Index (Protempa Framework 3.0-Alpha-13 API)

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

A

abbrevDisplayName(Value) - Method in class org.protempa.valueset.ValueSet: Returns an abbreviated display name for the specified value, if one is defined.
AbsoluteTimeGranularity - Class in org.protempa.proposition.value: Defines absolute time temporal granularities.
AbsoluteTimeGranularityFactory - Class in org.protempa.proposition.value: Access to AbsoluteTimeGranularity objects.
AbsoluteTimeGranularityFactory() - Constructor for class org.protempa.proposition.value.AbsoluteTimeGranularityFactory
AbsoluteTimeGranularityUtil - Class in org.protempa.proposition.value
AbsoluteTimeIntervalFactory - Class in org.protempa.proposition.interval: Factory for constructing intervals from Java dates.
AbsoluteTimeIntervalFactory() - Constructor for class org.protempa.proposition.interval.AbsoluteTimeIntervalFactory
AbsoluteTimeUnit - Class in org.protempa.proposition.value: Defines units of absolute time.
AbsoluteTimeUnitFactory - Class in org.protempa.proposition.value: Access to AbsoluteTimeUnit objects.
AbsoluteTimeUnitFactory() - Constructor for class org.protempa.proposition.value.AbsoluteTimeUnitFactory
AbstractAbstractionDefinition - Class in org.protempa: Definition of the constraints required to infer an abstract parameter.
AbstractAlgorithm - Class in org.protempa: Provides a skeletal implementation of the Algorithm interface.
AbstractAlgorithm(Algorithms, String) - Constructor for class org.protempa.AbstractAlgorithm
AbstractAlgorithmSourceBackend - Class in org.protempa.backend.asb: Skeletal implementation of the AlgorithmSourceBackend interface to minimize the effort required to implement it.
AbstractAlgorithmSourceBackend() - Constructor for class org.protempa.backend.asb.AbstractAlgorithmSourceBackend
AbstractBackend<E extends BackendUpdatedEvent> - Class in org.protempa.backend: Common interface for PROTEMPA backends.
AbstractBackend() - Constructor for class org.protempa.backend.AbstractBackend
AbstractCommonsAlgorithmSourceBackend - Class in org.protempa.backend
AbstractCommonsAlgorithmSourceBackend() - Constructor for class org.protempa.backend.AbstractCommonsAlgorithmSourceBackend
AbstractCommonsDataSourceBackend - Class in org.protempa.backend
AbstractCommonsDataSourceBackend() - Constructor for class org.protempa.backend.AbstractCommonsDataSourceBackend
AbstractCommonsKnowledgeSourceBackend - Class in org.protempa.backend
AbstractCommonsKnowledgeSourceBackend() - Constructor for class org.protempa.backend.AbstractCommonsKnowledgeSourceBackend
AbstractCommonsTermSourceBackend - Class in org.protempa.backend
AbstractCommonsTermSourceBackend() - Constructor for class org.protempa.backend.AbstractCommonsTermSourceBackend
AbstractConfigurations - Class in org.protempa.backend
AbstractConfigurations(BackendProvider) - Constructor for class org.protempa.backend.AbstractConfigurations
AbstractDataSourceBackend - Class in org.protempa.backend.dsb: Convenience class for implementing a data source backend.
AbstractDataSourceBackend() - Constructor for class org.protempa.backend.dsb.AbstractDataSourceBackend
AbstractDataStoreCreator<K,V> - Class in org.protempa.datastore
AbstractDataStoreCreator() - Constructor for class org.protempa.datastore.AbstractDataStoreCreator
AbstractDataStoreCreator(String) - Constructor for class org.protempa.datastore.AbstractDataStoreCreator
AbstractDestination - Class in org.protempa.dest
AbstractDestination() - Constructor for class org.protempa.dest.AbstractDestination
AbstractFilter - Class in org.protempa.backend.dsb.filter: An abstract class that makes implementing filters relatively easy.
AbstractFilter(String[]) - Constructor for class org.protempa.backend.dsb.filter.AbstractFilter: Instantiates the filter with the proposition ids that it is valid for.
AbstractFilterVisitor - Class in org.protempa.backend.dsb.filter
AbstractFilterVisitor() - Constructor for class org.protempa.backend.dsb.filter.AbstractFilterVisitor
AbstractionDefinition - Interface in org.protempa: Interface to definitions of the constraints required to infer an abstract parameter.
AbstractionDefinitionReadFromBackendEvent - Class in org.protempa
AbstractionDefinitionReadFromBackendEvent(Object) - Constructor for class org.protempa.AbstractionDefinitionReadFromBackendEvent
AbstractJavaAlgorithmBackend - Class in org.protempa.backend.asb.java: For accessing algorithms written in Java as subclasses of AbstractAlgorithm.
AbstractJavaAlgorithmBackend() - Constructor for class org.protempa.backend.asb.java.AbstractJavaAlgorithmBackend
AbstractJavaAlgorithmBackend(BackendInstanceSpec) - Constructor for class org.protempa.backend.asb.java.AbstractJavaAlgorithmBackend
AbstractKaplanMeyer - Class in org.protempa.proposition.stats: Calculates length frequencies of temporal propositions.
AbstractKnowledgeSourceBackend - Class in org.protempa.backend.ksb: Skeletal implementation of the KnowledgeSourceBackend interface to minimize the effort required to implement this interface.
AbstractKnowledgeSourceBackend() - Constructor for class org.protempa.backend.ksb.AbstractKnowledgeSourceBackend
AbstractParameter - Class in org.protempa.proposition: An parameter over an interval.
AbstractParameter(String, UniqueId) - Constructor for class org.protempa.proposition.AbstractParameter: Creates an abstract parameter with an id.
AbstractParameterFactory - Class in org.protempa: FIXME If there are two input propositions of the same type and value, the behavior is unpredictable (which one it chooses for an offset).
AbstractParameterIntervalSectioner - Class in org.protempa.proposition
AbstractParameterIntervalSectioner() - Constructor for class org.protempa.proposition.AbstractParameterIntervalSectioner
AbstractProposition - Class in org.protempa.proposition: Abstract class for implementing the various kinds of propositions.
AbstractProposition() - Constructor for class org.protempa.proposition.AbstractProposition: Here only for use by deserialization of Serializable subclasses of this class.
AbstractPropositionCheckedVisitor - Class in org.protempa.proposition.visitor
AbstractPropositionCheckedVisitor() - Constructor for class org.protempa.proposition.visitor.AbstractPropositionCheckedVisitor
AbstractPropositionDefinition - Class in org.protempa: Abstract base class for all knowledge definition classes.
AbstractPropositionDefinitionCheckedVisitor - Class in org.protempa: An abstract base class for implementing proposition definition visitors that may throw exceptions.
AbstractPropositionDefinitionCheckedVisitor() - Constructor for class org.protempa.AbstractPropositionDefinitionCheckedVisitor
AbstractPropositionDefinitionVisitor - Class in org.protempa: An abstract base class for implementing proposition definition visitors.
AbstractPropositionDefinitionVisitor() - Constructor for class org.protempa.AbstractPropositionDefinitionVisitor
AbstractPropositionVisitor - Class in org.protempa.proposition.visitor: An abstract base class for implementing proposition visitors.
AbstractPropositionVisitor() - Constructor for class org.protempa.proposition.visitor.AbstractPropositionVisitor
AbstractQueryResultsHandler - Class in org.protempa.dest
AbstractQueryResultsHandler() - Constructor for class org.protempa.dest.AbstractQueryResultsHandler
AbstractRelativeTimeUnit - Class in org.protempa.proposition.value: Base class for relative time units.
AbstractSource<S extends SourceUpdatedEvent,B extends Backend,E extends SourceUpdatedEvent,T extends BackendUpdatedEvent> - Class in org.protempa
AbstractTableColumnSpec - Class in org.protempa.dest.table
AbstractTableColumnSpec() - Constructor for class org.protempa.dest.table.AbstractTableColumnSpec
AbstractTermSourceBackend - Class in org.protempa.backend.tsb
AbstractTermSourceBackend() - Constructor for class org.protempa.backend.tsb.AbstractTermSourceBackend
AbstractTimeUnit - Class in org.protempa.proposition.value: Base class for defining time units.
accept(FilterVisitor) - Method in interface org.protempa.backend.dsb.filter.Filter: Performs some processing on this filter.
accept(FilterVisitor) - Method in class org.protempa.backend.dsb.filter.PositionFilter
accept(FilterVisitor) - Method in class org.protempa.backend.dsb.filter.PropertyValueFilter
accept(FilterVisitor) - Method in class org.protempa.backend.dsb.filter.ValueFilter
accept(PropositionDefinitionVisitor) - Method in class org.protempa.CompoundLowLevelAbstractionDefinition
accept(PropositionDefinitionVisitor) - Method in class org.protempa.ConstantDefinition
accept(PropositionDefinitionVisitor) - Method in class org.protempa.ContextDefinition
accept(PropositionDefinitionVisitor) - Method in class org.protempa.EventDefinition
accept(PropositionDefinitionVisitor) - Method in class org.protempa.HighLevelAbstractionDefinition
accept(PropositionDefinitionVisitor) - Method in class org.protempa.LowLevelAbstractionDefinition
accept(PropositionDefinitionVisitor) - Method in class org.protempa.PrimitiveParameterDefinition
accept(PropositionVisitor) - Method in class org.protempa.proposition.AbstractParameter
accept(PropositionVisitor) - Method in class org.protempa.proposition.Constant
accept(PropositionVisitor) - Method in class org.protempa.proposition.Context
accept(PropositionVisitor) - Method in class org.protempa.proposition.Event
accept(PropositionVisitor) - Method in class org.protempa.proposition.PrimitiveParameter
accept(PropositionVisitor) - Method in class org.protempa.proposition.Sequence
accept(ValueVisitor) - Method in class org.protempa.proposition.value.BooleanValue
accept(ValueVisitor) - Method in class org.protempa.proposition.value.DateValue
accept(ValueVisitor) - Method in class org.protempa.proposition.value.InequalityNumberValue
accept(ValueVisitor) - Method in class org.protempa.proposition.value.NominalValue
accept(ValueVisitor) - Method in class org.protempa.proposition.value.NumberValue
accept(ValueVisitor) - Method in class org.protempa.proposition.value.OrdinalValue
accept(ValueVisitor) - Method in class org.protempa.proposition.value.ValueList
accept(ValueVisitor) - Method in interface org.protempa.proposition.value.ValueVisitable: Performs some processing on a value.
accept(PropositionVisitor) - Method in interface org.protempa.proposition.visitor.PropositionVisitable: Performs some processing on a proposition.
accept(PropositionDefinitionVisitor) - Method in interface org.protempa.PropositionDefinitionVisitable: Performs some processing on a proposition definition.
accept(PropositionDefinitionVisitor) - Method in class org.protempa.SequentialTemporalPatternDefinition
accept(PropositionDefinitionVisitor) - Method in class org.protempa.SliceDefinition
acceptChecked(PropositionDefinitionCheckedVisitor) - Method in class org.protempa.CompoundLowLevelAbstractionDefinition
acceptChecked(PropositionDefinitionCheckedVisitor) - Method in class org.protempa.ConstantDefinition
acceptChecked(PropositionDefinitionCheckedVisitor) - Method in class org.protempa.ContextDefinition
acceptChecked(PropositionDefinitionCheckedVisitor) - Method in class org.protempa.EventDefinition
acceptChecked(PropositionDefinitionCheckedVisitor) - Method in class org.protempa.HighLevelAbstractionDefinition
acceptChecked(PropositionDefinitionCheckedVisitor) - Method in class org.protempa.LowLevelAbstractionDefinition
acceptChecked(PropositionDefinitionCheckedVisitor) - Method in class org.protempa.PrimitiveParameterDefinition
acceptChecked(PropositionCheckedVisitor) - Method in class org.protempa.proposition.AbstractParameter
acceptChecked(PropositionCheckedVisitor) - Method in class org.protempa.proposition.Constant
acceptChecked(PropositionCheckedVisitor) - Method in class org.protempa.proposition.Context
acceptChecked(PropositionCheckedVisitor) - Method in class org.protempa.proposition.Event
acceptChecked(PropositionCheckedVisitor) - Method in class org.protempa.proposition.PrimitiveParameter
acceptChecked(PropositionCheckedVisitor) - Method in interface org.protempa.proposition.visitor.PropositionCheckedVisitable: Performs some processing on a proposition that might throw a checked exception.
acceptChecked(PropositionDefinitionCheckedVisitor) - Method in interface org.protempa.PropositionDefinitionCheckedVisitable: Performs some processing on this proposition definition.
acceptChecked(PropositionDefinitionCheckedVisitor) - Method in class org.protempa.SequentialTemporalPatternDefinition
acceptChecked(PropositionDefinitionCheckedVisitor) - Method in class org.protempa.SliceDefinition
add(Object) - Method in class org.protempa.graph.DirectedGraph: Adds a vertex.
add(Weight) - Method in class org.protempa.graph.Weight: Creates a new weight with value equal to the sum of both weights.
add(ExtendedPropositionDefinition) - Method in class org.protempa.HighLevelAbstractionDefinition: Adds an extended proposition definition.
add(T) - Method in class org.protempa.proposition.Sequence
add(int, T) - Method in class org.protempa.proposition.Sequence
add(TemporalExtendedPropositionDefinition) - Method in class org.protempa.SliceDefinition: Adds a proposition id from which this slice definition is abstracted.
addAlgorithm(Algorithm) - Method in class org.protempa.Algorithms: Adds a new algorithm.
addAll(Collection<? extends T>) - Method in class org.protempa.proposition.Segment: Unsupported operation.
addAll(Collection<? extends T>) - Method in class org.protempa.proposition.Sequence
addAll(int, Collection<? extends T>) - Method in class org.protempa.proposition.Sequence
addBackendListener(BackendListener<E>) - Method in class org.protempa.backend.AbstractBackend
addBackendListener(BackendListener<E>) - Method in interface org.protempa.backend.Backend: Registers a listener that get called whenever a backend changes.
addCustomCliOptions(Options) - Method in class org.protempa.cli.CLI: Override to specify any custom command line options.
addDisplayNameOverride(String, String) - Method in class org.protempa.backend.BackendInstanceSpec
addPrimitiveParameterId(String) - Method in class org.protempa.LowLevelAbstractionDefinition: Adds a primitive parameter from which this abstraction is inferred.
addPropertyChangeListener(PropertyChangeListener) - Method in class org.protempa.AbstractPropositionDefinition
addPropertyChangeListener(String, PropertyChangeListener) - Method in class org.protempa.AbstractPropositionDefinition
addPropertyChangeListener(PropertyChangeListener) - Method in class org.protempa.proposition.AbstractProposition
addPropertyChangeListener(PropertyChangeListener) - Method in interface org.protempa.proposition.Proposition: Adds a PropertyChangeListener to the listener list.
addPropertyChangeListener(PropertyChangeListener) - Method in interface org.protempa.PropositionDefinition
addPropertyChangeListener(String, PropertyChangeListener) - Method in interface org.protempa.PropositionDefinition
addPropertyChangeListener(PropertyChangeListener) - Method in class org.protempa.query.And
addPropertyChangeListener(String, PropertyChangeListener) - Method in class org.protempa.query.And
addPropertyChangeListener(PropertyChangeListener) - Method in class org.protempa.query.DefaultQueryBuilder: Adds listeners for changes to this Query's properties.
addPropertyChangeListener(String, PropertyChangeListener) - Method in class org.protempa.query.DefaultQueryBuilder: Adds listeners for changes to the specified property.
addReference(String, UniqueId) - Method in class org.protempa.proposition.AbstractProposition
addRequiredOverride(String) - Method in class org.protempa.backend.BackendInstanceSpec
addSourceListener(SourceListener<S>) - Method in class org.protempa.AbstractSource: Adds a listener that gets called whenever something changes.
addSourceListener(SourceListener<S>) - Method in interface org.protempa.Source
addToPosition(long, int) - Method in class org.protempa.proposition.value.AbsoluteTimeUnit
addToPosition(long, int) - Method in class org.protempa.proposition.value.AbstractRelativeTimeUnit
addToPosition(long, int) - Method in interface org.protempa.proposition.value.Unit: Adds a length in these units to the given position.
addValueClassification(ValueClassification) - Method in class org.protempa.CompoundLowLevelAbstractionDefinition: Adds a value classification for the abstraction.
addValueDefinition(LowLevelAbstractionValueDefinition) - Method in class org.protempa.LowLevelAbstractionDefinition
AFTER - Static variable in class org.protempa.proposition.interval.Relation
AGE - Static variable in class org.protempa.dest.deid.DeidAttributes
Algorithm - Interface in org.protempa: Interface to algorithms for processing primitive parameters.
AlgorithmArguments - Class in org.protempa: Stores arguments to be passed into an algorithm for a given low-level abstraction value definition.
AlgorithmInitializationException - Exception in org.protempa: Thrown when an error occurs in algorithm initialization.
AlgorithmInitializationException() - Constructor for exception org.protempa.AlgorithmInitializationException
AlgorithmInitializationException(String, Throwable) - Constructor for exception org.protempa.AlgorithmInitializationException
AlgorithmInitializationException(String) - Constructor for exception org.protempa.AlgorithmInitializationException
AlgorithmInitializationException(Throwable) - Constructor for exception org.protempa.AlgorithmInitializationException
AlgorithmParameter - Class in org.protempa: Definition of an algorithm parameter.
AlgorithmParameter(String, ValueComparator[], ValueType) - Constructor for class org.protempa.AlgorithmParameter: Defines a parameter.
AlgorithmProcessingException - Exception in org.protempa: Throws when an error occurs in algorithm processing.
AlgorithmProcessingException() - Constructor for exception org.protempa.AlgorithmProcessingException
AlgorithmProcessingException(String, Throwable) - Constructor for exception org.protempa.AlgorithmProcessingException
AlgorithmProcessingException(String) - Constructor for exception org.protempa.AlgorithmProcessingException
AlgorithmProcessingException(Throwable) - Constructor for exception org.protempa.AlgorithmProcessingException
Algorithms - Class in org.protempa: The set of defined algorithms.
AlgorithmSource - Interface in org.protempa
AlgorithmSourceBackend - Interface in org.protempa.backend.asb: A set of algorithms for use in PROTEMPA pattern detection.
AlgorithmSourceBackendInitializationException - Exception in org.protempa.backend
AlgorithmSourceBackendInitializationException(String) - Constructor for exception org.protempa.backend.AlgorithmSourceBackendInitializationException
AlgorithmSourceBackendInitializationException(Throwable) - Constructor for exception org.protempa.backend.AlgorithmSourceBackendInitializationException
AlgorithmSourceBackendInitializationException(String, Throwable) - Constructor for exception org.protempa.backend.AlgorithmSourceBackendInitializationException
AlgorithmSourceBackendUpdatedEvent - Class in org.protempa.backend: The event generated when the algorithm source backend is updated.
AlgorithmSourceBackendUpdatedEvent(AlgorithmSourceBackend) - Constructor for class org.protempa.backend.AlgorithmSourceBackendUpdatedEvent: Constructs an event with the source AlgorithmSourceBackend that generated the event.
AlgorithmSourceException - Exception in org.protempa: Thrown when an error occurs in algorithm initialization or processing.
AlgorithmSourceImpl - Class in org.protempa: A read-only "interface" to an externally maintained set of pattern detection algorithm implementations.
AlgorithmSourceImpl(AlgorithmSourceBackend[]) - Constructor for class org.protempa.AlgorithmSourceImpl: Constructor for specifying a mix of AlgorithmSourceBackends and Properties objects specifying algorithm source backends.
AlgorithmSourceReadException - Exception in org.protempa: Thrown when an error occurs reading an algorithm.
AlgorithmSourceReadException() - Constructor for exception org.protempa.AlgorithmSourceReadException
AlgorithmSourceReadException(String, Throwable) - Constructor for exception org.protempa.AlgorithmSourceReadException
AlgorithmSourceReadException(String) - Constructor for exception org.protempa.AlgorithmSourceReadException
AlgorithmSourceReadException(Throwable) - Constructor for exception org.protempa.AlgorithmSourceReadException
AlgorithmSourceUpdatedEvent - Class in org.protempa: The event generated when the algorithm source is updated.
AlgorithmSourceUpdatedEvent(AlgorithmSource) - Constructor for class org.protempa.AlgorithmSourceUpdatedEvent: Constructs an event with the source AlgorithmSource that generated the event.
AllPropositionIntervalComparator - Class in org.protempa.proposition.comparator: For sorting propositions by interval, if they are temporal propositions.
AllPropositionIntervalComparator() - Constructor for class org.protempa.proposition.comparator.AllPropositionIntervalComparator
And<E> - Class in org.protempa.query: A list of PROTEMPA ids that are chained together by boolean and.
And() - Constructor for class org.protempa.query.And
And(E...) - Constructor for class org.protempa.query.And
andIterator() - Method in class org.protempa.backend.dsb.filter.AbstractFilter
andIterator() - Method in interface org.protempa.backend.dsb.filter.Filter: Returns an iterator over this filter and all subsequent filters in the chain.
Argument(String, boolean) - Constructor for class org.protempa.cli.CLI.Argument: Instantiates an instance with the name of the argument and whether or not it is required.
asBuilder() - Method in class org.protempa.Attribute
asBuilder() - Method in class org.protempa.DefaultSourceId
asBuilder() - Method in class org.protempa.NotRecordedSourceId
asBuilder() - Method in class org.protempa.proposition.value.BooleanValue
asBuilder() - Method in class org.protempa.proposition.value.DateValue
asBuilder() - Method in class org.protempa.proposition.value.InequalityNumberValue
asBuilder() - Method in class org.protempa.proposition.value.NominalValue
asBuilder() - Method in class org.protempa.proposition.value.NumberValue
asBuilder() - Method in interface org.protempa.proposition.value.NumericalValue
asBuilder() - Method in interface org.protempa.proposition.value.OrderedValue
asBuilder() - Method in class org.protempa.proposition.value.OrdinalValue
asBuilder() - Method in interface org.protempa.proposition.value.Value
asBuilder() - Method in class org.protempa.proposition.value.ValueList
asBuilder() - Method in interface org.protempa.SourceId
asBuilder() - Method in class org.protempa.valueset.ValueSet
asBuilder() - Method in class org.protempa.valueset.ValueSetElement
asDate(Long) - Static method in class org.protempa.proposition.value.AbsoluteTimeGranularityUtil
asPosition(Date) - Static method in class org.protempa.proposition.value.AbsoluteTimeGranularityUtil
AtLeastNColumnSpec - Class in org.protempa.dest.table
AtLeastNColumnSpec(int, Link[]) - Constructor for class org.protempa.dest.table.AtLeastNColumnSpec
AtLeastNColumnSpec(String, int, Link[]) - Constructor for class org.protempa.dest.table.AtLeastNColumnSpec
AtLeastNColumnSpec(String, int, Link[], String, String) - Constructor for class org.protempa.dest.table.AtLeastNColumnSpec
attribute(String) - Method in class org.protempa.AbstractPropositionDefinition
Attribute - Class in org.protempa
Attribute(String, Value) - Constructor for class org.protempa.Attribute
attribute(String) - Method in interface org.protempa.PropositionDefinition
AttributeBuilder - Class in org.protempa
AttributeBuilder() - Constructor for class org.protempa.AttributeBuilder

B

Backend<E extends BackendUpdatedEvent> - Interface in org.protempa.backend: Common interface for PROTEMPA backends.
BackendCloseException - Exception in org.protempa: Abstract class for exceptions that are thrown when an error occurs calling the data source.
BackendCloseException() - Constructor for exception org.protempa.BackendCloseException
BackendCloseException(String, Throwable) - Constructor for exception org.protempa.BackendCloseException
BackendCloseException(String) - Constructor for exception org.protempa.BackendCloseException
BackendCloseException(Throwable) - Constructor for exception org.protempa.BackendCloseException
BackendInfo - Annotation Type in org.protempa.backend.annotations
backendInfo(Backend) - Static method in class org.protempa.backend.CommonsBackend
BackendInitializationException - Exception in org.protempa.backend
BackendInitializationException(String) - Constructor for exception org.protempa.backend.BackendInitializationException
BackendInitializationException(Throwable) - Constructor for exception org.protempa.backend.BackendInitializationException
BackendInitializationException(String, Throwable) - Constructor for exception org.protempa.backend.BackendInitializationException
BackendInstanceSpec - Class in org.protempa.backend
BackendListener<E extends BackendUpdatedEvent> - Interface in org.protempa: Common interface for backend listeners.
BackendNewInstanceException - Exception in org.protempa.backend
BackendNewInstanceException() - Constructor for exception org.protempa.backend.BackendNewInstanceException
BackendNewInstanceException(String) - Constructor for exception org.protempa.backend.BackendNewInstanceException
BackendNewInstanceException(Throwable) - Constructor for exception org.protempa.backend.BackendNewInstanceException
BackendNewInstanceException(String, Throwable) - Constructor for exception org.protempa.backend.BackendNewInstanceException
BackendNotFoundException - Exception in org.protempa.backend
BackendProperty - Annotation Type in org.protempa.backend.annotations
BackendPropertySpec - Class in org.protempa.backend
BackendPropertySpec(String, String, String, BackendPropertyType, boolean, BackendPropertyValidator) - Constructor for class org.protempa.backend.BackendPropertySpec
BackendPropertyType - Enum in org.protempa.backend
BackendPropertyValidator<E> - Interface in org.protempa.backend
BackendProvider - Interface in org.protempa.backend: Interface for PROTEMPA backend provider modules.
BackendProviderInitializationException - Exception in org.protempa.backend
BackendProviderManager - Class in org.protempa.backend: Manages PROTEMPA's backend provider.
BackendProviderSpecLoaderException - Exception in org.protempa.backend
BackendProviderSpecLoaderException(Throwable) - Constructor for exception org.protempa.backend.BackendProviderSpecLoaderException
BackendProviderSpecLoaderException(String) - Constructor for exception org.protempa.backend.BackendProviderSpecLoaderException
BackendProviderSpecLoaderException(String, Throwable) - Constructor for exception org.protempa.backend.BackendProviderSpecLoaderException
BackendProviderSpecLoaderException() - Constructor for exception org.protempa.backend.BackendProviderSpecLoaderException
BackendSourceIdFactory - Class in org.protempa.backend
BackendSourceIdFactory(Backend) - Constructor for class org.protempa.backend.BackendSourceIdFactory
BackendSpec - Class in org.protempa.backend
BackendSpec(BackendProvider, String, String, BackendPropertySpec[]) - Constructor for class org.protempa.backend.BackendSpec
BackendSpecLoader - Class in org.protempa.backend: Loads
BackendSpecLoader(List<BackendSpec>) - Constructor for class org.protempa.backend.BackendSpecLoader
BackendSpecNotFoundException - Exception in org.protempa.backend
backendUpdated(AlgorithmSourceBackendUpdatedEvent) - Method in class org.protempa.AlgorithmSourceImpl
backendUpdated(E) - Method in interface org.protempa.BackendListener: Notifies a listener when it needs to reread data in the backend.
backendUpdated(DataSourceBackendUpdatedEvent) - Method in class org.protempa.DataSourceImpl
backendUpdated(KnowledgeSourceBackendUpdatedEvent) - Method in class org.protempa.KnowledgeSourceImpl
backendUpdated(TermSourceBackendUpdatedEvent) - Method in class org.protempa.TermSourceImpl
BackendUpdatedEvent - Class in org.protempa.backend: Backend updated events.
BackendUtil - Class in org.protempa.backend
BEFORE - Static variable in class org.protempa.proposition.interval.Relation
BellmanFord - Class in org.protempa.graph: An implementation of the Bellman-Ford single-source shortest paths algorithm.
BellmanFord.Mode - Enum in org.protempa.graph: For setting whether the Bellman-Ford algorithm should look for the shortest paths from a source or to a destination.
binarySearch(List<PrimitiveParameter>, long) - Static method in class org.protempa.proposition.PropositionUtil: Binary search for a primitive parameter by timestamp.
BIRTHDATE - Static variable in class org.protempa.dest.deid.DeidAttributes
BooleanValue - Class in org.protempa.proposition.value: A boolean value.
BooleanValue(boolean) - Constructor for class org.protempa.proposition.value.BooleanValue: Creates a new boolean value.
BooleanValue(Boolean) - Constructor for class org.protempa.proposition.value.BooleanValue: Creates a boolean value (true or false).
booleanValue() - Method in class org.protempa.proposition.value.BooleanValue: Returns the Java boolean corresponding to this object.
BooleanValueBuilder - Class in org.protempa.proposition.value
BooleanValueBuilder(BooleanValue) - Constructor for class org.protempa.proposition.value.BooleanValueBuilder
BooleanValueBuilder() - Constructor for class org.protempa.proposition.value.BooleanValueBuilder
build() - Method in class org.protempa.AttributeBuilder
build() - Method in class org.protempa.DefaultSourceIdBuilder
build() - Method in class org.protempa.dest.table.OutputConfigBuilder: Creates a new OutputConfig instance.
build() - Method in class org.protempa.dest.table.ValueOutputConfigBuilder: Creates a new ValueOutputConfig instance.
build() - Method in class org.protempa.NotRecordedSourceIdBuilder
build() - Method in class org.protempa.PropertyDefinitionBuilder
build() - Method in class org.protempa.proposition.value.BooleanValueBuilder
build() - Method in class org.protempa.proposition.value.DateValueBuilder
build() - Method in class org.protempa.proposition.value.InequalityNumberValueBuilder
build() - Method in class org.protempa.proposition.value.NominalValueBuilder
build() - Method in class org.protempa.proposition.value.NumberValueBuilder
build() - Method in interface org.protempa.proposition.value.NumericalValueBuilder
build() - Method in class org.protempa.proposition.value.OrdinalValueBuilder
build() - Method in interface org.protempa.proposition.value.ValueBuilder
build() - Method in class org.protempa.proposition.value.ValueListBuilder
build(KnowledgeSource, AlgorithmSource) - Method in class org.protempa.query.DefaultQueryBuilder
build(KnowledgeSource, AlgorithmSource) - Method in interface org.protempa.query.QueryBuilder: Builds a Query.
build() - Method in interface org.protempa.SourceIdBuilder
build() - Method in class org.protempa.valueset.ValueSetBuilder
build() - Method in class org.protempa.valueset.ValueSetElementBuilder
build(KnowledgeSource, AlgorithmSource) - Method in class org.protempa.xml.XMLConfiguration
buildConfiguration() - Method in class org.protempa.backend.ConfigurationsSupport
buildIntervalList(List<E>) - Method in class org.protempa.proposition.IntervalSectioner: Creates a chronologically ordered list of intervals and their associated propositions and values.
buildQuery(QueryBuilder) - Method in class org.protempa.Protempa: Convenience method for calling QueryBuilder.build(org.protempa.KnowledgeSource, org.protempa.AlgorithmSource) with this Protempa instance's knowledge source and algorithm source.

