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

A

addBridgeOntology(String) - Method in class owltools.ontologyrelease.OortConfiguration
 
addPath(String) - Method in class owltools.ontologyrelease.OortConfiguration
 
addSourceOntologyPrefix(String) - Method in class owltools.ontologyrelease.OortConfiguration
 
addToSkipFormatSet(String) - Method in class owltools.ontologyrelease.OortConfiguration
 
addValues(String, Collection<String>) - Static method in class owltools.ontologyrelease.OortConfiguration
Only public for testing purposes.
AfterLoading - Annotation Type in owltools.ontologyverification.annotations
 
afterLoading(OWLGraphWrapper) - Method in class owltools.ontologyverification.OntologyCheckHandler
Run tests for the ontology after loading it.
AfterMireot - Annotation Type in owltools.ontologyverification.annotations
 
afterMireot(OWLGraphWrapper) - Method in class owltools.ontologyverification.OntologyCheckHandler
Run tests for the ontology after mireoting.
AfterReasoning - Annotation Type in owltools.ontologyverification.annotations
 
afterReasoning(OWLGraphWrapper) - Method in class owltools.ontologyverification.OntologyCheckHandler
Run tests for the ontology after reasoning.
allowFileOverwrite(File) - Method in class owltools.ontologyrelease.OboOntologyReleaseRunner
Hook method to handle an unexpected file overwrite request.

B

BuildVersionId - Class in owltools.ontologyrelease
Deprecated. 
BuildVersionId() - Constructor for class owltools.ontologyrelease.BuildVersionId
Deprecated.  

C

Check - Annotation Type in owltools.ontologyverification.annotations
 
checkNew(File) - Method in class owltools.ontologyrelease.OboOntologyReleaseRunner
Check whether the file is new.
CheckResult - Class in owltools.ontologyverification
 
CheckResult.Status - Enum in owltools.ontologyverification
 
convertToMultiline(String) - Static method in class owltools.ontologyrelease.OboOntologyReleaseRunnerGui
 
createError(String) - Static method in class owltools.ontologyverification.CheckResult
 
createError(List<String>) - Static method in class owltools.ontologyverification.CheckResult
 
createMultiLineLabel(String) - Static method in class owltools.ontologyrelease.OboOntologyReleaseRunnerGui
 
createOortConfig(Properties) - Static method in class owltools.ontologyrelease.OortConfiguration
Create an OortConfiguration from the given Properties.
createProperties(OortConfiguration) - Static method in class owltools.ontologyrelease.OortConfiguration
Create a Properties object for the given configuration.
createRelease(Vector<String>) - Method in class owltools.ontologyrelease.OboOntologyReleaseRunner
 
createSuccess() - Static method in class owltools.ontologyverification.CheckResult
 
createSuccess(String) - Static method in class owltools.ontologyverification.CheckResult
 
createWarning(String) - Static method in class owltools.ontologyverification.CheckResult
 
createWarning(List<String>) - Static method in class owltools.ontologyverification.CheckResult
 

D

DEFAULT_INSTANCE - Static variable in class owltools.ontologyverification.OntologyCheckHandler
Default instance for convenient use.
DefaultOntologyChecks - Class in owltools.ontologyverification
 
DefaultOntologyChecks() - Constructor for class owltools.ontologyverification.DefaultOntologyChecks
 
disableReleaseButton() - Method in class owltools.ontologyrelease.gui.OortGuiMainFrame
 

