Range> getRanges() {
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123 public void setRanges(TreeSet<Range> ranges) {
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124 this.ranges = ranges;
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128 public String toString() {
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129 return "Score [method=" + method + ", ranges=" + ranges + ", scores="
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134 public int hashCode() {
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135 final int prime = 7;
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137 result = prime * result + ((method == null) ? 0 : method.hashCode());
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138 result = prime * result + ((ranges == null) ? 0 : ranges.hashCode());
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139 result = prime * result + ((scores == null) ? 0 : scores.hashCode());
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144 public boolean equals(Object obj) {
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149 if (getClass() != obj.getClass())
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151 Score other = (Score) obj;
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152 if (method == null) {
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153 if (other.method != null)
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155 } else if (!method.equals(other.method))
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157 if (ranges == null) {
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158 if (other.ranges != null)
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160 } else if (!ranges.equals(other.ranges))
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162 if (scores == null) {
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163 if (other.scores != null)
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165 } else if (!scores.equals(other.scores))
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171 * Outputs the List of Score objects into the Output stream. The output
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172 * format is as follows:
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176 * #MethodName <space separated list of values>
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180 * #KABAT 0.2 0.3 0.2 0 0.645 0.333 1 1 0 0
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181 * #SMERFS 0.645 0.333 1 1 0 0 0.2 0.3 0.2 0
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185 * The maximum precision for values is 3 digits, but can be less.
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188 * the list of scores to output
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190 * the stream to output the data to
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191 * @throws IOException
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192 * if the OutputStream cannot be written into
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193 * @throws NullPointerException
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194 * if the output stream is null
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196 public static void write(Set<Score> scores, OutputStream output)
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197 throws IOException {
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198 if (output == null) {
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199 throw new NullPointerException("OutputStream must be provided!");
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201 BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(
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203 for (Score score : scores) {
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204 writer.write("#" + score.method + " ");
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205 for (Float scoreVal : score.getScores()) {
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206 writer.write(NUMBER_FORMAT.format(scoreVal) + " ");
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208 writer.write("\n");
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