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

A

actionPerformed(ActionEvent) - Method in class edu.uchsc.ccp.knowtator.Knowtator
 
actionPerformed(ActionEvent) - Method in class edu.uchsc.ccp.knowtator.textsource.TextSourceSelector
 
actionPerformed(ActionEvent) - Method in class edu.uchsc.ccp.knowtator.ui.SpanEditPanel
 
actionPerformed(ActionEvent) - Method in class edu.uchsc.ccp.knowtator.wizards.CreateConsensusSetWizard
 
actionPerformed(ActionEvent) - Method in class edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog
 
actionPerformed(ActionEvent) - Method in class edu.uchsc.ccp.knowtator.wizards.IAAWizard
 
ACTIVE_CONFIGURATION - Static variable in class edu.uchsc.ccp.knowtator.ProjectSettings
 
ACTIVE_FILTERS_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
ADD_SLOT_MATCHER_CLICKED - Static variable in class edu.uchsc.ccp.knowtator.wizards.IAAWizard
 
addActiveFilter(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
addAnnotationCreatedListener(AnnotationCreatedListener) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
addAnnotationHighlights(Collection<Span>, Color, int) - Method in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 
addAssignment(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.DisplayColors
 
addAssignment(Cls, SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.DisplayColors
 
addComparedComplexFeature(String, ComplexFeatureMatchCriteria) - Method in class edu.uchsc.ccp.iaa.matcher.FeatureMatcher
 
addComparedSimpleFeatures(String) - Method in class edu.uchsc.ccp.iaa.matcher.FeatureMatcher
 
addCurrentAnnotationsChangedListener(CurrentAnnotationsChangedListener) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
addFastAnnotateListener(FastAnnotateListener) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
addFilterChangedListener(FilterChangedListener) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
addInverse(SimpleInstance, Slot, SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
This method was written and contributed by Angus Roberts.
addNotifyTextChangeListener(NotifyTextChangeListener) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
addRefreshAnnotationsDisplayListener(RefreshAnnotationsDisplayListener) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
addSelectedAnnotationChangeListener(SelectedAnnotationChangeListener) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
addSelectedClsChangeListener(SelectedClsChangeListener) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
addSelectedSpanChangeListener(SelectedSpanChangeListener) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
addSlotMention(SimpleInstance, SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
This method adds a slotMention to a class or instance mention.
addSpanEditListener(SpanEditListener) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
addTextSourceChangeListener(TextSourceChangeListener) - Method in class edu.uchsc.ccp.knowtator.TextSourceUtil
 
addTextSourceCollectionChangeListener(TextSourceCollectionChangeListener) - Method in class edu.uchsc.ccp.knowtator.TextSourceUtil
TextSourceCollection methods
addTextSourceToCollection(File) - Method in class edu.uchsc.ccp.knowtator.textsource.files.FileTextSourceCollection
This method allows a text source to be added to this TextSourceCollection on the fly.
addValueToSlotMention(SimpleInstance, Object) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
This method adds a value to a slotMention.
adjustSlotMentionForCardinality(Cls, Slot, SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
allwayIAA(Class) - Method in class edu.uchsc.ccp.iaa.IAA
 
allwayIAA(Matcher) - Method in class edu.uchsc.ccp.iaa.IAA
 
ANNOTATED_MENTION_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
AnnotatedClassWidget - Class in edu.uchsc.ccp.knowtator.widget
 
AnnotatedClassWidget() - Constructor for class edu.uchsc.ccp.knowtator.widget.AnnotatedClassWidget
 
Annotation - Class in edu.uchsc.ccp.iaa
 
Annotation() - Constructor for class edu.uchsc.ccp.iaa.Annotation
 
ANNOTATION_ANNOTATOR_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
ANNOTATION_CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
ANNOTATION_COMMENT_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
ANNOTATION_CREATION_DATE_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
ANNOTATION_ELEMENT_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
 
ANNOTATION_SPAN_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
ANNOTATION_TEXT - Static variable in class edu.uchsc.ccp.knowtator.BrowserTextUtil
 
ANNOTATION_TEXT_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
ANNOTATION_TEXT_SOURCE_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
AnnotationCleanup - Class in edu.uchsc.ccp.knowtator.util
 
AnnotationCleanup() - Constructor for class edu.uchsc.ccp.knowtator.util.AnnotationCleanup
 
annotationCreated(AnnotationCreatedEvent) - Method in interface edu.uchsc.ccp.knowtator.event.AnnotationCreatedListener
 
annotationCreated(AnnotationCreatedEvent) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
annotationCreated(AnnotationCreatedEvent) - Method in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 
AnnotationCreatedEvent - Class in edu.uchsc.ccp.knowtator.event
 
AnnotationCreatedEvent(Object, SimpleInstance) - Constructor for class edu.uchsc.ccp.knowtator.event.AnnotationCreatedEvent
 
AnnotationCreatedListener - Interface in edu.uchsc.ccp.knowtator.event
 
AnnotationInstanceDisplay - Class in edu.uchsc.ccp.knowtator.ui
 
AnnotationInstanceDisplay(KnowtatorProjectUtil, Project) - Constructor for class edu.uchsc.ccp.knowtator.ui.AnnotationInstanceDisplay
 
AnnotationInstanceDisplay(KnowtatorProjectUtil, Project, boolean, boolean) - Constructor for class edu.uchsc.ccp.knowtator.ui.AnnotationInstanceDisplay
 
AnnotationPicker - Class in edu.uchsc.ccp.knowtator.ui
The following code was copied and modified from edu.stanford.smi.protege.ui.DisplayUtilities written by the Protege team.
AnnotationPicker(KnowtatorManager, List<SimpleInstance>, boolean) - Constructor for class edu.uchsc.ccp.knowtator.ui.AnnotationPicker
 
ANNOTATIONS_ELEMENT_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
 
AnnotationSchemaFinder - Class in edu.uchsc.ccp.knowtator.ui
 
AnnotationSchemaFinder(KnowledgeBase, JTree) - Constructor for class edu.uchsc.ccp.knowtator.ui.AnnotationSchemaFinder
 
AnnotationSchemaFinder(KnowledgeBase, JTree, ResourceKey) - Constructor for class edu.uchsc.ccp.knowtator.ui.AnnotationSchemaFinder
 
AnnotationSchemaFinder(KnowledgeBase, JTree, String) - Constructor for class edu.uchsc.ccp.knowtator.ui.AnnotationSchemaFinder
 
AnnotationSchemaFinder(KnowledgeBase, JTree, String, Icon) - Constructor for class edu.uchsc.ccp.knowtator.ui.AnnotationSchemaFinder
 
AnnotationSchemaInstancesList - Class in edu.uchsc.ccp.knowtator.ui
 
AnnotationSchemaInstancesList(KnowtatorManager) - Constructor for class edu.uchsc.ccp.knowtator.ui.AnnotationSchemaInstancesList
 
AnnotationSchemaMenuItemFactory - Class in edu.uchsc.ccp.knowtator.ui
 
AnnotationSchemaMenuItemFactory() - Constructor for class edu.uchsc.ccp.knowtator.ui.AnnotationSchemaMenuItemFactory
 
AnnotationSchemaTree - Class in edu.uchsc.ccp.knowtator.ui
 
AnnotationSchemaTree(KnowtatorManager, Action, LazyTreeRoot) - Constructor for class edu.uchsc.ccp.knowtator.ui.AnnotationSchemaTree
 
annotationSelectionChanged(SelectedAnnotationChangeEvent) - Method in interface edu.uchsc.ccp.knowtator.event.SelectedAnnotationChangeListener
To get the currently selected annotation at any time call KnowtatorManager.getSelectedAnnotation().
annotationSelectionChanged(SelectedAnnotationChangeEvent) - Method in class edu.uchsc.ccp.knowtator.Knowtator
 
annotationSelectionChanged(SelectedAnnotationChangeEvent) - Method in class edu.uchsc.ccp.knowtator.ui.AnnotationInstanceDisplay
 
annotationSelectionChanged(SelectedAnnotationChangeEvent) - Method in class edu.uchsc.ccp.knowtator.ui.AnnotationSchemaInstancesList
 
annotationSelectionChanged(SelectedAnnotationChangeEvent) - Method in class edu.uchsc.ccp.knowtator.ui.AnnotationSchemaTree
 
annotationSelectionChanged(SelectedAnnotationChangeEvent) - Method in class edu.uchsc.ccp.knowtator.ui.MentionDisplay
 
AnnotationSpanIndex - Class in edu.uchsc.ccp.iaa
This class creates an index on a collection of annotations based on the proximity of the spans of the annotations.
AnnotationSpanIndex(Collection<Annotation>) - Constructor for class edu.uchsc.ccp.iaa.AnnotationSpanIndex
 
AnnotationSpanIndex(Collection<Annotation>, int) - Constructor for class edu.uchsc.ccp.iaa.AnnotationSpanIndex
 
AnnotationUtil - Class in edu.uchsc.ccp.knowtator
Authors: Philip V.
AnnotationUtil(KnowtatorManager) - Constructor for class edu.uchsc.ccp.knowtator.AnnotationUtil
 
ANNOTATOR_AFFILIATION_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
ANNOTATOR_CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
ANNOTATOR_ELEMENT_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
 
ANNOTATOR_FIRST_NAME_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
ANNOTATOR_ID_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
ANNOTATOR_LAST_NAME_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
ANNOTATOR_TEAM_CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
ANNOTATOR_TEAM_MEMBERS_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
ANNOTATOR_TEAM_NAME_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
AnnotatorUtil - Class in edu.uchsc.ccp.knowtator.util
 
AnnotatorUtil() - Constructor for class edu.uchsc.ccp.knowtator.util.AnnotatorUtil
 
ANY_FILTER - Static variable in class edu.uchsc.ccp.knowtator.FilterUtil
 
attemptClose(int) - Method in class edu.uchsc.ccp.knowtator.ui.ModalDialog
 
attemptDialogClose(int) - Static method in class edu.uchsc.ccp.knowtator.ui.ModalDialog
 

B

batchAnnotationSetChange(Component, KnowtatorProjectUtil, AnnotationUtil, FilterUtil) - Static method in class edu.uchsc.ccp.knowtator.util.AnnotatorUtil
 
batchAnnotationSetChange(SimpleInstance, KnowtatorProjectUtil, SimpleInstance, AnnotationUtil, FilterUtil) - Static method in class edu.uchsc.ccp.knowtator.util.AnnotatorUtil
This method sets the annotator slot value for a set of annotations.
batchAnnotatorChange(Component, KnowtatorProjectUtil, AnnotationUtil, FilterUtil) - Static method in class edu.uchsc.ccp.knowtator.util.AnnotatorUtil
This method provides dialogs which collect the annotator and filter instances needed to forward on to the other batchAnnotatorChange method.
batchAnnotatorChange(SimpleInstance, KnowtatorProjectUtil, SimpleInstance, AnnotationUtil, FilterUtil) - Static method in class edu.uchsc.ccp.knowtator.util.AnnotatorUtil
This method sets the annotator slot value for a set of annotations.
BOOLEAN_SLOT_MENTION_CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
BOOLEAN_SLOT_MENTION_ELEMENT_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
 
BOOLEAN_SLOT_MENTION_VALUE_ELEMENT_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
 
BrowserTextUtil - Class in edu.uchsc.ccp.knowtator
 
BrowserTextUtil(AnnotationUtil, MentionUtil, KnowtatorProjectUtil) - Constructor for class edu.uchsc.ccp.knowtator.BrowserTextUtil
Creates a new instance of BrowserText
buildXMLDocument(Document, Collection<SimpleInstance>, String, AnnotationUtil, MentionUtil) - Static method in class edu.uchsc.ccp.knowtator.xml.XMLExport
 

C

CANCEL - Static variable in class edu.uchsc.ccp.knowtator.wizards.WizardFrame
 
canClose(int) - Method in interface edu.uchsc.ccp.knowtator.ui.ModalDialog.CloseCallback
 
canGrowSpanLeft(Span) - Method in class edu.uchsc.ccp.knowtator.SpanUtil
 
canGrowSpanRight(Span) - Method in class edu.uchsc.ccp.knowtator.SpanUtil
 
canShrinkSpanLeft(Span) - Method in class edu.uchsc.ccp.knowtator.SpanUtil
 
canShrinkSpanRight(Span) - Method in class edu.uchsc.ccp.knowtator.SpanUtil
 
caretUpdate(CaretEvent) - Method in class edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog
 
caretUpdate(CaretEvent) - Method in class edu.uchsc.ccp.knowtator.wizards.IAAWizard
 
castSimpleInstances(Collection) - Static method in class edu.uchsc.ccp.knowtator.util.ProtegeUtil
It seems like there should be a better way of accomplishing this.
castStrings(Collection) - Static method in class edu.uchsc.ccp.knowtator.util.ProtegeUtil
 
CHANGE_SORT_METHOD - Static variable in class edu.uchsc.ccp.knowtator.Knowtator
 
charset - Variable in class edu.uchsc.ccp.knowtator.textsource.files.FileTextSource
 
CLASS_MATCH_CRITERIA_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
CLASS_MENTION_CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
CLASS_MENTION_ELEMENT_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
The name of the element that represents a class mention.
ClassAndSpanMatcher - Class in edu.uchsc.ccp.iaa.matcher
 
ClassAndSpanMatcher() - Constructor for class edu.uchsc.ccp.iaa.matcher.ClassAndSpanMatcher
 
classesMatch(Annotation, Annotation) - Static method in class edu.uchsc.ccp.iaa.Annotation
returns true only if both annotations have the same non-null annotationClass.
ClassHierarchy - Interface in edu.uchsc.ccp.iaa.matcher
 
ClassHierarchyImpl - Class in edu.uchsc.ccp.iaa.matcher
 
ClassHierarchyImpl(Map<String, Set<String>>) - Constructor for class edu.uchsc.ccp.iaa.matcher.ClassHierarchyImpl
 
ClassMatcher - Class in edu.uchsc.ccp.iaa.matcher
 
ClassMatcher() - Constructor for class edu.uchsc.ccp.iaa.matcher.ClassMatcher
 
cleanup(Component, KnowledgeBase, KnowtatorProjectUtil, TextSourceUtil, AnnotationUtil, MentionUtil, FilterUtil, Project) - Static method in class edu.uchsc.ccp.knowtator.util.AnnotationCleanup
 
cleanup(SimpleInstance, FilterUtil, Collection<SimpleInstance>, AnnotationUtil, MentionUtil, KnowledgeBase, KnowtatorProjectUtil) - Static method in class edu.uchsc.ccp.knowtator.util.AnnotationCleanup
 
clearAnnotationHighlights() - Method in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 
clearHighlights() - Method in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 
clearSelectionHighlights() - Method in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 
closeHTML() - Method in class edu.uchsc.ccp.knowtator.stats.KnowtatorIAA
 
CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.textsource.DefaultTextSource
 
CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.textsource.filelines.FileLinesTextSourceCollection
 
CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.textsource.filelines.FileLineTextSource
 
CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.textsource.files.FileTextSource
 
CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.textsource.files.FileTextSourceCollection
 
CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.textsource.generif.GeneRIFTextSource
 
CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.textsource.generif.GeneRIFTextSourceCollection
 
CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.textsource.TextSourceCollection
Corresponds to the Protege class name of the text sources that are retrieved by this collection.
clsSelectionChanged(SelectedClsChangeEvent) - Method in interface edu.uchsc.ccp.knowtator.event.SelectedClsChangeListener
To get the currently selected cls at any time call KnowtatorProjectUtil.getSelectedCls().
COLOR_ASSIGNMENT_CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
COLOR_ASSIGNMENTS_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
COLOR_CLASS_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
ColorFrameRenderer - Class in edu.uchsc.ccp.knowtator.ui
 
ColorFrameRenderer(KnowtatorManager) - Constructor for class edu.uchsc.ccp.knowtator.ui.ColorFrameRenderer
 
