Alignment API and Server 4.1.${version.update}

Uses of Interface
org.semanticweb.owl.align.Alignment

Packages that use Alignment
fr.inrialpes.exmo.align.impl   
fr.inrialpes.exmo.align.impl.aggr   
fr.inrialpes.exmo.align.impl.edoal   
fr.inrialpes.exmo.align.impl.eval   
fr.inrialpes.exmo.align.impl.method   
fr.inrialpes.exmo.align.impl.renderer   
fr.inrialpes.exmo.align.ling   
fr.inrialpes.exmo.align.parser   
fr.inrialpes.exmo.align.service   
fr.inrialpes.exmo.align.util   
org.semanticweb.owl.align   
 

Uses of Alignment in fr.inrialpes.exmo.align.impl
 

Classes in fr.inrialpes.exmo.align.impl that implement Alignment
 class BasicAlignment
          Represents a basic ontology alignment, i.e., a fully functionnal alignment for wich the type of aligned objects is not known.
 class DistanceAlignment
          The mother class for distance or similarity-based alignments.
 class ObjectAlignment
          Represents an OWL ontology alignment.
 class URIAlignment
          Represents an ontology alignment relating entities identified by their URIs
 

Fields in fr.inrialpes.exmo.align.impl declared as Alignment
protected  Alignment BasicEvaluator.align1
           
protected  Alignment BasicEvaluator.align2
           
 

Fields in fr.inrialpes.exmo.align.impl with type parameters of type Alignment
protected  HashSet<Alignment> BasicOntologyNetwork.alignments
           
 HashSet<Alignment> OntologyTriple.sourceAlignments
           
 HashSet<Alignment> OntologyTriple.targettingAlignments
           
 

Methods in fr.inrialpes.exmo.align.impl that return Alignment
 Alignment BasicAlignment.compose(Alignment align)
          The second alignment is composed with the first one meaning that for any pair (o, o', n, r) in O and (o',o", n', r') in O' the resulting alignment will contain: ( o, o", join(n,n'), compose(r, r')) iff compose(r,r') exists.
 Alignment BasicAlignment.diff(Alignment align)
          The second alignment is suppresed from the first one meaning that for any pair (o, o', n, r) in O and (o, o', n', r) in O' the resulting alignment will contain: ( o, o', diff(n,n'), r) any pair which is only in the first alignment is preserved.
 Alignment DistanceAlignment.extract(String type, Properties params)
          Extract the alignment form the Similarity There are theoretically 16 types of extractors composing the characteristics [q]estion mark = ?, one or zero relation [s]tar = *, one, zero or many relations [1] = 1, exactly one relation [p]lus = +, one or many relations for each place of the relation.
 Alignment DistanceAlignment.extractqq(double threshold, Properties params)
          Extract the alignment of a ?? type exact algorithm using the Hungarian method
 Alignment DistanceAlignment.extractqqgreedy(double threshold, Properties params)
          Greedy algorithm: 1) dump the part of the matrix distance above threshold in a sorted set 2) traverse the sorted set and each time a correspondence involving two entities that have no correspondence is encountered, add it to the alignment.
 Alignment DistanceAlignment.extractqs(double threshold, Properties params)
          Extract the alignment of a ?* type Complexity: O(n^2)
 Alignment BasicAlignment.inverse()
          A new alignment is created such that for any pair (o, o', n, r) in O the resulting alignment will contain: ( o', o, n, inverse(r)) iff compose(r) exists.
 Alignment BasicAlignment.join(Alignment align)
          The second alignment is join with the first one meaning that for any pair (o, o', n, r) in O and (o, o', n', r) in O' the resulting alignment will contain: ( o, o", join(n,n'), r) any pair which is in only one alignment is discarded.
 Alignment BasicAlignment.meet(Alignment align)
          The second alignment is meet with the first one meaning that for any pair (o, o', n, r) in O and (o, o', n', r) in O' the resulting alignment will contain: ( o, o', meet(n,n'), r) any pair which is in only one alignment is preserved.
 

