public class Sim2CommandRunner extends SimCommandRunner
CommandRunnerBase.OptionException
Modifier and Type | Field and Description |
---|---|
protected PrintStream |
resultOutStream |
bioentityDocument, eco, gafdoc
exitOnException, g, isDisposeReasonerOnExit, owlObjectCachedSet, pw, queryOntology, reasoner, reasonerName
Constructor and Description |
---|
Sim2CommandRunner() |
Modifier and Type | Method and Description |
---|---|
void |
attributeAllByAll(OwlSim sim,
Opts opts) |
void |
attributeAllByAllOld(Opts opts) |
void |
attributeSimilarityAllByAllPairwise(Opts opts)
Iterates through all individuals, generating similarity calculations for
each of its attributes (ontology classes).
|
void |
attributeSimilarityByPair(org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLNamedIndividual j)
Given two individuals, this fetches their respective attributes, computes
their similarity (LCS), and renders the scores for all attribute-pairs.
|
void |
classICPairs(Opts opts) |
void |
fsimAttTopSimJ(Opts opts) |
void |
fsimBasic(Opts opts) |
void |
fsimCompareAtts(Opts opts) |
void |
fsimCompareAttsLCS(Opts opts) |
void |
fsimCompareAttsLite(Opts opts) |
void |
fsimCompareAttsSimJ(Opts opts) |
void |
fsimFindMatches(Opts opts) |
void |
fsimSearchAll(Opts opts) |
void |
fsimTest(Opts opts) |
OwlSimFactory |
getOwlSimFactory() |
String |
getProperty(SimpleOwlSim.SimConfigurationProperty p) |
void |
instanceICValues(Opts opts)
Prints a tab-delimited report of the IC measures for each annotation (class)
made to each instance.
|
void |
instanceStats(Opts opts)
Computes & reports on some summary statistics on the loaded data set.
|
void |
learnClassDifferentia(Opts opts) |
protected void |
loadProperties(Opts opts) |
void |
mergeSim(Opts opts) |
void |
OLDinstanceICValues(Opts opts)
Deprecated.
|
void |
owlsimEnrichmentAnalysis(Opts opts) |
void |
owlsimEnrichmentAnalysisAllByAll(Opts opts) |
void |
removeDangningAnnotations(Opts opts) |
void |
runOwlSim(Opts opts)
Deprecated.
|
void |
runOwlSim(OwlSim owlsim,
Opts opts) |
void |
saveSim(Opts opts) |
void |
setOwlSimFactory(OwlSimFactory owlSimFactory) |
void |
setSimProperty(Opts opts) |
void |
showAttributeGroupings(Opts opts) |
void |
showAttributeGroupingsAsList(Opts opts)
Given a set of classes, will print the grouping class(es) for each
annotation in a comma-separated list.
|
void |
showAttributeGroupingsInTable(Opts opts)
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.
|
void |
showSimProperties(Opts opts) |
void |
simAttMatchOld(Opts opts)
Deprecated.
|
void |
simBasic(Opts opts)
Deprecated.
|
void |
simBasicStats(Opts opts)
This method will report to the user some metadata about the previous similarity
run.
