Creates a new AssemblyManager from two LUTs: (Mention -> IDPointer) and (IDPointer -> EntityEventRepresentation).
Creates a new AssemblyManager from two LUTs: (Mention -> IDPointer) and (IDPointer -> EntityEventRepresentation). These LUTs are used to populate the mentionStateToID and idToEERepresentation LUTs containing the same information. Subsequent updates to these LUTs create new LUTs. The motivation for the LUTs was to allow for changes in the mapping of a Mention -...-> EntityEventRepresentation to easily propagate in nested cases. For example, an update to the (Mention -> EntityEventRepresentation) mapping of a SimpleEvent Mention will propagate to the (Mention -> EntityEventRepresentation) mapping of any ComplexEvent Mention containing this SimpleEvent Mention.
Retrieves all EntityEventRepresentations found in AssemblyManager.idToEER
Retrieves all EntityEventRepresentations found in AssemblyManager.idToEER
the Set of Odin Mentions tracked by this AssemblyManager
Creates a Complex from a Binding Mention and updates the mentionStateToID and idToEER LUTs
Creates a Complex from a Binding Mention and updates the mentionStateToID and idToEER LUTs
an Odin Mention
a tuple of (Complex, IDPointer)
Create a SimpleEntity representation from a Mention and an optional set of optional modifications (useful for building output of SimpleEvent)
Create a SimpleEntity representation from a Mention and an optional set of optional modifications (useful for building output of SimpleEvent)
Whenever modifications are provided, the mentionStateToID LUT is NOT updated, so as to avoid a conflict with the existing mapping (see the description of mods for the motivation)
an Odin Mention
an optional set of AssemblyModification. This is useful for building the output of a SimpleEvent (any simple event other than a Binding), which is a set of SimpleEvent where the key PTM comes from the SimpleEvent (i.e., the PTM cannot be recovered by simply examining m out of context)
a SimpleEntity
Create a SimpleEntity representation from a Mention and an optional set of optional modifications (useful for building output of SimpleEvent)
Create a SimpleEntity representation from a Mention and an optional set of optional modifications (useful for building output of SimpleEvent)
Whenever modifications are provided, the mentionStateToID LUT is NOT updated, so as to avoid a conflict with the existing mapping (see the description of mods for the motivation)
an Odin Mention
an optional set of AssemblyModification. This is useful for building the output of a SimpleEvent (any simple event other than a Binding), which is a set of SimpleEvent where the key PTM comes from the SimpleEvent (i.e., the PTM cannot be recovered by simply examining m out of context)
a tuple of (IDPointer, SimpleEntity)
Returns "distinct" Set of Activations matching the provided polarity.
Returns "distinct" Set of Activations matching the provided polarity. Ignores differences in IDPointers.
a String to match against each Activation.polarity
a Set of Activations
Returns "distinct" Set of Activations.
Returns "distinct" Set of Activations. Ignores differences in IDPointers.
a Set of Regulation
Returns "distinct" Set of Activations matching the provided polarity and all evidence (Set[Mention]) corresponding to each Activation.
Returns "distinct" Set of Activations matching the provided polarity and all evidence (Set[Mention]) corresponding to each Activation.
a String to match against each Activation.polarity
Set[(Activation, Set[Mention])]
Returns "distinct" Set of Activations and all evidence (Set[Mention]) corresponding to each Activation.
Returns "distinct" Set of Activations and all evidence (Set[Mention]) corresponding to each Activation.
Set[(Regulation, Set[Mention])]
Returns "distinct" Set of Complexes.
Returns "distinct" Set of Complexes. Ignores differences in IDPointers.
a Set of Complexes
Returns "distinct" Set of Complexes and all evidence (Set[Mention]) corresponding to each Complex.
Returns "distinct" Set of Complexes and all evidence (Set[Mention]) corresponding to each Complex.
Set[(Complex, Set[Mention])]
Returns head of each group returned by groupedEERs.
Returns head of each group returned by groupedEERs.
a Set of EntityEventRepresentation
Gets distinct members of eers after grouping by EntityEventRepresentation.equivalenceHash.
Gets distinct members of eers after grouping by EntityEventRepresentation.equivalenceHash.
an EntityEventRepresentation Set
whether or not to ignore modifications when determining the distinct set of EERs
Returns Set of "distinct" EntityEventRepresentation with corresponding evidence.
