public class SimCommandRunner extends SolrCommandRunner
Modifier and Type | Field and Description |
---|---|
boolean |
exitOnException |
OWLGraphWrapper |
g |
boolean |
isDisposeReasonerOnExit |
Set<org.semanticweb.owlapi.model.OWLObject> |
owlObjectCachedSet |
protected ParserWrapper |
pw |
org.semanticweb.owlapi.model.OWLOntology |
queryOntology |
org.semanticweb.owlapi.reasoner.OWLReasoner |
reasoner |
String |
reasonerName |
bioentityDocument, eco, gafdoc
Constructor and Description |
---|
SimCommandRunner() |
Modifier and Type | Method and Description |
---|---|
void |
allClassIC(Opts opts) |
protected void |
exit(int code) |
void |
getAncestorsWithIC(Opts opts) |
void |
getIC(Opts opts) |
protected OWLPrettyPrinter |
getPrettyPrinter() |
String |
getProperty(SimpleOwlSim.SimConfigurationProperty p) |
void |
handlePrettyPrinter(Opts opts) |
void |
help() |
void |
helpFooter() |
void |
lcsx(Opts opts) |
void |
lcsxAll(Opts opts) |
protected void |
loadProperties(Opts opts) |
void |
mergeSim(Opts opts) |
void |
owlsimEnrichmentAnalysis(Opts opts) |
void |
phenoSim(Opts opts) |
org.semanticweb.owlapi.model.OWLClass |
resolveClass(String id) |
List<org.semanticweb.owlapi.model.OWLClass> |
resolveClassList(Opts opts) |
org.semanticweb.owlapi.model.OWLObject |
resolveEntity(Opts opts) |
org.semanticweb.owlapi.model.OWLObject |
resolveEntity(String id) |
Set<org.semanticweb.owlapi.model.OWLObject> |
resolveEntityList(Opts opts) |
org.semanticweb.owlapi.model.OWLObjectProperty |
resolveObjectProperty(String id) |
Set<org.semanticweb.owlapi.model.OWLObjectProperty> |
resolveObjectPropertyList(Opts opts) |
List<org.semanticweb.owlapi.model.OWLObjectProperty> |
resolveObjectPropertyListAsList(Opts opts) |
void |
run(Opts opts) |
void |
run(String[] args) |
void |
runOwlSim(Opts opts)
performs all by all individual comparison
|
void |
runSingleIteration(String[] args) |
void |
saveSim(Opts opts) |
void |
setSimMethod(Opts opts) |
void |
sim(Opts opts) |
void |
simAll(Opts opts) |
void |
simBasic(Opts opts) |
void |
simResume(Opts opts) |
void |
summarizeOntology(org.semanticweb.owlapi.model.OWLOntology ont) |
configRead, dumpShuntGraphs, experimentalLoadComplexAnnotationSolr, flexDumpOntologySolr, flexLoadOntologySolr, generalLoadOntologySolr, loadComplexAnnotationSolr, loadGAFsSolr, loadGPADsSolr, loadPANTHERGeneralSolr, loadPANTHERSolr, optimizeSolr, processCAFiles, processLegoCatalogs, processLegoFiles, processPantherTrees, purgeSolr, setSolrLogFile, setSolrUrl, solrSchemaDump
createDisjoint, createDisjoint, createDisjoint, createTaxonDisjointOverInTaxon, makeClassTaxonMatrix, makeTaxonSet
createExperimentalPredictions, createRdfXml, extractOntologySubsetByGaf, foldGafExtensions, gaCalculateSpecificity, gaf, gaf2oa, gaf2Owl, gaf2OwlSimple, gafCompareBasic, gafFoldInferences, gafQuery, gafRemoveRedundant, gafTermCounts, gafTermICValues, gafXpPredict, generateJsonGafStatistics, loadGpadGpi, mapToSlim, preCheckOntology, runGAFChecks, runOntologyPreCheck, setExperimentalGAFPredictionFile, setExperimentalGAFPredictionReportFile, setGAFPredictionFile, setGAFPredictionReportFile, setGAFReportFile, setGAFReportSummaryFile, setGAFTaxonModule, unfoldGafExtensions, writeGaf, writeGpad, writeGpi, writeXgmml
assertAboxInferences, assertInferredSubClassAxioms, createBioChebi, createExternalMappings, createPartOfLinks, createSlim, createSubsetTags, extractAnnotationValue, extractExtensionFile, filterExtensionFile, jsonLdToRdf, rdfToJsonLd, removeRedundantInferredSuperClassAxioms, removeRedundantSubclasses, removeSubsetEntities, runDAGCheck, runSingleIteration, verifyChanges
public OWLGraphWrapper g
public org.semanticweb.owlapi.model.OWLOntology queryOntology
public boolean exitOnException
public boolean isDisposeReasonerOnExit
public org.semanticweb.owlapi.reasoner.OWLReasoner reasoner
public String reasonerName
public Set<org.semanticweb.owlapi.model.OWLObject> owlObjectCachedSet
protected ParserWrapper pw
public String getProperty(SimpleOwlSim.SimConfigurationProperty p)
public void setSimMethod(Opts opts)
public void simAll(Opts opts) throws SimEngine.SimilarityAlgorithmException
public void lcsx(Opts opts)
public void getIC(Opts opts)
public void getAncestorsWithIC(Opts opts)
public void runOwlSim(Opts opts) throws UnknownOWLClassException
opts
- UnknownOWLClassException
protected void loadProperties(Opts opts) throws IOException
IOException
public void owlsimEnrichmentAnalysis(Opts opts) throws Exception
Exception
protected void exit(int code)
protected OWLPrettyPrinter getPrettyPrinter()
public void summarizeOntology(org.semanticweb.owlapi.model.OWLOntology ont)
public Set<org.semanticweb.owlapi.model.OWLObjectProperty> resolveObjectPropertyList(Opts opts)
public List<org.semanticweb.owlapi.model.OWLObjectProperty> resolveObjectPropertyListAsList(Opts opts)
public org.semanticweb.owlapi.model.OWLObject resolveEntity(Opts opts)
public org.semanticweb.owlapi.model.OWLObject resolveEntity(String id)
public org.semanticweb.owlapi.model.OWLObjectProperty resolveObjectProperty(String id)
public org.semanticweb.owlapi.model.OWLClass resolveClass(String id)
public void help()
public void helpFooter()
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