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

A

add(OWLAxiom) - Method in class org.obolibrary.obo2owl.Obo2Owl
 
addClause(Clause) - Method in class org.obolibrary.oboformat.model.Frame
 
addDefaultOntologyHeader(String) - Method in class org.obolibrary.oboformat.model.OBODoc
 
addFrame(Frame) - Method in class org.obolibrary.oboformat.model.OBODoc
 
addImportedOBODoc(OBODoc) - Method in class org.obolibrary.oboformat.model.OBODoc
 
addInstanceFrame(Frame) - Method in class org.obolibrary.oboformat.model.OBODoc
 
addOntologyAnnotation(OWLAnnotationProperty, OWLAnnotationValue) - Method in class org.obolibrary.obo2owl.Obo2Owl
 
addQualifierValue(QualifierValue) - Method in class org.obolibrary.oboformat.model.Clause
 
addRowGap(JPanel, GuiTools.GBHelper, int) - Static method in class org.obolibrary.gui.GuiTools
Add an additional row with a fixed size for layout purposes.
addTermFrame(Frame) - Method in class org.obolibrary.oboformat.model.OBODoc
 
addTypedefFrame(Frame) - Method in class org.obolibrary.oboformat.model.OBODoc
 
addValue(Object) - Method in class org.obolibrary.oboformat.model.Clause
 
addXref(Xref) - Method in class org.obolibrary.oboformat.model.Clause
 
advance(int) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream
 
advanceLine() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream
 
allowDangling - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 
anchorCenter() - Method in class org.obolibrary.gui.GuiTools.GBHelper
Set the anchor to center.
annotationFrames - Variable in class org.obolibrary.oboformat.model.OBODoc
 
annotationPropertyMap - Static variable in class org.obolibrary.obo2owl.Obo2Owl
 
annotationPropertyMap - Static variable in class org.obolibrary.obo2owl.Owl2Obo
 
apply(OWLOntologyChange) - Method in class org.obolibrary.obo2owl.Obo2Owl
 

B

buildAllOboOwlFiles(String, OBORunnerConfiguration, Logger) - Static method in class org.obolibrary.cli.OBODiffRunner
makes OWL from all selected ontologies.
buildAllOboOwlFiles(String, OBORunnerConfiguration, Logger) - Static method in class org.obolibrary.cli.OBORunner
makes OWL from all selected ontologies.
buildDir - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 

C

canStoreOntology(OWLOntologyFormat) - Method in class org.obolibrary.owl.LabelFunctionalSyntaxOntologyStorer
 
check() - Method in class org.obolibrary.oboformat.model.Frame
 
check() - Method in class org.obolibrary.oboformat.model.OBODoc
 
checkDanglingReferences(OBODoc) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
 
Clause - Class in org.obolibrary.oboformat.model
 
Clause(OBOFormatConstants.OboFormatTag) - Constructor for class org.obolibrary.oboformat.model.Clause
 
Clause(String) - Constructor for class org.obolibrary.oboformat.model.Clause
 
Clause(String, String) - Constructor for class org.obolibrary.oboformat.model.Clause
 
Clause(OBOFormatConstants.OboFormatTag, String) - Constructor for class org.obolibrary.oboformat.model.Clause
 
Clause() - Constructor for class org.obolibrary.oboformat.model.Clause
 
clauses - Variable in class org.obolibrary.oboformat.model.Frame
 
consume(String) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream
 
convert(String) - Method in class org.obolibrary.obo2owl.Obo2Owl
Creates an OBOFormatParser object to parse a file and then converts it using the convert method
convert(OBODoc, boolean) - Method in class org.obolibrary.obo2owl.Obo2Owl
 
convert(OBODoc) - Method in class org.obolibrary.obo2owl.Obo2Owl
Converts an OBO document to an OWL ontology
convert(OWLOntology) - Method in class org.obolibrary.obo2owl.Owl2Obo
 
convertURL(String, String) - Static method in class org.obolibrary.obo2owl.Obo2Owl
Static convenience method which: (1) creates an Obo2Owl bridge object (2) parses an obo file from a URL (3) converts that to an OWL ontology (4) saves the OWL ontology as RDF/XML
convertURL(String, String, String) - Static method in class org.obolibrary.obo2owl.Obo2Owl
See Obo2Owl.convertURL(String iri, String outFile)
createGCIOntology() - Method in class org.obolibrary.macro.MacroExpansionGCIVisitor
 
createTextField(String) - Static method in class org.obolibrary.gui.GuiTools
Create a new JTextField and set text value to a give default.

D

DEBUG - Static variable in class org.obolibrary.obo2owl.Obo2Owl
 
DEFAULT_CHARACTER_ENCODING - Static variable in class org.obolibrary.oboformat.parser.OBOFormatConstants
 
DEFAULT_IRI_PREFIX - Static variable in class org.obolibrary.obo2owl.Obo2Owl
Deprecated. 
DEFAULT_IRI_PREFIX - Static variable in class org.obolibrary.obo2owl.Obo2OWLConstants
 
defaultOnt - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 
Diff - Class in org.obolibrary.oboformat.diff
 
Diff(String, String, Frame, int) - Constructor for class org.obolibrary.oboformat.diff.Diff
 
Diff(String, String, Frame, Frame, Clause, int) - Constructor for class org.obolibrary.oboformat.diff.Diff
 
disableRunButton() - Method in class org.obolibrary.gui.GuiMainFrame
 
dispose() - Method in class org.obolibrary.macro.MacroExpansionGCIVisitor
Call this method to clear internal references.
dispose() - Method in class org.obolibrary.macro.MacroExpansionVisitor
Call this method to clear internal references.
dispose() - Method in class org.obolibrary.macro.ManchesterSyntaxTool
Call this method to dispose the internal data structures.
DocumentStructureException - Exception in org.obolibrary.oboformat.model
 
