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1 package middlewares;
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2
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3 import java.util.*;
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4 import java.io.*;
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5 import org.jdom.*;
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6 import org.jdom.input.*;
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7 import org.jdom.output.*;
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8
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9 /**
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10 * Used to construct the summary file based on the computation of an
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11 * EnrichmentStatsComputer object. It uses a file pattern to generate this file
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12 * dynamically.
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13 *
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14 * @author Ali Abdallah
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15 * @version 20.07.2011
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16 * @since Java 1.6
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17 */
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18
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19 public class XMLSummaryFileBuilder {
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20
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21 /**
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22 * The pattern file containing the structure of the summary without real
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23 * data.
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24 */
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25 static String xmlPatternFile;
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26
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27 /**
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28 * The summary file containing the computed data.
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29 */
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30 static String xmlOutputFile;
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31
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32 /**
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33 * An object with an abstract representation on an xml-file.
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34 */
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35 static Document doc;
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36
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37 /**
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38 * The leaf-tags containing data as text.
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39 */
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40 List<Element> leafs;
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41
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42 /**
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43 * The name of the current sample.
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44 */
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45 static String currSample;
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46
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47 /**
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48 * Creates and initializes a XMLSummaryFileBuilder object.
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49 *
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50 * @param xmlPatternFile the pattern file.
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51 * @param xmlOutputFile the output file.
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52 * @param currSample the current read alignment sample name without
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53 * the extension.
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54 */
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55 public XMLSummaryFileBuilder(String xmlPatternFile, String xmlOutputFile,
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56 String currSample) {
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57
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58 leafs = new ArrayList<Element>();
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59 XMLSummaryFileBuilder.xmlPatternFile = xmlPatternFile;
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60 XMLSummaryFileBuilder.xmlOutputFile = xmlOutputFile;
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61 XMLSummaryFileBuilder.currSample = currSample;
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62 SAXBuilder builder = new SAXBuilder();
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63 try {
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64 doc = builder.build(xmlPatternFile);
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65 } catch (JDOMException e) {
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66 e.printStackTrace();
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67 } catch (IOException e) {
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68 e.printStackTrace();
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69 }
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70 }
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71
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72 /**
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73 * Same as the constructor above but the pattern file is internally
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74 * specified.
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75 *
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76 * @param xmlOutputFile the output file.
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77 * @param currSample the current read alignment sample name without
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78 * the extension.
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79 */
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80 public XMLSummaryFileBuilder(String xmlOutputFile,
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81 String currSample) {
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82 this(Misc.binDir()+"/xmlFilePattern.xml", xmlOutputFile, currSample);
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83 }
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84
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85 /**
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86 * Computes all the leafs of the subtree with root e.
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87 *
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88 * @param e an Element.
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89 * @return all the leafs of the subtree with root e.
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90 */
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91 public Element[] getLeafs(Element e){
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92 @SuppressWarnings("unchecked")
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93 List<Element> children = e.getChildren();
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94 for(int i = 0; i < children.size(); i++){
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95 Element child = children.get(i);
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96 if(child.getChildren().size() == 0)
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97 leafs.add(child);
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98 else
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99 getLeafs(child);
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100 }
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101
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102 Object[] oleafs = leafs.toArray();
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103 Element[] eleafs = new Element[oleafs.length];
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104 for(int i = 0; i < eleafs.length; i++)
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105 eleafs[i] = (Element)oleafs[i];
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106
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107 return eleafs;
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108 }
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109
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110 /**
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111 * Same as the above method but the element is internally specified as the
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112 * root of the document.
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113 *
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114 * @return an array with all leaf elements of the document.
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115 */
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116 public Element[] getLeafs(){
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117 return getLeafs(doc.getRootElement());
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118 }
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119
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120 /**
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121 * Write the summary file created.
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122 * @param name the name of the file.
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123 */
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124 public void writeXMLFile(String name) {
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125 XMLOutputter outp = new XMLOutputter();
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126 outp.setFormat(Format.getPrettyFormat());
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127 try {
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128 outp.output(doc, new FileOutputStream(name));
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129 } catch (FileNotFoundException e) {
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130 e.printStackTrace();
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131 } catch (IOException e) {
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132 e.printStackTrace();
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133 }
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134 }
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135
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136 }
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