[2] | 1 | /* |
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| 2 | * To change this template, choose Tools | Templates |
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| 3 | * and open the template in the editor. |
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| 4 | */ |
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| 5 | package org.biohackathon.SPARQLBuilder.OWL; |
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| 6 | |
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| 7 | /** |
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| 8 | * |
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| 9 | * @author atsuko |
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| 10 | */ |
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[67] | 11 | import java.util.ArrayList; |
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| 12 | import java.util.LinkedList; |
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| 13 | import java.util.List; |
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| 14 | import java.util.ListIterator; |
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[2] | 15 | |
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| 16 | public class OWLClassGraph extends LabeledMultiDigraph{ |
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| 17 | String startClass; |
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| 18 | String endClass; |
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| 19 | int nsteps; |
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| 20 | int limit; |
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[34] | 21 | int th; |
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[47] | 22 | double concut; |
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| 23 | double divcut; |
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[2] | 24 | |
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| 25 | public class LinkAndPath{ |
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[67] | 26 | String originalClassURI; // originalClasssURI -classLink.propertyURI-> classLink.linkedClassURL |
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[2] | 27 | ClassLink classLink; |
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| 28 | List<ClassLink> path; |
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[45] | 29 | boolean converge; |
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[67] | 30 | |
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[2] | 31 | public LinkAndPath(ClassLink classLink, List<ClassLink> path){ |
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| 32 | this.classLink = classLink; |
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| 33 | this.path = path; |
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[45] | 34 | this.converge = false; |
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[2] | 35 | } |
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[45] | 36 | |
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[67] | 37 | public LinkAndPath(ClassLink classLink, List<ClassLink> path, String orinalClassURI, boolean converge){ |
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[45] | 38 | this.classLink = classLink; |
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| 39 | this.path = path; |
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[67] | 40 | this.originalClassURI = originalClassURI; |
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[45] | 41 | this.converge = converge; |
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| 42 | } |
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[2] | 43 | } |
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| 44 | |
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[3] | 45 | public OWLClassGraph(String startClass, String endClass){ |
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[2] | 46 | super(); |
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[3] | 47 | this.startClass = startClass; |
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| 48 | addNode(startClass); |
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| 49 | this.endClass = endClass; |
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| 50 | addNode(endClass); |
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[41] | 51 | nsteps = 3; |
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[3] | 52 | limit = 1000; |
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[34] | 53 | th = 0; |
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[47] | 54 | concut = 2.0; |
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[48] | 55 | divcut = - 2.0; |
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[2] | 56 | } |
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| 57 | |
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[67] | 58 | /* |
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[3] | 59 | public void generateGraph(List<List<ClassLink>> paths){ |
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[15] | 60 | ListIterator<List<ClassLink>> pit = paths.listIterator(); |
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| 61 | while( pit.hasNext() ){ |
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[21] | 62 | List<ClassLink> cls = pit.next(); |
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| 63 | String start = startClass; |
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| 64 | ListIterator<ClassLink> cit = cls.listIterator(); |
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| 65 | while ( cit.hasNext() ){ |
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| 66 | // KOKO |
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| 67 | } |
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[15] | 68 | } |
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[2] | 69 | } |
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[67] | 70 | */ |
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[2] | 71 | |
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[29] | 72 | public Path[] getPaths(OWLQueryBuilderImpl qb, int mode, boolean countLink){ |
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[47] | 73 | List<List<ClassLink>> paths = null; |
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| 74 | if ( mode <= 1){ |
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| 75 | paths = searchPaths(qb, mode, countLink); |
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| 76 | }else if ( mode == 2 ){ |
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[67] | 77 | paths = searchPathsWithCut(qb); |
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[47] | 78 | }else{ |
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| 79 | System.err.println("Mode is not correct"); |
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| 80 | return null; |
