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A

AbstractCheck - Class in owltools.ontologyverification.impl
Helper to reduce boiler plate code for an OntologyCheck.
AbstractCheck(String, String, boolean, OntologyCheckRunner.TimePoint) - Constructor for class owltools.ontologyverification.impl.AbstractCheck
 
AbstractReport() - Constructor for class owltools.ontologyrelease.reports.OntologyReportGenerator.AbstractReport
 
addBridgeOntology(String) - Method in class owltools.ontologyrelease.OortConfiguration
 
addPath(String) - Method in class owltools.ontologyrelease.OortConfiguration
 
addRewriteIRIMap(IRI, IRI) - Method in class owltools.ontologyrelease.OortConfiguration
Adds entry to rewrite map
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(OWLGraphWrapper) - Method in class owltools.ontologyverification.OntologyCheckHandler
Run tests for the ontology after loading it.
afterMireot(OWLGraphWrapper) - Method in class owltools.ontologyverification.OntologyCheckHandler
Run tests for the ontology after mireoting.
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.
AltIdInSignature - Class in owltools.ontologyverification.impl
 
AltIdInSignature() - Constructor for class owltools.ontologyverification.impl.AltIdInSignature
 
assertAllInferences(OWLGraphWrapper, String) - Static method in class owltools.cli.AssertInferenceTool
 
assertInferences(OWLGraphWrapper, boolean, boolean, boolean, boolean, boolean, InferenceBuilder.OWLClassFilter, BufferedWriter) - Static method in class owltools.cli.AssertInferenceTool
Assert inferred super class relationships and (optional) remove redundant ones.
assertInferences(OWLGraphWrapper, boolean, boolean, boolean, boolean, boolean, boolean, boolean, InferenceBuilder.OWLClassFilter, BufferedWriter) - Static method in class owltools.cli.AssertInferenceTool
 
AssertInferenceTool - Class in owltools.cli
Simple command-line tool to assert inferences and (optional) remove redundant relations
AssertInferenceTool() - Constructor for class owltools.cli.AssertInferenceTool
 
AssertInferredClassExpressions - Class in owltools.cli
 
AssertInferredClassExpressions() - Constructor for class owltools.cli.AssertInferredClassExpressions
 
AssertInferredClassExpressions.OWLClassFilter - Interface in owltools.cli
 

B

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

C

check(OWLGraphWrapper, Collection<OWLObject>) - Method in class owltools.ontologyverification.impl.AltIdInSignature
 
check(OWLClass, OWLGraphWrapper, Map<String, OWLObject>, List<CheckWarning>, OWLPrettyPrinter) - Method in class owltools.ontologyverification.impl.AltIdInSignature
 
check(OWLGraphWrapper, Collection<OWLObject>) - Method in class owltools.ontologyverification.impl.CycleCheck
 
check(OWLGraphWrapper, Collection<OWLObject>) - Method in class owltools.ontologyverification.impl.DanglingReferenceCheck
 
check(OWLClass, OWLGraphWrapper, List<CheckWarning>, OWLPrettyPrinter) - Method in class owltools.ontologyverification.impl.DanglingReferenceCheck
 
check(OWLGraphWrapper, Collection<OWLObject>) - Method in class owltools.ontologyverification.impl.NameRedundancyCheck
 
check(OWLGraphWrapper, Collection<OWLObject>) - Method in class owltools.ontologyverification.impl.ObsoleteClassInSignature
 
check(OWLClass, OWLGraphWrapper, List<CheckWarning>, OWLPrettyPrinter) - Method in class owltools.ontologyverification.impl.ObsoleteClassInSignature
 
check(OWLGraphWrapper, Collection<OWLObject>) - Method in class owltools.ontologyverification.impl.SelfReferenceInDefinition
 
check(OWLGraphWrapper, Collection<OWLObject>) - Method in interface owltools.ontologyverification.OntologyCheck
Run the check for the given ontology.
checkNew(File) - Method in class owltools.ontologyrelease.OboOntologyReleaseRunner
Check whether the file is new.
CheckSummary(boolean, int, String) - Constructor for class owltools.ontologyverification.OntologyCheckHandler.CheckSummary
 
