public class SimCommandRunner extends SolrCommandRunner
CommandRunner.OptionException
bioentityDocument, eco, gafdoc
exitOnException, g, isDisposeReasonerOnExit, owlObjectCachedSet, pw, queryOntology, reasoner, reasonerName
Constructor and Description |
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SimCommandRunner() |
Modifier and Type | Method and Description |
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void |
allClassIC(Opts opts) |
void |
getAncestorsWithIC(Opts opts) |
void |
getIC(Opts opts) |
String |
getProperty(SimpleOwlSim.SimConfigurationProperty p) |
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) |
void |
runOwlSim(Opts opts)
performs all by all individual comparison
|
void |
saveSim(Opts opts) |
void |
setSimMethod(Opts opts) |
void |
sim(Opts opts) |
void |
simAll(Opts opts) |
void |
simBasic(Opts opts) |
void |
simResume(Opts opts) |
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, fetchCandidateProcess, foldGafExtensions, gaCalculateSpecificity, gaf, gaf2Lego, gaf2LegoIndivduals, gaf2oa, gaf2Owl, gaf2OwlSimple, gafCompareBasic, gafFoldInferences, gafQuery, gafRemoveRedundant, gafTermCounts, gafTermICValues, gafXpPredict, generateJsonGafStatistics, generateMolecularModel, goMultiEnrichment, legoToAnnotations, loadGpadGpi, mapToSlim, preCheckOntology, runGAFChecks, runOntologyPreCheck, setExperimentalGAFPredictionFile, setExperimentalGAFPredictionReportFile, setGAFPredictionFile, setGAFPredictionReportFile, setGAFReportFile, setGAFReportSummaryFile, setGAFTaxonModule, unfoldGafExtensions, visualizeLego, writeGaf, writeGpad, writeGpi, writeLego, writeXgmml
assertAboxInferences, assertInferredSubClassAxioms, createBioChebi, createExternalMappings, createPartOfLinks, createSlim, createSubsetTags, exit, extractAnnotationValue, extractExtensionFile, filterExtensionFile, getPrettyPrinter, handlePrettyPrinter, help, helpFooter, jsonLdToRdf, parseArgString, rdfToJsonLd, removeRedundantInferredSuperClassAxioms, removeSubsetEntities, resolveClass, resolveClassList, resolveEntity, resolveEntity, resolveEntityList, resolveObjectProperty, resolveObjectPropertyList, resolveObjectPropertyListAsList, run, run, runDAGCheck, runSingleIteration, runSingleIteration, summarizeOntology, verifyChanges
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
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