Uses of Interface org.semanticweb.owl.align.Alignment (Alignment API and Server)
Date: 2010-03-31

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| Alignment API and Server 4.0
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## Uses of Interface
org.semanticweb.owl.align.Alignment

Packages that use Alignment
fr.inrialpes.exmo.align.impl |
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`
`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)`
`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.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
`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
`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 corresponding to the URI 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)`

Overview | Package | Class | Use | Tree | Deprecated | Index | Help
| Alignment API and Server 4.0
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