Methods in fr.inrialpes.exmo.align.impl that return types with arguments of type Alignment
 Set<Alignment> BasicOntologyNetwork.getAlignments()
           
 Set<Alignment> BasicOntologyNetwork.getSourceAlignments(URI onto)
           
 Set<Alignment> BasicOntologyNetwork.getTargetingAlignments(URI onto)
           
 

Methods in fr.inrialpes.exmo.align.impl with parameters of type Alignment
 void BasicOntologyNetwork.addAlignment(Alignment al)
           
 void DistanceAlignment.align(Alignment alignment, Properties params)
          Process matching - create distance data structures, - compute distance or similarity - extract alignment
 Alignment BasicAlignment.compose(Alignment align)
          The second alignment is composed with the first one meaning that for any pair (o, o', n, r) in O and (o',o", n', r') in O' the resulting alignment will contain: ( o, o", join(n,n'), compose(r, r')) iff compose(r,r') exists.
 Alignment BasicAlignment.diff(Alignment align)
          The second alignment is suppresed from the first one meaning that for any pair (o, o', n, r) in O and (o, o', n', r) in O' the resulting alignment will contain: ( o, o', diff(n,n'), r) any pair which is only in the first alignment is preserved.
 URI URICell.getObject1AsURI(Alignment al)
           
 URI ObjectCell.getObject1AsURI(Alignment al)
          Used to order the cells in an alignment: -- this > c iff this.getStrength() < c.getStrength() -- public int compareTo( Cell c ){ //if ( ! (c instanceof Cell) ) return 1; if ( c.getStrength() > getStrength() ) return 1; if ( getStrength() > c.getStrength() ) return -1; return 0; }
 URI BasicCell.getObject1AsURI(Alignment al)
           
 URI URICell.getObject2AsURI(Alignment al)
           
 URI ObjectCell.getObject2AsURI(Alignment al)
           
 URI BasicCell.getObject2AsURI(Alignment al)
           
 void BasicAlignment.ingest(Alignment alignment)
          Incorporate the cells of the alignment into its own alignment.
 void Similarity.initialize(LoadedOntology<Object> onto1, LoadedOntology<Object> onto2, Alignment align)
           
 void MatrixMeasure.initialize(LoadedOntology onto1, LoadedOntology onto2, Alignment align)
           
 void InstanceBasedMatrixMeasure.initialize(LoadedOntology onto1, LoadedOntology onto2, Alignment align)
           
 boolean IDDLOntologyNetwork.isEntailed(Alignment al)
           
 Alignment BasicAlignment.join(Alignment align)
          The second alignment is join with the first one meaning that for any pair (o, o', n, r) in O and (o, o', n', r) in O' the resulting alignment will contain: ( o, o", join(n,n'), r) any pair which is in only one alignment is discarded.
 void ObjectAlignment.loadInit(Alignment al)
           
 Alignment BasicAlignment.meet(Alignment align)
          The second alignment is meet with the first one meaning that for any pair (o, o', n, r) in O and (o, o', n', r) in O' the resulting alignment will contain: ( o, o', meet(n,n'), r) any pair which is in only one alignment is preserved.
 void BasicOntologyNetwork.remAlignment(Alignment al)
           
 

Constructors in fr.inrialpes.exmo.align.impl with parameters of type Alignment
BasicEvaluator(Alignment align1, Alignment align2)
          Creation
 

Uses of Alignment in fr.inrialpes.exmo.align.impl.aggr
 

Classes in fr.inrialpes.exmo.align.impl.aggr that implement Alignment
 class ConsensusAggregator
           
 

Methods in fr.inrialpes.exmo.align.impl.aggr with parameters of type Alignment
 void ConsensusAggregator.ingest(Alignment al)
          Extract the alignment from consensus
 

Uses of Alignment in fr.inrialpes.exmo.align.impl.edoal
 

Classes in fr.inrialpes.exmo.align.impl.edoal that implement Alignment
 class EDOALAlignment
          This class is an encapsulation of BasicAlignement so that it creates the structures required by the MappingDocument within the BasicAlignment
 

Methods in fr.inrialpes.exmo.align.impl.edoal with parameters of type Alignment
 URI EDOALCell.getObject1AsURI(Alignment al)
           
 URI EDOALCell.getObject2AsURI(Alignment al)
           
 void EDOALAlignment.loadInit(Alignment al)
           
 