Returns "distinct" Set of Entities.
Returns "distinct" Set of Entities. Ignores multiple instances of the same Entity.
a Set of Entity
Returns "distinct" Set of Entities and all evidence (Set[Mention]) corresponding to each Entity.
Returns "distinct" Set of Entities and all evidence (Set[Mention]) corresponding to each Entity.
Set[(Entity, Set[Mention])]
Returns "distinct" Set of Events.
Returns "distinct" Set of Events. Ignores multiple instances of the same Entity.
a Set of Event
Returns "distinct" Set of Events and all evidence (Set[Mention]) corresponding to each Event.
Returns "distinct" Set of Events and all evidence (Set[Mention]) corresponding to each Event.
Set[(SimpleEntity, Set[Mention])]
Retrieves the distinct Set of EER predecessors for the provided Mention (m).
Retrieves the distinct Set of EER predecessors for the provided Mention (m).
an Odin Mention
the Set of distinct EntityEventRepresentations known to causally precede the EER corresponding to M
Retrieves the distinct Set of EER predecessors for the provided EER.
Retrieves the distinct Set of EER predecessors for the provided EER.
an EntityEventRepresentation
the Set of distinct EntityEventRepresentations known to causally precede any EER corresponding to EntityEventRepresentation.equivalenceHash
Returns "distinct" Set of Regulations matching the provided polarity.
Returns "distinct" Set of Regulations matching the provided polarity. Ignores differences in IDPointers.
a String to match against each Regulation.polarity
a Set of Regulations
Returns "distinct" Set of Regulation.
Returns "distinct" Set of Regulation. Ignores differences in IDPointers.
a Set of Regulation
Returns "distinct" Set of Regulations matching the provided polarity and all evidence (Set[Mention]) corresponding to each Regulation.
Returns "distinct" Set of Regulations matching the provided polarity and all evidence (Set[Mention]) corresponding to each Regulation.
a String to match against each Regulation.polarity
Set[(Regulation, Set[Mention])]
Returns "distinct" Set of Regulations and all evidence (Set[Mention]) corresponding to each Regulation.
Returns "distinct" Set of Regulations and all evidence (Set[Mention]) corresponding to each Regulation.
Set[(Regulation, Set[Mention])]
Returns "distinct" Set of SimpleEntity.
Returns "distinct" Set of SimpleEntity. Ignores multiple instances of the same SimpleEntity.
a Set of SimpleEntity
Returns "distinct" Set of SimpleEntities and all evidence (Set[Mention]) corresponding to each SimpleEntity.
Returns "distinct" Set of SimpleEntities and all evidence (Set[Mention]) corresponding to each SimpleEntity.
Set[(SimpleEntity, Set[Mention])]
Returns "distinct" Set of SimpleEvents matching the provided event label.
Returns "distinct" Set of SimpleEvents matching the provided event label. Ignores differences in IDPointers.
a String to match against each SimpleEvent.label
a Set of SimpleEvents
Returns "distinct" Set of SimpleEvents.
Returns "distinct" Set of SimpleEvents. Ignores differences in IDPointers.
a Set of SimpleEvents
Returns "distinct" Set of SimpleEvent matching the provided event label and all evidence (Set[Mention]) corresponding to each SimpleEvent.
Returns "distinct" Set of SimpleEvent matching the provided event label and all evidence (Set[Mention]) corresponding to each SimpleEvent.
a String to match against each SimpleEvent.label
Set[(SimpleEvent, Set[Mention])]
Retrieves the distinct Set of EER successors for the provided Mention (m).
Retrieves the distinct Set of EER successors for the provided Mention (m).
an Odin Mention
the Set of distinct EntityEventRepresentations known to causally succeed any EER corresponding to eh
Retrieves the distinct Set of EER successors for the provided EER.
Retrieves the distinct Set of EER successors for the provided EER.
an EntityEventRepresentation
the Set of distinct EntityEventRepresentations known to causally succeed any EER corresponding to eh
Retrieves all Activations from the manager matching the provided polarity label.
Retrieves all Activations from the manager matching the provided polarity label. Note that these are non-distinct (Activations may differ in terms of their IDPointers).
a String to match against each Activation.polarity
Retrieves all Activations from the manager.
