fr.inrialpes.exmo.align.impl
Class BasicAlignment

java.lang.Object
  fr.inrialpes.exmo.align.impl.BasicAlignment

All Implemented Interfaces:

Cloneable, Iterable<Cell>, Alignment, Visitable

Direct Known Subclasses:

EDOALAlignment, ObjectAlignment, URIAlignment

public class BasicAlignment
extends Object
implements Alignment

Represents a basic ontology alignment, i.e., a fully functionnal alignment for wich the type of aligned objects is not known. In version 3.0 this class is virtually abstract. But it cannot be declared abstract because it uses its own constructor.

Version:

$Id: BasicAlignment.java 1348 2010-03-21 23:34:08Z euzenat $

Author:

Jérôme Euzenat, David Loup, Raphaël Troncy

Field Summary

protected int	debug
protected Extensions	extensions
protected Hashtable<Object,Set<Cell>>	hash1
protected Hashtable<Object,Set<Cell>>	hash2
protected String	level
protected BasicParameters	namespaces
protected Ontology<Object>	onto1
protected Ontology<Object>	onto2
protected long	time
protected String	type

Constructor Summary

BasicAlignment()

Method Summary

void	accept(AlignmentVisitor visitor)
Cell	addAlignCell(Object ob1, Object ob2)
Cell	addAlignCell(Object ob1, Object ob2, String relation, double measure) Cells are created and indexed at once
Cell	addAlignCell(String id, Object ob1, Object ob2, Relation relation, double measure)
Cell	addAlignCell(String id, Object ob1, Object ob2, Relation relation, double measure, Extensions extensions) Cell methods
protected void	addCell(Cell c)
void	cleanUp() Can be used for reducing the amount of memory taken by an alignment Does nothing in BasicAlignment.
Object	clone() Generate a copy of this alignment object It has the same content but a different id (no id indeed)
Alignment	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.
Cell	createCell(String id, Object ob1, Object ob2, Relation relation, double measure)
BasicAlignment	createNewAlignment(Object onto1, Object onto2) Algebraic part This is to be improved by (TODO): - improving cell equivalence (maybe not dependent on the confidence...
void	cut(double threshold) Default cut implementation For compatibility with API until version 1.1
void	cut(String method, double threshold) Cut refinement : - getting those cells with strength above n (hard) - getting the n best cells (best) - getting those cells with strength at worse n under the best (span) - getting the n% best cells (perc) - getting those cells with strength at worse n% of the best (prop) - getting all cells until a gap of n (hardgap) - getting all cells until a gap of n% of the last (propgap) Rule: threshold is betweew 1 and 0
void	cut2(double threshold) The cut function suppresses from an alignment all the cell over a particular threshold
Alignment	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.
void	dump(ContentHandler h) Housekeeping
Cell	getAlignCell1(Object ob) Cells are retrieved These primitives are deprecated.
Cell	getAlignCell2(Object ob) //@deprecated There is more than one cell about one object
Set<Cell>	getAlignCells1(Object ob) Cells are retrieved These primitives are deprecated.
Set<Cell>	getAlignCells2(Object ob)
Object	getAlignedObject1(Object ob) Each part of the cell can be queried independently.
Object	getAlignedObject2(Object ob)
Relation	getAlignedRelation1(Object ob)
Relation	getAlignedRelation2(Object ob)
double	getAlignedStrength1(Object ob)
double	getAlignedStrength2(Object ob)
ArrayList<Cell>	getArrayElements()
Enumeration<Cell>	getElements()
String	getExtension(String uri, String label)
Collection<String[]>	getExtensions() Extensions are a way to read and add other information (metadata) to the alignment structure itself.
URI	getFile1()
URI	getFile2()
String	getLevel()
Object	getOntology1() Alignment methods *
URI	getOntology1URI()
Object	getOntology2()
URI	getOntology2URI()
Ontology<Object>	getOntologyObject1()
Ontology<Object>	getOntologyObject2()
static Properties	getParameters()
String	getType()
String	getXNamespace(String label)
BasicParameters	getXNamespaces()
void	harden(double threshold) The harden function acts like threshold but put all weights to 1.
void	ingest(Alignment alignment) Incorporate the cells of the alignment into its own alignment.
void	init(Object onto1, Object onto2) Initialize the alignement before using it
void	init(Object onto1, Object onto2, Object cache) Initialises the Alignment object with two ontologies.
Alignment	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.
Iterator<Cell>	iterator()
Alignment	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	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.
int	nbCells()
void	remCell(Cell c)
void	removeAlignCell(Cell c)
void	render(AlignmentVisitor renderer) This should be rewritten in order to generate the axiom ontology instead of printing it! And then use ontology serialization for getting it printed.
void	setExtension(String uri, String label, String value)
void	setExtensions(Extensions ext)
void	setFile1(URI u) Alignment type: Currently defined a sa String.
void	setFile2(URI u)
void	setLevel(String level) Alignment type: Currently defined a sa String.
void	setOntology1(Object ontology)
void	setOntology2(Object ontology)
void	setType(String type) Alignment type: Currently defined a sa String.
void	setXNamespace(String label, String uri)
URIAlignment	toURIAlignment() Returns default exception for conversion to URIAlignments