C

calcShortestDistances(Object, DirectedGraph, BellmanFord.Mode) - Static method in class org.protempa.graph.BellmanFord: Calculates the distance of every object in a graph from a source object.
cancel() - Method in class org.protempa.dest.AbstractQueryResultsHandler
cancel() - Method in class org.protempa.dest.deid.DeidentifiedQueryResultsHandler
cancel() - Method in interface org.protempa.dest.QueryResultsHandler: Requests cancellation of whatever this object is currently doing.
cancel() - Method in class org.protempa.Protempa: Cancels an executing query.
chainLength() - Method in class org.protempa.backend.dsb.filter.AbstractFilter
changes - Variable in class org.protempa.AbstractPropositionDefinition
changes - Variable in class org.protempa.MinMaxGapFunction
changes - Variable in class org.protempa.SimpleGapFunction
checkArray(Object[], String) - Static method in class org.protempa.ProtempaUtil: Checks if the specified array is null, has length zero or has null values.
checkArrayForNullElement(Object[], String) - Static method in class org.protempa.ProtempaUtil: Checks if the specified array has any null elements.
children - Variable in class org.protempa.AbstractPropositionDefinition
CHILDREN_PROPERTY - Static variable in class org.protempa.AbstractPropositionDefinition
CipherDeidConfig - Interface in org.protempa.dest.deid
CipherEncryption - Class in org.protempa.dest.deid: Utility class for encrypting and decrypting strings.
CipherEncryption(CipherDeidConfig) - Constructor for class org.protempa.dest.deid.CipherEncryption
clear() - Method in class org.protempa.AlgorithmSourceImpl
clear() - Method in class org.protempa.DataSourceImpl
clear() - Method in class org.protempa.DataSourceResultMap
clear() - Method in class org.protempa.dest.xml.XmlPropositionVisitor
clear() - Method in class org.protempa.graph.DirectedGraph: Remove all vertices and edges.
clear() - Method in class org.protempa.KnowledgeSourceImpl
clear() - Method in class org.protempa.proposition.Sequence
clear() - Method in class org.protempa.Protempa: Clears resources created by this object and the data source, knowledge source and algorithm source.
clear() - Method in interface org.protempa.Source
clear() - Method in class org.protempa.TermSourceImpl
CLI - Class in org.protempa.cli: Convenience class for creating command line applications using PROTEMPA.
CLI() - Constructor for class org.protempa.cli.CLI: Instantiates this application.
CLI(String) - Constructor for class org.protempa.cli.CLI: Instantiates the application with a required shell command name.
CLI(CLI.Argument[]) - Constructor for class org.protempa.cli.CLI: Instantiates the application with optional arguments.
CLI(String, CLI.Argument[]) - Constructor for class org.protempa.cli.CLI: Instantiates the application with a required shell command name and optional arguments that are not prefixed with option syntax.
CLI(CLI.Argument[], boolean) - Constructor for class org.protempa.cli.CLI: Instantiates the application with a required shell command name and whether to create the configuration id option.
CLI(String, CLI.Argument[], boolean) - Constructor for class org.protempa.cli.CLI: Instantiates the application with a required shell command name, optional arguments that are not prefixed with option syntax, and whether to create the configuration id option.
CLI.Argument - Class in org.protempa.cli: For defining command line arguments that are not prefixed by the option syntax.
CLIException - Exception in org.protempa.cli
CLIException(Throwable) - Constructor for exception org.protempa.cli.CLIException
CLIException(String) - Constructor for exception org.protempa.cli.CLIException
CLIException(String, Throwable) - Constructor for exception org.protempa.cli.CLIException
CLIException() - Constructor for exception org.protempa.cli.CLIException
clone() - Method in class org.protempa.proposition.DefaultLocalUniqueId
clone() - Method in interface org.protempa.proposition.LocalUniqueId: Makes a shallow copy of this instance.
clone() - Method in class org.protempa.proposition.ProviderBasedLocalUniqueId
clone() - Method in class org.protempa.query.And
close() - Method in class org.protempa.AbstractAlgorithm
close() - Method in class org.protempa.AbstractSource: Removes this Source as a listener to the Backends provided to the constructor.
close() - Method in interface org.protempa.Algorithm
close() - Method in class org.protempa.AlgorithmSourceImpl
close() - Method in class org.protempa.backend.asb.AbstractAlgorithmSourceBackend: Implemented as a no-op.
close() - Method in class org.protempa.backend.asb.java.AbstractJavaAlgorithmBackend
close() - Method in interface org.protempa.backend.Backend: Releases any resources allocated by this backend.
close() - Method in class org.protempa.backend.dsb.AbstractDataSourceBackend
close() - Method in class org.protempa.backend.ksb.AbstractKnowledgeSourceBackend: Implemented as a no-op.
close() - Method in class org.protempa.backend.tsb.AbstractTermSourceBackend: Implemented as a no-op
close() - Method in class org.protempa.cli.CLI: Closes the instance of Protempa created by #initialize(java.lang.String).
close() - Method in class org.protempa.DataSourceBackendMultiplexingDataStreamingEventIterator: Closes resources associated with the iterators specified in the constructor.
close() - Method in class org.protempa.DataSourceImpl
close() - Method in interface org.protempa.DataStreamingEventIterator: Closes any IO or other resources opened by the iterator.
close() - Method in class org.protempa.dest.AbstractQueryResultsHandler
close() - Method in class org.protempa.dest.deid.DeidentifiedQueryResultsHandler
close() - Method in interface org.protempa.dest.QueryResultsHandler: Called by Protempa after #handleFinish() to clean up any resources used by the handler.
close() - Method in class org.protempa.KnowledgeSourceImpl
close() - Method in class org.protempa.MultiplexingDataStreamingEventIterator: Calls the underlying DataStreamingEventIterators DataStreamingEventIterator.close() method.
close() - Method in class org.protempa.Protempa: Closes resources created by this object and the data source, knowledge source, and algorithm source.
close() - Method in interface org.protempa.Source
close() - Method in class org.protempa.TermSourceImpl
closedUnexpectedly(SourceClosedUnexpectedlyEvent) - Method in interface org.protempa.SourceListener: The method that gets called when the source is closed unexpectedly, like when a connection to a server is lost.
CloseException - Exception in org.protempa
CloseException() - Constructor for exception org.protempa.CloseException
CloseException(String, Throwable) - Constructor for exception org.protempa.CloseException
CloseException(String) - Constructor for exception org.protempa.CloseException
CloseException(Throwable) - Constructor for exception org.protempa.CloseException
CollectionSizeExpression - Class in org.protempa: Sets a lower limit on the size of a collection.
CollectionSizeExpression(int) - Constructor for class org.protempa.CollectionSizeExpression
collectPropDefDescendantsUsingAllNarrower(boolean, String[]) - Method in interface org.protempa.backend.ksb.KnowledgeSourceBackend
collectPropDefDescendantsUsingAllNarrower(boolean, String[]) - Method in class org.protempa.backend.ksb.SimpleKnowledgeSourceBackend
collectPropDefDescendantsUsingAllNarrower(boolean, String...) - Method in interface org.protempa.KnowledgeSource
collectPropDefDescendantsUsingAllNarrower(boolean, String...) - Method in class org.protempa.KnowledgeSourceImpl
collectPropDefDescendantsUsingInverseIsA(String[]) - Method in interface org.protempa.backend.ksb.KnowledgeSourceBackend
collectPropDefDescendantsUsingInverseIsA(String[]) - Method in class org.protempa.backend.ksb.SimpleKnowledgeSourceBackend
collectPropDefDescendantsUsingInverseIsA(String...) - Method in interface org.protempa.KnowledgeSource
collectPropDefDescendantsUsingInverseIsA(String...) - Method in class org.protempa.KnowledgeSourceImpl
collectPropIdDescendantsUsingAllNarrower(boolean, String[]) - Method in interface org.protempa.backend.ksb.KnowledgeSourceBackend
collectPropIdDescendantsUsingAllNarrower(boolean, String[]) - Method in class org.protempa.backend.ksb.SimpleKnowledgeSourceBackend
collectPropIdDescendantsUsingAllNarrower(boolean, String...) - Method in interface org.protempa.KnowledgeSource
collectPropIdDescendantsUsingAllNarrower(boolean, String...) - Method in class org.protempa.KnowledgeSourceImpl
collectPropIdDescendantsUsingInverseIsA(String[]) - Method in interface org.protempa.backend.ksb.KnowledgeSourceBackend
collectPropIdDescendantsUsingInverseIsA(String[]) - Method in class org.protempa.backend.ksb.SimpleKnowledgeSourceBackend
collectPropIdDescendantsUsingInverseIsA(String...) - Method in interface org.protempa.KnowledgeSource
collectPropIdDescendantsUsingInverseIsA(String...) - Method in class org.protempa.KnowledgeSourceImpl
collectStatistics() - Method in class org.protempa.dest.map.MapQueryResultsHandler
columnNames(KnowledgeSource) - Method in class org.protempa.dest.table.AtLeastNColumnSpec
columnNames(KnowledgeSource) - Method in class org.protempa.dest.table.CountColumnSpec
columnNames(KnowledgeSource) - Method in class org.protempa.dest.table.DistanceBetweenColumnSpec
columnNames(String) - Method in class org.protempa.dest.table.PropositionColumnSpec
columnNames(KnowledgeSource) - Method in class org.protempa.dest.table.PropositionColumnSpec
columnNames(KnowledgeSource) - Method in class org.protempa.dest.table.PropositionValueColumnSpec
columnNames(KnowledgeSource) - Method in interface org.protempa.dest.table.TableColumnSpec: Gets the names of the columns representing one instance of a proposition or property.
columnValues(String, Proposition, Map<Proposition, List<Proposition>>, Map<Proposition, List<Proposition>>, Map<UniqueId, Proposition>, KnowledgeSourceCache, Map<String, String>, char, Writer) - Method in class org.protempa.dest.table.AtLeastNColumnSpec
columnValues(String, Proposition, Map<Proposition, List<Proposition>>, Map<Proposition, List<Proposition>>, Map<UniqueId, Proposition>, KnowledgeSourceCache, Map<String, String>, char, Writer) - Method in class org.protempa.dest.table.CountColumnSpec
columnValues(String, Proposition, Map<Proposition, List<Proposition>>, Map<Proposition, List<Proposition>>, Map<UniqueId, Proposition>, KnowledgeSourceCache, Map<String, String>, char, Writer) - Method in class org.protempa.dest.table.DistanceBetweenColumnSpec
columnValues(String, Proposition, Map<Proposition, List<Proposition>>, Map<Proposition, List<Proposition>>, Map<UniqueId, Proposition>, KnowledgeSourceCache, Map<String, String>, char, Writer) - Method in class org.protempa.dest.table.PropositionColumnSpec
columnValues(String, Proposition, Map<Proposition, List<Proposition>>, Map<Proposition, List<Proposition>>, Map<UniqueId, Proposition>, KnowledgeSourceCache, Map<String, String>, char, Writer) - Method in class org.protempa.dest.table.PropositionValueColumnSpec
columnValues(String, Proposition, Map<Proposition, List<Proposition>>, Map<Proposition, List<Proposition>>, Map<UniqueId, Proposition>, KnowledgeSourceCache, Map<String, String>, char, Writer) - Method in interface org.protempa.dest.table.TableColumnSpec: Gets the values of the specified propositions or properties for one row of data.
CommonsBackend - Class in org.protempa.backend
CommonsBackend() - Constructor for class org.protempa.backend.CommonsBackend
compare(Proposition, Proposition) - Method in class org.protempa.proposition.comparator.AllPropositionIntervalComparator: If comparing TemporalPropositions, compares their intervals; otherwise, a constant proposition compared to a temporal proposition will return -1, and a constant proposition compared to another constant proposition will return 0.
compare(TemporalProposition, TemporalProposition) - Method in class org.protempa.proposition.comparator.MaxFinishTemporalPropositionComparator
compare(TemporalProposition, TemporalProposition) - Method in class org.protempa.proposition.comparator.TemporalPropositionIntervalComparator
compare(Value) - Method in class org.protempa.proposition.value.BooleanValue: Returns ValueComparator.UNKNOWN, as boolean values do not have a natural order, unless the provided value is a value list, for which this method tests for membership in the list.
compare(Value) - Method in class org.protempa.proposition.value.DateValue: Compares this date value and another date value according to their natural order, or checks this date value for membership in a value list.
compare(Value) - Method in class org.protempa.proposition.value.InequalityNumberValue: Compares this value and another numerically, or checks this value for membership in a value list.
compare(Value) - Method in class org.protempa.proposition.value.NominalValue: Compares this nominal value and another lexically.
compare(Value) - Method in class org.protempa.proposition.value.NumberValue: Compares this value and another numerically, or checks this number value for membership in a value list.
compare(Value) - Method in class org.protempa.proposition.value.OrdinalValue: Compares this value and another according to the defined order, or checks this number value for membership in a value list.
compare(Value) - Method in interface org.protempa.proposition.value.Value: Returns whether the given value is greater, less than, equal to or not equal to this value.
compare(Value, Value) - Method in enum org.protempa.proposition.value.ValueComparator: Returns whether two values have the relationship specified by this value comparator.
compare(Value) - Method in class org.protempa.proposition.value.ValueList: Compares a value list for membership in another value list.
compare(PropositionDefinition, PropositionDefinition) - Method in class org.protempa.ProtempaUtil.PropositionDefinitionDisplayNameComparator
compareTo(Weight) - Method in class org.protempa.graph.Weight: Compares two Weight objects numerically.
compareTo(Interval) - Method in class org.protempa.proposition.interval.Interval
compareTo(Granularity) - Method in class org.protempa.proposition.value.AbsoluteTimeGranularity
compareTo(Unit) - Method in class org.protempa.proposition.value.AbsoluteTimeUnit
compareTo(DateValue) - Method in class org.protempa.proposition.value.DateValue
compareTo(NominalValue) - Method in class org.protempa.proposition.value.NominalValue
compareTo(NumberValue) - Method in class org.protempa.proposition.value.NumberValue
compareTo(Granularity) - Method in class org.protempa.proposition.value.RelativeDayGranularity
compareTo(Unit) - Method in class org.protempa.proposition.value.RelativeDayUnit
compareTo(Granularity) - Method in class org.protempa.proposition.value.RelativeHourGranularity
compareTo(Unit) - Method in class org.protempa.proposition.value.RelativeHourUnit
compareToLong(long) - Method in class org.protempa.graph.Weight
CompoundInterval<E extends TemporalProposition> - Class in org.protempa.proposition
CompoundLowLevelAbstractionDefinition - Class in org.protempa: An abstraction for representing compound low-level abstractions.
CompoundLowLevelAbstractionDefinition(String) - Constructor for class org.protempa.CompoundLowLevelAbstractionDefinition: Constructor for this class.
CompoundLowLevelAbstractionDefinition.ValueDefinitionMatchOperator - Enum in org.protempa: The different ways to consider the low-level abstraction value rules in a given interval
CompoundValuedInterval - Class in org.protempa.proposition: Represents an interval of multiple propositions and their values.
compute(Segment<PrimitiveParameter>, AlgorithmArguments) - Method in class org.protempa.AbstractAlgorithm
compute(Segment<PrimitiveParameter>, AlgorithmArguments) - Method in interface org.protempa.Algorithm: Computes whether or not a temporal abstraction exists in a segment of a time series.
compute(Segment<PrimitiveParameter>, AlgorithmArguments) - Method in class org.protempa.backend.asb.java.MinAlgorithm
compute(Segment<PrimitiveParameter>, AlgorithmArguments) - Method in class org.protempa.backend.asb.java.StateAlgorithm: Computes whether the values of a time sequence segment are above and/or below a specified value.
compute(Segment<PrimitiveParameter>, AlgorithmArguments) - Method in class org.protempa.backend.asb.java.TrendAlgorithm: Computes whether the slope of a linear regression line drawn through the values of a time sequence segment is above and/or below a specified value.
computeLength() - Method in class org.protempa.proposition.interval.Interval
Configuration - Class in org.protempa.backend
Configuration() - Constructor for class org.protempa.backend.Configuration
ConfigurationRemoveException - Exception in org.protempa.backend
ConfigurationRemoveException(Throwable) - Constructor for exception org.protempa.backend.ConfigurationRemoveException
ConfigurationRemoveException(String, Throwable) - Constructor for exception org.protempa.backend.ConfigurationRemoveException
ConfigurationRemoveException(String) - Constructor for exception org.protempa.backend.ConfigurationRemoveException
ConfigurationRemoveException() - Constructor for exception org.protempa.backend.ConfigurationRemoveException
Configurations - Interface in org.protempa.backend
ConfigurationsLoadException - Exception in org.protempa.backend
ConfigurationsLoadException(Throwable) - Constructor for exception org.protempa.backend.ConfigurationsLoadException
ConfigurationsLoadException(String, Throwable) - Constructor for exception org.protempa.backend.ConfigurationsLoadException
ConfigurationsLoadException(String) - Constructor for exception org.protempa.backend.ConfigurationsLoadException
ConfigurationsLoadException() - Constructor for exception org.protempa.backend.ConfigurationsLoadException
ConfigurationsNotFoundException - Exception in org.protempa.backend
ConfigurationsNotFoundException(Throwable) - Constructor for exception org.protempa.backend.ConfigurationsNotFoundException
ConfigurationsNotFoundException(String, Throwable) - Constructor for exception org.protempa.backend.ConfigurationsNotFoundException
ConfigurationsNotFoundException(String) - Constructor for exception org.protempa.backend.ConfigurationsNotFoundException
ConfigurationsNotFoundException() - Constructor for exception org.protempa.backend.ConfigurationsNotFoundException
ConfigurationsProvider - Interface in org.protempa.backend
ConfigurationsProviderManager - Class in org.protempa.backend: Class for getting PROTEMPA configurations.
ConfigurationsProviderManager() - Constructor for class org.protempa.backend.ConfigurationsProviderManager
ConfigurationsSaveException - Exception in org.protempa.backend
ConfigurationsSaveException(Throwable) - Constructor for exception org.protempa.backend.ConfigurationsSaveException
ConfigurationsSaveException(String, Throwable) - Constructor for exception org.protempa.backend.ConfigurationsSaveException
ConfigurationsSaveException(String) - Constructor for exception org.protempa.backend.ConfigurationsSaveException
ConfigurationsSaveException() - Constructor for exception org.protempa.backend.ConfigurationsSaveException
ConfigurationsSupport - Class in org.protempa.backend
ConfigurationsSupport(BackendProvider) - Constructor for class org.protempa.backend.ConfigurationsSupport
Constant - Class in org.protempa.proposition: A parameter with no temporal component.
Constant(String, UniqueId) - Constructor for class org.protempa.proposition.Constant: Creates a constant with an identifier String.
ConstantDefinition - Class in org.protempa
ConstantDefinition(String) - Constructor for class org.protempa.ConstantDefinition
contains(Object) - Method in class org.protempa.graph.DirectedGraph: Check to see if an object is a vertex.
CONTAINS - Static variable in class org.protempa.proposition.interval.Relation
contains(Object) - Method in class org.protempa.proposition.Segment
contains(Object) - Method in class org.protempa.proposition.Sequence
CONTAINS_OR_EQUALS - Static variable in class org.protempa.proposition.interval.Relation
containsAll(Collection<?>) - Method in class org.protempa.proposition.Sequence
containsEdge(Object, Object) - Method in class org.protempa.graph.DirectedGraph: Check to see if an edge has been set between two vertices.
containsKey(Object) - Method in class org.protempa.DataSourceResultMap
containsTerm(String) - Method in class org.protempa.TermSubsumption
containsValue(Object) - Method in class org.protempa.DataSourceResultMap
Context - Class in org.protempa.proposition: A state of affairs that, when interpreted over a time interval, can change the interpretation (abstraction) of one or more parameters within the scope of that time interval.
Context(String, UniqueId) - Constructor for class org.protempa.proposition.Context
ContextDefinition - Class in org.protempa: A context is a state of affairs that, when interpreted over a time interval, can change the interpretation of data or abstractions.
ContextDefinition(String) - Constructor for class org.protempa.ContextDefinition
ContextIntervalSectioner - Class in org.protempa.proposition
ContextIntervalSectioner() - Constructor for class org.protempa.proposition.ContextIntervalSectioner
ContextOffset - Class in org.protempa
ContextOffset() - Constructor for class org.protempa.ContextOffset
CountColumnSpec - Class in org.protempa.dest.table: Counts the number of instances of a proposition.
CountColumnSpec(Link[]) - Constructor for class org.protempa.dest.table.CountColumnSpec
CountColumnSpec(String, Link[], boolean) - Constructor for class org.protempa.dest.table.CountColumnSpec: Constructs a count column spec with an optional header name, the links to traverse and whether to count the number of unique proposition ids rather than the number of propositions.
createContext() - Method in class org.protempa.CollectionSizeExpression
createDataSourceConstraint() - Method in class org.protempa.AbstractAlgorithm
createDataSourceConstraint() - Method in interface org.protempa.Algorithm
createPropositionMap(List<T>) - Static method in class org.protempa.proposition.PropositionUtil: Divides a list of propositions up by id.
createResults(List<Proposition>) - Method in class org.protempa.dest.table.Link: Filters out propositions by applying the property constraint and index constraints.
CreateRuleBaseException - Exception in org.protempa
Criteria - Interface in org.protempa.dest.keyloader
CriteriaEvaluateException - Exception in org.protempa.dest.keyloader
CriteriaEvaluateException() - Constructor for exception org.protempa.dest.keyloader.CriteriaEvaluateException
CriteriaEvaluateException(String, Throwable) - Constructor for exception org.protempa.dest.keyloader.CriteriaEvaluateException
CriteriaEvaluateException(String) - Constructor for exception org.protempa.dest.keyloader.CriteriaEvaluateException
CriteriaEvaluateException(Throwable) - Constructor for exception org.protempa.dest.keyloader.CriteriaEvaluateException
CriteriaInitException - Exception in org.protempa.dest.keyloader
CriteriaInitException() - Constructor for exception org.protempa.dest.keyloader.CriteriaInitException
CriteriaInitException(String, Throwable) - Constructor for exception org.protempa.dest.keyloader.CriteriaInitException
CriteriaInitException(String) - Constructor for exception org.protempa.dest.keyloader.CriteriaInitException
CriteriaInitException(Throwable) - Constructor for exception org.protempa.dest.keyloader.CriteriaInitException
CycleDetectedException - Exception in org.protempa
CycleDetectedException(Collection<String>) - Constructor for exception org.protempa.CycleDetectedException

D

DATABASE_NAME - Static variable in class org.protempa.datastore.PropositionStoreCreator
DATABASE_NAME - Static variable in class org.protempa.datastore.UniqueIdUniqueIdStoreCreator
DATABASE_NAME - Static variable in class org.protempa.datastore.WorkingMemoryStoreCreator
DataSource - Interface in org.protempa
DataSourceBackend - Interface in org.protempa.backend.dsb: Interface for data source backends, which provide access to data sources for PROTEMPA.
DataSourceBackendException - Exception in org.protempa: Abstract class for exceptions that are thrown when an error occurs calling the data source.
DataSourceBackendFailedConfigurationValidationException - Exception in org.protempa.backend
DataSourceBackendFailedConfigurationValidationException(Throwable) - Constructor for exception org.protempa.backend.DataSourceBackendFailedConfigurationValidationException
DataSourceBackendFailedConfigurationValidationException(String, Throwable) - Constructor for exception org.protempa.backend.DataSourceBackendFailedConfigurationValidationException
DataSourceBackendFailedConfigurationValidationException(String) - Constructor for exception org.protempa.backend.DataSourceBackendFailedConfigurationValidationException
DataSourceBackendFailedConfigurationValidationException() - Constructor for exception org.protempa.backend.DataSourceBackendFailedConfigurationValidationException
DataSourceBackendFailedDataValidationException - Exception in org.protempa.backend
DataSourceBackendFailedDataValidationException(Throwable, DataValidationEvent[]) - Constructor for exception org.protempa.backend.DataSourceBackendFailedDataValidationException
DataSourceBackendFailedDataValidationException(String, Throwable, DataValidationEvent[]) - Constructor for exception org.protempa.backend.DataSourceBackendFailedDataValidationException
DataSourceBackendFailedDataValidationException(String, DataValidationEvent[]) - Constructor for exception org.protempa.backend.DataSourceBackendFailedDataValidationException
DataSourceBackendFailedDataValidationException(DataValidationEvent[]) - Constructor for exception org.protempa.backend.DataSourceBackendFailedDataValidationException
DataSourceBackendId - Class in org.protempa.proposition: A unique identifier for a data source backend.
DataSourceBackendInitializationException - Exception in org.protempa.backend
DataSourceBackendInitializationException(String) - Constructor for exception org.protempa.backend.DataSourceBackendInitializationException
DataSourceBackendInitializationException(Throwable) - Constructor for exception org.protempa.backend.DataSourceBackendInitializationException
DataSourceBackendInitializationException(String, Throwable) - Constructor for exception org.protempa.backend.DataSourceBackendInitializationException
DataSourceBackendMultiplexingDataStreamingEventIterator - Class in org.protempa
DataSourceBackendMultiplexingDataStreamingEventIterator(List<? extends DataStreamingEventIterator<Proposition>>, List<? extends DataStreamingEventIterator<UniqueIdPair>>) - Constructor for class org.protempa.DataSourceBackendMultiplexingDataStreamingEventIterator
DataSourceBackendReadException - Exception in org.protempa
DataSourceBackendReadException() - Constructor for exception org.protempa.DataSourceBackendReadException
DataSourceBackendReadException(String, Throwable) - Constructor for exception org.protempa.DataSourceBackendReadException
DataSourceBackendReadException(String) - Constructor for exception org.protempa.DataSourceBackendReadException
DataSourceBackendReadException(Throwable) - Constructor for exception org.protempa.DataSourceBackendReadException
DataSourceBackendSourceSystem - Class in org.protempa
DataSourceBackendUpdatedEvent - Class in org.protempa.backend: The event generated when the algorithm source backend is updated.
DataSourceBackendUpdatedEvent(DataSourceBackend) - Constructor for class org.protempa.backend.DataSourceBackendUpdatedEvent: Constructs an event with the source AlgorithmSourceBackend that generated the event.
DataSourceException - Exception in org.protempa: Abstract class for exceptions that are thrown when an error occurs calling the data source.
DataSourceFailedConfigurationValidationException - Exception in org.protempa
DataSourceFailedConfigurationValidationException() - Constructor for exception org.protempa.DataSourceFailedConfigurationValidationException
DataSourceFailedConfigurationValidationException(String, Throwable) - Constructor for exception org.protempa.DataSourceFailedConfigurationValidationException
DataSourceFailedConfigurationValidationException(String) - Constructor for exception org.protempa.DataSourceFailedConfigurationValidationException
DataSourceFailedConfigurationValidationException(Throwable) - Constructor for exception org.protempa.DataSourceFailedConfigurationValidationException
DataSourceFailedDataValidationException - Exception in org.protempa
DataSourceFailedDataValidationException(Throwable, DataValidationEvent[]) - Constructor for exception org.protempa.DataSourceFailedDataValidationException
DataSourceFailedDataValidationException(String, Throwable, DataValidationEvent[]) - Constructor for exception org.protempa.DataSourceFailedDataValidationException
DataSourceFailedDataValidationException(String, DataValidationEvent[]) - Constructor for exception org.protempa.DataSourceFailedDataValidationException
DataSourceFailedDataValidationException(DataValidationEvent[]) - Constructor for exception org.protempa.DataSourceFailedDataValidationException
DataSourceImpl - Class in org.protempa: Read-only access to a database.
DataSourceImpl(DataSourceBackend[]) - Constructor for class org.protempa.DataSourceImpl
DataSourceReadException - Exception in org.protempa: Thrown when there is an error retrieving data from the data source.
DataSourceReadException() - Constructor for exception org.protempa.DataSourceReadException
DataSourceReadException(String, Throwable) - Constructor for exception org.protempa.DataSourceReadException
DataSourceReadException(String) - Constructor for exception org.protempa.DataSourceReadException
DataSourceReadException(Throwable) - Constructor for exception org.protempa.DataSourceReadException
DataSourceReadException(List<DataSourceReadException>) - Constructor for exception org.protempa.DataSourceReadException
DataSourceResultMap - Class in org.protempa: The map implementation that is returned by the query methods.
DataSourceResultMap(List<? extends Map<String, List>>) - Constructor for class org.protempa.DataSourceResultMap
DataSourceUpdatedEvent - Class in org.protempa: The event generated when a data source is updated.
DataSourceUpdatedEvent(DataSource) - Constructor for class org.protempa.DataSourceUpdatedEvent: Constructs an event with the source DataSource that generated the event.
DataSourceValidationIncompleteException - Exception in org.protempa: Thrown if an error occurred during validation that prevented its completion.
DataSourceValidationIncompleteException(Throwable) - Constructor for exception org.protempa.DataSourceValidationIncompleteException: Instantiates the exception with another nested Throwable.
DataSourceValidationIncompleteException(String) - Constructor for exception org.protempa.DataSourceValidationIncompleteException: Instantiates the exception with an error message.
DataSourceValidationIncompleteException(String, Throwable) - Constructor for exception org.protempa.DataSourceValidationIncompleteException: Instantiates the exception with an error message and a nested Throwable.
DataSourceValidationIncompleteException() - Constructor for exception org.protempa.DataSourceValidationIncompleteException: Instantiates the exception with no information.
DataSourceWriteException - Exception in org.protempa: Thrown when there is an error retrieving data from the data source.
DataSourceWriteException() - Constructor for exception org.protempa.DataSourceWriteException
DataSourceWriteException(String, Throwable) - Constructor for exception org.protempa.DataSourceWriteException
DataSourceWriteException(String) - Constructor for exception org.protempa.DataSourceWriteException
DataSourceWriteException(Throwable) - Constructor for exception org.protempa.DataSourceWriteException
DataSourceWriteException(List<DataSourceWriteException>) - Constructor for exception org.protempa.DataSourceWriteException
DataStoreCreator<K,V> - Interface in org.protempa.datastore: An interface for defining classes that return external data stores.
DataStreamingEvent<E> - Class in org.protempa
DataStreamingEvent(String, List<E>) - Constructor for class org.protempa.DataStreamingEvent
DataStreamingEventIterator<E> - Interface in org.protempa: An iterator-like interface for iterating over DataStreamingEvents.
DataValidationEvent - Class in org.protempa.backend.dsb: Hold various validation messages that occur when verifying an input data source.
DataValidationEvent() - Constructor for class org.protempa.backend.dsb.DataValidationEvent
DateTimeFilter - Class in org.protempa.backend.dsb.filter: A filter for date/time ranges.
DateTimeFilter(String[], Date, Granularity, Date, Granularity) - Constructor for class org.protempa.backend.dsb.filter.DateTimeFilter: Creates a filter with a date/time range.
DateTimeFilter(String[], Date, Granularity, Date, Granularity, Interval.Side, Interval.Side) - Constructor for class org.protempa.backend.dsb.filter.DateTimeFilter: Creates a filter with a date/time range.
DateValue - Class in org.protempa.proposition.value: Represents dates and datetimes.
DateValue() - Constructor for class org.protempa.proposition.value.DateValue: Constructs a new date value object representing the current time.
DateValue(Date) - Constructor for class org.protempa.proposition.value.DateValue: Constructs a new date value from a Java date object.
DateValueBuilder - Class in org.protempa.proposition.value
DateValueBuilder() - Constructor for class org.protempa.proposition.value.DateValueBuilder
DateValueBuilder(DateValue) - Constructor for class org.protempa.proposition.value.DateValueBuilder
DAY - Static variable in class org.protempa.proposition.value.AbsoluteTimeGranularity
DAY - Static variable in class org.protempa.proposition.value.AbsoluteTimeUnit
DAY - Static variable in class org.protempa.proposition.value.RelativeDayGranularity
DAY - Static variable in class org.protempa.proposition.value.RelativeDayUnit
DEFAULT - Static variable in class org.protempa.GapFunction
DEFAULT_QUERY_MODE - Static variable in class org.protempa.query.Query
DEFAULT_VALUE_TYPE - Static variable in class org.protempa.PrimitiveParameterDefinition: The default value factory (ValueFactory.NOMINAL).
DefaultBackendPropertyValidator - Class in org.protempa.backend
DefaultBackendPropertyValidator() - Constructor for class org.protempa.backend.DefaultBackendPropertyValidator
DefaultInterval - Class in org.protempa.proposition.interval: A constraint representing a temporal abstraction interval.
DefaultLocalUniqueId - Class in org.protempa.proposition
DefaultLocalUniqueId() - Constructor for class org.protempa.proposition.DefaultLocalUniqueId
DefaultQueryBuilder - Class in org.protempa.query
DefaultQueryBuilder() - Constructor for class org.protempa.query.DefaultQueryBuilder
DefaultSourceId - Class in org.protempa
DefaultSourceIdBuilder - Class in org.protempa
DefaultSourceIdBuilder() - Constructor for class org.protempa.DefaultSourceIdBuilder
DefaultSourceIdFactory - Class in org.protempa
DefaultSourceIdFactory() - Constructor for class org.protempa.DefaultSourceIdFactory
DefaultStatistics - Class in org.protempa.dest
DefaultStatistics(int, Map<String, Integer>, Map<String, String>) - Constructor for class org.protempa.dest.DefaultStatistics
DefaultStatisticsBuilder - Class in org.protempa.dest
DefaultStatisticsBuilder() - Constructor for class org.protempa.dest.DefaultStatisticsBuilder
DefaultUniqueIdFactory - Class in org.protempa.proposition
DefaultUniqueIdFactory() - Constructor for class org.protempa.proposition.DefaultUniqueIdFactory
DeidAttributes - Class in org.protempa.dest.deid
DeidConfig - Interface in org.protempa.dest.deid
DeidentifiedDestination - Class in org.protempa.dest.deid
DeidentifiedDestination(Destination, DeidConfig) - Constructor for class org.protempa.dest.deid.DeidentifiedDestination
DeidentifiedQueryResultsHandler - Class in org.protempa.dest.deid: Implements de-identification.
deleteAllKeys() - Method in class org.protempa.backend.dsb.AbstractDataSourceBackend
deleteAllKeys() - Method in interface org.protempa.backend.dsb.DataSourceBackend
deleteAllKeys() - Method in interface org.protempa.DataSource
deleteAllKeys() - Method in class org.protempa.DataSourceImpl
deleteSession(QuerySession) - Method in class org.protempa.Protempa
Derivation - Class in org.protempa.dest.table: Traverses traversals from a proposition to/from a derived proposition.
Derivation(String[], Derivation.Behavior) - Constructor for class org.protempa.dest.table.Derivation
Derivation(String[], PropertyConstraint[], Derivation.Behavior) - Constructor for class org.protempa.dest.table.Derivation
Derivation(String[], PropertyConstraint[], Value[], Derivation.Behavior) - Constructor for class org.protempa.dest.table.Derivation
Derivation(String[], PropertyConstraint[], Value[], Derivation.Behavior, Relation) - Constructor for class org.protempa.dest.table.Derivation
Derivation(String[], PropertyConstraint[], Comparator<Proposition>, int, Derivation.Behavior) - Constructor for class org.protempa.dest.table.Derivation
Derivation(String[], PropertyConstraint[], Comparator<Proposition>, int, Value[], Derivation.Behavior) - Constructor for class org.protempa.dest.table.Derivation
Derivation(String[], PropertyConstraint[], Comparator<Proposition>, int, int, Derivation.Behavior) - Constructor for class org.protempa.dest.table.Derivation
Derivation(String[], PropertyConstraint[], Comparator<Proposition>, int, int, Value[], Derivation.Behavior, Relation) - Constructor for class org.protempa.dest.table.Derivation
Derivation.Behavior - Enum in org.protempa.dest.table: For configuring the direction of the traversal and how many derivation steps to traverse.
DERIVED - Static variable in class org.protempa.SourceSystem
DerivedSourceId - Class in org.protempa.proposition
Destination - Interface in org.protempa.dest
DestinationException - Exception in org.protempa.dest
DestinationInitException - Exception in org.protempa.dest
DestinationInitException() - Constructor for exception org.protempa.dest.DestinationInitException
DestinationInitException(String, Throwable) - Constructor for exception org.protempa.dest.DestinationInitException
DestinationInitException(String) - Constructor for exception org.protempa.dest.DestinationInitException
DestinationInitException(Throwable) - Constructor for exception org.protempa.dest.DestinationInitException
detachSession(QuerySession) - Method in class org.protempa.Protempa
DirectedGraph - Class in org.protempa.graph: A directed graph implementation.
DirectedGraph(int) - Constructor for class org.protempa.graph.DirectedGraph: Constructs an empty DirectedGraph with the specified initial vertex capacity.
DirectedGraph() - Constructor for class org.protempa.graph.DirectedGraph: Constructs an empty DirectedGraph with the default initial vertex capacity (10).
DISPLAY_NAME_NULL - Static variable in annotation type org.protempa.backend.annotations.BackendInfo
displayName(Value) - Method in class org.protempa.valueset.ValueSet: Returns a display name for the specified value, if one is defined.
distance(long, long, Granularity, Unit) - Method in class org.protempa.proposition.value.AbsoluteTimeGranularity
distance(long, long, Granularity, Unit) - Method in interface org.protempa.proposition.value.Granularity: Calculates the distance between two positions.
distance(long, long, Granularity, Unit) - Method in class org.protempa.proposition.value.RelativeDayGranularity
distance(long, long, Granularity, Unit) - Method in class org.protempa.proposition.value.RelativeHourGranularity
distanceBetween(Interval, Interval) - Static method in class org.protempa.proposition.interval.IntervalUtil
distanceBetween(Interval, Interval, Unit) - Static method in class org.protempa.proposition.interval.IntervalUtil
distanceBetween(TemporalProposition, TemporalProposition) - Static method in class org.protempa.proposition.PropositionUtil
distanceBetween(TemporalProposition, TemporalProposition, Unit) - Static method in class org.protempa.proposition.PropositionUtil
DistanceBetweenColumnSpec - Class in org.protempa.dest.table
DistanceBetweenColumnSpec(Link[]) - Constructor for class org.protempa.dest.table.DistanceBetweenColumnSpec
DistanceBetweenColumnSpec(String, Link[]) - Constructor for class org.protempa.dest.table.DistanceBetweenColumnSpec
DistanceBetweenColumnSpec(String, Link[], Unit) - Constructor for class org.protempa.dest.table.DistanceBetweenColumnSpec
distanceBetweenFormattedLong(Interval, Interval) - Static method in class org.protempa.proposition.interval.IntervalUtil
distanceBetweenFormattedLong(Interval, Interval, Unit) - Static method in class org.protempa.proposition.interval.IntervalUtil
distanceBetweenFormattedLong(TemporalProposition, TemporalProposition) - Static method in class org.protempa.proposition.PropositionUtil
distanceBetweenFormattedLong(TemporalProposition, TemporalProposition, Unit) - Static method in class org.protempa.proposition.PropositionUtil
distanceBetweenFormattedMedium(Interval, Interval) - Static method in class org.protempa.proposition.interval.IntervalUtil
distanceBetweenFormattedMedium(Interval, Interval, Unit) - Static method in class org.protempa.proposition.interval.IntervalUtil
distanceBetweenFormattedMedium(TemporalProposition, TemporalProposition) - Static method in class org.protempa.proposition.PropositionUtil
distanceBetweenFormattedMedium(TemporalProposition, TemporalProposition, Unit) - Static method in class org.protempa.proposition.PropositionUtil
distanceBetweenFormattedShort(Interval, Interval) - Static method in class org.protempa.proposition.interval.IntervalUtil
distanceBetweenFormattedShort(Interval, Interval, Unit) - Static method in class org.protempa.proposition.interval.IntervalUtil
distanceBetweenFormattedShort(TemporalProposition, TemporalProposition) - Static method in class org.protempa.proposition.PropositionUtil
distanceBetweenFormattedShort(TemporalProposition, TemporalProposition, Unit) - Static method in class org.protempa.proposition.PropositionUtil
doubleValue() - Method in class org.protempa.proposition.value.InequalityNumberValue
doubleValue() - Method in class org.protempa.proposition.value.NumberValue
doubleValue() - Method in interface org.protempa.proposition.value.NumericalValue: Gets this value as a double.
drillDown(String, QueryResultsHandler) - Method in class org.protempa.QuerySession
DURING - Static variable in class org.protempa.proposition.interval.Relation

E

earliest(long) - Method in class org.protempa.proposition.value.AbsoluteTimeGranularity
earliest(long) - Method in interface org.protempa.proposition.value.Granularity
earliest(long) - Method in class org.protempa.proposition.value.RelativeDayGranularity
earliest(long) - Method in class org.protempa.proposition.value.RelativeHourGranularity
Edge - Class in org.protempa.graph
edges() - Method in class org.protempa.graph.DirectedGraph: Create an iterator of edges.
edgesAsArray() - Method in class org.protempa.graph.DirectedGraph
EMPTY_KEY_SET_SPEC_ARRAY - Static variable in class org.protempa.KeySetSpec
encrypt(String, String) - Method in class org.protempa.dest.deid.CipherEncryption: Encrypts the provided string.
encrypt(String, String) - Method in interface org.protempa.dest.deid.Encryption: Encrypts the provided string.
encrypt(String, String) - Method in class org.protempa.dest.deid.MessageDigestEncryption
Encryption - Interface in org.protempa.dest.deid
EncryptionInitException - Exception in org.protempa.dest.deid
entrySet() - Method in class org.protempa.DataSourceResultMap
equals(Object) - Method in class org.protempa.AttributeBuilder
equals(Object) - Method in class org.protempa.backend.dsb.filter.PositionFilter
equals(Object) - Method in class org.protempa.backend.dsb.filter.PropertyValueFilter
equals(Object) - Method in class org.protempa.backend.dsb.filter.ValueFilter
equals(Object) - Method in class org.protempa.DataSourceBackendSourceSystem
equals(Object) - Method in class org.protempa.DefaultSourceIdBuilder
equals(Object) - Method in class org.protempa.dest.table.AtLeastNColumnSpec
equals(Object) - Method in class org.protempa.dest.table.CountColumnSpec
equals(Object) - Method in class org.protempa.dest.table.Derivation
equals(Object) - Method in class org.protempa.dest.table.DistanceBetweenColumnSpec
equals(Object) - Method in class org.protempa.dest.table.Link
equals(Object) - Method in class org.protempa.dest.table.OutputConfig
equals(Object) - Method in class org.protempa.dest.table.PropertyConstraint
equals(Object) - Method in class org.protempa.dest.table.PropositionColumnSpec
equals(Object) - Method in class org.protempa.dest.table.PropositionValueColumnSpec
equals(Object) - Method in class org.protempa.dest.table.Reference
equals(Object) - Method in class org.protempa.dest.table.ValueOutputConfig
equals(Object) - Method in class org.protempa.graph.Edge
equals(Object) - Method in class org.protempa.graph.Weight
equals(Object) - Method in class org.protempa.KeySetSpec
equals(Object) - Method in class org.protempa.NotRecordedSourceIdBuilder
equals(Object) - Method in class org.protempa.PropertyDefinitionBuilder
equals(Object) - Method in class org.protempa.proposition.AbstractProposition
equals(Object) - Method in class org.protempa.proposition.comparator.AllPropositionIntervalComparator
equals(Object) - Method in class org.protempa.proposition.DataSourceBackendId
equals(Object) - Method in class org.protempa.proposition.DerivedSourceId
equals(Object) - Method in class org.protempa.proposition.interval.Interval
EQUALS - Static variable in class org.protempa.proposition.interval.Relation
equals(Object) - Method in class org.protempa.proposition.interval.Relation
equals(Object) - Method in class org.protempa.proposition.ProviderBasedLocalUniqueId
equals(Object) - Method in class org.protempa.proposition.Sequence
equals(Object) - Method in class org.protempa.proposition.UniqueId
equals(Object) - Method in class org.protempa.proposition.value.AbsoluteTimeGranularity
equals(Object) - Method in class org.protempa.proposition.value.BooleanValue
equals(Object) - Method in class org.protempa.proposition.value.BooleanValueBuilder
equals(Object) - Method in class org.protempa.proposition.value.DateValue
equals(Object) - Method in class org.protempa.proposition.value.DateValueBuilder
equals(Object) - Method in class org.protempa.proposition.value.InequalityNumberValue
equals(Object) - Method in class org.protempa.proposition.value.InequalityNumberValueBuilder
equals(Object) - Method in class org.protempa.proposition.value.NominalValue: Compares this nominal value and another for string equality.
equals(Object) - Method in class org.protempa.proposition.value.NominalValueBuilder
equals(Object) - Method in class org.protempa.proposition.value.NumberValue
equals(Object) - Method in class org.protempa.proposition.value.NumberValueBuilder
equals(Object) - Method in class org.protempa.proposition.value.OrdinalValue
equals(Object) - Method in class org.protempa.proposition.value.OrdinalValueBuilder
equals(Object) - Method in class org.protempa.proposition.value.RelativeDayGranularity
equals(Object) - Method in class org.protempa.proposition.value.RelativeHourGranularity
equals(Object) - Method in class org.protempa.proposition.value.ValueListBuilder
equals(Object) - Method in class org.protempa.query.And
equals(Object) - Method in class org.protempa.query.Query
equals(Object) - Method in class org.protempa.valueset.ValueSetBuilder
equals(Object) - Method in class org.protempa.valueset.ValueSetElementBuilder
evaluate(Object, Tuple, Declaration[], Declaration[], WorkingMemory, Object) - Method in class org.protempa.CollectionSizeExpression
evaluate(List<Proposition>) - Method in interface org.protempa.dest.keyloader.Criteria
Event - Class in org.protempa.proposition: An external volitional action or process, such as the administration of a drug (as opposed to a measurable datum, such as temperature).
Event(String, UniqueId) - Constructor for class org.protempa.proposition.Event: Creates an event with an id and no attribute id.
EventDefinition - Class in org.protempa: Defines external acts upon an entity such as a patient.
EventDefinition(String) - Constructor for class org.protempa.EventDefinition
execute(Protempa, CommandLine) - Method in class org.protempa.cli.CLI: Implemented with whatever is done with the instance of PROTEMPA created with #initialize(java.lang.String), and processing of any arguments and command line options specified in CLI.addCustomCliOptions(org.apache.commons.cli.Options).
execute() - Method in class org.protempa.cli.CLI: Calls the code in CLI.execute(org.protempa.Protempa, org.apache.commons.cli.CommandLine).
execute(Protempa, CommandLine) - Method in class org.protempa.cli.PrintAbstractedFrom
execute(Protempa, CommandLine) - Method in class org.protempa.cli.PrintAbstractedInto
execute(Protempa, CommandLine) - Method in class org.protempa.cli.PrintInverseIsA
execute(Protempa, CommandLine) - Method in class org.protempa.cli.PrintIsA
execute(Protempa, CommandLine) - Method in class org.protempa.cli.PrintPropositionDefinition
execute(Protempa, CommandLine) - Method in class org.protempa.cli.PrintPropositionDefinitionsForTerm
execute(Protempa, CommandLine) - Method in class org.protempa.cli.PrintSubtreeInDataSource
execute(Protempa, CommandLine) - Method in class org.protempa.cli.PrintTerm
execute(Protempa, CommandLine) - Method in class org.protempa.cli.PrintTermChildren
execute(Protempa, CommandLine) - Method in class org.protempa.cli.ValidateDataSource
execute(TemporalProposition, TemporalProposition) - Method in class org.protempa.GapFunction: Returns whether two abstract parameters have a gap that satisfies the constraints of the gap function.
execute(Interval, Interval) - Method in class org.protempa.GapFunction: Returns whether two intervals have a gap that satisfies the constraints of the gap function.
execute(Interval, Interval) - Method in class org.protempa.MinMaxGapFunction
execute(Query, Destination) - Method in class org.protempa.Protempa: Executes a query.
execute(QueryResultsHandler) - Method in class org.protempa.QuerySession: This method returns the current data for the query session without any filter or drill down.
execute(Interval, Interval) - Method in class org.protempa.SimpleGapFunction: Executes the gap function.
ExtendedParameterDefinition - Class in org.protempa: Represents an instance of an abstraction definition with optional constraints on the instance's duration.
ExtendedParameterDefinition(String) - Constructor for class org.protempa.ExtendedParameterDefinition
ExtendedPropositionDefinition - Class in org.protempa
ExtendedPropositionDefinition(String) - Constructor for class org.protempa.ExtendedPropositionDefinition