COMMENT_ELEMENT_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
 
comparator() - Method in class edu.uchsc.ccp.knowtator.BrowserTextUtil
 
comparator(Comparator<SimpleInstance>) - Method in class edu.uchsc.ccp.knowtator.SpanUtil
 
comparator(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.ui.TextViewer
 
compare(SimpleInstance, SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.SlotMentionWidget.SlotMentionComparator
 
compareAnnotations(Annotation, Annotation, int, boolean, Set<String>) - Static method in class edu.uchsc.ccp.iaa.Annotation
This method compares two annotations with respect to their spans, annotation classes and simple features.
compareComplexFeature(Annotation, Annotation, String, int, boolean, Set<String>, boolean) - Static method in class edu.uchsc.ccp.iaa.Annotation
This method compares the complex features of two annotations.
compareComplexFeatureNames(Annotation, Annotation) - Static method in class edu.uchsc.ccp.iaa.Annotation
This method checks to see if two annotations have the same complex features but does not compare the values of the features.
compareFeatureNames(Annotation, Annotation) - Static method in class edu.uchsc.ccp.iaa.Annotation
 
compareSimpleFeature(Annotation, Annotation, String) - Static method in class edu.uchsc.ccp.iaa.Annotation
 
compareSimpleFeatureNames(Annotation, Annotation) - Static method in class edu.uchsc.ccp.iaa.Annotation
This method checks to see if two annotations have the same simple features but does not compare the values of the features.
compareSimpleFeatures(Annotation, Annotation) - Static method in class edu.uchsc.ccp.iaa.Annotation
Compares all of the simple features of two annotations
compareSimpleFeatures(Annotation, Annotation, Set<String>) - Static method in class edu.uchsc.ccp.iaa.Annotation
Compares the simple features of two annotations named in featureNames
compareSpans(SimpleInstance, SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
This method returns true if two annotations have exactly the same spans.
compareSpans(List<SimpleInstance>) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
compareTo(Object) - Method in class edu.uchsc.ccp.iaa.Span
 
compareTo(Span) - Method in class edu.uchsc.ccp.knowtator.Span
 
COMPLEX_SLOT_MATCH_CRITERIA_CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
COMPLEX_SLOT_MENTION_CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
COMPLEX_SLOT_MENTION_ELEMENT_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
The name of the element that represents a slot mention.
COMPLEX_SLOT_MENTION_VALUE_ELEMENT_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
 
ComplexFeatureMatchCriteria - Class in edu.uchsc.ccp.iaa.matcher
 
ComplexFeatureMatchCriteria(boolean, int, Set<String>, boolean) - Constructor for class edu.uchsc.ccp.iaa.matcher.ComplexFeatureMatchCriteria
 
ComplexSlotMentionValueWidget - Class in edu.uchsc.ccp.knowtator
 
ComplexSlotMentionValueWidget() - Constructor for class edu.uchsc.ccp.knowtator.ComplexSlotMentionValueWidget
 
CONFIGURATION_CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
CONSENSUS_FILTER - Static variable in class edu.uchsc.ccp.knowtator.FilterUtil
 
CONSENSUS_FILTER_CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
CONSENSUS_SET_CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
CONSENSUS_SET_CONSENSUS_FILTER_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
CONSENSUS_SET_INDIVIDUAL_FILTER_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
CONSENSUS_SET_TEAM_ANNOTATOR_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
ConsensusAnnotations - Class in edu.uchsc.ccp.knowtator.util
 
ConsensusAnnotations() - Constructor for class edu.uchsc.ccp.knowtator.util.ConsensusAnnotations
 
ConsensusException - Exception in edu.uchsc.ccp.knowtator.util
 
ConsensusException() - Constructor for exception edu.uchsc.ccp.knowtator.util.ConsensusException
 
ConsensusException(String) - Constructor for exception edu.uchsc.ccp.knowtator.util.ConsensusException
 
ConsensusException(String, Throwable) - Constructor for exception edu.uchsc.ccp.knowtator.util.ConsensusException
 
ConsensusException(Throwable) - Constructor for exception edu.uchsc.ccp.knowtator.util.ConsensusException
 
ConsensusSet - Class in edu.uchsc.ccp.knowtator.util
 
ConsensusSet(Set<SimpleInstance>, SimpleInstance, KnowtatorManager) - Constructor for class edu.uchsc.ccp.knowtator.util.ConsensusSet
 
ConsensusSet.ConsensusFrameAdapter - Class in edu.uchsc.ccp.knowtator.util
 
ConsensusSet.ConsensusFrameAdapter() - Constructor for class edu.uchsc.ccp.knowtator.util.ConsensusSet.ConsensusFrameAdapter
 
consolidateAnnotation(SimpleInstance, SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
consolidateAnnotations(SimpleInstance, SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.util.ConsensusSet
This method consolidates two anntotations into one.
consolidateAnnotations() - Method in class edu.uchsc.ccp.knowtator.util.ConsensusSet
 
contains(Span) - Method in class edu.uchsc.ccp.iaa.Span
 
contains(int) - Method in class edu.uchsc.ccp.iaa.Span
 
contains(Span) - Method in class edu.uchsc.ccp.knowtator.Span
 
contains(int) - Method in class edu.uchsc.ccp.knowtator.Span
 
convertAnnotation(SimpleInstance, boolean) - Method in class edu.uchsc.ccp.knowtator.stats.KnowtatorIAA
 
copyFile(File, File) - Static method in class edu.uchsc.ccp.util.io.FileCopy
 
copyKnowtatorFilesToProjectDirectory(Project) - Static method in class edu.uchsc.ccp.knowtator.util.ProjectUtil
 
copyKnowtatorFilesToProjectDirectory(Project, File) - Static method in class edu.uchsc.ccp.knowtator.util.ProjectUtil
 
copyKnowtatorFilesToProjectDirectory(File, File) - Static method in class edu.uchsc.ccp.knowtator.util.ProjectUtil
 
copyMention(SimpleInstance, Map<SimpleInstance, SimpleInstance>) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
CREATE_BUTTON_CLICKED - Static variable in class edu.uchsc.ccp.knowtator.wizards.CreateConsensusSetWizard
 
createAnnotation(Cls, List<Span>, String, String) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
createAnnotation(Cls, List<Span>, String, String, SimpleInstance, SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
createAnnotation(SimpleInstance, SimpleInstance, List<Span>, TextSource, SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
If the textSource does not have a corresponding instance in the kb, then one will be created.
createAnnotation(SimpleInstance, SimpleInstance, List<Span>, SimpleInstance, SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
createAnnotation(SimpleInstance, SimpleInstance, List<Span>, String, SimpleInstance, Collection<SimpleInstance>) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
createAnnotation(SimpleInstance, SimpleInstance, List<Span>, String, SimpleInstance, Collection<SimpleInstance>, String) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
Creates an annotation.
createAnnotation(Instance) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
calls createAnnotation(selectedClsOrInstance, true)
createAnnotation(Instance, boolean) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
createAnnotationMenuItem(KnowtatorManager, Frame, TextSourceUtil) - Static method in class edu.uchsc.ccp.knowtator.ui.AnnotationSchemaMenuItemFactory
 
createClassMention(Cls) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
createCls(KnowledgeBase) - Static method in class edu.uchsc.ccp.knowtator.textsource.filelines.FileLinesTextSourceCollection
 
createCls(KnowledgeBase) - Static method in class edu.uchsc.ccp.knowtator.textsource.files.FileTextSourceCollection
 
createCls(KnowledgeBase) - Static method in class edu.uchsc.ccp.knowtator.textsource.generif.GeneRIFTextSourceCollection
 
createCls(KnowledgeBase) - Static method in class edu.uchsc.ccp.knowtator.textsource.TextSourceCollection
This method ensures that the Protege cls definition corresponding to the text sources in this collection does exist.
createConsensusAnnotations(KnowtatorManager, SimpleInstance, String, Collection<SimpleInstance>) - Static method in class edu.uchsc.ccp.knowtator.util.ConsensusAnnotations
 
createConsensusSet(SimpleInstance, KnowtatorManager, SimpleInstance) - Static method in class edu.uchsc.ccp.knowtator.util.ConsensusAnnotations
 
createConsensusSet() - Method in class edu.uchsc.ccp.knowtator.wizards.CreateConsensusSetWizard
 
CreateConsensusSetWizard - Class in edu.uchsc.ccp.knowtator.wizards
 
CreateConsensusSetWizard(JFrame, KnowtatorManager) - Constructor for class edu.uchsc.ccp.knowtator.wizards.CreateConsensusSetWizard
 
createFastAnnotateMenuItem(KnowtatorManager, Frame) - Static method in class edu.uchsc.ccp.knowtator.ui.AnnotationSchemaMenuItemFactory
 
createFeatureMatcher(SimpleInstance, KnowtatorProjectUtil, String) - Static method in class edu.uchsc.ccp.knowtator.stats.KnowtatorIAA
 
createInstanceMention(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
createList() - Method in class edu.uchsc.ccp.knowtator.widget.AnnotatedClassWidget
 
createMention(Instance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
Creates a mention based on the passed in instance.
createNewProject(File) - Static method in class edu.uchsc.ccp.knowtator.util.ProjectUtil
 
createNewProject(File, File) - Static method in class edu.uchsc.ccp.knowtator.util.ProjectUtil
 
createRemoveClsFromToolbarMenuItem(KnowtatorManager, Frame) - Static method in class edu.uchsc.ccp.knowtator.ui.AnnotationSchemaMenuItemFactory
Creates and returns the menu item that will remove the selected class (button) from the fast annotation toolbar.
createSelectAnnotationMenuItems(KnowtatorManager, Frame, Component) - Static method in class edu.uchsc.ccp.knowtator.ui.AnnotationSchemaMenuItemFactory
 
createSlotMention(Slot) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
createTextSource(String) - Method in class edu.uchsc.ccp.knowtator.textsource.filelines.FileLinesTextSourceCollection
 
createTextSource(String) - Method in class edu.uchsc.ccp.knowtator.textsource.generif.GeneRIFTextSourceCollection
 
createTextSourceInstance(KnowledgeBase) - Method in class edu.uchsc.ccp.knowtator.textsource.DefaultTextSource
 
createTextSourceInstance(KnowledgeBase) - Method in class edu.uchsc.ccp.knowtator.textsource.generif.GeneRIFTextSource
 
createTextSourceInstance(KnowledgeBase) - Method in interface edu.uchsc.ccp.knowtator.textsource.TextSource
This is the generic method for creating a "knowtator text source" instance from a TextSource object.
CREATION_DATE_ELEMENT_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
The name of the element that represents the annotation creation date
crosses(Span) - Method in class edu.uchsc.ccp.iaa.Span
 
crosses(Span) - Method in class edu.uchsc.ccp.knowtator.Span
 
CURRENT_VERSION - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
currentAnnotationsChanged(CurrentAnnotationsChangeEvent) - Method in interface edu.uchsc.ccp.knowtator.event.CurrentAnnotationsChangedListener
 
currentAnnotationsChanged(CurrentAnnotationsChangeEvent) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
CurrentAnnotationsChangedListener - Interface in edu.uchsc.ccp.knowtator.event
 
CurrentAnnotationsChangeEvent - Class in edu.uchsc.ccp.knowtator.event
 
CurrentAnnotationsChangeEvent(Object, List<SimpleInstance>, List<SimpleInstance>) - Constructor for class edu.uchsc.ccp.knowtator.event.CurrentAnnotationsChangeEvent
 

D

DASHED_LINES - Static variable in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 
DEFAULT_ANNOTATION_COLOR - Static variable in class edu.uchsc.ccp.knowtator.DisplayColors
 
DEFAULT_ICON - Static variable in class edu.uchsc.ccp.knowtator.DisplayColors
 
DEFAULT_TOKEN_REGEX - Static variable in class edu.uchsc.ccp.knowtator.ProjectSettings
 
DefaultTextSource - Class in edu.uchsc.ccp.knowtator.textsource
 
DefaultTextSource() - Constructor for class edu.uchsc.ccp.knowtator.textsource.DefaultTextSource
Creates a new instance of TextSource
DefaultTextSource(String, String) - Constructor for class edu.uchsc.ccp.knowtator.textsource.DefaultTextSource
 
DefaultTextSource(String, String, String) - Constructor for class edu.uchsc.ccp.knowtator.textsource.DefaultTextSource
 
deleteAnnotation(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
deleted(FrameEvent) - Method in class edu.uchsc.ccp.knowtator.util.ConsensusSet.ConsensusFrameAdapter
 
deleteMention(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
This method deletes the mention of annotation.
deleteMention(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
deleteSelectedAnnotation() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
destroy() - Method in class edu.uchsc.ccp.knowtator.util.ConsensusSet
 
DISPLAY_COLOR_B_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
DISPLAY_COLOR_CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
DISPLAY_COLOR_G_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
DISPLAY_COLOR_NAME_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
DISPLAY_COLOR_R_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
DISPLAY_COLOR_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
DISPLAY_NAME - Static variable in class edu.uchsc.ccp.knowtator.textsource.filelines.FileLinesTextSourceCollection
 
DISPLAY_NAME - Static variable in class edu.uchsc.ccp.knowtator.textsource.files.FileTextSourceCollection
 
DISPLAY_NAME - Static variable in class edu.uchsc.ccp.knowtator.textsource.generif.GeneRIFTextSourceCollection
 
DISPLAY_NAME - Static variable in class edu.uchsc.ccp.knowtator.textsource.TextSourceCollection
This is the name that is displayed when users are asked what type of text source collection they would like to access.
displayAnnotationAuthor() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
DisplayColors - Class in edu.uchsc.ccp.knowtator
 
DisplayColors(KnowtatorManager) - Constructor for class edu.uchsc.ccp.knowtator.DisplayColors
Creates a new instance of DisplayColors
dispose() - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
dispose() - Method in class edu.uchsc.ccp.knowtator.Knowtator
removing the instance from currentInstances was interferring with the code that changes the type of an instance.
dispose() - Method in class edu.uchsc.ccp.knowtator.textsource.TextSourceSelector
 
duplicateSelectedAnnotation() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 

E

editSpans(List<Span>, SimpleInstance, String) - Method in class edu.uchsc.ccp.knowtator.SpanUtil
 
edu.uchsc.ccp.iaa - package edu.uchsc.ccp.iaa
 
edu.uchsc.ccp.iaa.html - package edu.uchsc.ccp.iaa.html
 
edu.uchsc.ccp.iaa.matcher - package edu.uchsc.ccp.iaa.matcher
 
edu.uchsc.ccp.knowtator - package edu.uchsc.ccp.knowtator
 
edu.uchsc.ccp.knowtator.event - package edu.uchsc.ccp.knowtator.event
 
edu.uchsc.ccp.knowtator.stats - package edu.uchsc.ccp.knowtator.stats
 
edu.uchsc.ccp.knowtator.textsource - package edu.uchsc.ccp.knowtator.textsource
 
edu.uchsc.ccp.knowtator.textsource.filelines - package edu.uchsc.ccp.knowtator.textsource.filelines
 
edu.uchsc.ccp.knowtator.textsource.files - package edu.uchsc.ccp.knowtator.textsource.files
 
edu.uchsc.ccp.knowtator.textsource.generif - package edu.uchsc.ccp.knowtator.textsource.generif
 
edu.uchsc.ccp.knowtator.ui - package edu.uchsc.ccp.knowtator.ui
 
edu.uchsc.ccp.knowtator.util - package edu.uchsc.ccp.knowtator.util
 
edu.uchsc.ccp.knowtator.widget - package edu.uchsc.ccp.knowtator.widget
 
edu.uchsc.ccp.knowtator.wizards - package edu.uchsc.ccp.knowtator.wizards
 
edu.uchsc.ccp.knowtator.xml - package edu.uchsc.ccp.knowtator.xml
 
edu.uchsc.ccp.util.io - package edu.uchsc.ccp.util.io
 
ENTREZ_GENE_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.textsource.generif.GeneRIFTextSource
 
equals(Object) - Method in class edu.uchsc.ccp.iaa.Span
 
equals(SimpleInstance, SimpleInstance, boolean) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
equals(Object) - Method in class edu.uchsc.ccp.knowtator.Span
 
equals(Object) - Method in class edu.uchsc.ccp.knowtator.textsource.DefaultTextSource
 
equals(Object) - Method in interface edu.uchsc.ccp.knowtator.textsource.TextSource
 
errorMatrix(Set<Annotation>, Map<Annotation, Set<Annotation>>) - Static method in class edu.uchsc.ccp.iaa.html.SpanMatcherHTML
 