DocumentStructureException(String) - Constructor for exception org.obolibrary.oboformat.model.DocumentStructureException
 
doesReadValue() - Method in class org.obolibrary.cli.OBORunnerConfiguration.Variable
 

E

enableRunButton() - Method in class org.obolibrary.gui.GuiMainFrame
 
eof() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream
 
eol() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream
 
equals(Object) - Method in class org.obolibrary.oboformat.model.Clause
 
equals(Object) - Method in class org.obolibrary.oboformat.model.QualifierValue
 
equals(Object) - Method in class org.obolibrary.oboformat.model.Xref
 
executeConversion(OBORunnerConfiguration) - Method in class org.obolibrary.gui.GuiMainFrame
Execute the actual conversion.
expand(Frame, String, String) - Method in class org.obolibrary.oboformat.parser.XrefExpander.EquivalenceExpansion
 
expand(Frame, String, String) - Method in class org.obolibrary.oboformat.parser.XrefExpander.GenusDifferentiaExpansion
 
expand(Frame, String, String) - Method in class org.obolibrary.oboformat.parser.XrefExpander.HasSubClassExpansion
 
expand(Frame, String, String) - Method in class org.obolibrary.oboformat.parser.XrefExpander.IsaExpansion
 
expand(Frame, String, String) - Method in class org.obolibrary.oboformat.parser.XrefExpander.RelationshipExpansion
 
expand(Frame, String, String) - Method in class org.obolibrary.oboformat.parser.XrefExpander.ReverseGenusDifferentiaExpansion
 
expand(Frame, String, String) - Method in class org.obolibrary.oboformat.parser.XrefExpander.Rule
 
expandAll() - Method in class org.obolibrary.macro.MacroExpansionVisitor
 
expandH() - Method in class org.obolibrary.gui.GuiTools.GBHelper
Expandable Height.
expandMacrosMode - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 
expandPrefix(String) - Method in class obo.obolibrary.idrules.IdTranslator
Expands an OBO prefix such as "GO" to "http://purl.obolibrary.org/obo/GO_" By default a prefix XX maps to http://purl.obolibrary.org/obo/XX_
expandW() - Method in class org.obolibrary.gui.GuiTools.GBHelper
Expandable Width.
expandXrefs() - Method in class org.obolibrary.oboformat.parser.XrefExpander
 
ExportLabelsAsOWL - Class in org.obolibrary.examples
Saves an OWL ontology consisting only of labels argument 1: a file path to an input obo file argument 2: a file path to an output owl file Example: java org.obolibrary.examples.ExportLabelsAsOWL human-phenotype-ontology.obo labels.owl
ExportLabelsAsOWL() - Constructor for class org.obolibrary.examples.ExportLabelsAsOWL
 

F

fill() - Method in class org.obolibrary.gui.GuiTools.GBHelper
Set the fill to both.
followImports - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 
forceEol() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream
 
forceParseNlOrEof() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
 
format - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 
Frame - Class in org.obolibrary.oboformat.model
 
Frame() - Constructor for class org.obolibrary.oboformat.model.Frame
 
Frame(Frame.FrameType) - Constructor for class org.obolibrary.oboformat.model.Frame
 
Frame.FrameType - Enum in org.obolibrary.oboformat.model
 
FrameMergeException - Exception in org.obolibrary.oboformat.model
 
FrameMergeException(String) - Constructor for exception org.obolibrary.oboformat.model.FrameMergeException
 
FrameStructureException - Exception in org.obolibrary.oboformat.model
 
FrameStructureException(String) - Constructor for exception org.obolibrary.oboformat.model.FrameStructureException
 
FrameStructureException(Frame, String) - Constructor for exception org.obolibrary.oboformat.model.FrameStructureException
 

G

getAnnotation() - Method in class org.obolibrary.oboformat.model.Xref
 
getClause(String) - Method in class org.obolibrary.oboformat.model.Frame
 
getClause(OBOFormatConstants.OboFormatTag) - Method in class org.obolibrary.oboformat.model.Frame
 
getClause1() - Method in class org.obolibrary.oboformat.diff.Diff
 
getClause2() - Method in class org.obolibrary.oboformat.diff.Diff
 
getClauses() - Method in class org.obolibrary.oboformat.model.Frame
 
getClauses(String) - Method in class org.obolibrary.oboformat.model.Frame
 
getClauses(OBOFormatConstants.OboFormatTag) - Method in class org.obolibrary.oboformat.model.Frame
 
getDefaultOboNamespace() - Method in interface org.obolibrary.oboformat.writer.OBOFormatWriter.NameProvider
Retrieve the default OBO namespace
getDefaultOboNamespace() - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter.OBODocNameProvider
 
getDescription() - Method in class org.obolibrary.cli.OBORunnerConfiguration.Variable
 
getDiffs(OBODoc, OBODoc) - Method in class org.obolibrary.oboformat.diff.OBODocDiffer
 
getFileSelector(Frame, boolean, String, String, String, String[]) - Static method in class org.obolibrary.gui.SelectDialog
Create a new dialog, which selects a file from the file system.
getFolderSelector(Frame, String, String) - Static method in class org.obolibrary.gui.SelectDialog
Create a new dialog, which selects a folder from the file system.
getFollowImports() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
 
getFrame1() - Method in class org.obolibrary.oboformat.diff.Diff
 
getFrame2() - Method in class org.obolibrary.oboformat.diff.Diff
 
getHeaderFrame() - Method in class org.obolibrary.oboformat.model.OBODoc
 
getId(IRI) - Method in class org.obolibrary.macro.ManchesterSyntaxTool
Translate the IRI into the short form as expected by the parser.
getId(OWLEntity) - Method in class org.obolibrary.macro.ManchesterSyntaxTool
Translate the OWLEntity identifier into the short form as expected by the parser.
getId() - Method in class org.obolibrary.oboformat.model.Frame
 