CheckWarning - Class in owltools.ontologyverification
Information about an error or warning as a result of an ontology check.
CheckWarning(String, String, boolean, IRI) - Constructor for class owltools.ontologyverification.CheckWarning
 
CheckWarning(String, String, boolean, IRI, String) - Constructor for class owltools.ontologyverification.CheckWarning
 
CheckWarning(String, String, boolean, List<IRI>, String) - Constructor for class owltools.ontologyverification.CheckWarning
 
convertToMultiline(String) - Static method in class owltools.ontologyrelease.OboOntologyReleaseRunnerGui
 
createMultiLineLabel(String) - Static method in class owltools.ontologyrelease.OboOntologyReleaseRunnerGui
 
createNameFiltered(Set<String>, OortConfiguration) - Static method in class owltools.ontologyrelease.logging.ExplicitReportFileHandler
 
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() - Method in class owltools.ontologyrelease.OboOntologyReleaseRunner
Create a release, use the OortConfiguration instance specified the in constructor.
createSuffixFiltered(Set<String>, OortConfiguration) - Static method in class owltools.ontologyrelease.logging.ExplicitReportFileHandler
 
CycleCheck - Class in owltools.ontologyverification.impl
Simple cycle check using the asserted super/sub class relations.
CycleCheck() - Constructor for class owltools.ontologyverification.impl.CycleCheck
 

D

DanglingReferenceCheck - Class in owltools.ontologyverification.impl
Check for dangling references in equivalence axioms.
DanglingReferenceCheck() - Constructor for class owltools.ontologyverification.impl.DanglingReferenceCheck
 
disableReleaseButton() - Method in class owltools.ontologyrelease.gui.OortGuiMainFrame
 
doWriteReport(String) - Method in class owltools.ontologyrelease.logging.ExplicitReportFileHandler
 

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.
equals(Object) - Method in class owltools.ontologyverification.CheckWarning
 
equals(Object) - Method in class owltools.ontologyverification.impl.AbstractCheck
 
errorCount - Variable in class owltools.ontologyverification.OntologyCheckHandler.CheckSummary
 
ErrorReportFileHandler - Class in owltools.ontologyrelease.logging
 
ErrorReportFileHandler(File, String) - Constructor for class owltools.ontologyrelease.logging.ErrorReportFileHandler
 
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.
ExplicitReportFileHandler - Class in owltools.ontologyrelease.logging
 
ExplicitReportFileHandler(OortConfiguration) - Constructor for class owltools.ontologyrelease.logging.ExplicitReportFileHandler
 
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

findCycles(OWLGraphWrapper) - Static method in class owltools.ontologyrelease.OboBasicDagCheck
Find cycles of any relationship.
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.
getAvailableChecks() - Static method in class owltools.ontologyrelease.OortConfiguration
Provide a list of all OntologyCheck's known to this configuration.
getBase() - Method in class owltools.ontologyrelease.OortConfiguration
 
getBridgeOntologies() - Method in class owltools.ontologyrelease.OortConfiguration
 
getCatalogXML() - Method in class owltools.ontologyrelease.OortConfiguration
 
getCheck() - Method in class owltools.ontologyverification.CheckWarning
 
getChunkLevel() - Method in class owltools.renderer.markdown.MarkdownRenderer
 
getDefaultFormat() - Method in class owltools.ontologyrelease.OortConfiguration
 
getErrorReportFile() - Method in class owltools.ontologyrelease.OortConfiguration
 
getExpressions(OWLOntology, Set<OWLObjectProperty>, AssertInferredClassExpressions.OWLClassFilter) - Static method in class owltools.cli.AssertInferredClassExpressions
 
getField() - Method in class owltools.ontologyverification.CheckWarning
 
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
 
getFilterSimpleProperties() - Method in class owltools.ontologyrelease.OortConfiguration
 
getGeneOntologyReports() - Static method in class owltools.ontologyrelease.reports.go.GeneOntologyReports
 
getHint() - Method in exception owltools.ontologyrelease.OboOntologyReleaseRunnerCheckException
 
getID() - Method in class owltools.ontologyverification.impl.AbstractCheck
 
getID() - Method in interface owltools.ontologyverification.OntologyCheck
 
getIgnoreSelectedEquivalentPairSet() - Method in class owltools.ontologyrelease.OortConfiguration
 