E

enableReleaseButton() - Method in class owltools.ontologyrelease.gui.OortGuiMainFrame
 
end(PrintWriter, OWLGraphWrapper) - Method in class owltools.ontologyrelease.reports.OntologyReportGenerator.AbstractReport
 
end(PrintWriter, OWLGraphWrapper) - Method in interface owltools.ontologyrelease.reports.OntologyReportGenerator.OntologyReport
End the report.
escape(String, char) - Static method in class owltools.ontologyrelease.OortConfiguration
Only public for testing purposes.
execute() - Method in class owltools.ontologyrelease.BuildVersionId
Deprecated. Run task.
execute() - Method in class owltools.ontologyrelease.GetOntologyId
Deprecated.  
execute() - Method in class owltools.ontologyrelease.OboProperty
Deprecated.  
executeRelease(OortGuiConfiguration) - Method in class owltools.ontologyrelease.gui.OortGuiMainFrame
Execute the actual release.
External2GoReports - Class in owltools.ontologyrelease.reports.go
Provide reports for all external to go mappings.
External2GoReports.External2GoKegg - Class in owltools.ontologyrelease.reports.go
 
External2GoReports.External2GoMetaCyc - Class in owltools.ontologyrelease.reports.go
 
External2GoReports.External2GoReactome - Class in owltools.ontologyrelease.reports.go
 
External2GoReports.External2GoResid - Class in owltools.ontologyrelease.reports.go
 
External2GoReports.External2GoRhea - Class in owltools.ontologyrelease.reports.go
 
External2GoReports.External2GoUmBbdEnzymeId - Class in owltools.ontologyrelease.reports.go
 
External2GoReports.External2GoUmBbdPathwayId - Class in owltools.ontologyrelease.reports.go
 
External2GoReports.External2GoUmBbdReactionId - Class in owltools.ontologyrelease.reports.go
 
External2GoReports.External2GoWikipedia - Class in owltools.ontologyrelease.reports.go
 

F

format(Date) - Static method in class owltools.ontologyrelease.OntologyVersionTools
Format a date into the canonical format of YYYY-MM-DD.

G

GeneOntologyReports - Class in owltools.ontologyrelease.reports.go
Provide all reports for the GeneOntology.
generate(OWLGraphWrapper) - Method in class owltools.ontologyrelease.OntologyMetadata
 
generateReports(OWLGraphWrapper) - Method in class owltools.ontologyrelease.reports.OntologyReportGenerator
Generate the internal reports for a given ontology.
getAdvancedPanel() - Method in class owltools.ontologyrelease.gui.OortGuiMainFrame
Retrieve advanced panel, create new if it not exists.
getBase() - Method in class owltools.ontologyrelease.OortConfiguration
 
getBridgeOntologies() - Method in class owltools.ontologyrelease.OortConfiguration
 
getCatalogXML() - Method in class owltools.ontologyrelease.OortConfiguration
 
getCheckName() - Method in class owltools.ontologyverification.CheckResult
 
getDefaultFormat() - Method in class owltools.ontologyrelease.OortConfiguration
 
getFile() - Method in class owltools.ontologyrelease.GetOntologyId
Deprecated.  
getFileHeader() - Method in class owltools.ontologyrelease.reports.OBOTermsAltIdsReport
 
getFileHeader() - Method in class owltools.ontologyrelease.reports.OBOTermsIdsObsoleteReport
 
getFileHeader() - Method in class owltools.ontologyrelease.reports.OBOTermsIdsReport
 
getFileHeader() - Method in class owltools.ontologyrelease.reports.ObsoletesAllReport
 
getFileHeader() - Method in class owltools.ontologyrelease.reports.ObsoletesExactReport
 
getFileHeader() - Method in class owltools.ontologyrelease.reports.ObsoletesInExactReport
 
getFileHeader() - Method in class owltools.ontologyrelease.reports.OntologyReportGenerator.AbstractReport
 
getGeneOntologyReports() - Static method in class owltools.ontologyrelease.reports.go.GeneOntologyReports
 
getHint() - Method in exception owltools.ontologyrelease.OboOntologyReleaseRunnerCheckException
 
getJustifyAssertedSubclassesFrom() - Method in class owltools.ontologyrelease.OortConfiguration
 
getMacroStrategy() - Method in class owltools.ontologyrelease.OortConfiguration
 
getMessage() - Method in exception owltools.ontologyrelease.OboOntologyReleaseRunnerCheckException
 
