A B C D E F G H I J L M N O P R S T U V W X

A

activateFastIdentification() - Method in class de.unima.alcomox.mapping.Mapping
Activates fast idpattern used for hast identification is e.g. hashsets.
activeMapping - Variable in class de.unima.alcomox.algorithms.AlcomoExtraction
 
activeSize() - Method in class de.unima.alcomox.algorithms.IndexMarker
 
addAxioms(Set<OWLAxiom>) - Method in class de.unima.alcomox.ontology.MergedOntology
 
addChild(IConcept) - Method in class de.unima.alcomox.ontology.IConcept
 
addCounter() - Method in class de.unima.alcomox.util.DataStorage
Adds the value of the counter as data value and restets the counter to 0.
addDisIntervals(ArrayList<Interval>) - Method in class de.unima.alcomox.ontology.IConcept
 
addMapping(String, Mapping) - Method in class de.unima.alcomox.mapping.MappingFamiliy
Adds a mapping to this family of mappings.
addParent(IConcept) - Method in class de.unima.alcomox.ontology.IConcept
 
addSubIntervals(ArrayList<Interval>) - Method in class de.unima.alcomox.ontology.IConcept
 
addValue(String) - Method in class de.unima.alcomox.util.DataStorage
 
addValue(int) - Method in class de.unima.alcomox.util.DataStorage
 
addValue(double) - Method in class de.unima.alcomox.util.DataStorage
 
adjustConceptConfidence(double) - Method in class de.unima.alcomox.mapping.Mapping
 
adjustPropertyConfidence(double) - Method in class de.unima.alcomox.mapping.Mapping
 
ALCOMO_URL - Static variable in class de.unima.alcomox.ExtractionProblem
The namespace for additionally created entities (domain and range concepts).
AlcomoException - Exception in de.unima.alcomox.exceptions
Every problem that might occur and cannot be solved is thrown as instance of this class.
AlcomoException(String) - Constructor for exception de.unima.alcomox.exceptions.AlcomoException
 
AlcomoExtraction - Class in de.unima.alcomox.algorithms
 
AlcomoExtraction(ExtractionProblem) - Constructor for class de.unima.alcomox.algorithms.AlcomoExtraction
Constructs an algorithm for solving an extraction problem.
AlcomoLogger - Class in de.unima.alcomox.util
A wrapper for the log4j logging mechanism.
AlcomoLogger(Class) - Constructor for class de.unima.alcomox.util.AlcomoLogger
Constructs a wrapper logger for the log4j logger for a certain class.
AlcomoOntology - Class in de.unima.alcomox.ontology
This abstract class represents an ontology used in the alcomo system.
AlcomoOntology(OWLOntology, OWLOntologyManager) - Constructor for class de.unima.alcomox.ontology.AlcomoOntology
 
AlcomoOntology() - Constructor for class de.unima.alcomox.ontology.AlcomoOntology
 
AlcomoProblem - Class in de.unima.alcomox
 
AlcomoProblem() - Constructor for class de.unima.alcomox.AlcomoProblem
 
AlcomoReasoner - Class in de.unima.alcomox.ontology
This abstract class represents a reasoner used in the alcomo system.
AlcomoReasoner(LocalOntology, LocalOntology, ExtractionProblem) - Constructor for class de.unima.alcomox.ontology.AlcomoReasoner
 
applyThreshhold(double) - Method in class de.unima.alcomox.mapping.Mapping
Applies a threshold on the mapping by removing every correspondence with a confidence below the threhold.
applyThresholdRelative(double) - Method in class de.unima.alcomox.mapping.Mapping
Applies a threshold such that the fraction of the rt worst correspondences are removed.
AStarSearch - Class in de.unima.alcomox.algorithms
A uniform cost search to solve an extraction problem. .
AStarSearch(ExtractionProblem) - Constructor for class de.unima.alcomox.algorithms.AStarSearch
Constructs a algorithm implementing a uniform cost search by spanning a tree where every node in the tree is a (sub) mapping.
attachValidatedMapping(Mapping) - Method in class de.unima.alcomox.ontology.CompleteReasoner
Adds a validated mapping that will be used in reasoning in a fixed way.

B

bind(LocalOntology, LocalOntology) - Method in class de.unima.alcomox.mapping.Mapping
Binds the mapping (more precise: the uris of the correspondences) to the internal representation of the entities.
bindMapping(Mapping) - Method in class de.unima.alcomox.AlcomoProblem
Sets a mapping as input mapping.
bindSourceOntology(LocalOntology) - Method in class de.unima.alcomox.AlcomoProblem
Sets an ontology as source ontology.
bindTargetOntology(LocalOntology) - Method in class de.unima.alcomox.AlcomoProblem
Sets an ontology as target ontology.
BLACKBOX_REASONER - Static variable in class de.unima.alcomox.Settings
The reasoner used internally in a black-box approach.

C

catchedException - Variable in exception de.unima.alcomox.exceptions.AlcomoException
 
Characteristic - Class in de.unima.alcomox.mapping
Characterises the relation between two mappings in terms of recall, precision and f-value.
Characteristic() - Constructor for class de.unima.alcomox.mapping.Characteristic
Constructs an empty characteristic which is a characteristic for an mapping of cardinality zero.
Characteristic(int, int, int) - Constructor for class de.unima.alcomox.mapping.Characteristic
Constructs a characteristic.
Characteristic(Mapping, Mapping) - Constructor for class de.unima.alcomox.mapping.Characteristic
Constructs a characteristic based by comparing two mappings.
characters(char[], int, int) - Method in class de.unima.alcomox.mapping.MappingReaderXml
 
checkBindings() - Method in class de.unima.alcomox.AlcomoProblem
 
closeInterval(int) - Method in class de.unima.alcomox.ontology.IConcept
 
compareTo(IndexMarker) - Method in class de.unima.alcomox.algorithms.IndexMarker
 
compareTo(LockMarker) - Method in class de.unima.alcomox.algorithms.LockMarker
 
compareTo(Correspondence) - Method in class de.unima.alcomox.mapping.Correspondence
 
compareTo(Mapping) - Method in class de.unima.alcomox.mapping.Mapping
 
compareTo(Interval) - Method in class de.unima.alcomox.ontology.Interval
 
CompleteReasoner - Class in de.unima.alcomox.ontology
This class represents a complete reasoner for conflict detection in mappings.
CompleteReasoner(LocalOntology, LocalOntology, ExtractionProblem) - Constructor for class de.unima.alcomox.ontology.CompleteReasoner
Constructs an reasoner for complete conflict detection.
computeFFromPR(double, double) - Static method in class de.unima.alcomox.mapping.Characteristic
 
ConflictPair - Class in de.unima.alcomox.ontology
A conflict pair is a conflict set of size 2 that can can be detected by incomplete and effient reasoning.
ConflictPair(Correspondence, Correspondence) - Constructor for class de.unima.alcomox.ontology.ConflictPair
 
ConflictSearch - Class in de.unima.alcomox.algorithms
 
ConflictSearch(ExtractionProblem) - Constructor for class de.unima.alcomox.algorithms.ConflictSearch
 
ConflictStore - Class in de.unima.alcomox.algorithms
 
ConflictStore(EfficientReasoner, Mapping) - Constructor for class de.unima.alcomox.algorithms.ConflictStore
Construct a conflict store where some conflicts are precomputed due to efficient reasoning.
ConflictStore(Mapping) - Constructor for class de.unima.alcomox.algorithms.ConflictStore
Constructs an empty conflict store where no efficient component is used for pre processing.
conflictsWithMapping(Correspondence, Mapping) - Method in class de.unima.alcomox.ontology.EfficientReasoner
 
contains(Correspondence) - Method in class de.unima.alcomox.mapping.Mapping
Checks if a given correspondence is contained in this mapping.
contains(Interval) - Method in class de.unima.alcomox.ontology.Interval
Compares this and that interval and checks whether this interval contains that interval.
contains(int) - Method in class de.unima.alcomox.ontology.Interval
Checks whether an index is contained in this interval.
containsCorrespondence(int, int) - Method in class de.unima.alcomox.mapping.MappingMatrix
 
containsLock(Coord) - Method in class de.unima.alcomox.algorithms.LockMarker
 
convertToEquivalenceCorrespondences() - Method in class de.unima.alcomox.mapping.Mapping
Converts all correspondences from the mapping that express a different semantic relation than equivalence to equivalence.
Coord - Class in de.unima.alcomox.algorithms
A Lock represent a locked coordinate in a mapping matrix.
Coord(int, int) - Constructor for class de.unima.alcomox.algorithms.Coord
 
copyFile(String, String) - Static method in class de.unima.alcomox.util.Tools
 
copyFile(File, File) - Static method in class de.unima.alcomox.util.Tools
 
Correspondence - Class in de.unima.alcomox.mapping
A correspondence represents a (simple) semantic relation between two entities belonging to different ontologies.
Correspondence(String, String, SemanticRelation) - Constructor for class de.unima.alcomox.mapping.Correspondence
Constructs an unbound correspondence with confidence value set to 1.0.
Correspondence(String, String, SemanticRelation, double) - Constructor for class de.unima.alcomox.mapping.Correspondence
Constructs an unbound correspondence with confidence value set to 1.0.
CORRESPONDENCE_PROBLEM - Static variable in exception de.unima.alcomox.exceptions.MappingException
 
