NegexAnnotator

java.lang.Object
- JCasAnnotator_ImplBase
- - org.apache.ctakes.ytex.uima.annotators.NegexAnnotator

```
public class NegexAnnotator
extends JCasAnnotator_ImplBase
```
Negex adapted to cTAKES. Checks negation status of named entities. Loads negex triggers from classpath: /org/apache/ctakes/ytex/uima/annotators/negex_triggers.txt
The meaning of the certainty and confidence attributes is nowhere documented for cTakes. There are several ways of handling 'maybes', see below. Default behavior: certainty attribute for negated & possible terms set to -1 Configure with following uima initialization parameters:
checkPossibilities : should we check for possibilities
negatePossibilities : should possibilities be negated, default = true? if true,
- negated: polarity=-1, confidence=1
- possible: polarity=-1, confidence=-1
- affirmed: polarity=1, confidence=1
negated: polarity=-1, confidence=1
possible: polarity=1, confidence=-1
affirmed: polarity=1, confidence=1

storeAsInterval

negated: polarity=-1, confidence = -1
possible: polarity=1, confidence = 0.5
affirmed: polarity=1, confidence = 1

Added support for negating arbitrary annotations. Set the targetTypeName to an annotation type. Will see if it is negated; if so will set the negated and possible boolean values on the annotation.

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`static class`	`NegexAnnotator.NamedEntityTargetAnnoFilter` only bother with IdentifiedAnnotations that have concepts
`static class`	`NegexAnnotator.NegexRule`
`static class`	`NegexAnnotator.NegexToken`
`static interface`	`NegexAnnotator.TargetAnnoFilter`

Field Summary

Fields
Modifier and Type	Field and Description
`private boolean`	`checkPossibilities`
`private java.util.List<NegexAnnotator.NegexRule>`	`listNegexRules`
`private static Log`	`log`
`private boolean`	`negatePossibilities`
`private boolean`	`storeAsInterval`
`private java.lang.String`	`targetTypeName`

Constructor Summary

Constructors
Constructor and Description

NegexAnnotator()

Constructors
Constructor and Description
`NegexAnnotator()`

Method Summary

Methods
Modifier and Type	Method and Description
`private void`	`annotateNegation(JCas aJCas, Sentence s, Annotation anno, NegexAnnotator.NegexToken t, boolean negated, boolean possible)` set the certainty/confidence flag on a named entity, and add a negation context annotation.
`private void`	`checkNegation(JCas aJCas, Sentence s, Annotation ne)` check the negation status of the specfied term in the specified sentence
`private void`	`checkNegation2(JCas aJCas, Sentence s, IdentifiedAnnotation ne, boolean negPoss)`
`private NegexAnnotator.NegexToken`	`findTokenByTag(java.lang.String tag, java.lang.String[] stopTags, boolean before, int neRelStart, int neRelEnd, NegexAnnotator.NegexToken[] tokens)`
`private boolean`	`getBooleanConfigParam(UimaContext aContext, java.lang.String param, boolean defaultVal)`
`private java.util.List<java.lang.String>`	`initalizeRuleList()`
`void`	`initialize(UimaContext aContext)`
`private java.util.List<NegexAnnotator.NegexRule>`	`initializeRules()`
`private void`	`negateAnnotations(JCas aJCas, AnnotationIndex sentenceIdx, AnnotationIndex targetIdx, NegexAnnotator.TargetAnnoFilter filter)`
`void`	`process(JCas aJCas)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

log
```
private static final Log log
```

listNegexRules

private java.util.List<NegexAnnotator.NegexRule> listNegexRules

negatePossibilities
```
private boolean negatePossibilities
```

checkPossibilities
```
private boolean checkPossibilities
```

storeAsInterval
```
private boolean storeAsInterval
```

targetTypeName

private java.lang.String targetTypeName

Constructor Detail
- NegexAnnotator
```
public NegexAnnotator()
```

Method Detail

initialize

public void initialize(UimaContext aContext)
                throws ResourceInitializationException

Throws:: ResourceInitializationException

getBooleanConfigParam

private boolean getBooleanConfigParam(UimaContext aContext,
                            java.lang.String param,
                            boolean defaultVal)

initalizeRuleList

private java.util.List<java.lang.String> initalizeRuleList()

initializeRules

private java.util.List<NegexAnnotator.NegexRule> initializeRules()

process
```
public void process(JCas aJCas)
```

negateAnnotations

private void negateAnnotations(JCas aJCas,
                     AnnotationIndex sentenceIdx,
                     AnnotationIndex targetIdx,
                     NegexAnnotator.TargetAnnoFilter filter)

findTokenByTag

private NegexAnnotator.NegexToken findTokenByTag(java.lang.String tag,
                                       java.lang.String[] stopTags,
                                       boolean before,
                                       int neRelStart,
                                       int neRelEnd,
                                       NegexAnnotator.NegexToken[] tokens)

checkNegation
```
private void checkNegation(JCas aJCas,
                 Sentence s,
                 Annotation ne)
```
check the negation status of the specfied term in the specified sentence

Parameters:
aJCas - for adding annotations
s - the sentence in which we will look
ne - the named entity whose negation status will be checked.
checkPoss - should possibility be checked?
negPoss - should possiblities be negated?

checkNegation2

private void checkNegation2(JCas aJCas,
                  Sentence s,
                  IdentifiedAnnotation ne,
                  boolean negPoss)

annotateNegation

private void annotateNegation(JCas aJCas,
                    Sentence s,
                    Annotation anno,
                    NegexAnnotator.NegexToken t,
                    boolean negated,
                    boolean possible)

set the certainty/confidence flag on a named entity, and add a negation context annotation.

Parameters:: aJCas -; s - used to figure out text span; ne - the certainty/confidence will be set to -1; t - the token; fSetCertainty - should we set the certainty (true) or confidence (false)

Class NegexAnnotator