|
void |
simDlQuery(Opts opts) |
void |
simLCS(Opts opts) |
void |
simLoadICCache(Opts opts) |
void |
simLoadLCSCache(Opts opts) |
void |
simPairwiseAttMatch(Opts opts) |
void |
simSaveICCache(Opts opts) |
void |
simSaveLCSCache(Opts opts) |
void |
simSavePhenodigmClassScores(Opts opts) |
void |
simSaveState(Opts opts) |
void |
simTest(Opts opts) |
void |
startSimServer(Opts opts) |
void |
useFastOwlSim(Opts opts) |
void |
useSimpleOwlSim(Opts opts) |
allClassIC, getAncestorsWithIC, getIC, lcsx, lcsxAll, phenoSim, setSimMethod, sim, simAll, simResume
configRead, dumpShuntGraphs, experimentalLoadComplexAnnotationSolr, flexDumpOntologySolr, flexLoadOntologySolr, generalLoadOntologySolr, loadComplexAnnotationSolr, loadGAFsSolr, loadGPADsSolr, loadModelAnnotations, loadPANTHERGeneralSolr, loadPANTHERSolr, optimizeSolr, processCAFiles, processLegoCatalogs, processLegoFiles, processModelFolder, processModelUrlPrefix, processPantherTrees, purgeSolr, setSolrLogFile, setSolrUrl, solrEcoSubsetName, solrSchemaDump, solrTaxonSubsetName
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, removeRedundantInferredSuperClassAxioms, removeRedundantInferredSVFs, removeRedundantSubclasses, removeRedundantSVFs, removeSubsetEntities, runDAGCheck, runSingleIteration, verifyChanges
exit, getPrettyPrinter, handlePrettyPrinter, help, helpFooter, printVersion, resolveClass, resolveClassList, resolveEntity, resolveEntity, resolveEntityList, resolveObjectProperty, resolveObjectPropertyList, resolveObjectPropertyListAsList, run, run, runSingleIteration, summarizeOntology
protected PrintStream resultOutStream
public String getProperty(SimpleOwlSim.SimConfigurationProperty p)
getProperty
in class SimCommandRunner
public void saveSim(Opts opts) throws Exception
saveSim
in class SimCommandRunner
Exception
public void mergeSim(Opts opts) throws Exception
mergeSim
in class SimCommandRunner
Exception
public void removeDangningAnnotations(Opts opts) throws Exception
Exception
public void attributeAllByAllOld(Opts opts) throws UnknownOWLClassException
UnknownOWLClassException
public void attributeAllByAll(OwlSim sim, Opts opts) throws UnknownOWLClassException
UnknownOWLClassException
public void attributeSimilarityAllByAllPairwise(Opts opts) throws UnknownOWLClassException
attributeAllByAll(owltools.sim2.OwlSim, owltools.cli.Opts)
, which outputs the comparison of any two attributes only
ever once, this method will necessarily output the
pairwise-comparison repeatedly, if the same two
attributes belong to two different sets of individuals.opts
- UnknownOWLClassException
public void attributeSimilarityByPair(org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLNamedIndividual j) throws UnknownOWLClassException
i
- j
- UnknownOWLClassException
@Deprecated public void runOwlSim(Opts opts) throws UnknownOWLClassException
runOwlSim
in class SimCommandRunner
opts
- UnknownOWLClassException
public void runOwlSim(OwlSim owlsim, Opts opts) throws UnknownOWLClassException
UnknownOWLClassException
protected void loadProperties(Opts opts) throws IOException
loadProperties
in class SimCommandRunner
IOException
@Deprecated public void simBasic(Opts opts) throws Exception
simBasic
in class SimCommandRunner
Exception
public void simBasicStats(Opts opts) throws Exception
opts
- Exception
@Deprecated public void simAttMatchOld(Opts opts) throws Exception
Exception
public void simSavePhenodigmClassScores(Opts opts) throws Exception
Exception
public void owlsimEnrichmentAnalysis(Opts opts) throws Exception
owlsimEnrichmentAnalysis
in class SimCommandRunner
Exception
public void owlsimEnrichmentAnalysisAllByAll(Opts opts) throws Exception
Exception
public void learnClassDifferentia(Opts opts) throws Exception
Exception
public void instanceStats(Opts opts) throws Exception
opts
- Exception
public void instanceICValues(Opts opts) throws Exception
opts
- Exception
@Deprecated public void OLDinstanceICValues(Opts opts) throws Exception
Exception
public void showAttributeGroupingsInTable(Opts opts) throws Exception
showAttributeGroupingsAsList(owltools.cli.Opts)
.opts
- Exception
public void showAttributeGroupingsAsList(Opts opts) throws Exception
showAttributeGroupingsInTable(owltools.cli.Opts)
opts
- Exception
public void showAttributeGroupings(Opts opts) throws Exception
Exception
public OwlSimFactory getOwlSimFactory()
public void setOwlSimFactory(OwlSimFactory owlSimFactory)
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