CorrespondenceException - Exception in de.unima.alcomox.exceptions
A correspondence exception handles every type of problems related to correspondences and their internal components.
CorrespondenceException(int, String, Exception) - Constructor for exception de.unima.alcomox.exceptions.CorrespondenceException
 
CorrespondenceException(int, String) - Constructor for exception de.unima.alcomox.exceptions.CorrespondenceException
 
CorrespondenceException(int) - Constructor for exception de.unima.alcomox.exceptions.CorrespondenceException
 
count() - Method in class de.unima.alcomox.util.DataStorage
 
createConceptEntity(OWLClass) - Static method in class de.unima.alcomox.ontology.EntityFactory
 
createDataPropertyEntity(OWLDataProperty, OWLClass) - Static method in class de.unima.alcomox.ontology.EntityFactory
 
createDataRow() - Method in class de.unima.alcomox.util.DataStorage
 
createObjectPropertyEntity(OWLObjectProperty, OWLClass, OWLClass) - Static method in class de.unima.alcomox.ontology.EntityFactory
Constructs an entity corresponding to an object property with both domain and range class extension.
createObjectPropertyEntity(OWLObjectProperty, OWLClass) - Static method in class de.unima.alcomox.ontology.EntityFactory
Constructs an entity corresponding to an object property with only a domain extension.
createUriClassReferences() - Method in class de.unima.alcomox.ontology.MergedOntology
 
CSEXACTNESS - Static variable in class de.unima.alcomox.ExtractionProblem
The conflict sensitivity exactness determines the exactness of the conflict sensitivity estimation.

D

DataStorage - Class in de.unima.alcomox.util
 
DataStorage() - Constructor for class de.unima.alcomox.util.DataStorage
Constructs a data storage.
DataStorage(String) - Constructor for class de.unima.alcomox.util.DataStorage
Constructs a data storage.
de.unima.alcomox - package de.unima.alcomox
 
de.unima.alcomox.algorithms - package de.unima.alcomox.algorithms
 
de.unima.alcomox.exceptions - package de.unima.alcomox.exceptions
 
de.unima.alcomox.mapping - package de.unima.alcomox.mapping
 
de.unima.alcomox.metric - package de.unima.alcomox.metric
 
de.unima.alcomox.ontology - package de.unima.alcomox.ontology
 
de.unima.alcomox.ontology.extowlapi - package de.unima.alcomox.ontology.extowlapi
 
de.unima.alcomox.util - package de.unima.alcomox.util
 
deactivate(int) - Method in class de.unima.alcomox.algorithms.IndexMarker
 
deactivateCounter() - Method in class de.unima.alcomox.util.DataStorage
 
deactivateLogger() - Static method in class de.unima.alcomox.util.Tools
 
deactivateStopWatch() - Method in class de.unima.alcomox.util.DataStorage
 
detectedNominal() - Method in class de.unima.alcomox.ontology.extowlapi.NominalAxiomDetector
Informs about the existence of a nominal in an axiom.
DiagnosisException - Exception in de.unima.alcomox.exceptions
A diagnosis exception handles every type of problems related to diagnosis with the human in the loop.
DiagnosisException(int, String, Exception) - Constructor for exception de.unima.alcomox.exceptions.DiagnosisException
 
DiagnosisException(int, String) - Constructor for exception de.unima.alcomox.exceptions.DiagnosisException
 
DiagnosisException(int) - Constructor for exception de.unima.alcomox.exceptions.DiagnosisException
 
DIS - Static variable in class de.unima.alcomox.mapping.SemanticRelation
Relation of disjointness, e.g.
DISABLE_REASONING - Static variable in class de.unima.alcomox.Settings
If activated no conflicts are computed except one-to-one conflicts.
disableExtendedStyle() - Method in class de.unima.alcomox.mapping.MappingWriterXml
 
displaySubtree(int) - Method in class de.unima.alcomox.ontology.IConcept
 

E

EfficientReasoner - Class in de.unima.alcomox.ontology
This class represents a reasoner for efficient pairwise but incomplete conflict detection.
EfficientReasoner(LocalOntology, LocalOntology, ExtractionProblem) - Constructor for class de.unima.alcomox.ontology.EfficientReasoner
Constructs an reasoner for efficient pairwise but incomplete conflict detection.
enableExtendedStyle() - Method in class de.unima.alcomox.mapping.MappingWriterXml
 
endElement(String, String, String) - Method in class de.unima.alcomox.mapping.MappingReaderXml
 
ENTITIES - Static variable in class de.unima.alcomox.ExtractionProblem
The entities parameter determines whether only concepts correspondences or correspondences between concepts and relations are accepted.
entities - Variable in class de.unima.alcomox.ontology.AlcomoOntology
 
ENTITIES_CONCEPTSPROPERTIES - Static variable in class de.unima.alcomox.ExtractionProblem
Concept and property correspondences.
ENTITIES_ONLYCONCEPTS - Static variable in class de.unima.alcomox.ExtractionProblem
Only concepts correspondences.
Entity - Class in de.unima.alcomox.ontology
 
Entity() - Constructor for class de.unima.alcomox.ontology.Entity
 
EntityFactory - Class in de.unima.alcomox.ontology
 
EntityFactory() - Constructor for class de.unima.alcomox.ontology.EntityFactory
 
equalizeBoundedMappingTrust() - Method in class de.unima.alcomox.ExtractionProblem
 
equals(Object) - Method in class de.unima.alcomox.algorithms.Coord
 
equals(Object) - Method in class de.unima.alcomox.algorithms.IndexMarker
 
equals(Object) - Method in class de.unima.alcomox.algorithms.LockMarker
 
equals(Object) - Method in class de.unima.alcomox.mapping.Correspondence
 
equals(Object) - Method in class de.unima.alcomox.mapping.Mapping
 
equals(Object) - Method in class de.unima.alcomox.mapping.SemanticRelation
Checks equality of this and that semantic relation.
equals(Object) - Method in class de.unima.alcomox.ontology.ConflictPair
 
equals(Object) - Method in class de.unima.alcomox.ontology.Interval
 
EQUIV - Static variable in class de.unima.alcomox.mapping.SemanticRelation
Relation of equivalence, e.g.
estimateConflictSensitivity(Correspondence, int) - Method in class de.unima.alcomox.ontology.EfficientReasoner
Estimates the conflict sensitivity by drawing a sample of randomly generated correspondences.
eval(LocalOntology, LocalOntology, Mapping) - Method in class de.unima.alcomox.metric.IncoherenceMetric
Runs an evaluation by applying the incoherence metric a.k.a maximum cardinality incoherence measure (as defined in Meilicke,Stuckenschmidt OM 2008).
evaluationSuccessful() - Method in class de.unima.alcomox.metric.IncoherenceMetric
Checks whether the evaluation was successful and generated a meaningful value.
evaluationTerminated() - Method in class de.unima.alcomox.metric.IncoherenceMetric
 
extractionProblem - Variable in class de.unima.alcomox.algorithms.AlcomoExtraction
 
ExtractionProblem - Class in de.unima.alcomox
 
ExtractionProblem(int, int, int) - Constructor for class de.unima.alcomox.ExtractionProblem
Constructs an extraction problem and specifies the way it will be solved.
ExtractionProblem() - Constructor for class de.unima.alcomox.ExtractionProblem
Constructs an extraction problem with standard settings (concepts and props, optimal, complete).
extractionProblem - Variable in class de.unima.alcomox.ontology.AlcomoOntology
 
extractionProblem - Variable in class de.unima.alcomox.ontology.AlcomoReasoner
 

F

factory - Variable in class de.unima.alcomox.ontology.AlcomoOntology
 
filterBySourceNamespace(String) - Method in class de.unima.alcomox.mapping.Mapping
Filters out every correspondence in this mapping that has not the specified source namespace.
filterByTargetNamespace(String) - Method in class de.unima.alcomox.mapping.Mapping
Filters out every correspondence in this mapping that has not the specified target namespace.
FORMAT_RDF - Static variable in class de.unima.alcomox.mapping.Mapping
Standard format of the OAEI.
FORMAT_TXT - Static variable in class de.unima.alcomox.mapping.Mapping
Simple text-based proprietary format.
freeReasoner() - Method in class de.unima.alcomox.ontology.AlcomoOntology
 