F

FALSE - Static variable in class org.protempa.proposition.value.BooleanValue
Filter - Interface in org.protempa.backend.dsb.filter: Specifies a filter on what propositions to return from a data source.
filter(Filter, QueryResultsHandler) - Method in class org.protempa.QuerySession
filterArrayToChain(Filter[]) - Static method in class org.protempa.backend.dsb.filter.AbstractFilter: Convert an array of AbstractFilter objects to a chain of filters by calling the AbstractFilter.setAnd(org.protempa.backend.dsb.filter.Filter) the method of each filter object.
filterChainToArray() - Method in class org.protempa.backend.dsb.filter.AbstractFilter: Return an array that contains all of the filters in the chain.
filterChainToArray() - Method in interface org.protempa.backend.dsb.filter.Filter: Return an array that contains all of the filters in the chain.
FilterVisitor - Interface in org.protempa.backend.dsb.filter
finalize() - Method in class org.protempa.AbstractAlgorithm
finish() - Method in class org.protempa.dest.AbstractQueryResultsHandler
finish() - Method in class org.protempa.dest.deid.DeidentifiedQueryResultsHandler
finish() - Method in class org.protempa.dest.keyloader.KeyLoaderQueryResultsHandler
finish() - Method in interface org.protempa.dest.QueryResultsHandler: Called by Protempa as soon as all query results have been retrieved from the data source.
finish() - Method in class org.protempa.dest.xml.XmlQueryResultsHandler
FINISHED_BY - Static variable in class org.protempa.proposition.interval.Relation
FINISHES - Static variable in class org.protempa.proposition.interval.Relation
fireAlgorithmSourceBackendUpdated() - Method in class org.protempa.backend.asb.AbstractAlgorithmSourceBackend: Notifies registered listeners that the backend has been updated.
fireBackendUpdated(E) - Method in class org.protempa.backend.AbstractBackend: Notifies all registered listeners when the backend has been updated.
fireClosedUnexpectedly(SourceClosedUnexpectedlyEvent<S, B, T>) - Method in class org.protempa.AbstractSource
fireKnowledgeSourceBackendUpdated() - Method in class org.protempa.backend.ksb.AbstractKnowledgeSourceBackend: Notifies registered listeners that the backend has been updated.
fireKnowledgeSourceBackendUpdated() - Method in class org.protempa.backend.ksb.SimpleKnowledgeSourceBackend: Make public so that tests can call it.
fireSourceUpdated(S) - Method in class org.protempa.AbstractSource: Notifies registered listeners that the source has been updated.
fireTermSourceBackendUpdated() - Method in class org.protempa.backend.test.MockTermSourceBackend: Make public so that tests can call it.
fireTermSourceBackendUpdated() - Method in class org.protempa.backend.tsb.AbstractTermSourceBackend
fireUnrecoverableError(UnrecoverableBackendErrorEvent) - Method in class org.protempa.backend.AbstractBackend: Notifies all registered listeners when an unrecoverable error has occurred in a backend.
first() - Method in class org.protempa.proposition.Segment
fromCls(Class<?>) - Static method in enum org.protempa.backend.BackendPropertyType
fromTerminologyAndCode(String, String) - Static method in class org.protempa.Term
fromTerms(Collection<String>) - Static method in class org.protempa.TermSubsumption
fromTerms(String...) - Static method in class org.protempa.TermSubsumption

