Package de.julielab.genemapper.uima

Class TaxIdSentenceLabelWriter

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.genemapper.uima.TaxIdSentenceLabelWriter

All Implemented Interfaces:

org.apache.uima.analysis_component.AnalysisComponent

public class TaxIdSentenceLabelWriter
extends org.apache.uima.analysis_component.JCasAnnotator_ImplBase

Field Summary

Fields

Modifier and Type	Field	Description
static String	PARAM_BASE_PATH
static String	PARAM_LEMMAS
static String	PARAM_LOWERCASING
static String	PARAM_MASK_ORGANISM_NAMES
static String	PARAM_TOKENIZATION

Constructor Summary

Constructors

Constructor	Description
TaxIdSentenceLabelWriter()

Method Summary

Modifier and Type	Method	Description
void	addTokenizedOutput(StringBuilder sb, de.julielab.jcore.utility.JCoReAnnotationIndexMerger merger, de.julielab.jcore.utility.index.JCoReOverlapAnnotationIndex<de.julielab.jcore.types.Organism> organismIndex)
void	addUntokenizedOutput(org.apache.uima.jcas.JCas jCas, StringBuilder sb, de.julielab.jcore.types.Sentence s)
void	collectionProcessComplete()
void	initialize(org.apache.uima.UimaContext aContext)
void	process(org.apache.uima.jcas.JCas jCas)

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_BASE_PATH

public static final String PARAM_BASE_PATH

See Also:

Constant Field Values

PARAM_TOKENIZATION

public static final String PARAM_TOKENIZATION

See Also:

Constant Field Values

PARAM_LEMMAS

public static final String PARAM_LEMMAS

See Also:

Constant Field Values

PARAM_LOWERCASING

public static final String PARAM_LOWERCASING

See Also:

Constant Field Values

PARAM_MASK_ORGANISM_NAMES

public static final String PARAM_MASK_ORGANISM_NAMES

See Also:

Constant Field Values

Constructor Detail

TaxIdSentenceLabelWriter

public TaxIdSentenceLabelWriter()

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 jCas)
             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

addUntokenizedOutput

public void addUntokenizedOutput(org.apache.uima.jcas.JCas jCas,
                                 StringBuilder sb,
                                 de.julielab.jcore.types.Sentence s)

addTokenizedOutput

public void addTokenizedOutput(StringBuilder sb,
                               de.julielab.jcore.utility.JCoReAnnotationIndexMerger merger,
                               de.julielab.jcore.utility.index.JCoReOverlapAnnotationIndex<de.julielab.jcore.types.Organism> organismIndex)

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