getMessages() - Method in class owltools.ontologyverification.CheckResult
 
getOboInOWLVersion(OWLOntology) - Static method in class owltools.ontologyrelease.OntologyVersionTools
Retrieve the ontology version from the OboInOwl remark.
getOboInOWLVersionDate(OWLOntology) - Static method in class owltools.ontologyrelease.OntologyVersionTools
Retrieve the ontology version from the OboInOwl remark and parse as Date.
GetOntologyId - Class in owltools.ontologyrelease
Deprecated. 
GetOntologyId() - Constructor for class owltools.ontologyrelease.GetOntologyId
Deprecated.  
getOntologyVersion(OWLOntology) - Static method in class owltools.ontologyrelease.OntologyVersionTools
Retrieve the ontology version as string.
getOntologyVersionDate(OWLOntology) - Static method in class owltools.ontologyrelease.OntologyVersionTools
Retrieve the ontology version as Date.
getOntologyVersionIRI(OWLOntology) - Static method in class owltools.ontologyrelease.OntologyVersionTools
Retrieve the ontology version as IRI.
getOwlOfnFormat() - Method in class owltools.ontologyrelease.OortConfiguration
 
getOwlXMLFormat() - Method in class owltools.ontologyrelease.OortConfiguration
 
getPaths() - Method in class owltools.ontologyrelease.OortConfiguration
 
getPropertyViews() - Method in class owltools.ontologyrelease.OortConfiguration
 
getQueryOntology() - Method in class owltools.ontologyrelease.OortConfiguration
 
getQueryOntologyReference() - Method in class owltools.ontologyrelease.OortConfiguration
 
getReasonerName() - Method in class owltools.ontologyrelease.OortConfiguration
 
getReasons() - Method in exception owltools.ontologyrelease.OboOntologyReleaseRunnerCheckException
 
getReportFileName() - Method in class owltools.ontologyrelease.reports.OBOTermsAltIdsReport
 
getReportFileName() - Method in class owltools.ontologyrelease.reports.OBOTermsIdsObsoleteReport
 
getReportFileName() - Method in class owltools.ontologyrelease.reports.OBOTermsIdsReport
 
getReportFileName() - Method in class owltools.ontologyrelease.reports.ObsoletesAllReport
 
getReportFileName() - Method in class owltools.ontologyrelease.reports.ObsoletesExactReport
 
getReportFileName() - Method in class owltools.ontologyrelease.reports.ObsoletesInExactReport
 
getReportFileName() - Method in interface owltools.ontologyrelease.reports.OntologyReportGenerator.OntologyReport
Get the target file name for this report.
getReports() - Static method in class owltools.ontologyrelease.reports.go.External2GoReports
Get all external reports.
getReportSubFolderName() - Method in class owltools.ontologyrelease.reports.OntologyReportGenerator.AbstractReport
 
getReportSubFolderName() - Method in interface owltools.ontologyrelease.reports.OntologyReportGenerator.OntologyReport
Get the sub folder name for the report
getSkipFormatSet() - Method in class owltools.ontologyrelease.OortConfiguration
 
getSourceOntologyPrefixes() - Method in class owltools.ontologyrelease.OortConfiguration
 
getStatus() - Method in class owltools.ontologyverification.CheckResult
 

H

handleTerm(PrintWriter, OWLClass, OWLGraphWrapper) - Method in class owltools.ontologyrelease.reports.OBOTermsAltIdsReport
 
handleTerm(PrintWriter, OWLClass, OWLGraphWrapper) - Method in class owltools.ontologyrelease.reports.OBOTermsIdsObsoleteReport
 
handleTerm(PrintWriter, OWLClass, OWLGraphWrapper) - Method in class owltools.ontologyrelease.reports.OBOTermsIdsReport
 
handleTerm(PrintWriter, OWLClass, OWLGraphWrapper) - Method in class owltools.ontologyrelease.reports.ObsoletesAllReport
 
handleTerm(PrintWriter, OWLClass, OWLGraphWrapper) - Method in class owltools.ontologyrelease.reports.ObsoletesExactReport
 
handleTerm(PrintWriter, OWLClass, OWLGraphWrapper) - Method in class owltools.ontologyrelease.reports.ObsoletesInExactReport
 
handleTerm(PrintWriter, OWLClass, OWLGraphWrapper) - Method in interface owltools.ontologyrelease.reports.OntologyReportGenerator.OntologyReport
Handle an OWLObject during the report.