getIdentifier(OWLObject) - Method in class org.obolibrary.obo2owl.Owl2Obo
 
getIdentifier(IRI) - Static method in class org.obolibrary.obo2owl.Owl2Obo
See table 5.9.2.
getIdentifierFromObject(OWLObject, OWLOntology, String) - Static method in class org.obolibrary.obo2owl.Owl2Obo
Retrieve the identifier for a given OWLObject.
getIdentifierFromObject(OWLObject, OWLOntology) - Static method in class org.obolibrary.obo2owl.Owl2Obo
Retrieve the identifier for a given OWLObject.
getIdref() - Method in class org.obolibrary.oboformat.model.Xref
 
getIDSpace(String) - Method in class org.obolibrary.oboformat.model.OBODoc
Looks up the ID prefix to IRI prefix mapping.
getImportedOBODocs() - Method in class org.obolibrary.oboformat.model.OBODoc
 
getInstanceFrame(String) - Method in class org.obolibrary.oboformat.model.OBODoc
 
getInstanceFrames() - Method in class org.obolibrary.oboformat.model.OBODoc
 
getIRI() - Method in enum org.obolibrary.obo2owl.Obo2OWLConstants.Obo2OWLVocabulary
 
getLabel() - Method in enum org.obolibrary.obo2owl.Obo2OWLConstants.Obo2OWLVocabulary
 
getLineNo() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream
 
getManager() - Method in class org.obolibrary.obo2owl.Obo2Owl
 
getManager() - Method in class org.obolibrary.obo2owl.Owl2Obo
 
getMappedTag() - Method in enum org.obolibrary.obo2owl.Obo2OWLConstants.Obo2OWLVocabulary
 
getName() - Method in class org.obolibrary.cli.OBORunnerConfiguration.Variable
 
getName(String) - Method in interface org.obolibrary.oboformat.writer.OBOFormatWriter.NameProvider
Try to retrieve the valid name for the given identifier.
getName(String) - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter.OBODocNameProvider
 
getNamespace() - Method in enum org.obolibrary.obo2owl.Obo2OWLConstants.Obo2OWLVocabulary
 
getObodoc() - Method in class org.obolibrary.obo2owl.Obo2Owl
 
getObodoc() - Method in class org.obolibrary.obo2owl.Owl2Obo
 
getOntologyId(OWLOntology) - Static method in class org.obolibrary.obo2owl.Owl2Obo
E.g.
getOntologyId(IRI) - Static method in class org.obolibrary.obo2owl.Owl2Obo
 
getOwlOntology() - Method in class org.obolibrary.obo2owl.Obo2Owl
 
getParameters() - Method in class org.obolibrary.cli.OBORunnerConfiguration.Variable
 
getQualifier() - Method in class org.obolibrary.oboformat.model.QualifierValue
 
getQualifierValues() - Method in class org.obolibrary.oboformat.model.Clause
 
getSelected() - Method in class org.obolibrary.gui.SelectDialog
Retrieve the selected file/folder.
getSelectedCanonicalPath() - Method in class org.obolibrary.gui.SelectDialog
Retrieve the canonical path of the selected folder.
getSetValueFailure() - Method in class org.obolibrary.cli.OBORunnerConfiguration.Variable
 
getShortName() - Method in enum org.obolibrary.obo2owl.Obo2OWLConstants.Obo2OWLVocabulary
 
getStrictConversion() - Method in class org.obolibrary.obo2owl.Owl2Obo
 
getStrings(JTextArea) - Static method in class org.obolibrary.gui.GuiTools
Retrieve the lines as a list of strings from a given JTextArea.
getTag() - Method in class org.obolibrary.oboformat.model.Clause
 
getTag(String) - Static method in class org.obolibrary.oboformat.parser.OBOFormatConstants
 
getTag() - Method in enum org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag
 
getTag() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream
 
getTags() - Method in class org.obolibrary.oboformat.model.Frame
 
getTagValue(String) - Method in class org.obolibrary.oboformat.model.Frame
 
getTagValue(OBOFormatConstants.OboFormatTag) - Method in class org.obolibrary.oboformat.model.Frame
 
getTagValue(String, Class<T>) - Method in class org.obolibrary.oboformat.model.Frame
 
getTagValue(OBOFormatConstants.OboFormatTag, Class<T>) - Method in class org.obolibrary.oboformat.model.Frame
 
getTagValues(OBOFormatConstants.OboFormatTag) - Method in class org.obolibrary.oboformat.model.Frame
 
getTagValues(String) - Method in class org.obolibrary.oboformat.model.Frame
 
getTagValues(OBOFormatConstants.OboFormatTag, Class<T>) - Method in class org.obolibrary.oboformat.model.Frame
 
getTagValues(String, Class<T>) - Method in class org.obolibrary.oboformat.model.Frame
 
getTagXrefs(String) - Method in class org.obolibrary.oboformat.model.Frame
 
getTargetDoc(String) - Method in class org.obolibrary.oboformat.parser.XrefExpander
 
getTargetFrame(String) - Method in class org.obolibrary.oboformat.parser.XrefExpander.Rule
 
getTermFrame(String) - Method in class org.obolibrary.oboformat.model.OBODoc
 
getTermFrame(String, boolean) - Method in class org.obolibrary.oboformat.model.OBODoc
 
getTermFrames() - Method in class org.obolibrary.oboformat.model.OBODoc
 
getType() - Method in class org.obolibrary.oboformat.diff.Diff
 
getType() - Method in class org.obolibrary.oboformat.model.Frame
 
getTypedefFrame(String) - Method in class org.obolibrary.oboformat.model.OBODoc
 
getTypedefFrame(String, boolean) - Method in class org.obolibrary.oboformat.model.OBODoc
 