EventHandler - Class in edu.uchsc.ccp.knowtator.event
 
EventHandler() - Constructor for class edu.uchsc.ccp.knowtator.event.EventHandler
 
expandToSplits(String, Span, int, int, Pattern) - Static method in class edu.uchsc.ccp.knowtator.SpanUtil
The purpose of this method is to "expand" the substringSpan such that the start and end of the returned span are at splits in the string.
ExportAnnotations - Class in edu.uchsc.ccp.knowtator.util
This class simply iterates over annotations and mentions in a Knowtator project and accesses the slot values of each.
ExportAnnotations(Project) - Constructor for class edu.uchsc.ccp.knowtator.util.ExportAnnotations
 
exportAnnotations() - Method in class edu.uchsc.ccp.knowtator.util.ExportAnnotations
 
exportMentions() - Method in class edu.uchsc.ccp.knowtator.util.ExportAnnotations
 

F

FADE_UNSELECTED_ANNOTATIONS - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
fastAnnotateAddCls(Frame) - Method in interface edu.uchsc.ccp.knowtator.event.FastAnnotateListener
Adds the given class to the fast annotate tool bar
fastAnnotateAddCls(Frame) - Method in class edu.uchsc.ccp.knowtator.Knowtator
 
fastAnnotateClsChange() - Method in interface edu.uchsc.ccp.knowtator.event.FastAnnotateListener
 
fastAnnotateClsChange() - Method in class edu.uchsc.ccp.knowtator.Knowtator
 
FastAnnotateListener - Interface in edu.uchsc.ccp.knowtator.event
 
fastAnnotateQuit() - Method in interface edu.uchsc.ccp.knowtator.event.FastAnnotateListener
 
fastAnnotateQuit() - Method in class edu.uchsc.ccp.knowtator.Knowtator
 
fastAnnotateRemoveCls(Frame) - Method in interface edu.uchsc.ccp.knowtator.event.FastAnnotateListener
Removes the given class from the fast annotate tool bar
fastAnnotateRemoveCls(Frame) - Method in class edu.uchsc.ccp.knowtator.Knowtator
 
fastAnnotateStart() - Method in interface edu.uchsc.ccp.knowtator.event.FastAnnotateListener
 
fastAnnotateStart() - Method in class edu.uchsc.ccp.knowtator.Knowtator
 
fastAnnotateToolBarContains(Frame) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
Finds out if the given frame is being shown in the fast annotate tool bar.
FeatureMatcher - Class in edu.uchsc.ccp.iaa.matcher
 
FeatureMatcher() - Constructor for class edu.uchsc.ccp.iaa.matcher.FeatureMatcher
 
FeatureMatcher(String) - Constructor for class edu.uchsc.ccp.iaa.matcher.FeatureMatcher
 
file - Variable in class edu.uchsc.ccp.knowtator.textsource.files.FileTextSource
 
FileCopy - Class in edu.uchsc.ccp.util.io
 
FileCopy() - Constructor for class edu.uchsc.ccp.util.io.FileCopy
 
FileLinesTextSourceCollection - Class in edu.uchsc.ccp.knowtator.textsource.filelines
 
FileLinesTextSourceCollection(String) - Constructor for class edu.uchsc.ccp.knowtator.textsource.filelines.FileLinesTextSourceCollection
 
FileLinesTextSourceCollection(File) - Constructor for class edu.uchsc.ccp.knowtator.textsource.filelines.FileLinesTextSourceCollection
 
FileLineTextSource - Class in edu.uchsc.ccp.knowtator.textsource.filelines
 
FileLineTextSource() - Constructor for class edu.uchsc.ccp.knowtator.textsource.filelines.FileLineTextSource
 
FileLineTextSource(String, String) - Constructor for class edu.uchsc.ccp.knowtator.textsource.filelines.FileLineTextSource
 
FileReadingUtil - Class in edu.uchsc.ccp.util.io
 
FileReadingUtil() - Constructor for class edu.uchsc.ccp.util.io.FileReadingUtil
 
FileTextSource - Class in edu.uchsc.ccp.knowtator.textsource.files
 
FileTextSource(File, String, Charset) - Constructor for class edu.uchsc.ccp.knowtator.textsource.files.FileTextSource
The name of the file with the rootPath prefix removed is the name of the FileTextSource.
FileTextSourceCollection - Class in edu.uchsc.ccp.knowtator.textsource.files
 
FileTextSourceCollection(String, Charset) - Constructor for class edu.uchsc.ccp.knowtator.textsource.files.FileTextSourceCollection
 
FileTextSourceCollection(File, Charset) - Constructor for class edu.uchsc.ccp.knowtator.textsource.files.FileTextSourceCollection
 
FILTER_ANNOTATOR_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
FILTER_CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
FILTER_INSTRUCTIONS - Static variable in class edu.uchsc.ccp.knowtator.wizards.CreateConsensusSetWizard
 
FILTER_NAME_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
FILTER_SET_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
FILTER_TYPE_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
FILTER_TYPES_NOT_SELECTABLE_FROM_TEXT_VIEWER - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
filterAnnotations(Collection<SimpleInstance>, SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.FilterUtil
 
filterAnnotations(Collection<SimpleInstance>, SimpleInstance, boolean, boolean) - Method in class edu.uchsc.ccp.knowtator.FilterUtil
 
filterAnnotations(Collection<SimpleInstance>, SimpleInstance, boolean) - Method in class edu.uchsc.ccp.knowtator.FilterUtil
 
filterChanged(FilterChangedEvent) - Method in interface edu.uchsc.ccp.knowtator.event.FilterChangedListener
 
filterChanged(FilterChangedEvent) - Method in class edu.uchsc.ccp.knowtator.Knowtator
 
filterChanged(FilterChangedEvent) - Method in class edu.uchsc.ccp.knowtator.ui.TextViewer
 
FilterChangedEvent - Class in edu.uchsc.ccp.knowtator.event
 
FilterChangedEvent(Object, SimpleInstance, boolean) - Constructor for class edu.uchsc.ccp.knowtator.event.FilterChangedEvent
 
FilterChangedListener - Interface in edu.uchsc.ccp.knowtator.event
 
FilterUtil - Class in edu.uchsc.ccp.knowtator
 
FilterUtil(KnowtatorManager) - Constructor for class edu.uchsc.ccp.knowtator.FilterUtil
Creates a new instance of FilterUtil
finalize() - Method in class edu.uchsc.ccp.knowtator.util.ConsensusSet
 
find(Component) - Method in class edu.uchsc.ccp.knowtator.textsource.filelines.FileLinesTextSourceCollection
 
find(Component) - Method in class edu.uchsc.ccp.knowtator.textsource.files.FileTextSourceCollection
 
find(Component) - Method in class edu.uchsc.ccp.knowtator.textsource.TextSourceCollection
 
FindAnnotateDialog - Class in edu.uchsc.ccp.knowtator.wizards
 
FindAnnotateDialog(Project, JFrame, KnowtatorTextPane, KnowtatorManager) - Constructor for class edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog
 
fireAnnotationCreated(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
The preferred way of creating an annotation is via KnowtatorManager.createAnnotation.
fireCurrentAnnotationsChanged() - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
fireFastAnnotateAddCls(Frame) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
fireFastAnnotateClsChange() - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
fireFastAnnotateQuit() - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
fireFastAnnotateRemoveCls(Frame) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
fireFastAnnotateStart() - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
fireFilterChanged(SimpleInstance, boolean) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
fireNotifyTextChanged(String) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
fireRefreshAnnotationsDisplay(boolean) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
fireSelectedAnnotationChanged(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
The preferred way of updating the currently selected annotation is via KnowtatorManager.setSelectedAnnotation().
fireSelectedClsChanged(Cls) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
The preferred way of updating the currently selected cls is via KnowtatorManager.setSelectedCls().
fireSelectedSpanChanged(List<Span>) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
The preferred way to update the currently selected spans is via KnowtatorManager.setSelectedSpans.
fireSpanEditted(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
fixKnowtatorProjectPath(Project) - Static method in class edu.uchsc.ccp.knowtator.util.ProjectUtil
 
fixKnowtatorProjectPath(Project, File) - Static method in class edu.uchsc.ccp.knowtator.util.ProjectUtil
Knowtator annotation projects require that the project knowtator.pprj is a directly included project - i.e.
FLOAT_SLOT_MENTION_CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
FLOAT_SLOT_MENTION_ELEMENT_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
 
FLOAT_SLOT_MENTION_VALUE_ELEMENT_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
 

G

GeneRIFTextSource - Class in edu.uchsc.ccp.knowtator.textsource.generif
 
GeneRIFTextSource(String, String[], String, String) - Constructor for class edu.uchsc.ccp.knowtator.textsource.generif.GeneRIFTextSource
 
GeneRIFTextSourceCollection - Class in edu.uchsc.ccp.knowtator.textsource.generif
This TextSourceCollection implementation is useful for GeneRIFs stored in in a single file line-by-line.
GeneRIFTextSourceCollection(String) - Constructor for class edu.uchsc.ccp.knowtator.textsource.generif.GeneRIFTextSourceCollection
 
GeneRIFTextSourceCollection(File) - Constructor for class edu.uchsc.ccp.knowtator.textsource.generif.GeneRIFTextSourceCollection
 
get(int) - Method in class edu.uchsc.ccp.knowtator.textsource.filelines.FileLinesTextSourceCollection
 
get(String) - Method in class edu.uchsc.ccp.knowtator.textsource.filelines.FileLinesTextSourceCollection
 
get(int) - Method in class edu.uchsc.ccp.knowtator.textsource.files.FileTextSourceCollection
 
get(String) - Method in class edu.uchsc.ccp.knowtator.textsource.files.FileTextSourceCollection
 
get(int) - Method in class edu.uchsc.ccp.knowtator.textsource.TextSourceCollection
 
get(String) - Method in class edu.uchsc.ccp.knowtator.textsource.TextSourceCollection
 
getActiveConfiguration(Project) - Static method in class edu.uchsc.ccp.knowtator.ProjectSettings
 
getActiveFilters() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getActiveFiltersSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getAddValueAction() - Method in class edu.uchsc.ccp.knowtator.SlotMentionValueWidget
 
getAllConnectedMentions(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
This method gathers all the mentions (e.g.
getAllwayMatches() - Method in class edu.uchsc.ccp.iaa.IAA
 
getAllwayMatchSets() - Method in class edu.uchsc.ccp.iaa.IAA
 
getAllwayNonmatches() - Method in class edu.uchsc.ccp.iaa.IAA
 
getAnnotatedMentionSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getAnnotation() - Method in class edu.uchsc.ccp.knowtator.event.SpanEditEvent
 
getAnnotationAnnotatorSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getAnnotationClass() - Method in class edu.uchsc.ccp.iaa.Annotation
 
getAnnotationClasses() - Method in class edu.uchsc.ccp.iaa.IAA
 
getAnnotationCls() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getAnnotationCommentSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getAnnotationComparator() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getAnnotationCreationDateSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getAnnotations(TextSource) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
Returns the "annotation" instances associated with a TextSource if the TextSource does not have a corresponding "text source" instance in the knowledgebase, then null is returned.
getAnnotations(String) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
getAnnotations(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
Does the work of finding all "annotation" instances that have the textSourceInstance as the value of "annotation_text_source" slot.
getAnnotationSets() - Method in class edu.uchsc.ccp.iaa.IAA
 
getAnnotationsOfClass(String, String) - Method in class edu.uchsc.ccp.iaa.IAA
 
getAnnotationsOfSameType(Annotation, String) - Method in class edu.uchsc.ccp.iaa.IAA
 
getAnnotationSpanSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getAnnotationTexts() - Method in class edu.uchsc.ccp.knowtator.stats.KnowtatorIAA
 
getAnnotationTextSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getAnnotationTextSourceSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getAnnotationUtil() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getAnnotator(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
getAnnotatorAffiliationSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getAnnotatorCls() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getAnnotatorFirstNameSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getAnnotatorIDSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getAnnotatorLastNameSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getAnnotators(SimpleInstance) - Static method in class edu.uchsc.ccp.knowtator.FilterUtil
Returns the annotators specified by the filter.
getAnnotatorTeamMembersSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getAnnotatorTeamNameSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getAReferencedSpan(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.SpanUtil
 
getBackgroundColor(Color) - Static method in class edu.uchsc.ccp.knowtator.DisplayColors
 
getBackgroundColor() - Method in class edu.uchsc.ccp.knowtator.ui.ColorFrameRenderer
 
getBooleanSlotMentionCls() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getBrowserText(SimpleInstance, int) - Method in class edu.uchsc.ccp.knowtator.BrowserTextUtil
 
getBrowserText(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.BrowserTextUtil
The BrowserSlotPattern in the Protege code does not work very well with annotations and their mentions.
getBrowserTextUtil() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getCandidateAnnotations(Annotation, AnnotationSpanIndex) - Static method in class edu.uchsc.ccp.iaa.html.IAA2HTML
 
getCentralDialogLocation(Component, JDialog) - Static method in class edu.uchsc.ccp.knowtator.wizards.WizardUtil
 
getClassMatchCriteriaSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getClassMentionCls() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getCloseAction(Component) - Static method in class edu.uchsc.ccp.knowtator.ui.ModalDialog
 
getColor(Frame) - Method in class edu.uchsc.ccp.knowtator.DisplayColors
 
getColorAssignmentCls() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getColorAssignments() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getColorAssignmentsSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getColorClassSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getComment(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
getComplexFeatureNames() - Method in class edu.uchsc.ccp.iaa.Annotation
 
getComplexFeatureValues(String) - Method in class edu.uchsc.ccp.iaa.Annotation
 
getComplexSlotMatchCriteriaCls() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getComplexSlotMentionCls() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getComplexSlotMentions(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
This method gets the complex slot mentions of a class mention or instance mention.
getComplexSlotsFromMatcherConfig(SimpleInstance, KnowtatorProjectUtil) - Static method in class edu.uchsc.ccp.knowtator.stats.KnowtatorIAA
 
getConfigurationCls() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getConsensusFilterCls() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getConsensusModeProgress() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getConsensusSetCls() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getConsensusSetConsensusFilterSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getConsensusSetIndividualFilterSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getConsensusSetName() - Method in class edu.uchsc.ccp.knowtator.wizards.CreateConsensusSetWizard
 
getConsensusSetTeamAnnotatorSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getConsolidatedAnnotationCountForFrame(Frame) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getContentPane() - Method in class edu.uchsc.ccp.knowtator.ui.TextViewer
 
getCoveredText(Annotation, String, String) - Static method in class edu.uchsc.ccp.iaa.Annotation
Returns the text covered by an annotation.
getCreatedAnnotation() - Method in class edu.uchsc.ccp.knowtator.event.AnnotationCreatedEvent
 
getCreationDate(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
getCurrentAnnotationCountForFrame(Frame) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getCurrentAnnotationsForFrame(Frame) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getCurrentDialog() - Static method in class edu.uchsc.ccp.knowtator.ui.ModalDialog
 
getCurrentFilteredAnnotations() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
Returns the annotations for the current text source that satisfy the currently selected filter.
getCurrentFilterIndex() - Method in class edu.uchsc.ccp.knowtator.FilterUtil
 
getCurrentPartiallyFilteredAnnotations() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
returns the annotations for the current text source that satisfy the currently selected filter ignoring the type constraint.
getCurrentSelectableFilteredAnnotations() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getCurrentTextSource() - Method in class edu.uchsc.ccp.knowtator.TextSourceUtil
 
getCurrentTextSourceCollection() - Method in class edu.uchsc.ccp.knowtator.TextSourceUtil
 
getDescription() - Method in class edu.uchsc.ccp.iaa.matcher.ClassAndSpanMatcher
 
getDescription() - Method in class edu.uchsc.ccp.iaa.matcher.ClassMatcher
 
getDescription() - Method in class edu.uchsc.ccp.iaa.matcher.FeatureMatcher
 
getDescription() - Method in interface edu.uchsc.ccp.iaa.matcher.Matcher
 
getDescription() - Method in class edu.uchsc.ccp.iaa.matcher.OverlappingSpanMatcher
 
getDescription() - Method in class edu.uchsc.ccp.iaa.matcher.SpanMatcher
 
getDescription() - Method in class edu.uchsc.ccp.iaa.matcher.SpansExactComplexFeatureMatcher
 
getDescription() - Method in class edu.uchsc.ccp.iaa.matcher.SpansExactSimpleFeatureMatcher
 