G

generalDescription - Variable in exception de.unima.alcomox.exceptions.AlcomoException
 
get(int) - Method in class de.unima.alcomox.mapping.Mapping
 
getActiveMapping() - Method in class de.unima.alcomox.algorithms.AlcomoExtraction
Returns the activated mapping (also referred to as the extracted mapping).
getActiveMapping(Mapping) - Method in class de.unima.alcomox.algorithms.IndexMarker
 
getAxioms() - Method in class de.unima.alcomox.ontology.AlcomoOntology
 
getChild(int, ConflictStore) - Method in class de.unima.alcomox.algorithms.IndexMarker
Constructs a child of an index-marker which ic the parent index-maker where on of the flags is set from true to false (one correspondence dismissed).
getChild(Coord) - Method in class de.unima.alcomox.algorithms.LockMarker
Constructs a child of this lock marker, where an additional lock has been added.
getChildren() - Method in class de.unima.alcomox.ontology.IConcept
 
getClasses() - Method in class de.unima.alcomox.ontology.AlcomoOntology
Returns alls classes in this ontology.
getConcept() - Method in class de.unima.alcomox.ontology.Entity
 
getConfidence(int) - Method in class de.unima.alcomox.algorithms.IndexMarker
 
getConfidence() - Method in class de.unima.alcomox.mapping.Correspondence
 
getConfidenceLowerBound() - Method in class de.unima.alcomox.mapping.Mapping
 
getConfidenceTotal() - Method in class de.unima.alcomox.mapping.Mapping
 
getConfidenceUpperBound() - Method in class de.unima.alcomox.mapping.Mapping
 
getConflicSets() - Method in class de.unima.alcomox.ExtractionProblem
Deprecated. Will be removed in following AlcomoVersions (was used in javasript based manual evaluation). Computes the set of all conflict sets in the efficient mode. This method will find most pairs of conflicting correspondences, conflict sets of higher cardinality are not yet supported.
getConflictingIndices(IndexMarker) - Method in class de.unima.alcomox.algorithms.ConflictStore
Checks whether there are still some conflicts unresolved with respect to the index marker.
getConflictingIndices(ArrayList<Integer>) - Method in class de.unima.alcomox.algorithms.ConflictStore
Checks whether there are still some conflicts unresolved with respect to a list of active correspondence indices.
getConflictPairs() - Method in class de.unima.alcomox.mapping.Mapping
 
getConflictSet(Mapping) - Method in class de.unima.alcomox.ontology.CompleteReasoner
 
getConflictSets() - Method in class de.unima.alcomox.algorithms.ConflictSearch
 
getCoord(Integer) - Method in class de.unima.alcomox.mapping.MappingMatrix
 
getCopy() - Method in class de.unima.alcomox.mapping.Mapping
Creates and returns a copy of this mapping.
getCorrespondence(int, int) - Method in class de.unima.alcomox.mapping.MappingMatrix
 
getCorrespondence1() - Method in class de.unima.alcomox.ontology.ConflictPair
 
getCorrespondence2() - Method in class de.unima.alcomox.ontology.ConflictPair
 
getCorrespondences() - Method in class de.unima.alcomox.mapping.Mapping
Returns the correspondences of this mapping as list.
getCorrespondences() - Method in class de.unima.alcomox.ontology.ConflictPair
 
getCorrespondencesAsSet() - Method in class de.unima.alcomox.mapping.Mapping
Returns the correspondences of this mapping as set.
getDataProperty() - Method in class de.unima.alcomox.ontology.Entity
 
getDegreeOfIncoherence() - Method in class de.unima.alcomox.metric.IncoherenceMetric
Returns the degree of incoherence.
getDifference(Mapping) - Method in class de.unima.alcomox.mapping.Mapping
Returns the set difference between this mapping and that mapping.
getDiscardedMapping() - Method in class de.unima.alcomox.ExtractionProblem
Returns the mapping discarded as results of solving this extraction problem.
getDisIntervals() - Method in class de.unima.alcomox.ontology.IConcept
 
getDistances() - Method in class de.unima.alcomox.mapping.MappingMatrix
 
getDomain() - Method in class de.unima.alcomox.ontology.Entity
 
getEntities() - Method in class de.unima.alcomox.ExtractionProblem
 
getEntityByUri(String) - Method in class de.unima.alcomox.ontology.LocalOntology
Resolves the uri reference and returns the entity that the uri refers to.
getErrorMessage() - Method in class de.unima.alcomox.metric.IncoherenceMetric
If the evaluation has not been successful, a string representations of caught exceptions can be retrieved.
getEstimatedTrustLoss() - Method in class de.unima.alcomox.algorithms.IndexMarker
 
getExtractedMapping() - Method in class de.unima.alcomox.ExtractionProblem
Returns the mapping extracted as results of solving this extraction problem.
getExtractionProblem() - Method in class de.unima.alcomox.ontology.AlcomoOntology
 
getF() - Method in class de.unima.alcomox.mapping.Characteristic
 
getFinalTrust() - Method in class de.unima.alcomox.algorithms.IndexMarker
 
getFMeasure() - Method in class de.unima.alcomox.mapping.Characteristic
Returns the f-measure.
getId() - Method in class de.unima.alcomox.mapping.Correspondence
 
getId() - Method in class de.unima.alcomox.ontology.IConcept
 
getId() - Method in class de.unima.alcomox.ontology.Interval
 
getIdPattern() - Method in class de.unima.alcomox.mapping.Mapping
 
getInactiveMapping() - Method in class de.unima.alcomox.algorithms.AlcomoExtraction
Returns the deactivated mapping (also referred to as the thrown, removed or rejected mapping).
getInactiveMapping(Mapping) - Method in class de.unima.alcomox.algorithms.IndexMarker
 
getIndex(int, int) - Method in class de.unima.alcomox.mapping.MappingMatrix
 
getIndicesAndSetConflicts(Mapping) - Method in class de.unima.alcomox.algorithms.ConflictStore
Returns the indices that refer to the correspondences of a given mapping and sets these indices as additional conflicts.0000000000000
getIntersection(Mapping) - Method in class de.unima.alcomox.mapping.Mapping
Returns the intersection between this mapping and that.
getInverse() - Method in class de.unima.alcomox.mapping.SemanticRelation
Returns the inverse semantic relation of this semantic relation.
getJaccardDimilarity(Mapping, Mapping) - Static method in class de.unima.alcomox.mapping.Similarity
 
getJoinedMapping(Mapping[]) - Static method in class de.unima.alcomox.mapping.Mapping
Joins the specified mappings into a single mapping that contains all correspondences of the specified mappings.
getJoinedMapping(Mapping[], double[]) - Static method in class de.unima.alcomox.mapping.Mapping
 
getLocalUnsatisfiableEntities() - Method in class de.unima.alcomox.ExtractionProblem
Returns the uris (as strings) of all unsatisfiable concepts of both local ontologies.
getLocks() - Method in class de.unima.alcomox.algorithms.LockMarker
 
getLower() - Method in class de.unima.alcomox.ontology.Interval
 
getMapping(String) - Method in interface de.unima.alcomox.mapping.MappingReader
 
getMapping(String) - Method in class de.unima.alcomox.mapping.MappingReaderTxt
 
getMapping(String) - Method in class de.unima.alcomox.mapping.MappingReaderXml
 
getMergedMappingVC() - Method in class de.unima.alcomox.mapping.MappingFamiliy
Returns the merged mapping where confindences have been computed in a way such that the following holds for two correspondences c1 and c2: (1) conf(c1) <h; conf(c2) iff less systems found c1 (Vote)
getMergedOntology() - Method in class de.unima.alcomox.ExtractionProblem
 
getMergedOntology() - Method in class de.unima.alcomox.ontology.CompleteReasoner
 
getMergedUnsatisfiableEntities() - Method in class de.unima.alcomox.ExtractionProblem
Returns the uris (as strings) of all unsatisfiable concepts of ther merged ontology based on the currecnt input mapping.
getMetaDescription() - Method in class de.unima.alcomox.mapping.Mapping
Returns different kinds of meta information about this mapping.
getNextExtId() - Method in class de.unima.alcomox.ontology.LocalOntology
 
