Package de.julielab.jcore.reader.bc2gm

Class BC2GMReader

  • All Implemented Interfaces:
    org.apache.uima.collection.base_cpm.BaseCollectionReader, org.apache.uima.collection.CollectionReader, org.apache.uima.resource.ConfigurableResource, org.apache.uima.resource.Resource
    public class BC2GMReader
extends org.apache.uima.fit.component.JCasCollectionReader_ImplBase

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static java.lang.String PARAM_GENES  
      static java.lang.String PARAM_SENTENCES  

      • Fields inherited from interface org.apache.uima.resource.Resource

        PARAM_AGGREGATE_SOFA_MAPPINGS, PARAM_CONFIG_MANAGER, PARAM_CONFIG_PARAM_SETTINGS, PARAM_EXTERNAL_OVERRIDE_SETTINGS, PARAM_PERFORMANCE_TUNING_SETTINGS, PARAM_RESOURCE_MANAGER, PARAM_UIMA_CONTEXT

    • Constructor Summary

      Constructors 
      Constructor Description
      BC2GMReader()  

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void close()  
      static java.util.TreeMap<java.lang.Integer,​java.lang.Integer> createNumWsMap​(java.lang.String input)
      Returns a map where for each white space position, the number of preceding non-whitespace characters from the beginning of input is returned.
      Thus, for each character-based offset o, the non-whitespace offset may be retrieved using the floor entry for o, retrieving its value and subtracting it from o.
      void getNext​(org.apache.uima.jcas.JCas cas)  
      org.apache.uima.util.Progress[] getProgress()  
      boolean hasNext()  
      void initialize​(org.apache.uima.UimaContext context)  

      • Methods inherited from class org.apache.uima.fit.component.JCasCollectionReader_ImplBase

        getLogger, getNext, initialize

      • Methods inherited from class org.apache.uima.collection.CollectionReader_ImplBase

        destroy, getCasInitializer, getProcessingResourceMetaData, initialize, isConsuming, reconfigure, setCasInitializer, typeSystemInit

      • Methods inherited from class org.apache.uima.resource.ConfigurableResource_ImplBase

        getConfigParameterValue, getConfigParameterValue, setConfigParameterValue, setConfigParameterValue

      • Methods inherited from class org.apache.uima.resource.Resource_ImplBase

        getCasManager, getMetaData, getRelativePathResolver, getResourceManager, getUimaContext, getUimaContextAdmin, setLogger, setMetaData

      • Methods inherited from class java.lang.Object

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

      • Methods inherited from interface org.apache.uima.resource.ConfigurableResource

        getConfigParameterValue, getConfigParameterValue, setConfigParameterValue, setConfigParameterValue

      • Methods inherited from interface org.apache.uima.resource.Resource

        getMetaData, getResourceManager, getUimaContext, getUimaContextAdmin, setLogger

    • Constructor Detail

      • BC2GMReader

        public BC2GMReader()

    • Method Detail

      • createNumWsMap

        public static java.util.TreeMap<java.lang.Integer,​java.lang.Integer> createNumWsMap​(java.lang.String input)
        Returns a map where for each white space position, the number of preceding non-whitespace characters from the beginning of input is returned.
        Thus, for each character-based offset o, the non-whitespace offset may be retrieved using the floor entry for o, retrieving its value and subtracting it from o.
        Parameters:
        input -
        Returns:

      • initialize

        public void initialize​(org.apache.uima.UimaContext context)
                throws org.apache.uima.resource.ResourceInitializationException
        Overrides:
        initialize in class org.apache.uima.fit.component.JCasCollectionReader_ImplBase
        Throws:
        org.apache.uima.resource.ResourceInitializationException

      • getNext

        public void getNext​(org.apache.uima.jcas.JCas cas)
             throws java.io.IOException,
                    org.apache.uima.collection.CollectionException
        Specified by:
        getNext in class org.apache.uima.fit.component.JCasCollectionReader_ImplBase
        Throws:
        java.io.IOException
        org.apache.uima.collection.CollectionException

      • close

        public void close()
           throws java.io.IOException
        Specified by:
        close in interface org.apache.uima.collection.base_cpm.BaseCollectionReader
        Overrides:
        close in class org.apache.uima.fit.component.JCasCollectionReader_ImplBase
        Throws:
        java.io.IOException

      • getProgress

        public org.apache.uima.util.Progress[] getProgress()

      • hasNext

        public boolean hasNext()
                throws java.io.IOException,
                       org.apache.uima.collection.CollectionException
        Throws:
        java.io.IOException
        org.apache.uima.collection.CollectionException