G

GapFunction - Class in org.protempa: A convenience class for implementing gap functions.
GapFunction() - Constructor for class org.protempa.GapFunction
get(Object) - Method in class org.protempa.DataSourceResultMap
get(String) - Method in class org.protempa.KnowledgeSourceCache
get(int) - Method in class org.protempa.proposition.Segment
get(int) - Method in class org.protempa.proposition.Sequence
get(String) - Method in class org.protempa.proposition.stats.AbstractKaplanMeyer
get(String, Value) - Method in class org.protempa.proposition.stats.AbstractKaplanMeyer
get(String) - Method in class org.protempa.QueryResults
getAbbrevatedName() - Method in class org.protempa.proposition.value.AbsoluteTimeGranularity
getAbbrevatedName() - Method in interface org.protempa.proposition.value.Granularity: Returns a shorter version of the granularity's name.
getAbbrevatedName() - Method in class org.protempa.proposition.value.RelativeDayGranularity
getAbbrevatedName() - Method in class org.protempa.proposition.value.RelativeHourGranularity
getAbbrevDisplayName() - Method in class org.protempa.Term
getAbbrevDisplayName() - Method in class org.protempa.valueset.ValueSetElement: Returns the value's abbreviated display name.
getAbbrevDisplayName() - Method in class org.protempa.valueset.ValueSetElementBuilder
getAbbrevDisplayNameHeading() - Method in class org.protempa.dest.table.OutputConfig
getAbbrevDisplayNameHeading() - Method in class org.protempa.dest.table.OutputConfigBuilder
getAbbreviatedDisplayName() - Method in class org.protempa.AbstractPropositionDefinition
getAbbreviatedDisplayName() - Method in class org.protempa.ExtendedPropositionDefinition
getAbbreviatedDisplayName() - Method in interface org.protempa.PropositionDefinition: This proposition definition's abbreviated display name.
getAbbreviatedName() - Method in class org.protempa.proposition.value.AbstractTimeUnit
getAbbreviatedName() - Method in interface org.protempa.proposition.value.Unit: Returns a short version of the unit's singular name.
getAbstractedFrom() - Method in interface org.protempa.AbstractionDefinition: Returns all proposition ids from which this abstract parameter is abstracted.
getAbstractedFrom() - Method in class org.protempa.CompoundLowLevelAbstractionDefinition
getAbstractedFrom() - Method in class org.protempa.HighLevelAbstractionDefinition
getAbstractedFrom() - Method in class org.protempa.LowLevelAbstractionDefinition
getAbstractedFrom() - Method in class org.protempa.SequentialTemporalPatternDefinition
getAbstractedFrom() - Method in class org.protempa.SliceDefinition
getAccessed() - Method in class org.protempa.AbstractPropositionDefinition
getAccessed() - Method in interface org.protempa.PropositionDefinition: Returns the timestamp of when this proposition definition was accessed from the knowledge source.
getAdvanceRowSkipEnd() - Method in class org.protempa.AbstractAlgorithm
getAdvanceRowSkipEnd() - Method in interface org.protempa.Algorithm
getAlgorithm(String) - Method in class org.protempa.Algorithms: Returns the algorithm with a given id.
getAlgorithm() - Method in interface org.protempa.dest.deid.MessageDigestDeidConfig
getAlgorithmClass(String) - Method in class org.protempa.backend.asb.java.AbstractJavaAlgorithmBackend: name is expected to be a fully-qualified class name in dot-format (e.g., my.algorithms.MockAlgorithm).
getAlgorithmId() - Method in class org.protempa.LowLevelAbstractionDefinition
getAlgorithms() - Method in class org.protempa.Algorithms: Returns all algorithms.
getAlgorithms() - Method in class org.protempa.backend.asb.java.JavaAlgorithmBackend
getAlgorithmSource() - Method in class org.protempa.Protempa: Gets the algorithm source.
getAlgorithmSourceBackendInstanceSpecs() - Method in class org.protempa.backend.ConfigurationsSupport
getAlgorithmSourceBackendSections() - Method in class org.protempa.backend.Configuration
getAlgorithmSourceBackendSpecLoader() - Method in interface org.protempa.backend.BackendProvider
getAlgorithmSourceBackendSpecLoader() - Static method in class org.protempa.backend.BackendProviderManager
getAlgorithmSourceBackendSpecLoader() - Method in class org.protempa.backend.test.MockBackendProvider
getAlgorithmsPropertiesResourceName() - Method in class org.protempa.backend.asb.java.AbstractJavaAlgorithmBackend
getAlgorithmsPropertiesResourceName() - Method in class org.protempa.backend.asb.java.JavaAlgorithmBackend
getAllowedValues() - Method in class org.protempa.dest.table.Derivation
getAllSections() - Method in class org.protempa.backend.Configuration
getAnd() - Method in class org.protempa.backend.dsb.filter.AbstractFilter
getAnd() - Method in interface org.protempa.backend.dsb.filter.Filter: Returns the next filter in the chain, if specified.
getAnded() - Method in class org.protempa.query.And
getArguments() - Method in class org.protempa.cli.CLI: Gets optional arguments that are not prefixed with option syntax.
getAttribute(String) - Method in class org.protempa.PropertyDefinition
getAttributeBuilders() - Method in class org.protempa.valueset.ValueSetElementBuilder
getAttributes() - Method in class org.protempa.AbstractPropositionDefinition
getAttributes() - Method in class org.protempa.PropertyDefinition
getAttributes() - Method in interface org.protempa.PropositionDefinition
getAttributes() - Method in class org.protempa.valueset.ValueSetElement
getBackend() - Method in class org.protempa.backend.AlgorithmSourceBackendUpdatedEvent
getBackend() - Method in class org.protempa.backend.BackendUpdatedEvent: Returns the source Backend (the same as what getSource() returns).
getBackend() - Method in class org.protempa.backend.DataSourceBackendUpdatedEvent
getBackend() - Method in class org.protempa.backend.KnowledgeSourceBackendUpdatedEvent
getBackend() - Method in class org.protempa.backend.TermSourceBackendUpdatedEvent
getBackendPropertySpec() - Method in class org.protempa.backend.test.MockBackendPropertySpec
getBackendProvider() - Method in class org.protempa.backend.AbstractConfigurations
getBackendProvider() - Static method in class org.protempa.backend.BackendProviderManager
getBackendProvider() - Method in class org.protempa.backend.BackendSpec
getBackendProviderClassLoader() - Static method in class org.protempa.backend.BackendProviderManager
getBackends() - Method in class org.protempa.AbstractSource: Gets the backends registered to this source.
getBackends() - Method in interface org.protempa.Source
getBackendSpec() - Method in class org.protempa.backend.BackendInstanceSpec
getBehavior() - Method in class org.protempa.dest.table.Derivation
getBigDecimal() - Method in class org.protempa.proposition.value.InequalityNumberValue
getBigDecimal() - Method in class org.protempa.proposition.value.NumberValue
getBigDecimal() - Method in interface org.protempa.proposition.value.NumericalValue: Gets this value as a BigDecimal.
getBoolean() - Method in class org.protempa.proposition.value.BooleanValue: Returns the Java Boolean corresponding to this object.
getCalendarUnits() - Method in class org.protempa.proposition.value.AbstractTimeUnit: The equivalent units in Calendar.
getCalendarUnits() - Method in class org.protempa.proposition.value.RelativeDayGranularity
getCalendarUnits() - Method in class org.protempa.proposition.value.RelativeHourGranularity
getChildren() - Method in class org.protempa.AbstractPropositionDefinition
getChildren() - Method in interface org.protempa.PropositionDefinition: Returns the ids of this proposition definition's children.
getChildrenToParents() - Method in class org.protempa.dest.DefaultStatistics
getChildrenToParents(String[]) - Method in class org.protempa.dest.DefaultStatistics
getChildrenToParents() - Method in class org.protempa.dest.DefaultStatisticsBuilder
getChildrenToParents() - Method in interface org.protempa.dest.Statistics
getChildrenToParents(String[]) - Method in interface org.protempa.dest.Statistics
getCipherAlgorithm() - Method in interface org.protempa.dest.deid.CipherDeidConfig
getCls() - Method in enum org.protempa.backend.BackendPropertyType
getCode() - Method in class org.protempa.Term
getColumnDelimiter() - Method in class org.protempa.dest.table.TableDestination
getColumnNameOverride() - Method in class org.protempa.dest.table.AtLeastNColumnSpec
getColumnNameOverride() - Method in class org.protempa.dest.table.CountColumnSpec
getColumnNamePrefixOverride() - Method in class org.protempa.dest.table.DistanceBetweenColumnSpec
getColumnNamePrefixOverride() - Method in class org.protempa.dest.table.PropositionColumnSpec
getColumnNamePrefixOverride() - Method in class org.protempa.dest.table.PropositionValueColumnSpec
getColumnSpecs() - Method in class org.protempa.dest.table.TableDestination
getComparator() - Method in class org.protempa.backend.dsb.filter.ValueFilter
getComparator() - Method in class org.protempa.dest.table.Link: A comparator for ordering the propositions at the end of the traversal.
getComparator() - Method in class org.protempa.proposition.value.InequalityNumberValue
getComparator() - Method in class org.protempa.proposition.value.InequalityNumberValueBuilder
getComparators() - Method in class org.protempa.AlgorithmParameter: Returns the allowed comparators for this parameter.
getComparatorString() - Method in enum org.protempa.proposition.value.ValueComparator: Gets the string associated with this comparator object.
getConfigurationId() - Method in class org.protempa.backend.Configuration
getConfigurations() - Method in interface org.protempa.backend.ConfigurationsProvider
getConfigurations() - Static method in class org.protempa.backend.ConfigurationsProviderManager: Convenience static method for getting configurations, like calling ConfigurationsProviderManager.getConfigurationsProvider() followed by ConfigurationsProvider.getConfigurations().
getConfigurationsId() - Method in class org.protempa.backend.AbstractBackend
getConfigurationsId() - Method in interface org.protempa.backend.Backend
getConfigurationsId() - Method in class org.protempa.backend.BackendInstanceSpec
getConfigurationsProvider() - Static method in class org.protempa.backend.ConfigurationsProviderManager: Gets the configurations provider found by service discovery or set with {@link #setConfigurationsProvider(org.protempa.backend.ConfigurationsProvider).
getConfigurationsProviderClassLoader() - Static method in class org.protempa.backend.ConfigurationsProviderManager
getConstraints() - Method in class org.protempa.dest.table.Link: Constraints on properties of the propositions at the end of the traversal.
getContextId() - Method in class org.protempa.CompoundLowLevelAbstractionDefinition
getContextId() - Method in class org.protempa.LowLevelAbstractionDefinition
getContextId() - Method in class org.protempa.proposition.AbstractParameter
getContextId() - Method in class org.protempa.TemporalExtendedAbstractParameterDefinition
getCorrespondingUnit() - Method in class org.protempa.proposition.value.AbsoluteTimeGranularity
getCorrespondingUnit() - Method in interface org.protempa.proposition.value.Granularity
getCorrespondingUnit() - Method in class org.protempa.proposition.value.RelativeDayGranularity
getCorrespondingUnit() - Method in class org.protempa.proposition.value.RelativeHourGranularity
getCounts() - Method in class org.protempa.dest.DefaultStatistics
getCounts(String[]) - Method in class org.protempa.dest.DefaultStatistics
getCounts() - Method in class org.protempa.dest.DefaultStatisticsBuilder
getCounts() - Method in interface org.protempa.dest.Statistics
getCounts(String[]) - Method in interface org.protempa.dest.Statistics
getCreated() - Method in class org.protempa.AbstractPropositionDefinition
getCreated() - Method in interface org.protempa.PropositionDefinition: Returns the timestamp of when this proposition definition was created, if the knowledge source backend maintains this information.
getCreateDate() - Method in class org.protempa.proposition.AbstractProposition
getCreateDate() - Method in interface org.protempa.proposition.Proposition: Gets the date this proposition was created in the source system, or for derived propositions, the date it was created through the temporal abstraction process.
getData() - Method in class org.protempa.DataStreamingEvent
getData() - Method in class org.protempa.proposition.stats.AbstractKaplanMeyer
getDataSource() - Method in class org.protempa.Protempa: Gets the data source.
getDataSourceBackendId() - Method in class org.protempa.backend.AbstractCommonsDataSourceBackend: Deprecated.
getDataSourceBackendInstanceSpecs() - Method in class org.protempa.backend.ConfigurationsSupport
getDataSourceBackendSections() - Method in class org.protempa.backend.Configuration
getDataSourceBackendSpecLoader() - Method in interface org.protempa.backend.BackendProvider
getDataSourceBackendSpecLoader() - Static method in class org.protempa.backend.BackendProviderManager
getDataSourceBackendSpecLoader() - Method in class org.protempa.backend.test.MockBackendProvider
getDate() - Method in class org.protempa.proposition.value.DateValue: Gets the date represented by this object as a Java Date.
getDate() - Method in class org.protempa.proposition.value.DateValueBuilder
getDeclaringPropId() - Method in class org.protempa.PropertyDefinition
getDeclaringPropId() - Method in class org.protempa.PropertyDefinitionBuilder
getDeleteDate() - Method in class org.protempa.proposition.AbstractProposition
getDeleteDate() - Method in interface org.protempa.proposition.Proposition: Gets the date this proposition was deleted from the source system, or for derived propositions, the date it was invalidated due to data changes.
getDerived(Proposition) - Method in class org.protempa.QuerySession: Gets the abstract propositions that were derived from the given proposition.
getDerived(Proposition, String[]) - Method in class org.protempa.QuerySession: Gets the abstract propositions with the given ids that were derived from the given proposition.
getDescription() - Method in interface org.protempa.AbstractionDefinition
getDescription() - Method in class org.protempa.AbstractPropositionDefinition
getDescription() - Method in class org.protempa.backend.BackendPropertySpec
getDescription() - Method in class org.protempa.KeySetSpec
getDescription() - Method in interface org.protempa.PropositionDefinition: A longer description of the proposition definition.
getDescription() - Method in class org.protempa.Term
getDescription() - Method in class org.protempa.Terminology
getDirectChildren() - Method in class org.protempa.Term: Returns a newly-created array of the ids of this term's direct children.
getDisplayName() - Method in class org.protempa.AbstractPropositionDefinition
getDisplayName() - Method in class org.protempa.backend.AbstractCommonsAlgorithmSourceBackend
getDisplayName() - Method in class org.protempa.backend.AbstractCommonsDataSourceBackend
getDisplayName() - Method in class org.protempa.backend.AbstractCommonsKnowledgeSourceBackend
getDisplayName() - Method in class org.protempa.backend.AbstractCommonsTermSourceBackend
getDisplayName() - Method in class org.protempa.backend.asb.java.JavaAlgorithmBackend
getDisplayName() - Method in interface org.protempa.backend.Backend: Returns the name of this backend for display in user interfaces.
getDisplayName(String) - Method in class org.protempa.backend.BackendInstanceSpec
getDisplayName() - Method in class org.protempa.backend.BackendPropertySpec
getDisplayName() - Method in interface org.protempa.backend.BackendProvider
getDisplayName() - Method in class org.protempa.backend.BackendSpec
getDisplayName() - Method in class org.protempa.backend.ksb.SimpleKnowledgeSourceBackend
getDisplayName() - Method in class org.protempa.backend.test.MockBackendProvider
getDisplayName() - Method in class org.protempa.backend.test.MockTermSourceBackend
getDisplayName() - Method in class org.protempa.backend.tsb.AbstractTermSourceBackend: A default implementation that returns null
getDisplayName() - Method in class org.protempa.dest.AbstractDestination: Returns this destination's display name for user interfaces.
getDisplayName() - Method in class org.protempa.dest.AbstractQueryResultsHandler: Returns this query result handler's display name for user interfaces.
getDisplayName() - Method in interface org.protempa.dest.Destination: Gets the destination's display name for user interfaces.
getDisplayName() - Method in class org.protempa.dest.keyloader.KeyLoaderDestination
getDisplayName() - Method in class org.protempa.dest.keyloader.KeyLoaderQueryResultsHandler
getDisplayName() - Method in interface org.protempa.dest.QueryResultsHandler: Gets the query result handler's display name for user interfaces.
getDisplayName() - Method in class org.protempa.ExtendedPropositionDefinition
getDisplayName() - Method in class org.protempa.KeySetSpec
getDisplayName() - Method in class org.protempa.PropertyDefinition: Returns the property's displayName.
getDisplayName() - Method in class org.protempa.PropertyDefinitionBuilder
getDisplayName() - Method in interface org.protempa.PropositionDefinition: This proposition definition's display name.
getDisplayName() - Method in class org.protempa.ReferenceDefinition
getDisplayName() - Method in class org.protempa.Term
getDisplayName() - Method in class org.protempa.valueset.ValueSet
getDisplayName() - Method in class org.protempa.valueset.ValueSetBuilder
getDisplayName() - Method in class org.protempa.valueset.ValueSetElement: Returns the value's display name.
getDisplayName() - Method in class org.protempa.valueset.ValueSetElementBuilder
getDisplayNameHeading() - Method in class org.protempa.dest.table.OutputConfig
getDisplayNameHeading() - Method in class org.protempa.dest.table.OutputConfigBuilder
getDownloadDate() - Method in class org.protempa.proposition.AbstractProposition
getDownloadDate() - Method in interface org.protempa.proposition.Proposition: Gets the date this proposition was downloaded from the source system.
getDownloaded() - Method in class org.protempa.AbstractPropositionDefinition
getDownloaded() - Method in interface org.protempa.PropositionDefinition: Returns the timestamp of when this proposition definition's information was downloaded from its source, e.g., a terminology standard, if such information is available.
getEdge(Object, Object) - Method in class org.protempa.graph.DirectedGraph
getEdgeCount() - Method in class org.protempa.graph.DirectedGraph: Get the total number of edges.
getElements() - Method in class org.protempa.proposition.value.ValueListBuilder
getEncryptionInstance() - Method in interface org.protempa.dest.deid.DeidConfig
getEnvironmentName() - Method in class org.protempa.datastore.AbstractDataStoreCreator
getExtendedPropositionDefinitions() - Method in class org.protempa.HighLevelAbstractionDefinition: Gets the extended proposition definitions that are part of this abstraction definition.
getFalseOutput() - Method in class org.protempa.dest.table.AtLeastNColumnSpec
getFilters() - Method in class org.protempa.query.DefaultQueryBuilder: Gets the filters to be applied to this query.
getFilters() - Method in class org.protempa.query.Query: Gets the filters to be applied to this query.
getFinish() - Method in class org.protempa.backend.dsb.filter.PositionFilter: Returns the finish position supplied in the constructor.
getFinish() - Method in class org.protempa.graph.Edge
getFinishAbstractParamValue() - Method in class org.protempa.TemporalPatternOffset
getFinishFormattedLong() - Method in class org.protempa.proposition.TemporalProposition: Returns the latest valid time of this proposition as a long string.
getFinishFormattedMedium() - Method in class org.protempa.proposition.TemporalProposition: Returns the earliest valid time of this proposition as a medium-length string.
getFinishFormattedShort() - Method in class org.protempa.proposition.TemporalProposition: Returns the earliest valid time of this proposition as a short string.
getFinishGranularity() - Method in class org.protempa.backend.dsb.filter.PositionFilter: Returns the Granularity with which to interpret the finish position.
getFinishGranularity() - Method in class org.protempa.proposition.interval.Interval: Returns the finish granularity.
getFinishGranularity() - Method in class org.protempa.proposition.Segment
getFinishHeading() - Method in class org.protempa.dest.table.OutputConfig
getFinishHeading() - Method in class org.protempa.dest.table.OutputConfigBuilder
getFinishIntervalSide() - Method in class org.protempa.ContextOffset
getFinishIntervalSide() - Method in class org.protempa.TemporalPatternOffset
getFinishOffset() - Method in class org.protempa.ContextOffset
getFinishOffset() - Method in class org.protempa.TemporalPatternOffset
getFinishOffsetUnits() - Method in class org.protempa.ContextOffset
getFinishOffsetUnits() - Method in class org.protempa.TemporalPatternOffset
getFinishSide() - Method in class org.protempa.backend.dsb.filter.PositionFilter: Returns the side of the proposition to which to apply the upper bound.
getFinishTemporalExtendedPropositionDefinition() - Method in class org.protempa.TemporalPatternOffset
getFirstIndex() - Method in class org.protempa.proposition.Segment
getFirstTemporalExtendedPropositionDefinition() - Method in class org.protempa.SequentialTemporalPatternDefinition
getFormatted() - Method in class org.protempa.cli.CLI.Argument: Gets the argument formatted as a string suitable for a usage statement.
getFormatted() - Method in class org.protempa.proposition.value.BooleanValue
getFormatted() - Method in class org.protempa.proposition.value.DateValue
getFormatted() - Method in class org.protempa.proposition.value.InequalityNumberValue
getFormatted() - Method in class org.protempa.proposition.value.NominalValue: Returns the same thing as NominalValue.getString().
getFormatted() - Method in class org.protempa.proposition.value.NumberValue
getFormatted() - Method in class org.protempa.proposition.value.OrdinalValue
getFormatted() - Method in interface org.protempa.proposition.value.Value: Returns a string representing this value for display purposes.
getFormatted() - Method in class org.protempa.proposition.value.ValueList
getFromAbstraction(String, UniqueId, Segment<? extends TemporalProposition>, List<? extends TemporalProposition>, Value, TemporalPatternOffset, TemporalExtendedPropositionDefinition[], String) - Static method in class org.protempa.AbstractParameterFactory
getFromIndex() - Method in class org.protempa.dest.table.Link: The start index of the propositions of interest at the end of the traversal step, after applying the proposition id constraints, property constraints and a comparator.
getGapFunction() - Method in class org.protempa.AbstractAbstractionDefinition
getGapFunction() - Method in interface org.protempa.AbstractionDefinition
getGapFunction() - Method in class org.protempa.ContextDefinition
getGapFunctionBetweenValues() - Method in class org.protempa.CompoundLowLevelAbstractionDefinition
getGranularity() - Method in class org.protempa.proposition.PrimitiveParameter: Returns the granularity of this parameter's timestamp.
getGranularityFactory() - Method in class org.protempa.backend.dsb.AbstractDataSourceBackend
getGranularityFactory() - Method in interface org.protempa.backend.dsb.DataSourceBackend
getGranularityFactory() - Method in interface org.protempa.DataSource: Returns an object for accessing the granularity of returned data from the schema adaptor for this data source.
getGranularityFactory() - Method in class org.protempa.DataSourceImpl: Returns an object for accessing the granularity of returned data from the schema adaptor for this data source.
getId() - Method in class org.protempa.AbstractAlgorithm
getId() - Method in class org.protempa.AbstractPropositionDefinition
getId() - Method in interface org.protempa.Algorithm: The algorithm's unique id.
getId() - Method in class org.protempa.backend.AbstractBackend
getId() - Method in class org.protempa.backend.AbstractCommonsAlgorithmSourceBackend
getId() - Method in class org.protempa.backend.AbstractCommonsDataSourceBackend
getId() - Method in class org.protempa.backend.AbstractCommonsKnowledgeSourceBackend
getId() - Method in class org.protempa.backend.AbstractCommonsTermSourceBackend
getId() - Method in interface org.protempa.backend.Backend
getId() - Method in class org.protempa.backend.BackendSpec
getId() - Method in class org.protempa.DataSourceBackendSourceSystem
getId() - Method in class org.protempa.dest.AbstractDestination
getId() - Method in class org.protempa.dest.AbstractQueryResultsHandler
getId() - Method in class org.protempa.dest.deid.DeidentifiedDestination
getId() - Method in class org.protempa.dest.deid.DeidentifiedQueryResultsHandler
getId() - Method in interface org.protempa.dest.Destination: Gets the destination's identifier string for logging and internal purposes.
getId() - Method in class org.protempa.dest.keyloader.KeyLoaderDestination
getId() - Method in class org.protempa.dest.keyloader.KeyLoaderQueryResultsHandler
getId() - Method in interface org.protempa.dest.QueryResultsHandler: Gets the query result handler's identifier string for logging and internal purposes.
getId() - Method in class org.protempa.KeySetSpec
getId() - Method in class org.protempa.LowLevelAbstractionValueDefinition
getId() - Method in class org.protempa.PropertyDefinition: Returns the property's id, which is unique in combination with a proposition id.
getId() - Method in class org.protempa.PropertyDefinitionBuilder
getId() - Method in class org.protempa.proposition.AbstractProposition
getId() - Method in class org.protempa.proposition.DefaultLocalUniqueId
getId() - Method in interface org.protempa.proposition.LocalUniqueId: Gets a string identifier that is unique to a proposition for all propositions with its proposition id.
getId() - Method in interface org.protempa.proposition.LocalUniqueIdValuesProvider
getId() - Method in interface org.protempa.proposition.Proposition: Gets this proposition's data type.
getId() - Method in class org.protempa.proposition.ProviderBasedLocalUniqueId
getId() - Method in interface org.protempa.PropositionDefinition: This proposition definition's id.
getId() - Method in class org.protempa.QuerySession: Gets the query session's unique identifier.
getId() - Method in class org.protempa.ReferenceDefinition: Gets the id of the reference.
getId() - Method in class org.protempa.Term
getId() - Method in class org.protempa.valueset.ValueSet: Returns the value set's unique identifier.
getId() - Method in class org.protempa.valueset.ValueSetBuilder
getIdHeading() - Method in class org.protempa.dest.table.OutputConfig
getIdHeading() - Method in class org.protempa.dest.table.OutputConfigBuilder
getInDataSource() - Method in class org.protempa.AbstractPropositionDefinition
getInDataSource() - Method in interface org.protempa.PropositionDefinition
getIndex() - Method in class org.protempa.proposition.value.OrdinalValue
getIndex() - Method in class org.protempa.proposition.value.OrdinalValueBuilder
getInducedBy() - Method in class org.protempa.ContextDefinition: Returns the id of the proposition definition that induces this context.
getInequality() - Method in class org.protempa.proposition.value.InequalityNumberValue
getInferredPropositionIds(KnowledgeSource, String[]) - Method in class org.protempa.dest.table.AtLeastNColumnSpec
getInferredPropositionIds(KnowledgeSource, String[]) - Method in class org.protempa.dest.table.CountColumnSpec
getInferredPropositionIds(KnowledgeSource, String[]) - Method in class org.protempa.dest.table.Derivation
getInferredPropositionIds(KnowledgeSource, String[]) - Method in class org.protempa.dest.table.DistanceBetweenColumnSpec
getInferredPropositionIds(KnowledgeSource, String[]) - Method in class org.protempa.dest.table.Link: Aggregates and returns the possible proposition ids on the right-hand side of the link.
getInferredPropositionIds(KnowledgeSource, String[]) - Method in class org.protempa.dest.table.PropositionColumnSpec
getInferredPropositionIds(KnowledgeSource, String[]) - Method in class org.protempa.dest.table.PropositionValueColumnSpec
getInferredPropositionIds(KnowledgeSource, String[]) - Method in class org.protempa.dest.table.Reference
getInferredPropositionIds(KnowledgeSource, String[]) - Method in interface org.protempa.dest.table.TableColumnSpec: Infers the ids of the propositions corresponding to the contents of this column.
getInstance() - Method in class org.protempa.backend.BackendInstanceSpec: Instantiates a new Backend and calls its Backend.initialize(org.protempa.backend.BackendInstanceSpec<?>) method before returning it.
getInstance() - Method in class org.protempa.backend.BackendSourceIdFactory
getInstance() - Method in class org.protempa.backend.test.MockBackendInstanceSpecFactory
getInstance(String) - Static method in class org.protempa.DataSourceBackendSourceSystem
getInstance(RuleBase) - Static method in class org.protempa.datastore.WorkingMemoryStoreCreator: Returns an instance of this class, which can be used to get either a permanent or temporary store.
getInstance(String) - Static method in class org.protempa.DefaultSourceId
getInstance(String) - Method in class org.protempa.DefaultSourceIdFactory
getInstance() - Method in class org.protempa.graph.WeightFactory
getInstance(Number) - Method in class org.protempa.graph.WeightFactory
getInstance(KnowledgeSource, Collection<PropositionDefinition>, boolean) - Method in class org.protempa.KnowledgeSourceCacheFactory
getInstance() - Static method in class org.protempa.NotRecordedSourceId
getInstance(String) - Static method in class org.protempa.proposition.DataSourceBackendId: Creates a data source backend id.
getInstance() - Method in class org.protempa.proposition.DefaultUniqueIdFactory
getInstance() - Static method in class org.protempa.proposition.DerivedSourceId
getInstance() - Method in class org.protempa.proposition.interval.AbsoluteTimeIntervalFactory
getInstance(Date, Granularity) - Method in class org.protempa.proposition.interval.AbsoluteTimeIntervalFactory
getInstance(Date, Granularity, Date, Granularity) - Method in class org.protempa.proposition.interval.AbsoluteTimeIntervalFactory
getInstance(Date, Date, Granularity, Date, Date, Granularity) - Method in class org.protempa.proposition.interval.AbsoluteTimeIntervalFactory
getInstance(Long, Long, Granularity, Long, Long, Granularity) - Method in class org.protempa.proposition.interval.IntervalFactory: Returns an interval specified by the given minimum start, maximum start, minimum finish and maximum finish and corresponding granularities.
getInstance(Long, Granularity, Long, Granularity) - Method in class org.protempa.proposition.interval.IntervalFactory: Returns at interval specified by the given start and finish and granularities.
getInstance(Long, Granularity) - Method in class org.protempa.proposition.interval.IntervalFactory: Returns an interval representing a position on the timeline or other axis at a specified granularity.
getInstance() - Method in class org.protempa.proposition.interval.IntervalFactory: Returns an unbounded interval.
getInstance() - Method in class org.protempa.proposition.ProviderBasedUniqueIdFactory
getInstance(String, String, String) - Method in class org.protempa.proposition.TemporalAbstractParameterFactory
getInstance(String, Date, Date) - Method in class org.protempa.proposition.TemporalAbstractParameterFactory
getInstance(String, String, SourceSystem) - Method in class org.protempa.proposition.TemporalEventFactory
getInstance(String, Date, SourceSystem) - Method in class org.protempa.proposition.TemporalEventFactory
getInstance(String, String, String, SourceSystem) - Method in class org.protempa.proposition.TemporalEventFactory
getInstance(String, Date, Date, SourceSystem) - Method in class org.protempa.proposition.TemporalEventFactory
getInstance(String, String, SourceSystem) - Method in class org.protempa.proposition.TemporalPrimitiveParameterFactory
getInstance(String, String, Value, SourceSystem) - Method in class org.protempa.proposition.TemporalPrimitiveParameterFactory
getInstance(String, Date, SourceSystem) - Method in class org.protempa.proposition.TemporalPrimitiveParameterFactory
getInstance() - Method in interface org.protempa.proposition.UniqueIdFactory
getInstance(Date) - Static method in class org.protempa.proposition.value.DateValue: Constructs a new date value from a Java date object.
getInstance() - Static method in class org.protempa.proposition.value.DateValue: Constructs a new date value representing the current time.
getInstance(String) - Static method in class org.protempa.proposition.value.NominalValue: Creates a new nominal value.
getInstance(double) - Static method in class org.protempa.proposition.value.NumberValue: Gets an instance of NumberValue representing a double.
getInstance(long) - Static method in class org.protempa.proposition.value.NumberValue
getInstance(BigDecimal) - Static method in class org.protempa.proposition.value.NumberValue
getInstance(V...) - Static method in class org.protempa.proposition.value.ValueList: Creates a list of the provided elements in the same order.
getInstance(E) - Method in interface org.protempa.SourceIdFactory
getInterpretationContext() - Method in class org.protempa.CompoundLowLevelAbstractionDefinition
getInterval() - Method in class org.protempa.proposition.CompoundInterval: Gets the interval for this compound interval.
getInterval() - Method in class org.protempa.proposition.Segment
getInterval() - Method in class org.protempa.proposition.TemporalProposition: The range of time over which this parameter's value is true.
getInValueType() - Method in class org.protempa.AbstractAlgorithm
getInValueType() - Method in interface org.protempa.Algorithm
getInverseIsA() - Method in class org.protempa.AbstractPropositionDefinition
getInverseIsA() - Method in interface org.protempa.PropositionDefinition: Returns the ids of the proposition definitions that have an is-a relationship with this proposition definition.
getInverseIsA() - Method in class org.protempa.Term: Returns a newly-created array of the ids of the terms with which this term has an inverse is-a relationship.
getKey(String) - Method in interface org.protempa.dest.deid.CipherDeidConfig: Returns a secret key used for de-identification.
getKeyAlgorithm() - Method in interface org.protempa.dest.deid.CipherDeidConfig
getKeyId() - Method in class org.protempa.DataStreamingEvent
getKeyId() - Method in class org.protempa.QueryResults.QueryResultsEntry
getKeyIdComparator() - Method in class org.protempa.backend.dsb.AbstractDataSourceBackend
getKeyIdComparator() - Method in interface org.protempa.backend.dsb.DataSourceBackend
getKeyIds() - Method in class org.protempa.query.DefaultQueryBuilder: Returns the key ids to be queried.
getKeyIds() - Method in class org.protempa.query.Query: Returns the key ids to be queried.
getKeyIds() - Method in class org.protempa.QueryResults
getKeyType() - Method in class org.protempa.backend.AbstractCommonsDataSourceBackend
getKeyType() - Method in class org.protempa.backend.dsb.AbstractDataSourceBackend
getKeyType() - Method in interface org.protempa.backend.dsb.DataSourceBackend
getKeyType() - Method in interface org.protempa.DataSource: Returns a string representing the type of keys in this data source (e.g., patient, case).
getKeyType() - Method in class org.protempa.DataSourceImpl: Returns a string representing the type of keys in this data source (e.g., patient, case).
getKeyTypeDisplayName() - Method in class org.protempa.backend.dsb.AbstractDataSourceBackend
getKeyTypeDisplayName() - Method in interface org.protempa.backend.dsb.DataSourceBackend
getKeyTypeDisplayName() - Method in interface org.protempa.DataSource: Returns a string representing the type of keys in this data source (e.g., patient, case) for display purposes.
getKeyTypeDisplayName() - Method in class org.protempa.DataSourceImpl: Returns a string representing the type of keys in this data source (e.g., patient, case) for display purposes.
getKeyTypePluralDisplayName() - Method in class org.protempa.backend.dsb.AbstractDataSourceBackend
getKeyTypePluralDisplayName() - Method in interface org.protempa.backend.dsb.DataSourceBackend
getKeyTypePluralDisplayName() - Method in interface org.protempa.DataSource: Returns a plural string representing the type of keys in this data source (e.g., patient, case) for display purposes.
getKeyTypePluralDisplayName() - Method in class org.protempa.DataSourceImpl: Returns a plural string representing the type of keys in this data source (e.g., patient, case) for display purposes.
getKnowledgeSource() - Method in class org.protempa.Protempa: Gets the knowledge source.
getKnowledgeSourceBackendInstanceSpecs() - Method in class org.protempa.backend.ConfigurationsSupport
getKnowledgeSourceBackendSections() - Method in class org.protempa.backend.Configuration
getKnowledgeSourceBackendSpecLoader() - Method in interface org.protempa.backend.BackendProvider
getKnowledgeSourceBackendSpecLoader() - Static method in class org.protempa.backend.BackendProviderManager
getKnowledgeSourceBackendSpecLoader() - Method in class org.protempa.backend.test.MockBackendProvider
getKnowledgeSourceSearchResults(String) - Method in interface org.protempa.backend.ksb.KnowledgeSourceBackend
getKnowledgeSourceSearchResults(String) - Method in class org.protempa.backend.ksb.SimpleKnowledgeSourceBackend
getLastIndex() - Method in class org.protempa.proposition.Segment
getLength() - Method in class org.protempa.proposition.value.AbstractTimeUnit
getLength() - Method in class org.protempa.proposition.value.RelativeDayGranularity
getLength() - Method in class org.protempa.proposition.value.RelativeHourGranularity
getLengthFormattedLong() - Method in class org.protempa.proposition.TemporalProposition
getLengthFormattedMedium() - Method in class org.protempa.proposition.TemporalProposition
getLengthFormattedShort() - Method in class org.protempa.proposition.TemporalProposition
getLengthHeading() - Method in class org.protempa.dest.table.OutputConfig
getLengthHeading() - Method in class org.protempa.dest.table.OutputConfigBuilder
getLengthUnit() - Method in class org.protempa.proposition.interval.Interval: Gets the units of the length.
getLine() - Method in class org.protempa.backend.dsb.DataValidationEvent
getLinks() - Method in class org.protempa.dest.table.AtLeastNColumnSpec
getLinks() - Method in class org.protempa.dest.table.CountColumnSpec
getLinks() - Method in class org.protempa.dest.table.DistanceBetweenColumnSpec
getLinks() - Method in class org.protempa.dest.table.PropositionColumnSpec
getLinks() - Method in class org.protempa.dest.table.PropositionValueColumnSpec
getLocalUniqueId() - Method in class org.protempa.proposition.UniqueId
getLongDateFormatNoYear() - Method in class org.protempa.proposition.value.AbsoluteTimeGranularity
getLongFormat() - Method in class org.protempa.proposition.value.AbsoluteTimeGranularity
getLongFormat() - Method in class org.protempa.proposition.value.AbstractTimeUnit
getLongFormat() - Method in interface org.protempa.proposition.value.Granularity
getLongFormat() - Method in class org.protempa.proposition.value.RelativeDayGranularity
getLongFormat() - Method in class org.protempa.proposition.value.RelativeHourGranularity
getLongFormat() - Method in interface org.protempa.proposition.value.Unit
getLowerBound() - Method in class org.protempa.valueset.ValueSet: Gets the lower bound of this value set, if specified.
getLowerBoundBuilder() - Method in class org.protempa.valueset.ValueSetBuilder
getLowLevelAbstractionDefinition() - Method in class org.protempa.LowLevelAbstractionValueDefinition
getLowLevelAbstractionId() - Method in class org.protempa.ValueClassification
getLowLevelAbstractionIds() - Method in class org.protempa.CompoundLowLevelAbstractionDefinition: Gets the IDs of the low-level abstraction that this abstraction is abstracted from.
getLowLevelAbstractionValue() - Method in class org.protempa.ValueClassification
getMatchingPropositionDefinitions(String) - Method in interface org.protempa.KnowledgeSource
getMatchingPropositionDefinitions(String) - Method in class org.protempa.KnowledgeSourceImpl: Gets the proposition Definitions from each backend that match the searchKey
getMaxDistanceBetween() - Method in class org.protempa.proposition.interval.Relation
getMaxDistanceBetweenFinishes() - Method in class org.protempa.proposition.interval.Relation
getMaxDistanceBetweenFinishesUnits() - Method in class org.protempa.proposition.interval.Relation
getMaxDistanceBetweenStarts() - Method in class org.protempa.proposition.interval.Relation
getMaxDistanceBetweenStartsUnits() - Method in class org.protempa.proposition.interval.Relation
getMaxDistanceBetweenUnits() - Method in class org.protempa.proposition.interval.Relation
getMaxFinish() - Method in class org.protempa.proposition.interval.Interval: Gets the maximum finish in the current finish granularity.
getMaximumDuration() - Method in class org.protempa.LowLevelAbstractionDefinition
getMaximumDurationUnits() - Method in class org.protempa.LowLevelAbstractionDefinition
getMaximumFinish() - Method in class org.protempa.backend.dsb.filter.PositionFilter: Returns the maximum finish position in Protempa's Long representation.
getMaximumFinish() - Method in class org.protempa.proposition.interval.DefaultInterval: ************************************************************************* MAXIMUM START
getMaximumFinish() - Method in class org.protempa.proposition.interval.Interval: Gets the maximum finish in internal PROTEMPA units.
getMaximumGap() - Method in class org.protempa.MinMaxGapFunction
getMaximumGap() - Method in class org.protempa.SimpleGapFunction: Returns the gap function's maximum gap value.
getMaximumGapBetweenValues() - Method in class org.protempa.LowLevelAbstractionDefinition
getMaximumGapBetweenValuesUnits() - Method in class org.protempa.LowLevelAbstractionDefinition
getMaximumGapUnit() - Method in class org.protempa.MinMaxGapFunction
getMaximumGapUnit() - Method in class org.protempa.SimpleGapFunction: Returns the units of the maximum gap value.
getMaximumLength() - Method in class org.protempa.proposition.interval.DefaultInterval: ************************************************************************* MAXIMUM DURATION
getMaximumLength() - Method in class org.protempa.proposition.interval.Interval: Gets the maximum length in internal PROTEMPA units.
getMaximumNumberOfValues() - Method in class org.protempa.AbstractAlgorithm
getMaximumNumberOfValues() - Method in interface org.protempa.Algorithm: Gets the default maximum sliding window width.
getMaximumNumberOfValues() - Method in class org.protempa.LowLevelAbstractionDefinition
getMaximumStart() - Method in class org.protempa.backend.dsb.filter.PositionFilter: Returns the maximum start position in Protempa's Long representation.
getMaximumStart() - Method in class org.protempa.proposition.interval.DefaultInterval: ************************************************************************* MAXIMUM START
getMaximumStart() - Method in class org.protempa.proposition.interval.Interval: Gets the maximum start in internal PROTEMPA units.
getMaxIndex() - Method in class org.protempa.SliceDefinition: Gets the upper limit of the range for this slice (exclusive).
getMaxLength() - Method in class org.protempa.proposition.interval.Interval: Gets the maximum length in the finest granularity of those defined for the start and finish.
getMaxLength() - Method in class org.protempa.TemporalExtendedPropositionDefinition
getMaxLengthUnit() - Method in class org.protempa.TemporalExtendedPropositionDefinition
getMaxOverlapping() - Method in class org.protempa.LowLevelAbstractionDefinition: Return the value of the max-overlapping restart search directive.
getMaxSpan() - Method in class org.protempa.proposition.interval.Relation
getMaxSpanUnits() - Method in class org.protempa.proposition.interval.Relation
getMaxStart() - Method in class org.protempa.proposition.interval.Interval: Gets the maximum start in the current start granularity.
getMediumDateFormatNoYear() - Method in class org.protempa.proposition.value.AbsoluteTimeGranularity
getMediumFormat() - Method in class org.protempa.proposition.value.AbsoluteTimeGranularity
getMediumFormat() - Method in class org.protempa.proposition.value.AbstractTimeUnit
getMediumFormat() - Method in interface org.protempa.proposition.value.Granularity
getMediumFormat() - Method in class org.protempa.proposition.value.RelativeDayGranularity
getMediumFormat() - Method in class org.protempa.proposition.value.RelativeHourGranularity
getMediumFormat() - Method in interface org.protempa.proposition.value.Unit
getMessage() - Method in class org.protempa.backend.dsb.DataValidationEvent
getMinDistanceBetween() - Method in class org.protempa.proposition.interval.Relation
getMinDistanceBetweenFinishes() - Method in class org.protempa.proposition.interval.Relation
getMinDistanceBetweenFinishesUnits() - Method in class org.protempa.proposition.interval.Relation
getMinDistanceBetweenStarts() - Method in class org.protempa.proposition.interval.Relation
getMinDistanceBetweenStartsUnits() - Method in class org.protempa.proposition.interval.Relation
getMinDistanceBetweenUnits() - Method in class org.protempa.proposition.interval.Relation
getMinFinish() - Method in class org.protempa.proposition.interval.Interval: Gets the minimum finish in the current finish granularity.
getMinimumDuration() - Method in class org.protempa.LowLevelAbstractionDefinition
getMinimumDurationUnits() - Method in class org.protempa.LowLevelAbstractionDefinition
getMinimumFinish() - Method in class org.protempa.backend.dsb.filter.PositionFilter: Returns the minimum finish position in Protempa's Long representation.
getMinimumFinish() - Method in class org.protempa.proposition.interval.DefaultInterval: ************************************************************************* MINIMUM FINISH
getMinimumFinish() - Method in class org.protempa.proposition.interval.Interval: Gets the minimum finish in internal PROTEMPA units.
getMinimumGap() - Method in class org.protempa.MinMaxGapFunction
getMinimumGapBetweenValues() - Method in class org.protempa.LowLevelAbstractionDefinition
getMinimumGapBetweenValuesUnits() - Method in class org.protempa.LowLevelAbstractionDefinition
getMinimumGapUnit() - Method in class org.protempa.MinMaxGapFunction
getMinimumLength() - Method in class org.protempa.proposition.interval.DefaultInterval: ************************************************************************* MINIMUM DURATION
getMinimumLength() - Method in class org.protempa.proposition.interval.Interval: Gets the minimum length in internal PROTEMPA units.
getMinimumNumberOfValues() - Method in class org.protempa.AbstractAlgorithm
getMinimumNumberOfValues() - Method in interface org.protempa.Algorithm: Gets the default minimum sliding window width.
getMinimumNumberOfValues() - Method in class org.protempa.CompoundLowLevelAbstractionDefinition: Gets the minimum number of consecutive intervals that must have the same value before this abstraction is asserted.
getMinimumNumberOfValues() - Method in class org.protempa.LowLevelAbstractionDefinition
getMinimumStart() - Method in class org.protempa.backend.dsb.filter.PositionFilter: Returns the minimum start position in Protempa's Long representation.
getMinimumStart() - Method in class org.protempa.proposition.interval.DefaultInterval: ************************************************************************* MINIMUM START
getMinimumStart() - Method in class org.protempa.proposition.interval.Interval: Gets the minimum start in internal PROTEMPA units.
getMinIndex() - Method in class org.protempa.SliceDefinition: Gets the lower limit of the range for this slice (inclusive).
getMinLength() - Method in class org.protempa.proposition.interval.Interval: Gets the minimum length in the finest granularity of those defined for the start and finish.
getMinLength() - Method in class org.protempa.TemporalExtendedPropositionDefinition
getMinLengthUnit() - Method in class org.protempa.TemporalExtendedPropositionDefinition
getMinSpan() - Method in class org.protempa.proposition.interval.Relation
getMinSpanUnits() - Method in class org.protempa.proposition.interval.Relation
getMinStart() - Method in class org.protempa.proposition.interval.Interval: Gets the minimum start in the current start granularity.
getN() - Method in class org.protempa.dest.table.AtLeastNColumnSpec
getName() - Method in class org.protempa.AlgorithmParameter: Returns the name of this parameter.
getName() - Method in class org.protempa.Attribute
getName() - Method in class org.protempa.AttributeBuilder
getName() - Method in class org.protempa.backend.BackendPropertySpec
getName() - Method in class org.protempa.cli.CLI.Argument: Returns the argument's name.
getName() - Method in class org.protempa.datastore.UniqueIdUniqueIdStoreCreator.Reference
getName() - Method in class org.protempa.proposition.value.AbsoluteTimeGranularity
getName() - Method in class org.protempa.proposition.value.AbstractTimeUnit
getName() - Method in interface org.protempa.proposition.value.Granularity: Returns the granularity's singular name.
getName() - Method in class org.protempa.proposition.value.RelativeDayGranularity
getName() - Method in class org.protempa.proposition.value.RelativeHourGranularity
getName() - Method in interface org.protempa.proposition.value.Unit: Returns the unit's singular name.
getName() - Method in class org.protempa.query.DefaultQueryBuilder
getName() - Method in class org.protempa.query.Query: Returns this query's identifier.
getName() - Method in class org.protempa.Terminology
getNumber() - Method in class org.protempa.proposition.value.InequalityNumberValue
getNumber() - Method in class org.protempa.proposition.value.NumberValue
getNumber() - Method in interface org.protempa.proposition.value.NumericalValue: Gets this value as a number.
getNumberOfKeys() - Method in class org.protempa.dest.DefaultStatistics
getNumberOfKeys() - Method in class org.protempa.dest.DefaultStatisticsBuilder
getNumberOfKeys() - Method in interface org.protempa.dest.Statistics
getNumberValue() - Method in class org.protempa.proposition.value.InequalityNumberValue
getNumberValue() - Method in class org.protempa.proposition.value.NumberValue
getNumberValue() - Method in interface org.protempa.proposition.value.NumericalValue: Gets the number value component of this numerical value.
getNumericalId() - Method in class org.protempa.proposition.DefaultLocalUniqueId
getNumericalId() - Method in interface org.protempa.proposition.LocalUniqueId: Gets a number that is to unique to the proposition for all propositions for a keyid with the same proposition id.
getNumericalId() - Method in interface org.protempa.proposition.LocalUniqueIdValuesProvider
getNumericalId() - Method in class org.protempa.proposition.ProviderBasedLocalUniqueId
getNumInstances() - Method in class org.protempa.dest.table.PropositionColumnSpec
getOffset() - Method in class org.protempa.ContextDefinition: Returns the start and finish of an interval of this context relative to its inducing interval.
getOffset(String) - Method in interface org.protempa.dest.deid.DeidConfig
getOutputConfig() - Method in class org.protempa.dest.table.PropositionColumnSpec
getParameterComp(String) - Method in class org.protempa.LowLevelAbstractionValueDefinition
getParameterComps() - Method in class org.protempa.LowLevelAbstractionValueDefinition
getParameters() - Method in class org.protempa.AbstractAlgorithm
getParameters() - Method in interface org.protempa.Algorithm
getParameters() - Method in class org.protempa.LowLevelAbstractionValueDefinition
getParameterValue(String) - Method in class org.protempa.LowLevelAbstractionValueDefinition
getPersistentStore() - Method in interface org.protempa.datastore.DataStoreCreator: Returns a permanent store with the given name.
getPersistentStore() - Method in class org.protempa.datastore.PropositionStoreCreator
getPersistentStore() - Method in class org.protempa.datastore.UniqueIdUniqueIdStoreCreator
getPersistentStore() - Method in class org.protempa.datastore.WorkingMemoryStoreCreator
getPluralName() - Method in class org.protempa.proposition.value.AbsoluteTimeGranularity
getPluralName() - Method in class org.protempa.proposition.value.AbstractTimeUnit
getPluralName() - Method in interface org.protempa.proposition.value.Granularity: Returns the granularity's plural name.
getPluralName() - Method in class org.protempa.proposition.value.RelativeDayGranularity
getPluralName() - Method in class org.protempa.proposition.value.RelativeHourGranularity
getPluralName() - Method in interface org.protempa.proposition.value.Unit: Returns the unit's plural name.
getPoint() - Method in exception org.protempa.proposition.stats.RegressionLine.NullValueException
getPosition() - Method in class org.protempa.proposition.PrimitiveParameter: Returns this parameter's timestamp (or other kind of position value).
getPositionFormattedLong() - Method in class org.protempa.proposition.PrimitiveParameter: Returns this parameter's timestamp as a long formatted string.
getPositionFormattedMedium() - Method in class org.protempa.proposition.PrimitiveParameter: Returns this parameter's timestamp as a medium-length formatted string.
getPositionFormattedShort() - Method in class org.protempa.proposition.PrimitiveParameter: Returns this parameter's timestamp as a short formatted string.
getProperty(String) - Method in class org.protempa.backend.BackendInstanceSpec
getProperty() - Method in class org.protempa.backend.dsb.filter.PropertyValueFilter: Gets the name of the specified property.
getProperty(String) - Method in class org.protempa.proposition.AbstractProposition
getProperty(String) - Method in interface org.protempa.proposition.Proposition: Gets the value of the specified property.
getPropertyConstraints() - Method in class org.protempa.ExtendedPropositionDefinition
getPropertyDefinitions() - Method in class org.protempa.AbstractPropositionDefinition
getPropertyDefinitions() - Method in interface org.protempa.PropositionDefinition
getPropertyName() - Method in class org.protempa.dest.table.PropertyConstraint: Returns the name of the property.
getPropertyName() - Method in class org.protempa.PropertyConstraint
getPropertyNames() - Method in class org.protempa.backend.BackendInstanceSpec
getPropertyNames() - Method in class org.protempa.dest.table.PropositionColumnSpec
getPropertyNames() - Method in class org.protempa.proposition.AbstractProposition
getPropertyNames() - Method in interface org.protempa.proposition.Proposition: Get the property names for the proposition
getPropertySpecs() - Method in class org.protempa.backend.BackendSpec
getPropertyValueAbbrevDisplayName() - Method in class org.protempa.dest.table.ValueOutputConfig
getPropertyValueAbbrevDisplayName() - Method in class org.protempa.dest.table.ValueOutputConfigBuilder
getPropertyValueDisplayName() - Method in class org.protempa.dest.table.ValueOutputConfig
getPropertyValueDisplayName() - Method in class org.protempa.dest.table.ValueOutputConfigBuilder
getPropId() - Method in class org.protempa.PropertyDefinition
getPropId() - Method in class org.protempa.PropertyDefinitionBuilder
getProposition() - Method in class org.protempa.UniqueIdPair
getPropositionDefinitions() - Method in class org.protempa.query.DefaultQueryBuilder: Returns an optional set of user-specified proposition definitions.
getPropositionDefinitions() - Method in class org.protempa.query.Query: Returns an optional set of user-specified proposition definitions.
getPropositionDefinitionsByTerm(And<TermSubsumption>) - Method in interface org.protempa.KnowledgeSource: Gets the mappings from term IDs to proposition IDs for each backend.
getPropositionDefinitionsByTerm(And<TermSubsumption>) - Method in class org.protempa.KnowledgeSourceImpl: Gets the mappings from term IDs to proposition IDs for each backend.
getPropositionId() - Method in class org.protempa.AbstractPropositionDefinition
getPropositionId() - Method in class org.protempa.ExtendedPropositionDefinition
getPropositionId() - Method in interface org.protempa.PropositionDefinition: The proposition id of propositions derived by this proposition definition.
getPropositionIds() - Method in class org.protempa.backend.dsb.filter.AbstractFilter
getPropositionIds() - Method in interface org.protempa.backend.dsb.filter.Filter: Returns the proposition ids for which this filter is valid.
getPropositionIds() - Method in class org.protempa.dest.table.Link: The ids of the propositions to traverse to.
getPropositionIds() - Method in class org.protempa.proposition.Sequence
getPropositionIds() - Method in class org.protempa.query.DefaultQueryBuilder: Returns the proposition ids to be queried.
getPropositionIds() - Method in class org.protempa.query.Query: Returns the proposition ids to be queried.
getPropositionIds() - Method in class org.protempa.ReferenceDefinition: Gets the allowed proposition ids for this reference.
getPropositionIdsSpecified() - Method in interface org.protempa.dest.keyloader.Criteria
getPropositionProperties() - Method in class org.protempa.dest.xml.XmlPropositionVisitor
getPropositions() - Method in class org.protempa.QueryResults.QueryResultsEntry
getPropositionsByTerm(String) - Method in class org.protempa.backend.ksb.AbstractKnowledgeSourceBackend: A default implementation that returns an empty list.
getPropositionsByTerm(String) - Method in interface org.protempa.backend.ksb.KnowledgeSourceBackend: Gets the proposition definitions for a given term.
getPropositionsByTermSubsumption(And<TermSubsumption>) - Method in class org.protempa.backend.ksb.AbstractKnowledgeSourceBackend: A default implementation that returns an empty List.
getPropositionsByTermSubsumption(And<TermSubsumption>) - Method in interface org.protempa.backend.ksb.KnowledgeSourceBackend: Gets the proposition definitions that are associated with the given AND clause of term subsumptions.
getPropositionValues() - Method in class org.protempa.dest.xml.XmlPropositionVisitor
getPropositionVisitor() - Method in class org.protempa.dest.table.PropositionColumnSpec
getProtempaSource() - Method in class org.protempa.AlgorithmSourceUpdatedEvent
getProtempaSource() - Method in class org.protempa.DataSourceUpdatedEvent
getProtempaSource() - Method in class org.protempa.KnowledgeSourceUpdatedEvent
getProtempaSource() - Method in class org.protempa.SourceClosedUnexpectedlyEvent: Returns the Source that closed unexpectedly.
getProtempaSource() - Method in class org.protempa.SourceUpdatedEvent: Returns the source Source (the same as what getSource() returns).
getProtempaSource() - Method in class org.protempa.TermSourceUpdatedEvent
getQuery() - Method in class org.protempa.QuerySession: Gets the initial query.
getQueryId() - Method in exception org.protempa.QueryException
getQueryMode() - Method in class org.protempa.query.DefaultQueryBuilder
getQueryMode() - Method in class org.protempa.query.Query
getQueryResultsHandler(Query, DataSource, KnowledgeSource) - Method in class org.protempa.dest.deid.DeidentifiedDestination
getQueryResultsHandler(Query, DataSource, KnowledgeSource) - Method in interface org.protempa.dest.Destination: Performs any initialization required for the query results handler's configuration.
getQueryResultsHandler(Query, DataSource, KnowledgeSource) - Method in class org.protempa.dest.keyloader.KeyLoaderDestination
getQueryResultsHandler(Query, DataSource, KnowledgeSource) - Method in class org.protempa.dest.map.MapDestination
getQueryResultsHandler(Query, DataSource, KnowledgeSource) - Method in class org.protempa.dest.proplist.PropositionListDestination
getQueryResultsHandler(Query, DataSource, KnowledgeSource) - Method in class org.protempa.dest.table.TableDestination
getQueryResultsHandler(Query, DataSource, KnowledgeSource) - Method in class org.protempa.dest.xml.XmlDestination
getReference() - Method in class org.protempa.UniqueIdPair
getReferenceDefinitions() - Method in class org.protempa.AbstractPropositionDefinition
getReferenceDefinitions() - Method in interface org.protempa.PropositionDefinition
getReferenceName() - Method in class org.protempa.UniqueIdPair
getReferenceNames() - Method in class org.protempa.dest.table.Reference: Gets the names of the reference(s) to be traversed.
getReferenceNames() - Method in class org.protempa.proposition.AbstractProposition
getReferenceNames() - Method in interface org.protempa.proposition.Proposition: Get the reference names for the proposition
getReferences(String) - Method in class org.protempa.proposition.AbstractProposition
getReferences(String) - Method in interface org.protempa.proposition.Proposition: Gets the global unique identifiers for the propositions that have the specified 1:N relationship with this proposition.
getReferences(Proposition, String) - Method in class org.protempa.QuerySession: Gets the references for a proposition with the specified reference name.
getRelatedTemporalExtendedPropositionDefinition() - Method in class org.protempa.SequentialTemporalPatternDefinition.SubsequentTemporalExtendedPropositionDefinition
getRelation() - Method in class org.protempa.dest.table.Derivation
getRelation(TemporalExtendedPropositionDefinition, TemporalExtendedPropositionDefinition) - Method in class org.protempa.HighLevelAbstractionDefinition: Gets the relation between two temporal extended proposition definitions.
getRelation(List<TemporalExtendedPropositionDefinition>) - Method in class org.protempa.HighLevelAbstractionDefinition
getRelation() - Method in class org.protempa.SequentialTemporalPatternDefinition.SubsequentTemporalExtendedPropositionDefinition
getReprFormat() - Method in class org.protempa.proposition.value.AbsoluteTimeGranularity
getResultMap() - Method in class org.protempa.dest.map.MapQueryResultsHandler: Gets the map of query results that have been handled.
getRMSError() - Method in class org.protempa.proposition.stats.RegressionLine: Returns the r.m.s.
getRowPropositionIds() - Method in class org.protempa.dest.table.TableDestination
getSalt(String) - Method in interface org.protempa.dest.deid.MessageDigestDeidConfig
getSelectedKeySetSpecs() - Method in class org.protempa.backend.dsb.AbstractDataSourceBackend
getSelectedKeySetSpecs() - Method in interface org.protempa.backend.dsb.DataSourceBackend
getSelectedKeySetSpecs() - Method in interface org.protempa.DataSource
getSelectedKeySetSpecs() - Method in class org.protempa.DataSourceImpl
getSemanticType() - Method in class org.protempa.Term
getSequence() - Method in class org.protempa.proposition.Segment
getShellCommand() - Method in class org.protempa.cli.CLI: Gets the shell command.
getShortDateFormatNoYear() - Method in class org.protempa.proposition.value.AbsoluteTimeGranularity
getShortDisplayName() - Method in class org.protempa.ExtendedPropositionDefinition
getShortFormat() - Method in class org.protempa.proposition.value.AbsoluteTimeGranularity
getShortFormat() - Method in class org.protempa.proposition.value.AbstractTimeUnit
getShortFormat() - Method in interface org.protempa.proposition.value.Granularity
getShortFormat() - Method in class org.protempa.proposition.value.RelativeDayGranularity
getShortFormat() - Method in class org.protempa.proposition.value.RelativeHourGranularity
getShortFormat() - Method in interface org.protempa.proposition.value.Unit
getSkip() - Method in class org.protempa.CompoundLowLevelAbstractionDefinition
getSkip() - Method in class org.protempa.LowLevelAbstractionDefinition: Return the value of the skip restart search directive.
getSkipEnd() - Method in class org.protempa.LowLevelAbstractionDefinition: Return the value of the skip-end restart search directive.
getSkipStart() - Method in class org.protempa.LowLevelAbstractionDefinition: Return the value of the skip-start restart search directive.
getSlidingWindowWidthMode() - Method in class org.protempa.LowLevelAbstractionDefinition: Gets the sliding window width mode.
getSourceId() - Method in class org.protempa.AbstractPropositionDefinition
getSourceId() - Method in class org.protempa.proposition.UniqueId
getSourceId() - Method in interface org.protempa.PropositionDefinition
getSourceId() - Method in class org.protempa.valueset.ValueSet: Returns the source of this value set.
getSourceIdBuilder() - Method in class org.protempa.valueset.ValueSetBuilder
getSourceIdStr() - Method in class org.protempa.DefaultSourceIdBuilder
getSourceSystem() - Method in class org.protempa.backend.dsb.AbstractDataSourceBackend
getSourceSystem() - Method in interface org.protempa.backend.dsb.DataSourceBackend
getSourceSystem() - Method in class org.protempa.KeySetSpec
getSourceSystem() - Method in class org.protempa.proposition.AbstractProposition
getSourceSystem() - Method in interface org.protempa.proposition.Proposition: Returns the data source type of the Proposition.
getStart() - Method in class org.protempa.backend.dsb.filter.PositionFilter: Returns the start position supplied in the constructor.
getStart() - Method in class org.protempa.graph.Edge
getStartAbstractParamValue() - Method in class org.protempa.TemporalPatternOffset
getStartFormattedLong() - Method in class org.protempa.proposition.TemporalProposition: Returns the earliest valid time of this proposition as a long string.
getStartFormattedMedium() - Method in class org.protempa.proposition.TemporalProposition: Returns the earliest valid time of this proposition as a medium-length string.
getStartFormattedShort() - Method in class org.protempa.proposition.TemporalProposition: Returns the earliest valid time of this proposition as a short string.
getStartGranularity() - Method in class org.protempa.backend.dsb.filter.PositionFilter: Returns the Granularity with which to interpret the start position.
getStartGranularity() - Method in class org.protempa.proposition.interval.Interval: Gets the start granularity.
getStartGranularity() - Method in class org.protempa.proposition.Segment
getStartIntervalSide() - Method in class org.protempa.ContextOffset
getStartIntervalSide() - Method in class org.protempa.TemporalPatternOffset
getStartOffset() - Method in class org.protempa.ContextOffset
getStartOffset() - Method in class org.protempa.TemporalPatternOffset
getStartOffsetUnits() - Method in class org.protempa.ContextOffset
getStartOffsetUnits() - Method in class org.protempa.TemporalPatternOffset
getStartOrTimestampHeading() - Method in class org.protempa.dest.table.OutputConfig
getStartOrTimestampHeading() - Method in class org.protempa.dest.table.OutputConfigBuilder
getStartSide() - Method in class org.protempa.backend.dsb.filter.PositionFilter: Returns the side of the proposition to which to apply the lower bound.
getStartTemporalExtendedPropositionDefinition() - Method in class org.protempa.TemporalPatternOffset
getStatistics() - Method in class org.protempa.dest.AbstractDestination
getStatistics() - Method in class org.protempa.dest.deid.DeidentifiedDestination
getStatistics() - Method in interface org.protempa.dest.Destination: Returns an instance that can be used to discover information about previous runs of data.
getString() - Method in class org.protempa.proposition.value.NominalValue: Gets the value as a Java String.
getStringRepresentation() - Method in class org.protempa.DataSourceBackendSourceSystem
getStringRepresentation() - Method in class org.protempa.DefaultSourceId
getStringRepresentation() - Method in class org.protempa.NotRecordedSourceId
getStringRepresentation() - Method in class org.protempa.proposition.UniqueId
getStringRepresentation() - Method in interface org.protempa.SourceId
getStringRepresentation() - Method in class org.protempa.SourceSystem
getSubContexts() - Method in class org.protempa.ContextDefinition: Returns the ids of other context definitions that, together with this one, have a specific meaning when their intervals intersect.
getSubsequentTemporalExtendedPropositionDefinitions() - Method in class org.protempa.SequentialTemporalPatternDefinition
getSubsumption(String) - Method in class org.protempa.backend.tsb.AbstractTermSourceBackend: A default implementation that returns null
getSubsumption(String) - Method in interface org.protempa.backend.tsb.TermSourceBackend: Retrieves all of the descendants of the term specified by the given ID.
getSupportedPropositionIds(DataSource, KnowledgeSource) - Method in class org.protempa.dest.AbstractDestination
getSupportedPropositionIds(DataSource, KnowledgeSource) - Method in class org.protempa.dest.deid.DeidentifiedDestination
getSupportedPropositionIds(DataSource, KnowledgeSource) - Method in interface org.protempa.dest.Destination: Infers from the query results handler's specification what propositions this query results handler supports in its output.
getSupportedPropositionIds(DataSource, KnowledgeSource) - Method in class org.protempa.dest.keyloader.KeyLoaderDestination
getSupportedPropositionIds(DataSource, KnowledgeSource) - Method in class org.protempa.dest.table.TableDestination: Infers a list of propositions to populate all of the specified columns.
getSupportedPropositionIds(DataSource, KnowledgeSource) - Method in class org.protempa.dest.xml.XmlDestination: Returns the proposition ids specified in the constructor.
getSupportedPropositionIds(Destination) - Method in class org.protempa.Protempa
GetSupportedPropositionIdsException - Exception in org.protempa.dest
GetSupportedPropositionIdsException() - Constructor for exception org.protempa.dest.GetSupportedPropositionIdsException
GetSupportedPropositionIdsException(String, Throwable) - Constructor for exception org.protempa.dest.GetSupportedPropositionIdsException
GetSupportedPropositionIdsException(String) - Constructor for exception org.protempa.dest.GetSupportedPropositionIdsException
GetSupportedPropositionIdsException(Throwable) - Constructor for exception org.protempa.dest.GetSupportedPropositionIdsException
getSurvivalCurveData() - Method in class org.protempa.proposition.stats.AbstractKaplanMeyer
getTemporalExtendedPropositionDefinitionPairs() - Method in class org.protempa.HighLevelAbstractionDefinition: Gets the temporal extended proposition definitions involved in relations as pairs.
getTemporalExtendedPropositionDefinitions() - Method in class org.protempa.SliceDefinition
getTemporalOffset() - Method in class org.protempa.HighLevelAbstractionDefinition
getTemporalOffset() - Method in class org.protempa.SequentialTemporalPatternDefinition
getTemporalPropositions() - Method in class org.protempa.proposition.CompoundInterval: Gets the abstract parameters that belong to this interval
getTermIds() - Method in class org.protempa.AbstractPropositionDefinition
getTermIds() - Method in interface org.protempa.PropositionDefinition: Gets the ids of the TermDefinitions associated with this proposition definition.
getTermIds() - Method in class org.protempa.query.DefaultQueryBuilder: Gets the term ids to be queried in disjunctive normal form.
getTermIds() - Method in class org.protempa.query.Query: Gets the term ids to be queried in disjunctive normal form.
getTerminology() - Method in class org.protempa.Term
getTerms() - Method in class org.protempa.TermSubsumption
getTermSource() - Method in class org.protempa.Protempa: Gets the term source.
getTermSourceBackendInstanceSpecs() - Method in class org.protempa.backend.ConfigurationsSupport
getTermSourceBackendSections() - Method in class org.protempa.backend.Configuration
getTermSourceBackendSpecLoader() - Method in interface org.protempa.backend.BackendProvider
getTermSourceBackendSpecLoader() - Static method in class org.protempa.backend.BackendProviderManager
getTermSourceBackendSpecLoader() - Method in class org.protempa.backend.test.MockBackendProvider
getTermSubsumption(String) - Method in interface org.protempa.TermSource: Gets the term subsumption for the given term ID.
getTermSubsumption(String) - Method in class org.protempa.TermSourceImpl: Gets the term subsumption for the given term ID.
getTimeFormat() - Method in class org.protempa.proposition.value.AbsoluteTimeGranularity
getTimestamp() - Method in class org.protempa.backend.dsb.DataValidationEvent
getToIndex() - Method in class org.protempa.dest.table.Link: The last index of the propositions of interest at the end of the traversal step exclusive, after applying the proposition id constraints, property constraints and a comparator.
getTrueOutput() - Method in class org.protempa.dest.table.AtLeastNColumnSpec
getType() - Method in class org.protempa.backend.BackendPropertySpec
getType() - Method in class org.protempa.backend.dsb.DataValidationEvent
getType() - Method in class org.protempa.dest.table.PropositionValueColumnSpec
getType() - Method in class org.protempa.proposition.value.BooleanValue
getType() - Method in class org.protempa.proposition.value.DateValue
getType() - Method in class org.protempa.proposition.value.InequalityNumberValue
getType() - Method in class org.protempa.proposition.value.NominalValue
getType() - Method in class org.protempa.proposition.value.NumberValue
getType() - Method in class org.protempa.proposition.value.OrdinalValue
getType() - Method in interface org.protempa.proposition.value.Value: Returns this object's type, guaranteed not null.
getType() - Method in class org.protempa.proposition.value.ValueList
getUniqueId() - Method in class org.protempa.datastore.UniqueIdUniqueIdStoreCreator.Reference
getUniqueId() - Method in class org.protempa.proposition.AbstractProposition
getUniqueId() - Method in interface org.protempa.proposition.Proposition: Gets this proposition's global unique identifier.
getUnitFactory() - Method in class org.protempa.backend.dsb.AbstractDataSourceBackend
getUnitFactory() - Method in interface org.protempa.backend.dsb.DataSourceBackend
getUnitFactory() - Method in interface org.protempa.DataSource: Returns the length units of returned data from this data source.
getUnitFactory() - Method in class org.protempa.DataSourceImpl: Returns the length units of returned data from this data source.
getUnits() - Method in class org.protempa.dest.table.DistanceBetweenColumnSpec
getUnits() - Method in class org.protempa.PrimitiveParameterDefinition: Returns the units for values of this primitive parameter.
getUnits() - Method in class org.protempa.proposition.value.AbsoluteTimeUnit
getUpdated() - Method in class org.protempa.AbstractPropositionDefinition
getUpdated() - Method in interface org.protempa.PropositionDefinition: Returns the timestamp of when this proposition definition was last updated, if the knowledge source backend maintains this information.
getUpdateDate() - Method in class org.protempa.proposition.AbstractProposition
getUpdateDate() - Method in interface org.protempa.proposition.Proposition: Gets the date this proposition was last updated in the source system, or for derived propositions, the date it was last updated through the temporal abstraction process.
getUpperBound() - Method in class org.protempa.valueset.ValueSet: Gets the upper bound of this value set, if specified.
getUpperBoundBuilder() - Method in class org.protempa.valueset.ValueSetBuilder
getURI() - Method in class org.protempa.backend.dsb.DataValidationEvent
getUsername() - Method in class org.protempa.query.DefaultQueryBuilder
getUsername() - Method in class org.protempa.query.Query
getVal() - Method in class org.protempa.proposition.value.InequalityNumberValueBuilder
getVal() - Method in class org.protempa.proposition.value.NominalValueBuilder
getVal() - Method in class org.protempa.proposition.value.NumberValueBuilder
getValidationEvents() - Method in exception org.protempa.backend.DataSourceBackendFailedDataValidationException
getValidationEvents() - Method in exception org.protempa.DataSourceFailedDataValidationException
getValidator() - Method in class org.protempa.backend.BackendPropertySpec
getValue() - Method in class org.protempa.Attribute
getValue() - Method in class org.protempa.backend.dsb.filter.ValueFilter
getValue() - Method in class org.protempa.dest.table.PropertyConstraint: Gets the value of the constraint.
getValue() - Method in class org.protempa.ExtendedParameterDefinition
getValue() - Method in class org.protempa.LowLevelAbstractionValueDefinition
getValue() - Method in class org.protempa.PropertyConstraint
getValue() - Method in interface org.protempa.proposition.Parameter: Gets the value of this parameter.
getValue() - Method in class org.protempa.proposition.TemporalParameter
getValue() - Method in class org.protempa.proposition.value.OrdinalValue: Returns the value.
getValue() - Method in class org.protempa.proposition.value.OrdinalValueBuilder
getValue() - Method in class org.protempa.TemporalExtendedParameterDefinition
getValue() - Method in class org.protempa.ValueClassification
getValue() - Method in class org.protempa.valueset.ValueSetElement: Returns the value.
getValueBuilder() - Method in class org.protempa.AttributeBuilder
getValueBuilder() - Method in class org.protempa.valueset.ValueSetElementBuilder
getValueClassifications() - Method in class org.protempa.CompoundLowLevelAbstractionDefinition
getValueComp() - Method in class org.protempa.PropertyConstraint
getValueComparator() - Method in class org.protempa.backend.dsb.filter.PropertyValueFilter: Gets the specified operator.
getValueComparator() - Method in class org.protempa.dest.table.PropertyConstraint: Gets the comparator of the constraint.
getValueDefinitionMatchOperator() - Method in class org.protempa.CompoundLowLevelAbstractionDefinition: Gets the operator that is applied to each interval's low-level abstraction values to determine the value to set for this abstraction.
getValueDefinitions() - Method in class org.protempa.LowLevelAbstractionDefinition
getValueDefinitions(String) - Method in class org.protempa.LowLevelAbstractionDefinition
getValueFormatted() - Method in interface org.protempa.proposition.Parameter: Returns this parameter's value formatted as a string.
getValueFormatted() - Method in class org.protempa.proposition.TemporalParameter
getValueHeading() - Method in class org.protempa.dest.table.OutputConfig
getValueHeading() - Method in class org.protempa.dest.table.OutputConfigBuilder
getValueOutputConfig() - Method in class org.protempa.dest.table.PropositionColumnSpec
getValues() - Method in class org.protempa.backend.dsb.filter.PropertyValueFilter: Gets the specified value.
getValues() - Method in class org.protempa.proposition.CompoundValuedInterval: Gets the proposition ID-value map for this interval
getValueSet(String) - Method in class org.protempa.KnowledgeSourceCache
getValueSetElementBuilders() - Method in class org.protempa.valueset.ValueSetBuilder
getValueSetElements() - Method in class org.protempa.valueset.ValueSet: Gets the elements of this value set, if specified.
getValueSetId() - Method in class org.protempa.PropertyDefinition: Returns the property's value set (for nominal and ordinal values).
getValueSetId() - Method in class org.protempa.PropertyDefinitionBuilder
getValueType() - Method in class org.protempa.AlgorithmParameter: Returns the type of value of this parameter.
getValueType() - Method in class org.protempa.CompoundLowLevelAbstractionDefinition
getValueType() - Method in class org.protempa.LowLevelAbstractionDefinition
getValueType() - Method in interface org.protempa.ParameterDefinition
getValueType() - Method in class org.protempa.PrimitiveParameterDefinition: Gets the value factory for this primitive parameter definition.
getValueType() - Method in class org.protempa.PropertyDefinition: Returns the property's value type.
getValueType() - Method in class org.protempa.PropertyDefinitionBuilder
getVersion() - Method in class org.protempa.AbstractPropositionDefinition
getVersion() - Method in interface org.protempa.PropositionDefinition: Returns the version number of this proposition definition, for knowledge source backends that maintain version information.
getVersion() - Method in class org.protempa.Terminology
getView(List<T>, Long, Long) - Static method in class org.protempa.proposition.PropositionUtil: Filters a list of temporal propositions by time.
getView(Map<String, List<T>>, Long, Long) - Static method in class org.protempa.proposition.PropositionUtil
getVisited() - Method in class org.protempa.graph.Edge
getWeight() - Method in class org.protempa.graph.Edge
Granularity - Interface in org.protempa.proposition.value: The units for a proposition's temporal or spatial position, represented as the distance from some origin.
GranularityFactory - Interface in org.protempa.proposition.value: Access to the granularity of data provided by a data source.
granularityStringToGranularity(String) - Static method in class org.protempa.proposition.value.AbsoluteTimeGranularity
greaterThan(long) - Method in class org.protempa.graph.Weight: Checks to see if this weight is greater than the given long value.