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| 81 | } |
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[2] | 82 | Path[] patharray = new Path[paths.size()]; |
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| 83 | ListIterator<List<ClassLink>> pit = paths.listIterator(); |
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| 84 | int i = 0; |
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| 85 | while ( pit.hasNext() ){ |
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[3] | 86 | patharray[i] = new Path(); |
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[2] | 87 | patharray[i].setStartClass(startClass); |
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| 88 | List<ClassLink> path = pit.next(); |
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| 89 | patharray[i].setClassLinks(path); |
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[8] | 90 | ListIterator<ClassLink> cit = path.listIterator(); |
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| 91 | int min = Integer.MAX_VALUE; |
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| 92 | while ( cit.hasNext() ){ |
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| 93 | ClassLink cl = cit.next(); |
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| 94 | if ( cl.getNumOfLinks() < min ){ |
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| 95 | min = cl.getNumOfLinks(); |
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| 96 | } |
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| 97 | } |
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| 98 | patharray[i].setWidth(min); |
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[2] | 99 | i++; |
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| 100 | } |
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| 101 | return patharray; |
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| 102 | } |
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[45] | 103 | |
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[32] | 104 | private List<List<ClassLink>> searchPaths(OWLQueryBuilderImpl qb, int mode, boolean countLinks){ |
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[15] | 105 | List<List<ClassLink>> paths = new ArrayList<>(); |
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[51] | 106 | ClassLink crrLink = new ClassLink(null,startClass,Direction.both,0,0,0,0,0); |
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[15] | 107 | List<LinkAndPath> lp = new LinkedList<>(); |
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[2] | 108 | lp.add(new LinkAndPath(crrLink, new LinkedList<ClassLink>())); |
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| 109 | try{ |
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| 110 | for ( int i = 0; i < nsteps; i++ ){ |
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| 111 | ListIterator<LinkAndPath> lit = lp.listIterator(); |
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[15] | 112 | List<LinkAndPath> nextlp = new LinkedList<>(); |
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[2] | 113 | while ( lit.hasNext() ){ |
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| 114 | LinkAndPath crrlp = lit.next(); |
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[3] | 115 | ClassLink[] classLinks = null; |
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| 116 | // Mode |
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| 117 | if ( mode == 0 ){ |
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[32] | 118 | classLinks = qb.getNextClass(null, crrlp.classLink.getLinkedClassURI(), limit, countLinks); |
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[3] | 119 | }else if ( mode == 1 ){ |
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[41] | 120 | classLinks = qb.getNextClassViaInstanceLink(null, crrlp.classLink.getLinkedClassURI(), limit); |
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[3] | 121 | }else{ System.err.println("Mode is not correct."); } |
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[2] | 122 | for ( int j = 0 ; j < classLinks.length; j++ ){ |
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[15] | 123 | List<ClassLink> crrpath = new LinkedList<>(crrlp.path); |
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[2] | 124 | crrpath.add(classLinks[j]); |
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| 125 | if ( classLinks[j].getLinkedClassURI().equals(endClass) ){ |
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[15] | 126 | paths.add(new LinkedList<>(crrpath)); |
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[34] | 127 | continue; |
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[2] | 128 | } |
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[34] | 129 | if ( countLinks == true && classLinks[j].getNumOfLinks() <= th){ |
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| 130 | continue; |
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| 131 | } |
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[2] | 132 | nextlp.add(new LinkAndPath(classLinks[j],crrpath)); |
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| 133 | } |
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| 134 | } |
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[3] | 135 | lp = nextlp; |
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[2] | 136 | } |
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[15] | 137 | }catch(Exception e){ |
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| 138 | System.err.println(e); |
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| 139 | } |
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[21] | 140 | return paths; |
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[2] | 141 | } |
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[45] | 142 | |
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| 143 | private List<List<ClassLink>> searchPathsWithCut(OWLQueryBuilderImpl qb){ |
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| 144 | List<List<ClassLink>> paths = new ArrayList<>(); |
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[51] | 145 | ClassLink crrLink = new ClassLink(null,startClass,Direction.both,0,0,0,0,0); |
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[45] | 146 | List<LinkAndPath> lp = new LinkedList<>(); |
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| 147 | lp.add(new LinkAndPath(crrLink, new LinkedList<ClassLink>())); |
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| 148 | try{ |
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| 149 | for ( int i = 0; i < nsteps; i++ ){ |
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| 150 | ListIterator<LinkAndPath> lit = lp.listIterator(); |