I

isAddImportsFromSupports() - Method in class owltools.ontologyrelease.OortConfiguration
 
isAddSupportFromImports() - Method in class owltools.ontologyrelease.OortConfiguration
 
isAllowEquivalentNamedClassPairs() - Method in class owltools.ontologyrelease.OortConfiguration
 
isAllowFileOverWrite() - Method in class owltools.ontologyrelease.OortConfiguration
 
isAsserted() - Method in class owltools.ontologyrelease.OortConfiguration
 
isAutoDetectBridgingOntology() - Method in class owltools.ontologyrelease.OortConfiguration
 
isCheckConsistency() - Method in class owltools.ontologyrelease.OortConfiguration
 
isDeprecated(OWLClass, OWLOntology, OWLAnnotationProperty) - Method in class owltools.ontologyrelease.OntologyMetadata
 
isEnforceEL() - Method in class owltools.ontologyrelease.OortConfiguration
 
isExecuteOntologyChecks() - Method in class owltools.ontologyrelease.OortConfiguration
 
isExpandMacros() - Method in class owltools.ontologyrelease.OortConfiguration
 
isExpandShortcutRelations() - Method in class owltools.ontologyrelease.OortConfiguration
 
isExpandXrefs() - Method in class owltools.ontologyrelease.OortConfiguration
 
isForceRelease() - Method in class owltools.ontologyrelease.OortConfiguration
 
isGafToOwl() - Method in class owltools.ontologyrelease.OortConfiguration
 
isJustifyAssertedSubclasses() - Method in class owltools.ontologyrelease.OortConfiguration
 
isOBOOntologyVersion(String) - Static method in class owltools.ontologyrelease.OntologyVersionTools
Check, whether the given version string is an OBO-specific IRI.
isQueryOntologyReferenceIsIRI() - Method in class owltools.ontologyrelease.OortConfiguration
 
isRecreateMireot() - Method in class owltools.ontologyrelease.OortConfiguration
 
isRemoveDanglingBeforeReasoning() - Method in class owltools.ontologyrelease.OortConfiguration
 
isRemoveQueryOntologyReference() - Method in class owltools.ontologyrelease.OortConfiguration
 
isRepairAnnotationCardinality() - Method in class owltools.ontologyrelease.OortConfiguration
 
isSimple() - Method in class owltools.ontologyrelease.OortConfiguration
 
isSkipFormat(String) - Method in class owltools.ontologyrelease.OortConfiguration
 
isTranslateDisjointsToEquivalents() - Method in class owltools.ontologyrelease.OortConfiguration
 
isUseQueryOntology() - Method in class owltools.ontologyrelease.OortConfiguration
 
isUseReleaseFolder() - Method in class owltools.ontologyrelease.OortConfiguration
 
isWriteELOntology() - Method in class owltools.ontologyrelease.OortConfiguration
 
isWriteLabelOWL() - Method in class owltools.ontologyrelease.OortConfiguration
 
isWriteMetadata() - Method in class owltools.ontologyrelease.OortConfiguration
 
isWriteSubsets() - Method in class owltools.ontologyrelease.OortConfiguration
 

L

loadConfig(File, OortConfiguration) - Static method in class owltools.ontologyrelease.OortConfiguration
Load the configuration from a property file into the given OortConfiguration.
loadOortConfig(Properties, OortConfiguration) - Static method in class owltools.ontologyrelease.OortConfiguration
Load the given Properties into the OortConfiguration.
log(StringBuilder, Level) - Method in class owltools.ontologyverification.OntologyCheckHandler
 
logger - Static variable in class owltools.ontologyrelease.OboOntologyReleaseRunner
 