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

onto1

protected Ontology<Object> onto1

onto2

protected Ontology<Object> onto2

debug

protected int debug

level

protected String level

type

protected String type

hash1

protected Hashtable<Object,Set<Cell>> hash1

hash2

protected Hashtable<Object,Set<Cell>> hash2

time

protected long time

extensions

protected Extensions extensions

namespaces

protected BasicParameters namespaces

Constructor Detail

BasicAlignment

public BasicAlignment()

Method Detail

accept

public void accept(AlignmentVisitor visitor)
            throws AlignmentException

Specified by:

accept in interface Visitable

Throws:

AlignmentException

init

public void init(Object onto1,
                 Object onto2,
                 Object cache)
          throws AlignmentException

Initialises the Alignment object with two ontologies. These two ontologies can be either an instance of fr.inrialpes.exmo.ontowrap.Ontology which will then replaced the one that was there at creation time or a "concrete" ontology which will be inserted in the fr.inrialpes.exmo.ontowrap.Ontology object.

Specified by:

init in interface Alignment

Throws:

AlignmentException

init

public void init(Object onto1,
                 Object onto2)
          throws AlignmentException

Description copied from interface: Alignment

Initialize the alignement before using it

Specified by:

init in interface Alignment

Throws:

AlignmentException

getParameters

public static Properties getParameters()

nbCells

public int nbCells()

Specified by:

nbCells in interface Alignment

getOntology1

public Object getOntology1()

Alignment methods *

Specified by:

getOntology1 in interface Alignment

getOntology2

public Object getOntology2()

Specified by:

getOntology2 in interface Alignment

getOntologyObject1

public Ontology<Object> getOntologyObject1()

getOntologyObject2

public Ontology<Object> getOntologyObject2()

getOntology1URI

public URI getOntology1URI()

Specified by:

getOntology1URI in interface Alignment

getOntology2URI

public URI getOntology2URI()

Specified by:

getOntology2URI in interface Alignment

setOntology1

public void setOntology1(Object ontology)
                  throws AlignmentException

Specified by:

setOntology1 in interface Alignment

Throws:

AlignmentException

setOntology2

public void setOntology2(Object ontology)
                  throws AlignmentException

Specified by:

setOntology2 in interface Alignment

Throws:

AlignmentException

setType

public void setType(String type)

Description copied from interface: Alignment

Alignment type: Currently defined a sa String. This string is supposed to contain two characters: among ?, 1, *, + Can be implemented otherwise

Specified by:

setType in interface Alignment

getType

public String getType()

Specified by:

getType in interface Alignment

setLevel

public void setLevel(String level)

Description copied from interface: Alignment

Alignment type: Currently defined a sa String. This string is supposed to contain two characters: among ?, 1, *, + Can be implemented otherwise

Specified by:

setLevel in interface Alignment

getLevel

public String getLevel()

Specified by:

getLevel in interface Alignment

getFile1

public URI getFile1()

Specified by:

getFile1 in interface Alignment

setFile1

public void setFile1(URI u)

Description copied from interface: Alignment

Alignment type: Currently defined a sa String. This string is supposed to contain two characters: among ?, 1, *, + Can be implemented otherwise

Specified by:

setFile1 in interface Alignment

getFile2

public URI getFile2()

Specified by:

getFile2 in interface Alignment

setFile2

public void setFile2(URI u)

