org.clulab.reach.grounding.IMKBProteinLookup.scala Maven / Gradle / Ivy

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package org.clulab.reach.grounding

import org.clulab.reach.grounding.ReachKBKeyTransforms._

/**
  * Class implementing alternate key lookups for protein knowledge bases.
  *   Written by Tom Hicks. 11/10/2015.
  *   Last Modified: Change to class, add IMKB ctor argument.
  */
class IMKBProteinLookup (

  /** The in-memory knowledge base that all lookups will work against. */
  memoryKB: InMemoryKB = new InMemoryKB()

) extends IMKBLookup (memoryKB) {

  /** Resolve the given text string to an optional entry in a knowledge base.
    * Return a resolution for the entry, if any found.
    */
  override def resolve (text:String): Resolutions =
    resolveAlt(text, proteinKeyTransforms)

  /** Resolve the given text string to an optional entry in a knowledge base,
    * for the single named species.
    * Return a resolution for the entry, if any found.
    */
  override def resolveByASpecies (text:String, species:String): Resolutions =
    resolveByASpeciesAlt(text, species, proteinKeyTransforms)

  /** Resolve the given text string to an optional group of entries in a knowledge base,
    * returning resolutions for all species entries found in the KB.
    */
  override def resolveBySpecies (text:String, speciesSet:SpeciesNameSet): Resolutions =
    resolveBySpeciesAlt(text, speciesSet, proteinKeyTransforms)

  /** Resolve the given text string to an optional entry in a knowledge base,
    * failing if the entry is not for humans.
    * Return a resolution for a human entry, if any found.
    */
  override def resolveHuman (text:String): Resolutions =
    resolveHumanAlt(text, proteinKeyTransforms)

  /** Resolve the given text string to an optional entry in a knowledge base which
    * explicitly does not have an associated species. Fail if all entries have species.
    * Return a resolution for the entry, if any found.
    */
  override def resolveNoSpecies (text:String): Resolutions =
    resolveNoSpeciesAlt(text, proteinKeyTransforms)

}