getIris() - Method in class owltools.ontologyverification.CheckWarning
 
getJustifyAssertedSubclassesFrom() - Method in class owltools.ontologyrelease.OortConfiguration
 
getLabel() - Method in class owltools.ontologyverification.impl.AbstractCheck
 
getLabel() - Method in interface owltools.ontologyverification.OntologyCheck
 
getMacroStrategy() - Method in class owltools.ontologyrelease.OortConfiguration
 
getMessage() - Method in exception owltools.ontologyrelease.OboOntologyReleaseRunnerCheckException
 
getMessage() - Method in class owltools.ontologyverification.CheckWarning
 
getOntologyCheck(String) - Static method in class owltools.ontologyrelease.OortConfiguration
 
getOntologyChecks() - Method in class owltools.ontologyrelease.OortConfiguration
 
getOntologyCheckShortName(OntologyCheck) - Static method in class owltools.ontologyrelease.OortConfiguration
 
GetOntologyId - Class in owltools.ontologyrelease
Deprecated.
GetOntologyId() - Constructor for class owltools.ontologyrelease.GetOntologyId
Deprecated.
 
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
getRewriteIRIMap() - Method in class owltools.ontologyrelease.OortConfiguration
 
getSkipFormatSet() - Method in class owltools.ontologyrelease.OortConfiguration
 
getSourceOntologyPrefixes() - Method in class owltools.ontologyrelease.OortConfiguration
 
getThreads() - Method in class owltools.ontologyrelease.OortConfiguration
 
getTimePoint() - Method in class owltools.ontologyverification.impl.AbstractCheck
 
getTimePoint() - Method in interface owltools.ontologyverification.OntologyCheck
Get the OntologyCheckRunner.TimePoint for this check.
If the check is to be run on multiple time points, create multiple instance.
getTraceReportFile() - Method in class owltools.ontologyrelease.OortConfiguration
 
getVersionSubdirectory() - Method in class owltools.ontologyrelease.OortConfiguration
 
GuiLogHandler - Class in owltools.ontologyrelease.logging
 
GuiLogHandler(BlockingQueue<String>) - Constructor for class owltools.ontologyrelease.logging.GuiLogHandler
 

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.
hashCode() - Method in class owltools.ontologyverification.CheckWarning
 
hashCode() - Method in class owltools.ontologyverification.impl.AbstractCheck
 

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
 
isCheckPotentialRedundant() - Method in class owltools.ontologyrelease.OortConfiguration
 
isCreateErrorModules() - 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
 
isFatal() - Method in class owltools.ontologyverification.CheckWarning
 
isFatal() - Method in class owltools.ontologyverification.impl.AbstractCheck
 
isFatal() - Method in interface owltools.ontologyverification.OntologyCheck
 
isForceRelease() - Method in class owltools.ontologyrelease.OortConfiguration
 
isGafToOwl() - Method in class owltools.ontologyrelease.OortConfiguration
 
isIgnoreLockFile() - Method in class owltools.ontologyrelease.OortConfiguration
 
isIgnoreObsolete() - Method in class owltools.ontologyverification.impl.NameRedundancyCheck
 
isJustifyAssertedSubclasses() - Method in class owltools.ontologyrelease.OortConfiguration
 
isQueryOntologyReferenceIsIRI() - Method in class owltools.ontologyrelease.OortConfiguration
 
isRecreateMireot() - Method in class owltools.ontologyrelease.OortConfiguration
 
isRelaxed() - Method in class owltools.ontologyrelease.OortConfiguration
 
isRemoveDanglingBeforeReasoning() - Method in class owltools.ontologyrelease.OortConfiguration
 
isRemoveQueryOntologyReference() - Method in class owltools.ontologyrelease.OortConfiguration
 
isRemoveRedunantAxioms() - Method in class owltools.ontologyrelease.OortConfiguration
 
isRemoveTrailingQualifiers() - Method in class owltools.ontologyrelease.OortConfiguration
 
isRepairAnnotationCardinality() - Method in class owltools.ontologyrelease.OortConfiguration
 
isRunOboBasicDagCheck() - 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
 
isUseIsInferred() - Method in class owltools.ontologyrelease.OortConfiguration
 
isUseQueryOntology() - Method in class owltools.ontologyrelease.OortConfiguration
 
isUseReleaseFolder() - Method in class owltools.ontologyrelease.OortConfiguration
 
isVersionReportFiles() - 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.
Log4jHandler - Class in owltools.ontologyrelease.logging
 
