A C D E F G H I K L M N O P R S T U W X

A

add(String) - Method in class org.apache.ctakes.utils.distsem.WordEmbeddings

add(K) - Method in class org.apache.ctakes.utils.struct.CounterMap

add(K, Integer) - Method in class org.apache.ctakes.utils.struct.CounterMap

add(K) - Method in class org.apache.ctakes.utils.struct.CounterTreeMap

add(K, Integer) - Method in class org.apache.ctakes.utils.struct.CounterTreeMap

addAnnotation(int, XcasAnnotation) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile

Inserts a new annotation with the specified internal id to this XcasFile.

addAnnotation(int, XcasAnnotation, String) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile

Inserts a new annotation, along with its position in the file, to this XcasFile object.

addAnnotation(int, XcasAnnotation, int, int) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile

Inserts a new annotation, along with its position in the file, to this XcasFile object.

addChild(SimpleTree) - Method in class org.apache.ctakes.utils.tree.SimpleTree

allFieldsValues() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation

Returns a string representation of all the attributes and references.

alog(double) - Static method in class org.apache.ctakes.utils.wiki.ApproximateMath

annotations - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasFile

annotationsClone() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile

ApproximateMath - Class in org.apache.ctakes.utils.wiki

ApproximateMath() - Constructor for class org.apache.ctakes.utils.wiki.ApproximateMath

ApproximateSimilarity - Class in org.apache.ctakes.utils.wiki

ApproximateSimilarity() - Constructor for class org.apache.ctakes.utils.wiki.ApproximateSimilarity

asqrt(int) - Static method in class org.apache.ctakes.utils.wiki.ApproximateMath

asqrt(double) - Static method in class org.apache.ctakes.utils.wiki.ApproximateMath

attributes - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation

ATTRIBUTES_TO_IGNORE - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const

C

cat - Variable in class org.apache.ctakes.utils.tree.SimpleTree

characters(char[], int, int) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasProcessor

children - Variable in class org.apache.ctakes.utils.tree.SimpleTree

clone() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation

Recursive, deep copy of this object, including attributes and references.

clone() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile

close() - Method in class org.apache.ctakes.utils.wiki.WikiIndex

Compare - Class in org.apache.ctakes.utils.xcas_comparison

This class illustrates the basic usage of this tool.

Compare() - Constructor for class org.apache.ctakes.utils.xcas_comparison.Compare

compareTo(XcasAnnotation) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation

Determines the order of this and the specified XcasAnnotation.

Const - Class in org.apache.ctakes.utils.xcas_comparison

Const() - Constructor for class org.apache.ctakes.utils.xcas_comparison.Const

containsKey(String) - Method in class org.apache.ctakes.utils.distsem.WordEmbeddings

ConvertAndCompare - Class in org.apache.ctakes.utils.xcas_comparison

ConvertAndCompare() - Constructor for class org.apache.ctakes.utils.xcas_comparison.ConvertAndCompare

CounterMap<K> - Class in org.apache.ctakes.utils.struct

CounterMap() - Constructor for class org.apache.ctakes.utils.struct.CounterMap

CounterTreeMap<K> - Class in org.apache.ctakes.utils.struct

CounterTreeMap() - Constructor for class org.apache.ctakes.utils.struct.CounterTreeMap

createInstance(String) - Static method in class org.apache.ctakes.utils.struct.MapFactory

D

defaultIndexPath - Static variable in class org.apache.ctakes.utils.wiki.WikiIndex

defaultMaxHits - Static variable in class org.apache.ctakes.utils.wiki.WikiIndex

defaultSearchField - Static variable in class org.apache.ctakes.utils.wiki.WikiIndex

description() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation

Returns a String representation of this object, including its type, and all attributes and references.