getNonReferingInputMapping() - Method in class de.unima.alcomox.ExtractionProblem
 
getNumOfInvolvedConflicts(int, IndexMarker) - Method in class de.unima.alcomox.algorithms.ConflictStore
 
getNumOfRulesCorrect() - Method in class de.unima.alcomox.mapping.Characteristic
 
getNumOfRulesGold() - Method in class de.unima.alcomox.mapping.Characteristic
 
getNumOfRulesMatcher() - Method in class de.unima.alcomox.mapping.Characteristic
 
getObjectProperty() - Method in class de.unima.alcomox.ontology.Entity
 
getP() - Method in class de.unima.alcomox.mapping.Characteristic
 
getParam(String) - Method in class de.unima.alcomox.ExtractionProblem
Returns the value of a parameter.
getPrecision() - Method in class de.unima.alcomox.mapping.Characteristic
Returns the precision.
getR() - Method in class de.unima.alcomox.mapping.Characteristic
 
getRandomEntity() - Method in class de.unima.alcomox.ontology.LocalOntology
 
getRandomEntity(boolean) - Method in class de.unima.alcomox.ontology.LocalOntology
 
getRange() - Method in class de.unima.alcomox.ontology.Entity
 
getRealDirectSuperClassesOfClass(OWLClass) - Method in class de.unima.alcomox.ontology.AlcomoOntology
Returns the set of all classes that direct are superclasses of the specified class The class itself is excluded.
getRecall() - Method in class de.unima.alcomox.mapping.Characteristic
Returns the recall.
getReferencedClassUris() - Method in class de.unima.alcomox.ontology.LocalOntology
 
getReferingInputMapping() - Method in class de.unima.alcomox.ExtractionProblem
 
getRelation() - Method in class de.unima.alcomox.mapping.Correspondence
 
getScore() - Method in class de.unima.alcomox.algorithms.LockMarker
 
getSourceEntity() - Method in class de.unima.alcomox.mapping.Correspondence
 
getSourceEntityId() - Method in class de.unima.alcomox.mapping.Correspondence
 
getSourceEntityUri() - Method in class de.unima.alcomox.mapping.Correspondence
 
getSourceNamespace() - Method in class de.unima.alcomox.mapping.Correspondence
 
getSubClassesOfClass(OWLClass) - Method in class de.unima.alcomox.ontology.AlcomoOntology
Returns the set of all classes that are subclasses of the specified class as well as the class itself.
getSubIntervals() - Method in class de.unima.alcomox.ontology.IConcept
 
getTargetEntity() - Method in class de.unima.alcomox.mapping.Correspondence
 
getTargetEntityId() - Method in class de.unima.alcomox.mapping.Correspondence
 
getTargetEntityUri() - Method in class de.unima.alcomox.mapping.Correspondence
 
getTargetNamespace() - Method in class de.unima.alcomox.mapping.Correspondence
 
getTopWeightedConflictingIndex(IndexMarker) - Method in class de.unima.alcomox.algorithms.ConflictStore
Computes the next index that has to be removed following a greedy strategy that first chooses according to conflicts in which a correspondence is involved, and next takes uses the confidence value.
getTransImpliedMapping(Mapping, Mapping) - Static method in class de.unima.alcomox.mapping.MappingClosure
 
getTrust() - Method in class de.unima.alcomox.algorithms.IndexMarker
 
getType() - Method in class de.unima.alcomox.mapping.SemanticRelation
 
getUnion(Mapping) - Method in class de.unima.alcomox.mapping.Mapping
Returns the union of this mapping and that.
getUnsatisfiableClasses() - Method in class de.unima.alcomox.ontology.AlcomoOntology
Returns all unsatisfiable classes in this ontology.
getUnsatisfiableClasses(Mapping) - Method in class de.unima.alcomox.ontology.CompleteReasoner
A complete method for computing the set of all unsatisfiable classes in the merged ontology..
getUpper() - Method in class de.unima.alcomox.ontology.Interval
 
getX() - Method in class de.unima.alcomox.algorithms.Coord
 
getY() - Method in class de.unima.alcomox.algorithms.Coord
 
Greedy - Class in de.unima.alcomox.algorithms
A greedy algoritm to solve an extraction problem.
Greedy(ExtractionProblem) - Constructor for class de.unima.alcomox.algorithms.Greedy
Constructs a greedy algorithm for solving the extraction problem.
GreedyMinimize - Class in de.unima.alcomox.algorithms
A uniform cost search to solve an extraction problem. .
GreedyMinimize(ExtractionProblem) - Constructor for class de.unima.alcomox.algorithms.GreedyMinimize
Constructs a algorithm implementing a greedy search that removes first those correspondences that are involved in most conflicts.

H

hasBeenInterrupted() - Method in class de.unima.alcomox.algorithms.AlcomoExtraction
Checks for an interrupt, stores current results and stops computation.
hasCommonSubClassWith(IConcept) - Method in class de.unima.alcomox.ontology.IConcept
 
hasCommonSubDisjointClassWith(IConcept) - Method in class de.unima.alcomox.ontology.IConcept
 
hashCode() - Method in class de.unima.alcomox.algorithms.Coord
 
hashCode() - Method in class de.unima.alcomox.algorithms.IndexMarker
 
hashCode() - Method in class de.unima.alcomox.algorithms.LockMarker
 
hashCode() - Method in class de.unima.alcomox.mapping.Correspondence
 
hashCode() - Method in class de.unima.alcomox.mapping.Mapping
 
hashCode() - Method in class de.unima.alcomox.mapping.SemanticRelation
 
hashCode() - Method in class de.unima.alcomox.ontology.ConflictPair
 
hasICommonSubClass(OWLClass, OWLClass) - Method in class de.unima.alcomox.ontology.IOntology
Checks whether two classes have a common named sublass (except NOTHING).
hasICommonSubDisjointClass(OWLClass, OWLClass) - Method in class de.unima.alcomox.ontology.IOntology
Checks whether there exists a class that is both a subclass of c1 and at the same time a class that is disjoint with c2.
hasNext() - Method in class de.unima.alcomox.algorithms.IndexMarker
 
HTML_DEBUG_DISPLAY_LABELS - Static variable in class de.unima.alcomox.Settings
Probably no longer used internally.
HungarianSearch - Class in de.unima.alcomox.algorithms
A uniform cost search using the hungarian method
HungarianSearch(ExtractionProblem) - Constructor for class de.unima.alcomox.algorithms.HungarianSearch
Constructs a algorithm implementing a uniform cost search by spanning a tree where every node in the tree is a (sub) mapping.

I

IConcept - Class in de.unima.alcomox.ontology
 
IConcept(OWLClass, int) - Constructor for class de.unima.alcomox.ontology.IConcept
 
idPattern - Variable in class de.unima.alcomox.mapping.Mapping
 
inactiveMapping - Variable in class de.unima.alcomox.algorithms.AlcomoExtraction
 
IncoherenceMetric - Class in de.unima.alcomox.metric
Replaces the old IMerasureProblem class and is under development at the moment to be used inside SEALS maybe via the Alignment API.
IncoherenceMetric() - Constructor for class de.unima.alcomox.metric.IncoherenceMetric
Constructs an incoherence metric with default timeout.
IncoherenceMetric(long) - Constructor for class de.unima.alcomox.metric.IncoherenceMetric
Constructs an incoherence metric with timeout specified in millis.
indexedConceptEntityUris - Variable in class de.unima.alcomox.ontology.AlcomoOntology
 
indexedPropertyEntityUris - Variable in class de.unima.alcomox.ontology.AlcomoOntology
 
