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

A

allClassIC(Opts) - Method in class owltools.cli.SimCommandRunner
 
assertAboxInferences(Opts) - Method in class owltools.cli.CommandRunner
 
assertInferredSubClassAxioms(Opts) - Method in class owltools.cli.CommandRunner
 
attributeAllByAll(OwlSim, Opts) - Method in class owltools.cli.Sim2CommandRunner
 
attributeAllByAllOld(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
attributeSimilarityAllByAllPairwise(Opts) - Method in class owltools.cli.Sim2CommandRunner
Iterates through all individuals, generating similarity calculations for each of its attributes (ontology classes).
attributeSimilarityByPair(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.cli.Sim2CommandRunner
Given two individuals, this fetches their respective attributes, computes their similarity (LCS), and renders the scores for all attribute-pairs.

B

BioChebiGenerator - Class in owltools.cli
Methods for creating the BioChEBI wrapper file for ChEBI.
BioChebiGenerator(Map<OWLObjectProperty, Set<OWLObjectProperty>>) - Constructor for class owltools.cli.BioChebiGenerator
 
bioentityDocument - Variable in class owltools.cli.GafCommandRunner
 

C

classICPairs(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
CLIMethod - Annotation Type in owltools.cli.tools
Annotation indicating, that this method can be called from the command line interface.
CommandLineInterface - Class in owltools.cli
Wrapper class to provide a stable class name for the main method.
CommandLineInterface() - Constructor for class owltools.cli.CommandLineInterface
 
CommandRunner - Class in owltools.cli
An instance of this class can execute owltools commands in sequence.
CommandRunner() - Constructor for class owltools.cli.CommandRunner
 
CommandRunner.OptionException - Exception in owltools.cli
 
CommandRunner.OptionException(String) - Constructor for exception owltools.cli.CommandRunner.OptionException
 
configRead(Opts) - Method in class owltools.cli.SolrCommandRunner
Output (STDOUT) a XML segment to put into the Solr schema file after reading the YAML file.
createBioChebi(File, String) - Static method in class owltools.cli.BioChebiGenerator
Create the GCIs for BioChEBI.
createBioChebi(OWLGraphWrapper, String) - Static method in class owltools.cli.BioChebiGenerator
Create the GCIs for BioChEBI.
createBioChebi(OWLGraphWrapper, Set<OWLClass>) - Static method in class owltools.cli.BioChebiGenerator
Create the GCIs for BioChEBI.
createBioChebi(Opts) - Method in class owltools.cli.CommandRunner
 
createDisjoint(OWLDataFactory, Set<OWLClass>, OWLObjectProperty) - Method in class owltools.cli.TaxonCommandRunner
 
createDisjoint(OWLDataFactory, OWLClass, OWLClass, OWLObjectProperty) - Method in class owltools.cli.TaxonCommandRunner
 
createDisjoint(OWLDataFactory, OWLClass, OWLClass) - Method in class owltools.cli.TaxonCommandRunner
 
createExperimentalPredictions(Opts) - Method in class owltools.cli.GafCommandRunner
 
createExternalMappings(Opts) - Method in class owltools.cli.CommandRunner
 
createPartOfLinks(Opts) - Method in class owltools.cli.CommandRunner
GeneOntology specific function to create links between molecular functions and their corresponding processes.
createRdfXml(Opts) - Method in class owltools.cli.GafCommandRunner
 
createSlim(Opts) - Method in class owltools.cli.CommandRunner
 
createSubsetTags(Opts) - Method in class owltools.cli.CommandRunner
Simple helper to create a subset tag for matching entities, allows to specify exceptions
createTaxonDisjointOverInTaxon(Opts) - Method in class owltools.cli.TaxonCommandRunner
 

D

dumpShuntGraphs(Opts) - Method in class owltools.cli.SolrCommandRunner
Used for generating output for units tests in other languages.