DistanceMetrics - Class in org.apache.ctakes.utils.distsem

DistanceMetrics() - Constructor for class org.apache.ctakes.utils.distsem.DistanceMetrics

documentScore - Variable in class org.apache.ctakes.utils.wiki.SearchResult

documentTitle - Variable in class org.apache.ctakes.utils.wiki.SearchResult

dotProd(svm_node[], svm_node[]) - Static method in class org.apache.ctakes.utils.kernel.Kernel

dumpCache() - Static method in class org.apache.ctakes.utils.wiki.ApproximateMath

E

endElement(String, String, String) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasProcessor

EnvironmentVariable - Class in org.apache.ctakes.utils.env

equals(Object) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation

Determines whether the specified object equals to this one.

equals(Object) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile

Checks whether the specified object has the same set of annotations.

escapeCat(String) - Static method in class org.apache.ctakes.utils.tree.SimpleTree

eval(Object, Object) - Method in class org.apache.ctakes.utils.kernel.Kernel

eval(Object, Object) - Method in class org.apache.ctakes.utils.kernel.PolyKernel

eval(Object, Object) - Method in class org.apache.ctakes.utils.kernel.RBFKernel

F

f - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasFile

frag2tree(String) - Static method in class org.apache.ctakes.utils.tree.FragmentUtils

FragmentUtils - Class in org.apache.ctakes.utils.tree

FragmentUtils() - Constructor for class org.apache.ctakes.utils.tree.FragmentUtils

fromString(String) - Static method in class org.apache.ctakes.utils.tree.SimpleTree

G

get(Object) - Method in class org.apache.ctakes.utils.struct.CounterMap

get(Object) - Method in class org.apache.ctakes.utils.struct.CounterTreeMap

get(String, K) - Static method in class org.apache.ctakes.utils.struct.MapFactory

getAE(File) - Static method in class org.apache.ctakes.utils.test.TestUtil

getAllAnnotations() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile

getAnnotation(int) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile

Returns the XcasAnnotation object associated with the specified internal id.

getAttribute(String) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation

Returns the value of the specified attribute.

getCosineSimilarity(String, String) - Method in class org.apache.ctakes.utils.wiki.WikiIndex

Send two queries to the index.

getCR(File) - Static method in class org.apache.ctakes.utils.test.TestUtil

getDimensionality() - Method in class org.apache.ctakes.utils.distsem.WordEmbeddings

getEmbeddings() - Method in class org.apache.ctakes.utils.distsem.WordVectorReader

getEmbeddings(String) - Static method in class org.apache.ctakes.utils.distsem.WordVectorReader

getEmbeddings(InputStream) - Static method in class org.apache.ctakes.utils.distsem.WordVectorReader

getEnv(String, UimaContext) - Static method in class org.apache.ctakes.utils.env.EnvironmentVariable

Get the value of some variable in the full (os, user, java, ctakes) environment.

getEnv(String) - Static method in class org.apache.ctakes.utils.env.EnvironmentVariable

Get the value of some variable in the full (os, user, java, ctakes) environment.

getFeatureStructureAtIndex(JCas, Class<T>, int) - Static method in class org.apache.ctakes.utils.test.TestUtil

getFeatureStructureSize(JCas, Class<T>) - Static method in class org.apache.ctakes.utils.test.TestUtil

getFileName() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile

getKeysSortedByValue() - Method in class org.apache.ctakes.utils.struct.CounterMap

getLength() - Method in class org.apache.ctakes.utils.distsem.WordVector

getMeanVector() - Method in class org.apache.ctakes.utils.distsem.WordEmbeddings

getPosition(XcasAnnotation) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile

Returns the line and column numbers of the specified XcasAnnotation.

getPositionOther(XcasAnnotation) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile

Finds an XcasAnnotation with the same attributes as specified, and returns its line and column numbers.

getPositionOwn(XcasAnnotation) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile

Returns the line and column numbers of the specified XcasAnnotation, which is included in this XcasFile object.

getPositionOwn(int) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile

Returns the line and column numbers of the XcasAnnotation, specified by the original XCAS internal _id field.

