Mercurial > repos > mikel-egana-aranguren > oppl

annotate src/GalaxyOWLAPI.java @ 21:ffde1fafa066 draft

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README corrected with proper installation instructions for mercurial (hg pull + hg update)
author Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Mon, 08 Oct 2012 13:10:44 +0200
parents cc270db37d33
children
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1 /**
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2 *
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3 */
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4 package es.upm.fi.dia.oeg.oppl.galaxy;
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5
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6 import java.io.BufferedWriter;
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7 import java.io.File;
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8 import java.io.IOException;
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9 import java.io.OutputStreamWriter;
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10 import java.util.ArrayList;
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11 import java.util.List;
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12 import java.util.Scanner;
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13 import java.util.Set;
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14
18
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15 import org.apache.log4j.Level;
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16 import org.apache.log4j.Logger;
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17 import org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxEditorParser;
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18 import org.coode.owlapi.obo.parser.OBOOntologyFormat;
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19 import org.coode.parsers.BidirectionalShortFormProviderAdapter;
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20 import org.semanticweb.HermiT.Reasoner;
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21 import org.semanticweb.elk.owlapi.ElkReasonerFactory;
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22 import org.semanticweb.owlapi.apibinding.OWLManager;
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23 import org.semanticweb.owlapi.expression.OWLEntityChecker;
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24 import org.semanticweb.owlapi.expression.ParserException;
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25 import org.semanticweb.owlapi.expression.ShortFormEntityChecker;
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26 import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
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27 import org.semanticweb.owlapi.io.SystemOutDocumentTarget;
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28 import org.semanticweb.owlapi.model.AddAxiom;
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29 import org.semanticweb.owlapi.model.IRI;
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30 import org.semanticweb.owlapi.model.OWLAnnotation;
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31 import org.semanticweb.owlapi.model.OWLAnnotationProperty;
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32 import org.semanticweb.owlapi.model.OWLAxiom;
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33 import org.semanticweb.owlapi.model.OWLClass;
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34 import org.semanticweb.owlapi.model.OWLClassExpression;
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35 import org.semanticweb.owlapi.model.OWLDataFactory;
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36 import org.semanticweb.owlapi.model.OWLLiteral;
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37 import org.semanticweb.owlapi.model.OWLNamedIndividual;
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38 import org.semanticweb.owlapi.model.OWLOntology;
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39 import org.semanticweb.owlapi.model.OWLOntologyChange;
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40 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
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41 import org.semanticweb.owlapi.model.OWLOntologyManager;
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42 import org.semanticweb.owlapi.model.OWLOntologyStorageException;
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43 import org.semanticweb.owlapi.reasoner.InferenceType;
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44 import org.semanticweb.owlapi.reasoner.OWLReasoner;
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45 import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
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46 import org.semanticweb.owlapi.util.BidirectionalShortFormProvider;
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47 import org.semanticweb.owlapi.util.InferredAxiomGenerator;
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48 import org.semanticweb.owlapi.util.InferredClassAssertionAxiomGenerator;
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49 import org.semanticweb.owlapi.util.InferredDisjointClassesAxiomGenerator;
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50 import org.semanticweb.owlapi.util.InferredOntologyGenerator;
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51 import org.semanticweb.owlapi.util.InferredSubClassAxiomGenerator;
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52 import org.semanticweb.owlapi.util.InferredSubDataPropertyAxiomGenerator;
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53 import org.semanticweb.owlapi.util.InferredSubObjectPropertyAxiomGenerator;
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54 import org.semanticweb.owlapi.util.OWLEntityRenamer;
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55 import org.semanticweb.owlapi.util.OWLOntologyImportsClosureSetProvider;
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56 import org.semanticweb.owlapi.util.OWLOntologyMerger;
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57 import org.semanticweb.owlapi.util.SimpleShortFormProvider;
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58 import org.semanticweb.owlapi.vocab.OWL2Datatype;
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59 import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;
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60 import org.semanticweb.owlapi.reasoner.Node;
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61
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62 import uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory;
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63
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64 import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
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65
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66 /**
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67 * A wrapper of the OWL API
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68 *
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69 * @author Mikel Egana Aranguren
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70 */
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71 public class GalaxyOWLAPI {
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72 private OWLOntologyManager manager;
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73 private OWLOntology ontology;
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74 private OWLReasonerFactory reasonerFactory;
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75 private OWLReasoner reasoner;
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76
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77 public GalaxyOWLAPI (){
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78 manager = OWLManager.createOWLOntologyManager();
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79 }
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80 public OWLOntologyManager getOWLManager(){
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81 return manager;
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82 }
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83 public OWLOntology getMainOntology(){
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84 return ontology;
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85 }
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86 public OWLReasoner getReasoner(){