getTypedefFrames() - Method in class org.obolibrary.oboformat.model.OBODoc
 
getUntranslatableAxioms() - Method in class org.obolibrary.obo2owl.Owl2Obo
 
getValue() - Method in class org.obolibrary.cli.OBORunnerConfiguration.Variable
 
getValue() - Method in class org.obolibrary.oboformat.model.Clause
 
getValue(Class<T>) - Method in class org.obolibrary.oboformat.model.Clause
 
getValue() - Method in class org.obolibrary.oboformat.model.QualifierValue
 
getValue2() - Method in class org.obolibrary.oboformat.model.Clause
 
getValue2(Class<T>) - Method in class org.obolibrary.oboformat.model.Clause
 
getValues() - Method in class org.obolibrary.oboformat.model.Clause
 
getVariables() - Method in class org.obolibrary.cli.OBORunnerConfiguration
 
getVocabularyObj(String) - Static method in class org.obolibrary.obo2owl.Obo2OWLConstants
 
getXrefs() - Method in class org.obolibrary.oboformat.model.Clause
 
GuiAdvancedDirectionSpecificPanel - Class in org.obolibrary.gui
GUI elements for the advanced settings of the converter
GuiAdvancedDirectionSpecificPanel(boolean, boolean, boolean, String, boolean, boolean) - Constructor for class org.obolibrary.gui.GuiAdvancedDirectionSpecificPanel
Create GUI panel for advanced settings specific for either conversion direction with the given default values.
GuiAdvancedPanel - Class in org.obolibrary.gui
GUI elements for the advanced settings of the converter
GuiAdvancedPanel(Frame, Collection<String>, Collection<String>, String) - Constructor for class org.obolibrary.gui.GuiAdvancedPanel
Create GUI panel for advanced settings with the given default values.
GuiLogPanel - Class in org.obolibrary.gui
Panel for rendering the log in the GUI.
GuiLogPanel(BlockingQueue<String>) - Constructor for class org.obolibrary.gui.GuiLogPanel
Construct a new LogPanel using the given log message queue.
GuiMainFrame - Class in org.obolibrary.gui
GUI main frame, calls all constructors for the sub components.
GuiMainFrame() - Constructor for class org.obolibrary.gui.GuiMainFrame
Default constructor, required only for testing the GUI as bean.
GuiMainFrame(BlockingQueue<String>, OBORunnerConfiguration) - Constructor for class org.obolibrary.gui.GuiMainFrame
Main constructor.
GuiMainPanel - Class in org.obolibrary.gui
GUI component for the minimum number of configurations required for the conversion.
GuiMainPanel(GuiMainFrame, Iterable<String>, String, boolean) - Constructor for class org.obolibrary.gui.GuiMainPanel
Constructor allows to build a panel with default values
GuiTools - Class in org.obolibrary.gui
Tools for the layout and handling of the GUI components.
GuiTools() - Constructor for class org.obolibrary.gui.GuiTools
 
GuiTools.GBHelper - Class in org.obolibrary.gui
Simplify the GridBagConstrains handling.
GuiTools.GBHelper() - Constructor for class org.obolibrary.gui.GuiTools.GBHelper
 
GuiTools.SizedJPanel - Class in org.obolibrary.gui
All tabbed panels should have the same preferred size.
GuiTools.SizedJPanel() - Constructor for class org.obolibrary.gui.GuiTools.SizedJPanel
 

H

handleDuplicateClause(Frame, Clause) - Method in class org.obolibrary.obo2owl.Owl2Obo
Handle a duplicate clause in a frame during translation.
hashCode() - Method in class org.obolibrary.oboformat.model.QualifierValue
 
headerDateFormat - Static variable in class org.obolibrary.oboformat.parser.OBOFormatConstants
Date format for OboFormatTag.TAG_DATE Use Thread local to ensure thread safety, as SimpleDateFormat is not thread safe.
headerFrame - Variable in class org.obolibrary.oboformat.model.OBODoc
 
height(int) - Method in class org.obolibrary.gui.GuiTools.GBHelper
Sets the height of the area in terms of rows.

I

id - Variable in class org.obolibrary.oboformat.model.Frame
 
idSpace - Variable in class org.obolibrary.oboformat.parser.XrefExpander.Rule
 
IdTranslator - Class in obo.obolibrary.idrules
This class will eventually replace the id to uri translation in Owl2Obo and OboO2Owl It is currently in-progress.
IdTranslator() - Constructor for class obo.obolibrary.idrules.IdTranslator
 
importedOBODocs - Variable in class org.obolibrary.oboformat.model.OBODoc
 
indentLeft(int) - Method in class org.obolibrary.gui.GuiTools.GBHelper
Increase indent in the left.
indentRight(int) - Method in class org.obolibrary.gui.GuiTools.GBHelper
Increase indent in the left.
indexOf(char) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream
 
init() - Method in class org.obolibrary.oboformat.model.Frame
 
instanceFrameMap - Variable in class org.obolibrary.oboformat.model.OBODoc
 
InvalidXrefMapException - Exception in org.obolibrary.oboformat.parser
 
InvalidXrefMapException() - Constructor for exception org.obolibrary.oboformat.parser.InvalidXrefMapException
 
InvalidXrefMapException(String, Throwable) - Constructor for exception org.obolibrary.oboformat.parser.InvalidXrefMapException
 
InvalidXrefMapException(String) - Constructor for exception org.obolibrary.oboformat.parser.InvalidXrefMapException
 
InvalidXrefMapException(Throwable) - Constructor for exception org.obolibrary.oboformat.parser.InvalidXrefMapException
 
IRI_PROP_isReversiblePropertyChain - Static variable in class org.obolibrary.obo2owl.Obo2Owl
 
isCheckStructure() - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter
 
isDisableDocumentChecking - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 
isEmpty() - Method in class org.obolibrary.cli.OBORunnerConfiguration.Variable
 
isExpandMacros - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 
isOboToOwl - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 
isTreatXrefsAsEquivalent(String) - Method in class org.obolibrary.oboformat.model.OBODoc
 
isURI(String) - Method in class obo.obolibrary.idrules.IdTranslator
True if id starts with a standard URI prefix (http, ftp, https) followed by a ":".