Uses of Alignment in fr.inrialpes.exmo.align.impl.eval
 

Methods in fr.inrialpes.exmo.align.impl.eval with parameters of type Alignment
protected  double ExtPREvaluator.computeEffSimilarity(Cell c1, Alignment s2)
          Effort-based relaxed precision and recal similarity Note: it will be better if the parameters were replaced by the actual sibling (choice) Table 3 of [Ehrig2005]
protected  double ExtPREvaluator.computePrecisionOrientedSimilarity(Cell c1, Alignment s2)
          Oriented relaxed precision and recal similarity Table 4 (& 5) of [Ehrig2005]
protected  double ExtPREvaluator.computeRecallOrientedSimilarity(Cell c1, Alignment s2)
          Oriented relaxed precision and recal similarity Table 6 (& 7) of [Ehrig2005]
protected  double ExtPREvaluator.computeSymSimilarity(Cell c1, Alignment s2)
          Symmetric relaxed precision and recal similarity This computes similarity depending on structural measures: the similarity is symALPHA^(val1+val2), symALPHA being lower than 1.
 void AveragePRGraphEvaluator.evalAlignment(Alignment align1, Alignment align2)
           
 void GraphEvaluator.ingest(Alignment al, Alignment ref)
           
 void AveragePRGraphEvaluator.ingest(Alignment al, Alignment reference)
           
 boolean GraphEvaluator.isCorrect(Cell c, Alignment ref)
           
 

Constructors in fr.inrialpes.exmo.align.impl.eval with parameters of type Alignment
DiffEvaluator(Alignment align1, Alignment align2)
          Creation Initiate Evaluator for precision and recall
ExtPREvaluator(Alignment align1, Alignment align2)
          Creation
PRecEvaluator(Alignment align1, Alignment align2)
          Creation Initiate Evaluator for precision and recall
SemPRecEvaluator(Alignment align1, Alignment align2)
          Creation Initiate Evaluator for precision and recall
SymMeanEvaluator(Alignment align1, Alignment align2)
          Creation
 

Uses of Alignment in fr.inrialpes.exmo.align.impl.method
 

Classes in fr.inrialpes.exmo.align.impl.method that implement Alignment
 class ClassStructAlignment
          Establishes an alignment based on the comparison of the properties that classes have in common.
 class EditDistNameAlignment
          This class aligns ontology with regard to the editing distance between class names.
 class NameAndPropertyAlignment
          This class has been built for ISWC experiments with bibliography.
 class NameEqAlignment
          Matches two oontologies based on the equality of the name of their entities.
 class SMOANameAlignment
          This class aligns ontology with regard to the editing distance between class names.
 class StringDistAlignment
          Represents an OWL ontology alignment.
 class StrucSubsDistAlignment
          This class has been built for ISWC experiments with bibliography.
 class SubsDistNameAlignment
          This class implements alignment based on substring distance of class and property labels THIS CLASS IS ONLY HERE FOR COMPATIBILITY PURPOSES
 

Methods in fr.inrialpes.exmo.align.impl.method with parameters of type Alignment
 void StrucSubsDistAlignment.align(Alignment alignment, Properties params)
          Processing
 void StringDistAlignment.align(Alignment alignment, Properties params)
           
 void NameAndPropertyAlignment.align(Alignment alignment, Properties params)
          Processing
 void ClassStructAlignment.align(Alignment alignment, Properties params)
          Processing
 

Uses of Alignment in fr.inrialpes.exmo.align.impl.renderer
 

Fields in fr.inrialpes.exmo.align.impl.renderer declared as Alignment
(package private)  Alignment XSLTRendererVisitor.alignment
           
(package private)  Alignment XMLMetadataRendererVisitor.alignment
           
(package private)  Alignment SWRLRendererVisitor.alignment
           
(package private)  Alignment SKOSRendererVisitor.alignment
           
(package private)  Alignment SEKTMappingRendererVisitor.alignment
           
(package private)  Alignment RDFRendererVisitor.alignment
           
(package private)  Alignment OWLAxiomsRendererVisitor.alignment
           
(package private)  Alignment HTMLRendererVisitor.alignment
           
(package private)  Alignment HTMLMetadataRendererVisitor.alignment
           
(package private)  Alignment COWLMappingRendererVisitor.alignment
           
 