IndexMarker - Class in de.unima.alcomox.algorithms
An index marker is an array of flags that inform wether or not a correspondence of a mapping is active or not.
IndexMarker(Mapping, ConflictStore) - Constructor for class de.unima.alcomox.algorithms.IndexMarker
Constructs an index-marker of size specified by a mapping.
infoP(double) - Method in class de.unima.alcomox.util.AlcomoLogger
Logs a double interpreted as progress in percentage as info message.
infoPEnd() - Method in class de.unima.alcomox.util.AlcomoLogger
Logs a end sign for a series of progress infos as info message followed by a newline.
infoPStart() - Method in class de.unima.alcomox.util.AlcomoLogger
Logs a start sign for a series of progress infos as info message.
infoPStart(String) - Method in class de.unima.alcomox.util.AlcomoLogger
Logs a start sign for a series of progress infos as info message.
infoS(String) - Method in class de.unima.alcomox.util.AlcomoLogger
Logs a statement as info message.
infoW(String) - Method in class de.unima.alcomox.util.AlcomoLogger
Logs a word as info message.
init() - Method in class de.unima.alcomox.AlcomoProblem
 
init() - Method in class de.unima.alcomox.ExtractionProblem
 
init(ExtractionProblem) - Method in class de.unima.alcomox.ontology.IOntology
Initializes an IOntology by setting up an additional interval tree, that represents very fast index structures highly beneficial in the pattern-based reasoning. 22
init(ExtractionProblem) - Method in class de.unima.alcomox.ontology.LocalOntology
Inits this extandable ontology and binds it to the extraction problem.
initialized - Variable in class de.unima.alcomox.AlcomoProblem
 
initOrResetIndex() - Method in class de.unima.alcomox.algorithms.IndexMarker
 
initReasoner() - Method in class de.unima.alcomox.ontology.AlcomoOntology
 
initReasonerWithoutClassification() - Method in class de.unima.alcomox.ontology.AlcomoOntology
 
inputMapping - Variable in class de.unima.alcomox.AlcomoProblem
 
interpretPartOfAsDisjointness() - Method in class de.unima.alcomox.ExtractionProblem
 
Interval - Class in de.unima.alcomox.ontology
An interval represents a sub branch of classes in an interval tree.
Interval(int) - Constructor for class de.unima.alcomox.ontology.Interval
Constructs an interval be explicitly defining the lower border, while the upper border is set to -1 to mark the interval as an open interval.
Interval(int, int) - Constructor for class de.unima.alcomox.ontology.Interval
 
INVALID_CONFIDENCE_VALUE - Static variable in exception de.unima.alcomox.exceptions.CorrespondenceException
 
INVALID_FORMAT - Static variable in exception de.unima.alcomox.exceptions.DiagnosisException
 
INVALID_FORMAT - Static variable in exception de.unima.alcomox.exceptions.MappingException
 
INVALID_FORMAT - Static variable in exception de.unima.alcomox.exceptions.OntologyException
 
INVALID_OPERATION - Static variable in exception de.unima.alcomox.exceptions.PCFException
 
INVALID_PARAM - Static variable in exception de.unima.alcomox.exceptions.PCFException
 
INVALID_PARAM_COMBINATION - Static variable in exception de.unima.alcomox.exceptions.PCFException
 
INVALID_SEMANTIC_RELATION - Static variable in exception de.unima.alcomox.exceptions.CorrespondenceException
 
invert() - Method in class de.unima.alcomox.mapping.Correspondence
 
invert() - Method in class de.unima.alcomox.mapping.Mapping
Inverts this mapping.
invertRelation() - Method in class de.unima.alcomox.mapping.Correspondence
 
IO_ERROR - Static variable in exception de.unima.alcomox.exceptions.DiagnosisException
 
IO_ERROR - Static variable in exception de.unima.alcomox.exceptions.MappingException
 
IO_ERROR - Static variable in exception de.unima.alcomox.exceptions.OntologyException
 
IOntology - Class in de.unima.alcomox.ontology
 
IOntology(String) - Constructor for class de.unima.alcomox.ontology.IOntology
 
isActive(int) - Method in class de.unima.alcomox.algorithms.IndexMarker
 
isClosed() - Method in class de.unima.alcomox.ontology.Interval
 
isCoherentExtraction() - Method in class de.unima.alcomox.ExtractionProblem
Checks with complete reasoning wether the extracted mapping is coherent.
isConcept() - Method in class de.unima.alcomox.ontology.Entity
 
isConflictPair(Correspondence, Correspondence) - Method in class de.unima.alcomox.ontology.EfficientReasoner
Checks wether two correspondences are in conflict.
isConflictSet(Mapping) - Method in class de.unima.alcomox.ontology.CompleteReasoner
A complete method for checking if a set of correspondences induces a conflict.
isConflictSet(Mapping) - Method in class de.unima.alcomox.ontology.EfficientReasoner
 
isDataProperty() - Method in class de.unima.alcomox.ontology.Entity
 
isDisjointClassWithClass(OWLClass, OWLClass) - Method in class de.unima.alcomox.ontology.AlcomoOntology
Checks wether two classes are disjoint.
isDisjointWith(IConcept) - Method in class de.unima.alcomox.ontology.IConcept
 
isEquivOrSub() - Method in class de.unima.alcomox.mapping.Correspondence
 
isEquivOrSuper() - Method in class de.unima.alcomox.mapping.Correspondence
 
isIDisjointClassWithClass(OWLClass, OWLClass) - Method in class de.unima.alcomox.ontology.IOntology
 
isISubClassOfClass(OWLClass, OWLClass) - Method in class de.unima.alcomox.ontology.IOntology
 
isObjectProperty() - Method in class de.unima.alcomox.ontology.Entity
 
isSubClassOf(IConcept) - Method in class de.unima.alcomox.ontology.IConcept
 
isSubClassOfClass(OWLClass, OWLClass) - Method in class de.unima.alcomox.ontology.AlcomoOntology
Checks wether first class is subclass of second class.
isUnique() - Method in class de.unima.alcomox.mapping.Mapping
 
isUnsatisfiable(OWLClass) - Method in class de.unima.alcomox.ontology.AlcomoOntology
Checks the unsatisfiability of a class.
isUnsatisfiable(OWLClass) - Method in class de.unima.alcomox.ontology.LocalOntology
 
iterator() - Method in class de.unima.alcomox.algorithms.LockMarker
 
iterator() - Method in class de.unima.alcomox.mapping.Mapping
 

J

join(Characteristic) - Method in class de.unima.alcomox.mapping.Characteristic
Joins this mapping with another mapping by summing up relevant characteristics in absolute numbers.
joinToEquivalence() - Method in class de.unima.alcomox.mapping.Mapping
Joins all pairs like a < b and a > b into equivalence correspondences a = b in place.

L

loadedOntCounter - Static variable in class de.unima.alcomox.ontology.LocalOntology
 
LocalOntology - Class in de.unima.alcomox.ontology
This class represents a local possibly extended ontology.
LocalOntology(String) - Constructor for class de.unima.alcomox.ontology.LocalOntology
Constructs an ontology, thats a kind of wrapper for an owl ontology, by reading a file specified by a filepath or url.
LockMarker - Class in de.unima.alcomox.algorithms
A lock marker is an array of flags that inform wether or not a correspondence of a mapping is active or not.
LockMarker() - Constructor for class de.unima.alcomox.algorithms.LockMarker
Constructs an empty list of locks as lock-marker.
log - Variable in class de.unima.alcomox.algorithms.AlcomoExtraction
 
log - Variable in class de.unima.alcomox.algorithms.ConflictStore
 
log - Variable in class de.unima.alcomox.mapping.Mapping
 
log - Variable in class de.unima.alcomox.ontology.AlcomoOntology
 
log - Variable in class de.unima.alcomox.ontology.AlcomoReasoner
 
LOG4J_PROPERTY_FILE - Static variable in class de.unima.alcomox.Settings
Defines the path to the log4j property file.

M

main(String[]) - Static method in class de.unima.alcomox.ontology.IOntology
 
mainDescription - Variable in exception de.unima.alcomox.exceptions.AlcomoException
 
makeVisible() - Method in class de.unima.alcomox.util.DataStorage
 
manager - Variable in class de.unima.alcomox.ontology.AlcomoOntology
 
MANY_TO_ONE - Static variable in class de.unima.alcomox.Settings
If activated only many to one (from source to target) are extracted.
mapping - Variable in class de.unima.alcomox.algorithms.AlcomoExtraction
 
Mapping - Class in de.unima.alcomox.mapping
A mapping is a ordered list of correspondences.
Mapping() - Constructor for class de.unima.alcomox.mapping.Mapping
Constructs a mapping with an empty list of correspondences.
Mapping(String, int) - Constructor for class de.unima.alcomox.mapping.Mapping
Constructs a mapping from a mapping given in a file.
Mapping(String) - Constructor for class de.unima.alcomox.mapping.Mapping
Constructs a mapping from a mapping given in a file, that has to be formated in the alignment API format.
Mapping(ArrayList<Correspondence>) - Constructor for class de.unima.alcomox.mapping.Mapping
Constructs a mapping with the given list of correspondences.
Mapping(Set<Correspondence>) - Constructor for class de.unima.alcomox.mapping.Mapping
Constructs a mapping with the given set of correspondences.
MappingClosure - Class in de.unima.alcomox.mapping
Unready stuff, base4d on some idea that does not work for the banchmark testcase.
MappingClosure() - Constructor for class de.unima.alcomox.mapping.MappingClosure
 
