[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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| 18 | |
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| 19 | public class LinkAndPath{ |
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| 20 | ClassLink classLink; |
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| 21 | List<ClassLink> path; |
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| 22 | public LinkAndPath(ClassLink classLink, List<ClassLink> path){ |
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| 23 | this.classLink = classLink; |
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| 24 | this.path = path; |
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| 25 | } |
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| 26 | } |
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| 27 | |
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[3] | 28 | public OWLClassGraph(String startClass, String endClass){ |
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[2] | 29 | super(); |
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[3] | 30 | this.startClass = startClass; |
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| 31 | addNode(startClass); |
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| 32 | this.endClass = endClass; |
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| 33 | addNode(endClass); |
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| 34 | nsteps = 2; |
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| 35 | limit = 1000; |
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[2] | 36 | } |
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| 37 | |
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[3] | 38 | public void generateGraph(List<List<ClassLink>> paths){ |
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| 39 | |
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[2] | 40 | } |
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| 41 | |
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| 42 | public Path[] getPaths(OWLQueryBuilderImpl qb){ |
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[3] | 43 | //List<List<ClassLink>> paths = searchPathsFromOWL(qb); |
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| 44 | List<List<ClassLink>> paths = searchPathsFromInstances(qb); |
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[2] | 45 | Path[] patharray = new Path[paths.size()]; |
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| 46 | ListIterator<List<ClassLink>> pit = paths.listIterator(); |
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| 47 | int i = 0; |
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| 48 | while ( pit.hasNext() ){ |
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[3] | 49 | patharray[i] = new Path(); |
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[2] | 50 | patharray[i].setStartClass(startClass); |
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| 51 | List<ClassLink> path = pit.next(); |
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| 52 | patharray[i].setClassLinks(path); |
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| 53 | i++; |
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| 54 | } |
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| 55 | return patharray; |
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| 56 | } |
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| 57 | |
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| 58 | private List<List<ClassLink>> searchPathsFromOWL(OWLQueryBuilderImpl qb){ |
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[3] | 59 | return searchPathsEngine(qb, 0); |
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| 60 | } |
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| 61 | |
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| 62 | private List<List<ClassLink>> searchPathsFromInstances(OWLQueryBuilderImpl qb){ |
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| 63 | return searchPathsEngine(qb, 1); |
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| 64 | } |
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| 65 | |
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| 66 | private List<List<ClassLink>> searchPathsEngine(OWLQueryBuilderImpl qb, int mode){ |
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[2] | 67 | List<List<ClassLink>> paths = new ArrayList<List<ClassLink>>(); |
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| 68 | ClassLink crrLink = new ClassLink(null,startClass,Direction.both); |
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| 69 | List<LinkAndPath> lp = new LinkedList<LinkAndPath>(); |
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| 70 | lp.add(new LinkAndPath(crrLink, new LinkedList<ClassLink>())); |
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| 71 | try{ |
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| 72 | for ( int i = 0; i < nsteps; i++ ){ |
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| 73 | ListIterator<LinkAndPath> lit = lp.listIterator(); |
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| 74 | List<LinkAndPath> nextlp = new LinkedList<LinkAndPath>(); |
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| 75 | while ( lit.hasNext() ){ |
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| 76 | LinkAndPath crrlp = lit.next(); |
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| 77 | if ( crrlp.classLink.getLinkedClassURI().equals(endClass) ){ continue; } |
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[3] | 78 | ClassLink[] classLinks = null; |
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| 79 | // Mode |
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| 80 | if ( mode == 0 ){ |
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| 81 | classLinks = qb.getNextClass(null, crrlp.classLink.getLinkedClassURI(), limit); |
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| 82 | }else if ( mode == 1 ){ |
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| 83 | classLinks = qb.getNextClassViaInstanceLink(null, crrlp.classLink.getLinkedClassURI(), limit); |
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| 84 | }else{ System.err.println("Mode is not correct."); } |
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[2] | 85 | for ( int j = 0 ; j < classLinks.length; j++ ){ |
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| 86 | List<ClassLink> crrpath = new LinkedList<ClassLink>(crrlp.path); |
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| 87 | crrpath.add(classLinks[j]); |
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| 88 | if ( classLinks[j].getLinkedClassURI().equals(endClass) ){ |
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| 89 | paths.add(new LinkedList<ClassLink>(crrpath)); |
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| 90 | } |
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| 91 | nextlp.add(new LinkAndPath(classLinks[j],crrpath)); |
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| 92 | } |
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| 93 | } |
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[3] | 94 | lp = nextlp; |
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[2] | 95 | } |
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| 96 | }catch(Exception e){ System.err.println(e);} |
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[3] | 97 | return paths; |
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[2] | 98 | } |
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| 99 | } |
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