Specified by:

setFile2 in interface Alignment

getExtensions

public Collection<String[]> getExtensions()

Description copied from interface: Alignment

Extensions are a way to read and add other information (metadata) to the alignment structure itself. getExtensions returns a set of tripes: uri*label*value all three being String

Specified by:

getExtensions in interface Alignment

setExtensions

public void setExtensions(Extensions ext)

setExtension

public void setExtension(String uri,
                         String label,
                         String value)

Specified by:

setExtension in interface Alignment

getExtension

public String getExtension(String uri,
                           String label)

Specified by:

getExtension in interface Alignment

getXNamespaces

public BasicParameters getXNamespaces()

setXNamespace

public void setXNamespace(String label,
                          String uri)

getXNamespace

public String getXNamespace(String label)

getElements

public Enumeration<Cell> getElements()

Specified by:

getElements in interface Alignment

iterator

public Iterator<Cell> iterator()

Specified by:

iterator in interface Iterable<Cell>

Specified by:

iterator in interface Alignment

getArrayElements

public ArrayList<Cell> getArrayElements()

addAlignCell

public Cell addAlignCell(String id,
                         Object ob1,
                         Object ob2,
                         Relation relation,
                         double measure,
                         Extensions extensions)
                  throws AlignmentException

Cell methods

Throws:

AlignmentException

addAlignCell

public Cell addAlignCell(String id,
                         Object ob1,
                         Object ob2,
                         Relation relation,
                         double measure)
                  throws AlignmentException

Throws:

AlignmentException

addAlignCell

public Cell addAlignCell(Object ob1,
                         Object ob2,
                         String relation,
                         double measure)
                  throws AlignmentException

Description copied from interface: Alignment

Cells are created and indexed at once

Specified by:

addAlignCell in interface Alignment

Throws:

AlignmentException

addAlignCell

public Cell addAlignCell(Object ob1,
                         Object ob2)
                  throws AlignmentException

Specified by:

addAlignCell in interface Alignment

Throws:

AlignmentException

createCell

public Cell createCell(String id,
                       Object ob1,
                       Object ob2,
                       Relation relation,
                       double measure)
                throws AlignmentException

Throws:

AlignmentException

addCell

protected void addCell(Cell c)
                throws AlignmentException

Throws:

AlignmentException

remCell

public void remCell(Cell c)
             throws AlignmentException

Specified by:

remCell in interface Alignment

Throws:

AlignmentException

getAlignCells1

public Set<Cell> getAlignCells1(Object ob)
                         throws AlignmentException

Description copied from interface: Alignment

Cells are retrieved These primitives are deprecated. Use getAlignCells1 and getAlignCells2 instead. Reason: this applies only for 1:1 alignments Some implementations might act cleverly (retrieving the best value). Basic implementations may raise the exception

Specified by:

getAlignCells1 in interface Alignment

Throws:

AlignmentException

getAlignCells2

public Set<Cell> getAlignCells2(Object ob)
                         throws AlignmentException

Specified by:

getAlignCells2 in interface Alignment

Throws:

AlignmentException

getAlignCell1

public Cell getAlignCell1(Object ob)
                   throws AlignmentException

Description copied from interface: Alignment

Cells are retrieved These primitives are deprecated. Use getAlignCells1 and getAlignCells2 instead. Reason: this applies only for 1:1 alignments Some implementations might act cleverly (retrieving the best value). Basic implementations may raise the exception //@deprecated There is more than one cell about one object

Specified by:

getAlignCell1 in interface Alignment

Throws:

AlignmentException

getAlignCell2

public Cell getAlignCell2(Object ob)
                   throws AlignmentException

Description copied from interface: Alignment

//@deprecated There is more than one cell about one object

Specified by:

getAlignCell2 in interface Alignment

Throws:

AlignmentException

getAlignedObject1

public Object getAlignedObject1(Object ob)
                         throws AlignmentException

Description copied from interface: Alignment

Each part of the cell can be queried independently. These primitives are deprecated. Use getAlignCells1 and getAlignCells2 instead. Reason: this applies only for 1:1 alignments Some implementations might act cleverly (retrieving the best value). Basic implementations may raise the exception

Specified by:

getAlignedObject1 in interface Alignment

Throws:

AlignmentException

getAlignedObject2

public Object getAlignedObject2(Object ob)
                         throws AlignmentException