M

main(String[]) - Static method in class owltools.ontologyrelease.OboOntologyReleaseRunner
 
main(String[]) - Static method in class owltools.ontologyrelease.OboOntologyReleaseRunnerGui
 

O

OboOntologyReleaseRunner - Class in owltools.ontologyrelease
This class is a command line utility which builds an ontology release.
OboOntologyReleaseRunner(OortConfiguration, File) - Constructor for class owltools.ontologyrelease.OboOntologyReleaseRunner
 
OboOntologyReleaseRunnerCheckException - Exception in owltools.ontologyrelease
OORT Exception indicating a failed check during the release process.
OboOntologyReleaseRunnerCheckException(String) - Constructor for exception owltools.ontologyrelease.OboOntologyReleaseRunnerCheckException
 
OboOntologyReleaseRunnerCheckException(String, List<String>) - Constructor for exception owltools.ontologyrelease.OboOntologyReleaseRunnerCheckException
 
OboOntologyReleaseRunnerCheckException(String, List<String>, String) - Constructor for exception owltools.ontologyrelease.OboOntologyReleaseRunnerCheckException
 
OboOntologyReleaseRunnerGui - Class in owltools.ontologyrelease
GUI access for ontology release runner.
OboOntologyReleaseRunnerGui() - Constructor for class owltools.ontologyrelease.OboOntologyReleaseRunnerGui
 
OboProperty - Class in owltools.ontologyrelease
Deprecated. 
OboProperty() - Constructor for class owltools.ontologyrelease.OboProperty
Deprecated.  
OboProperty(boolean, Project) - Constructor for class owltools.ontologyrelease.OboProperty
Deprecated.  
OboProperty(boolean) - Constructor for class owltools.ontologyrelease.OboProperty
Deprecated.  
OBOTermsAltIdsReport - Class in owltools.ontologyrelease.reports
OntologyReportGenerator.OntologyReport for GeneOntology terms with alternative identifiers.
OBOTermsAltIdsReport(OWLGraphWrapper) - Constructor for class owltools.ontologyrelease.reports.OBOTermsAltIdsReport
 
OBOTermsAltIdsReport(String) - Constructor for class owltools.ontologyrelease.reports.OBOTermsAltIdsReport
 
OBOTermsAltIdsReport(String, String) - Constructor for class owltools.ontologyrelease.reports.OBOTermsAltIdsReport
 
OBOTermsIdsObsoleteReport - Class in owltools.ontologyrelease.reports
OntologyReportGenerator.OntologyReport for obsolete GeneOntology terms.
OBOTermsIdsObsoleteReport(OWLGraphWrapper) - Constructor for class owltools.ontologyrelease.reports.OBOTermsIdsObsoleteReport
 
OBOTermsIdsObsoleteReport(String) - Constructor for class owltools.ontologyrelease.reports.OBOTermsIdsObsoleteReport
 
OBOTermsIdsObsoleteReport(String, String) - Constructor for class owltools.ontologyrelease.reports.OBOTermsIdsObsoleteReport
 
OBOTermsIdsReport - Class in owltools.ontologyrelease.reports
OntologyReportGenerator.OntologyReport for identifiers and labels of all GeneOntology terms.
OBOTermsIdsReport(OWLGraphWrapper) - Constructor for class owltools.ontologyrelease.reports.OBOTermsIdsReport
 
OBOTermsIdsReport(String) - Constructor for class owltools.ontologyrelease.reports.OBOTermsIdsReport
 
OBOTermsIdsReport(String, String) - Constructor for class owltools.ontologyrelease.reports.OBOTermsIdsReport
 
