Package de.julielab.jules.ae.genemapping

Class GeneMappingAnnotator

  • All Implemented Interfaces:
    org.apache.uima.analysis_component.AnalysisComponent
    public class GeneMappingAnnotator
extends org.apache.uima.analysis_component.JCasAnnotator_ImplBase

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void initialize​(org.apache.uima.UimaContext aContext)
      initiaziation of GeneMapper: load the index, get some parameters
      void process​(org.apache.uima.jcas.JCas aJCas)
      The process method.

      • 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, collectionProcessComplete, 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

      • COMPONENT_ID

        public static final java.lang.String COMPONENT_ID

      • CONTEXT_WINDOW_SIZE

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

      • ENTITY_MAPPING_TYPES

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

      • MAPPER_CONFIG_FILE

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

    • Constructor Detail

      • GeneMappingAnnotator

        public GeneMappingAnnotator()

    • Method Detail

      • initialize

        public void initialize​(org.apache.uima.UimaContext aContext)
                throws org.apache.uima.resource.ResourceInitializationException
        initiaziation of GeneMapper: load the index, get some parameters
        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 aJCas)
             throws org.apache.uima.analysis_engine.AnalysisEngineProcessException
        The process method. loop over all entity types to be considered and do a mapping for all entities of this type
        Specified by:
        process in class org.apache.uima.analysis_component.JCasAnnotator_ImplBase
        Throws:
        org.apache.uima.analysis_engine.AnalysisEngineProcessException