MappingException - Exception in de.unima.alcomox.exceptions
A mapping exception handles every type of problems related to mappings and catches internally thrown correspondence exceptions.
MappingException(int, String, Exception) - Constructor for exception de.unima.alcomox.exceptions.MappingException
 
MappingException(int, String) - Constructor for exception de.unima.alcomox.exceptions.MappingException
 
MappingException(int) - Constructor for exception de.unima.alcomox.exceptions.MappingException
 
MappingFamiliy - Class in de.unima.alcomox.mapping
A mapping familiy is a set of mapping togeterh with the information which matcher generated which mapping.
MappingFamiliy() - Constructor for class de.unima.alcomox.mapping.MappingFamiliy
Constructs an empty mapping family.
MappingMatrix - Class in de.unima.alcomox.mapping
 
MappingMatrix(Mapping) - Constructor for class de.unima.alcomox.mapping.MappingMatrix
 
MappingReader - Interface in de.unima.alcomox.mapping
The MappingReader defines the interface for its implementing classes that can be used to read Mappings from xml as well as txt-files.
MappingReaderTxt - Class in de.unima.alcomox.mapping
A mapping reader for txt format reads mappings from txt-files.
MappingReaderTxt() - Constructor for class de.unima.alcomox.mapping.MappingReaderTxt
 
MappingReaderXml - Class in de.unima.alcomox.mapping
A mapping reader for rdf/xml format reads mappings from rdf-files.
MappingReaderXml() - Constructor for class de.unima.alcomox.mapping.MappingReaderXml
 
MappingWriter - Interface in de.unima.alcomox.mapping
The MappingReader defines the interface for its implementing classes that can be used to write Mappings to xml as well as txt-files.
MappingWriterTxt - Class in de.unima.alcomox.mapping
A MappingWriterTxt writes Mappings to txt-files.
MappingWriterTxt() - Constructor for class de.unima.alcomox.mapping.MappingWriterTxt
 
MappingWriterXml - Class in de.unima.alcomox.mapping
A MappingWriterXml writes Mappings to xml-files.
MappingWriterXml() - Constructor for class de.unima.alcomox.mapping.MappingWriterXml
 
MergedOntology - Class in de.unima.alcomox.ontology
This class represents an e(X)tendable ontology.
MergedOntology(OWLOntology, OWLOntologyManager) - Constructor for class de.unima.alcomox.ontology.MergedOntology
 
METHOD - Static variable in class de.unima.alcomox.ExtractionProblem
The method parameter determines whether greedy or optimal strategy (with respect to confidences) is chosen.
METHOD_GREEDY - Static variable in class de.unima.alcomox.ExtractionProblem
Greedy method, formerly refered to as naive descending, now referred to as local optimal diagnosis.
METHOD_GREEDY_MINIMIZE - Static variable in class de.unima.alcomox.ExtractionProblem
Greedy method that generates an minimal hitting set over all pattern-based conflicts by iteratively deleting the correspondence that is involved in the highest number of conflicts.
METHOD_OPTIMAL - Static variable in class de.unima.alcomox.ExtractionProblem
Method to find an optimal solution (a minimum weighted hitting set).
METHOD_OPTIMAL_HUN - Static variable in class de.unima.alcomox.ExtractionProblem
Method to find an optimal 1:1 solution (a minimum weighted hitting set).
mirror - Static variable in class de.unima.alcomox.util.DataStorage
 
MISSING_BINDING - Static variable in exception de.unima.alcomox.exceptions.PCFException
 
MISSING_NAMESPACE - Static variable in exception de.unima.alcomox.exceptions.CorrespondenceException
 
MISSING_PARAM - Static variable in exception de.unima.alcomox.exceptions.PCFException
 
MODIFICATION_FAILED - Static variable in exception de.unima.alcomox.exceptions.OntologyException
 
modifyToEquivalenceCorrespondences() - Method in class de.unima.alcomox.mapping.Mapping
 
myOntId - Variable in class de.unima.alcomox.ontology.LocalOntology
 

N

NA - Static variable in class de.unima.alcomox.mapping.SemanticRelation
Relation thats not available.
next() - Method in class de.unima.alcomox.algorithms.IndexMarker
 
NominalAxiomDetector - Class in de.unima.alcomox.ontology.extowlapi
 
NominalAxiomDetector(Set<OWLEntity>) - Constructor for class de.unima.alcomox.ontology.extowlapi.NominalAxiomDetector
 
NominalAxiomTranscriber - Class in de.unima.alcomox.ontology.extowlapi
 
NominalAxiomTranscriber(Set<OWLEntity>) - Constructor for class de.unima.alcomox.ontology.extowlapi.NominalAxiomTranscriber
 
NON_REFERING - Static variable in exception de.unima.alcomox.exceptions.CorrespondenceException
 
normalize(double) - Method in class de.unima.alcomox.mapping.Mapping
Sets all correspondences in this mapping to the same value.
normalize() - Method in class de.unima.alcomox.mapping.Mapping
Normalizes the confidences of the correspondences to the range [0.0, 1.0].
normalize(double, double) - Method in class de.unima.alcomox.mapping.Mapping
Normalizes the confidences of the correspondences to a given range.
NOTHING - Variable in class de.unima.alcomox.ontology.AlcomoOntology
 

O

ONE_TO_MANY - Static variable in class de.unima.alcomox.Settings
If activated only one to many (from source to target) alignments are extracted.
ONE_TO_ONE - Static variable in class de.unima.alcomox.Settings
If activated only strict one to one alignments are extracted.
ONE_TO_ONE_ONLYEQUIV - Static variable in class de.unima.alcomox.Settings
If activated, the chosen one to one setting, holds only for equivalenve relations.
ontology - Variable in class de.unima.alcomox.ontology.AlcomoOntology
 
OntologyException - Exception in de.unima.alcomox.exceptions
An ontology exception handles every type of problems related to ontologies.
OntologyException(int, String, Exception) - Constructor for exception de.unima.alcomox.exceptions.OntologyException
 
OntologyException(int, String) - Constructor for exception de.unima.alcomox.exceptions.OntologyException
 
OntologyException(int) - Constructor for exception de.unima.alcomox.exceptions.OntologyException
 
openInterval(int) - Method in class de.unima.alcomox.ontology.IConcept
 
overlaps(Interval) - Method in class de.unima.alcomox.ontology.Interval
Compares this and that interval and checks whether this overlaps with that (see also the cases in the in line comments).

P

partOfAsDisjointness() - Method in class de.unima.alcomox.ExtractionProblem
Calling this method adds disjointness axioms for each part-of axiom.
PCFException - Exception in de.unima.alcomox.exceptions
An PCF exception handles problems related to parameter (P) like imvalid combinations of parameters, as well as things related to the control flow (CF) like the invalid order of method calls.
PCFException(int, String, Exception) - Constructor for exception de.unima.alcomox.exceptions.PCFException
 
PCFException(int, String) - Constructor for exception de.unima.alcomox.exceptions.PCFException
 
PCFException(int) - Constructor for exception de.unima.alcomox.exceptions.PCFException
 
pop() - Method in class de.unima.alcomox.mapping.Mapping
Removes the last correspondence from this mapping.
PRE_CLASSIFY - Static variable in class de.unima.alcomox.Settings
If activated the ontologies are always classifed before e.g. subsumption queries are asked.
printTimestamps() - Static method in class de.unima.alcomox.util.AlcomoLogger
 
PROPERTY_RANGE_EXTENSION - Static variable in class de.unima.alcomox.Settings
Very important property, if false only domain restrictions are checked by efficient reasoning methods.
push(Correspondence) - Method in class de.unima.alcomox.mapping.Mapping
Adds a correspondence at the end of a mapping.
push(Mapping) - Method in class de.unima.alcomox.mapping.Mapping
Adds each correspondence of another mapping at the end of this mapping.