E

eco - Variable in class owltools.cli.GafCommandRunner
 
exit(int) - Method in class owltools.cli.CommandRunner
 
exitOnException - Variable in class owltools.cli.CommandRunner
 
expand(OWLOntology, Set<OWLClass>) - Method in class owltools.cli.BioChebiGenerator
Create the GCIs for BioChEBI.
experimentalLoadComplexAnnotationSolr(Opts) - Method in class owltools.cli.SolrCommandRunner
Experimental method for trying out the loading of complex_annotation doc type
extractAnnotationValue(Opts) - Method in class owltools.cli.CommandRunner
 
extractExtensionFile(Opts) - Method in class owltools.cli.CommandRunner
Extract all xps (OWLEquivalentClassesAxiom) from the loaded ontology.
extractOntologySubsetByGaf(Opts) - Method in class owltools.cli.GafCommandRunner
 

F

fetchCandidateProcess(Opts) - Method in class owltools.cli.GafCommandRunner
 
filterExtensionFile(Opts) - Method in class owltools.cli.CommandRunner
Retain only subclass of axioms and intersection of axioms if they contain a class in it's signature of a given set of parent terms.
flexDumpOntologySolr(Opts) - Method in class owltools.cli.SolrCommandRunner
Dump experimental flexible loader output to JSON(?) blob.
flexLoadOntologySolr(Opts) - Method in class owltools.cli.SolrCommandRunner
Flexible loader for ontologies--uses the YAML config to find loading functions.
foldGafExtensions(Opts) - Method in class owltools.cli.GafCommandRunner
 
fsimAttTopSimJ(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
fsimBasic(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
fsimCompareAtts(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
fsimCompareAttsLCS(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
fsimCompareAttsLite(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
fsimCompareAttsSimJ(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
fsimFindMatches(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
fsimSearchAll(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
fsimTest(Opts) - Method in class owltools.cli.Sim2CommandRunner
 

G

g - Variable in class owltools.cli.CommandRunner
 
gaCalculateSpecificity(Opts) - Method in class owltools.cli.GafCommandRunner
 
gaf(Opts) - Method in class owltools.cli.GafCommandRunner
Used for loading GAFs into memory
gaf2Lego(Opts) - Method in class owltools.cli.GafCommandRunner
 
gaf2LegoIndivduals(Opts) - Method in class owltools.cli.GafCommandRunner
Translate the GeneAnnotations into a lego all individual OWL representation.
gaf2oa(Opts) - Method in class owltools.cli.GafCommandRunner
 
gaf2Owl(Opts) - Method in class owltools.cli.GafCommandRunner
 
gaf2OwlSimple(Opts) - Method in class owltools.cli.GafCommandRunner
Created to mimic the translation to OWL for GAF checks
GafCommandRunner - Class in owltools.cli
GAF tools for command-line, includes validation of GAF files.
GafCommandRunner() - Constructor for class owltools.cli.GafCommandRunner
 
gafCompareBasic(Opts) - Method in class owltools.cli.GafCommandRunner
 
gafdoc - Variable in class owltools.cli.GafCommandRunner
 
gafFoldInferences(Opts) - Method in class owltools.cli.GafCommandRunner
 
gafQuery(Opts) - Method in class owltools.cli.GafCommandRunner
 
gafRemoveRedundant(Opts) - Method in class owltools.cli.GafCommandRunner
 
gafTermCounts(Opts) - Method in class owltools.cli.GafCommandRunner
 
gafTermICValues(Opts) - Method in class owltools.cli.GafCommandRunner
 
gafXpPredict(Opts) - Method in class owltools.cli.GafCommandRunner
 
generalLoadOntologySolr(Opts) - Method in class owltools.cli.SolrCommandRunner
Trivial hard-wired (and optional) method for loading collected ontology information into the "general" schema (general-config.yaml) for GO.
generateJsonGafStatistics(Opts) - Method in class owltools.cli.GafCommandRunner
 