Methods in fr.inrialpes.exmo.align.impl.renderer with parameters of type Alignment
 void XSLTRendererVisitor.visit(Alignment align)
           
 void XMLMetadataRendererVisitor.visit(Alignment align)
           
 void SWRLRendererVisitor.visit(Alignment align)
           
 void SKOSRendererVisitor.visit(Alignment align)
           
 void SEKTMappingRendererVisitor.visit(Alignment align)
           
 void RDFRendererVisitor.visit(Alignment align)
           
 void OWLAxiomsRendererVisitor.visit(Alignment align)
           
 void HTMLRendererVisitor.visit(Alignment align)
           
 void HTMLMetadataRendererVisitor.visit(Alignment align)
           
 void COWLMappingRendererVisitor.visit(Alignment align)
           
 

Uses of Alignment in fr.inrialpes.exmo.align.ling
 

Classes in fr.inrialpes.exmo.align.ling that implement Alignment
 class JWNLAlignment
          This Class uses JWNLDistances to align two ontologies.
 

Methods in fr.inrialpes.exmo.align.ling with parameters of type Alignment
 void JWNLAlignment.align(Alignment alignment, Properties prop)
          Processing
 

Uses of Alignment in fr.inrialpes.exmo.align.parser
 

Fields in fr.inrialpes.exmo.align.parser declared as Alignment
protected  Alignment XMLParser.alignment
          the alignment that is parsed We always create a URIAlignment (we could also use a BasicAlignment).
protected  Alignment AlignmentParser.alignment
          the alignment that is parsed We always create a URIAlignment (we could also use a BasicAlignment).
 

Methods in fr.inrialpes.exmo.align.parser that return Alignment
private  Alignment AlignmentParser.callParser(Object o)
          Parses the document given in parameter If the current process has links (import or include) to others documents then they are parsed.
private  Alignment AlignmentParser.callParser(RDFParser p, Object o)
           
private  Alignment AlignmentParser.callParser(XMLParser p, Object o)
          This dispatch is ridiculous, but that's life
 Alignment XMLParser.parse(InputStream s)
          Parses a string instead of a URI
 Alignment AlignmentParser.parse(InputStream s)
          Parses an inputStream
 Alignment XMLParser.parse(Reader r)
          Parses a reader, used for reading from a string
 Alignment AlignmentParser.parse(Reader r)
          Parses a the content of a reader
 Alignment XMLParser.parse(String uri)
          Parses the document corresponding to the URI given in parameter If the current process has links (import or include) to others documents then they are parsed.
 Alignment AlignmentParser.parse(String uri)
          Parses a URI expressed as a String
 Alignment AlignmentParser.parse(String uri, Hashtable loaded)
          Deprecated. use parse( URI ) instead
 Alignment AlignmentParser.parse(URI uri)
          Parses a URI
 Alignment AlignmentParser.parseString(String s)
          Parses the content of a string
 

Uses of Alignment in fr.inrialpes.exmo.align.service
 

Classes in fr.inrialpes.exmo.align.service that implement Alignment
 class WSAlignment
          Represents an ontology alignment relating entities identified by their URIs
 

Fields in fr.inrialpes.exmo.align.service declared as Alignment
private  Alignment QueryMediator.alignment
           
 

Fields in fr.inrialpes.exmo.align.service with type parameters of type Alignment
(package private)  Hashtable<String,Alignment> CacheImpl.alignmentTable
           
(package private)  Hashtable<URI,Set<Alignment>> CacheImpl.ontologyTable
           
 

Methods in fr.inrialpes.exmo.align.service that return Alignment
 Alignment CacheImpl.getAlignment(String id)
          retrieve full alignment from id (and cache it)
 Alignment CacheImpl.getMetadata(String id)
          retrieve alignment metadata from id This is more difficult because we return the alignment we have disreagarding if it is complete o only metadata
protected  Alignment CacheImpl.retrieveAlignment(String id, Alignment alignment)
          loads the full alignments from the database and put them in the alignmentTable hastable should be invoked when: ( result.getExtension(CACHED) == "" && result.getExtension(STORED) != "") {
protected  Alignment CacheImpl.retrieveDescription(String id)
          loads the description of alignments from the database and set them in an alignment object Beware, the Alignment API has two attributes: onto1 is the Ontology object uri1 is the URI object from which loading the ontologies In the database we store: ontology1 the URI string of the ontology file1 the URI string from which loading the ontologies uri1 which should be the same as the last one...
 