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| 151 | List<LinkAndPath> nextlp = new LinkedList<>(); |
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| 152 | while ( lit.hasNext() ){ |
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| 153 | LinkAndPath crrlp = lit.next(); |
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| 154 | ClassLink[] classLinks = null; |
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[53] | 155 | classLinks = qb.getNextClass(null, crrlp.classLink.getLinkedClassURI(), limit, true); |
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[45] | 156 | for ( int j = 0 ; j < classLinks.length; j++ ){ |
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[53] | 157 | if ( classLinks[j].getNumOfLinks() == 0 ){ continue; } |
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[45] | 158 | List<ClassLink> crrpath = new LinkedList<>(crrlp.path); |
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| 159 | crrpath.add(classLinks[j]); |
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| 160 | if ( classLinks[j].getLinkedClassURI().equals(endClass) ){ |
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| 161 | paths.add(new LinkedList<>(crrpath)); |
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| 162 | continue; |
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| 163 | } |
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[67] | 164 | if (classLinks[j].getNumOfLinks() <= th ){ |
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| 165 | continue; //cut by the number of instances |
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| 166 | } |
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| 167 | // Divergence & Convergence Decision |
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[45] | 168 | boolean con = false; |
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[47] | 169 | boolean div = false; |
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[52] | 170 | if ( decideConvergence(classLinks[j]) ){ // convergence |
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[45] | 171 | con = true; |
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| 172 | } |
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[52] | 173 | if ( decideDivergence(classLinks[j]) ){ // divergence |
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[47] | 174 | div = true; |
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| 175 | } |
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| 176 | if ( crrlp.converge == true && div == true ){ // converge & 縲diverge |
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[67] | 177 | continue; // cut by the differences of entropies |
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[45] | 178 | } |
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[67] | 179 | // crr & next are the same arcs |
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| 180 | if ( crrlp.classLink.getPropertyURI().equals(classLinks[j].getPropertyURI()) && |
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| 181 | crrlp.classLink.getDirection() != classLinks[j].getDirection() && |
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| 182 | crrlp.originalClassURI.equals( classLinks[j].getLinkedClassURI()) ){ |
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| 183 | continue; |
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| 184 | } |
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| 185 | |
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| 186 | nextlp.add(new LinkAndPath(classLinks[j], crrpath, crrlp.classLink.getLinkedClassURI(), con)); |
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[45] | 187 | } |
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| 188 | } |
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| 189 | lp = nextlp; |
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| 190 | } |
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| 191 | }catch(Exception e){ |
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| 192 | System.err.println(e); |
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| 193 | } |
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| 194 | return paths; |
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| 195 | } |
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[47] | 196 | |
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[52] | 197 | private boolean decideConvergence(ClassLink classLink){ |
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| 198 | double con = getValueForConvergence(classLink.getNumOfOriginInstances(), |
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| 199 | classLink.getNumOfLinkedInstances(), |
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| 200 | classLink.getNumOfLinks()); |
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| 201 | if ( con > concut ){ |
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| 202 | return true; |
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| 203 | } |
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| 204 | return false; |
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| 205 | } |
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| 206 | |
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| 207 | private boolean decideDivergence(ClassLink classLink){ |
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| 208 | double con = getValueForConvergence(classLink.getNumOfOriginInstances(), |
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| 209 | classLink.getNumOfLinkedInstances(), |
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| 210 | classLink.getNumOfLinks()); |
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| 211 | if ( con < divcut ){ |
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| 212 | return true; |
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| 213 | } |
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| 214 | return false; |
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| 215 | } |
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| 216 | |
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[47] | 217 | private double getValueForConvergence(int numOfOriginInstances, int numOfLinkedInstances, int numOfLinks){ |
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[48] | 218 | //return (double) numOfLinks / (double) numOfLinkedInstances ; |
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[50] | 219 | // Convergence plus, Divergence minus |
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| 220 | return Math.log((double)numOfOriginInstances) - Math.log((double)numOfLinkedInstances); |
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[47] | 221 | } |
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[2] | 222 | } |
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