getDescription() - Method in class edu.uchsc.ccp.iaa.matcher.SpansOverlapSimpleFeatureMatcher
 
getDescription() - Method in class edu.uchsc.ccp.iaa.matcher.SubclassMatcher
 
getDirectory() - Method in class edu.uchsc.ccp.knowtator.textsource.files.FileTextSourceCollection
 
getDisplayColorBSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getDisplayColorCls() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getDisplayColorGSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getDisplayColorNameSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getDisplayColorRSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getDisplayColors() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getDisplayColorSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getDocID() - Method in class edu.uchsc.ccp.iaa.Annotation
 
getEnd() - Method in class edu.uchsc.ccp.iaa.Span
 
getEnd() - Method in class edu.uchsc.ccp.knowtator.Span
 
getEntrezIDs() - Method in class edu.uchsc.ccp.knowtator.textsource.generif.GeneRIFTextSource
 
getExactlyOverlappingAnnotations(Annotation) - Method in class edu.uchsc.ccp.iaa.AnnotationSpanIndex
 
getExactlyOverlappingAnnotations(Annotation, String) - Method in class edu.uchsc.ccp.iaa.IAA
 
getFadeUnselectedAnnotations() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getFadeUnselectedAnnotationsSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getFastAnnotateFrame() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getFeatureNames() - Method in class edu.uchsc.ccp.iaa.Annotation
 
getFile() - Method in class edu.uchsc.ccp.knowtator.textsource.filelines.FileLinesTextSourceCollection
 
getFile() - Method in class edu.uchsc.ccp.knowtator.textsource.files.FileTextSource
 
getFilter() - Method in class edu.uchsc.ccp.knowtator.wizards.CreateConsensusSetWizard
 
getFilter() - Method in class edu.uchsc.ccp.knowtator.wizards.IAAWizard
 
getFilterAnnotatorSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getFilterCls() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getFilteredAnnotations() - Method in class edu.uchsc.ccp.knowtator.event.CurrentAnnotationsChangeEvent
 
getFilterNameSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getFilterSetSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getFilterTypeSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getFilterTypesNotSelectableFromTextViewerSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getFilterUtil() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getFirstSpan(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.SpanUtil
 
getFloatSlotMentionCls() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getHumanAnnotatorCls() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getIAAClass() - Method in class edu.uchsc.ccp.iaa.matcher.SubclassMatcher
 
getIcon(Color) - Method in class edu.uchsc.ccp.knowtator.DisplayColors
 
getIndex(TextSource) - Method in class edu.uchsc.ccp.knowtator.textsource.filelines.FileLinesTextSourceCollection
 
getIndex(TextSource) - Method in class edu.uchsc.ccp.knowtator.textsource.files.FileTextSourceCollection
 
getIndex(TextSource) - Method in class edu.uchsc.ccp.knowtator.textsource.TextSourceCollection
 
getInstance() - Static method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
getInstanceMentionCls() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getIntegerSlotMentionCls() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getInvalidFloatDescription(String, Cls, Slot) - Method in class edu.uchsc.ccp.knowtator.SlotMentionValueWidget
The code for this method was copied from edu.stanford.smi.protege.widget.FloatFieldWidget and modified slightly
getInvalidIntegerDescription(String, Cls, Slot) - Method in class edu.uchsc.ccp.knowtator.SlotMentionValueWidget
The code for this method was copied from edu.stanford.smi.protege.widget.IntegerFieldWidget and modified slightly
getKnowledgeBase() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getKnowledgeBase() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getKnowtatorProjectDirectory() - Static method in class edu.uchsc.ccp.knowtator.util.ProjectUtil
This method returns the default location of the knowtator project files: knowtator.pprj, knowtator.pins, knowtator.pont, new-project.pprj, etc.
getKnowtatorProjectUtil() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getKnowtatorSupportClassesVersion() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getKnowtatorSupportClassesVersion(KnowledgeBase) - Static method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getKnowtatorSupportCls() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getLastSelectedAnnotation() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getMatcherInfo(String) - Method in class edu.uchsc.ccp.iaa.IAA
 
getMatchingFrames(String, int) - Method in class edu.uchsc.ccp.knowtator.ui.AnnotationSchemaFinder
 
getMatchSpans() - Method in class edu.uchsc.ccp.iaa.matcher.FeatureMatcher
 
getMention(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
getMentionAnnotation(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
getMentionAnnotationSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getMentionClassSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getMentionCls() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getMentionCls(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
If the mention is a "class mention" then the Cls corresponding to the mentioned class is returned.
getMentionedBy(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
getMentionedInSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getMentionFrame(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
getMentionInstance(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
getMentionInstanceSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getMentionSlots(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
getMentionSlotSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getMentionSlotValueSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getMentionUtil() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getName() - Method in class edu.uchsc.ccp.iaa.matcher.ClassAndSpanMatcher
 
getName() - Method in class edu.uchsc.ccp.iaa.matcher.ClassMatcher
 
getName() - Method in class edu.uchsc.ccp.iaa.matcher.FeatureMatcher
 
getName() - Method in interface edu.uchsc.ccp.iaa.matcher.Matcher
 
getName() - Method in class edu.uchsc.ccp.iaa.matcher.OverlappingSpanMatcher
 
getName() - Method in class edu.uchsc.ccp.iaa.matcher.SpanMatcher
 
getName() - Method in class edu.uchsc.ccp.iaa.matcher.SpansExactComplexFeatureMatcher
 
getName() - Method in class edu.uchsc.ccp.iaa.matcher.SpansExactSimpleFeatureMatcher
 
getName() - Method in class edu.uchsc.ccp.iaa.matcher.SpansOverlapSimpleFeatureMatcher
 
getName() - Method in class edu.uchsc.ccp.iaa.matcher.SubclassMatcher
 
getName() - Method in class edu.uchsc.ccp.knowtator.textsource.DefaultTextSource
 
getName() - Method in class edu.uchsc.ccp.knowtator.textsource.filelines.FileLinesTextSourceCollection
 
getName() - Method in class edu.uchsc.ccp.knowtator.textsource.files.FileTextSourceCollection
 
getName() - Method in interface edu.uchsc.ccp.knowtator.textsource.TextSource
 
getName() - Method in class edu.uchsc.ccp.knowtator.textsource.TextSourceCollection
 
getNearbyAnnotations(Annotation) - Method in class edu.uchsc.ccp.iaa.AnnotationSpanIndex
 
getNewFilter() - Method in class edu.uchsc.ccp.knowtator.event.FilterChangedEvent
 
getNextAnnotation() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getNextFilter(int) - Method in class edu.uchsc.ccp.knowtator.FilterUtil
 
getNontrivialAllwayMatches() - Method in class edu.uchsc.ccp.iaa.IAA
 
getNontrivialAllwayNonmatches() - Method in class edu.uchsc.ccp.iaa.IAA
 
getNontrivialPairwiseMatches() - Method in class edu.uchsc.ccp.iaa.IAA
 
getNontrivialPairwiseNonmatches() - Method in class edu.uchsc.ccp.iaa.IAA
 
getOutputDirectory() - Method in class edu.uchsc.ccp.knowtator.wizards.IAAWizard
 
getOverlappingAnnotations(Annotation) - Method in class edu.uchsc.ccp.iaa.AnnotationSpanIndex
 
getOverlappingAnnotations(Annotation, String) - Method in class edu.uchsc.ccp.iaa.IAA
 
getPairwiseMatches() - Method in class edu.uchsc.ccp.iaa.IAA
 
getPairwiseMatchPairs() - Method in class edu.uchsc.ccp.iaa.IAA
 
getPairwiseNonmatches() - Method in class edu.uchsc.ccp.iaa.IAA
 
getPartiallyFilteredAnnotations() - Method in class edu.uchsc.ccp.knowtator.event.CurrentAnnotationsChangeEvent
 
getPositionComparator(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getPreviousAnnotation() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getPreviousFilter(int) - Method in class edu.uchsc.ccp.knowtator.FilterUtil
 
getPropogateTrivialMatchSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getProtegeClsName() - Method in class edu.uchsc.ccp.knowtator.textsource.DefaultTextSource
 
getProtegeClsName() - Method in interface edu.uchsc.ccp.knowtator.textsource.TextSource
Every implementation of TextSource corresponds to a subclass of "knowtator text source" which is a class defined knowtator.pprj (which is the project that must be included in order to run Knowtator.)
getRecentTextSourceCollection(Project) - Static method in class edu.uchsc.ccp.knowtator.ProjectSettings
 
getRecentTextSourceCollectionIndex(Project) - Static method in class edu.uchsc.ccp.knowtator.ProjectSettings
 
getRelatedAnnotations(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
Returns all annotations that are related to the passed in annotation.
getRelatedMentions(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
This method returns all class mentions or instance mentions related to the passed in mention via slot mentions.
getRelatedMentions(SimpleInstance, Slot) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
This method returns all class mentions or instance mentions related to the passed in mention via slot mentions whose mentioned slot is the passed in slot.
getRemoveValueAction() - Method in class edu.uchsc.ccp.knowtator.SlotMentionValueWidget
 
getRenderer() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getRendererAnnotationDisplayText(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.ui.ColorFrameRenderer
 
getResult() - Method in class edu.uchsc.ccp.iaa.matcher.MatchResult
 
getRootClses() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getRootClsesSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getSelectedAnnotation() - Method in class edu.uchsc.ccp.knowtator.event.SelectedAnnotationChangeEvent
 
getSelectedAnnotation() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
This is the preferred way to obtain the currently selected annotation
getSelectedAnnotationSet() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getSelectedAnnotationSetSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getSelectedAnnotator() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getSelectedAnnotatorSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getSelectedCls() - Method in class edu.uchsc.ccp.knowtator.event.SelectedClsChangeEvent
 
getSelectedCls() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
This is the preferred way to obtain the currently selected cls (i.e.
getSelectedFilter() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getSelectedFiltersCls() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getSelectedFilterSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getSelectedFiltersSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getSelectedIndices() - Method in class edu.uchsc.ccp.knowtator.SpanWidget
 
getSelectedSpanIndices() - Method in class edu.uchsc.ccp.knowtator.ui.AnnotationInstanceDisplay
 
getSelectedSpans() - Method in class edu.uchsc.ccp.knowtator.event.SelectedSpanChangeEvent
 
getSelectedSpans() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
This is the preferred way to obtain the currently selected spans (i.e.
getSelectedSpans() - Method in class edu.uchsc.ccp.knowtator.ui.AnnotationInstanceDisplay
Returns a list Span objects corresponding to the span strings selected in the span widget If there are no spans selected, then the first span listed in the span widget is returned.
getSelectedTextColor() - Method in class edu.uchsc.ccp.knowtator.ui.TextViewer
 
getSelection() - Method in class edu.uchsc.ccp.knowtator.ui.AnnotationPicker
 
getSetCls() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getSetDescriptionSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getSetName() - Method in class edu.uchsc.ccp.iaa.Annotation
 
getSetNames() - Method in class edu.uchsc.ccp.iaa.IAA
 
getSetNameSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getSets(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
getSets(SimpleInstance) - Static method in class edu.uchsc.ccp.knowtator.FilterUtil
 
getSetSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getShortestAnnotation(Collection<Annotation>) - Static method in class edu.uchsc.ccp.iaa.Annotation
This method returns the shortest annotation - that is the annotation whose span is the shortest.
getShortestAnnotation(Collection<SimpleInstance>) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
This method returns the shortest annotation - that is the annotation whose span is the shortest.
getShowAllFilter() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getShowInstances(Project) - Static method in class edu.uchsc.ccp.knowtator.ProjectSettings
 
getShowNoneFilter() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getSimpleFeatureNames() - Method in class edu.uchsc.ccp.iaa.Annotation
 
getSimpleFeatureValues(String) - Method in class edu.uchsc.ccp.iaa.Annotation
 
getSimpleSlotMatchCriteriaCls() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getSimpleSlotsFromMatcherConfig(SimpleInstance, KnowtatorProjectUtil) - Static method in class edu.uchsc.ccp.knowtator.stats.KnowtatorIAA
 
getSingleSet(Map<String, Set<Annotation>>) - Static method in class edu.uchsc.ccp.iaa.html.IAA2HTML
 
getSize() - Method in class edu.uchsc.ccp.iaa.Annotation
 
getSize() - Method in class edu.uchsc.ccp.iaa.Span
 
getSize(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
getSize() - Method in class edu.uchsc.ccp.knowtator.Span
 
getSlotFillerCandidates(SimpleInstance, Slot, List<SimpleInstance>) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
getSlotLabel(Cls, Slot, Project) - Static method in class edu.uchsc.ccp.knowtator.util.ProtegeUtil
 
getSlotMatchCriteriaSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getSlotMatcherConfig() - Method in class edu.uchsc.ccp.knowtator.wizards.IAAWizard
 
getSlotMatcherConfigCls() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getSlotMatcherSimpleSlotsSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getSlotMatcherSlotSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getSlotMention(SimpleInstance, Slot) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
gets a slot mention for the given slot of a class mention or instance mention.
getSlotMentionCls() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getSlotMentions(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
This method gets the slot mentions of a class mention or instance mention.
getSlotMentionSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getSlotMentionSlot(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
getSlotMentionValues(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
getSpanMatchCriteriaSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getSpans() - Method in class edu.uchsc.ccp.iaa.Annotation
 
getSpans(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
Returns a list of Span objects that correspond to the span values given to an annotation instance.
getSpans(SimpleInstance, boolean) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
Returns a list of Span objects that correspond to the span values given to an annotation instance.
getSpanUtil() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getStart() - Method in class edu.uchsc.ccp.iaa.Span
 
getStart() - Method in class edu.uchsc.ccp.knowtator.Span
 
getStringSlotMentionCls() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getSubclasses(String) - Method in interface edu.uchsc.ccp.iaa.matcher.ClassHierarchy
 
getSubclasses(String) - Method in class edu.uchsc.ccp.iaa.matcher.ClassHierarchyImpl
 
getSubclasses() - Method in class edu.uchsc.ccp.iaa.matcher.SubclassMatcher
 
getSubtextSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getSubtextSlotSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getTeamAnnotator() - Method in class edu.uchsc.ccp.knowtator.util.ConsensusSet
 
getTeamAnnotatorCls() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getText(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
getText() - Method in class edu.uchsc.ccp.knowtator.textsource.DefaultTextSource
It might be prudent for extensions of this class to override this method such that the member variable text is not used - esp.
getText(List<Span>) - Method in class edu.uchsc.ccp.knowtator.textsource.DefaultTextSource
 
getText(List<Span>, String) - Static method in class edu.uchsc.ccp.knowtator.textsource.DefaultTextSource
 
getText() - Method in class edu.uchsc.ccp.knowtator.textsource.files.FileTextSource
 
getText() - Method in interface edu.uchsc.ccp.knowtator.textsource.TextSource
 
getText(List<Span>) - Method in interface edu.uchsc.ccp.knowtator.textsource.TextSource
Returns the text corresponding to the spans passed in.
getTextPane() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getTextPane() - Method in class edu.uchsc.ccp.knowtator.ui.TextViewer
 
getTextSource(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
getTextSource() - Method in class edu.uchsc.ccp.knowtator.textsource.TextSourceChangedEvent
 
getTextSource() - Method in class edu.uchsc.ccp.knowtator.textsource.TextSourceChangeEvent
 
getTextSource(Instance) - Method in class edu.uchsc.ccp.knowtator.TextSourceUtil
 
getTextSourceAnnotationComment(Instance) - Method in class edu.uchsc.ccp.knowtator.TextSourceUtil
 
getTextSourceAnnotationComment(TextSource) - Method in class edu.uchsc.ccp.knowtator.TextSourceUtil
 
getTextSourceAnnotationsMap() - Method in class edu.uchsc.ccp.knowtator.stats.KnowtatorIAA
 
getTextSourceCls() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getTextSourceCollection() - Method in class edu.uchsc.ccp.knowtator.textsource.TextSourceCollectionChangeEvent
 
getTextSourceInstance(TextSource, boolean) - Method in class edu.uchsc.ccp.knowtator.TextSourceUtil
This method finds a "text source" instance in the knowledgebase for the given TextSouce object.
getTextSources() - Method in class edu.uchsc.ccp.knowtator.wizards.CreateConsensusSetWizard
 
getTextSources() - Method in class edu.uchsc.ccp.knowtator.wizards.IAAWizard
 
getTextSourceUtil() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getTokenRegex() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getTokenRegexSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getTrivialAllwayMatches() - Method in class edu.uchsc.ccp.iaa.IAA
 
getTrivialAllwayNonmatches() - Method in class edu.uchsc.ccp.iaa.IAA
 
getTrivialPairwiseMatches() - Method in class edu.uchsc.ccp.iaa.IAA
 
getTrivialPairwiseNonmatches() - Method in class edu.uchsc.ccp.iaa.IAA
 
getTscImplementationsCls() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getTscImplementationsSlot() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
getTypes(SimpleInstance) - Static method in class edu.uchsc.ccp.knowtator.FilterUtil
Returns the types specified by the filter.
getVerticalDistance(SimpleInstance, SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getVerticalDistance(SimpleInstance, SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.ui.TextViewer
Calculates the verticle distance in pixels between annotation1 and annotation2 as they appear in the text.
getVisibleFilteredAnnotations() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getVisibleSpan() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
getVisibleSpan() - Method in class edu.uchsc.ccp.knowtator.ui.TextViewer
 