generateMolecularModel(Opts) - Method in class owltools.cli.GafCommandRunner
 
getAncestorsWithIC(Opts) - Method in class owltools.cli.SimCommandRunner
 
getIC(Opts) - Method in class owltools.cli.SimCommandRunner
 
getOwlSimFactory() - Method in class owltools.cli.Sim2CommandRunner
 
getPrettyPrinter() - Method in class owltools.cli.CommandRunner
 
getProperty(SimpleOwlSim.SimConfigurationProperty) - Method in class owltools.cli.Sim2CommandRunner
 
getProperty(SimpleOwlSim.SimConfigurationProperty) - Method in class owltools.cli.SimCommandRunner
 
goMultiEnrichment(Opts) - Method in class owltools.cli.GafCommandRunner
 

H

handlePrettyPrinter(Opts) - Method in class owltools.cli.CommandRunner
 
help() - Method in class owltools.cli.CommandRunner
 
helpFooter() - Method in class owltools.cli.CommandRunner
 

I

IdTools - Class in owltools.cli
Convenience tool to convert IRI style Id suffixes into OBO style identifier.
IdTools() - Constructor for class owltools.cli.IdTools
 
instanceICValues(Opts) - Method in class owltools.cli.Sim2CommandRunner
Prints a tab-delimited report of the IC measures for each annotation (class) made to each instance.
instanceStats(Opts) - Method in class owltools.cli.Sim2CommandRunner
Computes & reports on some summary statistics on the loaded data set.
isDisposeReasonerOnExit - Variable in class owltools.cli.CommandRunner
 

J

JsCommandRunner - Class in owltools.cli
Provide a JavaScript interpreter for OWLTools.
JsCommandRunner() - Constructor for class owltools.cli.JsCommandRunner
 
jsonLdToRdf(Opts) - Method in class owltools.cli.CommandRunner
 

L

lcsx(Opts) - Method in class owltools.cli.SimCommandRunner
 
lcsxAll(Opts) - Method in class owltools.cli.SimCommandRunner
 
learnClassDifferentia(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
legoToAnnotations(Opts) - Method in class owltools.cli.GafCommandRunner
 
loadComplexAnnotationSolr(Opts) - Method in class owltools.cli.SolrCommandRunner
Experimental method for trying out the loading of complex_annotation doc type.
loadGAFsSolr(Opts) - Method in class owltools.cli.SolrCommandRunner
Used for loading a list of GAFs into GOlr.
loadGpadGpi(Opts) - Method in class owltools.cli.GafCommandRunner
 
loadGPADsSolr(Opts) - Method in class owltools.cli.SolrCommandRunner
Used for loading a list of GPAD pairs into GOlr.
loadPANTHERGeneralSolr(Opts) - Method in class owltools.cli.SolrCommandRunner
Requires the --read-panther argument (or something else that fills the pSet object).
loadPANTHERSolr(Opts) - Method in class owltools.cli.SolrCommandRunner
Requires the --read-panther argument (or something else that fills the pSet object).
loadProperties(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
loadProperties(Opts) - Method in class owltools.cli.SimCommandRunner
 

M

main(String[]) - Static method in class owltools.cli.BioChebiGenerator
Main method.
main(String[]) - Static method in class owltools.cli.CommandLineInterface
 
makeClassTaxonMatrix(Opts) - Method in class owltools.cli.TaxonCommandRunner
 
makeTaxonSet(Opts) - Method in class owltools.cli.TaxonCommandRunner
 
mapToSlim(Opts) - Method in class owltools.cli.GafCommandRunner
 
mergeSim(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
mergeSim(Opts) - Method in class owltools.cli.SimCommandRunner
 

O

OLDinstanceICValues(Opts) - Method in class owltools.cli.Sim2CommandRunner
Deprecated.
optimizeSolr(Opts) - Method in class owltools.cli.SolrCommandRunner
Requires the --solr-url argument.
owlObjectCachedSet - Variable in class owltools.cli.CommandRunner
 
owlsimEnrichmentAnalysis(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
owlsimEnrichmentAnalysis(Opts) - Method in class owltools.cli.SimCommandRunner
 
owlsimEnrichmentAnalysisAllByAll(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
owltools.cli - package owltools.cli
CLI - Command Line Interface
owltools.cli.tools - package owltools.cli.tools
 