getPositionSimilar(XcasAnnotation) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile

Finds an XcasAnnotation of the same type as specified, and a same text span, then returns its line and column number.

getReference(String) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation

Returns the referenced XcasAnnotations of the specified attribute.

getSimilarity(String, String) - Method in class org.apache.ctakes.utils.distsem.WordEmbeddings

getSimilarWords(String, int) - Method in class org.apache.ctakes.utils.distsem.WordEmbeddings

getTermFreqVectors(String) - Method in class org.apache.ctakes.utils.wiki.WikiIndex

getType() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation

getValue(int) - Method in class org.apache.ctakes.utils.distsem.WordVector

getVector(String) - Method in class org.apache.ctakes.utils.distsem.WordEmbeddings

H

hasAnnotation(int) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile

Checks whether this XCAS file has an annotation with the specified id.

hasAnnotation(XcasAnnotation) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile

Checks whether this XCAS file has the specified XcasAnnotation.

HIDDEN_TEXT - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const

I

ID - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const

idf(long, long) - Method in class org.apache.ctakes.utils.wiki.ApproximateSimilarity

init() - Static method in class org.apache.ctakes.utils.xcas_comparison.Const

initialize() - Method in class org.apache.ctakes.utils.wiki.WikiIndex

insertAttribute(String, String) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation

Inserts an (attribute, value) pair to this XcasAnnotation.

insertChild(int, SimpleTree) - Method in class org.apache.ctakes.utils.tree.SimpleTree

insertIntReference(String, int[]) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation

insertReference(String, XcasAnnotation) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation

isLeaf() - Method in class org.apache.ctakes.utils.tree.SimpleTree

K

Kernel - Class in org.apache.ctakes.utils.kernel

Kernel() - Constructor for class org.apache.ctakes.utils.kernel.Kernel

keySet() - Method in class org.apache.ctakes.utils.struct.CounterTreeMap

L

LinearKernel - Class in org.apache.ctakes.utils.kernel

LinearKernel() - Constructor for class org.apache.ctakes.utils.kernel.LinearKernel

LinearKernel(boolean) - Constructor for class org.apache.ctakes.utils.kernel.LinearKernel

M

main(String[]) - Static method in class org.apache.ctakes.utils.distsem.DistanceMetrics

main(String[]) - Static method in class org.apache.ctakes.utils.tree.SimpleTree

main(String[]) - Static method in class org.apache.ctakes.utils.wiki.TestCosineSimilarity

main(String[]) - Static method in class org.apache.ctakes.utils.xcas_comparison.Compare

main(String[]) - Static method in class org.apache.ctakes.utils.xcas_comparison.ConvertAndCompare

MapFactory - Class in org.apache.ctakes.utils.struct

MapFactory() - Constructor for class org.apache.ctakes.utils.struct.MapFactory

N

NOT_PRESENT - Static variable in class org.apache.ctakes.utils.env.EnvironmentVariable

O

org.apache.ctakes.utils.distsem - package org.apache.ctakes.utils.distsem

org.apache.ctakes.utils.env - package org.apache.ctakes.utils.env

org.apache.ctakes.utils.kernel - package org.apache.ctakes.utils.kernel

org.apache.ctakes.utils.struct - package org.apache.ctakes.utils.struct

org.apache.ctakes.utils.test - package org.apache.ctakes.utils.test

org.apache.ctakes.utils.tree - package org.apache.ctakes.utils.tree

org.apache.ctakes.utils.wiki - package org.apache.ctakes.utils.wiki

org.apache.ctakes.utils.xcas_comparison - package org.apache.ctakes.utils.xcas_comparison

P

parent - Variable in class org.apache.ctakes.utils.tree.SimpleTree

PolyKernel - Class in org.apache.ctakes.utils.kernel

PolyKernel(int, double, boolean) - Constructor for class org.apache.ctakes.utils.kernel.PolyKernel