R

rangeIds - Static variable in class de.unima.alcomox.ontology.LocalOntology
 
reasoner - Variable in class de.unima.alcomox.ontology.AlcomoOntology
 
REASONING - Static variable in class de.unima.alcomox.ExtractionProblem
The reasoning parameter determines whether efficient (incomplete) pairwise reasoning or complete reasoning is used to detect conflicts.
REASONING_BRUTEFORCE - Static variable in class de.unima.alcomox.ExtractionProblem
Brute force complete reasoning.
REASONING_COMPLETE - Static variable in class de.unima.alcomox.ExtractionProblem
Complete reasoning.
REASONING_D - Static variable in class de.unima.alcomox.ExtractionProblem
Brute force complete reasoning.
REASONING_EFFICIENT - Static variable in class de.unima.alcomox.ExtractionProblem
Pairwise incomplete conflict reasoning.
REASONING_ERROR - Static variable in exception de.unima.alcomox.exceptions.OntologyException
 
rebuild(OWLAxiom) - Method in class de.unima.alcomox.ontology.extowlapi.NominalAxiomTranscriber
 
rebuild(OWLSubClassOfAxiom) - Method in class de.unima.alcomox.ontology.extowlapi.NominalAxiomTranscriber
 
rebuild(OWLEquivalentClassesAxiom) - Method in class de.unima.alcomox.ontology.extowlapi.NominalAxiomTranscriber
 
rebuild(OWLDisjointUnionAxiom) - Method in class de.unima.alcomox.ontology.extowlapi.NominalAxiomTranscriber
 
rebuild(OWLDisjointClassesAxiom) - Method in class de.unima.alcomox.ontology.extowlapi.NominalAxiomTranscriber
 
rebuild(OWLDataPropertyDomainAxiom) - Method in class de.unima.alcomox.ontology.extowlapi.NominalAxiomTranscriber
 
rebuild(OWLObjectPropertyDomainAxiom) - Method in class de.unima.alcomox.ontology.extowlapi.NominalAxiomTranscriber
 
rebuild(OWLObjectPropertyRangeAxiom) - Method in class de.unima.alcomox.ontology.extowlapi.NominalAxiomTranscriber
 
reduceToEquivalenceCorrespondences() - Method in class de.unima.alcomox.mapping.Mapping
Remove all correspondences from the mapping that express a different semantic relation than equivalence.
REFERENCE_MISSING - Static variable in exception de.unima.alcomox.exceptions.OntologyException
 
refine() - Method in class de.unima.alcomox.ontology.IConcept
Sorts the subsumption and disjointness intervals and joins them if possible.
remove() - Method in class de.unima.alcomox.algorithms.IndexMarker
 
remove(int) - Method in class de.unima.alcomox.mapping.Mapping
Removes a correspondence at a specified index.
REMOVE_INDIVIDUALS - Static variable in class de.unima.alcomox.Settings
If true, instances are removed before processing to avoid incoherencies.
removeAxioms(Set<OWLAxiom>) - Method in class de.unima.alcomox.ontology.MergedOntology
 
replaceSourceNamespace(String) - Method in class de.unima.alcomox.mapping.Mapping
 
replaceSubstring(String, String) - Method in class de.unima.alcomox.mapping.Mapping
Helper method for easy working with different version of alignments that encoded version numbers in uris (like for each year of the benchmark track).
replaceTargetNamespace(String) - Method in class de.unima.alcomox.mapping.Mapping
 
reset() - Method in class de.unima.alcomox.ontology.extowlapi.NominalAxiomDetector
Resets the flag that indicates wether or not a nominal has been found.
resetCounter() - Method in class de.unima.alcomox.util.DataStorage
Returns the value of the counter and resets it to 0.
resetTimer() - Static method in class de.unima.alcomox.util.AlcomoLogger
 
resetValidatedMapping() - Method in class de.unima.alcomox.ontology.CompleteReasoner
Removes an (incrementally) attached validated mapping.
run() - Method in class de.unima.alcomox.algorithms.AlcomoExtraction
Solves the eaxtraction problem by selecting a part of the mapping as activated and the remainder as inactive.
run() - Method in class de.unima.alcomox.algorithms.AStarSearch
 
run() - Method in class de.unima.alcomox.algorithms.ConflictSearch
 
run() - Method in class de.unima.alcomox.algorithms.Greedy
 
run() - Method in class de.unima.alcomox.algorithms.GreedyMinimize
 
run() - Method in class de.unima.alcomox.algorithms.HungarianSearch
 

S

searchInvalidCorrespondence(Mapping) - Method in class de.unima.alcomox.ontology.CompleteReasoner
Searches binary and returns a correspondence being part of a conflict.
SemanticRelation - Class in de.unima.alcomox.mapping
A semantic relation can be used to express equivalence, subsumption or disjointness between entities of different ontologies.
SemanticRelation(int) - Constructor for class de.unima.alcomox.mapping.SemanticRelation
Constructs a semantic relation of a certain type.
setConcept(OWLClass) - Method in class de.unima.alcomox.ontology.Entity
 
setConcurrentExecution(boolean) - Method in class de.unima.alcomox.util.ThreadTimer
Disable the concurrent execution of the "own" thread and the regular application thread.
setConfidence(double) - Method in class de.unima.alcomox.mapping.Correspondence
 
setConflictPairs(Set<ConflictPair>) - Method in class de.unima.alcomox.mapping.Mapping
 
setCorrespondences(AbstractList<Correspondence>) - Method in class de.unima.alcomox.mapping.Mapping
Sets a list of correspondences as correspondences of the mapping.
setCorrespondences(Set<Correspondence>) - Method in class de.unima.alcomox.mapping.Mapping
Sets a set of correspondences as correspondences of the mapping.
setDataProperty(OWLDataProperty) - Method in class de.unima.alcomox.ontology.Entity
 
setDomain(OWLClass) - Method in class de.unima.alcomox.ontology.Entity
 
setExtractionProblem(ExtractionProblem) - Method in class de.unima.alcomox.ontology.AlcomoOntology
 
setFactory() - Method in class de.unima.alcomox.ontology.AlcomoOntology
 
setFactory(OWLDataFactory) - Method in class de.unima.alcomox.ontology.extowlapi.NominalAxiomTranscriber
 
setLocalOntology(LocalOntology) - Method in class de.unima.alcomox.ontology.extowlapi.NominalAxiomTranscriber
 
setLower(int) - Method in class de.unima.alcomox.ontology.Interval
 
setMapping(Mapping) - Method in class de.unima.alcomox.algorithms.AlcomoExtraction
 
setObjectProperty(OWLObjectProperty) - Method in class de.unima.alcomox.ontology.Entity
 
setOntologyCore(OWLOntology) - Method in class de.unima.alcomox.ontology.extowlapi.NominalAxiomTranscriber
 
setRange(OWLClass) - Method in class de.unima.alcomox.ontology.Entity
 
setRelation(SemanticRelation) - Method in class de.unima.alcomox.mapping.Correspondence
 
setScore(double) - Method in class de.unima.alcomox.algorithms.LockMarker
 
setSourceEntity(Entity) - Method in class de.unima.alcomox.mapping.Correspondence
 
setSourceEntityUri(String) - Method in class de.unima.alcomox.mapping.Correspondence
 
setSourceNamespace(String) - Method in class de.unima.alcomox.mapping.Correspondence
 
setSourceOntology(LocalOntology) - Method in class de.unima.alcomox.algorithms.AlcomoExtraction
 
setTargetEntity(Entity) - Method in class de.unima.alcomox.mapping.Correspondence
 
setTargetEntityUri(String) - Method in class de.unima.alcomox.mapping.Correspondence
 
setTargetNamespace(String) - Method in class de.unima.alcomox.mapping.Correspondence
 
setTargetOntology(LocalOntology) - Method in class de.unima.alcomox.algorithms.AlcomoExtraction
 
Settings - Class in de.unima.alcomox
 
Settings() - Constructor for class de.unima.alcomox.Settings
 
Settings.BlackBoxReasoner - Enum in de.unima.alcomox
It is possible tochoose between different reasoners that act internally as black box oracle.
setTopConfidence() - Method in class de.unima.alcomox.mapping.Correspondence
Sets the confidence value to 1.0 without need to catch a Exception.
setUpper(int) - Method in class de.unima.alcomox.ontology.Interval
 
shrinkTill(Correspondence) - Method in class de.unima.alcomox.mapping.Mapping
Removes every correspondence from the first one till the specified correspondence inclusive.
Similarity - Class in de.unima.alcomox.mapping
 