ObsoletesAllReport - Class in owltools.ontologyrelease.reports
OntologyReportGenerator.OntologyReport for obsolete terms with a direct or possible replacement
ObsoletesAllReport(OWLGraphWrapper) - Constructor for class owltools.ontologyrelease.reports.ObsoletesAllReport
 
ObsoletesAllReport(String) - Constructor for class owltools.ontologyrelease.reports.ObsoletesAllReport
 
ObsoletesExactReport - Class in owltools.ontologyrelease.reports
OntologyReportGenerator.OntologyReport for obsolete terms with a direct replacement
ObsoletesExactReport(OWLGraphWrapper) - Constructor for class owltools.ontologyrelease.reports.ObsoletesExactReport
 
ObsoletesExactReport(String) - Constructor for class owltools.ontologyrelease.reports.ObsoletesExactReport
 
ObsoletesInExactReport - Class in owltools.ontologyrelease.reports
OntologyReportGenerator.OntologyReport for obsolete terms with possible replacements (consider)
ObsoletesInExactReport(OWLGraphWrapper) - Constructor for class owltools.ontologyrelease.reports.ObsoletesInExactReport
 
ObsoletesInExactReport(String) - Constructor for class owltools.ontologyrelease.reports.ObsoletesInExactReport
 
OntologyCheckHandler - Class in owltools.ontologyverification
Handle the ontology checks for an ontology and its reporting via a Logger.
OntologyCheckHandler(boolean, Class<?>...) - Constructor for class owltools.ontologyverification.OntologyCheckHandler
Create a new instance.
OntologyCheckRunner - Class in owltools.ontologyverification
Identify and run ontology checks for an ontology (OWLGraphWrapper).
OntologyMetadata - Class in owltools.ontologyrelease
 
OntologyMetadata(PrintWriter) - Constructor for class owltools.ontologyrelease.OntologyMetadata
 
OntologyMetadata() - Constructor for class owltools.ontologyrelease.OntologyMetadata
 
OntologyMetadata.MetadataField - Enum in owltools.ontologyrelease
 
OntologyMetadata.MetadataQualifier - Enum in owltools.ontologyrelease
 
OntologyReportGenerator - Class in owltools.ontologyrelease.reports
Basic tool for generating ontology reports on a term basis.
OntologyReportGenerator(List<OntologyReportGenerator.OntologyReport>, File) - Constructor for class owltools.ontologyrelease.reports.OntologyReportGenerator
 
OntologyReportGenerator.AbstractReport - Class in owltools.ontologyrelease.reports
Abstract helper class for OntologyReportGenerator.OntologyReport.
OntologyReportGenerator.AbstractReport() - Constructor for class owltools.ontologyrelease.reports.OntologyReportGenerator.AbstractReport
 
OntologyReportGenerator.OntologyReport - Interface in owltools.ontologyrelease.reports
Ontology report to be run with the OntologyReportGenerator.
OntologyVersionTools - Class in owltools.ontologyrelease
Tools to handle the writing and reading of version information of owl ontology files.
OortConfiguration - Class in owltools.ontologyrelease
Parameters for OboOntologyReleaseRunner.
OortConfiguration() - Constructor for class owltools.ontologyrelease.OortConfiguration
 
OortConfiguration.MacroStrategy - Enum in owltools.ontologyrelease
 
OortGuiAdvancedPanel - Class in owltools.ontologyrelease.gui
Panel containing advanced options for the release manager.
OortGuiAdvancedPanel(Frame, OortConfiguration) - Constructor for class owltools.ontologyrelease.gui.OortGuiAdvancedPanel
Create the panel with the given default values.
OortGuiConfiguration - Class in owltools.ontologyrelease.gui
Parameters for OboOntologyReleaseRunnerGui with different default values.
OortGuiConfiguration() - Constructor for class owltools.ontologyrelease.gui.OortGuiConfiguration
 
OortGuiMainFrame - Class in owltools.ontologyrelease.gui
GUI main frame, calls all constructors for the sub components.
OortGuiMainFrame(OortGuiConfiguration) - Constructor for class owltools.ontologyrelease.gui.OortGuiMainFrame
 
