Package de.julielab.jcore.ae.linnaeus

Class LinnaeusSpeciesAnnotator

  • All Implemented Interfaces:
    org.apache.uima.analysis_component.AnalysisComponent
    public class LinnaeusSpeciesAnnotator
extends org.apache.uima.analysis_component.JCasAnnotator_ImplBase
    Uses the Linnaeus software (http://linnaeus.sourceforge.net/) to detect species mentions and map them to NCBI taxonomy IDs.
    Author:
    faessler

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static java.lang.String PARAM_CONFIG_FILE  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void collectionProcessComplete()  
      void initialize​(org.apache.uima.UimaContext aContext)  
      void process​(org.apache.uima.jcas.JCas cas)  

      • Methods inherited from class org.apache.uima.analysis_component.JCasAnnotator_ImplBase

        getRequiredCasInterface, process

      • Methods inherited from class org.apache.uima.analysis_component.Annotator_ImplBase

        getCasInstancesRequired, hasNext, next

      • Methods inherited from class org.apache.uima.analysis_component.AnalysisComponent_ImplBase

        batchProcessComplete, destroy, getContext, getResultSpecification, reconfigure, setResultSpecification

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • PARAM_CONFIG_FILE

        public static final java.lang.String PARAM_CONFIG_FILE
        See Also:
        Constant Field Values

    • Constructor Detail

      • LinnaeusSpeciesAnnotator

        public LinnaeusSpeciesAnnotator()

    • Method Detail

      • initialize

        public void initialize​(org.apache.uima.UimaContext aContext)
                throws org.apache.uima.resource.ResourceInitializationException
        Specified by:
        initialize in interface org.apache.uima.analysis_component.AnalysisComponent
        Overrides:
        initialize in class org.apache.uima.analysis_component.AnalysisComponent_ImplBase
        Throws:
        org.apache.uima.resource.ResourceInitializationException

      • process

        public void process​(org.apache.uima.jcas.JCas cas)
             throws org.apache.uima.analysis_engine.AnalysisEngineProcessException
        Specified by:
        process in class org.apache.uima.analysis_component.JCasAnnotator_ImplBase
        Throws:
        org.apache.uima.analysis_engine.AnalysisEngineProcessException

      • collectionProcessComplete

        public void collectionProcessComplete()
                               throws org.apache.uima.analysis_engine.AnalysisEngineProcessException
        Specified by:
        collectionProcessComplete in interface org.apache.uima.analysis_component.AnalysisComponent
        Overrides:
        collectionProcessComplete in class org.apache.uima.analysis_component.AnalysisComponent_ImplBase
        Throws:
        org.apache.uima.analysis_engine.AnalysisEngineProcessException