assembly

Type Members

1. class Activation extends ComplexEvent

   

   Representation of a Activation.

2. class AssemblyExporter extends AnyRef

   

3. class AssemblyManager extends Serializable

   

4. trait AssemblyModification extends AnyRef

   

   Trait for modifications/features associated with an edu.arizona.sista.assembly.Entity.

5. trait AssemblySieve extends AnyRef

   

6. class Complex extends Entity

   

   A Entity representation of a Binding Mention.

7. trait ComplexEvent extends Event

   

   Representation of a ComplexEvent.

8. trait Entity extends EntityEventRepresentation

   

   Trait for entity representations of a Mention.

9. trait EntityEventRepresentation extends Serializable

   

   Trait used for entity/event representations of a Mention.

10. case class EntityLabel(label: String) extends AssemblyModification with Product with Serializable

    

    The label associated with an Entity ( Protein, GGP, etc.)

    The label associated with an Entity ( Protein, GGP, etc.)

    label

    the label associated with an Entity

11. trait Event extends EntityEventRepresentation

    

    Trait for an Event representation of a Mention.

12. type GroundingID = String

    

13. type IDPointer = Int

    

14. case class MutantEntity(mutantType: String) extends AssemblyModification with Product with Serializable

    

    A representation of a mutated form of an Entity.

    A representation of a mutated form of an Entity. Mutation sites, if present, are encoded in mutantType.

    mutantType

    the type of mutation (see edu.arizona.sista.reach.mentions.Mutant.label)

15. case class PTM(label: String, site: Option[String]) extends AssemblyModification with Product with Serializable

    

    A representation of a post-translational modification (PTM) ( Phosphorylation, Ubiquitination, etc.) associated with an Entity.

    A representation of a post-translational modification (PTM) ( Phosphorylation, Ubiquitination, etc.) associated with an Entity.

    label

    the ptm

    site

    an Option[String] representing the Site of the PTM

16. case class PrecedenceRelation(before: Int, after: Int, evidence: Set[Mention], foundBy: String) extends Product with Serializable

    

    Stores precedence information for two distinct EntityEventRepresentation

    Stores precedence information for two distinct EntityEventRepresentation

    before

    EntityEventRepresentation.equivalenceHash identifying the EER that precedes PrecedenceRelation.after

    after

    EntityEventRepresentation.equivalenceHash identifying the EER that follows PrecedenceRelation.before

    evidence

    the mentions that serve as evidence for this precedence relation

    foundBy

    the name of the Sieve which found this relation

17. class Regulation extends ComplexEvent

    

    Representation of a Regulation.

18. case class Row(input: String, output: String, controller: String, eventID: String, eventLabel: String, precededBy: Set[String], negated: Boolean, evidence: Set[Mention], sourceRepresentation: EntityEventRepresentation) extends Product with Serializable

    

19. type Sieve = (Seq[Mention], AssemblyManager) ⇒ AssemblyManager

    

20. class SieveMixture extends AssemblySieve

    

21. class Sieves extends AnyRef

    

    Contains all sieves of the signature (mentions: Seq[Mention], manager: AssemblyManager) => AssemblyManager.

22. class SimpleEntity extends Entity

    

    A SimpleEntity representation of a Mention of a Protein, GGP, Simple_chemical, etc.

    A SimpleEntity representation of a Mention of a Protein, GGP, Simple_chemical, etc. (see the children of "Entity" in the taxonomy)

23. class SimpleEvent extends Event

    

    Representation for any Mention with the label SimpleEvent.

    Representation for any Mention with the label SimpleEvent. Note that a Binding is represented using a Complex.