Package de.julielab.jcore.ae.linnaeus

Class LinnaeusSpeciesAnnotator

java.lang.Object

org.apache.uima.analysis_component.AnalysisComponent_ImplBase

org.apache.uima.analysis_component.Annotator_ImplBase

org.apache.uima.analysis_component.JCasAnnotator_ImplBase

de.julielab.jcore.ae.linnaeus.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 String	PARAM_CONFIG_FILE
static String	RES_KEY_LINNAEUS_MATCHER

Constructor Summary

Constructors

Constructor	Description
LinnaeusSpeciesAnnotator()

Method Summary

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

RES_KEY_LINNAEUS_MATCHER

public static final String RES_KEY_LINNAEUS_MATCHER

See Also:

Constant Field Values

PARAM_CONFIG_FILE

public static final 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