org.clulab.reach.assembly.representations
SimpleEntity
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package representations
IDPointer assigned to this SimpleEntity by the AssemblyManager
GroundingID for the SimpleEntity
a Set of AssemblyModification, such as representations.PTM and EntityLabel.
These are relevant to the identity of the SimpleEntity and describe its state (ex. Phosphorylated @ Ser123).
the Mention from which this SimpleEntity was constructed
a pointer to the AssemblyManager instance that produced this SimpleEntity
Whether or not the SimpleEntity contains the provided IDPointer.
Whether or not the SimpleEntity contains the provided IDPointer.
an IDPointer identifying some EntityEventRepresentation
true or false
Whether or not the EntityEventRepresentation was produced by a Mention resolved through coref.
Whether or not the EntityEventRepresentation was produced by a Mention resolved through coref.
true or false
Used by isEquivalentTo to compare against another SimpleEntity.
Used by isEquivalentTo to compare against another SimpleEntity.
The Set of Mentions serving as textual evidence for this EntityEventRepresentation.
The Set of Mentions serving as textual evidence for this EntityEventRepresentation.
Set[Mention]
Returns the Set of representations.PTM contained in modifications matching the given label.
Returns the Set of representations.PTM contained in modifications matching the given label.
the label used to filter representations.PTM
Returns the Set of representations.PTM contained in modifications.
GroundingID for the SimpleEntity
Checks to see if a coref mention has an antecedent.
Checks to see if a coref mention has an antecedent.
If the mentions made it through the coref component of reach,
the only mentions that might have an antecedent should be those with a "Generic_*"
this is just a broader, fail-safe check...
an Odin Mention
true if cm has an antecedent; false otherwise
Checks whether evidence contains a Negation modification
Checks whether evidence contains a Negation modification
an Odin Mention
true or false
Used to compare against another SimpleEntity.
Used to compare against another SimpleEntity.
Based on the equality of equivalenceHash to that of another SimpleEntity.
the thing to compare against
true or false
a pointer to the AssemblyManager instance that produced this SimpleEntity
a pointer to the AssemblyManager instance that produced this SimpleEntity
a Set of AssemblyModification, such as representations.PTM and EntityLabel.
a Set of AssemblyModification, such as representations.PTM and EntityLabel.
These are relevant to the identity of the SimpleEntity and describe its state (ex. Phosphorylated @ Ser123).
Hash representing the modifications.
Hash representing the modifications.
Used by equivalenceHash for isEquivalentTo comparisons.
an Int hash based on the hashcodes of the modifications
Check if SimpleEvent is negated
Check if SimpleEvent is negated
true or false
the Mention from which this SimpleEntity was constructed
the Mention from which this SimpleEntity was constructed
Summary making use of grounding, modifications, coref, and manager.
Summary making use of grounding, modifications, coref, and manager.
a String summary of the SimpleEntity
IDPointer assigned to this SimpleEntity by the AssemblyManager
IDPointer assigned to this SimpleEntity by the AssemblyManager
Find SimpleEntities with simple same grounding
A SimpleEntity representation of a Mention of a Protein, GGP, Simple_chemical, etc. (see the children of "Entity" in the taxonomy)