[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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| 11 | import java.util.*; |
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| 12 | |
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| 13 | public class OWLClassGraph extends LabeledMultiDigraph{ |
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| 14 | String startClass; |
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| 15 | String endClass; |
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| 16 | int nsteps; |
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| 17 | int limit; |
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[34] | 18 | int th; |
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[45] | 19 | double cut; |
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[2] | 20 | |
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| 21 | public class LinkAndPath{ |
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| 22 | ClassLink classLink; |
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| 23 | List<ClassLink> path; |
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[45] | 24 | boolean converge; |
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[2] | 25 | public LinkAndPath(ClassLink classLink, List<ClassLink> path){ |
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| 26 | this.classLink = classLink; |
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| 27 | this.path = path; |
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[45] | 28 | this.converge = false; |
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[2] | 29 | } |
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[45] | 30 | |
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| 31 | public LinkAndPath(ClassLink classLink, List<ClassLink> path, boolean converge){ |
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| 32 | this.classLink = classLink; |
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| 33 | this.path = path; |
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| 34 | this.converge = converge; |
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| 35 | } |
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[2] | 36 | } |
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| 37 | |
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[3] | 38 | public OWLClassGraph(String startClass, String endClass){ |
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[2] | 39 | super(); |
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[3] | 40 | this.startClass = startClass; |
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| 41 | addNode(startClass); |
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| 42 | this.endClass = endClass; |
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| 43 | addNode(endClass); |
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[41] | 44 | nsteps = 3; |
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[3] | 45 | limit = 1000; |
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[34] | 46 | th = 0; |
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[45] | 47 | cut = 2.0; |
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[2] | 48 | } |
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| 49 | |
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[3] | 50 | public void generateGraph(List<List<ClassLink>> paths){ |
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[15] | 51 | ListIterator<List<ClassLink>> pit = paths.listIterator(); |
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| 52 | while( pit.hasNext() ){ |
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[21] | 53 | List<ClassLink> cls = pit.next(); |
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| 54 | String start = startClass; |
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| 55 | ListIterator<ClassLink> cit = cls.listIterator(); |
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| 56 | while ( cit.hasNext() ){ |
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| 57 | // KOKO |
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| 58 | } |
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[15] | 59 | } |
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[2] | 60 | } |
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| 61 | |
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[29] | 62 | public Path[] getPaths(OWLQueryBuilderImpl qb, int mode, boolean countLink){ |
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| 63 | List<List<ClassLink>> paths = searchPaths(qb, mode, countLink); |
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[2] | 64 | Path[] patharray = new Path[paths.size()]; |
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| 65 | ListIterator<List<ClassLink>> pit = paths.listIterator(); |
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| 66 | int i = 0; |
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| 67 | while ( pit.hasNext() ){ |
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[3] | 68 | patharray[i] = new Path(); |
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[2] | 69 | patharray[i].setStartClass(startClass); |
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| 70 | List<ClassLink> path = pit.next(); |
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| 71 | patharray[i].setClassLinks(path); |
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[8] | 72 | ListIterator<ClassLink> cit = path.listIterator(); |
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| 73 | int min = Integer.MAX_VALUE; |
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| 74 | while ( cit.hasNext() ){ |
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| 75 | ClassLink cl = cit.next(); |
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| 76 | if ( cl.getNumOfLinks() < min ){ |
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| 77 | min = cl.getNumOfLinks(); |
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| 78 | } |
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| 79 | } |
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| 80 | patharray[i].setWidth(min); |
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[2] | 81 | i++; |
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| 82 | } |
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| 83 | return patharray; |
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| 84 | } |
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[45] | 85 | |
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[32] | 86 | private List<List<ClassLink>> searchPaths(OWLQueryBuilderImpl qb, int mode, boolean countLinks){ |
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[15] | 87 | List<List<ClassLink>> paths = new ArrayList<>(); |
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[8] | 88 | ClassLink crrLink = new ClassLink(null,startClass,Direction.both,0); |
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[15] | 89 | List<LinkAndPath> lp = new LinkedList<>(); |