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87 return reasoner;
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88 }
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89
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90 public void loadMainOntology(String OWLFilePath) throws OWLOntologyCreationException{
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91 File owl_file = new File(OWLFilePath);
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92 ontology = manager.loadOntologyFromOntologyDocument(owl_file);
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93 }
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94
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95 // public void loadImportedOntology(IRI importedOntologyIRI) throws OWLOntologyCreationException{
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96 // manager.loadOntologyFromOntologyDocument(importedOntologyIRI);
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97 // }
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98
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99 // OWLLink: The problem is that Racer, for example, listens in 8080, the same port as Galaxy
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100 // I have to change Racer settings and OWLLink settings
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101 // OWLlinkHTTPXMLReasonerFactory factory = new OWLlinkHTTPXMLReasonerFactory();
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102 // reasoner = factory.createReasoner(OWL_ontology);
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103
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104 public void setReasonerPellet (){
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105 reasonerFactory = new PelletReasonerFactory();
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106 reasoner = reasonerFactory.createReasoner(ontology);
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107 }
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108 public void setReasonerFaCT (){
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109 reasonerFactory = new FaCTPlusPlusReasonerFactory();
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110 reasoner = reasonerFactory.createReasoner(ontology);
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111 }
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112 public void setReasonerHermit (){
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113 reasonerFactory = new Reasoner.ReasonerFactory();
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114 reasoner = reasonerFactory.createReasoner(ontology);
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115 }
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116 public void setReasonerElk (){
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117 reasonerFactory = new ElkReasonerFactory();
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118 Logger.getLogger("org.semanticweb.elk").setLevel(Level.OFF);
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119 reasoner = reasonerFactory.createReasoner(ontology);
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120 }
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121 public void disposeReasoner(){
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122 reasoner.dispose();
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123 }
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124 public void merge (String ontologyIRI) throws OWLOntologyCreationException, OWLOntologyStorageException{
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125 OWLOntologyMerger merger = new OWLOntologyMerger(manager);
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126 // OWLOntologyMerger merger = new OWLOntologyMerger(new OWLOntologyImportsClosureSetProvider(manager, ontology));
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127 IRI mergedOntologyIRI = IRI.create(ontologyIRI);
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128 // OWLOntology merged_ontology = merger.createMergedOntology(manager, mergedOntologyIRI);
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129 ontology = merger.createMergedOntology(manager, mergedOntologyIRI);
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130 // manager.saveOntology(ontology, new RDFXMLOntologyFormat(), new SystemOutDocumentTarget());
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131 }
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132
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133 public OWLClassExpression parseMOSClassExpression (String expr) throws ParserException{
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134 Set<OWLOntology> importsClosure = ontology.getImportsClosure();
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135 BidirectionalShortFormProvider bidiShortFormProvider = new BidirectionalShortFormProviderAdapter(manager, importsClosure, new SimpleShortFormProvider());
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136 OWLEntityChecker entityChecker = new ShortFormEntityChecker(bidiShortFormProvider);
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137 ManchesterOWLSyntaxEditorParser MOSparser = new ManchesterOWLSyntaxEditorParser(manager.getOWLDataFactory(), expr);
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138 MOSparser.setOWLEntityChecker(entityChecker);
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139 return MOSparser.parseClassExpression();
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140 }
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141
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142 public Set<OWLNamedIndividual> getIndividuals (OWLClassExpression expr){
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143 return (reasoner.getInstances(expr, false)).getFlattened();
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144 }
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145 public Set<OWLClass> getEquivalentClasses (OWLClassExpression expr){
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146 Node<OWLClass> equivalentClasses = reasoner.getEquivalentClasses(expr);
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147 Set<OWLClass> result;
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148 if (expr.isAnonymous()) {
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149 result = equivalentClasses.getEntities();
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150 }
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151 else {
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152 result = equivalentClasses.getEntitiesMinus(expr.asOWLClass());
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153 }
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154 return result;
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155 }
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156
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157 public Set<OWLClass> getDirectSuperClasses (OWLClassExpression expr){
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158 return (reasoner.getSuperClasses(expr, true)).getFlattened();
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159 }
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160
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161 public Set<OWLClass> getAncestors (OWLClassExpression expr){
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162 return (reasoner.getSuperClasses(expr, false)).getFlattened();
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163 }
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164
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165 public Set<OWLClass> getDirectSubClasses (OWLClassExpression expr){
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166 return (reasoner.getSubClasses(expr, true)).getFlattened();
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167 }
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168
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169 public Set<OWLClass> getDescendants (OWLClassExpression expr){
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170 return (reasoner.getSubClasses(expr, false)).getFlattened();
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171 }
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172
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173 // CLASS_ASSERTIONS Denotes the computation of the direct types of individuals for each individual in the signature of the imports closure of the root ontology.