Log4jHandler(Logger, boolean) - Constructor for class owltools.ontologyrelease.logging.Log4jHandler
 
logError(String, Throwable) - Method in class owltools.ontologyrelease.logging.ErrorReportFileHandler
 
logError(String, Throwable) - Method in class owltools.ontologyrelease.logging.ExplicitReportFileHandler
 
logError(String, Throwable) - Method in class owltools.ontologyrelease.logging.GuiLogHandler
 
logError(String, Throwable) - Method in class owltools.ontologyrelease.logging.Log4jHandler
 
logError(String, Throwable) - Method in interface owltools.ontologyrelease.logging.LogHandler
 
logError(String, Throwable) - Method in class owltools.ontologyrelease.logging.TraceReportFileHandler
 
logError(String) - Method in class owltools.ontologyrelease.ReleaseRunnerFileTools
 
logError(String, Exception) - Method in class owltools.ontologyrelease.ReleaseRunnerFileTools
 
LogHandler - Interface in owltools.ontologyrelease.logging
 
logInfo(String) - Method in class owltools.ontologyrelease.logging.ErrorReportFileHandler
 
logInfo(String) - Method in class owltools.ontologyrelease.logging.ExplicitReportFileHandler
 
logInfo(String) - Method in class owltools.ontologyrelease.logging.GuiLogHandler
 
logInfo(String) - Method in class owltools.ontologyrelease.logging.Log4jHandler
 
logInfo(String) - Method in interface owltools.ontologyrelease.logging.LogHandler
 
logInfo(String) - Method in class owltools.ontologyrelease.logging.TraceReportFileHandler
 
logInfo(String) - Method in class owltools.ontologyrelease.ReleaseRunnerFileTools
 
logWarn(String, Throwable) - Method in class owltools.ontologyrelease.logging.ErrorReportFileHandler
 
logWarn(String, Throwable) - Method in class owltools.ontologyrelease.logging.ExplicitReportFileHandler
 
logWarn(String, Throwable) - Method in class owltools.ontologyrelease.logging.GuiLogHandler
 
logWarn(String, Throwable) - Method in class owltools.ontologyrelease.logging.Log4jHandler
 
logWarn(String, Throwable) - Method in interface owltools.ontologyrelease.logging.LogHandler
 
logWarn(String, Throwable) - Method in class owltools.ontologyrelease.logging.TraceReportFileHandler
 
logWarn(String) - Method in class owltools.ontologyrelease.ReleaseRunnerFileTools
 
logWarn(String, Exception) - Method in class owltools.ontologyrelease.ReleaseRunnerFileTools
 

M

main(String[]) - Static method in class owltools.cli.AssertInferenceTool
 
main(String[]) - Static method in class owltools.cli.AssertInferredClassExpressions
 
main(String[]) - Static method in class owltools.cli.Obo2Obo
 
main(String[]) - Static method in class owltools.ontologyrelease.OboOntologyReleaseRunner
 
main(String[]) - Static method in class owltools.ontologyrelease.OboOntologyReleaseRunnerGui
 
MarkdownRenderer - Class in owltools.renderer.markdown
Fairly hacky md renderer, geared towards storing md in github.
MarkdownRenderer() - Constructor for class owltools.renderer.markdown.MarkdownRenderer
 
MAX_REFERENCING_AXIOMS - Variable in class owltools.renderer.markdown.MarkdownRenderer
 
message - Variable in class owltools.ontologyverification.OntologyCheckHandler.CheckSummary
 

N

NameRedundancyCheck - Class in owltools.ontologyverification.impl
Check for redundant names in labels and synonyms (scope EXACT).
By default all obsoleted objects are ignored.
NameRedundancyCheck() - Constructor for class owltools.ontologyverification.impl.NameRedundancyCheck
 

O

Obo2Obo - Class in owltools.cli
Read an OBO file and write it back out as OBO, useful for sorting hand-edited OBO files.
Obo2Obo() - Constructor for class owltools.cli.Obo2Obo
 