GO_CLICKED - Static variable in class edu.uchsc.ccp.knowtator.wizards.IAAWizard
 
greaterThan(Span) - Method in class edu.uchsc.ccp.iaa.Span
 
greaterThan(Span) - Method in class edu.uchsc.ccp.knowtator.Span
 
GROW_ANNOTATION_LEFT - Static variable in class edu.uchsc.ccp.knowtator.SpanUtil
 
GROW_ANNOTATION_LEFT_WORD - Static variable in class edu.uchsc.ccp.knowtator.SpanUtil
 
GROW_ANNOTATION_RIGHT - Static variable in class edu.uchsc.ccp.knowtator.SpanUtil
 
GROW_ANNOTATION_RIGHT_WORD - Static variable in class edu.uchsc.ccp.knowtator.SpanUtil
 

H

handleAddAction() - Method in class edu.uchsc.ccp.knowtator.ComplexSlotMentionValueWidget
At the moment the only value you can add is a mention from another annotation.
handleAddAction() - Method in class edu.uchsc.ccp.knowtator.SlotMentionValueWidget
 
handleAddAction() - Method in class edu.uchsc.ccp.knowtator.SpanWidget
 
handleCreateAction() - Method in class edu.uchsc.ccp.knowtator.ComplexSlotMentionValueWidget
 
handleCreateAction() - Method in class edu.uchsc.ccp.knowtator.SpanWidget
 
handleRemoveAction(Collection) - Method in class edu.uchsc.ccp.knowtator.ComplexSlotMentionValueWidget
 
handleRemoveAction(Collection) - Method in class edu.uchsc.ccp.knowtator.SlotMentionValueWidget
 
handleRemoveAction(Collection) - Method in class edu.uchsc.ccp.knowtator.SpanWidget
 
handleViewAction(Instance) - Method in class edu.uchsc.ccp.knowtator.ComplexSlotMentionValueWidget
 
handleViewAction(String) - Method in class edu.uchsc.ccp.knowtator.SpanWidget
 
HAS_SLOT_MENTION_ELEMENT_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
 
hashCode() - Method in class edu.uchsc.ccp.iaa.Span
 
hashCode() - Method in class edu.uchsc.ccp.knowtator.Span
 
hashCode() - Method in class edu.uchsc.ccp.knowtator.textsource.DefaultTextSource
 
hashCode() - Method in interface edu.uchsc.ccp.knowtator.textsource.TextSource
 
hasNext() - Method in interface edu.uchsc.ccp.knowtator.textsource.TextSourceIterator
 
hasSlotMention(SimpleInstance, Slot) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
hasSlotValue(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
hasTeamAnnotator(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
hideHighlights() - Method in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 
highlightAnnotationTemp(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
written to provide a way for AnnotationPicker and AnnotationSchemaTree context menu to temporarily highlight an annotation.
highlightSelectedInstance(SimpleInstance, boolean) - Method in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 
highlightSpans(boolean) - Method in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 
highlightSpans(SimpleInstance, List<SimpleInstance>, boolean) - Method in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 
HTMLUtil - Class in edu.uchsc.ccp.iaa.html
 
HTMLUtil() - Constructor for class edu.uchsc.ccp.iaa.html.HTMLUtil
 
HUMAN_ANNOTATOR_CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 

I

IAA - Class in edu.uchsc.ccp.iaa
 
IAA(Set<String>) - Constructor for class edu.uchsc.ccp.iaa.IAA
 
IAA(Set<String>, Set<Annotation>) - Constructor for class edu.uchsc.ccp.iaa.IAA
 
IAA2HTML - Class in edu.uchsc.ccp.iaa.html
 
IAA2HTML() - Constructor for class edu.uchsc.ccp.iaa.html.IAA2HTML
 
IAA_CONFIG - Static variable in class edu.uchsc.ccp.knowtator.wizards.IAAWizard
 
IAA_CONFIG_DISPLAY - Static variable in class edu.uchsc.ccp.knowtator.wizards.IAAWizard
 
IAA_DIRECTORY - Static variable in class edu.uchsc.ccp.knowtator.wizards.IAAWizard
 
IAA_FILTER - Static variable in class edu.uchsc.ccp.knowtator.wizards.IAAWizard
 
IAA_TEXTSOURCES - Static variable in class edu.uchsc.ccp.knowtator.wizards.IAAWizard
 
IAA_WELCOME_MESSAGE - Static variable in class edu.uchsc.ccp.knowtator.wizards.IAAWizard
 
IAAException - Exception in edu.uchsc.ccp.iaa
 
IAAException() - Constructor for exception edu.uchsc.ccp.iaa.IAAException
 
IAAException(String) - Constructor for exception edu.uchsc.ccp.iaa.IAAException
 
IAAException(String, Throwable) - Constructor for exception edu.uchsc.ccp.iaa.IAAException
 
IAAException(Throwable) - Constructor for exception edu.uchsc.ccp.iaa.IAAException
 
IAAWizard - Class in edu.uchsc.ccp.knowtator.wizards
 
IAAWizard(Project, KnowledgeBase, KnowtatorProjectUtil, JFrame) - Constructor for class edu.uchsc.ccp.knowtator.wizards.IAAWizard
 
ID_ATTRIBUTE_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
 
IGNORE_SPANS_COMPARISON - Static variable in class edu.uchsc.ccp.iaa.Annotation
 
indexOfComponent(Container, Component) - Static method in class edu.uchsc.ccp.knowtator.ui.SwingUtils
Gets the index of the component inside the given panel.
init() - Method in class edu.uchsc.ccp.knowtator.TextSourceUtil
 
initGUI() - Method in class edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog
 
initHTML(String, String) - Static method in class edu.uchsc.ccp.iaa.html.HTMLUtil
 
initHTML(PrintStream, String, String, String, String) - Static method in class edu.uchsc.ccp.iaa.html.IAA2HTML
 
initHTML(String, String) - Static method in class edu.uchsc.ccp.iaa.html.IAA2HTML
 
initialize() - Method in class edu.uchsc.ccp.knowtator.ComplexSlotMentionValueWidget
 
initialize() - Method in class edu.uchsc.ccp.knowtator.Knowtator
 
initialize() - Method in class edu.uchsc.ccp.knowtator.SimpleSlotMentionValueWidget
 
initialize() - Method in class edu.uchsc.ccp.knowtator.SlotMentionValueWidget
 
initialize() - Method in class edu.uchsc.ccp.knowtator.SlotMentionWidget
 
initialize() - Method in class edu.uchsc.ccp.knowtator.SpanWidget
 
initialize() - Method in class edu.uchsc.ccp.knowtator.ui.TextViewer
 
initializeSlotMentions(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
this method takes a mention and initializes slot mentions for slots that do not yet have a slotMention for the mention.
INSTANCE_MENTION_CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
INSTANCE_MENTION_ELEMENT_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
The name of the element that represents an instance mention.
INTEGER_SLOT_MENTION_CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
INTEGER_SLOT_MENTION_ELEMENT_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
 
INTEGER_SLOT_MENTION_VALUE_ELEMENT_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
 
intersects(Span) - Method in class edu.uchsc.ccp.iaa.Span
we need some junit tests
intersects(List<Span>, List<Span>) - Static method in class edu.uchsc.ccp.iaa.Span
 
intersects(Span) - Method in class edu.uchsc.ccp.knowtator.Span
we need some junit tests
intersects(List<Span>, List<Span>) - Static method in class edu.uchsc.ccp.knowtator.Span
 
InvalidSpanException - Exception in edu.uchsc.ccp.knowtator
 
InvalidSpanException() - Constructor for exception edu.uchsc.ccp.knowtator.InvalidSpanException
Creates a new instance of InvalidSpanException
InvalidSpanException(String) - Constructor for exception edu.uchsc.ccp.knowtator.InvalidSpanException
 
InvalidSpanException(String, Throwable) - Constructor for exception edu.uchsc.ccp.knowtator.InvalidSpanException
 
InvalidSpanException(Throwable) - Constructor for exception edu.uchsc.ccp.knowtator.InvalidSpanException
 
isAnnotation(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
isAnnotationVisible(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
isBooleanSlotMention(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
isClassAndSpanMatcherSelected() - Method in class edu.uchsc.ccp.knowtator.wizards.IAAWizard
 
isClassMatcherSelected() - Method in class edu.uchsc.ccp.knowtator.wizards.IAAWizard
 
isClassMention(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
isClsLicensedByFilter(SimpleInstance, Frame) - Method in class edu.uchsc.ccp.knowtator.FilterUtil
 
isComplexFeature(String) - Method in class edu.uchsc.ccp.iaa.Annotation
 
isComplexSlotMention(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
Determines whether an instance is a complex slot mention.
isConsensusFilter(SimpleInstance) - Static method in class edu.uchsc.ccp.knowtator.FilterUtil
 
isConsensusMode() - Method in class edu.uchsc.ccp.knowtator.event.FilterChangedEvent
 
isConsensusMode() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
isFastAnnotateMode() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
isFloatSlotMention(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
isGoClicked() - Method in class edu.uchsc.ccp.knowtator.wizards.IAAWizard
 
isInstanceMention(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
isIntegerSlotMention(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
isKnowtatorSupportClassesCurrent() - Method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
isKnowtatorSupportClassesCurrent(KnowledgeBase) - Static method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
isMention(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
isSimpleFeature(String) - Method in class edu.uchsc.ccp.iaa.Annotation
 
isSimpleSlotMention(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
isSlotMention(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
isSpanMatcherSelected() - Method in class edu.uchsc.ccp.knowtator.wizards.IAAWizard
 
isStringSlotMention(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
isSubclassMatcherSelected() - Method in class edu.uchsc.ccp.knowtator.wizards.IAAWizard
 
isSuitable(Project, Collection) - Static method in class edu.uchsc.ccp.knowtator.Knowtator
 
isSuitable(Cls, Slot, Facet) - Static method in class edu.uchsc.ccp.knowtator.SimpleSlotMentionValueWidget
 
isSuitable(Cls, Slot, Facet) - Static method in class edu.uchsc.ccp.knowtator.SlotMentionValueWidget
 
isTeamAnnotator(SimpleInstance) - Static method in class edu.uchsc.ccp.knowtator.util.AnnotatorUtil
 
isValid(int, int) - Static method in class edu.uchsc.ccp.iaa.Span
 
isValid(int, int) - Static method in class edu.uchsc.ccp.knowtator.Span
 
isVisible(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.ui.TextViewer
 
iterator() - Method in class edu.uchsc.ccp.knowtator.textsource.filelines.FileLinesTextSourceCollection
 
iterator() - Method in class edu.uchsc.ccp.knowtator.textsource.files.FileTextSourceCollection
 
iterator() - Method in class edu.uchsc.ccp.knowtator.textsource.TextSourceCollection
provides an easy way for a script to iterate through all TextSources in a collection.

K

Knowtator - Class in edu.uchsc.ccp.knowtator
Authors: Philip V.
Knowtator() - Constructor for class edu.uchsc.ccp.knowtator.Knowtator
 
KNOWTATOR_MANAGER - Static variable in class edu.uchsc.ccp.knowtator.Knowtator
This string is used to give a hash key for the AnnotationUtil that will be passed to the knowledge base as client information that other objects can access.
KNOWTATOR_SUPPORT_CLASSES_VERSION - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
KNOWTATOR_SUPPORT_CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
KNOWTATOR_VERSION_CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
KnowtatorIAA - Class in edu.uchsc.ccp.knowtator.stats
 
KnowtatorIAA(File, SimpleInstance, Collection<SimpleInstance>, Project, Collection<Slot>, Collection<Slot>, KnowtatorManager, TextSourceCollection, AnnotationUtil, MentionUtil, FilterUtil) - Constructor for class edu.uchsc.ccp.knowtator.stats.KnowtatorIAA
 
KnowtatorManager - Class in edu.uchsc.ccp.knowtator
 
KnowtatorManager(KnowtatorProjectUtil) - Constructor for class edu.uchsc.ccp.knowtator.KnowtatorManager
 
KnowtatorProjectUtil - Class in edu.uchsc.ccp.knowtator
 
KnowtatorProjectUtil(KnowledgeBase) - Constructor for class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
KnowtatorProjectUtil(KnowledgeBase, Component) - Constructor for class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
Creates a new instance of KnowtatorKBUtil
KnowtatorTextPane - Class in edu.uchsc.ccp.knowtator.ui
 
KnowtatorTextPane(KnowtatorManager) - Constructor for class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 
KnowtatorXMLException - Exception in edu.uchsc.ccp.knowtator.xml
 
KnowtatorXMLException() - Constructor for exception edu.uchsc.ccp.knowtator.xml.KnowtatorXMLException
Creates a new instance of InvalidSpanException
KnowtatorXMLException(String) - Constructor for exception edu.uchsc.ccp.knowtator.xml.KnowtatorXMLException
 
KnowtatorXMLException(String, Throwable) - Constructor for exception edu.uchsc.ccp.knowtator.xml.KnowtatorXMLException
 
KnowtatorXMLException(Throwable) - Constructor for exception edu.uchsc.ccp.knowtator.xml.KnowtatorXMLException
 

L

length() - Method in class edu.uchsc.ccp.iaa.Span
 
length() - Method in class edu.uchsc.ccp.knowtator.Span
 
lengthComparator() - Method in class edu.uchsc.ccp.knowtator.SpanUtil
 
lessThan(Span) - Method in class edu.uchsc.ccp.iaa.Span
 
lessThan(Span) - Method in class edu.uchsc.ccp.knowtator.Span
 

M

main(String[]) - Static method in class edu.uchsc.ccp.knowtator.Knowtator
For testing/debuging purposes only.
main(String[]) - Static method in class edu.uchsc.ccp.util.io.FileReadingUtil
 
match(Annotation, Set<Annotation>, Matcher, MatchResult) - Method in class edu.uchsc.ccp.iaa.IAA
 
match(Annotation, String, Set<Annotation>, IAA, MatchResult) - Method in class edu.uchsc.ccp.iaa.matcher.ClassAndSpanMatcher
 
match(Annotation, String, IAA, Set<Annotation>) - Static method in class edu.uchsc.ccp.iaa.matcher.ClassAndSpanMatcher
This is a static version of the above match method that can be called by other matcher implementations.
match(Annotation, String, Set<Annotation>, IAA, MatchResult) - Method in class edu.uchsc.ccp.iaa.matcher.ClassMatcher
This method will return an annotation with the same class and spans.
match(Annotation, String, IAA, Set<Annotation>) - Static method in class edu.uchsc.ccp.iaa.matcher.ClassMatcher
 
match(Annotation, String, Set<Annotation>, IAA, MatchResult) - Method in class edu.uchsc.ccp.iaa.matcher.FeatureMatcher
 
match(Annotation, String, Set<Annotation>, IAA, MatchResult) - Method in interface edu.uchsc.ccp.iaa.matcher.Matcher
 
match(Annotation, String, Set<Annotation>, IAA, MatchResult) - Method in class edu.uchsc.ccp.iaa.matcher.OverlappingSpanMatcher
 
match(Annotation, String, Set<Annotation>, IAA, MatchResult) - Method in class edu.uchsc.ccp.iaa.matcher.SpanMatcher
This method will return an annotation with the same class and spans.
match(Annotation, String, Set<Annotation>, IAA, MatchResult) - Method in class edu.uchsc.ccp.iaa.matcher.SpansExactComplexFeatureMatcher
This method will return an annotation that has the exact same spans and complex features.
match(Annotation, String, IAA, Set<Annotation>, MatchResult) - Static method in class edu.uchsc.ccp.iaa.matcher.SpansExactComplexFeatureMatcher
This method will return an annotation that has the exact same spans and simple features.
match(Annotation, String, Set<Annotation>, IAA, MatchResult) - Method in class edu.uchsc.ccp.iaa.matcher.SpansExactSimpleFeatureMatcher
This method will return an annotation that has the exact same spans and simple features.
match(Annotation, String, IAA, Set<Annotation>, MatchResult) - Static method in class edu.uchsc.ccp.iaa.matcher.SpansExactSimpleFeatureMatcher
This method will return an annotation that has the exact same spans and simple features.
match(Annotation, String, Set<Annotation>, IAA, MatchResult) - Method in class edu.uchsc.ccp.iaa.matcher.SpansOverlapSimpleFeatureMatcher
This method will return an annotation that has overlapping spans and the same simple features.
match(Annotation, String, Set<Annotation>, IAA, MatchResult) - Method in class edu.uchsc.ccp.iaa.matcher.SubclassMatcher
This method will return a match from ClassMatcher.
MATCH_RESULT_UNASSIGNED - Static variable in class edu.uchsc.ccp.iaa.matcher.MatchResult
 