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174
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175 public void addCLASS_ASSERTIONS(){
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176 reasoner.precomputeInferences(InferenceType.CLASS_ASSERTIONS);
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177 List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
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178 gens.add(new InferredClassAssertionAxiomGenerator());
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179 InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
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180 iog.fillOntology(manager, ontology);
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181 }
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182
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183 // CLASS_HIERARCHY Denotes the computation of the class hierarchy.
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184
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185 public void addCLASS_HIERARCHY(){
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186 reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
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187 List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
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188 gens.add(new InferredSubClassAxiomGenerator());
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189 InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
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190 iog.fillOntology(manager, ontology);
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191 }
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192
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193 // DATA_PROPERTY_ASSERTIONS Denotes the computation of relationships between individuals and data property values for each individual in the signature of the imports closure of the root ontology.
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194 // public void addDATA_PROPERTY_ASSERTIONS(){
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195 // reasoner.precomputeInferences(InferenceType.DATA_PROPERTY_ASSERTIONS);
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196 // List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
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197 // gens.add(new InferredDataPropertyAxiomGenerator());
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198 // InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
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199 // iog.fillOntology(manager, ontology);
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200 // }
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201
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202 // DATA_PROPERTY_HIERARCHY Denotes the computation of the data property hierarchy.
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203
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204 public void addDATA_PROPERTY_HIERARCHY(){
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205 reasoner.precomputeInferences(InferenceType.DATA_PROPERTY_HIERARCHY);
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206 List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
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207 gens.add(new InferredSubDataPropertyAxiomGenerator());
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208 InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
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209 iog.fillOntology(manager, ontology);
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210 }
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211
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212 // DIFFERENT_INDIVIDUALS Denotes the computation of sets of individuals that are different from each individual in the signature of the imports closure of the root ontology.
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213
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214 // public void addDIFFERENT_INDIVIDUALS(){
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215 // reasoner.precomputeInferences(InferenceType.DIFFERENT_INDIVIDUALS);
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216 // List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
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217 // gens.add(new Inferred);
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218 // InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
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219 // iog.fillOntology(manager, ontology);
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220 // }
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221
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222 // DISJOINT_CLASSES Denotes the computation of sets of classes that are disjoint for each class in the signature of the imports closure of the root ontology.
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223
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224 public void addDISJOINT_CLASSES(){
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225 reasoner.precomputeInferences(InferenceType.DISJOINT_CLASSES);
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226 List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
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227 gens.add(new InferredDisjointClassesAxiomGenerator());
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228 InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
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229 iog.fillOntology(manager, ontology);
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230 }
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231
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232 // OBJECT_PROPERTY_ASSERTIONS Denotes the computation of relationships between individuals in the signature of the imports closure of the root ontology.
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233
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234 // public void addOBJECT_PROPERTY_ASSERTIONS(){
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235 // reasoner.precomputeInferences(InferenceType.OBJECT_PROPERTY_ASSERTIONS);
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236 // List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
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237 // gens.add(new InferredObjectPropertyAxiomGenerator<OWLAxiom>() {
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238 // };());
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239 // InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
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240 // iog.fillOntology(manager, ontology);
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241 // }
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242
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243 // OBJECT_PROPERTY_HIERARCHY Denotes the computation of the object property hierarchy.