H

handleQueryResult(String, List<Proposition>, Map<Proposition, List<Proposition>>, Map<Proposition, List<Proposition>>, Map<UniqueId, Proposition>) - Method in class org.protempa.dest.deid.DeidentifiedQueryResultsHandler
handleQueryResult(String, List<Proposition>, Map<Proposition, List<Proposition>>, Map<Proposition, List<Proposition>>, Map<UniqueId, Proposition>) - Method in class org.protempa.dest.keyloader.KeyLoaderQueryResultsHandler
handleQueryResult(String, List<Proposition>, Map<Proposition, List<Proposition>>, Map<Proposition, List<Proposition>>, Map<UniqueId, Proposition>) - Method in class org.protempa.dest.map.MapQueryResultsHandler: Puts handled keys and propositions into the map returned by MapQueryResultsHandler.getResultMap().
handleQueryResult(String, List<Proposition>, Map<Proposition, List<Proposition>>, Map<Proposition, List<Proposition>>, Map<UniqueId, Proposition>) - Method in class org.protempa.dest.proplist.PropositionListQueryResultsHandler: Writes a keys worth of data in tab delimited format optionally sorted.
handleQueryResult(String, List<Proposition>, Map<Proposition, List<Proposition>>, Map<Proposition, List<Proposition>>, Map<UniqueId, Proposition>) - Method in interface org.protempa.dest.QueryResultsHandler: Handles a single query result, which is the list of propositions associated with the given key.
handleQueryResult(String, List<Proposition>, Map<Proposition, List<Proposition>>, Map<Proposition, List<Proposition>>, Map<UniqueId, Proposition>) - Method in class org.protempa.dest.table.TableQueryResultsHandler
handleQueryResult(String, List<Proposition>, Map<Proposition, List<Proposition>>, Map<Proposition, List<Proposition>>, Map<UniqueId, Proposition>) - Method in class org.protempa.dest.xml.XmlQueryResultsHandler
hasAbstractionDefinition(String) - Method in interface org.protempa.KnowledgeSource
hasAbstractionDefinition(String) - Method in class org.protempa.KnowledgeSourceImpl
hasAlgorithm(String) - Method in class org.protempa.Algorithms: Returns whether an algorithm exists with the given id.
hasAttribute(String) - Method in class org.protempa.PropertyDefinition
hasComparator(ValueComparator) - Method in class org.protempa.AlgorithmParameter: Returns true if the given value comparator is allowed for this parameter.
hasContextDefinition(String) - Method in interface org.protempa.KnowledgeSource
hasContextDefinition(String) - Method in class org.protempa.KnowledgeSourceImpl
hasEqualFields(ExtendedPropositionDefinition) - Method in class org.protempa.ExtendedParameterDefinition
hasEqualFields(ExtendedPropositionDefinition) - Method in class org.protempa.ExtendedPropositionDefinition
hasEqualFields(ExtendedPropositionDefinition) - Method in class org.protempa.TemporalExtendedAbstractParameterDefinition
hasEqualFields(ExtendedPropositionDefinition) - Method in class org.protempa.TemporalExtendedParameterDefinition
hasEqualFields(ExtendedPropositionDefinition) - Method in class org.protempa.TemporalExtendedPropositionDefinition
hashCode() - Method in class org.protempa.AttributeBuilder
hashCode() - Method in class org.protempa.backend.dsb.filter.PositionFilter
hashCode() - Method in class org.protempa.backend.dsb.filter.PropertyValueFilter
hashCode() - Method in class org.protempa.backend.dsb.filter.ValueFilter
hashCode() - Method in class org.protempa.DataSourceBackendSourceSystem
hashCode() - Method in class org.protempa.DefaultSourceIdBuilder
hashCode() - Method in class org.protempa.dest.table.AtLeastNColumnSpec
hashCode() - Method in class org.protempa.dest.table.CountColumnSpec
hashCode() - Method in class org.protempa.dest.table.Derivation
hashCode() - Method in class org.protempa.dest.table.DistanceBetweenColumnSpec
hashCode() - Method in class org.protempa.dest.table.Link
hashCode() - Method in class org.protempa.dest.table.OutputConfig
hashCode() - Method in class org.protempa.dest.table.PropertyConstraint
hashCode() - Method in class org.protempa.dest.table.PropositionColumnSpec
hashCode() - Method in class org.protempa.dest.table.PropositionValueColumnSpec
hashCode() - Method in class org.protempa.dest.table.Reference
hashCode() - Method in class org.protempa.dest.table.ValueOutputConfig
hashCode() - Method in class org.protempa.ExtendedPropositionDefinition
hashCode() - Method in class org.protempa.graph.Edge
hashCode() - Method in class org.protempa.graph.Weight
hashCode() - Method in class org.protempa.KeySetSpec
hashCode() - Method in class org.protempa.NotRecordedSourceIdBuilder
hashCode() - Method in class org.protempa.PropertyDefinitionBuilder
hashCode() - Method in class org.protempa.proposition.AbstractProposition
hashCode() - Method in class org.protempa.proposition.DataSourceBackendId
hashCode() - Method in class org.protempa.proposition.DerivedSourceId
hashCode() - Method in class org.protempa.proposition.interval.Interval
hashCode() - Method in class org.protempa.proposition.interval.Relation
hashCode() - Method in class org.protempa.proposition.ProviderBasedLocalUniqueId
hashCode() - Method in class org.protempa.proposition.Sequence
hashCode() - Method in class org.protempa.proposition.UniqueId
hashCode() - Method in class org.protempa.proposition.value.AbsoluteTimeGranularity
hashCode() - Method in class org.protempa.proposition.value.BooleanValue
hashCode() - Method in class org.protempa.proposition.value.BooleanValueBuilder
hashCode() - Method in class org.protempa.proposition.value.DateValue
hashCode() - Method in class org.protempa.proposition.value.DateValueBuilder
hashCode() - Method in class org.protempa.proposition.value.InequalityNumberValue
hashCode() - Method in class org.protempa.proposition.value.InequalityNumberValueBuilder
hashCode() - Method in class org.protempa.proposition.value.NominalValue
hashCode() - Method in class org.protempa.proposition.value.NominalValueBuilder
hashCode() - Method in class org.protempa.proposition.value.NumberValue
hashCode() - Method in class org.protempa.proposition.value.NumberValueBuilder
hashCode() - Method in class org.protempa.proposition.value.OrdinalValue
hashCode() - Method in class org.protempa.proposition.value.OrdinalValueBuilder
hashCode() - Method in class org.protempa.proposition.value.RelativeDayGranularity
hashCode() - Method in class org.protempa.proposition.value.RelativeHourGranularity
hashCode() - Method in class org.protempa.proposition.value.ValueListBuilder
hashCode() - Method in class org.protempa.query.And
hashCode() - Method in class org.protempa.query.Query
hashCode() - Method in class org.protempa.valueset.ValueSetBuilder
hashCode() - Method in class org.protempa.valueset.ValueSetElementBuilder
hasNegativeCycle(Object, DirectedGraph, BellmanFord.Mode) - Static method in class org.protempa.graph.BellmanFord: Determines if there are any negative cycles found.
hasNext() - Method in interface org.protempa.DataStreamingEventIterator: Returns true if the iteration has more DataStreamingEvents.
hasNext() - Method in class org.protempa.MultiplexingDataStreamingEventIterator
hasNext() - Method in class org.protempa.QueryResults.QueryResultsIterator
hasPropositionDefinition(String) - Method in interface org.protempa.KnowledgeSource
hasPropositionDefinition(String) - Method in class org.protempa.KnowledgeSourceImpl
hasRelation(Interval, Interval) - Method in class org.protempa.proposition.interval.Relation: Determines whether the given intervals have this relation.
hasSpec(String) - Method in class org.protempa.backend.BackendSpecLoader
hasTemporalPropositionDefinition(String) - Method in interface org.protempa.KnowledgeSource
hasTemporalPropositionDefinition(String) - Method in class org.protempa.KnowledgeSourceImpl
hasValueSet(String) - Method in interface org.protempa.KnowledgeSource
hasValueSet(String) - Method in class org.protempa.KnowledgeSourceImpl
HighLevelAbstractionDefinition - Class in org.protempa: Definition of an extended parameter that's a high-level abstraction.
HighLevelAbstractionDefinition(String) - Constructor for class org.protempa.HighLevelAbstractionDefinition
HIPAA_IDENTIFIER_TYPE - Static variable in class org.protempa.dest.deid.DeidAttributes
HOUR - Static variable in class org.protempa.proposition.value.AbsoluteTimeGranularity
HOUR - Static variable in class org.protempa.proposition.value.AbsoluteTimeUnit
HOUR - Static variable in class org.protempa.proposition.value.RelativeHourGranularity
HOUR - Static variable in class org.protempa.proposition.value.RelativeHourUnit

I

includes(ValueComparator) - Method in enum org.protempa.proposition.value.ValueComparator: Returns whether this ValueComparator is the same as or includes the specified ValueComparator.
incr() - Method in interface org.protempa.proposition.LocalUniqueIdValuesProvider
indexOf(Object) - Method in class org.protempa.proposition.Segment
indexOf(Object) - Method in class org.protempa.proposition.Sequence
InequalityNumberValue - Class in org.protempa.proposition.value: Represents a test result that is outside of the reportable range of the test and thus is reported prefixed with a greater than or less than sign.
InequalityNumberValue(ValueComparator, double) - Constructor for class org.protempa.proposition.value.InequalityNumberValue: Creates a new InequalityNumberValue with the given comparator and value.
InequalityNumberValue(ValueComparator, BigDecimal) - Constructor for class org.protempa.proposition.value.InequalityNumberValue: Creates a new InequalityNumberValue with the given comparator and value.
InequalityNumberValueBuilder - Class in org.protempa.proposition.value
InequalityNumberValueBuilder() - Constructor for class org.protempa.proposition.value.InequalityNumberValueBuilder
InequalityNumberValueBuilder(InequalityNumberValue) - Constructor for class org.protempa.proposition.value.InequalityNumberValueBuilder
init(String) - Method in class org.protempa.backend.ConfigurationsSupport
init(KnowledgeSource) - Method in interface org.protempa.dest.keyloader.Criteria
init(Long, Granularity, Long, Granularity, Long, Unit) - Method in class org.protempa.proposition.interval.Interval
init(Long, Long, Granularity, Long, Long, Granularity, Long, Long, Unit) - Method in class org.protempa.proposition.interval.Interval
initComputed() - Method in class org.protempa.proposition.interval.Interval
initialize(AlgorithmArguments) - Method in class org.protempa.AbstractAlgorithm
initialize(AlgorithmArguments) - Method in interface org.protempa.Algorithm
initialize(BackendInstanceSpec<?>) - Method in class org.protempa.backend.AbstractBackend
initialize(BackendInstanceSpec<?>) - Method in class org.protempa.backend.AbstractCommonsAlgorithmSourceBackend
initialize(BackendInstanceSpec) - Method in class org.protempa.backend.AbstractCommonsDataSourceBackend
initialize(BackendInstanceSpec) - Method in class org.protempa.backend.AbstractCommonsKnowledgeSourceBackend
initialize(BackendInstanceSpec) - Method in class org.protempa.backend.AbstractCommonsTermSourceBackend
initialize(BackendInstanceSpec) - Method in class org.protempa.backend.asb.java.AbstractJavaAlgorithmBackend: Reads the properties file containing the list of algorithm classes.
initialize(BackendInstanceSpec<?>) - Method in interface org.protempa.backend.Backend: Initializes the backend from a BackendInstanceSpec.
initialize(Object, BackendInstanceSpec) - Static method in class org.protempa.backend.CommonsBackend: Sets the fields corresponding to the properties in the configuration.
initialize(BackendInstanceSpec) - Method in class org.protempa.backend.ksb.SimpleKnowledgeSourceBackend
initialize(BackendInstanceSpec<?>) - Method in class org.protempa.backend.test.MockTermSourceBackend
initialize() - Method in class org.protempa.cli.CLI: Initializes PROTEMPA with the specified configuration.
initializeAbstractProposition(String, UniqueId) - Method in class org.protempa.proposition.AbstractProposition: Assigns fields specified in the constructor.
initializeExecuteAndClose() - Method in class org.protempa.cli.CLI: Like calling #initialize(java.lang.String), CLI.execute() and CLI.close() in succession.
initializeProperties() - Method in class org.protempa.proposition.AbstractProposition
initializePropertyChangeSupport() - Method in class org.protempa.proposition.AbstractProposition
initializeReferences() - Method in class org.protempa.proposition.AbstractProposition
internAll(String[]) - Static method in class org.protempa.ProtempaUtil: Replaces every element of the supplied string array with an interned copy as created by String.intern().
Interval - Class in org.protempa.proposition.interval: A representation of an interval, designed according to the definition of an interval in Combi et al.
Interval.Side - Enum in org.protempa.proposition.interval
INTERVAL_FACTORY - Static variable in class org.protempa.proposition.TemporalProposition
intervalCreator() - Method in class org.protempa.proposition.Segment
IntervalFactory - Class in org.protempa.proposition.interval: A factory for creating Interval objects.
IntervalFactory() - Constructor for class org.protempa.proposition.interval.IntervalFactory
IntervalSectioner<E extends TemporalProposition,K extends CompoundInterval<E>> - Class in org.protempa.proposition: A factory for creating order lists of CompoundValuedIntervals based on input propositions.
IntervalUtil - Class in org.protempa.proposition.interval
InvalidConfigurationException - Exception in org.protempa.backend
InvalidConfigurationException(String) - Constructor for exception org.protempa.backend.InvalidConfigurationException
InvalidConfigurationException(Throwable) - Constructor for exception org.protempa.backend.InvalidConfigurationException
InvalidConfigurationException(String, Throwable) - Constructor for exception org.protempa.backend.InvalidConfigurationException
InvalidConfigurationException() - Constructor for exception org.protempa.backend.InvalidConfigurationException
InvalidPropertyNameException - Exception in org.protempa.backend: Thrown if a property name in a configuration is invalid.
InvalidPropertyNameException(String) - Constructor for exception org.protempa.backend.InvalidPropertyNameException
InvalidPropertyValueException - Exception in org.protempa.backend: Thrown if a property value in a configuration is invalid.
InvalidPropertyValueException(String) - Constructor for exception org.protempa.backend.InvalidPropertyValueException
InvalidPropertyValueException(String, Throwable) - Constructor for exception org.protempa.backend.InvalidPropertyValueException
InvalidPropertyValueException(String, Object, Throwable) - Constructor for exception org.protempa.backend.InvalidPropertyValueException
InvalidPropositionIdException - Exception in org.protempa: Thrown when a proposition id was not found in the knowledge source or in the user-defined proposition definitions.
inverse() - Method in class org.protempa.proposition.interval.Relation
invertSign() - Method in class org.protempa.graph.Weight: Creates a new weight with the opposite sign.
IS_HIPAA_IDENTIFIER - Static variable in class org.protempa.dest.deid.DeidAttributes
isAllowed(Class<?>) - Static method in enum org.protempa.backend.BackendPropertyType
isAllowPartialMatches() - Method in class org.protempa.SequentialTemporalPatternDefinition: Returns whether an interval will be generated if only the first, first and second, etc.
isBackendProviderClassLoaderSpecified() - Static method in class org.protempa.backend.BackendProviderManager: Indicates whether BackendProviderManager.setBackendProviderClassLoader(java.lang.ClassLoader) has been called.
isCachingEnabled() - Method in class org.protempa.QuerySession: Returns whether the proposition and derived caches are enabled.
isClosed() - Method in class org.protempa.AbstractSource
isConcatenable() - Method in class org.protempa.CompoundLowLevelAbstractionDefinition
isConcatenable() - Method in class org.protempa.ConstantDefinition: By definition, constants are not concatenable.
isConcatenable() - Method in class org.protempa.ContextDefinition
isConcatenable() - Method in class org.protempa.EventDefinition: By definition, events are not concatenable.
isConcatenable() - Method in class org.protempa.HighLevelAbstractionDefinition: Returns whether this type of high-level abstraction is concatenable.
isConcatenable() - Method in class org.protempa.LowLevelAbstractionDefinition: Returns whether this type of low-level abstraction is concatenable.
isConcatenable() - Method in class org.protempa.PrimitiveParameterDefinition: By definition, primitive parameters are not concatenable.
isConcatenable() - Method in interface org.protempa.PropositionDefinition: Returns whether instances of this proposition definition are concatenable.
isConcatenable() - Method in class org.protempa.SequentialTemporalPatternDefinition
isConcatenable() - Method in class org.protempa.SliceDefinition: By definition, slice abstractions are not concatenable.
isConfigurationIdEnabled() - Method in class org.protempa.cli.CLI: Whether the configuration option will be created.
isConfigurationsProviderClassLoaderSpecified() - Static method in class org.protempa.backend.ConfigurationsProviderManager: Indicates whether ConfigurationsProviderManager.setConfigurationsProviderClassLoader(java.lang.ClassLoader) has been called.
isCountUnique() - Method in class org.protempa.dest.table.CountColumnSpec
isDerived() - Method in class org.protempa.DataSourceBackendSourceSystem
isDerived() - Method in class org.protempa.SourceSystem
isEmpty() - Method in class org.protempa.DataSourceResultMap
isEmpty() - Method in class org.protempa.graph.DirectedGraph: Check to see if there are any vertices defined.
isEmpty() - Method in class org.protempa.proposition.Sequence
isEqual(long) - Method in class org.protempa.graph.Weight: Checks if this weight has the same value as the given long.
isEqual(Object) - Method in class org.protempa.proposition.AbstractParameter
isEqual(Object) - Method in class org.protempa.proposition.AbstractProposition
isEqual(Object) - Method in class org.protempa.proposition.Constant
isEqual(Object) - Method in class org.protempa.proposition.Event
isEqual(Object) - Method in class org.protempa.proposition.PrimitiveParameter
isEqual(Object) - Method in interface org.protempa.proposition.Proposition: Determines if the specified object is a Proposition and has the same field values as this proposition.
isEqual(Object) - Method in class org.protempa.proposition.TemporalParameter
isEqual(Object) - Method in class org.protempa.proposition.TemporalProposition
isFatal() - Method in class org.protempa.backend.dsb.DataValidationEvent
isGetStatisticsSupported() - Method in class org.protempa.dest.AbstractDestination
isGetStatisticsSupported() - Method in class org.protempa.dest.deid.DeidentifiedDestination
isGetStatisticsSupported() - Method in interface org.protempa.dest.Destination
isHeaderWritten() - Method in class org.protempa.dest.table.TableDestination
isInfinity() - Method in class org.protempa.graph.Weight: Checks if this weight has value of positive or negative infinity.
isInherited() - Method in class org.protempa.PropertyDefinition
isInstance(Object) - Method in enum org.protempa.backend.BackendPropertyType
isInstance(Value) - Method in enum org.protempa.proposition.value.ValueType: Returns whether a value is an instance of this value type.
isInValueSet(Value) - Method in class org.protempa.valueset.ValueSet: Returns whether the specified value is in the value set.
isLengthGreaterThan(int, Unit) - Method in class org.protempa.proposition.interval.Interval
isLengthLessThan(int, Unit) - Method in class org.protempa.proposition.interval.Interval
isMatch(Proposition) - Method in class org.protempa.dest.table.Link: Returns whether a proposition has one of the proposition ids specified by the link.
isMergedInterval() - Method in class org.protempa.SliceDefinition
isNegativeInfinity() - Method in class org.protempa.graph.Weight: Checks if this weight has value of negative infinity.
isOrdered() - Method in class org.protempa.valueset.ValueSet
isOrdered() - Method in class org.protempa.valueset.ValueSetBuilder
isPositiveInfinity() - Method in class org.protempa.graph.Weight: Checks if this weight has value of positive infinity.
isRequired(String) - Method in class org.protempa.backend.BackendInstanceSpec
isRequired() - Method in class org.protempa.backend.BackendPropertySpec
isRequired() - Method in class org.protempa.cli.CLI.Argument: Returns whether the argument is required.
isSatisfiedBy(Proposition) - Method in class org.protempa.PropertyConstraint: Returns whether a proposition satisfies this constraint.
isShowPropertyValueAbbrevDisplayName() - Method in class org.protempa.dest.table.ValueOutputConfig
isShowPropertyValueAbbrevDisplayName() - Method in class org.protempa.dest.table.ValueOutputConfigBuilder
isShowPropertyValueDisplayName() - Method in class org.protempa.dest.table.ValueOutputConfig
isShowPropertyValueDisplayName() - Method in class org.protempa.dest.table.ValueOutputConfigBuilder
isSolid() - Method in class org.protempa.CompoundLowLevelAbstractionDefinition
isSolid() - Method in class org.protempa.ConstantDefinition: By definition, there can be multiple constants with the same id.
isSolid() - Method in class org.protempa.ContextDefinition
isSolid() - Method in class org.protempa.EventDefinition: Returns whether intervals of this type are solid, i.e., never hold over properly overlapping intervals.
isSolid() - Method in class org.protempa.HighLevelAbstractionDefinition: Returns whether intervals of this type are solid, i.e., never hold over properly overlapping intervals.
isSolid() - Method in class org.protempa.LowLevelAbstractionDefinition: Returns whether intervals of this type are solid, i.e., never hold over properly overlapping intervals.
isSolid() - Method in class org.protempa.PrimitiveParameterDefinition: By definition, primitive parameters are solid.
isSolid() - Method in interface org.protempa.PropositionDefinition: Returns whether intervals of this type are solid, i.e., never hold over properly overlapping intervals.
isSolid() - Method in class org.protempa.SequentialTemporalPatternDefinition: Returns whether intervals of this type are solid, i.e., never hold over properly overlapping intervals.
isSolid() - Method in class org.protempa.SliceDefinition: Returns whether intervals of this type are solid, i.e., never hold over properly overlapping intervals.
isValid() - Method in class org.protempa.proposition.interval.DefaultInterval
isValidatePropositionIds() - Static method in class org.protempa.query.DefaultQueryBuilder
isValue() - Method in class org.protempa.proposition.value.BooleanValueBuilder
iterator() - Method in class org.protempa.backend.BackendSpecLoader
iterator() - Method in class org.protempa.graph.DirectedGraph: Create an iterator of vertices.
iterator() - Method in class org.protempa.proposition.Sequence
iterator() - Method in class org.protempa.QueryResults

J

JavaAlgorithmBackend - Class in org.protempa.backend.asb.java
JavaAlgorithmBackend() - Constructor for class org.protempa.backend.asb.java.JavaAlgorithmBackend

K

KeyCreateException - Exception in org.protempa.dest.deid
KeyCreateException() - Constructor for exception org.protempa.dest.deid.KeyCreateException
KeyCreateException(String, Throwable) - Constructor for exception org.protempa.dest.deid.KeyCreateException
KeyCreateException(String) - Constructor for exception org.protempa.dest.deid.KeyCreateException
KeyCreateException(Throwable) - Constructor for exception org.protempa.dest.deid.KeyCreateException
KeyLoaderDestination - Class in org.protempa.dest.keyloader
KeyLoaderDestination(Criteria) - Constructor for class org.protempa.dest.keyloader.KeyLoaderDestination
KeyLoaderDestination(String, Criteria) - Constructor for class org.protempa.dest.keyloader.KeyLoaderDestination
KeyLoaderDestination(String, String, Criteria) - Constructor for class org.protempa.dest.keyloader.KeyLoaderDestination
KeyLoaderQueryResultsHandler - Class in org.protempa.dest.keyloader
keySet() - Method in class org.protempa.DataSourceResultMap
KeySetSpec - Class in org.protempa
KeySetSpec(SourceSystem, String, String, String) - Constructor for class org.protempa.KeySetSpec
KnowledgeSource - Interface in org.protempa
KnowledgeSourceBackend - Interface in org.protempa.backend.ksb: Translates from an arbitrary knowledge base to a PROTEMPA knowledge base.
KnowledgeSourceBackendInitializationException - Exception in org.protempa.backend
KnowledgeSourceBackendInitializationException(String) - Constructor for exception org.protempa.backend.KnowledgeSourceBackendInitializationException
KnowledgeSourceBackendInitializationException(Throwable) - Constructor for exception org.protempa.backend.KnowledgeSourceBackendInitializationException
KnowledgeSourceBackendInitializationException(String, Throwable) - Constructor for exception org.protempa.backend.KnowledgeSourceBackendInitializationException
KnowledgeSourceBackendUpdatedEvent - Class in org.protempa.backend: The event generated when the knowledge source backend is updated.
KnowledgeSourceBackendUpdatedEvent(KnowledgeSourceBackend) - Constructor for class org.protempa.backend.KnowledgeSourceBackendUpdatedEvent: Constructs an event with the source KnowledgeSourceBackend that generated the event.
KnowledgeSourceCache - Class in org.protempa
KnowledgeSourceCache(Map<String, PropositionDefinition>, Map<String, ValueSet>) - Constructor for class org.protempa.KnowledgeSourceCache
KnowledgeSourceCacheFactory - Class in org.protempa
KnowledgeSourceCacheFactory() - Constructor for class org.protempa.KnowledgeSourceCacheFactory
KnowledgeSourceException - Exception in org.protempa
KnowledgeSourceImpl - Class in org.protempa: A read-only "interface" to an externally-maintained knowledge base.
KnowledgeSourceImpl(KnowledgeSourceBackend...) - Constructor for class org.protempa.KnowledgeSourceImpl
KnowledgeSourceReadException - Exception in org.protempa
KnowledgeSourceReadException() - Constructor for exception org.protempa.KnowledgeSourceReadException
KnowledgeSourceReadException(String, Throwable) - Constructor for exception org.protempa.KnowledgeSourceReadException
KnowledgeSourceReadException(String) - Constructor for exception org.protempa.KnowledgeSourceReadException
KnowledgeSourceReadException(Throwable) - Constructor for exception org.protempa.KnowledgeSourceReadException
KnowledgeSourceUpdatedEvent - Class in org.protempa: The event generated when the knowledge source is updated.
KnowledgeSourceUpdatedEvent(KnowledgeSource) - Constructor for class org.protempa.KnowledgeSourceUpdatedEvent: Constructs an event with the source KnowledgeSource that generated the event.
KSUtil - Class in org.protempa.backend.ksb

L

last() - Method in class org.protempa.proposition.Segment
lastIndexOf(Object) - Method in class org.protempa.proposition.Segment
lastIndexOf(Object) - Method in class org.protempa.proposition.Sequence
latest(long) - Method in class org.protempa.proposition.value.AbsoluteTimeGranularity
latest(long) - Method in interface org.protempa.proposition.value.Granularity
latest(long) - Method in class org.protempa.proposition.value.RelativeDayGranularity
latest(long) - Method in class org.protempa.proposition.value.RelativeHourGranularity
length(TemporalProposition, Unit) - Method in class org.protempa.proposition.stats.AbstractKaplanMeyer
length(TemporalProposition, Unit) - Method in class org.protempa.proposition.stats.MaxLengthKaplanMeyer
length(TemporalProposition, Unit) - Method in class org.protempa.proposition.stats.MinLengthKaplanMeyer
length(int) - Method in class org.protempa.proposition.value.AbstractRelativeTimeUnit
lengthInBaseUnit(long) - Method in class org.protempa.proposition.value.RelativeDayGranularity
lengthInBaseUnit(long) - Method in class org.protempa.proposition.value.RelativeHourGranularity
lessThan(long) - Method in class org.protempa.graph.Weight: Checks to see if this weight is less than the given long value.
Link - Class in org.protempa.dest.table: Representation of links between propositions in the PROTEMPA virtual data model.
LinkTraverser - Class in org.protempa.dest.table
LinkTraverser() - Constructor for class org.protempa.dest.table.LinkTraverser
LinkValidationFailedException - Exception in org.protempa.dest.table
LinkValidationFailedException(Throwable) - Constructor for exception org.protempa.dest.table.LinkValidationFailedException
LinkValidationFailedException(String) - Constructor for exception org.protempa.dest.table.LinkValidationFailedException
LinkValidationFailedException(String, Throwable) - Constructor for exception org.protempa.dest.table.LinkValidationFailedException
LinkValidationFailedException() - Constructor for exception org.protempa.dest.table.LinkValidationFailedException
listIterator() - Method in class org.protempa.proposition.Sequence
listIterator(int) - Method in class org.protempa.proposition.Sequence
load(String) - Method in interface org.protempa.backend.Configurations: Reads all of the backend specifications from the specified configurations conforming to the given backend spec.
load(String) - Method in class org.protempa.backend.ConfigurationsSupport
loadSpec(String) - Method in class org.protempa.backend.BackendSpecLoader
LocalUniqueId - Interface in org.protempa.proposition: A unique identifier for a proposition retrieved from a data source backend.
LocalUniqueIdValuesProvider - Interface in org.protempa.proposition
longValue() - Method in class org.protempa.proposition.value.NumberValue
LowLevelAbstractionDefinition - Class in org.protempa: Definition of low-level abstraction.
LowLevelAbstractionDefinition(String) - Constructor for class org.protempa.LowLevelAbstractionDefinition
LowLevelAbstractionFinder - Class in org.protempa
LowLevelAbstractionValueDefinition - Class in org.protempa
LowLevelAbstractionValueDefinition(LowLevelAbstractionDefinition, String) - Constructor for class org.protempa.LowLevelAbstractionValueDefinition

M

main(String[]) - Static method in class org.protempa.cli.PrintAbstractedFrom
main(String[]) - Static method in class org.protempa.cli.PrintAbstractedInto
main(String[]) - Static method in class org.protempa.cli.PrintInverseIsA
main(String[]) - Static method in class org.protempa.cli.PrintIsA
main(String[]) - Static method in class org.protempa.cli.PrintPropositionDefinition
main(String[]) - Static method in class org.protempa.cli.PrintPropositionDefinitionsForTerm
main(String[]) - Static method in class org.protempa.cli.PrintSubtreeInDataSource
main(String[]) - Static method in class org.protempa.cli.PrintTerm
main(String[]) - Static method in class org.protempa.cli.PrintTermChildren
main(String[]) - Static method in class org.protempa.cli.ValidateDataSource
MalformedTermIdException - Exception in org.protempa
MalformedTermIdException() - Constructor for exception org.protempa.MalformedTermIdException
MalformedTermIdException(String) - Constructor for exception org.protempa.MalformedTermIdException
MalformedTermIdException(Throwable) - Constructor for exception org.protempa.MalformedTermIdException
MalformedTermIdException(String, Throwable) - Constructor for exception org.protempa.MalformedTermIdException
MapDestination - Class in org.protempa.dest.map
MapQueryResultsHandler - Class in org.protempa.dest.map: An implementation of QueryResultsHandler that stores the results in a map that may be accessed later for post-processing.
max(Weight, Weight) - Static method in class org.protempa.graph.Weight: Gets the larger of the two given weights.
MaxFinishTemporalPropositionComparator - Class in org.protempa.proposition.comparator: For sorting temporal propositions by time interval.
MaxFinishTemporalPropositionComparator() - Constructor for class org.protempa.proposition.comparator.MaxFinishTemporalPropositionComparator
maximumDistance(long, long, Unit) - Method in class org.protempa.proposition.value.AbsoluteTimeGranularity
maximumDistance(long, long, Unit) - Method in interface org.protempa.proposition.value.Granularity
maximumDistance(long, long, Unit) - Method in class org.protempa.proposition.value.RelativeDayGranularity
maximumDistance(long, long, Unit) - Method in class org.protempa.proposition.value.RelativeHourGranularity
maxLengthIn(Unit) - Method in class org.protempa.proposition.interval.Interval
MaxLengthKaplanMeyer - Class in org.protempa.proposition.stats: Calculates survival based on temporal propositions' maxlength.
MaxLengthKaplanMeyer() - Constructor for class org.protempa.proposition.stats.MaxLengthKaplanMeyer
MaxLengthKaplanMeyer(Unit) - Constructor for class org.protempa.proposition.stats.MaxLengthKaplanMeyer
MEETS - Static variable in class org.protempa.proposition.interval.Relation
merge(Configuration) - Method in class org.protempa.backend.Configuration
MessageDigestDeidConfig - Interface in org.protempa.dest.deid
MessageDigestEncryption - Class in org.protempa.dest.deid
MessageDigestEncryption(MessageDigestDeidConfig) - Constructor for class org.protempa.dest.deid.MessageDigestEncryption
MET_BY - Static variable in class org.protempa.proposition.interval.Relation
min(Weight, Weight) - Static method in class org.protempa.graph.Weight: Gets the smaller of the two given weights.
MinAlgorithm - Class in org.protempa.backend.asb.java: Determines if the minimum value of a segment is at most a defined threshold.
MinAlgorithm(Algorithms, String) - Constructor for class org.protempa.backend.asb.java.MinAlgorithm
minimumDistance(long, long, Unit) - Method in class org.protempa.proposition.value.AbsoluteTimeGranularity
minimumDistance(long, long, Unit) - Method in interface org.protempa.proposition.value.Granularity
minimumDistance(long, long, Unit) - Method in class org.protempa.proposition.value.RelativeDayGranularity
minimumDistance(long, long, Unit) - Method in class org.protempa.proposition.value.RelativeHourGranularity
minLengthIn(Unit) - Method in class org.protempa.proposition.interval.Interval
MinLengthKaplanMeyer - Class in org.protempa.proposition.stats: Calculates survival based on the minlength of temporal propositions.
MinLengthKaplanMeyer() - Constructor for class org.protempa.proposition.stats.MinLengthKaplanMeyer
MinLengthKaplanMeyer(Unit) - Constructor for class org.protempa.proposition.stats.MinLengthKaplanMeyer
MinMaxGapFunction - Class in org.protempa
MinMaxGapFunction() - Constructor for class org.protempa.MinMaxGapFunction: Instantiates an instance with the default minimum and maximum gap and units.
MinMaxGapFunction(Integer, Unit, Integer, Unit) - Constructor for class org.protempa.MinMaxGapFunction
MINUTE - Static variable in class org.protempa.proposition.value.AbsoluteTimeGranularity
MINUTE - Static variable in class org.protempa.proposition.value.AbsoluteTimeUnit
MockBackendInstanceSpecFactory> - Class in org.protempa.backend.test
MockBackendInstanceSpecFactory(List<BackendPropertySpec>) - Constructor for class org.protempa.backend.test.MockBackendInstanceSpecFactory
MockBackendPropertySpec - Class in org.protempa.backend.test
MockBackendPropertySpec(String, BackendPropertyType) - Constructor for class org.protempa.backend.test.MockBackendPropertySpec
MockBackendProvider - Class in org.protempa.backend.test
MockBackendProvider() - Constructor for class org.protempa.backend.test.MockBackendProvider
MockTermSourceBackend - Class in org.protempa.backend.test
MockTermSourceBackend() - Constructor for class org.protempa.backend.test.MockTermSourceBackend
modCount - Variable in class org.protempa.proposition.Segment
MONTH - Static variable in class org.protempa.proposition.value.AbsoluteTimeGranularity
MONTH - Static variable in class org.protempa.proposition.value.AbsoluteTimeUnit
MRN - Static variable in class org.protempa.dest.deid.DeidAttributes
MultiplexingDataStreamingEventIterator - Class in org.protempa: Iterator-like access to DataStreamingEvents.