L

LabelFunctionalFormat - Class in org.obolibrary.owl
Format for serializing an OWL ontology in a functional syntax format and labels instead of identifiers.
LabelFunctionalFormat() - Constructor for class org.obolibrary.owl.LabelFunctionalFormat
 
LabelFunctionalSyntaxOntologyStorer - Class in org.obolibrary.owl
Implement the writer for LabelFunctionalFormat.
LabelFunctionalSyntaxOntologyStorer() - Constructor for class org.obolibrary.owl.LabelFunctionalSyntaxOntologyStorer
 
LOAD - Static variable in class org.obolibrary.gui.SelectDialog
 

M

MacroExpansionGCIVisitor - Class in org.obolibrary.macro
 
MacroExpansionGCIVisitor(OWLOntology) - Constructor for class org.obolibrary.macro.MacroExpansionGCIVisitor
 
MacroExpansionVisitor - Class in org.obolibrary.macro
 
MacroExpansionVisitor(OWLOntology) - Constructor for class org.obolibrary.macro.MacroExpansionVisitor
 
main(String[]) - Static method in class org.obolibrary.cli.OBODiffRunner
 
main(String[]) - Static method in class org.obolibrary.cli.OBORunner
 
main(String[]) - Static method in class org.obolibrary.cli.OBORunnerGui
 
main(String[]) - Static method in class org.obolibrary.examples.ExportLabelsAsOWL
 
main(String[]) - Static method in class org.obolibrary.oboformat.diff.OBODocDiffer
 
ManchesterSyntaxTool - Class in org.obolibrary.macro
wrapper for parsing Manchester Syntax
ManchesterSyntaxTool(OWLOntology) - Constructor for class org.obolibrary.macro.ManchesterSyntaxTool
Create a new parser instance for the given ontology.
ManchesterSyntaxTool(OWLOntology, Collection<OWLOntology>) - Constructor for class org.obolibrary.macro.ManchesterSyntaxTool
Create a new parser instance for the given ontologies.
ManchesterSyntaxTool(OWLOntology, Collection<OWLOntology>, boolean) - Constructor for class org.obolibrary.macro.ManchesterSyntaxTool
Create a new parser instance for the given ontologies.
merge(Frame) - Method in class org.obolibrary.oboformat.model.Frame
 
mergeContents(OBODoc) - Method in class org.obolibrary.oboformat.model.OBODoc
 

N

nextChar() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream
 
nextCol() - Method in class org.obolibrary.gui.GuiTools.GBHelper
Moves the helper's cursor to the right one column.
nextRow() - Method in class org.obolibrary.gui.GuiTools.GBHelper
Moves the helper's cursor to first col in next row.

O

obo.obolibrary.idrules - package obo.obolibrary.idrules
 
Obo2Owl - Class in org.obolibrary.obo2owl
 
Obo2Owl() - Constructor for class org.obolibrary.obo2owl.Obo2Owl
 
Obo2Owl(OWLOntologyManager) - Constructor for class org.obolibrary.obo2owl.Obo2Owl
 
Obo2OWLConstants - Class in org.obolibrary.obo2owl
 
Obo2OWLConstants() - Constructor for class org.obolibrary.obo2owl.Obo2OWLConstants
 
Obo2OWLConstants.Obo2OWLVocabulary - Enum in org.obolibrary.obo2owl
 
OBODiffRunner - Class in org.obolibrary.cli
command line access to obo2owl
OBODiffRunner() - Constructor for class org.obolibrary.cli.OBODiffRunner
 
OBODoc - Class in org.obolibrary.oboformat.model
An OBODoc is a container for a header frame and zero or more entity frames
OBODoc() - Constructor for class org.obolibrary.oboformat.model.OBODoc
 
OBODocDiffer - Class in org.obolibrary.oboformat.diff
Diffs two OBO Documents.
OBODocDiffer() - Constructor for class org.obolibrary.oboformat.diff.OBODocDiffer
 
OBOFormatConstants - Class in org.obolibrary.oboformat.parser
 
OBOFormatConstants() - Constructor for class org.obolibrary.oboformat.parser.OBOFormatConstants
 
OBOFormatConstants.OboFormatTag - Enum in org.obolibrary.oboformat.parser
 
OBOFormatDanglingReferenceException - Exception in org.obolibrary.oboformat.parser
 
OBOFormatDanglingReferenceException() - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatDanglingReferenceException
 
OBOFormatDanglingReferenceException(String) - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatDanglingReferenceException
 
OBOFormatDanglingReferenceException(Throwable) - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatDanglingReferenceException
 
OBOFormatDanglingReferenceException(String, Throwable) - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatDanglingReferenceException
 
OBOFormatException - Exception in org.obolibrary.oboformat.parser
 
OBOFormatException() - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatException
 
OBOFormatException(String) - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatException
 
OBOFormatException(Throwable) - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatException
 
OBOFormatException(String, Throwable) - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatException
 
OBOFormatParser - Class in org.obolibrary.oboformat.parser
implements the OBO Format 1.4 specification
OBOFormatParser() - Constructor for class org.obolibrary.oboformat.parser.OBOFormatParser
 
OBOFormatParser(OBOFormatParser.MyStream) - Constructor for class org.obolibrary.oboformat.parser.OBOFormatParser
 
OBOFormatParser.MyStream - Class in org.obolibrary.oboformat.parser
 
OBOFormatParser.MyStream() - Constructor for class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream
 
