Package de.julielab.genemapper.uima

Class GeneMentionTaxIdCountWriter

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.GeneMentionTaxIdCountWriter

All Implemented Interfaces:

org.apache.uima.analysis_component.AnalysisComponent

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

Field Summary

Fields

Modifier and Type	Field	Description
static String	PARAM_OUTPUT_PATH

Constructor Summary

Constructors

Constructor	Description
GeneMentionTaxIdCountWriter()

Method Summary

Modifier and Type	Method	Description
void	batchProcessComplete()
void	collectionProcessComplete()
void	incrementCountsForCoveredOrganisms(String normalizedGeneName, de.julielab.jcore.types.Annotation a, Consumer<de.julielab.genemapper.uima.GeneMentionTaxIdCountWriter.GeneOccurrenceCount> npIncrementer, Set<de.julielab.genemapper.uima.GeneMentionTaxIdCountWriter.GeneNameTaxPair> mentionsCountedForDoc, de.julielab.jcore.utility.index.JCoReTreeMapAnnotationIndex<Long,de.julielab.jcore.types.Organism> orgIndex, Map<de.julielab.genemapper.uima.GeneMentionTaxIdCountWriter.GeneNameTaxPair,de.julielab.genemapper.uima.GeneMentionTaxIdCountWriter.GeneOccurrenceCount> counts)
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

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_OUTPUT_PATH

public static final String PARAM_OUTPUT_PATH

See Also:

Constant Field Values

Constructor Detail

GeneMentionTaxIdCountWriter

public GeneMentionTaxIdCountWriter()

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)

Specified by:

process in class org.apache.uima.analysis_component.JCasAnnotator_ImplBase

batchProcessComplete

public void batchProcessComplete()

Specified by:

batchProcessComplete in interface org.apache.uima.analysis_component.AnalysisComponent

Overrides:

batchProcessComplete in class org.apache.uima.analysis_component.AnalysisComponent_ImplBase

incrementCountsForCoveredOrganisms

public void incrementCountsForCoveredOrganisms(String normalizedGeneName,
                                               de.julielab.jcore.types.Annotation a,
                                               Consumer<de.julielab.genemapper.uima.GeneMentionTaxIdCountWriter.GeneOccurrenceCount> npIncrementer,
                                               Set<de.julielab.genemapper.uima.GeneMentionTaxIdCountWriter.GeneNameTaxPair> mentionsCountedForDoc,
                                               de.julielab.jcore.utility.index.JCoReTreeMapAnnotationIndex<Long,de.julielab.jcore.types.Organism> orgIndex,
                                               Map<de.julielab.genemapper.uima.GeneMentionTaxIdCountWriter.GeneNameTaxPair,de.julielab.genemapper.uima.GeneMentionTaxIdCountWriter.GeneOccurrenceCount> counts)

collectionProcessComplete

public void collectionProcessComplete()

Specified by:

collectionProcessComplete in interface org.apache.uima.analysis_component.AnalysisComponent

Overrides:

collectionProcessComplete in class org.apache.uima.analysis_component.AnalysisComponent_ImplBase