P

parseArgString(String) - Method in class owltools.cli.CommandRunner
 
phenoSim(Opts) - Method in class owltools.cli.SimCommandRunner
 
preCheckOntology(String, String) - Method in class owltools.cli.GafCommandRunner
 
processCAFiles(Opts) - Method in class owltools.cli.SolrCommandRunner
Used for reading the lego files to be used for loading complex annotations.
processLegoCatalogs(Opts) - Method in class owltools.cli.SolrCommandRunner
Used for reading the ontology catalogs to be used for loading complex annotations.
processLegoFiles(Opts) - Method in class owltools.cli.SolrCommandRunner
Used for reading the lego files to be used for loading complex annotations.
processPantherTrees(Opts) - Method in class owltools.cli.SolrCommandRunner
Used for applying the panther trees to the currently data run.
purgeSolr(Opts) - Method in class owltools.cli.SolrCommandRunner
Manually purge the index to try again.
pw - Variable in class owltools.cli.CommandRunner
 

Q

queryOntology - Variable in class owltools.cli.CommandRunner
 

R

rdfToJsonLd(Opts) - Method in class owltools.cli.CommandRunner
 
reasoner - Variable in class owltools.cli.CommandRunner
 
reasonerName - Variable in class owltools.cli.CommandRunner
 
removeDangningAnnotations(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
removeRedundantInferredSuperClassAxioms(Opts) - Method in class owltools.cli.CommandRunner
 
removeSubsetEntities(Opts) - Method in class owltools.cli.CommandRunner
 
resolveClass(String) - Method in class owltools.cli.CommandRunner
 
resolveClassList(Opts) - Method in class owltools.cli.CommandRunner
 
resolveEntity(Opts) - Method in class owltools.cli.CommandRunner
 
resolveEntity(String) - Method in class owltools.cli.CommandRunner
 
resolveEntityList(Opts) - Method in class owltools.cli.CommandRunner
 
resolveObjectProperty(String) - Method in class owltools.cli.CommandRunner
 
resolveObjectPropertyList(Opts) - Method in class owltools.cli.CommandRunner
 
resolveObjectPropertyListAsList(Opts) - Method in class owltools.cli.CommandRunner
 
resultOutStream - Variable in class owltools.cli.Sim2CommandRunner
 
run(String[]) - Method in class owltools.cli.CommandRunner
 
run(Opts) - Method in class owltools.cli.CommandRunner
 
runDAGCheck(Opts) - Method in class owltools.cli.CommandRunner
 
runGAFChecks(Opts) - Method in class owltools.cli.GafCommandRunner
 
runJavaScript(Opts) - Method in class owltools.cli.JsCommandRunner
Run the given js with the current graph (and reasoner).
runOntologyPreCheck(Opts) - Method in class owltools.cli.GafCommandRunner
Similar method to '--run-reasoner', but not only checks for unsatisfiable classes, but also checks first for a consistent ontology.
runOwlSim(Opts) - Method in class owltools.cli.Sim2CommandRunner
Deprecated.
runOwlSim(OwlSim, Opts) - Method in class owltools.cli.Sim2CommandRunner
 
runOwlSim(Opts) - Method in class owltools.cli.SimCommandRunner
performs all by all individual comparison
runSingleIteration(String[]) - Method in class owltools.cli.CommandRunner
 
runSingleIteration(Opts) - Method in class owltools.cli.CommandRunner
 

S

saveSim(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
saveSim(Opts) - Method in class owltools.cli.SimCommandRunner
 
setExperimentalGAFPredictionFile(Opts) - Method in class owltools.cli.GafCommandRunner
 
setExperimentalGAFPredictionReportFile(Opts) - Method in class owltools.cli.GafCommandRunner
 
