org.apache.ctakes.dictionary.lookup2.ae

Class AbstractJCasTermAnnotator

java.lang.Object

org.apache.uima.analysis_component.AnalysisComponent_ImplBase

org.apache.uima.analysis_component.Annotator_ImplBase

org.apache.uima.analysis_component.JCasAnnotator_ImplBase

org.apache.uima.fit.component.JCasAnnotator_ImplBase

org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator

All Implemented Interfaces:

JCasTermAnnotator, WindowProcessor, org.apache.uima.analysis_component.AnalysisComponent

Direct Known Subclasses:

DefaultJCasTermAnnotator, OverlapJCasTermAnnotator

public abstract class AbstractJCasTermAnnotator
extends org.apache.uima.fit.component.JCasAnnotator_ImplBase
implements JCasTermAnnotator, WindowProcessor

Performs the basic initialization with uima context, including the parse of the dictionary specifications file. Has a

Author: SPF Affiliation: CHIP-NLP Date: 12/6/13

Field Summary

Fields

Modifier and Type	Field and Description
protected int	_minimumLookupSpan

Fields inherited from interface org.apache.ctakes.dictionary.lookup2.ae.JCasTermAnnotator

DEFAULT_DICT_DESC_PATH, DEFAULT_EXCLUSION_TAGS, DEFAULT_LOOKUP_WINDOW, DEFAULT_MINIMUM_SPAN, DICTIONARY_DESCRIPTOR_KEY, PARAM_EXC_TAGS_KEY, PARAM_MIN_SPAN_KEY, PARAM_WINDOW_ANNOT_KEY

Constructor Summary

Constructors

Constructor and Description
AbstractJCasTermAnnotator()

Method Summary

Modifier and Type	Method and Description
protected void	getAnnotationsInWindow(org.apache.uima.jcas.JCas jcas, org.apache.uima.cas.text.AnnotationFS window, List<FastLookupToken> allTokens, Collection<Integer> lookupTokenIndices) For the given lookup window fills two collections with 1) All tokens in the window, and 2) indexes of tokens in the window to be used for lookup
Collection<RareWordDictionary>	getDictionaries()
void	initialize(org.apache.uima.UimaContext uimaContext)
boolean	isWindowOk(org.apache.uima.jcas.tcas.Annotation window) Skip windows that are section headers/footers.
protected static int	parseInt(Object value, String name, int defaultValue)
void	process(org.apache.uima.jcas.JCas jcas)
void	processWindow(org.apache.uima.jcas.JCas jcas, org.apache.uima.jcas.tcas.Annotation window, Map<RareWordDictionary,CollectionMap<TextSpan,Long,? extends Collection<Long>>> dictionaryTerms) Processes a window of annotations for dictionary terms

Methods inherited from class org.apache.uima.fit.component.JCasAnnotator_ImplBase

getLogger

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

Methods inherited from interface org.apache.ctakes.dictionary.lookup2.ae.JCasTermAnnotator

findTerms

Methods inherited from interface org.apache.uima.analysis_component.AnalysisComponent

batchProcessComplete, collectionProcessComplete, destroy, getCasInstancesRequired, getRequiredCasInterface, hasNext, next, process, reconfigure, setResultSpecification

Field Detail

_minimumLookupSpan

protected int _minimumLookupSpan

Constructor Detail

AbstractJCasTermAnnotator

public AbstractJCasTermAnnotator()

Method Detail

initialize

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

Specified by:

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

Overrides:

initialize in class org.apache.uima.fit.component.JCasAnnotator_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

getDictionaries

public Collection<RareWordDictionary> getDictionaries()

Specified by:

getDictionaries in interface JCasTermAnnotator

Returns:

Dictionaries that are used by this WindowProcessor

isWindowOk

public boolean isWindowOk(org.apache.uima.jcas.tcas.Annotation window)

Skip windows that are section headers/footers. Kludge, but worth doing todo read these string values as parameters from uimaContext Some windows should be skipped entirely, such as "[section *]"

Specified by:

isWindowOk in interface WindowProcessor

Parameters:

window - annotation in which to search for terms

Returns:

true if window should be processed, false if it should not

processWindow

public void processWindow(org.apache.uima.jcas.JCas jcas,
                          org.apache.uima.jcas.tcas.Annotation window,
                          Map<RareWordDictionary,CollectionMap<TextSpan,Long,? extends Collection<Long>>> dictionaryTerms)

Processes a window of annotations for dictionary terms

Specified by:

processWindow in interface WindowProcessor

Parameters:

jcas - -

window - annotation in which to search for terms

dictionaryTerms - map of entity types and terms for those types in the window

getAnnotationsInWindow

protected void getAnnotationsInWindow(org.apache.uima.jcas.JCas jcas,
                                      org.apache.uima.cas.text.AnnotationFS window,
                                      List<FastLookupToken> allTokens,
                                      Collection<Integer> lookupTokenIndices)

For the given lookup window fills two collections with 1) All tokens in the window, and 2) indexes of tokens in the window to be used for lookup

Parameters:

jcas - -

window - annotation lookup window

allTokens - filled with all tokens, including punctuation, etc.

lookupTokenIndices - filled with indices of tokens to use for lookup

parseInt

protected static int parseInt(Object value,
                              String name,
                              int defaultValue)