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244
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245 public void addOBJECT_PROPERTY_HIERARCHY(){
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246 reasoner.precomputeInferences(InferenceType.OBJECT_PROPERTY_HIERARCHY);
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247 List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
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248 gens.add(new InferredSubObjectPropertyAxiomGenerator());
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249 InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
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250 iog.fillOntology(manager, ontology);
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251 }
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252
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253 // SAME_INDIVIDUAL Denotes the computation of individuals that are interpreted as the same object for each individual in the imports closure of the root ontology.
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254
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255 // public void addSAME_INDIVIDUAL(){
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256 // reasoner.precomputeInferences(InferenceType.SAME_INDIVIDUAL);
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257 // List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
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258 // gens.add(new Infer);
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259 // InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
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260 // iog.fillOntology(manager, ontology);
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261 // }
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262
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263 public void saveOntology (boolean OWL) throws OWLOntologyStorageException, IOException, OWLOntologyCreationException{
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264 // OWL format
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265 if(OWL){
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266 manager.saveOntology(ontology, new RDFXMLOntologyFormat(), new SystemOutDocumentTarget());
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267 }
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268 // OBO format
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269 else{
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270 // OWL API generates bad OBO but OBOformat doesn't work either so I correct the OWL API problems (More predictable) in a temporary file
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271 // Very inefficient but no time for another solution
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272
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273 OWLDataFactory factory = manager.getOWLDataFactory();
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274 OWLEntityRenamer renamer = new OWLEntityRenamer (manager, manager.getOntologies());
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275 OWLAnnotationProperty label = factory.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI());
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276 for(OWLClass cls : ontology.getClassesInSignature()){
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277 // Remove annotations (OWL API generates bad OBO annotations)
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278
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279 // Keep rdfs:label
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280 String class_name = null;
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281 for (OWLAnnotation annotation : cls.getAnnotations(ontology, label)){
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282 if (annotation.getValue() instanceof OWLLiteral) {
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283 OWLLiteral val = (OWLLiteral) annotation.getValue();
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284 class_name = val.getLiteral();
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285 }
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286 }
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287
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288 // I have to remove all the annotations cause I don't know which ones are rendered properly
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289 manager.removeAxioms(ontology,ontology.getAnnotationAssertionAxioms(cls.getIRI()));
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290
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291 // Add rdfs:label again
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292 OWLAnnotation labelAnno = factory.getOWLAnnotation(factory.getOWLAnnotationProperty(
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293 OWLRDFVocabulary.RDFS_LABEL.getIRI()),factory.getOWLLiteral(class_name,OWL2Datatype.XSD_STRING));
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294 OWLAxiom ax = factory.getOWLAnnotationAssertionAxiom(cls.getIRI(), labelAnno);
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295 manager.applyChange(new AddAxiom(ontology, ax));
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296
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297 // Rename entities
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298 String cls_IRI = cls.getIRI().toString();
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299 String cls_proper_IRI = cls_IRI.replace("_", ":");
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300 List<OWLOntologyChange> changes = renamer.changeIRI(cls, IRI.create(cls_proper_IRI));
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301 manager.applyChanges(changes);
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302 }
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303
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304 File file = new File("tmp.obo");
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305 manager.saveOntology(ontology, new OBOOntologyFormat(), IRI.create(file.toURI()));
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306 BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(System.out));
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307 Scanner input = new Scanner(file);
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308 String buffer = "";
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309
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310 while(input.hasNext()){
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311 String nextLine = input.nextLine();
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312 if(nextLine.contains("[Term]") || nextLine.contains("[Typedef]")){
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313 if(buffer.isEmpty()){
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314 bw.write(buffer);
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Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
315 bw.newLine();
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parents:
diff changeset
316 }
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parents:
diff changeset
317 }
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
318 if(!nextLine.contains("is_a: Thing") && !nextLine.contains("auto-generated-by:") && !nextLine.contains("id_space:") && !nextLine.contains("! ----")){
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
319 if(!nextLine.isEmpty() && !buffer.contains("relationship:")){
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
320 bw.write(nextLine);
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
321 bw.newLine();
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
322 }
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
323 }
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
324 buffer = nextLine;
6ca67b155e32 Imports simplified, new tool for inference added
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parents:
diff changeset
325 }
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
326 input.close();
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
327 bw.close();
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
328 file.delete();
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
329 }
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
330 }
6ca67b155e32 Imports simplified, new tool for inference added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
331 }