1 | /* |
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2 | * To change this license header, choose License Headers in Project Properties. |
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3 | * To change this template file, choose Tools | Templates |
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4 | * and open the template in the editor. |
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5 | */ |
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6 | |
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7 | package org.biohackathon.SPARQLBuilder.OWL; |
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8 | |
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9 | import java.io.*; |
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10 | import java.util.*; |
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11 | |
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12 | /** |
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13 | * |
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14 | * @author atsuko |
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15 | */ |
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16 | |
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17 | public class QueryPathGenerator { |
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18 | //private String sparqlEndpoint = null; |
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19 | private RDFSchemaAnalyzerFactory factory = null; |
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20 | //private RDFSchemaAnalyzer analyzer = null; |
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21 | private HashMap<String, RDFSchemaAnalyzer> analyzers = null; |
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22 | private OWLClassGraph graph; |
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23 | |
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24 | private Map<String, String> clabels; |
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25 | |
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26 | private static final String CDIR = "cdata"; |
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27 | private static final String ODIR = "owldata"; |
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28 | |
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29 | public QueryPathGenerator(){ |
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30 | factory = new RDFSchemaAnalyzerFactory(CDIR); |
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31 | } |
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32 | |
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33 | /* |
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34 | public QueryPathGenerator(String sparqlEndpoint){ |
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35 | factory = new RDFSchemaAnalyzerFactory(CDIR); |
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36 | setSPARQLendpoint(sparqlEndpoint); |
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37 | } |
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38 | */ |
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39 | |
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40 | /*public void setOWLClassGraph(String startClass){ |
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41 | graph = new OWLClassGraph(analyzer, sparqlEndpoint, startClass); |
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42 | }*/ |
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43 | |
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44 | public SClass[] getClassesByEndpoint(String ep){ |
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45 | RDFSchemaAnalyzer analyzer = analyzers.get(ep); |
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46 | try { |
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47 | return analyzer.getOWLClasses(null, null, null, true); |
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48 | }catch(Exception e){ |
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49 | System.err.println(e); |
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50 | return null; |
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51 | } |
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52 | } |
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53 | |
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54 | public SClass[] getClasses(String keyword){ |
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55 | return getClassList(keyword).toArray(new SClass[0]); |
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56 | } |
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57 | |
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58 | public List<SClass> getClassList(String keyword){ |
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59 | Iterator<RDFSchemaAnalyzer> ait = analyzers.values().iterator(); |
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60 | List<SClass> cl = new LinkedList<SClass>(); |
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61 | try { |
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62 | while ( ait.hasNext() ){ |
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63 | RDFSchemaAnalyzer analyzer = ait.next(); |
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64 | cl.addAll(analyzer.getOWLClassList(null, null, null, true)); |
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65 | } |
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66 | }catch(Exception e){ |
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67 | System.err.println(e); |
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68 | return null; |
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69 | } |
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70 | return cl; |
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71 | } |
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72 | |
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73 | public Path[] getPaths(String startClass, String endClass){ |
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74 | if (startClass == null || endClass == null){ |
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75 | return null; |
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76 | } |
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77 | if ( graph == null ){ |
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78 | //setOWLClassGraph(startClass); |
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79 | } |
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80 | return graph.getPaths(startClass, endClass); |
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81 | } |
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82 | |
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83 | /* |
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84 | public void setSPARQLendpoint(String sparqlEndpoint){ |
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85 | this.sparqlEndpoint = sparqlEndpoint; |
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86 | setAnalyzer(); |
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87 | } |
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88 | */ |
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89 | |
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90 | public RDFSchemaAnalyzerFactory getFactory(){ |
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91 | return factory; |
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92 | } |
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93 | |
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94 | /* |
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95 | private void setAnalyzer(){ |
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96 | try { |
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97 | analyzer = factory.create(sparqlEndpoint); |
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98 | } catch (Exception e) { |
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99 | System.err.println(e); |
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100 | } |
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101 | } |
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102 | */ |
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103 | |
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104 | public String getClassLabel(String classURI){ |
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105 | return clabels.get(classURI); |
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106 | } |
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107 | |
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108 | public void setClassLabels(SClass[] classes){ |
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109 | clabels = new HashMap<String, String>(); |
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110 | Map<String, String> extLabels = getClassLabelsFromExternal(); |
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111 | |
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112 | for ( int i = 0 ; i < classes.length; i++ ){ |
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113 | String classURI = classes[i].getClassURI(); |
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114 | |
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115 | Label[] labels = classes[i].getLabels(); |