Matcher - Interface in edu.uchsc.ccp.iaa.matcher
 
matches(Annotation, String, IAA, Set<Annotation>, boolean) - Static method in class edu.uchsc.ccp.iaa.matcher.ClassAndSpanMatcher
 
matches(Annotation, String, IAA, Set<Annotation>) - Static method in class edu.uchsc.ccp.iaa.matcher.ClassMatcher
 
MatchResult - Class in edu.uchsc.ccp.iaa.matcher
 
MatchResult() - Constructor for class edu.uchsc.ccp.iaa.matcher.MatchResult
 
MENTION_ANNOTATION_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
MENTION_CLASS_ELEMENT_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
The name of the element that represents the mentioned class of a class mention.
MENTION_CLASS_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
MENTION_CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
MENTION_ELEMENT_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
 
MENTION_INSTANCE_ELEMENT_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
The name of the element that represents the mentioned instance of an instance mention.
MENTION_INSTANCE_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
MENTION_SLOT_ELEMENT_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
The name of the element that represents the mentioned slot of a slot mention.
MENTION_SLOT_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
MENTION_SLOT_VALUE_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
MentionDisplay - Class in edu.uchsc.ccp.knowtator.ui
 
MentionDisplay(KnowtatorManager, Project) - Constructor for class edu.uchsc.ccp.knowtator.ui.MentionDisplay
 
MentionDisplay(MentionUtil, AnnotationUtil, Project) - Constructor for class edu.uchsc.ccp.knowtator.ui.MentionDisplay
 
MENTIONED_IN_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
MentionUtil - Class in edu.uchsc.ccp.knowtator
 
MentionUtil(KnowtatorProjectUtil) - Constructor for class edu.uchsc.ccp.knowtator.MentionUtil
Creates a new instance of MentionUtil
merge(Span, Span) - Static method in class edu.uchsc.ccp.knowtator.Span
This method takes two spans that intersect and returns a Span that "merges" the two spans.
MergeAnnotations - Class in edu.uchsc.ccp.knowtator.util
 
MergeAnnotations(Project, Project, TextSourceUtil, Component) - Constructor for class edu.uchsc.ccp.knowtator.util.MergeAnnotations
This class facilitates the merging of an annotation project with a 'master' annotation project.
mergeAnnotations(SimpleInstance, Collection<SimpleInstance>) - Method in class edu.uchsc.ccp.knowtator.util.MergeAnnotations
 
mergeAnnotations(Component, Project, TextSourceUtil) - Static method in class edu.uchsc.ccp.knowtator.util.MergeAnnotations
 
ModalDialog - Class in edu.uchsc.ccp.knowtator.ui
This code was copied directly from the Protege source code from edu.stanford.smi.protege.util.ModalDialog I copied the code so that I could modify it so that I could move the location of the where the dialog appears.
ModalDialog.CloseCallback - Interface in edu.uchsc.ccp.knowtator.ui
 
MODE_CLOSE - Static variable in class edu.uchsc.ccp.knowtator.ui.ModalDialog
 
MODE_OK_CANCEL - Static variable in class edu.uchsc.ccp.knowtator.ui.ModalDialog
 
MODE_YES_NO - Static variable in class edu.uchsc.ccp.knowtator.ui.ModalDialog
 
MODE_YES_NO_CANCEL - Static variable in class edu.uchsc.ccp.knowtator.ui.ModalDialog
 
mouseDragged(MouseEvent) - Method in class edu.uchsc.ccp.knowtator.ui.AnnotationPicker
 
mouseMoved(MouseEvent) - Method in class edu.uchsc.ccp.knowtator.ui.AnnotationPicker
 

N

name - Variable in class edu.uchsc.ccp.knowtator.textsource.DefaultTextSource
 
NAME_INSTRUCTIONS - Static variable in class edu.uchsc.ccp.knowtator.wizards.CreateConsensusSetWizard
 
namesToTextSource - Variable in class edu.uchsc.ccp.knowtator.textsource.filelines.FileLinesTextSourceCollection
 
next() - Method in interface edu.uchsc.ccp.knowtator.textsource.TextSourceIterator
 
NEXT - Static variable in class edu.uchsc.ccp.knowtator.wizards.WizardFrame
 
NO_LINES - Static variable in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 
NONCONSENSUS_FILTER - Static variable in class edu.uchsc.ccp.knowtator.FilterUtil
 
NONTRIVIAL_MATCH - Static variable in class edu.uchsc.ccp.iaa.matcher.MatchResult
 
NONTRIVIAL_NONMATCH - Static variable in class edu.uchsc.ccp.iaa.matcher.MatchResult
 
notifyTextChanged(String) - Method in interface edu.uchsc.ccp.knowtator.event.NotifyTextChangeListener
 
notifyTextChanged(String) - Method in class edu.uchsc.ccp.knowtator.Knowtator
 
NotifyTextChangeListener - Interface in edu.uchsc.ccp.knowtator.event
 

O

onDoubleClick(Object) - Method in class edu.uchsc.ccp.knowtator.ComplexSlotMentionValueWidget
 
open(Project) - Static method in class edu.uchsc.ccp.knowtator.textsource.filelines.FileLinesTextSourceCollection
 
open(Project, Component) - Static method in class edu.uchsc.ccp.knowtator.textsource.filelines.FileLinesTextSourceCollection
 
open(Project) - Static method in class edu.uchsc.ccp.knowtator.textsource.files.FileTextSourceCollection
 
open(Project, Component) - Static method in class edu.uchsc.ccp.knowtator.textsource.files.FileTextSourceCollection
 
open(Project, Component) - Static method in class edu.uchsc.ccp.knowtator.textsource.generif.GeneRIFTextSourceCollection
 
open(Project) - Static method in class edu.uchsc.ccp.knowtator.textsource.generif.GeneRIFTextSourceCollection
 
open(Project) - Static method in class edu.uchsc.ccp.knowtator.textsource.TextSourceCollection
This method should return the text source collection most recently opened by the provided project.
open(Project, Component) - Static method in class edu.uchsc.ccp.knowtator.textsource.TextSourceCollection
 
openProject(String) - Static method in class edu.uchsc.ccp.knowtator.util.ProjectUtil
 
OPTION_CANCEL - Static variable in class edu.uchsc.ccp.knowtator.ui.ModalDialog
 
OPTION_CLOSE - Static variable in class edu.uchsc.ccp.knowtator.ui.ModalDialog
 
OPTION_NO - Static variable in class edu.uchsc.ccp.knowtator.ui.ModalDialog
 
OPTION_OK - Static variable in class edu.uchsc.ccp.knowtator.ui.ModalDialog
 
OPTION_YES - Static variable in class edu.uchsc.ccp.knowtator.ui.ModalDialog
 
OverlappingSpanMatcher - Class in edu.uchsc.ccp.iaa.matcher
 
OverlappingSpanMatcher() - Constructor for class edu.uchsc.ccp.iaa.matcher.OverlappingSpanMatcher
 
ownSlotValueChanged(FrameEvent) - Method in class edu.uchsc.ccp.knowtator.util.ConsensusSet.ConsensusFrameAdapter
 

P

pairwiseIAA(Class) - Method in class edu.uchsc.ccp.iaa.IAA
This method performs pairwise IAA for each combination of annotators.
pairwiseIAA(Matcher) - Method in class edu.uchsc.ccp.iaa.IAA
 
parseSpan(String) - Static method in class edu.uchsc.ccp.iaa.Span
 
parseSpan(String) - Static method in class edu.uchsc.ccp.knowtator.Span
 
pickAnnotationsFromCollection(Component, KnowtatorManager, List<SimpleInstance>, String) - Static method in class edu.uchsc.ccp.knowtator.ui.AnnotationPicker
 
pickAnnotationsFromCollection(Component, KnowtatorManager, List<SimpleInstance>, String, boolean) - Static method in class edu.uchsc.ccp.knowtator.ui.AnnotationPicker
 
PMID_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.textsource.generif.GeneRIFTextSource
 
PREVIOUS - Static variable in class edu.uchsc.ccp.knowtator.wizards.WizardFrame
 
printIAA(IAA, Matcher, File, int, Map<Annotation, String>, Map<Annotation, String>) - Static method in class edu.uchsc.ccp.iaa.html.IAA2HTML
 
printIAA(IAA, Matcher, File, int, Map<Annotation, String>, Map<Annotation, String>) - Static method in class edu.uchsc.ccp.iaa.html.SpanMatcherHTML
 
printIAA(IAA, SubclassMatcher, File, int, Map<Annotation, String>, Map<Annotation, String>) - Static method in class edu.uchsc.ccp.iaa.html.SubclassMatcherHTML
 
printInstances(PrintStream, Map<String, Set<Annotation>>, List<String>, Map<Annotation, String>, Map<Annotation, String>, Map<Annotation, Set<Annotation>>) - Static method in class edu.uchsc.ccp.iaa.html.IAA2HTML
 
printMatchData(PrintStream, Set<String>, String, File, Map<String, Set<Annotation>>, Map<Annotation, String>, Map<Annotation, String>, Set<String>, IAA) - Static method in class edu.uchsc.ccp.iaa.html.IAA2HTML
 
printNonmatchData(PrintStream, Set<String>, String, File, Map<String, Set<Annotation>>, AnnotationSpanIndex, Map<Annotation, String>, Map<Annotation, String>, Set<String>, IAA) - Static method in class edu.uchsc.ccp.iaa.html.IAA2HTML
 
printPairwiseAgreement(PrintStream, Set<String>, Map<String, Map<String, Set<Annotation>>>, Map<String, Map<String, Set<Annotation>>>, NumberFormat) - Static method in class edu.uchsc.ccp.iaa.html.IAA2HTML
 
PROJECT_RECENT_TSC - Static variable in class edu.uchsc.ccp.knowtator.ProjectSettings
Records the most recent type of TextSourceCollection (tsc) used by this project.
PROJECT_RECENT_TSC_INDEX - Static variable in class edu.uchsc.ccp.knowtator.ProjectSettings
 
PROJECT_SETTING_RECENT_CHARSET - Static variable in class edu.uchsc.ccp.knowtator.textsource.files.FileTextSourceCollection
 
PROJECT_SETTING_RECENT_DIRECTORY - Static variable in class edu.uchsc.ccp.knowtator.textsource.files.FileTextSourceCollection
 
PROJECT_SETTING_RECENT_FILE - Static variable in class edu.uchsc.ccp.knowtator.textsource.filelines.FileLinesTextSourceCollection
 
PROJECT_SETTING_RECENT_FILE - Static variable in class edu.uchsc.ccp.knowtator.textsource.generif.GeneRIFTextSourceCollection
 
ProjectSettings - Class in edu.uchsc.ccp.knowtator
 
ProjectSettings() - Constructor for class edu.uchsc.ccp.knowtator.ProjectSettings
 
ProjectUtil - Class in edu.uchsc.ccp.knowtator.util
 
ProjectUtil() - Constructor for class edu.uchsc.ccp.knowtator.util.ProjectUtil
 
PROPOGATE_TRIVIAL_MATCH_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
protegeClsName - Variable in class edu.uchsc.ccp.knowtator.textsource.DefaultTextSource
 
ProtegeUtil - Class in edu.uchsc.ccp.knowtator.util
 
ProtegeUtil() - Constructor for class edu.uchsc.ccp.knowtator.util.ProtegeUtil
 

Q

quitFastAnnotate() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 

R

readFile(InputStream, Charset) - Static method in class edu.uchsc.ccp.knowtator.textsource.files.FileTextSource
 
readFileLines(String) - Static method in class edu.uchsc.ccp.util.io.FileReadingUtil
Reads in a text file and returns it as an array of Strings.
readFileLines(String, String) - Static method in class edu.uchsc.ccp.util.io.FileReadingUtil
 
readFileLines(InputStream) - Static method in class edu.uchsc.ccp.util.io.FileReadingUtil
 
readFileLines(InputStream, String) - Static method in class edu.uchsc.ccp.util.io.FileReadingUtil
 
readFromXML(Component, KnowledgeBase, KnowtatorProjectUtil, TextSourceUtil, AnnotationUtil, MentionUtil, FilterUtil, Project) - Static method in class edu.uchsc.ccp.knowtator.xml.XMLImport
 
readFromXML(File, KnowledgeBase, KnowtatorProjectUtil, AnnotationUtil, FilterUtil, MentionUtil, TextSourceUtil) - Static method in class edu.uchsc.ccp.knowtator.xml.XMLImport
 
recreateConsensusAnnotations(SimpleInstance, SimpleInstance, KnowtatorManager) - Static method in class edu.uchsc.ccp.knowtator.util.ConsensusAnnotations
 
refreshAnnotationsDisplay(boolean) - Method in interface edu.uchsc.ccp.knowtator.event.RefreshAnnotationsDisplayListener
 
refreshAnnotationsDisplay(boolean) - Method in class edu.uchsc.ccp.knowtator.Knowtator
 
refreshAnnotationsDisplay(boolean) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
refreshAnnotationsDisplay(boolean) - Method in class edu.uchsc.ccp.knowtator.ui.AnnotationSchemaInstancesList
 
refreshAnnotationsDisplay(boolean) - Method in class edu.uchsc.ccp.knowtator.ui.AnnotationSchemaTree
 
refreshAnnotationsDisplay(boolean) - Method in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 
RefreshAnnotationsDisplayListener - Interface in edu.uchsc.ccp.knowtator.event
 