Methods in fr.inrialpes.exmo.align.service that return types with arguments of type Alignment
protected  Collection<Alignment> CacheImpl.alignments()
           
 Collection<Alignment> AServProtocolManager.alignments()
           
 Set<Alignment> CacheImpl.getAlignments(URI uri)
           
 Set<Alignment> CacheImpl.getAlignments(URI uri1, URI uri2)
          returns the alignments between two ontologies if one of the ontologies is null, then return them all
protected  Enumeration<Alignment> CacheImpl.listAlignments()
           
 

Methods in fr.inrialpes.exmo.align.service with parameters of type Alignment
 void WSAlignment.align(Alignment alignment, Properties params)
          Process matching This does not work with regular AServ web service because it returns an URL
protected  void CacheImpl.flushAlignment(Alignment alignment)
          unload the cells of an alignment...
 boolean CacheImpl.isAlignmentStored(Alignment alignment)
           
 String CacheImpl.recordAlignment(String id, Alignment alignment, boolean force)
          records alignment identified by id
 String CacheImpl.recordNewAlignment(Alignment alignment, boolean force)
          records newly created alignment
 String CacheImpl.recordNewAlignment(String id, Alignment al, boolean force)
          records alignment identified by id
 void OysterDirectory.register(Alignment al)
          Register an alignment to the directory (if necessary)
 void Directory.register(Alignment al)
          Register an alignment to the directory (if necessary)
 void CacheImpl.resetCacheStamp(Alignment result)
           
protected  Alignment CacheImpl.retrieveAlignment(String id, Alignment alignment)
          loads the full alignments from the database and put them in the alignmentTable hastable should be invoked when: ( result.getExtension(CACHED) == "" && result.getExtension(STORED) != "") {
static String QueryMediator.rewriteSPARQLQuery(String aQuery, Alignment align)
           
 

Constructors in fr.inrialpes.exmo.align.service with parameters of type Alignment
QueryMediator(Alignment a)
           
QueryMediator(QueryProcessor proc, Alignment a)
           
 

Uses of Alignment in fr.inrialpes.exmo.align.util
 

Methods in fr.inrialpes.exmo.align.util that return Alignment
 Alignment Procalign.run(String[] args)
           
 

Uses of Alignment in org.semanticweb.owl.align
 

Subinterfaces of Alignment in org.semanticweb.owl.align
 interface AlignmentProcess
          Represents an executable alignment
 

Methods in org.semanticweb.owl.align that return Alignment
 Alignment Alignment.compose(Alignment align)
           
 Alignment Alignment.diff(Alignment align)
           
 Alignment Alignment.inverse()
          Algebra of alignment manipulation operations: compose, join, meet.
 Alignment Alignment.join(Alignment align)
           
 Alignment Alignment.meet(Alignment align)
           
 

Methods in org.semanticweb.owl.align that return types with arguments of type Alignment
 Set<Alignment> OntologyNetwork.getAlignments()
           
 Set<Alignment> OntologyNetwork.getSourceAlignments(URI onto)
           
 Set<Alignment> OntologyNetwork.getTargetingAlignments(URI onto)
           
 

Methods in org.semanticweb.owl.align with parameters of type Alignment
 void OntologyNetwork.addAlignment(Alignment al)
           
 void AlignmentProcess.align(Alignment alignment, Properties param)
          The align method computes the alignment from the ontologies.
 Alignment Alignment.compose(Alignment align)
           
 Alignment Alignment.diff(Alignment align)
           
 URI Cell.getObject1AsURI(Alignment al)
           
 URI Cell.getObject2AsURI(Alignment al)
           
 boolean LogicOntologyNetwork.isEntailed(Alignment al)
           
 Alignment Alignment.join(Alignment align)
           
 Alignment Alignment.meet(Alignment align)
           
 void OntologyNetwork.remAlignment(Alignment al)
           
 


Alignment API and Server 4.1.${version.update}

(C) INRIA & friends, 2003-${curryear}