OBOFormatParser.MyStream(BufferedReader) - Constructor for class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream
 
OBOFormatWriter - Class in org.obolibrary.oboformat.writer
 
OBOFormatWriter() - Constructor for class org.obolibrary.oboformat.writer.OBOFormatWriter
 
OBOFormatWriter.NameProvider - Interface in org.obolibrary.oboformat.writer
Provide names for given OBO identifiers.
OBOFormatWriter.OBODocNameProvider - Class in org.obolibrary.oboformat.writer
Default implementation of a OBOFormatWriter.NameProvider using an underlying OBODoc.
OBOFormatWriter.OBODocNameProvider(OBODoc) - Constructor for class org.obolibrary.oboformat.writer.OBOFormatWriter.OBODocNameProvider
 
oboIdToIRI(String) - Method in class org.obolibrary.obo2owl.Obo2Owl
 
OBORunner - Class in org.obolibrary.cli
command line access to obo2owl
OBORunner() - Constructor for class org.obolibrary.cli.OBORunner
 
OBORunnerConfigCLIReader - Class in org.obolibrary.cli
 
OBORunnerConfigCLIReader() - Constructor for class org.obolibrary.cli.OBORunnerConfigCLIReader
 
OBORunnerConfiguration - Class in org.obolibrary.cli
 
OBORunnerConfiguration() - Constructor for class org.obolibrary.cli.OBORunnerConfiguration
 
OBORunnerConfiguration.ExpandMacrosModeOptions - Enum in org.obolibrary.cli
 
OBORunnerConfiguration.Variable<T> - Class in org.obolibrary.cli
 
OBORunnerConfiguration.Variable(String, T) - Constructor for class org.obolibrary.cli.OBORunnerConfiguration.Variable
 
OBORunnerGui - Class in org.obolibrary.cli
GUI access for converter.
OBORunnerGui() - Constructor for class org.obolibrary.cli.OBORunnerGui
 
OIOVOCAB_IRI_PREFIX - Static variable in class org.obolibrary.obo2owl.Obo2OWLConstants
 
omitOntsToDownload - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 
ontsToDownload - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 
org.obolibrary.cli - package org.obolibrary.cli
 
org.obolibrary.examples - package org.obolibrary.examples
 
org.obolibrary.gui - package org.obolibrary.gui
 
org.obolibrary.macro - package org.obolibrary.macro
 
org.obolibrary.obo2owl - package org.obolibrary.obo2owl
 
org.obolibrary.oboformat.diff - package org.obolibrary.oboformat.diff
 
org.obolibrary.oboformat.model - package org.obolibrary.oboformat.model
 
org.obolibrary.oboformat.parser - package org.obolibrary.oboformat.parser
 
org.obolibrary.oboformat.writer - package org.obolibrary.oboformat.writer
 
org.obolibrary.owl - package org.obolibrary.owl
 
outFile - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 
outputdir - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 
OWL2_DATE_LITERAL_FORMAT - Static variable in class org.obolibrary.obo2owl.Obo2OWLConstants
 
Owl2Obo - Class in org.obolibrary.obo2owl
 
Owl2Obo() - Constructor for class org.obolibrary.obo2owl.Owl2Obo
 
Owl2Obo.UntranslatableAxiomException - Exception in org.obolibrary.obo2owl
 
Owl2Obo.UntranslatableAxiomException(String, Throwable) - Constructor for exception org.obolibrary.obo2owl.Owl2Obo.UntranslatableAxiomException
 
Owl2Obo.UntranslatableAxiomException(String) - Constructor for exception org.obolibrary.obo2owl.Owl2Obo.UntranslatableAxiomException
 
owlObjectToTag(OWLObject) - Static method in class org.obolibrary.obo2owl.Owl2Obo
 

P

parse(String) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
Parses a local file or URL to an OBODoc
parse(File) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
Parses a local file to an OBODoc
parse(URL) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
Parses a remote URL to an OBODoc
parse(BufferedReader) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
 
parseEntityFrame(OBODoc) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
 
parseHeaderClause(Frame) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
 
parseHeaderClauseNl(Frame) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
header-clause ::= format-version-TVP | ...
parseHeaderFrame(Frame) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
 
parseIdLine(Frame) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
 
parseManchesterExpression(String) - Method in class org.obolibrary.macro.ManchesterSyntaxTool
Parse a class expression in Manchester syntax.
parseManchesterExpressionFrames(String) - Method in class org.obolibrary.macro.ManchesterSyntaxTool
Parse frame expressions in Manchester syntax.
parseNlChar() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
 
parseOBODoc(OBODoc) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
 
parseOneOrMoreWs() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
 
parseSynonymXrefs(Clause, boolean) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
 
parseTermFrame(OBODoc) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
term-frame ::= nl* '[Term]' nl id-Tag Class-ID EOL { term-frame-clause EOL }
parseTermFrameClause(Clause) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
 
parseTermFrameClauseEOL(Frame) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
 
parseTypedefFrame(OBODoc) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
Typedef-frame ::= nl* '[Typedef]' nl id-Tag Class-ID EOL { Typedef-frame-clause EOL }
parseTypedefFrameClause(Clause) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
 
parseTypedefFrameClauseEOL(Frame) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
 
parseUnquotedString(Clause) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
 
parseURL(String) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
Parses a remote URL to an OBODoc
parseWs() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
 
parseWsOptCmtNl() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
 
parseZeroOrMoreWs() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
 
parseZeroOrMoreWsOptCmtNl() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
 
paths - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 
peekCharIs(char) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream
 
prepare() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream
 

Q

qualifier - Variable in class org.obolibrary.oboformat.model.QualifierValue
 
QualifierValue - Class in org.obolibrary.oboformat.model
 
QualifierValue(String, String) - Constructor for class org.obolibrary.oboformat.model.QualifierValue
 