Retrieves all Activations from the manager. Note that these are non-distinct (Activations may differ in terms of their IDPointers).
Returns a Regulation for a Mention m with the appropriate label.
Returns a Regulation for a Mention m with the appropriate label.
an Odin Mention. Must have the label "Complex".
Retrieves all Complexes from the manager.
Retrieves all Complexes from the manager. Note that these are non-distinct (Complexes may differ in terms of their IDPointers).
Retrieves an EntityEventRepresentation associated with the given IDPointer.
Retrieves an EntityEventRepresentation for a Mention.
Retrieves an EntityEventRepresentation for a Mention. Assumes an EntityEventRepresentation for the given Mention already exists.
an Odin Mention
an EntityEventRepresentation
Retrieves the Set of EntityEventRepresentation tracked by the manager.
Retrieves the Set of EntityEventRepresentation tracked by the manager.
Set[EntityEventRepresentation]
Retrieves all Entities from the manager.
Retrieves all Entities from the manager. Note that these are non-distinct.
Returns an Entity for a Mention with the appropriate labels.
Returns an Entity for a Mention with the appropriate labels.
an Odin Mention. Must have the label "Entity"
Get non-distinct equivalent EERs matching the provided equivalenceHash (eh)
Get non-distinct equivalent EERs matching the provided equivalenceHash (eh)
an EntityEventRepresentation.equivalenceHash
Returns an Event for a Mention with the appropriate labels.
Returns an Event for a Mention with the appropriate labels.
an Odin Mention.
Retrieves all Events from the manager.
Retrieves all Events from the manager. Note that these are non-distinct (Events may differ in terms of their IDPointers).
Collects mentions pointing to a given EntityEventRepresentation.
Collects mentions pointing to a given EntityEventRepresentation.
an EntityEventRepresentation
a sequence of Mention serving as textual evidence of the given representation
Retrieves ID from an EntityEventRepresentation.uniqueID
Retrieves ID from an EntityEventRepresentation.uniqueID
an EntityEventRepresentation
the IDPointer for the repr
Retrieve the set of mentions currently tracked by the manager
Gets the polarity of a mention.
Gets the polarity of a mention. Should only be relevant to ComplexEvents
an Odin Mention
AssemblyManager.positive, AssemblyManager.negative, or AssemblyManager.unknown
Retrieves the set of PrecedenceRelations for all Events
Retrieves the Set of PrecedenceRelations corresponding to the provided Mention
Retrieves the Set of PrecedenceRelations corresponding to the provided Mention
an Odin Mention
Retrieves the Set of PrecedenceRelations corresponding to the provided EntityEventRepresentation.equivalenceHash (eh)
Retrieves the Set of PrecedenceRelations corresponding to the provided EntityEventRepresentation.equivalenceHash (eh)
an EntityEventRepresentation
Returns a Regulation for a Mention m with the label "Regulation"
Returns a Regulation for a Mention m with the label "Regulation"
an Odin Mention. Must have the label "Regulation"
Retrieves all Regulations from the manager matching the provided polarity label.
Retrieves all Regulations from the manager matching the provided polarity label. Note that these are non-distinct (Regulations may differ in terms of their IDPointers).
a String to match against each Regulation.polarity
Retrieves all Regulations from the manager.
Retrieves all Regulations from the manager. Note that these are non-distinct (Regulations may differ in terms of their IDPointers).
Retrieves all SimpleEntities from the manager.
Retrieves all SimpleEntities from the manager. Note that these are non-distinct.
Retrieves all SimpleEntities containing the given
Retrieves all SimpleEntities containing the given
an AssemblyModification
a Set of SimpleEntities sharing mod
Returns a SimpleEntity for a Mention with the appropriate labels.
Returns a SimpleEntity for a Mention with the appropriate labels.
an Odin Mention. Must have the label "Entity" and not the label "Complex".
Returns a SimpleEvent for a Mention m with the appropriate labels.
Returns a SimpleEvent for a Mention m with the appropriate labels.
an Odin Mention. Must have the label "SimpleEvent".
Retrieves all SimpleEvents from the manager matching the provided event label.