OboBasicDagCheck - Class in owltools.ontologyrelease
 
OboBasicDagCheck() - Constructor for class owltools.ontologyrelease.OboBasicDagCheck
 
OboOntologyReleaseRunner - Class in owltools.ontologyrelease
This class is a command line utility which builds an ontology release.
OboOntologyReleaseRunner(OortConfiguration, File, List<LogHandler>) - 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
 
ObsoleteClassInSignature - Class in owltools.ontologyverification.impl
 
ObsoleteClassInSignature() - Constructor for class owltools.ontologyverification.impl.ObsoleteClassInSignature
 
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
 
OntologyCheck - Interface in owltools.ontologyverification
Methods for executing and describing an ontology check.
OntologyCheckHandler - Class in owltools.ontologyverification
Handle the ontology checks for an ontology and its reporting to the LogHandler.
OntologyCheckHandler(boolean, List<OntologyCheck>, List<LogHandler>) - Constructor for class owltools.ontologyverification.OntologyCheckHandler
Create a new instance.
OntologyCheckHandler.CheckSummary - Class in owltools.ontologyverification
 
OntologyCheckRunner - Class in owltools.ontologyverification
Identify and run ontology checks for an ontology (OWLGraphWrapper) via the OntologyCheck interface.
OntologyCheckRunner.TimePoint - Enum in owltools.ontologyverification
 
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.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.cli - package owltools.cli
 
owltools.ontologyrelease - package owltools.ontologyrelease
Oort - OBO Ontology Release Tool (OORT)
owltools.ontologyrelease.gui - package owltools.ontologyrelease.gui
 
owltools.ontologyrelease.logging - package owltools.ontologyrelease.logging
 
owltools.ontologyrelease.reports - package owltools.ontologyrelease.reports
 
owltools.ontologyrelease.reports.go - package owltools.ontologyrelease.reports.go
 
owltools.ontologyverification - package owltools.ontologyverification
 
owltools.ontologyverification.impl - package owltools.ontologyverification.impl
 
owltools.renderer.markdown - package owltools.renderer.markdown
 

P

parseVersion(String) - Static method in class owltools.ontologyrelease.OntologyVersionTools
Try to parse the IRI as a version IRI 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.
ReleaseRunnerFileTools - Class in owltools.ontologyrelease
Provide a staging directory for the release runners.
removeFromSkipFormatSet(String) - Method in class owltools.ontologyrelease.OortConfiguration
 
render(OWLOntology, String) - Method in class owltools.renderer.markdown.MarkdownRenderer
 
render(OWLOntology) - Method in class owltools.renderer.markdown.MarkdownRenderer
 
render(OWLClass) - Method in class owltools.renderer.markdown.MarkdownRenderer
 
render(OWLObjectProperty) - Method in class owltools.renderer.markdown.MarkdownRenderer
 
render(OWLAnnotationProperty) - Method in class owltools.renderer.markdown.MarkdownRenderer
 
renderAbout(OWLClass) - Method in class owltools.renderer.markdown.MarkdownRenderer
 
renderMessageString() - Method in exception owltools.ontologyrelease.OboOntologyReleaseRunnerCheckException
Render the exception in an human readable form and suitable for appending to a logger.
report(String, CharSequence) - Method in class owltools.ontologyrelease.logging.ErrorReportFileHandler
 
report(String, CharSequence) - Method in class owltools.ontologyrelease.logging.ExplicitReportFileHandler
 
report(String, CharSequence) - Method in class owltools.ontologyrelease.logging.GuiLogHandler
 
report(String, CharSequence) - Method in class owltools.ontologyrelease.logging.Log4jHandler
 
report(String, CharSequence) - Method in interface owltools.ontologyrelease.logging.LogHandler
 
report(String, CharSequence) - Method in class owltools.ontologyrelease.logging.TraceReportFileHandler
 
report(String, CharSequence) - Method in class owltools.ontologyrelease.ReleaseRunnerFileTools
 
report(StringBuilder, OntologyCheckRunner.TimePoint) - Method in class owltools.ontologyverification.OntologyCheckHandler
 
report(StringBuilder, OntologyCheck, Collection<CheckWarning>, String) - Method in class owltools.ontologyverification.OntologyCheckHandler
 
reportHeader(StringBuilder) - Method in class owltools.ontologyverification.OntologyCheckHandler
 
run(Opts) - Method in class owltools.cli.Obo2Obo
 

S

SelfReferenceInDefinition - Class in owltools.ontologyverification.impl
Check, whether the class is defined using the class itself.
SelfReferenceInDefinition() - Constructor for class owltools.ontologyverification.impl.SelfReferenceInDefinition
 
