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

A

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

B

BuildPear - Class in org.apache.ctakes.utils.build

Build a PEAR file for this project
Looks for BuildPear.properties file for classpath and datapath values to use for PEAR.
Expects the properties file to be in the same directory as this class file.

BuildPear() - Constructor for class org.apache.ctakes.utils.build.BuildPear

BuildPipelinePears - Class in org.apache.ctakes.utils.build

This class is used to edu.mayo.bmi.utils.build the PEAR files for the pipeline.

BuildPipelinePears() - Constructor for class org.apache.ctakes.utils.build.BuildPipelinePears

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

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

createDirIfNotExist(String) - Static method in class org.apache.ctakes.utils.build.BuildPear

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.

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

EnvironmentVariable() - Constructor for class org.apache.ctakes.utils.env.EnvironmentVariable

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

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

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

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.

getString(String[], int) - Static method in class org.apache.ctakes.utils.build.BuildPipelinePears

getString(String[], int) - Static method in class org.apache.ctakes.utils.build.InstallPearSilently

getString(String[], int) - Static method in class org.apache.ctakes.utils.build.InstallPipelineFromPears

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

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

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

InstallPearSilently - Class in org.apache.ctakes.utils.build

This class is used to install a pear file locally in a directory chosen by the user and then run the installed AE in CVD.

InstallPearSilently() - Constructor for class org.apache.ctakes.utils.build.InstallPearSilently

InstallPearSilently.RunInstallation - Class in org.apache.ctakes.utils.build

The RunInstallation class implements a thread that is used to run the installation.

InstallPearSilently.RunInstallation(File, File) - Constructor for class org.apache.ctakes.utils.build.InstallPearSilently.RunInstallation

Constructor that sets a given input PEAR file and a given installation directory.

InstallPipelineFromPears - Class in org.apache.ctakes.utils.build

This class is used to install a pear file locally in a directory chosen by the user and then run the installed AE in CVD.

InstallPipelineFromPears() - Constructor for class org.apache.ctakes.utils.build.InstallPipelineFromPears

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.build.BuildPear

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

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

Starts the application.

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

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

N

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

O

org.apache.ctakes.utils.build - package org.apache.ctakes.utils.build

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.

Q

quote(String) - Static method in class org.apache.ctakes.utils.build.BuildPear

Quote the string, using double quotes if the string contains any single quotes, otherwise using single quotes.

quote(String) - Static method in class org.apache.ctakes.utils.build.BuildPipelinePears

quote(String) - Static method in class org.apache.ctakes.utils.build.InstallPearSilently

quote(String) - Static method in class org.apache.ctakes.utils.build.InstallPipelineFromPears

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

run() - Method in class org.apache.ctakes.utils.build.InstallPearSilently.RunInstallation

Runs the PEAR installation process.

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.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

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