REMOVE_SLOT_MATCHER_CLICKED - Static variable in class edu.uchsc.ccp.knowtator.wizards.IAAWizard
 
removeAnnotationCreatedListener(AnnotationCreatedListener) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
removeCurrentAnnotationsChangedListener(CurrentAnnotationsChangedListener) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
removeEmptySlotMentions(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
removeFastAnnotateFrame(Frame) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
Removes the given frame (class) from the fast annotate tool bar.
removeFastAnnotateListener(FastAnnotateListener) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
removeFilterChangedListener(FilterChangedListener) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
removeInverse(SimpleInstance, Slot, SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
This method was written and contributed by Angus Roberts.
removeNotifyTextChangeListner(NotifyTextChangeListener) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
removeRefreshSpanHighlightsListener(RefreshAnnotationsDisplayListener) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
removeSelectedAnnotationChangeListener(SelectedAnnotationChangeListener) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
removeSelectedClsChangeListener(SelectedClsChangeListener) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
removeSelectedSpanChangeListener(SelectedSpanChangeListener) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
removeSpanEditListner(SpanEditListener) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
removeTextSourceChangeListener(TextSourceChangeListener) - Method in class edu.uchsc.ccp.knowtator.TextSourceUtil
 
removeTextSourceCollectionChangeListener(TextSourceCollectionChangeListener) - Method in class edu.uchsc.ccp.knowtator.TextSourceUtil
 
removeValueFromSlotMention(SimpleInstance, Object) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
repaint() - Method in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 
reset() - Method in class edu.uchsc.ccp.iaa.IAA
 
resetProtegeTitle(Project) - Static method in class edu.uchsc.ccp.knowtator.Knowtator
This code was copied and modified from ProjectManager.updateUI()
restartConsensusMode() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
RESULT_ERROR - Static variable in class edu.uchsc.ccp.knowtator.ui.ModalDialog
 
retrieveAllAnnotations() - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
returnsTrivials() - Method in class edu.uchsc.ccp.iaa.matcher.ClassAndSpanMatcher
 
returnsTrivials() - Method in class edu.uchsc.ccp.iaa.matcher.ClassMatcher
 
returnsTrivials() - Method in class edu.uchsc.ccp.iaa.matcher.FeatureMatcher
 
returnsTrivials() - Method in interface edu.uchsc.ccp.iaa.matcher.Matcher
 
returnsTrivials() - Method in class edu.uchsc.ccp.iaa.matcher.OverlappingSpanMatcher
 
returnsTrivials() - Method in class edu.uchsc.ccp.iaa.matcher.SpanMatcher
 
returnsTrivials() - Method in class edu.uchsc.ccp.iaa.matcher.SpansExactComplexFeatureMatcher
 
returnsTrivials() - Method in class edu.uchsc.ccp.iaa.matcher.SpansExactSimpleFeatureMatcher
 
returnsTrivials() - Method in class edu.uchsc.ccp.iaa.matcher.SpansOverlapSimpleFeatureMatcher
 
returnsTrivials() - Method in class edu.uchsc.ccp.iaa.matcher.SubclassMatcher
 
ROOT_CLSES_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
runClassAndSpanIAA() - Method in class edu.uchsc.ccp.knowtator.stats.KnowtatorIAA
 
runClassIAA() - Method in class edu.uchsc.ccp.knowtator.stats.KnowtatorIAA
 
runFeatureMatcherIAA(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.stats.KnowtatorIAA
 
runFeatureMatcherIAA(SimpleInstance, String) - Method in class edu.uchsc.ccp.knowtator.stats.KnowtatorIAA
 
runSpanIAA() - Method in class edu.uchsc.ccp.knowtator.stats.KnowtatorIAA
 
runSubclassIAA() - Method in class edu.uchsc.ccp.knowtator.stats.KnowtatorIAA
 

S

save(Project) - Method in class edu.uchsc.ccp.knowtator.textsource.filelines.FileLinesTextSourceCollection
 
save(Project) - Method in class edu.uchsc.ccp.knowtator.textsource.files.FileTextSourceCollection
contribution from Angus Roberts saves a relative path if the directory is under the protege project directory
save(Project) - Method in class edu.uchsc.ccp.knowtator.textsource.generif.GeneRIFTextSourceCollection
 
save(Project) - Method in class edu.uchsc.ccp.knowtator.textsource.TextSourceCollection
This method saves information about this text source collection to the Protege project.
saveProject(Project) - Static method in class edu.uchsc.ccp.knowtator.util.ProjectUtil
 
saveProjectAs(Project, File) - Static method in class edu.uchsc.ccp.knowtator.util.ProjectUtil
 
saveProjectAs(Project, File, File) - Static method in class edu.uchsc.ccp.knowtator.util.ProjectUtil
This method provides a programmatic way to safely save a Knowtator project with a different name.
select(Component) - Method in class edu.uchsc.ccp.knowtator.textsource.filelines.FileLinesTextSourceCollection
 
select(Component) - Method in class edu.uchsc.ccp.knowtator.textsource.files.FileTextSourceCollection
 
select(Component) - Method in class edu.uchsc.ccp.knowtator.textsource.TextSourceCollection
 
select(int) - Method in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 
select(int, int) - Method in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 
select(Span) - Method in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 
select(Span, boolean) - Method in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 
select(Collection<Span>) - Method in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 
SELECT_FILTER - Static variable in class edu.uchsc.ccp.knowtator.Knowtator
 
SELECT_NEXT_ANNOTATION - Static variable in class edu.uchsc.ccp.knowtator.Knowtator
 
SELECT_NEXT_ANNOTATION_FILTER - Static variable in class edu.uchsc.ccp.knowtator.Knowtator
 
SELECT_PREVIOUS_ANNOTATION - Static variable in class edu.uchsc.ccp.knowtator.Knowtator
 
SELECT_PREVIOUS_ANNOTATION_FILTER - Static variable in class edu.uchsc.ccp.knowtator.Knowtator
 
SELECTED_ANNOTATION_SET_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
SELECTED_ANNOTATOR_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
SELECTED_FILTER_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
SELECTED_FILTERS_CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
SELECTED_FILTERS_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
SelectedAnnotationChangeEvent - Class in edu.uchsc.ccp.knowtator.event
 
SelectedAnnotationChangeEvent(Object, SimpleInstance) - Constructor for class edu.uchsc.ccp.knowtator.event.SelectedAnnotationChangeEvent
 
SelectedAnnotationChangeListener - Interface in edu.uchsc.ccp.knowtator.event
 
SelectedClsChangeEvent - Class in edu.uchsc.ccp.knowtator.event
 
SelectedClsChangeEvent(Object, Cls) - Constructor for class edu.uchsc.ccp.knowtator.event.SelectedClsChangeEvent
 
SelectedClsChangeListener - Interface in edu.uchsc.ccp.knowtator.event
 
SelectedSpanChangeEvent - Class in edu.uchsc.ccp.knowtator.event
 
SelectedSpanChangeEvent(Object, List<Span>) - Constructor for class edu.uchsc.ccp.knowtator.event.SelectedSpanChangeEvent
 
SelectedSpanChangeListener - Interface in edu.uchsc.ccp.knowtator.event
 
selectFilterInstance() - Method in class edu.uchsc.ccp.knowtator.Knowtator
 
SELECTION_ITEMS_COUNT_THRESHOLD - Static variable in class edu.uchsc.ccp.knowtator.ui.AnnotationSchemaMenuItemFactory
 
selectionChanged(SelectionEvent) - Method in class edu.uchsc.ccp.knowtator.ui.AnnotationSchemaTree
 
selectNextAnnotation() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
The "next" annotation is defined as the annotation (if it exists) that is of the same type as the currently selected annotation that is 'next' according to the sort order defined by the currently selected comparator.
selectNextFilter(int) - Method in class edu.uchsc.ccp.knowtator.FilterUtil
 
selectPreviousAnnotation() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
The "previous" annotation is defined as the annotation (if it exists) that is of the same type as the currently selected annotation that is 'next' according to the sort order defined by the currently selected comparator.
selectPreviousFilter(int) - Method in class edu.uchsc.ccp.knowtator.FilterUtil
 
selectTextSourceCollection(Component) - Method in class edu.uchsc.ccp.knowtator.TextSourceUtil
 
SET_CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
SET_DESCRIPTION_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
SET_NAME_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
SET_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
setActiveConfiguration(Project, SimpleInstance) - Static method in class edu.uchsc.ccp.knowtator.ProjectSettings
 
setActiveFilters(Collection<SimpleInstance>) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
setAnnotationClass(String) - Method in class edu.uchsc.ccp.iaa.Annotation
 
setAnnotationComparator(Comparator<SimpleInstance>) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
setAnnotations(Set<Annotation>) - Method in class edu.uchsc.ccp.iaa.IAA
 
setAnnotationUtil(AnnotationUtil) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
setAnnotationUtil(AnnotationUtil) - Method in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 
setAnnotator(SimpleInstance, SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
setComment(SimpleInstance, String) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
setComplexFeature(String, Set<Annotation>) - Method in class edu.uchsc.ccp.iaa.Annotation
 
setComplexFeature(String, Annotation) - Method in class edu.uchsc.ccp.iaa.Annotation
 
setCreationDate(SimpleInstance, String) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
setCurrentTextSource(TextSource) - Method in class edu.uchsc.ccp.knowtator.TextSourceUtil
 
setCurrentTextSourceCollection(TextSourceCollection) - Method in class edu.uchsc.ccp.knowtator.TextSourceUtil
 
setDisplayColors(DisplayColors) - Method in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 
setDocID(String) - Method in class edu.uchsc.ccp.iaa.Annotation
 
setEditable(boolean) - Method in class edu.uchsc.ccp.knowtator.SlotMentionValueWidget
 
setFastAnnotateFrame(Frame) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
setIAAClass(String) - Method in class edu.uchsc.ccp.iaa.matcher.SubclassMatcher
Sets the class of the
setInstance(Instance) - Method in class edu.uchsc.ccp.knowtator.ComplexSlotMentionValueWidget
 
setKnowtatorManager(KnowtatorManager) - Method in class edu.uchsc.ccp.knowtator.event.EventHandler
 
setMatchClasses(boolean) - Method in class edu.uchsc.ccp.iaa.matcher.FeatureMatcher
 
setMatcherInfo(String, Object) - Method in class edu.uchsc.ccp.iaa.IAA
 
setMatchSpans(int) - Method in class edu.uchsc.ccp.iaa.matcher.FeatureMatcher
 
setMention(SimpleInstance, SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
setMentionAnnotations(SimpleInstance, Collection<SimpleInstance>) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
setMentionCls(SimpleInstance, Cls) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
This method sets the cls that is mentioned by a class mention.
setMentionInstance(SimpleInstance, SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
This method sets the instance that is mentioned by an instance mention.
setMentionSlot(SimpleInstance, Slot) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
This method sets the slot that is mentioned by a slot mention.
setMentionUtil(MentionUtil) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
setNotifyText(String) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
setProjectAnnotationSet(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
setProjectAnnotator(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
setRecentTextSourceCollection(Project, TextSourceCollection) - Static method in class edu.uchsc.ccp.knowtator.ProjectSettings
 
setRecentTextSourceCollectionIndex(Project, int) - Static method in class edu.uchsc.ccp.knowtator.ProjectSettings
 
setResult(int) - Method in class edu.uchsc.ccp.iaa.matcher.MatchResult
 
setScrollPane(JScrollPane) - Method in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 
setSelectedAnnotation(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
This is the preferred way to set the curently selected annotation.
setSelectedAnnotationSet(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
setSelectedAnnotator(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
setSelectedCls(Cls) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
This is the preferred way to set the curently selected cls (i.e.
setSelectedFilter(SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
setSelectedIndices(int[]) - Method in class edu.uchsc.ccp.knowtator.SpanWidget
 
setSelectedSpanIndices(int[]) - Method in class edu.uchsc.ccp.knowtator.ui.AnnotationInstanceDisplay
 
setSelectedSpans(List<Span>) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
This is the preferred way to set the currently selected spans.
setSet(SimpleInstance, SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
setSetName(String) - Method in class edu.uchsc.ccp.iaa.Annotation
 
setSets(SimpleInstance, Collection<SimpleInstance>) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
setShowInstances(Project, boolean) - Static method in class edu.uchsc.ccp.knowtator.ProjectSettings
 
setSimpleFeature(String, Set<Object>) - Method in class edu.uchsc.ccp.iaa.Annotation
 
setSimpleFeature(String, Object) - Method in class edu.uchsc.ccp.iaa.Annotation
 
setSlotMentionValues(SimpleInstance, List<Object>) - Method in class edu.uchsc.ccp.knowtator.MentionUtil
 
setSpan(Span) - Method in class edu.uchsc.ccp.iaa.Annotation
 
setSpans(List<Span>) - Method in class edu.uchsc.ccp.iaa.Annotation
 
setSpans(SimpleInstance, List<Span>, String) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
Sets the spans slot for an annotation instance.
setText(SimpleInstance, String) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
setText(String) - Method in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 
setTextPane(KnowtatorTextPane) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
setTextSource(SimpleInstance, SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
setTextSourceAnnotationComment(Instance, String) - Method in class edu.uchsc.ccp.knowtator.TextSourceUtil
 
setTextSourceAnnotationComment(TextSource, String) - Method in class edu.uchsc.ccp.knowtator.TextSourceUtil
 
setTextSourceDisplayText(String) - Method in class edu.uchsc.ccp.knowtator.ui.TextViewer
 
setTextSourceUtil(TextSourceUtil) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
setTextViewer(TextViewer) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
setup(Component, Object, boolean, boolean) - Method in class edu.uchsc.ccp.knowtator.ui.ColorFrameRenderer
 
setValues(Collection) - Method in class edu.uchsc.ccp.knowtator.ComplexSlotMentionValueWidget
 
setValues(Collection) - Method in class edu.uchsc.ccp.knowtator.SimpleSlotMentionValueWidget
 
setValues(Collection) - Method in class edu.uchsc.ccp.knowtator.SlotMentionValueWidget
 
setValues(Collection) - Method in class edu.uchsc.ccp.knowtator.SlotMentionWidget
 
setVisible(boolean) - Method in class edu.uchsc.ccp.knowtator.wizards.CreateConsensusSetWizard
 
setVisible(boolean) - Method in class edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog
 
setVisible(boolean) - Method in class edu.uchsc.ccp.knowtator.wizards.IAAWizard
 
shortest(List<Span>) - Static method in class edu.uchsc.ccp.iaa.Span
 
shortest(List<Span>) - Static method in class edu.uchsc.ccp.knowtator.Span
 
SHOW_INSTANCES - Static variable in class edu.uchsc.ccp.knowtator.ProjectSettings
 
showAllHighlights() - Method in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 
showAnnotationHighlights() - Method in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 
showDialog(Component, Component, String, int, Point) - Static method in class edu.uchsc.ccp.knowtator.ui.ModalDialog
 
showDialog(Component, Component, String, int, ModalDialog.CloseCallback, Point) - Static method in class edu.uchsc.ccp.knowtator.ui.ModalDialog
 
showDialog(Component, Component, String, int, ModalDialog.CloseCallback, boolean, Point) - Static method in class edu.uchsc.ccp.knowtator.ui.ModalDialog
 
showFrame(WizardFrame) - Method in class edu.uchsc.ccp.knowtator.wizards.CreateConsensusSetWizard
 
showFrame(WizardFrame) - Method in class edu.uchsc.ccp.knowtator.wizards.IAAWizard
 
showMessageDialog(Component, String, Point) - Static method in class edu.uchsc.ccp.knowtator.ui.ModalDialog
 
showMessageDialog(Component, String, String, Point) - Static method in class edu.uchsc.ccp.knowtator.ui.ModalDialog
 
showMessageDialog(Component, String, int, Point) - Static method in class edu.uchsc.ccp.knowtator.ui.ModalDialog
 
showMessageDialog(Component, String, String, int, Point) - Static method in class edu.uchsc.ccp.knowtator.ui.ModalDialog
 
showSelectionHighlights() - Method in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 
SHRINK_ANNOTATION_LEFT - Static variable in class edu.uchsc.ccp.knowtator.SpanUtil
 
SHRINK_ANNOTATION_LEFT_WORD - Static variable in class edu.uchsc.ccp.knowtator.SpanUtil
 
SHRINK_ANNOTATION_RIGHT - Static variable in class edu.uchsc.ccp.knowtator.SpanUtil
 
SHRINK_ANNOTATION_RIGHT_WORD - Static variable in class edu.uchsc.ccp.knowtator.SpanUtil
 
shrinkLeft(String, Span, Pattern) - Static method in class edu.uchsc.ccp.knowtator.SpanUtil
 
shrinkRight(String, Span, Pattern) - Static method in class edu.uchsc.ccp.knowtator.SpanUtil
 
SIMPLE_SLOT_MATCH_CRITERIA_CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
SimpleSlotMentionValueWidget - Class in edu.uchsc.ccp.knowtator
This class will hopefully replace SlotMentionValueWidget if I can ever get it to work the way I want it to.
SimpleSlotMentionValueWidget() - Constructor for class edu.uchsc.ccp.knowtator.SimpleSlotMentionValueWidget
 
size() - Method in class edu.uchsc.ccp.knowtator.textsource.filelines.FileLinesTextSourceCollection
 
size() - Method in class edu.uchsc.ccp.knowtator.textsource.files.FileTextSourceCollection
 
size() - Method in class edu.uchsc.ccp.knowtator.textsource.TextSourceCollection
 
SLOT_MATCH_CRITERIA_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
SLOT_MATCHER_CONFIG_CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
SLOT_MATCHER_SIMPLE_SLOTS_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
SLOT_MATCHER_SLOT_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
SLOT_MENTION_CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
SLOT_MENTION_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
SlotMentionValueWidget - Class in edu.uchsc.ccp.knowtator
 