qualifierValues - Variable in class org.obolibrary.oboformat.model.Clause
 

R

readConfig(String[]) - Static method in class org.obolibrary.cli.OBORunnerConfigCLIReader
 
rel - Variable in class org.obolibrary.oboformat.parser.XrefExpander.GenusDifferentiaExpansion
 
rel - Variable in class org.obolibrary.oboformat.parser.XrefExpander.RelationshipExpansion
 
rel - Variable in class org.obolibrary.oboformat.parser.XrefExpander.ReverseGenusDifferentiaExpansion
 
rest() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream
 
runConversion(OBORunnerConfiguration, Logger) - Static method in class org.obolibrary.cli.OBODiffRunner
 
runConversion(OBORunnerConfiguration, Logger) - Static method in class org.obolibrary.cli.OBORunner
 

S

s - Variable in class org.obolibrary.oboformat.parser.OBOFormatParser
 
SAVE - Static variable in class org.obolibrary.gui.SelectDialog
 
SelectDialog - Class in org.obolibrary.gui
Wrapper for the native FileDialog.
SelectDialog() - Constructor for class org.obolibrary.gui.SelectDialog
 
setAnnotation(String) - Method in class org.obolibrary.oboformat.model.Xref
 
setCheckStructure(boolean) - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter
 
setClause1(Clause) - Method in class org.obolibrary.oboformat.diff.Diff
 
setClause2(Clause) - Method in class org.obolibrary.oboformat.diff.Diff
 
setClauses(Collection<Clause>) - Method in class org.obolibrary.oboformat.model.Frame
 
setFollowImports(boolean) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
 
setFrame1(Frame) - Method in class org.obolibrary.oboformat.diff.Diff
 
setFrame2(Frame) - Method in class org.obolibrary.oboformat.diff.Diff
 
setHeaderFrame(Frame) - Method in class org.obolibrary.oboformat.model.OBODoc
 
setId(String) - Method in class org.obolibrary.oboformat.model.Frame
 
setIdref(String) - Method in class org.obolibrary.oboformat.model.Xref
 
setImportedOBODocs(Collection<OBODoc>) - Method in class org.obolibrary.oboformat.model.OBODoc
 
setManager(OWLOntologyManager) - Method in class org.obolibrary.obo2owl.Obo2Owl
 
setManager(OWLOntologyManager) - Method in class org.obolibrary.obo2owl.Owl2Obo
 
setObodoc(OBODoc) - Method in class org.obolibrary.obo2owl.Obo2Owl
 
setObodoc(OBODoc) - Method in class org.obolibrary.obo2owl.Owl2Obo
 
setOwlOntology(OWLOntology) - Method in class org.obolibrary.obo2owl.Obo2Owl
 
setQualifier(String) - Method in class org.obolibrary.oboformat.model.QualifierValue
 
setQualifierValues(Collection<QualifierValue>) - Method in class org.obolibrary.oboformat.model.Clause
 
setReader(BufferedReader) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser
 
setRealValue(T) - Method in class org.obolibrary.cli.OBORunnerConfiguration.Variable
 
setStrictConversion(boolean) - Method in class org.obolibrary.obo2owl.Owl2Obo
 
setTag(String) - Method in class org.obolibrary.oboformat.model.Clause
 
setType(String) - Method in class org.obolibrary.oboformat.diff.Diff
 
setType(Frame.FrameType) - Method in class org.obolibrary.oboformat.model.Frame
 
setUp() - Method in class org.obolibrary.oboformat.parser.XrefExpander
 
setValue(String) - Method in class org.obolibrary.cli.OBORunnerConfiguration.Variable
 
setValue(Object) - Method in class org.obolibrary.oboformat.model.Clause
 
setValue(Object) - Method in class org.obolibrary.oboformat.model.QualifierValue
 
setValues(Collection<Object>) - Method in class org.obolibrary.oboformat.model.Clause
 
setXrefs(Collection<Xref>) - Method in class org.obolibrary.oboformat.model.Clause
 
show() - Method in class org.obolibrary.gui.SelectDialog
Show the dialog to the user for selection.
showHelp - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 
showMemory() - Static method in class org.obolibrary.cli.OBODiffRunner
 
showMemory() - Static method in class org.obolibrary.cli.OBORunner
 
sortTermClauses(List<Clause>) - Static method in class org.obolibrary.oboformat.writer.OBOFormatWriter
Sort a list of term frame clauses according to in the OBO format specified tag and value order.
storeOntology(OWLOntologyManager, OWLOntology, Writer, OWLOntologyFormat) - Method in class org.obolibrary.owl.LabelFunctionalSyntaxOntologyStorer
 
strictConversion - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 

T

tag - Variable in class org.obolibrary.oboformat.model.Clause
 
TAGS - Static variable in class org.obolibrary.oboformat.parser.OBOFormatConstants
 
termFrameMap - Variable in class org.obolibrary.oboformat.model.OBODoc
 
tgt - Variable in class org.obolibrary.oboformat.parser.XrefExpander.GenusDifferentiaExpansion
 
tgt - Variable in class org.obolibrary.oboformat.parser.XrefExpander.ReverseGenusDifferentiaExpansion
 
toString() - Method in class org.obolibrary.cli.OBORunnerConfiguration.Variable
 
toString() - Method in class org.obolibrary.oboformat.diff.Diff
 
toString() - Method in class org.obolibrary.oboformat.model.Clause
 
toString() - Method in class org.obolibrary.oboformat.model.Frame
 
toString() - Method in class org.obolibrary.oboformat.model.OBODoc
 
toString() - Method in class org.obolibrary.oboformat.model.QualifierValue
 
toString() - Method in class org.obolibrary.oboformat.model.Xref
 
toString() - Method in enum org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag
 