N

nameForErrors() - Method in class org.protempa.backend.AbstractCommonsAlgorithmSourceBackend
nameForErrors() - Method in class org.protempa.backend.AbstractCommonsDataSourceBackend
nameForErrors() - Method in class org.protempa.backend.AbstractCommonsKnowledgeSourceBackend
nameForErrors() - Method in class org.protempa.backend.AbstractCommonsTermSourceBackend
nameForErrors(Backend) - Static method in class org.protempa.backend.CommonsBackend
nameToGranularity(String) - Static method in class org.protempa.proposition.value.AbsoluteTimeGranularity
nameToUnit(String) - Static method in class org.protempa.proposition.value.AbsoluteTimeUnit
NEG_EPSILON - Static variable in class org.protempa.graph.WeightFactory: Special value representing the smallest possible negative value.
NEG_INFINITY - Static variable in class org.protempa.graph.WeightFactory: Special value representing negative infinity.
neighbors(Object) - Method in class org.protempa.graph.DirectedGraph: Create an iterator of all vertices that share an edge with a vertex.
newAlgorithmSourceBackendSection(String) - Method in class org.protempa.backend.AbstractConfigurations
newAlgorithmSourceBackendSection(String) - Method in interface org.protempa.backend.Configurations
newAlgorithmSourceInstance() - Method in class org.protempa.SourceFactory
newBackendInstanceSpec() - Method in class org.protempa.backend.BackendSpec
newCacheStore() - Method in class org.protempa.datastore.AbstractDataStoreCreator
newCacheStore() - Method in interface org.protempa.datastore.DataStoreCreator: Returns a new cache store.
newCompoundInterval(Interval, Set<AbstractParameter>) - Method in class org.protempa.proposition.AbstractParameterIntervalSectioner
newCompoundInterval(Interval, Set<Context>) - Method in class org.protempa.proposition.ContextIntervalSectioner
newCompoundInterval(Interval, Set<E>) - Method in class org.protempa.proposition.IntervalSectioner
newDataSourceBackendSection(String) - Method in class org.protempa.backend.AbstractConfigurations
newDataSourceBackendSection(String) - Method in interface org.protempa.backend.Configurations
newDataSourceInstance() - Method in class org.protempa.SourceFactory
newInstance(String) - Method in interface org.protempa.backend.BackendProvider
newInstance(String) - Method in class org.protempa.backend.test.MockBackendProvider
newInstance(String) - Static method in class org.protempa.Protempa
newInstance(SourceFactory) - Static method in class org.protempa.Protempa
newInstance(String, boolean) - Static method in class org.protempa.Protempa
newInstance(SourceFactory, boolean) - Static method in class org.protempa.Protempa
newKnowledgeSourceBackendSection(String) - Method in class org.protempa.backend.AbstractConfigurations
newKnowledgeSourceBackendSection(String) - Method in interface org.protempa.backend.Configurations
newKnowledgeSourceInstance() - Method in class org.protempa.SourceFactory
newTermSourceBackendSection(String) - Method in class org.protempa.backend.AbstractConfigurations
newTermSourceBackendSection(String) - Method in interface org.protempa.backend.Configurations
newTermSourceInstance() - Method in class org.protempa.SourceFactory
next() - Method in interface org.protempa.DataStreamingEventIterator: Returns the next DataStreamingEvent in the iteration.
next() - Method in class org.protempa.MultiplexingDataStreamingEventIterator
next() - Method in class org.protempa.QueryResults.QueryResultsIterator
nextDatabaseName() - Method in class org.protempa.datastore.AbstractDataStoreCreator
nextDatabaseName() - Method in class org.protempa.datastore.PropositionStoreCreator
nextDatabaseName() - Method in class org.protempa.datastore.UniqueIdUniqueIdStoreCreator
nextDatabaseName() - Method in class org.protempa.datastore.WorkingMemoryStoreCreator
NominalValue - Class in org.protempa.proposition.value: Represents a String value.
NominalValue(String) - Constructor for class org.protempa.proposition.value.NominalValue: Creates a new nominal value with the given value.
NominalValueBuilder - Class in org.protempa.proposition.value
NominalValueBuilder() - Constructor for class org.protempa.proposition.value.NominalValueBuilder
NominalValueBuilder(NominalValue) - Constructor for class org.protempa.proposition.value.NominalValueBuilder
NoSuchAlgorithmException - Exception in org.protempa
NoSuchAlgorithmException(Throwable) - Constructor for exception org.protempa.NoSuchAlgorithmException
NoSuchAlgorithmException(String) - Constructor for exception org.protempa.NoSuchAlgorithmException
NoSuchAlgorithmException(String, Throwable) - Constructor for exception org.protempa.NoSuchAlgorithmException
NoSuchAlgorithmException() - Constructor for exception org.protempa.NoSuchAlgorithmException
NotRecordedSourceId - Class in org.protempa
NotRecordedSourceIdBuilder - Class in org.protempa
NotRecordedSourceIdBuilder() - Constructor for class org.protempa.NotRecordedSourceIdBuilder
numActiveColumns() - Method in class org.protempa.dest.table.OutputConfig
NumberValue - Class in org.protempa.proposition.value: Represents a number, either integral or floating point, with unbounded upper and lower limit (subject to available memory).
NumberValue(long) - Constructor for class org.protempa.proposition.value.NumberValue
NumberValue(double) - Constructor for class org.protempa.proposition.value.NumberValue
NumberValue(BigDecimal) - Constructor for class org.protempa.proposition.value.NumberValue
NumberValueBuilder - Class in org.protempa.proposition.value
NumberValueBuilder() - Constructor for class org.protempa.proposition.value.NumberValueBuilder
NumberValueBuilder(NumberValue) - Constructor for class org.protempa.proposition.value.NumberValueBuilder
NumericalValue - Interface in org.protempa.proposition.value: Represents numerical values.
NumericalValueBuilder - Interface in org.protempa.proposition.value

O

OrderedValue - Interface in org.protempa.proposition.value: A marker interface for indicating that an implementation of Value represents values that have an intrinsic order.
OrderedValueBuilder - Interface in org.protempa.proposition.value
OrdinalValue - Class in org.protempa.proposition.value: Represents ordinal string values.
OrdinalValueBuilder - Class in org.protempa.proposition.value
OrdinalValueBuilder() - Constructor for class org.protempa.proposition.value.OrdinalValueBuilder
OrdinalValueBuilder(OrdinalValue) - Constructor for class org.protempa.proposition.value.OrdinalValueBuilder
org.protempa - package org.protempa
org.protempa.backend - package org.protempa.backend
org.protempa.backend.annotations - package org.protempa.backend.annotations
org.protempa.backend.asb - package org.protempa.backend.asb
org.protempa.backend.asb.java - package org.protempa.backend.asb.java
org.protempa.backend.dsb - package org.protempa.backend.dsb
org.protempa.backend.dsb.filter - package org.protempa.backend.dsb.filter
org.protempa.backend.ksb - package org.protempa.backend.ksb
org.protempa.backend.test - package org.protempa.backend.test
org.protempa.backend.tsb - package org.protempa.backend.tsb
org.protempa.cli - package org.protempa.cli
org.protempa.datastore - package org.protempa.datastore
org.protempa.dest - package org.protempa.dest
org.protempa.dest.deid - package org.protempa.dest.deid
org.protempa.dest.keyloader - package org.protempa.dest.keyloader
org.protempa.dest.map - package org.protempa.dest.map
org.protempa.dest.proplist - package org.protempa.dest.proplist
org.protempa.dest.table - package org.protempa.dest.table
org.protempa.dest.xml - package org.protempa.dest.xml
org.protempa.graph - package org.protempa.graph
org.protempa.proposition - package org.protempa.proposition
org.protempa.proposition.comparator - package org.protempa.proposition.comparator
org.protempa.proposition.interval - package org.protempa.proposition.interval
org.protempa.proposition.stats - package org.protempa.proposition.stats
org.protempa.proposition.value - package org.protempa.proposition.value
org.protempa.proposition.visitor - package org.protempa.proposition.visitor
org.protempa.query - package org.protempa.query
org.protempa.valueset - package org.protempa.valueset
org.protempa.xml - package org.protempa.xml
OTHER - Static variable in class org.protempa.dest.deid.DeidAttributes
OutputConfig - Class in org.protempa.dest.table: An immutable class for configurating TableColumnSpecs.
OutputConfig() - Constructor for class org.protempa.dest.table.OutputConfig
OutputConfig(boolean, boolean, boolean, boolean, boolean, boolean, boolean, String, String, String, String, String, String, String) - Constructor for class org.protempa.dest.table.OutputConfig
OutputConfigBuilder - Class in org.protempa.dest.table: A bean-like class for creating OutputConfig configuration objects.
OutputConfigBuilder() - Constructor for class org.protempa.dest.table.OutputConfigBuilder
OVERLAPPED_BY - Static variable in class org.protempa.proposition.interval.Relation
OVERLAPS - Static variable in class org.protempa.proposition.interval.Relation

P

parameter(String) - Method in class org.protempa.AbstractAlgorithm
parameter(String) - Method in interface org.protempa.Algorithm: Returns the named parameter.
Parameter - Interface in org.protempa.proposition: Represents a single element of patient data or information, such as a time-stamped raw data value or an inferred interval.
ParameterDefinition - Interface in org.protempa
parse(String, String) - Method in enum org.protempa.backend.BackendPropertyType
parse(String) - Static method in class org.protempa.proposition.value.BooleanValue: Parses a boolean from a string.
parse(String) - Static method in class org.protempa.proposition.value.DateValue: Parses a date from a string.
parse(String) - Static method in class org.protempa.proposition.value.InequalityNumberValue: Parses a number with an inequality from a string, e.g., "> 100".
parse(String) - Static method in class org.protempa.proposition.value.NumberValue: Parses a number from a string.
parse(String) - Static method in enum org.protempa.proposition.value.ValueComparator: Gets the comparison object corresponding to the given mathematical comparison symbol.
parse(String) - Method in enum org.protempa.proposition.value.ValueType: Creates a Value instance by parsing the given string.
parseGranularityFactory(String) - Method in class org.protempa.backend.AbstractCommonsDataSourceBackend
parseProperty(String, String) - Method in class org.protempa.backend.BackendInstanceSpec
parseProperty(BackendInstanceSpec, BackendPropertySpec, String) - Method in enum org.protempa.backend.BackendPropertyType
parseUnitFactory(String) - Method in class org.protempa.backend.AbstractCommonsDataSourceBackend
POS_EPSILON - Static variable in class org.protempa.graph.WeightFactory: Special value representing the smallest possible positive value.
POS_INFINITY - Static variable in class org.protempa.graph.WeightFactory: Special value representing positive infinity.
PositionFilter - Class in org.protempa.backend.dsb.filter: A filter for a position (e.g., date/time) range.
PositionFilter(String[], Long, Granularity, Long, Granularity) - Constructor for class org.protempa.backend.dsb.filter.PositionFilter: Creates a filter with a position range.
PositionFilter(String[], Long, Granularity, Long, Granularity, Interval.Side, Interval.Side) - Constructor for class org.protempa.backend.dsb.filter.PositionFilter: Initializes a filter with a position range.
prepare(Query) - Method in class org.protempa.Protempa: Create a QuerySession object, which can be used by the caller to further filter or drill the results of the initial query that is passed in.
PrimitiveParameter - Class in org.protempa.proposition: A raw data parameter with a timestamp (or other position value).
PrimitiveParameter(String, UniqueId) - Constructor for class org.protempa.proposition.PrimitiveParameter: Creates a parameter with an identification string.
PrimitiveParameterDefinition - Class in org.protempa: Defines measurable or observable time-stamped data types.
PrimitiveParameterDefinition(String) - Constructor for class org.protempa.PrimitiveParameterDefinition
PrintAbstractedFrom - Class in org.protempa.cli
PrintAbstractedFrom() - Constructor for class org.protempa.cli.PrintAbstractedFrom
PrintAbstractedInto - Class in org.protempa.cli
PrintAbstractedInto() - Constructor for class org.protempa.cli.PrintAbstractedInto
printException(Exception) - Method in class org.protempa.cli.CLI: Prints to the console an exception's message and its nested exception's message (if any).
PrintInverseIsA - Class in org.protempa.cli
PrintInverseIsA() - Constructor for class org.protempa.cli.PrintInverseIsA
PrintIsA - Class in org.protempa.cli
PrintIsA() - Constructor for class org.protempa.cli.PrintIsA
PrintPropositionDefinition - Class in org.protempa.cli: Prints a specified proposition definition to the console.
PrintPropositionDefinition() - Constructor for class org.protempa.cli.PrintPropositionDefinition
PrintPropositionDefinitionsForTerm - Class in org.protempa.cli: Prints the ids of the proposition definitions that are associated with a given term.
PrintPropositionDefinitionsForTerm() - Constructor for class org.protempa.cli.PrintPropositionDefinitionsForTerm
PrintSubtreeInDataSource - Class in org.protempa.cli
PrintSubtreeInDataSource() - Constructor for class org.protempa.cli.PrintSubtreeInDataSource
PrintTerm - Class in org.protempa.cli: Prints a specified term to the console.
PrintTerm() - Constructor for class org.protempa.cli.PrintTerm
PrintTermChildren - Class in org.protempa.cli: Prints a term's children.
PrintTermChildren() - Constructor for class org.protempa.cli.PrintTermChildren
processOptionsAndArgs(String[]) - Method in class org.protempa.cli.CLI: Processes command line options.
PROPERTIES_BASE_NAME_NULL - Static variable in annotation type org.protempa.backend.annotations.BackendInfo
PropertyConstraint - Class in org.protempa.dest.table: Specifies a constraint on the value of a proposition property.
PropertyConstraint(String, ValueComparator, Value) - Constructor for class org.protempa.dest.table.PropertyConstraint: Constructs a property constraint with a property name, comparator and one or more values.
PropertyConstraint - Class in org.protempa
PropertyConstraint() - Constructor for class org.protempa.PropertyConstraint
propertyDefinition(String) - Method in class org.protempa.AbstractPropositionDefinition
PropertyDefinition - Class in org.protempa: Defines a property of a proposition definition.
PropertyDefinition(String, String, String, ValueType, String, String) - Constructor for class org.protempa.PropertyDefinition
PropertyDefinition(String, String, String, ValueType, String, String, Attribute[]) - Constructor for class org.protempa.PropertyDefinition: Initializes the property definition with a displayName, a value type and a value set.
propertyDefinition(String) - Method in interface org.protempa.PropositionDefinition
PropertyDefinitionBuilder - Class in org.protempa
PropertyDefinitionBuilder() - Constructor for class org.protempa.PropertyDefinitionBuilder
PropertyDefinitionBuilder(PropertyDefinition) - Constructor for class org.protempa.PropertyDefinitionBuilder
PropertyValueFilter - Class in org.protempa.backend.dsb.filter: For specifying constraints on the value of a property of a proposition.
PropertyValueFilter(String[], String, ValueComparator, Value...) - Constructor for class org.protempa.backend.dsb.filter.PropertyValueFilter: Instantiate with the proposition ids to which this filter applies, the property to which this filter applies, the operator and a value.
Proposition - Interface in org.protempa.proposition: A data element.
PropositionCheckedVisitable - Interface in org.protempa.proposition.visitor: Interface for accepting a proposition visitor that might throw a checked exception.
PropositionCheckedVisitor - Interface in org.protempa.proposition.visitor: Interface for classes that do processing on propositions.
PropositionColumnSpec - Class in org.protempa.dest.table
PropositionColumnSpec(String[]) - Constructor for class org.protempa.dest.table.PropositionColumnSpec
PropositionColumnSpec(String, String[]) - Constructor for class org.protempa.dest.table.PropositionColumnSpec
PropositionColumnSpec(String[], OutputConfig, ValueOutputConfig) - Constructor for class org.protempa.dest.table.PropositionColumnSpec
PropositionColumnSpec(String[], OutputConfig, ValueOutputConfig, Link[]) - Constructor for class org.protempa.dest.table.PropositionColumnSpec
PropositionColumnSpec(String[], OutputConfig, ValueOutputConfig, Link[], int) - Constructor for class org.protempa.dest.table.PropositionColumnSpec
PropositionColumnSpec(String, String[], OutputConfig, ValueOutputConfig, Link[], int) - Constructor for class org.protempa.dest.table.PropositionColumnSpec
PropositionDefinition - Interface in org.protempa: Foundation type for all objects that go in a Knowledge Base.
PropositionDefinitionCheckedVisitable - Interface in org.protempa: Interface for accepting a proposition definition visitor.
PropositionDefinitionCheckedVisitor - Interface in org.protempa: Interface for classes that do processing on abstraction definitions and may throw an exception.
PropositionDefinitionDisplayNameComparator() - Constructor for class org.protempa.ProtempaUtil.PropositionDefinitionDisplayNameComparator: Instantiates this comparator with the default display name style (Style.REGULAR.
PropositionDefinitionDisplayNameComparator(ProtempaUtil.PropositionDefinitionDisplayNameComparator.Style) - Constructor for class org.protempa.ProtempaUtil.PropositionDefinitionDisplayNameComparator: Instantiates this comparator to use the short or long display names when doing comparisons.
PropositionDefinitionVisitable - Interface in org.protempa: Interface for accepting a proposition definition visitor.
PropositionDefinitionVisitor - Interface in org.protempa: Interface for classes that do processing on abstraction definitions.
PropositionListDestination - Class in org.protempa.dest.proplist: Destination containing one row per proposition, with delimited columns containing attributes of each proposition.
PropositionListQueryResultsHandler - Class in org.protempa.dest.proplist: An implementation of QueryResultsHandler providing functionality for writing the results to an output stream in a tab-delimited format.
PropositionListQueryResultsHandler(BufferedWriter) - Constructor for class org.protempa.dest.proplist.PropositionListQueryResultsHandler: Instantiates this handler to write to a Writer.
PropositionListQueryResultsHandler(BufferedWriter, boolean) - Constructor for class org.protempa.dest.proplist.PropositionListQueryResultsHandler
PropositionListQueryResultsHandler(BufferedWriter, List<? extends Comparator<Proposition>>) - Constructor for class org.protempa.dest.proplist.PropositionListQueryResultsHandler: Instantiates this handler to write to a Writer with optional sorting of propositions.
PropositionListQueryResultsHandler(BufferedWriter, List<? extends Comparator<Proposition>>, boolean) - Constructor for class org.protempa.dest.proplist.PropositionListQueryResultsHandler
PropositionStoreCreator - Class in org.protempa.datastore: A permanent store mapping key IDs to lists of propositions.
PropositionStoreCreator() - Constructor for class org.protempa.datastore.PropositionStoreCreator
PropositionStoreCreator(String) - Constructor for class org.protempa.datastore.PropositionStoreCreator
PropositionUtil - Class in org.protempa.proposition
PropositionValueColumnSpec - Class in org.protempa.dest.table: Creates a column with an aggregation of primitive parameters with numerical values.
PropositionValueColumnSpec(Link[], PropositionValueColumnSpec.Type) - Constructor for class org.protempa.dest.table.PropositionValueColumnSpec
PropositionValueColumnSpec(String, Link[], PropositionValueColumnSpec.Type) - Constructor for class org.protempa.dest.table.PropositionValueColumnSpec
PropositionValueColumnSpec.Type - Enum in org.protempa.dest.table
PropositionVisitable - Interface in org.protempa.proposition.visitor: Interface for accepting a proposition visitor.
PropositionVisitor - Interface in org.protempa.proposition.visitor: Interface for classes that do processing on propositions.
Protempa - Class in org.protempa: Main PROTEMPA API.
Protempa(DataSource, KnowledgeSource, AlgorithmSource, TermSource) - Constructor for class org.protempa.Protempa: Constructor that configures PROTEMPA not to cache found abstract parameters.
Protempa(DataSource, KnowledgeSource, AlgorithmSource, TermSource, boolean) - Constructor for class org.protempa.Protempa: Constructor that lets the user specify whether or not to cache found abstract parameters.
ProtempaAlreadyClosedException - Exception in org.protempa: A cause of FinderExceptions when a query is attempted while Protempa is closed.
ProtempaAlreadyClosedException() - Constructor for exception org.protempa.ProtempaAlreadyClosedException
ProtempaException - Exception in org.protempa: Base class for PROTEMPA checked exceptions.
ProtempaException() - Constructor for exception org.protempa.ProtempaException
ProtempaException(String, Throwable) - Constructor for exception org.protempa.ProtempaException
ProtempaException(String) - Constructor for exception org.protempa.ProtempaException
ProtempaException(Throwable) - Constructor for exception org.protempa.ProtempaException
ProtempaStartupException - Exception in org.protempa: Exception for errors that occur when PROTEMPA is being initialized.
ProtempaUtil - Class in org.protempa: Utility methods for the PROTEMPA project.
ProtempaUtil.PropositionDefinitionDisplayNameComparator - Class in org.protempa: Comparator for comparing proposition definitions by display name.
ProtempaUtil.PropositionDefinitionDisplayNameComparator.Style - Enum in org.protempa: For specifying which display name style to use.
ProviderBasedLocalUniqueId - Class in org.protempa.proposition
ProviderBasedLocalUniqueId(LocalUniqueIdValuesProvider) - Constructor for class org.protempa.proposition.ProviderBasedLocalUniqueId
ProviderBasedUniqueIdFactory - Class in org.protempa.proposition
ProviderBasedUniqueIdFactory(LocalUniqueIdValuesProvider) - Constructor for class org.protempa.proposition.ProviderBasedUniqueIdFactory
put(String, List) - Method in class org.protempa.DataSourceResultMap
putAll(Map<? extends String, ? extends List>) - Method in class org.protempa.DataSourceResultMap

Q

Query - Class in org.protempa.query: Base query implementation.
Query(String[], Filter, String[], And<String>[], PropositionDefinition[], QueryMode) - Constructor for class org.protempa.query.Query: Creates new Query instance with a default identifier.
Query(String, String[], Filter, String[], And<String>[], PropositionDefinition[], QueryMode) - Constructor for class org.protempa.query.Query: Creates new Query instance.
Query(String, String, String[], Filter, String[], And<String>[], PropositionDefinition[], QueryMode) - Constructor for class org.protempa.query.Query
QueryBuilder - Interface in org.protempa.query: A query specification.
QueryBuildException - Exception in org.protempa.query
QueryBuildException(Throwable) - Constructor for exception org.protempa.query.QueryBuildException
QueryBuildException(String, Throwable) - Constructor for exception org.protempa.query.QueryBuildException
QueryBuildException(String) - Constructor for exception org.protempa.query.QueryBuildException
QueryBuildException() - Constructor for exception org.protempa.query.QueryBuildException
QueryException - Exception in org.protempa: Thrown when a Protempa query fails.
QueryException(String, Throwable) - Constructor for exception org.protempa.QueryException
QueryMode - Enum in org.protempa.query
QueryResults - Class in org.protempa
QueryResults.QueryResultsEntry - Class in org.protempa
QueryResults.QueryResultsIterator - Class in org.protempa
QueryResultsHandler - Interface in org.protempa.dest: Interface defining the operations for handling results of a Protempa query.
QueryResultsHandlerCloseException - Exception in org.protempa.dest
QueryResultsHandlerCloseException() - Constructor for exception org.protempa.dest.QueryResultsHandlerCloseException
QueryResultsHandlerCloseException(String, Throwable) - Constructor for exception org.protempa.dest.QueryResultsHandlerCloseException
QueryResultsHandlerCloseException(String) - Constructor for exception org.protempa.dest.QueryResultsHandlerCloseException
QueryResultsHandlerCloseException(Throwable) - Constructor for exception org.protempa.dest.QueryResultsHandlerCloseException
QueryResultsHandlerInitException - Exception in org.protempa.dest
QueryResultsHandlerInitException() - Constructor for exception org.protempa.dest.QueryResultsHandlerInitException
QueryResultsHandlerInitException(String, Throwable) - Constructor for exception org.protempa.dest.QueryResultsHandlerInitException
QueryResultsHandlerInitException(String) - Constructor for exception org.protempa.dest.QueryResultsHandlerInitException
QueryResultsHandlerInitException(Throwable) - Constructor for exception org.protempa.dest.QueryResultsHandlerInitException
QueryResultsHandlerProcessingException - Exception in org.protempa.dest
QueryResultsHandlerProcessingException() - Constructor for exception org.protempa.dest.QueryResultsHandlerProcessingException
QueryResultsHandlerProcessingException(String, Throwable) - Constructor for exception org.protempa.dest.QueryResultsHandlerProcessingException
QueryResultsHandlerProcessingException(String) - Constructor for exception org.protempa.dest.QueryResultsHandlerProcessingException
QueryResultsHandlerProcessingException(Throwable) - Constructor for exception org.protempa.dest.QueryResultsHandlerProcessingException
QueryResultsHandlerValidationFailedException - Exception in org.protempa.dest
QueryResultsHandlerValidationFailedException(Throwable) - Constructor for exception org.protempa.dest.QueryResultsHandlerValidationFailedException
QueryResultsHandlerValidationFailedException(String) - Constructor for exception org.protempa.dest.QueryResultsHandlerValidationFailedException
QueryResultsHandlerValidationFailedException(String, Throwable) - Constructor for exception org.protempa.dest.QueryResultsHandlerValidationFailedException
QueryResultsHandlerValidationFailedException() - Constructor for exception org.protempa.dest.QueryResultsHandlerValidationFailedException
QuerySession - Class in org.protempa: Models a query followed by data exploration.
QueryValidationException - Exception in org.protempa

R

readAbstractedFrom(AbstractionDefinition) - Method in interface org.protempa.KnowledgeSource
readAbstractedFrom(String) - Method in interface org.protempa.KnowledgeSource
readAbstractedFrom(AbstractionDefinition) - Method in class org.protempa.KnowledgeSourceImpl
readAbstractedFrom(String) - Method in class org.protempa.KnowledgeSourceImpl
readAbstractedInto(String) - Method in interface org.protempa.backend.ksb.KnowledgeSourceBackend
readAbstractedInto(String) - Method in class org.protempa.backend.ksb.SimpleKnowledgeSourceBackend
readAbstractedInto(PropositionDefinition) - Method in interface org.protempa.KnowledgeSource
readAbstractedInto(String) - Method in interface org.protempa.KnowledgeSource
readAbstractedInto(PropositionDefinition) - Method in class org.protempa.KnowledgeSourceImpl
readAbstractedInto(String) - Method in class org.protempa.KnowledgeSourceImpl
readAbstractionDefinition(String) - Method in interface org.protempa.backend.ksb.KnowledgeSourceBackend
readAbstractionDefinition(String) - Method in class org.protempa.backend.ksb.SimpleKnowledgeSourceBackend
readAbstractionDefinition(String) - Method in interface org.protempa.KnowledgeSource
readAbstractionDefinition(String) - Method in class org.protempa.KnowledgeSourceImpl
readAbstractionDefinitions(String[]) - Method in interface org.protempa.backend.ksb.KnowledgeSourceBackend
readAbstractionDefinitions(String[]) - Method in class org.protempa.backend.ksb.SimpleKnowledgeSourceBackend
readAbstractionDefinitions(String...) - Method in interface org.protempa.KnowledgeSource
readAbstractionDefinitions(String...) - Method in class org.protempa.KnowledgeSourceImpl
readAbstractProposition(ObjectInputStream) - Method in class org.protempa.proposition.AbstractProposition
readAlgorithm(String) - Method in interface org.protempa.AlgorithmSource: Read an algorithm with the given id.
readAlgorithm(String) - Method in class org.protempa.AlgorithmSourceImpl: Read an algorithm with the given id.
readAlgorithm(String, Algorithms) - Method in interface org.protempa.backend.asb.AlgorithmSourceBackend: Reads an algorithm from this backend.
readAlgorithm(String, Algorithms) - Method in class org.protempa.backend.asb.java.AbstractJavaAlgorithmBackend
readAlgorithms() - Method in interface org.protempa.AlgorithmSource: Reads all algorithms in this algorithm source.
readAlgorithms() - Method in class org.protempa.AlgorithmSourceImpl: Reads all algorithms in this algorithm source.
readAlgorithms(Algorithms) - Method in interface org.protempa.backend.asb.AlgorithmSourceBackend: Read the available algorithms.
readAlgorithms(Algorithms) - Method in class org.protempa.backend.asb.java.AbstractJavaAlgorithmBackend
readContextDefinition(String) - Method in interface org.protempa.backend.ksb.KnowledgeSourceBackend
readContextDefinition(String) - Method in class org.protempa.backend.ksb.SimpleKnowledgeSourceBackend
readContextDefinition(String) - Method in interface org.protempa.KnowledgeSource
readContextDefinition(String) - Method in class org.protempa.KnowledgeSourceImpl
readContextDefinitions(String[]) - Method in interface org.protempa.backend.ksb.KnowledgeSourceBackend
readContextDefinitions(String[]) - Method in class org.protempa.backend.ksb.SimpleKnowledgeSourceBackend
readContextDefinitions(String...) - Method in interface org.protempa.KnowledgeSource
readContextDefinitions(String...) - Method in class org.protempa.KnowledgeSourceImpl
readInducedBy(String) - Method in interface org.protempa.KnowledgeSource
readInducedBy(ContextDefinition) - Method in interface org.protempa.KnowledgeSource
readInducedBy(String) - Method in class org.protempa.KnowledgeSourceImpl
readInducedBy(ContextDefinition) - Method in class org.protempa.KnowledgeSourceImpl
readInduces(String) - Method in interface org.protempa.backend.ksb.KnowledgeSourceBackend
readInduces(String) - Method in class org.protempa.backend.ksb.SimpleKnowledgeSourceBackend
readInduces(String) - Method in interface org.protempa.KnowledgeSource
readInduces(TemporalPropositionDefinition) - Method in interface org.protempa.KnowledgeSource
readInduces(TemporalPropositionDefinition) - Method in class org.protempa.KnowledgeSourceImpl
readInduces(String) - Method in class org.protempa.KnowledgeSourceImpl
readInverseIsA(PropositionDefinition) - Method in interface org.protempa.KnowledgeSource
readInverseIsA(String) - Method in interface org.protempa.KnowledgeSource
readInverseIsA(PropositionDefinition) - Method in class org.protempa.KnowledgeSourceImpl
readInverseIsA(String) - Method in class org.protempa.KnowledgeSourceImpl
readIsA(String) - Method in interface org.protempa.backend.ksb.KnowledgeSourceBackend
readIsA(String) - Method in class org.protempa.backend.ksb.SimpleKnowledgeSourceBackend
readIsA(PropositionDefinition) - Method in interface org.protempa.KnowledgeSource
readIsA(String) - Method in interface org.protempa.KnowledgeSource
readIsA(PropositionDefinition) - Method in class org.protempa.KnowledgeSourceImpl
readIsA(String) - Method in class org.protempa.KnowledgeSourceImpl
readParents(PropositionDefinition) - Method in interface org.protempa.KnowledgeSource
readParents(String) - Method in interface org.protempa.KnowledgeSource
readParents(PropositionDefinition) - Method in class org.protempa.KnowledgeSourceImpl
readParents(String) - Method in class org.protempa.KnowledgeSourceImpl
readPropositionDefinition(String) - Method in interface org.protempa.backend.ksb.KnowledgeSourceBackend: Reads a proposition definition into the given PROTEMPA knowledge base.
readPropositionDefinition(String) - Method in class org.protempa.backend.ksb.SimpleKnowledgeSourceBackend
readPropositionDefinition(String) - Method in interface org.protempa.KnowledgeSource: Returns the specified proposition definition.
readPropositionDefinition(String) - Method in class org.protempa.KnowledgeSourceImpl: Returns the specified proposition definition.
readPropositionDefinitions(String[]) - Method in interface org.protempa.backend.ksb.KnowledgeSourceBackend
readPropositionDefinitions(String[]) - Method in class org.protempa.backend.ksb.SimpleKnowledgeSourceBackend
readPropositionDefinitions(String...) - Method in interface org.protempa.KnowledgeSource
readPropositionDefinitions(String...) - Method in class org.protempa.KnowledgeSourceImpl
readPropositions(Set<String>, Set<String>, Filter, QuerySession, QueryResultsHandler) - Method in interface org.protempa.backend.dsb.DataSourceBackend
readPropositions(Set<String>, Set<String>, Filter, QuerySession, QueryResultsHandler) - Method in interface org.protempa.DataSource
readPropositions(Set<String>, Set<String>, Filter, QuerySession, QueryResultsHandler) - Method in class org.protempa.DataSourceImpl
readQueryAsXML(File, KnowledgeSource, AlgorithmSource) - Static method in class org.protempa.xml.XMLConfiguration: Read XML from the specified file that describes a Protempa query and create the query.
readQueryAsXML(URL, KnowledgeSource, AlgorithmSource) - Static method in class org.protempa.xml.XMLConfiguration: Read XML from the specified URL that describes a Protempa query and create the query.
readQueryAsXML(Reader, KnowledgeSource, AlgorithmSource) - Static method in class org.protempa.xml.XMLConfiguration: Read XML from the specified Reader that describes a Protempa query and create the query.
readQueryAsXML(InputStream, KnowledgeSource, AlgorithmSource) - Static method in class org.protempa.xml.XMLConfiguration: Read XML from the specified input stream that describes a Protempa query and create the query.
readQueryAsXML(String, KnowledgeSource, AlgorithmSource) - Static method in class org.protempa.xml.XMLConfiguration: Read XML from the specified string that describes a Protempa query and create the query.
readSubContextOfs(String) - Method in interface org.protempa.backend.ksb.KnowledgeSourceBackend
readSubContextOfs(String) - Method in class org.protempa.backend.ksb.SimpleKnowledgeSourceBackend
readSubContextOfs(String) - Method in interface org.protempa.KnowledgeSource
readSubContextOfs(ContextDefinition) - Method in interface org.protempa.KnowledgeSource
readSubContextOfs(String) - Method in class org.protempa.KnowledgeSourceImpl
readSubContextOfs(ContextDefinition) - Method in class org.protempa.KnowledgeSourceImpl
readSubContexts(String) - Method in interface org.protempa.KnowledgeSource
readSubContexts(ContextDefinition) - Method in interface org.protempa.KnowledgeSource
readSubContexts(String) - Method in class org.protempa.KnowledgeSourceImpl
readSubContexts(ContextDefinition) - Method in class org.protempa.KnowledgeSourceImpl
readTableQueryResultsHandlerAsXML(URL, BufferedWriter, KnowledgeSource) - Static method in class org.protempa.xml.XMLConfiguration: Read XML from the specified URL that describes a Protempa TableQueryResultsHandler and create the TableQueryResultsHandler.
readTableQueryResultsHandlerAsXML(Reader, BufferedWriter, KnowledgeSource) - Static method in class org.protempa.xml.XMLConfiguration: Read XML from the specified Reader that describes a Protempa TableQueryResultsHandler and create the TableQueryResultsHandler.
readTableQueryResultsHandlerAsXML(InputStream, BufferedWriter, KnowledgeSource) - Static method in class org.protempa.xml.XMLConfiguration: Read XML from the specified InputStream that describes a Protempa TableQueryResultsHandler and create the TableQueryResultsHandler.
readTableQueryResultsHandlerAsXML(String, BufferedWriter, KnowledgeSource) - Static method in class org.protempa.xml.XMLConfiguration: Read XML from the specified string that describes a Protempa TableQueryResultsHandler and create the TableQueryResultsHandler.
readTableQueryResultsHandlerFactoryAsXML(File, BufferedWriter, KnowledgeSource) - Static method in class org.protempa.xml.XMLConfiguration: Read XML from the specified file that describes a Protempa TableQueryResultsHandler and create the TableQueryResultsHandler.
readTemporalParameter(ObjectInputStream) - Method in class org.protempa.proposition.TemporalParameter
readTemporalProposition(ObjectInputStream) - Method in class org.protempa.proposition.TemporalProposition: Called while deserializing a temporal proposition.
readTemporalPropositionDefinition(String) - Method in interface org.protempa.backend.ksb.KnowledgeSourceBackend
readTemporalPropositionDefinition(String) - Method in class org.protempa.backend.ksb.SimpleKnowledgeSourceBackend
readTemporalPropositionDefinition(String) - Method in interface org.protempa.KnowledgeSource
readTemporalPropositionDefinition(String) - Method in class org.protempa.KnowledgeSourceImpl
readTemporalPropositionDefinitions(String[]) - Method in interface org.protempa.backend.ksb.KnowledgeSourceBackend
readTemporalPropositionDefinitions(String[]) - Method in class org.protempa.backend.ksb.SimpleKnowledgeSourceBackend
readTemporalPropositionDefinitions(String...) - Method in interface org.protempa.KnowledgeSource
readTemporalPropositionDefinitions(String...) - Method in class org.protempa.KnowledgeSourceImpl
readTerm(String) - Method in class org.protempa.backend.tsb.AbstractTermSourceBackend: A default implementation that returns null
readTerm(String) - Method in interface org.protempa.backend.tsb.TermSourceBackend: Reads a term from the given terminology
readTerm(String) - Method in interface org.protempa.TermSource
readTerm(String) - Method in class org.protempa.TermSourceImpl
readTerms(String[]) - Method in class org.protempa.backend.tsb.AbstractTermSourceBackend: A default implementation that returns null
readTerms(String[]) - Method in interface org.protempa.backend.tsb.TermSourceBackend: Reads an array of terms from the given terminology
readValueSet(String) - Method in class org.protempa.backend.ksb.AbstractKnowledgeSourceBackend: A default implementation that returns null.
readValueSet(String) - Method in interface org.protempa.backend.ksb.KnowledgeSourceBackend: Reads the value set from the knowledge base and returns it.
readValueSet(String) - Method in interface org.protempa.KnowledgeSource
readValueSet(String) - Method in class org.protempa.KnowledgeSourceImpl
reattachSession(QuerySession) - Method in class org.protempa.Protempa
recalculateChildren() - Method in class org.protempa.AbstractPropositionDefinition
recalculateChildren() - Method in class org.protempa.CompoundLowLevelAbstractionDefinition
recalculateChildren() - Method in class org.protempa.ConstantDefinition
recalculateChildren() - Method in class org.protempa.ContextDefinition
recalculateChildren() - Method in class org.protempa.EventDefinition
recalculateChildren() - Method in class org.protempa.HighLevelAbstractionDefinition
recalculateChildren() - Method in class org.protempa.LowLevelAbstractionDefinition
recalculateChildren() - Method in class org.protempa.PrimitiveParameterDefinition
recalculateChildren() - Method in class org.protempa.SequentialTemporalPatternDefinition
recalculateChildren() - Method in class org.protempa.SliceDefinition
Reference(String, UniqueId) - Constructor for class org.protempa.datastore.UniqueIdUniqueIdStoreCreator.Reference
Reference - Class in org.protempa.dest.table: Specifies reference traversals from one proposition to other propositions.
Reference(String[]) - Constructor for class org.protempa.dest.table.Reference: Creates an instance that specifies traversals using the specified references from a proposition to all referred-to propositions.
Reference(String[], String[]) - Constructor for class org.protempa.dest.table.Reference: Creates an instance that specifies traversals using the specified references from a proposition only to propositions with the given ids.
Reference(String[], String[], PropertyConstraint[]) - Constructor for class org.protempa.dest.table.Reference: Creates an instance that specifies traversals using the specified references from a proposition only to propositions with the given ids and that satisfy the specified constraints.
Reference(String[], String[], PropertyConstraint[], Comparator<Proposition>, int) - Constructor for class org.protempa.dest.table.Reference: Creates an instance that specifies traversals using the specified references from a proposition only to propositions with the given ids and that satisfy the specified constraints.
Reference(String[], String[], PropertyConstraint[], Comparator<Proposition>, int, int) - Constructor for class org.protempa.dest.table.Reference: Creates an instance that specifies traversals using the specified references from a proposition only to propositions with the given ids and that satisfy the specified constraints.
Reference(String) - Constructor for class org.protempa.dest.table.Reference: Creates an instance that specifies traversals using the specified reference from a proposition to all referred-to propositions.
Reference(String, String[]) - Constructor for class org.protempa.dest.table.Reference: Creates an instance that specifies traversals using the specified reference from a proposition only to propositions with the given ids.
Reference(String, String[], PropertyConstraint[]) - Constructor for class org.protempa.dest.table.Reference: Creates an instance that specifies traversals using the specified references from a proposition only to propositions with the given ids and that satisfy the specified property constraints.
Reference(String, String[], PropertyConstraint[], Comparator<Proposition>, int) - Constructor for class org.protempa.dest.table.Reference: Creates an instance that specifies traversals using the specified reference from a proposition only to propositions with the given ids and that satisfy the specified property constraints.
Reference(String, String[], PropertyConstraint[], Comparator<Proposition>, int, int) - Constructor for class org.protempa.dest.table.Reference: Creates an instance that specifies traversals using the specified reference from a proposition only to propositions with the given ids and that satisfy the specified constraints.
referenceDefinition(String) - Method in class org.protempa.AbstractPropositionDefinition
referenceDefinition(String) - Method in interface org.protempa.PropositionDefinition: Returns the reference definition with the given name.
ReferenceDefinition - Class in org.protempa: Defines a proposition definition's references.
ReferenceDefinition(String, String, String[]) - Constructor for class org.protempa.ReferenceDefinition
RegressionLine - Class in org.protempa.proposition.stats: A class for manipulating regression lines.
RegressionLine(Segment<PrimitiveParameter>) - Constructor for class org.protempa.proposition.stats.RegressionLine: Creates a new regression line of points.
RegressionLine.NullValueException - Exception in org.protempa.proposition.stats
Relation - Class in org.protempa.proposition.interval: A representation of the temporal relationship between two intervals, as described in Stillman et al.
Relation() - Constructor for class org.protempa.proposition.interval.Relation
Relation(Integer, Unit, Integer, Unit, Integer, Unit, Integer, Unit, Integer, Unit, Integer, Unit, Integer, Unit, Integer, Unit) - Constructor for class org.protempa.proposition.interval.Relation: Constructs a new Relation between two intervals from Weights and Units.
RelativeDayGranularity - Class in org.protempa.proposition.value: Defines units of relative time.
RelativeDayGranularityFactory - Class in org.protempa.proposition.value: Access to RelativeDayGranularity objects.
RelativeDayGranularityFactory() - Constructor for class org.protempa.proposition.value.RelativeDayGranularityFactory
RelativeDayUnit - Class in org.protempa.proposition.value: Defines units of relative time.
RelativeDayUnitFactory - Class in org.protempa.proposition.value: Access to RelativeDayUnit objects.
RelativeDayUnitFactory() - Constructor for class org.protempa.proposition.value.RelativeDayUnitFactory
RelativeHourGranularity - Class in org.protempa.proposition.value: Defines units of relative time.
RelativeHourGranularityFactory - Class in org.protempa.proposition.value: Access to RelativeHourGranularity objects.
RelativeHourGranularityFactory() - Constructor for class org.protempa.proposition.value.RelativeHourGranularityFactory
RelativeHourUnit - Class in org.protempa.proposition.value: Defines units of relative time.
RelativeHourUnitFactory - Class in org.protempa.proposition.value: Access to RelativeHourUnit objects.
RelativeHourUnitFactory() - Constructor for class org.protempa.proposition.value.RelativeHourUnitFactory
remove(String) - Method in interface org.protempa.backend.Configurations: Deletes the configurations with the specified id.
remove(Object) - Method in class org.protempa.DataSourceResultMap
remove(Object) - Method in class org.protempa.graph.DirectedGraph: Remove a vertex and all edges between the vertex and other vertices.
remove(ExtendedPropositionDefinition) - Method in class org.protempa.HighLevelAbstractionDefinition: Removes an extended proposition definition, and all relations involving it.
remove(Object) - Method in class org.protempa.proposition.Sequence
remove(int) - Method in class org.protempa.proposition.Sequence
remove() - Method in class org.protempa.QueryResults.QueryResultsIterator
removeAll(Collection<?>) - Method in class org.protempa.proposition.Sequence
removeAllRelations(TemporalExtendedPropositionDefinition) - Method in class org.protempa.HighLevelAbstractionDefinition: Removes all relations involving a temporal extended proposition definition.
removeBackendListener(BackendListener<E>) - Method in class org.protempa.backend.AbstractBackend
removeBackendListener(BackendListener<E>) - Method in interface org.protempa.backend.Backend: Unregisters a listener so that changes to the backend are no longer sent.
removeDisplayNameOverride(String) - Method in class org.protempa.backend.BackendInstanceSpec
removePrimitiveParameterId(String) - Method in class org.protempa.LowLevelAbstractionDefinition: Removes a primitive parameter from which this abstraction is inferred.
removePropertyChangeListener(PropertyChangeListener) - Method in class org.protempa.AbstractPropositionDefinition
removePropertyChangeListener(String, PropertyChangeListener) - Method in class org.protempa.AbstractPropositionDefinition
removePropertyChangeListener(PropertyChangeListener) - Method in class org.protempa.proposition.AbstractProposition
removePropertyChangeListener(PropertyChangeListener) - Method in interface org.protempa.proposition.Proposition: Removes a PropertyChangeListener from the listener list.
removePropertyChangeListener(PropertyChangeListener) - Method in interface org.protempa.PropositionDefinition
removePropertyChangeListener(String, PropertyChangeListener) - Method in interface org.protempa.PropositionDefinition
removePropertyChangeListener(PropertyChangeListener) - Method in class org.protempa.query.And
removePropertyChangeListener(String, PropertyChangeListener) - Method in class org.protempa.query.And
removePropertyChangeListener(PropertyChangeListener) - Method in class org.protempa.query.DefaultQueryBuilder: Removes listeners for changes to this Query's properties.
removePropertyChangeListener(String, PropertyChangeListener) - Method in class org.protempa.query.DefaultQueryBuilder: Removes listeners for changes to the specified property.
removeRelation(TemporalExtendedPropositionDefinition, TemporalExtendedPropositionDefinition) - Method in class org.protempa.HighLevelAbstractionDefinition: Removes a relation between two temporal extended proposition definitions.
removeRequiredOverride(String) - Method in class org.protempa.backend.BackendInstanceSpec
removeSourceListener(SourceListener<S>) - Method in class org.protempa.AbstractSource: Removes a listener so that changes to the source are no longer sent.
removeSourceListener(SourceListener<S>) - Method in interface org.protempa.Source
replace() - Method in class org.protempa.proposition.value.BooleanValue
replace() - Method in class org.protempa.proposition.value.DateValue
replace() - Method in class org.protempa.proposition.value.InequalityNumberValue
replace() - Method in class org.protempa.proposition.value.NominalValue
replace() - Method in class org.protempa.proposition.value.NumberValue
replace() - Method in class org.protempa.proposition.value.OrdinalValue
replace() - Method in interface org.protempa.proposition.value.Value: Returns a value from a cache that is equal to this one, if such a value exists.
replace() - Method in class org.protempa.proposition.value.ValueList
reset() - Method in class org.protempa.AbstractAbstractionDefinition
reset() - Method in class org.protempa.AbstractPropositionDefinition: Resets this proposition definition to default values.
reset() - Method in class org.protempa.dest.table.OutputConfigBuilder
reset() - Method in class org.protempa.dest.table.ValueOutputConfigBuilder
reset() - Method in class org.protempa.HighLevelAbstractionDefinition
reset() - Method in class org.protempa.LowLevelAbstractionDefinition
reset() - Method in class org.protempa.PrimitiveParameterDefinition
reset() - Method in class org.protempa.SequentialTemporalPatternDefinition
reset() - Method in class org.protempa.SliceDefinition
resetState(Sequence<T>) - Method in class org.protempa.proposition.Segment
resetState(Sequence<T>, int, int) - Method in class org.protempa.proposition.Segment
retainAll(Collection<?>) - Method in class org.protempa.proposition.Sequence
RuleBaseInstantiationException - Exception in org.protempa
RuleBaseInstantiationException(Throwable) - Constructor for exception org.protempa.RuleBaseInstantiationException
RuleBaseInstantiationException(String) - Constructor for exception org.protempa.RuleBaseInstantiationException
RuleBaseInstantiationException(String, Throwable) - Constructor for exception org.protempa.RuleBaseInstantiationException
RuleBaseInstantiationException() - Constructor for exception org.protempa.RuleBaseInstantiationException
RuleCreationException - Exception in org.protempa: Thrown when an error occurs translating abstraction definitions into rules.
RuleCreationException() - Constructor for exception org.protempa.RuleCreationException
RuleCreationException(String, Throwable) - Constructor for exception org.protempa.RuleCreationException
RuleCreationException(String) - Constructor for exception org.protempa.RuleCreationException
RuleCreationException(Throwable) - Constructor for exception org.protempa.RuleCreationException

