Package de.julielab.genemapper.uima

Class GeneMapperAnnotator

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.GeneMapperAnnotator

All Implemented Interfaces:

org.apache.uima.analysis_component.AnalysisComponent

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

Field Summary

Fields

Modifier and Type	Field	Description
static String	COMPONENT_ID
static String	CONTEXT_WINDOW_SIZE
static String	ENTITY_MAPPING_TYPES
static String	MAPPER_CONFIG_FILE
static String	REMOVE_EXISTING_RESOURCE_ENTRIES
static String	TOKEN_CONTEXT

Constructor Summary

Constructors

Constructor	Description
GeneMapperAnnotator()

Method Summary

Modifier and Type	Method	Description
void	initialize(org.apache.uima.UimaContext aContext)	initialization 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 String COMPONENT_ID

CONTEXT_WINDOW_SIZE

public static final String CONTEXT_WINDOW_SIZE

See Also:

Constant Field Values

TOKEN_CONTEXT

public static final String TOKEN_CONTEXT

See Also:

Constant Field Values

ENTITY_MAPPING_TYPES

public static final String ENTITY_MAPPING_TYPES

See Also:

Constant Field Values

MAPPER_CONFIG_FILE

public static final String MAPPER_CONFIG_FILE

See Also:

Constant Field Values

REMOVE_EXISTING_RESOURCE_ENTRIES

public static final String REMOVE_EXISTING_RESOURCE_ENTRIES

See Also:

Constant Field Values

Constructor Detail

GeneMapperAnnotator

public GeneMapperAnnotator()

Method Detail

initialize

public void initialize(org.apache.uima.UimaContext aContext)
                throws org.apache.uima.resource.ResourceInitializationException

initialization 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