setGAFPredictionFile(Opts) - Method in class owltools.cli.GafCommandRunner
 
setGAFPredictionReportFile(Opts) - Method in class owltools.cli.GafCommandRunner
 
setGAFReportFile(Opts) - Method in class owltools.cli.GafCommandRunner
 
setGAFReportSummaryFile(Opts) - Method in class owltools.cli.GafCommandRunner
 
setGAFTaxonModule(Opts) - Method in class owltools.cli.GafCommandRunner
 
setOwlSimFactory(OwlSimFactory) - Method in class owltools.cli.Sim2CommandRunner
 
setSimMethod(Opts) - Method in class owltools.cli.SimCommandRunner
 
setSimProperty(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
setSolrLogFile(Opts) - Method in class owltools.cli.SolrCommandRunner
Set an optional file to use for logging load data (can be consumed by AmiGO 2).
setSolrUrl(Opts) - Method in class owltools.cli.SolrCommandRunner
Set an optional Solr URL to use with Solr options so they don't have to be specified separately for every option.
showAttributeGroupings(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
showAttributeGroupingsAsList(Opts) - Method in class owltools.cli.Sim2CommandRunner
Given a set of classes, will print the grouping class(es) for each annotation in a comma-separated list.
showAttributeGroupingsInTable(Opts) - Method in class owltools.cli.Sim2CommandRunner
Given a set of classes, will print a table of grouping class(es) for each annotation, and show a binary flag if the given annotation belongs to that class.
showSimProperties(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
sim(Opts) - Method in class owltools.cli.SimCommandRunner
 
Sim2CommandRunner - Class in owltools.cli
Semantic similarity and information content.
Sim2CommandRunner() - Constructor for class owltools.cli.Sim2CommandRunner
 
simAll(Opts) - Method in class owltools.cli.SimCommandRunner
 
simAttMatchOld(Opts) - Method in class owltools.cli.Sim2CommandRunner
Deprecated.
simBasic(Opts) - Method in class owltools.cli.Sim2CommandRunner
Deprecated.
simBasic(Opts) - Method in class owltools.cli.SimCommandRunner
 
simBasicStats(Opts) - Method in class owltools.cli.Sim2CommandRunner
This method will report to the user some metadata about the previous similarity run.
SimCommandRunner - Class in owltools.cli
Semantic similarity and information content.
SimCommandRunner() - Constructor for class owltools.cli.SimCommandRunner
 
simDlQuery(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
simLCS(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
simLoadICCache(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
simLoadLCSCache(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
simPairwiseAttMatch(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
simResume(Opts) - Method in class owltools.cli.SimCommandRunner
 
simSaveICCache(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
simSaveLCSCache(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
simSavePhenodigmClassScores(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
simSaveState(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
simTest(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
SolrCommandRunner - Class in owltools.cli
Solr/GOlr loading.
SolrCommandRunner() - Constructor for class owltools.cli.SolrCommandRunner
 
solrSchemaDump(Opts) - Method in class owltools.cli.SolrCommandRunner
Output (STDOUT) XML segment to put into the Solr schema file after reading the YAML configuration file(s).
startSimServer(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
summarizeOntology(OWLOntology) - Method in class owltools.cli.CommandRunner
 

T

TaxonCommandRunner - Class in owltools.cli
Command-line module for taxon constraints.
TaxonCommandRunner() - Constructor for class owltools.cli.TaxonCommandRunner
 

U

unfoldGafExtensions(Opts) - Method in class owltools.cli.GafCommandRunner
 
useFastOwlSim(Opts) - Method in class owltools.cli.Sim2CommandRunner
 
useSimpleOwlSim(Opts) - Method in class owltools.cli.Sim2CommandRunner
 

V

verifyChanges(Opts) - Method in class owltools.cli.CommandRunner
 
visualizeLego(Opts) - Method in class owltools.cli.GafCommandRunner
Deprecated.

W

writeGaf(Opts) - Method in class owltools.cli.GafCommandRunner
 
writeGpad(Opts) - Method in class owltools.cli.GafCommandRunner
 
writeGpi(Opts) - Method in class owltools.cli.GafCommandRunner
 
writeLego(OWLOntology, String, String) - Method in class owltools.cli.GafCommandRunner
Deprecated.
writeXgmml(Opts) - Method in class owltools.cli.GafCommandRunner
 
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