S

save(Configuration) - Method in interface org.protempa.backend.Configurations: Writes the provided backend specifications to the configurations with the specified id.
SECOND - Static variable in class org.protempa.proposition.value.AbsoluteTimeGranularity
SECOND - Static variable in class org.protempa.proposition.value.AbsoluteTimeUnit
Segment<T extends TemporalProposition> - Class in org.protempa.proposition: A segment of a sequence of Parameter objects provided to Detector instances' satisfiedBy() method.
Segment(Sequence<T>, int, int) - Constructor for class org.protempa.proposition.Segment
Segment(Sequence<T>) - Constructor for class org.protempa.proposition.Segment
Segment(Segment<T>) - Constructor for class org.protempa.proposition.Segment
Sequence<T extends TemporalProposition> - Class in org.protempa.proposition: A list of Propositions sorted chronologically.
Sequence(String) - Constructor for class org.protempa.proposition.Sequence
Sequence(String, int) - Constructor for class org.protempa.proposition.Sequence
Sequence(Set<String>) - Constructor for class org.protempa.proposition.Sequence
Sequence(String, List<T>) - Constructor for class org.protempa.proposition.Sequence
Sequence(Set<String>, List<T>) - Constructor for class org.protempa.proposition.Sequence
SequentialTemporalPatternDefinition - Class in org.protempa
SequentialTemporalPatternDefinition(String) - Constructor for class org.protempa.SequentialTemporalPatternDefinition
SequentialTemporalPatternDefinition.SubsequentTemporalExtendedPropositionDefinition - Class in org.protempa
set(int, T) - Method in class org.protempa.proposition.Sequence
setAbbrevDisplayName(String) - Method in class org.protempa.Term
setAbbrevDisplayName(String) - Method in class org.protempa.valueset.ValueSetElementBuilder
setAbbrevDisplayNameHeading(String) - Method in class org.protempa.dest.table.OutputConfigBuilder
setAbbreviatedDisplayName(String) - Method in class org.protempa.AbstractPropositionDefinition: Sets this knowledge definition's abbreviated display name.
setAbbreviatedDisplayName(String) - Method in class org.protempa.ExtendedPropositionDefinition
setAccessed(Date) - Method in class org.protempa.AbstractPropositionDefinition
setAdvanceRowSkipEnd(int) - Method in class org.protempa.AbstractAlgorithm
setAlgorithmId(String) - Method in class org.protempa.LowLevelAbstractionDefinition
setAlgorithms(String) - Method in class org.protempa.backend.asb.java.JavaAlgorithmBackend
setAlgorithmSourceBackendSections(List<BackendInstanceSpec<AlgorithmSourceBackend>>) - Method in class org.protempa.backend.Configuration
setAllowPartialMatches(boolean) - Method in class org.protempa.SequentialTemporalPatternDefinition: Sets whether to match if only the first, first and second, etc.
setAnd(Filter) - Method in class org.protempa.backend.dsb.filter.AbstractFilter
setAnded(List<E>) - Method in class org.protempa.query.And
setAttributeBuilders(AttributeBuilder[]) - Method in class org.protempa.valueset.ValueSetElementBuilder
setAttributes(Attribute[]) - Method in class org.protempa.AbstractPropositionDefinition
setBackendProvider(BackendProvider) - Static method in class org.protempa.backend.BackendProviderManager
setBackendProviderClassLoader(ClassLoader) - Static method in class org.protempa.backend.BackendProviderManager: Sets the class loader to use for loading a BackendProvider.
setChildrenToParents(Map<String, String>) - Method in class org.protempa.dest.DefaultStatisticsBuilder
setComparator(ValueComparator) - Method in class org.protempa.proposition.value.InequalityNumberValueBuilder
setConcatenable(boolean) - Method in class org.protempa.CompoundLowLevelAbstractionDefinition: Sets whether this type of compound low-level abstraction is concatenable.
setConcatenable(boolean) - Method in class org.protempa.HighLevelAbstractionDefinition: Sets whether this type of high-level abstraction is concatenable.
setConcatenable(boolean) - Method in class org.protempa.LowLevelAbstractionDefinition: Sets whether this type of low-level abstraction is concatenable.
setConcatenable(boolean) - Method in class org.protempa.SequentialTemporalPatternDefinition: Sets whether this type of high-level abstraction is concatenable.
setConfigurationId(String) - Method in class org.protempa.backend.Configuration
setConfigurationsId(String) - Method in class org.protempa.backend.BackendInstanceSpec
setConfigurationsProvider(ConfigurationsProvider) - Static method in class org.protempa.backend.ConfigurationsProviderManager: Sets the configurations provider, overriding any configurations provider that was found by service discovery.
setConfigurationsProviderClassLoader(ClassLoader) - Static method in class org.protempa.backend.ConfigurationsProviderManager
setContextId(String) - Method in class org.protempa.CompoundLowLevelAbstractionDefinition
setContextId(String) - Method in class org.protempa.LowLevelAbstractionDefinition
setContextId(String) - Method in class org.protempa.proposition.AbstractParameter
setCounts(Map<String, Integer>) - Method in class org.protempa.dest.DefaultStatisticsBuilder
setCreated(Date) - Method in class org.protempa.AbstractPropositionDefinition
setCreateDate(Date) - Method in class org.protempa.proposition.AbstractProposition: Sets the date this proposition was created according to the source system from which it was obtained, or for derived propositions, the date it was created through the temporal abstraction process.
setDataSourceBackendId(String) - Method in class org.protempa.backend.AbstractCommonsDataSourceBackend: Deprecated.
setDataSourceBackendSections(List<BackendInstanceSpec<DataSourceBackend>>) - Method in class org.protempa.backend.Configuration
setDate(Date) - Method in class org.protempa.proposition.value.DateValueBuilder
setDeclaringPropId(String) - Method in class org.protempa.PropertyDefinitionBuilder
setDeleteDate(Date) - Method in class org.protempa.proposition.AbstractProposition: Sets the date this proposition was deleted from the source system.
setDescription(String) - Method in class org.protempa.AbstractPropositionDefinition
setDescription(String) - Method in class org.protempa.Term
setDescription(String) - Method in class org.protempa.Terminology
setDirectChildren(String[]) - Method in class org.protempa.Term
setDisplayName(String) - Method in class org.protempa.AbstractPropositionDefinition: Sets this proposition definition's human-readable display name.
setDisplayName(String) - Method in class org.protempa.ExtendedPropositionDefinition
setDisplayName(String) - Method in class org.protempa.PropertyDefinitionBuilder
setDisplayName(String) - Method in class org.protempa.Term
setDisplayName(String) - Method in class org.protempa.valueset.ValueSetBuilder
setDisplayName(String) - Method in class org.protempa.valueset.ValueSetElementBuilder
setDisplayNameHeading(String) - Method in class org.protempa.dest.table.OutputConfigBuilder
setDownloadDate(Date) - Method in class org.protempa.proposition.AbstractProposition: Sets the date this proposition was downloaded from the source system.
setDownloaded(Date) - Method in class org.protempa.AbstractPropositionDefinition
setEdge(Object, Object, Weight) - Method in class org.protempa.graph.DirectedGraph: Set the edge between two vertices.
setElements(ValueBuilder<V>[]) - Method in class org.protempa.proposition.value.ValueListBuilder
setFatal(boolean) - Method in class org.protempa.backend.dsb.DataValidationEvent
setFilters(Filter) - Method in class org.protempa.query.DefaultQueryBuilder: Sets the filters to apply to this query.
setFinishAbstractParamValue(Value) - Method in class org.protempa.TemporalPatternOffset
setFinishHeading(String) - Method in class org.protempa.dest.table.OutputConfigBuilder
setFinishIntervalSide(Interval.Side) - Method in class org.protempa.ContextOffset
setFinishIntervalSide(Interval.Side) - Method in class org.protempa.TemporalPatternOffset
setFinishOffset(Integer) - Method in class org.protempa.ContextOffset
setFinishOffset(int) - Method in class org.protempa.TemporalPatternOffset
setFinishOffsetUnits(Unit) - Method in class org.protempa.ContextOffset
setFinishOffsetUnits(Unit) - Method in class org.protempa.TemporalPatternOffset
setFinishTemporalExtendedPropositionDefinition(TemporalExtendedPropositionDefinition) - Method in class org.protempa.TemporalPatternOffset
setFirstTemporalExtendedPropositionDefinition(TemporalExtendedPropositionDefinition) - Method in class org.protempa.SequentialTemporalPatternDefinition
setGapFunction(GapFunction) - Method in class org.protempa.AbstractAbstractionDefinition
setGapFunction(GapFunction) - Method in class org.protempa.ContextDefinition
setGapFunctionBetweenValues(GapFunction) - Method in class org.protempa.CompoundLowLevelAbstractionDefinition
setGranularity(Granularity) - Method in class org.protempa.proposition.PrimitiveParameter: Sets the granularity of this parameter's timestamp.
setGranularityFactory(GranularityFactory) - Method in class org.protempa.backend.dsb.AbstractDataSourceBackend
setId(String) - Method in class org.protempa.backend.AbstractBackend
setId(String) - Method in class org.protempa.backend.AbstractCommonsAlgorithmSourceBackend
setId(String) - Method in class org.protempa.backend.AbstractCommonsDataSourceBackend
setId(String) - Method in class org.protempa.backend.AbstractCommonsKnowledgeSourceBackend
setId(String) - Method in class org.protempa.backend.AbstractCommonsTermSourceBackend
setId(String) - Method in class org.protempa.PropertyDefinitionBuilder
setId(String) - Method in class org.protempa.valueset.ValueSetBuilder
setIdHeading(String) - Method in class org.protempa.dest.table.OutputConfigBuilder
setInDataSource(boolean) - Method in class org.protempa.AbstractPropositionDefinition
setIndex(int) - Method in class org.protempa.proposition.value.OrdinalValueBuilder
setInducedBy(TemporalExtendedPropositionDefinition[]) - Method in class org.protempa.ContextDefinition
setInterpretationContext(ContextDefinition) - Method in class org.protempa.CompoundLowLevelAbstractionDefinition
setInterval(Interval) - Method in class org.protempa.proposition.AbstractParameter
setInterval(Interval) - Method in class org.protempa.proposition.Context
setInterval(Interval) - Method in class org.protempa.proposition.Event
setInterval(Interval) - Method in class org.protempa.proposition.TemporalProposition: Sets the valid interval.
setInValueType(ValueType) - Method in class org.protempa.AbstractAlgorithm
setInverseIsA(String...) - Method in class org.protempa.AbstractPropositionDefinition: Sets the children of this proposition definition.
setInverseIsA(String[]) - Method in class org.protempa.Term
setKeyIdComparator(Comparator<Object>) - Method in class org.protempa.backend.dsb.AbstractDataSourceBackend
setKeyIds(String[]) - Method in class org.protempa.query.DefaultQueryBuilder: Sets the key ids to be queried.
setKeyType(String) - Method in class org.protempa.backend.AbstractCommonsDataSourceBackend
setKeyType(String) - Method in class org.protempa.backend.dsb.AbstractDataSourceBackend
setKnowledgeSourceBackendSections(List<BackendInstanceSpec<KnowledgeSourceBackend>>) - Method in class org.protempa.backend.Configuration
setLengthHeading(String) - Method in class org.protempa.dest.table.OutputConfigBuilder
setLine(Long) - Method in class org.protempa.backend.dsb.DataValidationEvent
setLowerBoundBuilder(OrderedValueBuilder) - Method in class org.protempa.valueset.ValueSetBuilder
setMaximumDuration(Integer) - Method in class org.protempa.LowLevelAbstractionDefinition
setMaximumDurationUnits(Unit) - Method in class org.protempa.LowLevelAbstractionDefinition
setMaximumGap(Integer) - Method in class org.protempa.MinMaxGapFunction
setMaximumGap(Integer) - Method in class org.protempa.SimpleGapFunction: Sets the the gap function's maximum gap value.
setMaximumGapBetweenValues(Integer) - Method in class org.protempa.LowLevelAbstractionDefinition
setMaximumGapBetweenValuesUnits(Unit) - Method in class org.protempa.LowLevelAbstractionDefinition
setMaximumGapUnit(Unit) - Method in class org.protempa.MinMaxGapFunction
setMaximumGapUnit(Unit) - Method in class org.protempa.SimpleGapFunction: Sets the maximum gap value's units.
setMaximumNumberOfValues(int) - Method in class org.protempa.AbstractAlgorithm: Sets the default maximum sliding window width.
setMaximumNumberOfValues(int) - Method in class org.protempa.LowLevelAbstractionDefinition
setMaxIndex(int) - Method in class org.protempa.SliceDefinition: Sets the upper limit of the range for this slice (exclusive).
setMaxLength(Integer) - Method in class org.protempa.TemporalExtendedPropositionDefinition
setMaxLengthUnit(Unit) - Method in class org.protempa.TemporalExtendedPropositionDefinition
setMaxOverlapping(int) - Method in class org.protempa.LowLevelAbstractionDefinition: Enable the max-overlapping restart search directive.
setMergedInterval(boolean) - Method in class org.protempa.SliceDefinition
setMessage(String) - Method in class org.protempa.backend.dsb.DataValidationEvent
setMinimumDuration(Integer) - Method in class org.protempa.LowLevelAbstractionDefinition
setMinimumDurationUnits(Unit) - Method in class org.protempa.LowLevelAbstractionDefinition
setMinimumGap(Integer) - Method in class org.protempa.MinMaxGapFunction
setMinimumGapBetweenValues(Integer) - Method in class org.protempa.LowLevelAbstractionDefinition
setMinimumGapBetweenValuesUnits(Unit) - Method in class org.protempa.LowLevelAbstractionDefinition
setMinimumGapUnit(Unit) - Method in class org.protempa.MinMaxGapFunction
setMinimumNumberOfValues(int) - Method in class org.protempa.AbstractAlgorithm: Sets the default minimum sliding window width.
setMinimumNumberOfValues(int) - Method in class org.protempa.CompoundLowLevelAbstractionDefinition: Sets the minimum number of consecutive intervals that must have the same value before this abstraction is asserted.
setMinimumNumberOfValues(int) - Method in class org.protempa.LowLevelAbstractionDefinition
setMinIndex(int) - Method in class org.protempa.SliceDefinition: Sets the lower limit of the range for this slice (inclusive).
setMinLength(Integer) - Method in class org.protempa.TemporalExtendedPropositionDefinition
setMinLengthUnit(Unit) - Method in class org.protempa.TemporalExtendedPropositionDefinition
setName(String) - Method in class org.protempa.AttributeBuilder
setName(String) - Method in class org.protempa.query.DefaultQueryBuilder
setNumberOfKeys(int) - Method in class org.protempa.dest.DefaultStatisticsBuilder
setOffset(ContextOffset) - Method in class org.protempa.ContextDefinition: Sets the start and finish of an interval of this context relative to its inducing interval.
setOrdered(boolean) - Method in class org.protempa.valueset.ValueSetBuilder
setParameterComp(String, ValueComparator) - Method in class org.protempa.LowLevelAbstractionValueDefinition
setParameters(AlgorithmParameter[]) - Method in class org.protempa.AbstractAlgorithm
setParameterValue(String, Value) - Method in class org.protempa.LowLevelAbstractionValueDefinition
setPosition(Long) - Method in class org.protempa.proposition.PrimitiveParameter: Sets this parameter's timestamp (or other kind of position value).
setProperty(String, Object) - Method in class org.protempa.backend.BackendInstanceSpec
setProperty(BackendPropertySpec, Object) - Method in class org.protempa.backend.BackendInstanceSpec
setProperty(BackendInstanceSpec, BackendPropertySpec, Object) - Method in enum org.protempa.backend.BackendPropertyType
setProperty(String, Value) - Method in class org.protempa.proposition.AbstractProposition
setPropertyConstraints(PropertyConstraint[]) - Method in class org.protempa.ExtendedPropositionDefinition
setPropertyDefinitions(PropertyDefinition...) - Method in class org.protempa.AbstractPropositionDefinition
setPropertyName(String) - Method in class org.protempa.PropertyConstraint
setPropertyValueAbbrevDisplayName(String) - Method in class org.protempa.dest.table.ValueOutputConfigBuilder
setPropertyValueDisplayName(String) - Method in class org.protempa.dest.table.ValueOutputConfigBuilder
setPropId(String) - Method in class org.protempa.PropertyDefinitionBuilder
setPropositionDefinitions(PropositionDefinition[]) - Method in class org.protempa.query.DefaultQueryBuilder: Returns an optional set of user-specified proposition definitions.
setPropositionId(String) - Method in class org.protempa.AbstractPropositionDefinition: Sets the proposition id of propositions derived by this proposition definition.
setPropositionIds(String[]) - Method in class org.protempa.query.DefaultQueryBuilder: Sets the proposition ids to be queried.
setQueryMode(QueryMode) - Method in class org.protempa.query.DefaultQueryBuilder
setReferenceDefinitions(ReferenceDefinition...) - Method in class org.protempa.AbstractPropositionDefinition
setReferences(String, List<UniqueId>) - Method in class org.protempa.proposition.AbstractProposition
setRelation(TemporalExtendedPropositionDefinition, TemporalExtendedPropositionDefinition, Relation) - Method in class org.protempa.HighLevelAbstractionDefinition: Sets the relation between the two temporal extended proposition definitions.
setSemanticType(String) - Method in class org.protempa.Term
setShowAbbrevDisplayName(boolean) - Method in class org.protempa.dest.table.OutputConfigBuilder
setShowDisplayName(boolean) - Method in class org.protempa.dest.table.OutputConfigBuilder
setShowFinish(boolean) - Method in class org.protempa.dest.table.OutputConfigBuilder
setShowId(boolean) - Method in class org.protempa.dest.table.OutputConfigBuilder
setShowLength(boolean) - Method in class org.protempa.dest.table.OutputConfigBuilder
setShowPropertyValueAbbrevDisplayName(boolean) - Method in class org.protempa.dest.table.ValueOutputConfigBuilder
setShowPropertyValueDisplayName(boolean) - Method in class org.protempa.dest.table.ValueOutputConfigBuilder
setShowStartOrTimestamp(boolean) - Method in class org.protempa.dest.table.OutputConfigBuilder
setShowValue(boolean) - Method in class org.protempa.dest.table.OutputConfigBuilder
setSkip(int) - Method in class org.protempa.CompoundLowLevelAbstractionDefinition
setSkip(int) - Method in class org.protempa.LowLevelAbstractionDefinition: Enable the skip restart search directive.
setSkipEnd(int) - Method in class org.protempa.LowLevelAbstractionDefinition: Enable the skip-end restart search directive.
setSkipStart(int) - Method in class org.protempa.LowLevelAbstractionDefinition: Enable the skip-start restart search directive.
setSlidingWindowWidthMode(SlidingWindowWidthMode) - Method in class org.protempa.LowLevelAbstractionDefinition: Sets the sliding window width mode.
setSolid(boolean) - Method in class org.protempa.HighLevelAbstractionDefinition: Sets whether intervals of this type are solid, i.e., never hold over properly overlapping intervals.
setSolid(boolean) - Method in class org.protempa.SequentialTemporalPatternDefinition: Sets whether intervals of this type are solid, i.e., never hold over properly overlapping intervals.
setSourceId(SourceId) - Method in class org.protempa.AbstractPropositionDefinition
setSourceIdBuilder(SourceIdBuilder) - Method in class org.protempa.valueset.ValueSetBuilder
setSourceIdStr(String) - Method in class org.protempa.DefaultSourceIdBuilder
setSourceSystem(SourceSystem) - Method in class org.protempa.proposition.AbstractProposition
setStartAbstractParamValue(Value) - Method in class org.protempa.TemporalPatternOffset
setStartIntervalSide(Interval.Side) - Method in class org.protempa.ContextOffset
setStartIntervalSide(Interval.Side) - Method in class org.protempa.TemporalPatternOffset
setStartOffset(Integer) - Method in class org.protempa.ContextOffset
setStartOffset(int) - Method in class org.protempa.TemporalPatternOffset
setStartOffsetUnits(Unit) - Method in class org.protempa.ContextOffset
setStartOffsetUnits(Unit) - Method in class org.protempa.TemporalPatternOffset
setStartOrTimestampHeading(String) - Method in class org.protempa.dest.table.OutputConfigBuilder
setStartTemporalExtendedPropositionDefinition(TemporalExtendedPropositionDefinition) - Method in class org.protempa.TemporalPatternOffset
setSubContexts(String[]) - Method in class org.protempa.ContextDefinition: Sets the ids of other context definitions that, together with this one, have a specific meaning when their intervals intersect.
setSubsequentTemporalExtendedPropositionDefinitions(SequentialTemporalPatternDefinition.SubsequentTemporalExtendedPropositionDefinition[]) - Method in class org.protempa.SequentialTemporalPatternDefinition
setTemporalOffset(TemporalPatternOffset) - Method in class org.protempa.HighLevelAbstractionDefinition
setTemporalOffset(TemporalPatternOffset) - Method in class org.protempa.SequentialTemporalPatternDefinition
setTermIds(String...) - Method in class org.protempa.AbstractPropositionDefinition: Assigns this proposition with associated TermDefinition ids.
setTermIds(And<String>[]) - Method in class org.protempa.query.DefaultQueryBuilder: Sets the term ids to be queried in disjunctive normal form.
setTermSourceBackendSections(List<BackendInstanceSpec<TermSourceBackend>>) - Method in class org.protempa.backend.Configuration
setTimestamp(Date) - Method in class org.protempa.backend.dsb.DataValidationEvent
setType(String) - Method in class org.protempa.backend.dsb.DataValidationEvent
setType(PropositionValueColumnSpec.Type) - Method in class org.protempa.dest.table.PropositionValueColumnSpec
setUnitFactory(UnitFactory) - Method in class org.protempa.backend.dsb.AbstractDataSourceBackend
setUnits(String) - Method in class org.protempa.PrimitiveParameterDefinition: Sets the units for values of this primitive parameter.
setUpdated(Date) - Method in class org.protempa.AbstractPropositionDefinition
setUpdateDate(Date) - Method in class org.protempa.proposition.AbstractProposition: Sets the date this proposition was last updated according to the source system from which it was obtained, or for derived propositions, the date it was last updated through the temporal abstraction process.
setUpperBoundBuilder(OrderedValueBuilder) - Method in class org.protempa.valueset.ValueSetBuilder
setURI(URI) - Method in class org.protempa.backend.dsb.DataValidationEvent
setUsername(String) - Method in class org.protempa.query.DefaultQueryBuilder
setVal(BigDecimal) - Method in class org.protempa.proposition.value.InequalityNumberValueBuilder
setVal(String) - Method in class org.protempa.proposition.value.NominalValueBuilder
setVal(BigDecimal) - Method in class org.protempa.proposition.value.NumberValueBuilder
setValidatePropositionIds(boolean) - Static method in class org.protempa.query.DefaultQueryBuilder: Set the value of the flag that determined whether the build method validates proposition IDs.
setValue(Value) - Method in class org.protempa.ExtendedParameterDefinition
setValue(Value) - Method in class org.protempa.LowLevelAbstractionValueDefinition
setValue(Value) - Method in class org.protempa.PropertyConstraint
setValue(Value) - Method in class org.protempa.proposition.TemporalParameter
setValue(boolean) - Method in class org.protempa.proposition.value.BooleanValueBuilder
setValue(String) - Method in class org.protempa.proposition.value.OrdinalValueBuilder
setValue(Value) - Method in class org.protempa.TemporalExtendedParameterDefinition
setValueBuilder(ValueBuilder) - Method in class org.protempa.AttributeBuilder
setValueBuilder(ValueBuilder) - Method in class org.protempa.valueset.ValueSetElementBuilder
setValueComp(ValueComparator) - Method in class org.protempa.PropertyConstraint
setValueDefinitionMatchOperator(CompoundLowLevelAbstractionDefinition.ValueDefinitionMatchOperator) - Method in class org.protempa.CompoundLowLevelAbstractionDefinition: Sets the operator that is applied to each interval's low-level abstraction values to determine the value to set for this abstraction.
setValueHeading(String) - Method in class org.protempa.dest.table.OutputConfigBuilder
setValueSetElementBuilders(ValueSetElementBuilder[]) - Method in class org.protempa.valueset.ValueSetBuilder
setValueSetId(String) - Method in class org.protempa.PropertyDefinitionBuilder
setValueType(ValueType) - Method in class org.protempa.LowLevelAbstractionDefinition
setValueType(ValueType) - Method in class org.protempa.PrimitiveParameterDefinition: Sets the value factory for this primitive parameter definition.
setValueType(ValueType) - Method in class org.protempa.PropertyDefinitionBuilder
setVersion(String) - Method in class org.protempa.AbstractPropositionDefinition
setVersion(String) - Method in class org.protempa.Terminology
setVisited(boolean) - Method in class org.protempa.graph.Edge
showAbbrevDisplayName() - Method in class org.protempa.dest.table.OutputConfig
showAbbrevDisplayName() - Method in class org.protempa.dest.table.OutputConfigBuilder
showDisplayName() - Method in class org.protempa.dest.table.OutputConfig
showDisplayName() - Method in class org.protempa.dest.table.OutputConfigBuilder
showFinish() - Method in class org.protempa.dest.table.OutputConfig
showFinish() - Method in class org.protempa.dest.table.OutputConfigBuilder
showId() - Method in class org.protempa.dest.table.OutputConfig
showId() - Method in class org.protempa.dest.table.OutputConfigBuilder
showLength() - Method in class org.protempa.dest.table.OutputConfig
showLength() - Method in class org.protempa.dest.table.OutputConfigBuilder
showStartOrTimestamp() - Method in class org.protempa.dest.table.OutputConfig
showStartOrTimestamp() - Method in class org.protempa.dest.table.OutputConfigBuilder
showValue() - Method in class org.protempa.dest.table.OutputConfig
showValue() - Method in class org.protempa.dest.table.OutputConfigBuilder
SimpleGapFunction - Class in org.protempa: Implements a gap function with a simple max range: if one interval is before the second and the distance between them is less than or equal to the supplied maximum gap, then the function returns true, otherwise it returns false.
SimpleGapFunction() - Constructor for class org.protempa.SimpleGapFunction: Instantiates an instance with the default maximum gap and units.
SimpleGapFunction(Integer, Unit) - Constructor for class org.protempa.SimpleGapFunction: Initializes a gap function with a maximum gap and units.
SimpleInterval - Class in org.protempa.proposition.interval: An Interval for completely specified minimum and maximum starts and finishes, and 0 duration.
SimpleKnowledgeSourceBackend - Class in org.protempa.backend.ksb
SimpleKnowledgeSourceBackend() - Constructor for class org.protempa.backend.ksb.SimpleKnowledgeSourceBackend
SimpleKnowledgeSourceBackend(PropositionDefinition...) - Constructor for class org.protempa.backend.ksb.SimpleKnowledgeSourceBackend
size() - Method in class org.protempa.DataSourceResultMap
size() - Method in class org.protempa.graph.DirectedGraph: Get the number of vertices.
size() - Method in class org.protempa.proposition.Segment
size() - Method in class org.protempa.proposition.Sequence
SliceDefinition - Class in org.protempa
SliceDefinition(String) - Constructor for class org.protempa.SliceDefinition
SlidingWindowWidthMode - Enum in org.protempa: For specifying whether a low-level abstraction definition's or aggregation definition's sliding window width should be the algorithm's default (DEFAULT), the entire width of a time series (ALL), or a specified minimum and maximum number of values (RANGE).
Source<S extends SourceUpdatedEvent,B extends Backend,T extends BackendUpdatedEvent> - Interface in org.protempa
SourceClosedUnexpectedlyEvent<S extends SourceUpdatedEvent,B extends Backend,T extends BackendUpdatedEvent> - Class in org.protempa
SourceClosedUnexpectedlyEvent(Source<S, B, T>) - Constructor for class org.protempa.SourceClosedUnexpectedlyEvent: Initializes the event with the Source that closed unexpectedly.
SourceCloseException - Exception in org.protempa: Class for exceptions that are thrown when an error occurs while closing a data, knowledge, algorithm or term source.
SourceFactory - Class in org.protempa
SourceFactory(Configuration) - Constructor for class org.protempa.SourceFactory
SourceFactory(Configurations, String) - Constructor for class org.protempa.SourceFactory
SourceFactory(String) - Constructor for class org.protempa.SourceFactory
SourceId - Class in org.protempa.proposition
SourceId() - Constructor for class org.protempa.proposition.SourceId
SourceId - Interface in org.protempa: Interface for classes that specify the source of proposition definitions and value sets.
SourceIdBuilder - Interface in org.protempa
SourceIdFactory<E> - Interface in org.protempa
SourceListener<E extends SourceUpdatedEvent> - Interface in org.protempa: Listener interface for when the source changes.
SourceSystem - Class in org.protempa
sourceUpdated(E) - Method in interface org.protempa.SourceListener: The method that gets called when the source is updated.
SourceUpdatedEvent - Class in org.protempa: Source updated events.
start(Collection<PropositionDefinition>) - Method in class org.protempa.dest.AbstractQueryResultsHandler
start(Collection<PropositionDefinition>) - Method in class org.protempa.dest.deid.DeidentifiedQueryResultsHandler
start(Collection<PropositionDefinition>) - Method in class org.protempa.dest.keyloader.KeyLoaderQueryResultsHandler
start(Collection<PropositionDefinition>) - Method in interface org.protempa.dest.QueryResultsHandler: Called by Protempa prior to the first invocation of QueryResultsHandler.handleQueryResult(java.lang.String, java.util.List, java.util.Map, java.util.Map, java.util.Map).
start(Collection<PropositionDefinition>) - Method in class org.protempa.dest.table.TableQueryResultsHandler
start(Collection<PropositionDefinition>) - Method in class org.protempa.dest.xml.XmlQueryResultsHandler
STARTED_BY - Static variable in class org.protempa.proposition.interval.Relation
STARTS - Static variable in class org.protempa.proposition.interval.Relation
StateAlgorithm - Class in org.protempa.backend.asb.java: Detects whether the values of a time sequence segment are above and/or below a specified value.
StateAlgorithm(Algorithms, String) - Constructor for class org.protempa.backend.asb.java.StateAlgorithm
Statistics - Interface in org.protempa.dest: Collect various statistics about the data in the dataset previously written out.
StatisticsException - Exception in org.protempa.dest
StatisticsException() - Constructor for exception org.protempa.dest.StatisticsException
StatisticsException(String, Throwable) - Constructor for exception org.protempa.dest.StatisticsException
StatisticsException(String) - Constructor for exception org.protempa.dest.StatisticsException
StatisticsException(Throwable) - Constructor for exception org.protempa.dest.StatisticsException
subList(int, int) - Method in class org.protempa.proposition.Sequence
SubsequentTemporalExtendedPropositionDefinition(Relation, TemporalExtendedPropositionDefinition) - Constructor for class org.protempa.SequentialTemporalPatternDefinition.SubsequentTemporalExtendedPropositionDefinition
subtract(Weight) - Method in class org.protempa.graph.Weight: Creates a new weight the value equal to the difference between the two weights.