toString() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream
 
translateIdToIRIString(String) - Method in class obo.obolibrary.idrules.IdTranslator
 
translateIRI(IRI) - Method in class obo.obolibrary.idrules.IdTranslator
 
trGenericClause(OWLAnnotationSubject, String, Clause) - Method in class org.obolibrary.obo2owl.Obo2Owl
 
trHeaderFrame(Frame) - Method in class org.obolibrary.obo2owl.Obo2Owl
 
trLiteral(Object) - Method in class org.obolibrary.obo2owl.Obo2Owl
 
trRel(String, String, Collection<QualifierValue>) - Method in class org.obolibrary.obo2owl.Obo2Owl
 
trTagToIRI(String) - Static method in class org.obolibrary.obo2owl.Obo2Owl
 
trTermFrame(Frame) - Method in class org.obolibrary.obo2owl.Obo2Owl
 
trTypedefFrame(Frame) - Method in class org.obolibrary.obo2owl.Obo2Owl
 
type - Variable in class org.obolibrary.oboformat.model.Frame
 
typedefFrameMap - Variable in class org.obolibrary.oboformat.model.OBODoc
 

U

untranslatableAxiomsFile - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 

V

value - Variable in class org.obolibrary.cli.OBORunnerConfiguration.Variable
 
value - Variable in class org.obolibrary.oboformat.model.QualifierValue
 
valueOf(String) - Static method in enum org.obolibrary.cli.OBORunnerConfiguration.ExpandMacrosModeOptions
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.obolibrary.obo2owl.Obo2OWLConstants.Obo2OWLVocabulary
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.obolibrary.oboformat.model.Frame.FrameType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag
Returns the enum constant of this type with the specified name.
values() - Static method in enum org.obolibrary.cli.OBORunnerConfiguration.ExpandMacrosModeOptions
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.obolibrary.obo2owl.Obo2OWLConstants.Obo2OWLVocabulary
Returns an array containing the constants of this enum type, in the order they are declared.
values - Variable in class org.obolibrary.oboformat.model.Clause
 
values() - Static method in enum org.obolibrary.oboformat.model.Frame.FrameType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag
Returns an array containing the constants of this enum type, in the order they are declared.
version - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 

W

width(int) - Method in class org.obolibrary.gui.GuiTools.GBHelper
Sets the width of the area in terms of rows.
write(String, BufferedWriter) - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter
 
write(URL, BufferedWriter) - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter
 
write(BufferedReader, BufferedWriter) - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter
 
write(OBODoc, String) - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter
 
write(OBODoc, BufferedWriter) - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter
 
write(OBODoc, BufferedWriter, OBOFormatWriter.NameProvider) - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter
 
write(Frame, BufferedWriter, OBOFormatWriter.NameProvider) - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter
 
write(Clause, BufferedWriter, OBOFormatWriter.NameProvider) - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter
 
writeDef(Clause, BufferedWriter) - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter
 
writeHeader(Frame, BufferedWriter, OBOFormatWriter.NameProvider) - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter
 
writeLabelOWL - Variable in class org.obolibrary.cli.OBORunnerConfiguration
 
writePropertyValue(Clause, BufferedWriter) - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter
 
writeSynonym(Clause, BufferedWriter) - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter
 

X

Xref - Class in org.obolibrary.oboformat.model
 
Xref(String) - Constructor for class org.obolibrary.oboformat.model.Xref
 
xref - Variable in class org.obolibrary.oboformat.parser.XrefExpander.Rule
 
XrefExpander - Class in org.obolibrary.oboformat.parser
 
XrefExpander(OBODoc) - Constructor for class org.obolibrary.oboformat.parser.XrefExpander
 
XrefExpander(OBODoc, String) - Constructor for class org.obolibrary.oboformat.parser.XrefExpander
 
XrefExpander(OBODoc, OBODoc) - Constructor for class org.obolibrary.oboformat.parser.XrefExpander
 
XrefExpander.EquivalenceExpansion - Class in org.obolibrary.oboformat.parser
 
XrefExpander.EquivalenceExpansion() - Constructor for class org.obolibrary.oboformat.parser.XrefExpander.EquivalenceExpansion
 
XrefExpander.GenusDifferentiaExpansion - Class in org.obolibrary.oboformat.parser
 
XrefExpander.GenusDifferentiaExpansion(String, String) - Constructor for class org.obolibrary.oboformat.parser.XrefExpander.GenusDifferentiaExpansion
 
XrefExpander.HasSubClassExpansion - Class in org.obolibrary.oboformat.parser
 
XrefExpander.HasSubClassExpansion() - Constructor for class org.obolibrary.oboformat.parser.XrefExpander.HasSubClassExpansion
 
XrefExpander.IsaExpansion - Class in org.obolibrary.oboformat.parser
 
XrefExpander.IsaExpansion() - Constructor for class org.obolibrary.oboformat.parser.XrefExpander.IsaExpansion
 
XrefExpander.RelationshipExpansion - Class in org.obolibrary.oboformat.parser
 
XrefExpander.RelationshipExpansion(String) - Constructor for class org.obolibrary.oboformat.parser.XrefExpander.RelationshipExpansion
 
XrefExpander.ReverseGenusDifferentiaExpansion - Class in org.obolibrary.oboformat.parser
 
XrefExpander.ReverseGenusDifferentiaExpansion(String, String) - Constructor for class org.obolibrary.oboformat.parser.XrefExpander.ReverseGenusDifferentiaExpansion
 
XrefExpander.Rule - Class in org.obolibrary.oboformat.parser
 
XrefExpander.Rule() - Constructor for class org.obolibrary.oboformat.parser.XrefExpander.Rule
 
xrefs - Variable in class org.obolibrary.oboformat.model.Clause
 

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