SlotMentionValueWidget() - Constructor for class edu.uchsc.ccp.knowtator.SlotMentionValueWidget
 
SlotMentionWidget - Class in edu.uchsc.ccp.knowtator
This class is a simple extension of the ContainsWidget that simply overrides the setValues method so that the slot mentions of a class mention or instance mention will always be in a predictable order - rather than a random order(!) The order of the slots is currently alphabetical by the slot name.
SlotMentionWidget() - Constructor for class edu.uchsc.ccp.knowtator.SlotMentionWidget
 
SlotMentionWidget.SlotMentionComparator - Class in edu.uchsc.ccp.knowtator
 
SlotMentionWidget.SlotMentionComparator() - Constructor for class edu.uchsc.ccp.knowtator.SlotMentionWidget.SlotMentionComparator
 
SOLID_LINES - Static variable in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 
sortByType(Set<String>, Collection<Annotation>) - Static method in class edu.uchsc.ccp.iaa.html.IAA2HTML
 
Span - Class in edu.uchsc.ccp.iaa
 
Span(int, int) - Constructor for class edu.uchsc.ccp.iaa.Span
 
Span - Class in edu.uchsc.ccp.knowtator
 
Span(int, int) - Constructor for class edu.uchsc.ccp.knowtator.Span
 
SPAN_ELEMENT_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
 
SPAN_END_ATTRIBUTE_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
 
SPAN_MATCH_CRITERIA_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
SPAN_START_ATTRIBUTE_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
 
SpanEditEvent - Class in edu.uchsc.ccp.knowtator.event
 
SpanEditEvent(Object, SimpleInstance) - Constructor for class edu.uchsc.ccp.knowtator.event.SpanEditEvent
 
SpanEditListener - Interface in edu.uchsc.ccp.knowtator.event
 
SpanEditPanel - Class in edu.uchsc.ccp.knowtator.ui
 
SpanEditPanel(KnowtatorManager, AnnotationInstanceDisplay) - Constructor for class edu.uchsc.ccp.knowtator.ui.SpanEditPanel
 
spanEditted(SpanEditEvent) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
spanEditted(SpanEditEvent) - Method in interface edu.uchsc.ccp.knowtator.event.SpanEditListener
To get the currently selected spans at any time call KnowtatorProjectUtil.getSelectedSpans()
SpanMatcher - Class in edu.uchsc.ccp.iaa.matcher
 
SpanMatcher() - Constructor for class edu.uchsc.ccp.iaa.matcher.SpanMatcher
 
SpanMatcherHTML - Class in edu.uchsc.ccp.iaa.html
 
SpanMatcherHTML() - Constructor for class edu.uchsc.ccp.iaa.html.SpanMatcherHTML
 
SPANNED_TEXT_ELEMENT_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
 
SPANS_EXACT_COMPARISON - Static variable in class edu.uchsc.ccp.iaa.Annotation
 
SPANS_OVERLAP_COMPARISON - Static variable in class edu.uchsc.ccp.iaa.Annotation
 
spanSelectionChanged(SelectedSpanChangeEvent) - Method in interface edu.uchsc.ccp.knowtator.event.SelectedSpanChangeListener
To get the currently selected spans at any time call KnowtatorProjectUtil.getSelectedSpans()
spanSelectionChanged(SelectedSpanChangeEvent) - Method in class edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog
 
SpansExactComplexFeatureMatcher - Class in edu.uchsc.ccp.iaa.matcher
 
SpansExactComplexFeatureMatcher() - Constructor for class edu.uchsc.ccp.iaa.matcher.SpansExactComplexFeatureMatcher
 
SpansExactSimpleFeatureMatcher - Class in edu.uchsc.ccp.iaa.matcher
 
SpansExactSimpleFeatureMatcher() - Constructor for class edu.uchsc.ccp.iaa.matcher.SpansExactSimpleFeatureMatcher
 
spansLength(List<Span>) - Method in class edu.uchsc.ccp.knowtator.SpanUtil
 
spansMatch(Annotation, Annotation) - Static method in class edu.uchsc.ccp.iaa.Annotation
 
spansMatch(List<Annotation>) - Static method in class edu.uchsc.ccp.iaa.Annotation
 
spansMatch(List<Span>, List<Span>) - Static method in class edu.uchsc.ccp.iaa.Span
This method assumes that the both lists of spans are sorted the same way and that a span in one list at the same index as a span in the other list should be the same.
spansMatch(List<Span>, List<Span>) - Static method in class edu.uchsc.ccp.knowtator.Span
 
spansOverlap(Annotation, Annotation) - Static method in class edu.uchsc.ccp.iaa.Annotation
 
spansOverlap(SimpleInstance, SimpleInstance) - Method in class edu.uchsc.ccp.knowtator.AnnotationUtil
 
SpansOverlapSimpleFeatureMatcher - Class in edu.uchsc.ccp.iaa.matcher
 
SpansOverlapSimpleFeatureMatcher() - Constructor for class edu.uchsc.ccp.iaa.matcher.SpansOverlapSimpleFeatureMatcher
 
SpanUtil - Class in edu.uchsc.ccp.knowtator
 
SpanUtil(KnowtatorManager) - Constructor for class edu.uchsc.ccp.knowtator.SpanUtil
Creates a new instance of SpanUtil
SpanWidget - Class in edu.uchsc.ccp.knowtator
 
SpanWidget() - Constructor for class edu.uchsc.ccp.knowtator.SpanWidget
 
startFastAnnotate() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
startFastAnnotate(Frame) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
This method allows you to start fast annotation mode and set the fast annotation class in one convenient method.
STRING_SLOT_MENTION_CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
STRING_SLOT_MENTION_ELEMENT_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
 
STRING_SLOT_MENTION_VALUE_ELEMENT_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
 
SubclassMatcher - Class in edu.uchsc.ccp.iaa.matcher
This matcher is very similar to ClassMatcher.
SubclassMatcher(ClassHierarchy) - Constructor for class edu.uchsc.ccp.iaa.matcher.SubclassMatcher
 
SubclassMatcherHTML - Class in edu.uchsc.ccp.iaa.html
 
SubclassMatcherHTML() - Constructor for class edu.uchsc.ccp.iaa.html.SubclassMatcherHTML
 
substring(String, Span) - Static method in class edu.uchsc.ccp.iaa.Span
 
substring(String, Span) - Static method in class edu.uchsc.ccp.knowtator.Span
 
SUBTEXT_SLOT_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
SwingUtils - Class in edu.uchsc.ccp.knowtator.ui
Class designed to contain various static utility functions that can be useful when creating a Java Swing application.
SwingUtils() - Constructor for class edu.uchsc.ccp.knowtator.ui.SwingUtils
 

T

text - Variable in class edu.uchsc.ccp.knowtator.textsource.DefaultTextSource
 
TEXT_SOURCE_ATTRIBUTE_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
 
TEXT_SOURCE_CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
TEXT_SOURCES_INSTRUCTIONS - Static variable in class edu.uchsc.ccp.knowtator.wizards.CreateConsensusSetWizard
 
TextSource - Interface in edu.uchsc.ccp.knowtator.textsource
We recommend that instead of implementing this interface that you extend DefaultTextSource.
TextSourceAccessException - Exception in edu.uchsc.ccp.knowtator.textsource
 
TextSourceAccessException() - Constructor for exception edu.uchsc.ccp.knowtator.textsource.TextSourceAccessException
Creates a new instance of TextSourceAccessException
TextSourceAccessException(String) - Constructor for exception edu.uchsc.ccp.knowtator.textsource.TextSourceAccessException
 
TextSourceAccessException(String, Throwable) - Constructor for exception edu.uchsc.ccp.knowtator.textsource.TextSourceAccessException
 
TextSourceAccessException(Throwable) - Constructor for exception edu.uchsc.ccp.knowtator.textsource.TextSourceAccessException
 
textSourceChanged(TextSourceChangeEvent) - Method in class edu.uchsc.ccp.knowtator.Knowtator
 
textSourceChanged(TextSourceChangeEvent) - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
textSourceChanged(TextSourceChangeEvent) - Method in class edu.uchsc.ccp.knowtator.SpanUtil
 
textSourceChanged(TextSourceChangeEvent) - Method in interface edu.uchsc.ccp.knowtator.textsource.TextSourceChangeListener
 
textSourceChanged(TextSourceChangeEvent) - Method in class edu.uchsc.ccp.knowtator.textsource.TextSourceSelector
 
textSourceChanged(TextSourceChangeEvent) - Method in class edu.uchsc.ccp.knowtator.ui.TextViewer
 
textSourceChanged(TextSourceChangeEvent) - Method in class edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog
 
TextSourceChangedEvent - Class in edu.uchsc.ccp.knowtator.textsource
 
TextSourceChangedEvent(TextSource) - Constructor for class edu.uchsc.ccp.knowtator.textsource.TextSourceChangedEvent
 
TextSourceChangeEvent - Class in edu.uchsc.ccp.knowtator.textsource
 
TextSourceChangeEvent(TextSource) - Constructor for class edu.uchsc.ccp.knowtator.textsource.TextSourceChangeEvent
 
TextSourceChangeListener - Interface in edu.uchsc.ccp.knowtator.textsource
 
TextSourceCollection - Class in edu.uchsc.ccp.knowtator.textsource
Authors: Philip V.
TextSourceCollection() - Constructor for class edu.uchsc.ccp.knowtator.textsource.TextSourceCollection
 
textSourceCollectionChanged(TextSourceCollectionChangeEvent) - Method in interface edu.uchsc.ccp.knowtator.textsource.TextSourceCollectionChangeListener
 
textSourceCollectionChanged(TextSourceCollectionChangeEvent) - Method in class edu.uchsc.ccp.knowtator.textsource.TextSourceSelector
 
TextSourceCollectionChangeEvent - Class in edu.uchsc.ccp.knowtator.textsource
 
TextSourceCollectionChangeEvent(TextSourceCollection) - Constructor for class edu.uchsc.ccp.knowtator.textsource.TextSourceCollectionChangeEvent
 
TextSourceCollectionChangeListener - Interface in edu.uchsc.ccp.knowtator.textsource
 
TextSourceIterator - Interface in edu.uchsc.ccp.knowtator.textsource
 
TextSourceSelector - Class in edu.uchsc.ccp.knowtator.textsource
 
TextSourceSelector(Project, TextSourceUtil, JToolBar, Component) - Constructor for class edu.uchsc.ccp.knowtator.textsource.TextSourceSelector
Creates a new instance of TextSourceSelector
textSourceToIndex - Variable in class edu.uchsc.ccp.knowtator.textsource.filelines.FileLinesTextSourceCollection
 
TextSourceUtil - Class in edu.uchsc.ccp.knowtator
This class helps one to find a "text source" instance in the knowledgebase given a TextSource object or vice versa.
TextSourceUtil(AnnotationUtil, KnowtatorProjectUtil) - Constructor for class edu.uchsc.ccp.knowtator.TextSourceUtil
 
TextViewer - Class in edu.uchsc.ccp.knowtator.ui
 
TextViewer(KnowtatorTextPane, KnowtatorManager) - Constructor for class edu.uchsc.ccp.knowtator.ui.TextViewer
 
TO_CONFIG_FRAME - Static variable in class edu.uchsc.ccp.knowtator.wizards.IAAWizard
 
TO_FILTER_FRAME - Static variable in class edu.uchsc.ccp.knowtator.wizards.CreateConsensusSetWizard
 
TO_FILTER_FRAME - Static variable in class edu.uchsc.ccp.knowtator.wizards.IAAWizard
 
TO_NAME_FRAME - Static variable in class edu.uchsc.ccp.knowtator.wizards.CreateConsensusSetWizard
 
TO_OUTPUT_FRAME - Static variable in class edu.uchsc.ccp.knowtator.wizards.IAAWizard
 
TO_TEXTSOURCES_FRAME - Static variable in class edu.uchsc.ccp.knowtator.wizards.CreateConsensusSetWizard
 
TO_TEXTSOURCES_FRAME - Static variable in class edu.uchsc.ccp.knowtator.wizards.IAAWizard
 
TO_WELCOME_FRAME - Static variable in class edu.uchsc.ccp.knowtator.wizards.CreateConsensusSetWizard
 
TO_WELCOME_FRAME - Static variable in class edu.uchsc.ccp.knowtator.wizards.IAAWizard
 
toHTML() - Method in class edu.uchsc.ccp.iaa.Annotation
this needs to be moved out of this class
toHTML(boolean) - Method in class edu.uchsc.ccp.iaa.Annotation
 
TOKEN_REGEX_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
toString() - Method in class edu.uchsc.ccp.iaa.Span
 
toString() - Method in class edu.uchsc.ccp.knowtator.Span
 
toString() - Method in class edu.uchsc.ccp.knowtator.textsource.DefaultTextSource
 
toString() - Method in interface edu.uchsc.ccp.knowtator.textsource.TextSource
 
toString(String) - Static method in class edu.uchsc.ccp.util.io.FileReadingUtil
 
toString(InputStream) - Static method in class edu.uchsc.ccp.util.io.FileReadingUtil
 
TRIVIAL_MATCH - Static variable in class edu.uchsc.ccp.iaa.matcher.MatchResult
 
TRIVIAL_NONMATCH - Static variable in class edu.uchsc.ccp.iaa.matcher.MatchResult
 
trivialCompare(Set, Set) - Static method in class edu.uchsc.ccp.iaa.Annotation
 
TSC_IMPLEMENTATION_SLOT_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
TSC_IMPLEMENTATIONS_CLS_NAME - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 

U

UNVERSIONED - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
updateCurrentAnnotations() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 
updateKnowtatorProject(Project) - Static method in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
updateTokenRegex() - Method in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 
updateVisibleFilteredAnnotations() - Method in class edu.uchsc.ccp.knowtator.KnowtatorManager
 

V

V001 - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
V002 - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
V003 - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
V004 - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
V005 - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
V006 - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
V007 - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
VALUE_ATTRIBUTE_NAME - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLConstants
 
valueChanged(ListSelectionEvent) - Method in class edu.uchsc.ccp.knowtator.ui.AnnotationPicker
 
VERSION_BEING_UPDATED - Static variable in class edu.uchsc.ccp.knowtator.KnowtatorProjectUtil
 
VERTICAL_LINES - Static variable in class edu.uchsc.ccp.knowtator.ui.KnowtatorTextPane
 

W

WELCOME_MESSAGE - Static variable in class edu.uchsc.ccp.knowtator.wizards.CreateConsensusSetWizard
 
WizardFrame - Class in edu.uchsc.ccp.knowtator.wizards
 
WizardFrame(JFrame, String) - Constructor for class edu.uchsc.ccp.knowtator.wizards.WizardFrame
 
WizardFrame(JFrame, String, Dimension) - Constructor for class edu.uchsc.ccp.knowtator.wizards.WizardFrame
 
WizardUtil - Class in edu.uchsc.ccp.knowtator.wizards
 
WizardUtil() - Constructor for class edu.uchsc.ccp.knowtator.wizards.WizardUtil
 
writeToXML(Component, KnowledgeBase, KnowtatorProjectUtil, TextSourceUtil, AnnotationUtil, MentionUtil, FilterUtil, Project) - Static method in class edu.uchsc.ccp.knowtator.xml.XMLExport
 
writeToXML(SimpleInstance, SimpleInstance, File, AnnotationUtil, FilterUtil, MentionUtil) - Static method in class edu.uchsc.ccp.knowtator.xml.XMLExport
 

X

XML_EXPORT_DIRECTORY - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLExport
 
XML_IMPORT_DIRECTORY - Static variable in class edu.uchsc.ccp.knowtator.xml.XMLImport
 
XMLConstants - Class in edu.uchsc.ccp.knowtator.xml
 
XMLConstants() - Constructor for class edu.uchsc.ccp.knowtator.xml.XMLConstants
 
XMLExport - Class in edu.uchsc.ccp.knowtator.xml
 
XMLExport() - Constructor for class edu.uchsc.ccp.knowtator.xml.XMLExport
 
XMLImport - Class in edu.uchsc.ccp.knowtator.xml
 
XMLImport() - Constructor for class edu.uchsc.ccp.knowtator.xml.XMLImport
 

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