Similarity() - Constructor for class de.unima.alcomox.mapping.Similarity
 
size() - Method in class de.unima.alcomox.algorithms.IndexMarker
 
size() - Method in class de.unima.alcomox.algorithms.LockMarker
 
size() - Method in class de.unima.alcomox.mapping.Mapping
Returns the size of the mapping.
solve() - Method in class de.unima.alcomox.AlcomoProblem
 
solve() - Method in class de.unima.alcomox.ExtractionProblem
Solves the extraction problem.
solved - Variable in class de.unima.alcomox.AlcomoProblem
 
sortDescending() - Method in class de.unima.alcomox.mapping.Mapping
 
sourceOntology - Variable in class de.unima.alcomox.AlcomoProblem
 
sourceOntology - Variable in class de.unima.alcomox.algorithms.AlcomoExtraction
 
sourceOntology - Variable in class de.unima.alcomox.ontology.AlcomoReasoner
 
specificDescription - Variable in exception de.unima.alcomox.exceptions.AlcomoException
 
splitToSubsumptionCorrespondences() - Method in class de.unima.alcomox.mapping.Mapping
Splits all equivalence correspondences in this mapping into subsumption correspondences in both directions.
start() - Method in class de.unima.alcomox.util.ThreadTimer
Method to start the timer, which will kill the thread after a specified period of time if no result deliviered.
startClock() - Method in class de.unima.alcomox.util.DataStorage
 
startElement(String, String, String, Attributes) - Method in class de.unima.alcomox.mapping.MappingReaderXml
 
StateAnalyzer - Class in de.unima.alcomox.algorithms
 
StateAnalyzer(Mapping) - Constructor for class de.unima.alcomox.algorithms.StateAnalyzer
 
store(Correspondence[]) - Method in class de.unima.alcomox.algorithms.StateAnalyzer
 
strictEvaluationActive() - Static method in class de.unima.alcomox.mapping.Characteristic
 
SUB - Static variable in class de.unima.alcomox.mapping.SemanticRelation
Relation of subsumption, e.g.
subMapping(int) - Method in class de.unima.alcomox.mapping.Mapping
Returns a submapping of this mapping from index 0 to indexInclusive.
SUPER - Static variable in class de.unima.alcomox.mapping.SemanticRelation
Relation of supsumption, e.g.

T

takeTime(String) - Static method in class de.unima.alcomox.util.AlcomoLogger
 
takeTime() - Method in class de.unima.alcomox.util.DataStorage
 
targetOntology - Variable in class de.unima.alcomox.AlcomoProblem
 
targetOntology - Variable in class de.unima.alcomox.algorithms.AlcomoExtraction
 
targetOntology - Variable in class de.unima.alcomox.ontology.AlcomoReasoner
 
terminatedCorrectly() - Method in class de.unima.alcomox.algorithms.AlcomoExtraction
 
TEST_INTERVALTREE_MODE - Static variable in class de.unima.alcomox.ontology.EfficientReasoner
 
THING - Variable in class de.unima.alcomox.ontology.AlcomoOntology
 
ThreadTimer - Class in de.unima.alcomox.util
 
ThreadTimer(Thread, long) - Constructor for class de.unima.alcomox.util.ThreadTimer
Constructor for a thread.
toAxioms(Mapping) - Method in class de.unima.alcomox.ontology.MergedOntology
 
toDecimalFormat(double) - Static method in class de.unima.alcomox.util.Tools
 
toDecimalFormat(double, String) - Static method in class de.unima.alcomox.util.Tools
 
Tools - Class in de.unima.alcomox.util
 
Tools() - Constructor for class de.unima.alcomox.util.Tools
 
toShortDesc() - Method in class de.unima.alcomox.mapping.Characteristic
 
toShortString() - Method in class de.unima.alcomox.mapping.Correspondence
 
toShortString() - Method in class de.unima.alcomox.mapping.Mapping
 
toShortString() - Method in class de.unima.alcomox.ontology.AlcomoOntology
Returns a short string representation of this ontology.
toString() - Method in class de.unima.alcomox.algorithms.ConflictStore
 
toString() - Method in class de.unima.alcomox.algorithms.Coord
 
toString() - Method in class de.unima.alcomox.algorithms.StateAnalyzer
 
toString() - Method in exception de.unima.alcomox.exceptions.AlcomoException
Returns a human understandable string representation.
toString() - Method in class de.unima.alcomox.mapping.Characteristic
Returns a string representation.
toString() - Method in class de.unima.alcomox.mapping.Correspondence
 
toString() - Method in class de.unima.alcomox.mapping.Mapping
 
toString() - Method in class de.unima.alcomox.mapping.MappingFamiliy
 
toString() - Method in class de.unima.alcomox.mapping.MappingMatrix
 
toString() - Method in class de.unima.alcomox.mapping.SemanticRelation
Returns the string representation of this semantic relation.
toString() - Method in class de.unima.alcomox.ontology.AlcomoOntology
Returns a string representation of this ontology.
toString() - Method in class de.unima.alcomox.ontology.ConflictPair
 
toString() - Method in class de.unima.alcomox.ontology.Entity
 
toString() - Method in class de.unima.alcomox.ontology.IConcept
 
toString() - Method in class de.unima.alcomox.ontology.Interval
 
toString() - Method in class de.unima.alcomox.util.DataStorage
 
toVeryShortString() - Method in class de.unima.alcomox.mapping.Mapping
 
typeOfReasoning - Variable in class de.unima.alcomox.algorithms.AlcomoExtraction
 

U

useDiffuseEvaluation() - Static method in class de.unima.alcomox.mapping.Characteristic
 

V

valueOf(String) - Static method in enum de.unima.alcomox.Settings.BlackBoxReasoner
Returns the enum constant of this type with the specified name.
values() - Static method in enum de.unima.alcomox.Settings.BlackBoxReasoner
Returns an array containing the constants of this enum type, in the order they are declared.
visit(OWLObjectOneOf) - Method in class de.unima.alcomox.ontology.extowlapi.NominalAxiomDetector
 
visit(OWLObjectHasValue) - Method in class de.unima.alcomox.ontology.extowlapi.NominalAxiomDetector
 
visit(OWLObjectIntersectionOf) - Method in class de.unima.alcomox.ontology.extowlapi.NominalAxiomTranscriber
 
visit(OWLObjectUnionOf) - Method in class de.unima.alcomox.ontology.extowlapi.NominalAxiomTranscriber
 
visit(OWLObjectComplementOf) - Method in class de.unima.alcomox.ontology.extowlapi.NominalAxiomTranscriber
 
visit(OWLObjectSomeValuesFrom) - Method in class de.unima.alcomox.ontology.extowlapi.NominalAxiomTranscriber
 
visit(OWLObjectAllValuesFrom) - Method in class de.unima.alcomox.ontology.extowlapi.NominalAxiomTranscriber
 
visit(OWLObjectMinCardinality) - Method in class de.unima.alcomox.ontology.extowlapi.NominalAxiomTranscriber
 
visit(OWLObjectExactCardinality) - Method in class de.unima.alcomox.ontology.extowlapi.NominalAxiomTranscriber
 
visit(OWLObjectMaxCardinality) - Method in class de.unima.alcomox.ontology.extowlapi.NominalAxiomTranscriber
 
visit(OWLClass) - Method in class de.unima.alcomox.ontology.extowlapi.NominalAxiomTranscriber
 
visit(OWLObjectOneOf) - Method in class de.unima.alcomox.ontology.extowlapi.NominalAxiomTranscriber
 
visit(OWLObjectHasValue) - Method in class de.unima.alcomox.ontology.extowlapi.NominalAxiomTranscriber
 
visit(OWLObjectHasSelf) - Method in class de.unima.alcomox.ontology.extowlapi.NominalAxiomTranscriber
 

W

warnS(String) - Method in class de.unima.alcomox.util.AlcomoLogger
Logs a statement as warning.
write(String, int) - Method in class de.unima.alcomox.mapping.Mapping
 
write(String) - Method in class de.unima.alcomox.mapping.Mapping
Writes a mapping in RDF format to a specified path.
write(String) - Method in class de.unima.alcomox.ontology.AlcomoOntology
Writes the ontology into a file.
write(String) - Method in class de.unima.alcomox.ontology.MergedOntology
 
writeMapping(String, Mapping) - Method in interface de.unima.alcomox.mapping.MappingWriter
 
writeMapping(String, Mapping) - Method in class de.unima.alcomox.mapping.MappingWriterTxt
 
writeMapping(String, Mapping) - Method in class de.unima.alcomox.mapping.MappingWriterXml
 
writeMergedOntology(String, Mapping) - Method in class de.unima.alcomox.ontology.MergedOntology
Dont you ever use this, very bad hack for generating merged ontology without helper classes.
writeToFile(String, String) - Static method in class de.unima.alcomox.util.Tools
 

X

xxx - Static variable in class de.unima.alcomox.ontology.LocalOntology
 

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