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[2] | 90 | lp.add(new LinkAndPath(crrLink, new LinkedList<ClassLink>())); |
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| 91 | try{ |
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| 92 | for ( int i = 0; i < nsteps; i++ ){ |
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| 93 | ListIterator<LinkAndPath> lit = lp.listIterator(); |
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[15] | 94 | List<LinkAndPath> nextlp = new LinkedList<>(); |
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[2] | 95 | while ( lit.hasNext() ){ |
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| 96 | LinkAndPath crrlp = lit.next(); |
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[3] | 97 | ClassLink[] classLinks = null; |
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| 98 | // Mode |
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| 99 | if ( mode == 0 ){ |
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[32] | 100 | classLinks = qb.getNextClass(null, crrlp.classLink.getLinkedClassURI(), limit, countLinks); |
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[3] | 101 | }else if ( mode == 1 ){ |
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[41] | 102 | classLinks = qb.getNextClassViaInstanceLink(null, crrlp.classLink.getLinkedClassURI(), limit); |
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[3] | 103 | }else{ System.err.println("Mode is not correct."); } |
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[2] | 104 | for ( int j = 0 ; j < classLinks.length; j++ ){ |
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[15] | 105 | List<ClassLink> crrpath = new LinkedList<>(crrlp.path); |
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[2] | 106 | crrpath.add(classLinks[j]); |
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| 107 | if ( classLinks[j].getLinkedClassURI().equals(endClass) ){ |
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[15] | 108 | paths.add(new LinkedList<>(crrpath)); |
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[34] | 109 | continue; |
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[2] | 110 | } |
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[34] | 111 | if ( countLinks == true && classLinks[j].getNumOfLinks() <= th){ |
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| 112 | continue; |
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| 113 | } |
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[2] | 114 | nextlp.add(new LinkAndPath(classLinks[j],crrpath)); |
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| 115 | } |
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| 116 | } |
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[3] | 117 | lp = nextlp; |
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[2] | 118 | } |
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[15] | 119 | }catch(Exception e){ |
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| 120 | System.err.println(e); |
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| 121 | } |
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[21] | 122 | return paths; |
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[2] | 123 | } |
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[45] | 124 | |
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| 125 | private List<List<ClassLink>> searchPathsWithCut(OWLQueryBuilderImpl qb){ |
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| 126 | List<List<ClassLink>> paths = new ArrayList<>(); |
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| 127 | ClassLink crrLink = new ClassLink(null,startClass,Direction.both,0); |
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| 128 | List<LinkAndPath> lp = new LinkedList<>(); |
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| 129 | lp.add(new LinkAndPath(crrLink, new LinkedList<ClassLink>())); |
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| 130 | try{ |
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| 131 | for ( int i = 0; i < nsteps; i++ ){ |
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| 132 | ListIterator<LinkAndPath> lit = lp.listIterator(); |
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| 133 | List<LinkAndPath> nextlp = new LinkedList<>(); |
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| 134 | while ( lit.hasNext() ){ |
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| 135 | LinkAndPath crrlp = lit.next(); |
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| 136 | ClassLink[] classLinks = null; |
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| 137 | classLinks = qb.getNextClassViaInstanceLink(null, crrlp.classLink.getLinkedClassURI(), limit); |
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| 138 | for ( int j = 0 ; j < classLinks.length; j++ ){ |
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| 139 | List<ClassLink> crrpath = new LinkedList<>(crrlp.path); |
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| 140 | crrpath.add(classLinks[j]); |
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| 141 | if ( classLinks[j].getLinkedClassURI().equals(endClass) ){ |
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| 142 | paths.add(new LinkedList<>(crrpath)); |
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| 143 | continue; |
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| 144 | } |
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| 145 | boolean con = false; |
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| 146 | double cont = 1.0; |
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| 147 | if ( cont > th ){ // shrink |
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| 148 | con = true; |
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| 149 | } |
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| 150 | if ( crrlp.converge == true && con == false ){ // converge & 縲diverge |
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| 151 | continue; // cut |
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| 152 | } |
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| 153 | nextlp.add(new LinkAndPath(classLinks[j], crrpath, con)); |
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| 154 | } |
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| 155 | } |
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| 156 | lp = nextlp; |
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| 157 | } |
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| 158 | }catch(Exception e){ |
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| 159 | System.err.println(e); |
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| 160 | } |
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| 161 | return paths; |
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| 162 | } |
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| 163 | |
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[2] | 164 | } |
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