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116 | String label = null; |
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117 | for ( int j = 0 ; j < labels.length; j++ ){ |
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118 | if ( labels[j].getLanguage() == null ){ |
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119 | label = labels[j].getLabel(); |
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120 | break; |
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121 | }else if ( labels[j].getLanguage().equals("en") || labels[j].getLanguage().equals("") ){ |
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122 | label = labels[j].getLabel(); |
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123 | break; |
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124 | } |
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125 | } |
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126 | if ( label == null ){ |
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127 | label = extLabels.get(classURI); |
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128 | } |
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129 | if ( label == null ){ |
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130 | String[] uris = classURI.split("/"); |
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131 | String tmplabel = uris[uris.length-1]; |
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132 | String[] tmplabel2 = tmplabel.split("#"); |
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133 | label = tmplabel2[tmplabel2.length-1]; |
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134 | } |
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135 | clabels.put(classURI, label); |
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136 | } |
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137 | } |
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138 | |
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139 | public static String getClassLabelfromList(String classURI, SClass[] classes){ |
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140 | if ( classURI == null ){ |
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141 | return ""; |
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142 | } |
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143 | SClass sclass = null; |
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144 | for ( int i = 0 ; i < classes.length; i++ ){ |
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145 | if ( classURI.equals(classes[i].getClassURI()) ){ |
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146 | return getClassLabelfromClass(classes[i]); |
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147 | } |
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148 | } |
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149 | return ""; |
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150 | } |
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151 | |
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152 | public static String getClassLabelfromClass(SClass sclass){ |
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153 | Label[] labels = sclass.getLabels(); |
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154 | for ( int i = 0 ; i < labels.length; i++ ){ |
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155 | if ( labels[i].getLanguage() == null ){ |
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156 | return labels[i].getLabel(); |
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157 | }else if ( labels[i].getLanguage().equals("en") ){ |
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158 | return labels[i].getLabel(); |
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159 | } |
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160 | } |
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161 | String[] url = sclass.getClassURI().split("/"); |
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162 | String tmplabel = url[url.length-1]; |
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163 | String[] tmplabel2 = tmplabel.split("#"); |
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164 | String label = tmplabel2[tmplabel2.length-1]; |
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165 | return label; |
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166 | } |
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167 | |
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168 | public Map<String, String> getClassLabelsFromExternal(){ |
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169 | return OWLLabelReader.readLabels(ODIR); |
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170 | } |
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171 | |
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172 | public OWLClassGraph getOWLClassGraph(){ |
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173 | /*if ( graph == null ){ |
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174 | graph = new OWLClassGraph(analyzer); |
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175 | }*/ |
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176 | return graph; |
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177 | } |
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178 | |
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179 | /* |
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180 | public SClass[] getReachableClasses(){ |
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181 | List<String> clURIs = graph.getReachableClasses(); |
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182 | SClass[] orgclasses = null; |
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183 | try { |
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184 | orgclasses = analyzer.getOWLClasses(null, null, null, true); |
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185 | }catch( Exception e ){ |
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186 | System.err.println(e); |
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187 | return null; |
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188 | } |
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189 | HashMap<String, SClass> orgmap = new HashMap<String, SClass>(); |
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190 | for (int i = 0; i < orgclasses.length; i++ ){ |
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191 | orgmap.put(orgclasses[i].getClassURI(), orgclasses[i]); |
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192 | } |
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193 | |
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194 | SClass[] classes = new SClass[clURIs.size()]; |
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195 | int j = 0; |
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196 | ListIterator<String> uit = clURIs.listIterator(); |
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197 | while(uit.hasNext()){ |
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198 | String u = uit.next(); |
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199 | SClass cl = orgmap.get(u); |
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200 | classes[j] = cl; |
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201 | j++; |
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202 | } |
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203 | return classes; |
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204 | } |
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205 | */ |
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206 | |
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207 | public SortedSet<String> getSortedClasses(SClass[] classes){ |
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208 | setClassLabels(classes); |
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209 | SortedSet<String> sortedClasses = new TreeSet<String>(); |
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210 | for (int i = 0 ; i < classes.length; i++ ){ |
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211 | String uri = classes[i].getClassURI(); |
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212 | String label = getClassLabel(uri); |
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213 | StringBuilder classbuilder = new StringBuilder(label); |
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214 | classbuilder.append(" "); |
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215 | classbuilder.append(classes[i].getNumOfInstances()); |
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216 | classbuilder.append(" "); |
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217 | classbuilder.append(uri); |
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218 | sortedClasses.add(classbuilder.toString()); |
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219 | } |
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220 | |
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221 | return sortedClasses; |
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222 | } |
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223 | } |
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