T

TableColumnSpec - Interface in org.protempa.dest.table: Specification of a column or sequence of columns in a delimited file that represent a proposition or property.
TableColumnSpecValidationFailedException - Exception in org.protempa.dest.table
TableColumnSpecValidationFailedException(Throwable) - Constructor for exception org.protempa.dest.table.TableColumnSpecValidationFailedException
TableColumnSpecValidationFailedException(String) - Constructor for exception org.protempa.dest.table.TableColumnSpecValidationFailedException
TableColumnSpecValidationFailedException(String, Throwable) - Constructor for exception org.protempa.dest.table.TableColumnSpecValidationFailedException
TableColumnSpecValidationFailedException() - Constructor for exception org.protempa.dest.table.TableColumnSpecValidationFailedException
TableDestination - Class in org.protempa.dest.table
TableDestination(BufferedWriter, char, String[], TableColumnSpec[], boolean) - Constructor for class org.protempa.dest.table.TableDestination
TableQueryResultsHandler - Class in org.protempa.dest.table
TemporalAbstractParameterFactory - Class in org.protempa.proposition: Generate instances of AbstractParameter based on the provided date format, and time granularity.
TemporalAbstractParameterFactory(DateFormat, Granularity, UniqueIdFactory) - Constructor for class org.protempa.proposition.TemporalAbstractParameterFactory
TemporalEventFactory - Class in org.protempa.proposition: Generate instances of Event based on the provided date format and granularity.
TemporalEventFactory(DateFormat, Granularity, UniqueIdFactory) - Constructor for class org.protempa.proposition.TemporalEventFactory
TemporalExtendedAbstractParameterDefinition - Class in org.protempa
TemporalExtendedAbstractParameterDefinition(String) - Constructor for class org.protempa.TemporalExtendedAbstractParameterDefinition
TemporalExtendedAbstractParameterDefinition(String, Value) - Constructor for class org.protempa.TemporalExtendedAbstractParameterDefinition
TemporalExtendedAbstractParameterDefinition(String, Value, String) - Constructor for class org.protempa.TemporalExtendedAbstractParameterDefinition
TemporalExtendedParameterDefinition - Class in org.protempa
TemporalExtendedParameterDefinition(String) - Constructor for class org.protempa.TemporalExtendedParameterDefinition
TemporalExtendedParameterDefinition(String, Value) - Constructor for class org.protempa.TemporalExtendedParameterDefinition
TemporalExtendedPropositionDefinition - Class in org.protempa
TemporalExtendedPropositionDefinition(String) - Constructor for class org.protempa.TemporalExtendedPropositionDefinition
TemporalParameter - Class in org.protempa.proposition
TemporalParameter() - Constructor for class org.protempa.proposition.TemporalParameter: Here only for use by deserialization.
TemporalPatternOffset - Class in org.protempa: Defines offsets for the interval of an abstract parameter defined by a complex abstract parameter definition.
TemporalPatternOffset() - Constructor for class org.protempa.TemporalPatternOffset
TemporalPrimitiveParameterFactory - Class in org.protempa.proposition: Generate instances of PrimitiveParameter based on the provided date format and granularity.
TemporalPrimitiveParameterFactory(DateFormat, Granularity, UniqueIdFactory) - Constructor for class org.protempa.proposition.TemporalPrimitiveParameterFactory
TemporalProposition - Class in org.protempa.proposition: A proposition with a valid timestamp or interval.
TemporalProposition() - Constructor for class org.protempa.proposition.TemporalProposition: Here only for use by deserialization.
TemporalPropositionDefinition - Interface in org.protempa
TemporalPropositionIntervalComparator - Class in org.protempa.proposition.comparator: For sorting temporal propositions by interval.
TemporalPropositionIntervalComparator() - Constructor for class org.protempa.proposition.comparator.TemporalPropositionIntervalComparator
Term - Class in org.protempa: Represents a term pulled from a terminology in PROTEMPA.
Terminology - Class in org.protempa: Represents a terminology in PROTEMPA
TermSource - Interface in org.protempa
TermSourceBackend - Interface in org.protempa.backend.tsb: Interface for term source backends
TermSourceBackendInitializationException - Exception in org.protempa.backend
TermSourceBackendInitializationException(String) - Constructor for exception org.protempa.backend.TermSourceBackendInitializationException
TermSourceBackendInitializationException(Throwable) - Constructor for exception org.protempa.backend.TermSourceBackendInitializationException
TermSourceBackendInitializationException(String, Throwable) - Constructor for exception org.protempa.backend.TermSourceBackendInitializationException
TermSourceBackendUpdatedEvent - Class in org.protempa.backend
TermSourceBackendUpdatedEvent(TermSourceBackend) - Constructor for class org.protempa.backend.TermSourceBackendUpdatedEvent
TermSourceException - Exception in org.protempa
TermSourceException() - Constructor for exception org.protempa.TermSourceException
TermSourceException(String, Throwable) - Constructor for exception org.protempa.TermSourceException
TermSourceException(String) - Constructor for exception org.protempa.TermSourceException
TermSourceException(Throwable) - Constructor for exception org.protempa.TermSourceException
TermSourceImpl - Class in org.protempa
TermSourceImpl(TermSourceBackend[]) - Constructor for class org.protempa.TermSourceImpl
TermSourceReadException - Exception in org.protempa
TermSourceReadException() - Constructor for exception org.protempa.TermSourceReadException
TermSourceReadException(String, Throwable) - Constructor for exception org.protempa.TermSourceReadException
TermSourceReadException(String) - Constructor for exception org.protempa.TermSourceReadException
TermSourceReadException(Throwable) - Constructor for exception org.protempa.TermSourceReadException
TermSourceUpdatedEvent - Class in org.protempa
TermSourceUpdatedEvent(TermSource) - Constructor for class org.protempa.TermSourceUpdatedEvent
TermSubsumption - Class in org.protempa
TermSubsumption() - Constructor for class org.protempa.TermSubsumption
toArray() - Method in class org.protempa.proposition.Sequence
toArray(E[]) - Method in class org.protempa.proposition.Sequence
toDefaultStatistics() - Method in class org.protempa.dest.DefaultStatisticsBuilder
toGranularity(String) - Method in class org.protempa.proposition.value.AbsoluteTimeGranularityFactory
toGranularity(String) - Method in interface org.protempa.proposition.value.GranularityFactory: Translates the name of a granularity unit into a Granularity object.
toGranularity(String) - Method in class org.protempa.proposition.value.RelativeDayGranularityFactory
toGranularity(String) - Method in class org.protempa.proposition.value.RelativeHourGranularityFactory
toSQLString(Long) - Static method in class org.protempa.proposition.value.AbsoluteTimeGranularity: Convenience method to translate a timestamp into the format expected by SQL.
toString() - Method in class org.protempa.AbstractAbstractionDefinition
toString() - Method in class org.protempa.AbstractAlgorithm
toString() - Method in class org.protempa.AbstractPropositionDefinition
toString() - Method in class org.protempa.AlgorithmArguments
toString() - Method in class org.protempa.AlgorithmParameter
toString() - Method in class org.protempa.Algorithms
toString() - Method in class org.protempa.Attribute
toString() - Method in class org.protempa.backend.BackendInstanceSpec
toString() - Method in class org.protempa.backend.BackendPropertySpec
toString() - Method in class org.protempa.backend.BackendSpec
toString() - Method in class org.protempa.backend.dsb.filter.AbstractFilter
toString() - Method in class org.protempa.backend.dsb.filter.PositionFilter
toString() - Method in class org.protempa.backend.dsb.filter.PropertyValueFilter
toString() - Method in class org.protempa.CompoundLowLevelAbstractionDefinition
toString() - Method in class org.protempa.ContextOffset
toString() - Method in class org.protempa.DataSourceBackendSourceSystem
toString() - Method in class org.protempa.DataStreamingEvent
toString() - Method in class org.protempa.dest.table.Derivation
toString() - Method in class org.protempa.dest.table.Link
toString() - Method in class org.protempa.dest.table.PropertyConstraint
toString() - Method in class org.protempa.dest.table.Reference
toString() - Method in class org.protempa.ExtendedParameterDefinition
toString() - Method in class org.protempa.ExtendedPropositionDefinition
toString() - Method in class org.protempa.graph.Edge
toString() - Method in class org.protempa.graph.Weight
toString() - Method in class org.protempa.HighLevelAbstractionDefinition
toString() - Method in class org.protempa.KeySetSpec
toString() - Method in class org.protempa.LowLevelAbstractionDefinition
toString() - Method in class org.protempa.LowLevelAbstractionValueDefinition
toString() - Method in class org.protempa.MinMaxGapFunction
toString() - Method in class org.protempa.PrimitiveParameterDefinition
toString() - Method in class org.protempa.PropertyDefinition
toString() - Method in class org.protempa.PropertyDefinitionBuilder
toString() - Method in class org.protempa.proposition.AbstractParameter
toString() - Method in class org.protempa.proposition.AbstractProposition
toString() - Method in class org.protempa.proposition.CompoundInterval
toString() - Method in class org.protempa.proposition.CompoundValuedInterval
toString() - Method in class org.protempa.proposition.Constant
toString() - Method in class org.protempa.proposition.DataSourceBackendId
toString() - Method in class org.protempa.proposition.DerivedSourceId
toString() - Method in class org.protempa.proposition.Event
toString() - Method in enum org.protempa.proposition.interval.Interval.Side
toString() - Method in class org.protempa.proposition.interval.Interval
toString() - Method in class org.protempa.proposition.interval.Relation
toString() - Method in class org.protempa.proposition.PrimitiveParameter
toString() - Method in class org.protempa.proposition.ProviderBasedLocalUniqueId
toString() - Method in class org.protempa.proposition.Sequence
toString() - Method in class org.protempa.proposition.TemporalParameter
toString() - Method in class org.protempa.proposition.TemporalProposition
toString() - Method in class org.protempa.proposition.UniqueId
toString() - Method in class org.protempa.proposition.value.AbsoluteTimeGranularity
toString() - Method in class org.protempa.proposition.value.AbstractTimeUnit: Returns the unit's name.
toString() - Method in class org.protempa.proposition.value.BooleanValue
toString() - Method in class org.protempa.proposition.value.BooleanValueBuilder
toString() - Method in class org.protempa.proposition.value.DateValue
toString() - Method in class org.protempa.proposition.value.DateValueBuilder
toString() - Method in class org.protempa.proposition.value.InequalityNumberValue
toString() - Method in class org.protempa.proposition.value.InequalityNumberValueBuilder
toString() - Method in class org.protempa.proposition.value.NominalValue
toString() - Method in class org.protempa.proposition.value.NominalValueBuilder
toString() - Method in class org.protempa.proposition.value.NumberValue
toString() - Method in class org.protempa.proposition.value.NumberValueBuilder
toString() - Method in class org.protempa.proposition.value.OrdinalValue
toString() - Method in class org.protempa.proposition.value.OrdinalValueBuilder
toString() - Method in class org.protempa.proposition.value.RelativeDayGranularity
toString() - Method in class org.protempa.proposition.value.RelativeHourGranularity
toString() - Method in class org.protempa.proposition.value.ValueList
toString() - Method in class org.protempa.proposition.value.ValueListBuilder
toString() - Method in class org.protempa.query.DefaultQueryBuilder
toString() - Method in class org.protempa.query.Query
toString() - Method in class org.protempa.SequentialTemporalPatternDefinition
toString() - Method in class org.protempa.SimpleGapFunction
toString() - Method in class org.protempa.SliceDefinition
toString() - Method in class org.protempa.TemporalExtendedAbstractParameterDefinition
toString() - Method in class org.protempa.TemporalExtendedParameterDefinition
toString() - Method in class org.protempa.TemporalExtendedPropositionDefinition
toString() - Method in class org.protempa.TemporalPatternOffset
toString() - Method in class org.protempa.UniqueIdPair
toString() - Method in class org.protempa.ValueClassification
toString() - Method in class org.protempa.valueset.ValueSet
toString() - Method in class org.protempa.valueset.ValueSetBuilder
toString() - Method in class org.protempa.valueset.ValueSetElement
toString() - Method in class org.protempa.valueset.ValueSetElementBuilder
toUnit(String) - Method in class org.protempa.proposition.value.AbsoluteTimeUnitFactory
toUnit(String) - Method in class org.protempa.proposition.value.RelativeDayUnitFactory
toUnit(String) - Method in class org.protempa.proposition.value.RelativeHourUnitFactory
toUnit(String) - Method in interface org.protempa.proposition.value.UnitFactory: Translates the name of a length unit into a Unit object
traverseLinks(Link[], Proposition, Map<Proposition, List<Proposition>>, Map<Proposition, List<Proposition>>, Map<UniqueId, Proposition>, KnowledgeSourceCache) - Method in class org.protempa.dest.table.LinkTraverser: Traverses links from a proposition to a list of propositions.
TrendAlgorithm - Class in org.protempa.backend.asb.java: Detects whether the slope of a linear regression line drawn through the values of a time sequence segment is above and/or below a specified value.
TrendAlgorithm(Algorithms, String) - Constructor for class org.protempa.backend.asb.java.TrendAlgorithm
TRUE - Static variable in class org.protempa.proposition.value.BooleanValue

U

UniqueId - Class in org.protempa.proposition: A global unique identifier for Propositions.
UniqueId(UniqueId) - Constructor for class org.protempa.proposition.UniqueId: Copy constructor.
UniqueId(SourceId, LocalUniqueId) - Constructor for class org.protempa.proposition.UniqueId: Instantiates a new unique identifier.
UniqueIdFactory - Interface in org.protempa.proposition
UniqueIdPair - Class in org.protempa
UniqueIdPair(String, UniqueId, UniqueId) - Constructor for class org.protempa.UniqueIdPair
UniqueIdUniqueIdStoreCreator - Class in org.protempa.datastore
UniqueIdUniqueIdStoreCreator() - Constructor for class org.protempa.datastore.UniqueIdUniqueIdStoreCreator
UniqueIdUniqueIdStoreCreator(String) - Constructor for class org.protempa.datastore.UniqueIdUniqueIdStoreCreator
UniqueIdUniqueIdStoreCreator.Reference - Class in org.protempa.datastore
Unit - Interface in org.protempa.proposition.value: The units for a length.
UnitFactory - Interface in org.protempa.proposition.value: Access to the length units of data provided by a data source.
UNKNOWN - Static variable in class org.protempa.SourceSystem
UnrecoverableBackendErrorEvent - Class in org.protempa.backend
UnrecoverableBackendErrorEvent(Object) - Constructor for class org.protempa.backend.UnrecoverableBackendErrorEvent
unrecoverableErrorOccurred(UnrecoverableBackendErrorEvent) - Method in class org.protempa.AbstractSource
unrecoverableErrorOccurred(UnrecoverableBackendErrorEvent) - Method in interface org.protempa.BackendListener: Some unrecoverable error occurred while using a backend module, like a connection to a server was lost.
unsetMaxOverlapping() - Method in class org.protempa.LowLevelAbstractionDefinition: Disable the max-overlapping restart search directive.
unsetSkip() - Method in class org.protempa.LowLevelAbstractionDefinition: Disable the skip restart search directive.
unsetSkipEnd() - Method in class org.protempa.LowLevelAbstractionDefinition: Disable the skip-end restart search directive.
unsetSkipStart() - Method in class org.protempa.LowLevelAbstractionDefinition: Disable the skip-start restart search directive.
Util - Class in org.protempa.dest.table
Util - Class in org.protempa.dest
Util() - Constructor for class org.protempa.dest.Util
Util - Class in org.protempa.dest.xml
Util - Class in org.protempa.proposition.value

V

v - Variable in class org.protempa.proposition.interval.Interval
validate(Object) - Method in class org.protempa.backend.BackendPropertySpec: Checks if the value null but required, then checks if the value has the right type, then calls the specified validator's BackendPropertyValidator.validate(java.lang.String, java.lang.Object) method.
validate(String, E) - Method in interface org.protempa.backend.BackendPropertyValidator
validate(String, Object) - Method in class org.protempa.backend.DefaultBackendPropertyValidator
validate() - Method in class org.protempa.dest.AbstractQueryResultsHandler
validate() - Method in class org.protempa.dest.deid.DeidentifiedQueryResultsHandler
validate() - Method in interface org.protempa.dest.QueryResultsHandler: Validates this query results handler's specification.
validate(KnowledgeSource) - Method in class org.protempa.dest.table.AtLeastNColumnSpec
validate(KnowledgeSource) - Method in class org.protempa.dest.table.CountColumnSpec
validate(KnowledgeSource) - Method in class org.protempa.dest.table.DistanceBetweenColumnSpec
validate(KnowledgeSource) - Method in class org.protempa.dest.table.PropositionColumnSpec
validate(KnowledgeSource) - Method in class org.protempa.dest.table.PropositionValueColumnSpec
validate(KnowledgeSource) - Method in interface org.protempa.dest.table.TableColumnSpec: Validates the fields of this column specification against the knowledge source.
validate() - Method in class org.protempa.dest.table.TableQueryResultsHandler
validate() - Method in class org.protempa.dest.xml.XmlQueryResultsHandler
validateConfiguration(KnowledgeSource) - Method in interface org.protempa.backend.dsb.DataSourceBackend
validateData(KnowledgeSource) - Method in interface org.protempa.backend.dsb.DataSourceBackend
ValidateDataSource - Class in org.protempa.cli: Validates the data source for consistency between the knowledge source and the database mappings.
ValidateDataSource() - Constructor for class org.protempa.cli.ValidateDataSource
validateDataSourceBackendConfigurations() - Method in class org.protempa.Protempa
validateDataSourceBackendData() - Method in class org.protempa.Protempa: Runs each data source backend's data validation routine.
value(String) - Method in class org.protempa.AlgorithmArguments
value() - Method in class org.protempa.graph.Weight: Gets the value of this weight.
Value - Interface in org.protempa.proposition.value: A value (number, string, category, etc.).
ValueBuilder<V extends Value> - Interface in org.protempa.proposition.value
ValueClassification - Class in org.protempa
ValueClassification(String, String, String) - Constructor for class org.protempa.ValueClassification
valueComp(String) - Method in class org.protempa.AlgorithmArguments
ValueComparator - Enum in org.protempa.proposition.value: Represents the possible valid comparisons between two Value objects.
ValueComparatorFormatException - Exception in org.protempa.proposition.value
ValueComparatorFormatException() - Constructor for exception org.protempa.proposition.value.ValueComparatorFormatException
ValueFilter - Class in org.protempa.backend.dsb.filter
ValueFilter(String[], ValueComparator, Value) - Constructor for class org.protempa.backend.dsb.filter.ValueFilter
ValueList<V extends Value> - Class in org.protempa.proposition.value: Represents lists of values.
ValueList(int) - Constructor for class org.protempa.proposition.value.ValueList
ValueList() - Constructor for class org.protempa.proposition.value.ValueList: Creates an empty list of values.
ValueList(List<V>) - Constructor for class org.protempa.proposition.value.ValueList: Creates a list of values from the provided List of values.
ValueListBuilder<V extends Value> - Class in org.protempa.proposition.value
ValueListBuilder() - Constructor for class org.protempa.proposition.value.ValueListBuilder
ValueListBuilder(ValueList<V>) - Constructor for class org.protempa.proposition.value.ValueListBuilder
valueOf(String) - Static method in enum org.protempa.backend.BackendPropertyType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.protempa.CompoundLowLevelAbstractionDefinition.ValueDefinitionMatchOperator: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.protempa.dest.table.Derivation.Behavior: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.protempa.dest.table.PropositionValueColumnSpec.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.protempa.graph.BellmanFord.Mode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.protempa.proposition.interval.Interval.Side: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.protempa.proposition.value.ValueComparator: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.protempa.proposition.value.ValueType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.protempa.ProtempaUtil.PropositionDefinitionDisplayNameComparator.Style: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.protempa.query.QueryMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.protempa.SlidingWindowWidthMode: Returns the enum constant of this type with the specified name.
ValueOutputConfig - Class in org.protempa.dest.table
ValueOutputConfig() - Constructor for class org.protempa.dest.table.ValueOutputConfig
ValueOutputConfig(boolean, boolean, String, String) - Constructor for class org.protempa.dest.table.ValueOutputConfig
ValueOutputConfigBuilder - Class in org.protempa.dest.table
ValueOutputConfigBuilder() - Constructor for class org.protempa.dest.table.ValueOutputConfigBuilder
values() - Static method in enum org.protempa.backend.BackendPropertyType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.protempa.CompoundLowLevelAbstractionDefinition.ValueDefinitionMatchOperator: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Method in class org.protempa.DataSourceResultMap
values() - Static method in enum org.protempa.dest.table.Derivation.Behavior: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.protempa.dest.table.PropositionValueColumnSpec.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.protempa.graph.BellmanFord.Mode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.protempa.proposition.interval.Interval.Side: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.protempa.proposition.value.ValueComparator: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.protempa.proposition.value.ValueType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.protempa.ProtempaUtil.PropositionDefinitionDisplayNameComparator.Style: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.protempa.query.QueryMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.protempa.SlidingWindowWidthMode: Returns an array containing the constants of this enum type, in the order they are declared.
ValueSet - Class in org.protempa.valueset: For specifying value sets.
ValueSet(String, String, OrderedValue, OrderedValue, SourceId) - Constructor for class org.protempa.valueset.ValueSet
ValueSet(String, String, ValueSetElement[], SourceId) - Constructor for class org.protempa.valueset.ValueSet
ValueSet(String, String, ValueSetElement[], boolean, SourceId) - Constructor for class org.protempa.valueset.ValueSet: Instantiates a new value set with the specified values (value set elements).
ValueSetBuilder - Class in org.protempa.valueset
ValueSetBuilder() - Constructor for class org.protempa.valueset.ValueSetBuilder
ValueSetElement - Class in org.protempa.valueset: For specifying the values of a value set.
ValueSetElement(Value) - Constructor for class org.protempa.valueset.ValueSetElement
ValueSetElement(Value, String) - Constructor for class org.protempa.valueset.ValueSetElement
ValueSetElement(Value, String, String) - Constructor for class org.protempa.valueset.ValueSetElement
ValueSetElement(Value, String, String, Attribute[]) - Constructor for class org.protempa.valueset.ValueSetElement: Instantiates a value of a value set.
ValueSetElementBuilder - Class in org.protempa.valueset
ValueSetElementBuilder() - Constructor for class org.protempa.valueset.ValueSetElementBuilder
ValueType - Enum in org.protempa.proposition.value: Represents types of values of propositions and properties, and provides a method for parsing them from strings.
ValueVisitable - Interface in org.protempa.proposition.value: Interface for accepting a value.
ValueVisitor - Interface in org.protempa.proposition.value: Interface for classes that do processing on propositions.
visit(Collection<PropositionDefinition>) - Method in class org.protempa.AbstractPropositionDefinitionCheckedVisitor: Processes a collection of proposition definitions.
visit(EventDefinition) - Method in class org.protempa.AbstractPropositionDefinitionCheckedVisitor: Processes event definitions.
visit(ConstantDefinition) - Method in class org.protempa.AbstractPropositionDefinitionCheckedVisitor: Processes constant definitions.
visit(HighLevelAbstractionDefinition) - Method in class org.protempa.AbstractPropositionDefinitionCheckedVisitor: Processes high-level abstraction definitions.
visit(LowLevelAbstractionDefinition) - Method in class org.protempa.AbstractPropositionDefinitionCheckedVisitor: Processes low-level abstraction definitions.
visit(CompoundLowLevelAbstractionDefinition) - Method in class org.protempa.AbstractPropositionDefinitionCheckedVisitor: Processes compound low-level abstraction definitions.
visit(PrimitiveParameterDefinition) - Method in class org.protempa.AbstractPropositionDefinitionCheckedVisitor: Processes primitive parameter definitions.
visit(SliceDefinition) - Method in class org.protempa.AbstractPropositionDefinitionCheckedVisitor: Processes slice abstraction definitions.
visit(SequentialTemporalPatternDefinition) - Method in class org.protempa.AbstractPropositionDefinitionCheckedVisitor: Processes pair abstraction definitions.
visit(Collection<? extends PropositionDefinition>) - Method in class org.protempa.AbstractPropositionDefinitionVisitor: Processes a collection of proposition definitions.
visit(EventDefinition) - Method in class org.protempa.AbstractPropositionDefinitionVisitor: Processes event definitions.
visit(HighLevelAbstractionDefinition) - Method in class org.protempa.AbstractPropositionDefinitionVisitor: Processes high-level abstraction definitions.
visit(LowLevelAbstractionDefinition) - Method in class org.protempa.AbstractPropositionDefinitionVisitor: Processes low-level abstraction definitions.
visit(CompoundLowLevelAbstractionDefinition) - Method in class org.protempa.AbstractPropositionDefinitionVisitor: Processes compound low-level abstraction definitions.
visit(PrimitiveParameterDefinition) - Method in class org.protempa.AbstractPropositionDefinitionVisitor: Processes primitive parameter definitions.
visit(SliceDefinition) - Method in class org.protempa.AbstractPropositionDefinitionVisitor: Processes slice abstraction definitions.
visit(ConstantDefinition) - Method in class org.protempa.AbstractPropositionDefinitionVisitor: Processes constant definitions.
visit(SequentialTemporalPatternDefinition) - Method in class org.protempa.AbstractPropositionDefinitionVisitor: Processes constant definitions.
visit(PositionFilter) - Method in class org.protempa.backend.dsb.filter.AbstractFilterVisitor
visit(ValueFilter) - Method in class org.protempa.backend.dsb.filter.AbstractFilterVisitor
visit(PropertyValueFilter) - Method in class org.protempa.backend.dsb.filter.AbstractFilterVisitor
visit(PropertyValueFilter) - Method in interface org.protempa.backend.dsb.filter.FilterVisitor
visit(PositionFilter) - Method in interface org.protempa.backend.dsb.filter.FilterVisitor
visit(ValueFilter) - Method in interface org.protempa.backend.dsb.filter.FilterVisitor
visit(AbstractParameter) - Method in class org.protempa.dest.xml.XmlPropositionVisitor
visit(Event) - Method in class org.protempa.dest.xml.XmlPropositionVisitor
visit(PrimitiveParameter) - Method in class org.protempa.dest.xml.XmlPropositionVisitor
visit(Constant) - Method in class org.protempa.dest.xml.XmlPropositionVisitor
visit(AbstractParameter) - Method in class org.protempa.proposition.stats.AbstractKaplanMeyer
visit(Event) - Method in class org.protempa.proposition.stats.AbstractKaplanMeyer
visit(PrimitiveParameter) - Method in class org.protempa.proposition.stats.AbstractKaplanMeyer
visit(NominalValue) - Method in interface org.protempa.proposition.value.ValueVisitor: Processes a nominal value.
visit(OrdinalValue) - Method in interface org.protempa.proposition.value.ValueVisitor: Processes an ordinal value.
visit(BooleanValue) - Method in interface org.protempa.proposition.value.ValueVisitor: Processes a boolean value.
visit(ValueList<? extends Value>) - Method in interface org.protempa.proposition.value.ValueVisitor: Processes a list of values.
visit(NumberValue) - Method in interface org.protempa.proposition.value.ValueVisitor: Processes a number value.
visit(InequalityNumberValue) - Method in interface org.protempa.proposition.value.ValueVisitor: Processes an inequality number value.
visit(DateValue) - Method in interface org.protempa.proposition.value.ValueVisitor: Processes a date value.
visit(Map<String, List<Proposition>>) - Method in class org.protempa.proposition.visitor.AbstractPropositionCheckedVisitor
visit(Collection<? extends Proposition>) - Method in class org.protempa.proposition.visitor.AbstractPropositionCheckedVisitor
visit(PrimitiveParameter) - Method in class org.protempa.proposition.visitor.AbstractPropositionCheckedVisitor
visit(Event) - Method in class org.protempa.proposition.visitor.AbstractPropositionCheckedVisitor
visit(AbstractParameter) - Method in class org.protempa.proposition.visitor.AbstractPropositionCheckedVisitor
visit(Constant) - Method in class org.protempa.proposition.visitor.AbstractPropositionCheckedVisitor
visit(Context) - Method in class org.protempa.proposition.visitor.AbstractPropositionCheckedVisitor
visit(Map<String, List<Proposition>>) - Method in class org.protempa.proposition.visitor.AbstractPropositionVisitor
visit(Collection<? extends Proposition>) - Method in class org.protempa.proposition.visitor.AbstractPropositionVisitor
visit(AbstractParameter) - Method in class org.protempa.proposition.visitor.AbstractPropositionVisitor: Processes abstract parameters.
visit(Event) - Method in class org.protempa.proposition.visitor.AbstractPropositionVisitor: Processes events.
visit(PrimitiveParameter) - Method in class org.protempa.proposition.visitor.AbstractPropositionVisitor: Processes primitive parameters.
visit(Constant) - Method in class org.protempa.proposition.visitor.AbstractPropositionVisitor: Processes constants.
visit(Context) - Method in class org.protempa.proposition.visitor.AbstractPropositionVisitor: Processes contexts.
visit(Map<String, List<Proposition>>) - Method in interface org.protempa.proposition.visitor.PropositionCheckedVisitor: Processes results from a PROTEMPA finder method.
visit(Collection<? extends Proposition>) - Method in interface org.protempa.proposition.visitor.PropositionCheckedVisitor: Processes a collection of propositions.
visit(PrimitiveParameter) - Method in interface org.protempa.proposition.visitor.PropositionCheckedVisitor: Processes a primitive parameter.
visit(Event) - Method in interface org.protempa.proposition.visitor.PropositionCheckedVisitor: Processes an event.
visit(AbstractParameter) - Method in interface org.protempa.proposition.visitor.PropositionCheckedVisitor: Processes an abstract parameter.
visit(Constant) - Method in interface org.protempa.proposition.visitor.PropositionCheckedVisitor: Processes a constant parameter.
visit(Context) - Method in interface org.protempa.proposition.visitor.PropositionCheckedVisitor: Processes a context.
visit(Map<String, List<Proposition>>) - Method in interface org.protempa.proposition.visitor.PropositionVisitor: Processes results from a PROTEMPA finder method.
visit(Collection<? extends Proposition>) - Method in interface org.protempa.proposition.visitor.PropositionVisitor: Processes a collection of propositions.
visit(PrimitiveParameter) - Method in interface org.protempa.proposition.visitor.PropositionVisitor: Processes a primitive parameter.
visit(Event) - Method in interface org.protempa.proposition.visitor.PropositionVisitor: Processes an event.
visit(AbstractParameter) - Method in interface org.protempa.proposition.visitor.PropositionVisitor: Processes an abstract parameter.
visit(Constant) - Method in interface org.protempa.proposition.visitor.PropositionVisitor: Processes a constant.
visit(Context) - Method in interface org.protempa.proposition.visitor.PropositionVisitor: Processes a context.
visit(Collection<PropositionDefinition>) - Method in interface org.protempa.PropositionDefinitionCheckedVisitor: Process a collection of proposition definitions.
visit(LowLevelAbstractionDefinition) - Method in interface org.protempa.PropositionDefinitionCheckedVisitor: Process a low-level abstraction definition
visit(CompoundLowLevelAbstractionDefinition) - Method in interface org.protempa.PropositionDefinitionCheckedVisitor: Process a compound low-level abstraction definition
visit(HighLevelAbstractionDefinition) - Method in interface org.protempa.PropositionDefinitionCheckedVisitor: Process a high-level abstraction definition
visit(SliceDefinition) - Method in interface org.protempa.PropositionDefinitionCheckedVisitor: Process a slice definition.
visit(EventDefinition) - Method in interface org.protempa.PropositionDefinitionCheckedVisitor: Process an event definition.
visit(PrimitiveParameterDefinition) - Method in interface org.protempa.PropositionDefinitionCheckedVisitor: Process a primitive parameter definition.
visit(ConstantDefinition) - Method in interface org.protempa.PropositionDefinitionCheckedVisitor: Process a constant definition.
visit(SequentialTemporalPatternDefinition) - Method in interface org.protempa.PropositionDefinitionCheckedVisitor: Process a pair abstraction definition.
visit(ContextDefinition) - Method in interface org.protempa.PropositionDefinitionCheckedVisitor: Process a context definition.
visit(Collection<? extends PropositionDefinition>) - Method in interface org.protempa.PropositionDefinitionVisitor: Process a collection of proposition definitions.
visit(LowLevelAbstractionDefinition) - Method in interface org.protempa.PropositionDefinitionVisitor: Process a low-level abstraction definition
visit(CompoundLowLevelAbstractionDefinition) - Method in interface org.protempa.PropositionDefinitionVisitor: Process a compound low-level abstraction definition
visit(HighLevelAbstractionDefinition) - Method in interface org.protempa.PropositionDefinitionVisitor: Process a high-level abstraction definition
visit(SliceDefinition) - Method in interface org.protempa.PropositionDefinitionVisitor: Process a slice definition.
visit(EventDefinition) - Method in interface org.protempa.PropositionDefinitionVisitor: Process an event definition.
visit(PrimitiveParameterDefinition) - Method in interface org.protempa.PropositionDefinitionVisitor: Process a primitive parameter definition.
visit(ConstantDefinition) - Method in interface org.protempa.PropositionDefinitionVisitor: Process a constant definition.
visit(SequentialTemporalPatternDefinition) - Method in interface org.protempa.PropositionDefinitionVisitor: Process a pair definition.
visit(ContextDefinition) - Method in interface org.protempa.PropositionDefinitionVisitor: Process a temporal context.
visitAll(Filter) - Method in class org.protempa.backend.dsb.filter.AbstractFilterVisitor
visitAll(Filter) - Method in interface org.protempa.backend.dsb.filter.FilterVisitor

W

WEEK - Static variable in class org.protempa.proposition.value.AbsoluteTimeUnit
Weight - Class in org.protempa.graph: Like a Long except that there are special values representing positive infinity, negative infinity, positive epsilon (smallest positive value), and negative epsilon (smallest negative value).
WeightFactory - Class in org.protempa.graph
WeightFactory() - Constructor for class org.protempa.graph.WeightFactory
withId(String) - Static method in class org.protempa.Term: Creates and returns a new Term with the given identifier
WorkingMemoryStoreCreator - Class in org.protempa.datastore: A class to generate permanent stores mapping key IDs to Drools working memory objects.
WorkingMemoryStoreCreator(RuleBase) - Constructor for class org.protempa.datastore.WorkingMemoryStoreCreator
WorkingMemoryStoreCreator(RuleBase, String) - Constructor for class org.protempa.datastore.WorkingMemoryStoreCreator
writeAbstractProposition(ObjectOutputStream) - Method in class org.protempa.proposition.AbstractProposition
writeKeys(Set<String>) - Method in class org.protempa.backend.dsb.AbstractDataSourceBackend
writeKeys(Set<String>) - Method in interface org.protempa.backend.dsb.DataSourceBackend
writeKeys(Set<String>) - Method in interface org.protempa.DataSource
writeKeys(Set<String>) - Method in class org.protempa.DataSourceImpl
writeQueryAsXML(Query, File) - Static method in class org.protempa.xml.XMLConfiguration: Write the given Protempa query to the specified file.
writeQueryAsXML(Query, File, boolean) - Static method in class org.protempa.xml.XMLConfiguration: Write the given protempa query to the specified file.
writeQueryAsXML(Query, Writer, boolean) - Static method in class org.protempa.xml.XMLConfiguration: Write the given protempa query to the specified file.
writeTableDestinationAsXML(TableDestination, File, KnowledgeSource) - Static method in class org.protempa.xml.XMLConfiguration: Write the given TableDestination query to the specified file.
writeTableDestinationAsXML(TableDestination, File, boolean, KnowledgeSource) - Static method in class org.protempa.xml.XMLConfiguration: Write the given TableDestination query to the specified file.
writeTableDestinationAsXML(TableDestination, Writer, boolean, KnowledgeSource) - Static method in class org.protempa.xml.XMLConfiguration: Write the given TableDestination query using the specified Writer.
writeTemporalParameter(ObjectOutputStream) - Method in class org.protempa.proposition.TemporalParameter
writeTemporalProposition(ObjectOutputStream) - Method in class org.protempa.proposition.TemporalProposition: Called while serializing a temporal proposition.

X

XMLConfiguration - Class in org.protempa.xml: This class takes a Protempa configuration information such as a query and generates equivalent XML that conforms to the schema in protempa_query.xsd.
XMLConfiguration(File) - Constructor for class org.protempa.xml.XMLConfiguration: Call this constructor to use this class as a QueryBuilder.
XmlDestination - Class in org.protempa.dest.xml
XmlDestination(Writer, Map<String, String>, String, String[]) - Constructor for class org.protempa.dest.xml.XmlDestination: Constructor
XmlPropositionVisitor - Class in org.protempa.dest.xml
XmlPropositionVisitor(KnowledgeSource) - Constructor for class org.protempa.dest.xml.XmlPropositionVisitor
XmlQueryResultsHandler - Class in org.protempa.dest.xml
XmlQueryResultsHandlerException - Exception in org.protempa.dest.xml
XmlQueryResultsHandlerException(Throwable) - Constructor for exception org.protempa.dest.xml.XmlQueryResultsHandlerException

Y

YEAR - Static variable in class org.protempa.proposition.value.AbsoluteTimeGranularity
YEAR - Static variable in class org.protempa.proposition.value.AbsoluteTimeUnit

Z

ZERO - Static variable in class org.protempa.graph.WeightFactory: Special value representing zero.

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