org.ohnlp.ae.medxn

Class MedAttrAnnotator

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.ohnlp.ae.medxn.MedAttrAnnotator

All Implemented Interfaces:

org.apache.uima.analysis_component.AnalysisComponent

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

Author:

Sunghwan Sohn Extract medication attributes defined in regExPatterns

Field Summary

Fields

Modifier and Type	Field and Description
static String	ALLOW_MULT_ANNO
static String	REGEX_FILE

Constructor Summary

Constructors

Constructor and Description
MedAttrAnnotator()

Method Summary

Modifier and Type	Method and Description
protected void	addToJCas2(org.apache.uima.jcas.JCas jcas, List<org.ohnlp.ae.medxn.MedAttrAnnotator.Attribute> annot)
protected List<org.ohnlp.ae.medxn.MedAttrAnnotator.Attribute>	getAttribute2(String text) Find and return medication attributes in text
protected Map<String,List<String>>	getRegEx(InputStream input) Return regular expression patterns for med attributes
void	initialize(org.apache.uima.UimaContext uimaContext)
void	process(org.apache.uima.jcas.JCas jcas)
protected List<org.ohnlp.ae.medxn.MedAttrAnnotator.Attribute>	removeOverlap(List<org.ohnlp.ae.medxn.MedAttrAnnotator.Attribute> attr) Remove duplicates or take a longer attribute if subsumed and return the updated list of Attribute

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

REGEX_FILE

public static final String REGEX_FILE

See Also:

Constant Field Values

ALLOW_MULT_ANNO

public static final String ALLOW_MULT_ANNO

See Also:

Constant Field Values

Constructor Detail

MedAttrAnnotator

public MedAttrAnnotator()

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.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

addToJCas2

protected void addToJCas2(org.apache.uima.jcas.JCas jcas,
                          List<org.ohnlp.ae.medxn.MedAttrAnnotator.Attribute> annot)

getAttribute2

protected List<org.ohnlp.ae.medxn.MedAttrAnnotator.Attribute> getAttribute2(String text)

Find and return medication attributes in text

Parameters:

text - String to extract attributes

Returns:

List of Attribute classes

removeOverlap

protected List<org.ohnlp.ae.medxn.MedAttrAnnotator.Attribute> removeOverlap(List<org.ohnlp.ae.medxn.MedAttrAnnotator.Attribute> attr)

Remove duplicates or take a longer attribute if subsumed and return the updated list of Attribute

Parameters:

attr - List of Attribute class

Returns:

List of Attribute class without duplicates/overlaps

getRegEx

protected Map<String,List<String>> getRegEx(InputStream input)

Return regular expression patterns for med attributes

Parameters:

input - file name of the regEx file

Returns:

Map of attribute regular expression (key:tag, val:List of regular expression patterns)