Retrieves all SimpleEvents from the manager matching the provided event label. Note that these are non-distinct (SimpleEvents may differ in terms of their IDPointers).
a String to match against each SimpleEvent.label
Retrieves all SimpleEvents from the manager.
Retrieves all SimpleEvents from the manager. Note that these are non-distinct (SimpleEvents may differ in terms of their IDPointers).
Returns groups of equivalent EntityEventRepresentation, ignoring differences due to IDPointer references.
A (mostly) human readable printout of the (key, value) pairs in the mentionStateToID] LUT
A high-level summary of a Mention m
A high-level summary of a Mention m
an Odin Mention
a high-level String representation of m
Builds a Set[AssemblyModfication] from the modifcations belonging to a Mention m.
Builds a Set[AssemblyModfication] from the modifcations belonging to a Mention m. Currently, only a subset of Mention org.clulab.reach.mentions.Modification are considered relevant to assembly: PTM Mutant
Additionally, a Mention corresponding to an Entity will include an EntityLabel AssemblyModification encoding its label (ex. Family)
an Odin Mention
Set[AssemblyModification]
Retrieves the non-distinct Set of EER predecessors for the provided Mention (m).
Retrieves the non-distinct Set of EER predecessors for the provided Mention (m).
an Odin Mention
the Set of non-distinct EntityEventRepresentations known to causally precede the EER corresponding to m
Retrieves the non-distinct Set of EER predecessors for the provided EER.
Retrieves the non-distinct Set of EER predecessors for the provided EER.
an EntityEventRepresentation
the Set of non-distinct EntityEventRepresentations known to causally precede eer
Removes mention and corresponding EntityEventRepresentation associated with the provided id.
Removes mention and corresponding EntityEventRepresentation associated with the provided id. If the corresponding EntityEventRepresentation is a SimpleEvent, remove its output as well.
an IDPointer used to identify mentions and EntityEventRepresentations for removal
Removes entries referencing the given EntityEventRepresentation.
Removes entries referencing the given EntityEventRepresentation.
an EntityEventRepresentation used to identify mentions and EntityEventRepresentations for removal
Removes mention and corresponding EERepresentation from the AssemblyManager
Removes entries referencing the any of the given IDPointer.
Removes entries referencing the any of the given IDPointer.
a Seq[IDPointer] used to identify mentions and EntityEventRepresentations for removal
Stores a PrecedenceRelation in EERtoPrecedenceRelations for the EERs corresponding to "before" and "after"
Stores a PrecedenceRelation in EERtoPrecedenceRelations for the EERs corresponding to "before" and "after"
an EntityEventRepresentation that causally precedes "after"
an EntityEventRepresentation that (causally) follows "before"
the name of the sieve or procedure that discovered this precedence relation
Stores a PrecedenceRelation in EERtoPrecedenceRelations connecting "before" and "after".
Stores a PrecedenceRelation in EERtoPrecedenceRelations connecting "before" and "after". Tracks "before" and "after" Mentions and produces EERs, is not already present.
an Odin Mention that causally precedes "after"
an Odin Mention that (causally) follows "before"
a Set of Odin Mentions serving as evidence for the precedence relation
the name of the sieve or procedure that discovered this precedence relation
Retrieves the non-distinct Set of EER successors for the provided Mention (m).
Retrieves the non-distinct Set of EER successors for the provided Mention (m).
an Odin Mention
the Set of non-distinct EntityEventRepresentations known to causally succeed the EER corresponding to m
Retrieves the non-distinct Set of EER successors for the provided EER.
Retrieves the non-distinct Set of EER successors for the provided EER.
an EntityEventRepresentation
the Set of non-distinct EntityEventRepresentations known to causally succeed eer
Creates an EntityEventRepresentation if m is a valid Mention See isValidMention for details on validation check
Creates an EntityEventRepresentation if m is a valid Mention See isValidMention for details on validation check
an Odin Mention
Creates an EntityEventRepresentation for each valid Mention See isValidMention for details on validation check
Creates an EntityEventRepresentation for each valid Mention See isValidMention for details on validation check
a sequence of Mention to store in the AssemblyManager LUTs
Retrieves all tracked Mentions from AssemblyManager.mentionStateToID
Retrieves all tracked Mentions from AssemblyManager.mentionStateToID
the Set of Odin Mentions tracked by this AssemblyManager