OortGuiMainFrame(BlockingQueue<String>, OortGuiConfiguration) - Constructor for class owltools.ontologyrelease.gui.OortGuiMainFrame
Main constructor.
OortGuiMainPanel - Class in owltools.ontologyrelease.gui
GUI component for the minimum number of configurations required for the release manager.
OortGuiMainPanel(Frame, OortConfiguration) - Constructor for class owltools.ontologyrelease.gui.OortGuiMainPanel
Constructor allows to build a panel with default values.
OortGuiMenuBar - Class in owltools.ontologyrelease.gui
Menu bar for OORT.
OortGuiMenuBar(OortGuiMainFrame, OortConfiguration) - Constructor for class owltools.ontologyrelease.gui.OortGuiMenuBar
Create a new menu instance.
OortGuiQueryOntologyPanel - Class in owltools.ontologyrelease.gui
 
OortGuiQueryOntologyPanel(Frame, OortConfiguration) - Constructor for class owltools.ontologyrelease.gui.OortGuiQueryOntologyPanel
 
owltools.ontologyrelease - package owltools.ontologyrelease
Oort - OBO Ontology Release Tool (OORT)
owltools.ontologyrelease.gui - package owltools.ontologyrelease.gui
 
owltools.ontologyrelease.reports - package owltools.ontologyrelease.reports
 
owltools.ontologyrelease.reports.go - package owltools.ontologyrelease.reports.go
 
owltools.ontologyverification - package owltools.ontologyverification
 
owltools.ontologyverification.annotations - package owltools.ontologyverification.annotations
 

P

parseVersion(String) - Static method in class owltools.ontologyrelease.OntologyVersionTools
Try to parse the string as a Date using the both patterns for version IRI and OboInOwl.
PropertyView - Class in owltools.ontologyrelease
 
PropertyView() - Constructor for class owltools.ontologyrelease.PropertyView
 

R

readConfig(File) - Static method in class owltools.ontologyrelease.OortConfiguration
Read from a configuration property file and load it into a new OortConfiguration object.
removeFromSkipFormatSet(String) - Method in class owltools.ontologyrelease.OortConfiguration
 
renderMessageString() - Method in exception owltools.ontologyrelease.OboOntologyReleaseRunnerCheckException
Render the exception in an human readable form and suitable for appending to a logger.
report(StringBuilder, CheckResult, CheckResult.Status) - Method in class owltools.ontologyverification.OntologyCheckHandler
 
reportHeader(StringBuilder) - Method in class owltools.ontologyverification.OntologyCheckHandler
 

S

selfReferenceInDefinition(OWLGraphWrapper) - Method in class owltools.ontologyverification.DefaultOntologyChecks
Check, whether the class is defined using the class itself.
setAddImportsFromSupports(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setAddSupportFromImports(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setAllowEquivalentNamedClassPairs(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setAllowFileOverWrite(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
Set allowFileOverWrite
setAllowOverwrite(boolean) - Method in class owltools.ontologyrelease.gui.OortGuiAdvancedPanel
 
setAsserted(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
Set asserted
setAutoDetectBridgingOntology(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setBase(File) - Method in class owltools.ontologyrelease.OortConfiguration
 
setBridgeOntologies(List<String>) - Method in class owltools.ontologyrelease.OortConfiguration
 
setCatalogXML(String) - Method in class owltools.ontologyrelease.OortConfiguration
 
setCheckConsistency(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setEnforceEL(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setExecuteOntologyChecks(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setExpandMacros(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setExpandShortcutRelations(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setExpandXrefs(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
Set export bridges
setFile(File) - Method in class owltools.ontologyrelease.BuildVersionId
Deprecated. The file in which the build number is stored.
setFile(String) - Method in class owltools.ontologyrelease.GetOntologyId
Deprecated.  
setForceRelease(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setGafToOwl(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setJustifyAssertedSubclasses(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setJustifyAssertedSubclassesFrom(String) - Method in class owltools.ontologyrelease.OortConfiguration
 