Specified by:

getAlignedObject2 in interface Alignment

Throws:

AlignmentException

getAlignedRelation1

public Relation getAlignedRelation1(Object ob)
                             throws AlignmentException

Specified by:

getAlignedRelation1 in interface Alignment

Throws:

AlignmentException

getAlignedRelation2

public Relation getAlignedRelation2(Object ob)
                             throws AlignmentException

Specified by:

getAlignedRelation2 in interface Alignment

Throws:

AlignmentException

getAlignedStrength1

public double getAlignedStrength1(Object ob)
                           throws AlignmentException

Specified by:

getAlignedStrength1 in interface Alignment

Throws:

AlignmentException

getAlignedStrength2

public double getAlignedStrength2(Object ob)
                           throws AlignmentException

Specified by:

getAlignedStrength2 in interface Alignment

Throws:

AlignmentException

removeAlignCell

public void removeAlignCell(Cell c)
                     throws AlignmentException

Throws:

AlignmentException

cut2

public void cut2(double threshold)
          throws AlignmentException

The cut function suppresses from an alignment all the cell over a particular threshold

Throws:

AlignmentException

cut

public void cut(double threshold)
         throws AlignmentException

Default cut implementation For compatibility with API until version 1.1

Specified by:

cut in interface Alignment

Throws:

AlignmentException

cut

public void cut(String method,
                double threshold)
         throws AlignmentException

Cut refinement : - getting those cells with strength above n (hard) - getting the n best cells (best) - getting those cells with strength at worse n under the best (span) - getting the n% best cells (perc) - getting those cells with strength at worse n% of the best (prop) - getting all cells until a gap of n (hardgap) - getting all cells until a gap of n% of the last (propgap) Rule: threshold is betweew 1 and 0

Specified by:

cut in interface Alignment

Throws:

AlignmentException

toURIAlignment

public URIAlignment toURIAlignment()
                            throws AlignmentException

Returns default exception for conversion to URIAlignments

Throws:

AlignmentException

harden

public void harden(double threshold)
            throws AlignmentException

The harden function acts like threshold but put all weights to 1.

Specified by:

harden in interface Alignment

Throws:

AlignmentException

createNewAlignment

public BasicAlignment createNewAlignment(Object onto1,
                                         Object onto2)
                                  throws AlignmentException

Algebraic part This is to be improved by (TODO): - improving cell equivalence (maybe not dependent on the confidence... and grounding it on abstract data types) - using algebraic meet and join for relations and confidences (the type of relation used can be declared in the alignment) - check compatibility and setup for type and level - conserve extensions if necessary

Throws:

AlignmentException

diff

public Alignment diff(Alignment align)
               throws AlignmentException

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.

Specified by:

diff in interface Alignment

Throws:

AlignmentException

meet

public Alignment meet(Alignment align)
               throws AlignmentException

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.

Specified by:

meet in interface Alignment

Throws:

AlignmentException

join

public Alignment join(Alignment align)
               throws AlignmentException

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.

Specified by:

join in interface Alignment

Throws:

AlignmentException

compose

public Alignment compose(Alignment align)
                  throws AlignmentException

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.

Specified by:

compose in interface Alignment

Throws:

AlignmentException

inverse

public Alignment inverse()
                  throws AlignmentException

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.

Specified by:

inverse in interface Alignment

Throws:

AlignmentException

dump

public void dump(ContentHandler h)

Housekeeping

Specified by:

dump in interface Alignment

ingest

public void ingest(Alignment alignment)
            throws AlignmentException

Incorporate the cells of the alignment into its own alignment. Note: for the moment, this does not copy but really incorporates. So, if hardening is applied, then the ingested alignmment will be modified as well. JE: May be a "force" boolean for really ingesting or copying may be useful

Throws:

AlignmentException

clone

public Object clone()

Generate a copy of this alignment object It has the same content but a different id (no id indeed)

Specified by:

clone in interface Alignment

Overrides:

clone in class Object

render

public void render(AlignmentVisitor renderer)
            throws AlignmentException

This should be rewritten in order to generate the axiom ontology instead of printing it! And then use ontology serialization for getting it printed.

Specified by:

render in interface Alignment

Throws:

AlignmentException

cleanUp

public void cleanUp()

Can be used for reducing the amount of memory taken by an alignment Does nothing in BasicAlignment.