PolyKernel() - Constructor for class org.apache.ctakes.utils.kernel.PolyKernel

positions - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasFile

printCommon() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasDiff

Prints common elements along with their attributes in the two XCAS files to stdout.

printDiff() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasDiff

Prints elements that are unique to each XCAS file to stdout.

printDiff(XcasFile, XcasFile) - Static method in class org.apache.ctakes.utils.xcas_comparison.XcasDiff

Prints elements that are unique to each XCAS file to stdout.

printHTML(Writer) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasDiff

Writes an HTML summary of the comparison of the two XCAS files.

printHTML(XcasFile, XcasFile, Writer) - Static method in class org.apache.ctakes.utils.xcas_comparison.XcasDiff

Writes an HTML summary of the comparison of the two specified XCAS files.

printUniq(int) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasDiff

Prints elements that are unique to XCAS file i.

process(String) - Static method in class org.apache.ctakes.utils.xcas_comparison.XcasFile

Creates a new XcasFile object from the specified file.

process(File) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasProcessor

Parses the specified file and returns a parsed XcasFile object.

process(String) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasProcessor

Parses the specified file and returns a parsed XcasFile object.

processAE(AnalysisEngine, File) - Static method in class org.apache.ctakes.utils.test.TestUtil

This method simply calls #createAnalysisEngineJCas(File, File, String) with the charSetName equal to "UTF-8".

processAE(AnalysisEngine, File, String) - Static method in class org.apache.ctakes.utils.test.TestUtil

This method reads in the text from the text file using the provided character set and then calls #getJCas(File, String)

processAE(AnalysisEngine, String) - Static method in class org.apache.ctakes.utils.test.TestUtil

This method creates a JCas for the provided analysis engine descriptor file and then processes the provided text and returns the JCas.

put(String, K, V) - Static method in class org.apache.ctakes.utils.struct.MapFactory

R

RBFKernel - Class in org.apache.ctakes.utils.kernel

RBFKernel(double) - Constructor for class org.apache.ctakes.utils.kernel.RBFKernel

recalculate() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasDiff

Calculates the differences or recalculates after the two files are updated.

REF_PREFIX - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const

references - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation

refIntArrays - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation

removeChild(int) - Method in class org.apache.ctakes.utils.tree.SimpleTree

S

search(String) - Method in class org.apache.ctakes.utils.wiki.WikiIndex

Search the index.

SearchResult - Class in org.apache.ctakes.utils.wiki

SearchResult(String, float) - Constructor for class org.apache.ctakes.utils.wiki.SearchResult

setDocumentLocator(Locator) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasProcessor

setGeneralizeLeaf(boolean) - Method in class org.apache.ctakes.utils.tree.SimpleTree

setType(String) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation

Sets the type name of this annotation.

shallowCopy() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation

Clones this object, its attributes, and reference keys.

shortType() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation

Returns a short description of this XcasAnnotation's type, specifically, the last segment as separated by dots.

SimpleTree - Class in org.apache.ctakes.utils.tree

SimpleTree(String) - Constructor for class org.apache.ctakes.utils.tree.SimpleTree

SimpleTree(String, SimpleTree) - Constructor for class org.apache.ctakes.utils.tree.SimpleTree

SimpleTree(String, SimpleTree, boolean) - Constructor for class org.apache.ctakes.utils.tree.SimpleTree

size() - Method in class org.apache.ctakes.utils.distsem.WordVector

size() - Method in class org.apache.ctakes.utils.struct.CounterTreeMap

startElement(String, String, String, Attributes) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasProcessor

T

testConfigParam(UimaContext, String, String, Object) - Static method in class org.apache.ctakes.utils.test.TestUtil

testConfigParam(UimaContext, String, String, Object, Integer) - Static method in class org.apache.ctakes.utils.test.TestUtil

TestCosineSimilarity - Class in org.apache.ctakes.utils.wiki

TestCosineSimilarity() - Constructor for class org.apache.ctakes.utils.wiki.TestCosineSimilarity