setMacroStrategy(OortConfiguration.MacroStrategy) - Method in class owltools.ontologyrelease.OortConfiguration
Set the OortConfiguration.MacroStrategy
setOboInOWLVersion(OWLOntology, String) - Static method in class owltools.ontologyrelease.OntologyVersionTools
Set the OboInOWL remark to the given ontology version.
setOboInOWLVersion(OWLOntology, Date) - Static method in class owltools.ontologyrelease.OntologyVersionTools
Set the OboInOWL remark to the given date.
setOntologyVersion(OWLOntology, String) - Static method in class owltools.ontologyrelease.OntologyVersionTools
Set the ontology version IRI in the OntologyID to the given string.
setOntologyVersion(OWLOntology, Date, String, String) - Static method in class owltools.ontologyrelease.OntologyVersionTools
Set the ontology version IRI in the OntologyID.
setOntologyVersion(OWLOntology, IRI) - Static method in class owltools.ontologyrelease.OntologyVersionTools
Set the ontology version IRI in the OntologyID.
setPropertyViews(Set<PropertyView>) - Method in class owltools.ontologyrelease.OortConfiguration
 
setQueryOntology(String) - Method in class owltools.ontologyrelease.OortConfiguration
 
setQueryOntologyReference(String) - Method in class owltools.ontologyrelease.OortConfiguration
 
setQueryOntologyReferenceIsIRI(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setReasonerName(String) - Method in class owltools.ontologyrelease.OortConfiguration
Set the reasoner name
setRecreateMireot(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
Set recreateMireot
setRemoveDanglingBeforeReasoning(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setRemoveQueryOntologyReference(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setRepairAnnotationCardinality(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setSimple(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
Set simple.
setSkipFormatSet(Set<String>) - Method in class owltools.ontologyrelease.OortConfiguration
 
setSourceOntologyPrefixes(Set<String>) - Method in class owltools.ontologyrelease.OortConfiguration
 
setTranslateDisjointsToEquivalents(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setUseQueryOntology(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setUseReleaseFolder(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setWriteELOntology(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setWriteLabelOWL(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setWriteMetadata(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setWriteSubsets(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
start(PrintWriter, OWLGraphWrapper) - Method in class owltools.ontologyrelease.reports.OntologyReportGenerator.AbstractReport
 
start(PrintWriter, OWLGraphWrapper) - Method in interface owltools.ontologyrelease.reports.OntologyReportGenerator.OntologyReport
Start the report.
summary(int, int, int, int, int) - Method in class owltools.ontologyverification.OntologyCheckHandler
 

T

toString() - Method in class owltools.ontologyrelease.OortConfiguration
 
toString() - Method in class owltools.ontologyverification.CheckResult
 

U

unescape(String) - Static method in class owltools.ontologyrelease.OortConfiguration
Only public for testing purposes.

V

valueOf(String) - Static method in enum owltools.ontologyrelease.OntologyMetadata.MetadataField
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.ontologyrelease.OntologyMetadata.MetadataQualifier
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.ontologyrelease.OortConfiguration.MacroStrategy
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.ontologyverification.CheckResult.Status
Returns the enum constant of this type with the specified name.
values() - Static method in enum owltools.ontologyrelease.OntologyMetadata.MetadataField
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.ontologyrelease.OntologyMetadata.MetadataQualifier
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.ontologyrelease.OortConfiguration.MacroStrategy
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.ontologyverification.CheckResult.Status
Returns an array containing the constants of this enum type, in the order they are declared.

W

writeConfig(File, OortConfiguration) - Static method in class owltools.ontologyrelease.OortConfiguration
Write the given OortConfiguration into the file as properties.
writeTabs(PrintWriter, CharSequence...) - Method in class owltools.ontologyrelease.reports.OntologyReportGenerator.AbstractReport
 

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