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
 
setCheckPotentialRedundant(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setChunkLevel(int) - Method in class owltools.renderer.markdown.MarkdownRenderer
 
setCreateErrorModules(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setEnforceEL(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setErrorReportFile(String) - 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
setFatal(boolean) - Method in class owltools.ontologyverification.impl.AbstractCheck
 
setFatal(boolean) - Method in interface owltools.ontologyverification.OntologyCheck
Set the fatal parameter of the check.
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.
 
setFilterSimpleProperties(List<String>) - Method in class owltools.ontologyrelease.OortConfiguration
 
setForceRelease(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setGafToOwl(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setIgnoreLockFile(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setIgnoreObsolete(boolean) - Method in class owltools.ontologyverification.impl.NameRedundancyCheck
 
setIgnoreSelectedEquivalentPairSet(Set<String>) - 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
setOntologyChecks(List<OntologyCheck>) - Method in class owltools.ontologyrelease.OortConfiguration
 
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
setRelaxed(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setRemoveDanglingBeforeReasoning(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setRemoveQueryOntologyReference(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setRemoveRedunantAxioms(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setRemoveTrailingQualifiers(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setRepairAnnotationCardinality(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setRewriteIRIMap(Map<IRI, IRI>) - Method in class owltools.ontologyrelease.OortConfiguration
 
setRunOboBasicDagCheck(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
 
setThreads(int) - Method in class owltools.ontologyrelease.OortConfiguration
 
setTimePoint(OntologyCheckRunner.TimePoint) - Method in class owltools.ontologyverification.impl.AbstractCheck
 
setTimePoint(OntologyCheckRunner.TimePoint) - Method in interface owltools.ontologyverification.OntologyCheck
Set the OntologyCheckRunner.TimePoint for this ontology check instance.
setTraceReportFile(String) - Method in class owltools.ontologyrelease.OortConfiguration
 
setTranslateDisjointsToEquivalents(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setUseIsInferred(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setUseQueryOntology(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setUseReleaseFolder(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setVersionReportFiles(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
 
setVersionSubdirectory(String) - 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
 
SHORT_HAND - Static variable in class owltools.ontologyverification.impl.AltIdInSignature
 
SHORT_HAND - Static variable in class owltools.ontologyverification.impl.CycleCheck
 
SHORT_HAND - Static variable in class owltools.ontologyverification.impl.DanglingReferenceCheck
 
SHORT_HAND - Static variable in class owltools.ontologyverification.impl.NameRedundancyCheck
 
SHORT_HAND - Static variable in class owltools.ontologyverification.impl.ObsoleteClassInSignature
 
SHORT_HAND - Static variable in class owltools.ontologyverification.impl.SelfReferenceInDefinition
 
STAGING_DIRECTORY_NAME - Static variable in class owltools.ontologyrelease.ReleaseRunnerFileTools
 
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.
success - Variable in class owltools.ontologyverification.OntologyCheckHandler.CheckSummary
 
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.CheckWarning
 
TraceReportFileHandler - Class in owltools.ontologyrelease.logging
 
TraceReportFileHandler(File, String) - Constructor for class owltools.ontologyrelease.logging.TraceReportFileHandler
 

U

unescape(String) - Static method in class owltools.ontologyrelease.OortConfiguration
Only public for testing purposes.
use(OWLClass) - Method in interface owltools.cli.AssertInferredClassExpressions.OWLClassFilter
 

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.OntologyCheckRunner.TimePoint
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.OntologyCheckRunner.TimePoint
Returns an array containing the constants of this enum type, in the order they are declared.
verifyExistingInferences(OWLGraphWrapper, BufferedWriter, boolean, boolean) - Static method in class owltools.cli.AssertInferenceTool
 

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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