TestUtil - Class in org.apache.ctakes.utils.test

TestUtil() - Constructor for class org.apache.ctakes.utils.test.TestUtil

tf(int) - Method in class org.apache.ctakes.utils.wiki.ApproximateSimilarity

toString() - Method in class org.apache.ctakes.utils.tree.SimpleTree

toString() - Method in class org.apache.ctakes.utils.wiki.SearchResult

type - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation

U

UIMA_ARRAY_INDEX_KEYWORD - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const

UIMA_ARRAY_SIZE_KEYWORD - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const

UIMA_CAS - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const

UIMA_EMPTY_FSLIST - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const

UIMA_FSARRAY - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const

UIMA_INTARRAY - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const

UIMA_LIST_HEAD_KEYWORD - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const

UIMA_LIST_TAIL_KEYWORD - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const

UIMA_NONEMPTY_FSLIST - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const

UIMA_REF_SOFA - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const

UIMA_SOFA - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const

UIMA_SOFA_STRING - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const

UIMA_TCAS_DOCUMENT - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const

W

WikiIndex - Class in org.apache.ctakes.utils.wiki

A wrapper for a wikipedia lucene index.

WikiIndex(int, String, String, boolean) - Constructor for class org.apache.ctakes.utils.wiki.WikiIndex

WikiIndex(int, String, String) - Constructor for class org.apache.ctakes.utils.wiki.WikiIndex

WikiIndex() - Constructor for class org.apache.ctakes.utils.wiki.WikiIndex

WordEmbeddings - Class in org.apache.ctakes.utils.distsem

WordEmbeddings(int) - Constructor for class org.apache.ctakes.utils.distsem.WordEmbeddings

WordEmbeddings(Map<String, WordVector>) - Constructor for class org.apache.ctakes.utils.distsem.WordEmbeddings

WordVector - Class in org.apache.ctakes.utils.distsem

WordVector(String, double[]) - Constructor for class org.apache.ctakes.utils.distsem.WordVector

WordVectorReader - Class in org.apache.ctakes.utils.distsem

WordVectorReader(InputStream) - Constructor for class org.apache.ctakes.utils.distsem.WordVectorReader

X

XcasAnnotation - Class in org.apache.ctakes.utils.xcas_comparison

An XcasAnnotation object represents an element under the CAS tag in an XCAS file.

XcasAnnotation() - Constructor for class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation

Default constructor.

XcasAnnotation(String) - Constructor for class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation

Constructs an object with the specified type.

XcasDiff - Class in org.apache.ctakes.utils.xcas_comparison

An XcasDiff object represents the comparison results of two XCAS files.

XcasDiff() - Constructor for class org.apache.ctakes.utils.xcas_comparison.XcasDiff

Default constructor.

XcasDiff(XcasFile, XcasFile) - Constructor for class org.apache.ctakes.utils.xcas_comparison.XcasDiff

Construct an XCASDiff object from two XcasFile objects.

XcasFile - Class in org.apache.ctakes.utils.xcas_comparison

An XcasFile wraps all XcasAnnotationss in it and also contains their position information in terms of line and column numbers.

XcasFile() - Constructor for class org.apache.ctakes.utils.xcas_comparison.XcasFile

Default constructor.

XcasFile(String) - Constructor for class org.apache.ctakes.utils.xcas_comparison.XcasFile

Constructs an XcasFile with the specified name.

XcasFile(File) - Constructor for class org.apache.ctakes.utils.xcas_comparison.XcasFile

Constructs an XcasFile with the specified name.

XcasProcessor - Class in org.apache.ctakes.utils.xcas_comparison

A SAX parser that parses an XCAS file.

XcasProcessor() - Constructor for class org.apache.ctakes.utils.xcas_comparison.XcasProcessor

Default constructor.

A C D E F G H I K L M N O P R S T U W X