Package | Description |
---|---|
owltools.cli |
CLI - Command Line Interface
|
Modifier and Type | Method and Description |
---|---|
void |
SimCommandRunner.allClassIC(Opts opts) |
void |
CommandRunner.assertAboxInferences(Opts opts) |
void |
CommandRunner.assertInferredSubClassAxioms(Opts opts) |
void |
Sim2CommandRunner.classICPairs(Opts opts) |
void |
SolrCommandRunner.configRead(Opts opts)
Output (STDOUT) a XML segment to put into the Solr schema file after reading the YAML file.
|
void |
CommandRunner.createBioChebi(Opts opts) |
void |
GafCommandRunner.createExperimentalPredictions(Opts opts) |
void |
CommandRunner.createExternalMappings(Opts opts) |
void |
CommandRunner.createPartOfLinks(Opts opts)
GeneOntology specific function to create links between molecular
functions and their corresponding processes.
|
void |
GafCommandRunner.createRdfXml(Opts opts) |
void |
CommandRunner.createSlim(Opts opts) |
void |
CommandRunner.createSubsetTags(Opts opts)
Simple helper to create a subset tag for matching entities, allows to specify exceptions
|
void |
TaxonCommandRunner.createTaxonDisjointOverInTaxon(Opts opts) |
void |
SolrCommandRunner.dumpShuntGraphs(Opts opts)
Used for generating output for units tests in other languages.
|
void |
SolrCommandRunner.experimentalLoadComplexAnnotationSolr(Opts opts)
Experimental method for trying out the loading of complex_annotation doc type
|
void |
CommandRunner.extractAnnotationValue(Opts opts) |
void |
CommandRunner.extractExtensionFile(Opts opts)
Extract all xps (
OWLEquivalentClassesAxiom ) from the loaded
ontology. |
void |
GafCommandRunner.extractOntologySubsetByGaf(Opts opts) |
void |
GafCommandRunner.fetchCandidateProcess(Opts opts) |
void |
CommandRunner.filterExtensionFile(Opts opts)
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.
|
void |
SolrCommandRunner.flexDumpOntologySolr(Opts opts)
Dump experimental flexible loader output to JSON(?) blob.
|
void |
SolrCommandRunner.flexLoadOntologySolr(Opts opts)
Flexible loader for ontologies--uses the YAML config to find loading functions.
|
void |
GafCommandRunner.foldGafExtensions(Opts opts) |
void |
Sim2CommandRunner.fsimAttTopSimJ(Opts opts) |
void |
Sim2CommandRunner.fsimBasic(Opts opts) |
void |
Sim2CommandRunner.fsimCompareAtts(Opts opts) |
void |
Sim2CommandRunner.fsimCompareAttsLCS(Opts opts) |
void |
Sim2CommandRunner.fsimCompareAttsLite(Opts opts) |
void |
Sim2CommandRunner.fsimCompareAttsSimJ(Opts opts) |
void |
Sim2CommandRunner.fsimFindMatches(Opts opts) |
void |
Sim2CommandRunner.fsimSearchAll(Opts opts) |
void |
Sim2CommandRunner.fsimTest(Opts opts) |
void |
GafCommandRunner.gaCalculateSpecificity(Opts opts) |
void |
GafCommandRunner.gaf(Opts opts)
Used for loading GAFs into memory
|
void |
GafCommandRunner.gaf2Lego(Opts opts) |
void |
GafCommandRunner.gaf2LegoIndivduals(Opts opts)
Translate the GeneAnnotations into a lego all individual OWL representation.
|
void |
GafCommandRunner.gaf2oa(Opts opts) |
void |
GafCommandRunner.gaf2Owl(Opts opts) |
void |
GafCommandRunner.gaf2OwlSimple(Opts opts)
Created to mimic the translation to OWL for GAF checks
|
void |
GafCommandRunner.gafCompareBasic(Opts opts) |
void |
GafCommandRunner.gafFoldInferences(Opts opts) |
void |
GafCommandRunner.gafQuery(Opts opts) |
void |
GafCommandRunner.gafRemoveRedundant(Opts opts) |
void |
GafCommandRunner.gafTermCounts(Opts opts) |
void |
GafCommandRunner.gafTermICValues(Opts opts) |
void |
GafCommandRunner.gafXpPredict(Opts opts) |
void |
SolrCommandRunner.generalLoadOntologySolr(Opts opts)
Trivial hard-wired (and optional) method for loading collected
ontology information into the "general" schema (general-config.yaml) for GO.
|
void |
GafCommandRunner.generateJsonGafStatistics(Opts opts) |
void |
GafCommandRunner.generateMolecularModel(Opts opts) |
void |
SimCommandRunner.getAncestorsWithIC(Opts opts) |
void |
SimCommandRunner.getIC(Opts opts) |
void |
GafCommandRunner.goMultiEnrichment(Opts opts) |
void |
CommandRunner.handlePrettyPrinter(Opts opts) |
void |
Sim2CommandRunner.instanceICValues(Opts opts)
Prints a tab-delimited report of the IC measures for each annotation (class)
made to each instance.
|
void |
Sim2CommandRunner.instanceStats(Opts opts)
Computes & reports on some summary statistics on the loaded data set.
|
void |
CommandRunner.jsonLdToRdf(Opts opts) |
void |
SimCommandRunner.lcsx(Opts opts) |
void |
SimCommandRunner.lcsxAll(Opts opts) |
void |
Sim2CommandRunner.learnClassDifferentia(Opts opts) |
void |
GafCommandRunner.legoToAnnotations(Opts opts) |
void |
SolrCommandRunner.loadComplexAnnotationSolr(Opts opts)
Experimental method for trying out the loading of complex_annotation doc type.
|
void |
SolrCommandRunner.loadGAFsSolr(Opts opts)
Used for loading a list of GAFs into GOlr.
|
void |
GafCommandRunner.loadGpadGpi(Opts opts) |
void |
SolrCommandRunner.loadGPADsSolr(Opts opts)
Used for loading a list of GPAD pairs into GOlr.
|
void |
SolrCommandRunner.loadPANTHERGeneralSolr(Opts opts)
Requires the --read-panther argument (or something else that fills the pSet object).
|
void |
SolrCommandRunner.loadPANTHERSolr(Opts opts)
Requires the --read-panther argument (or something else that fills the pSet object).
|
void |
TaxonCommandRunner.makeClassTaxonMatrix(Opts opts) |
void |
TaxonCommandRunner.makeTaxonSet(Opts opts) |
void |
GafCommandRunner.mapToSlim(Opts opts) |
void |
SimCommandRunner.mergeSim(Opts opts) |
void |
Sim2CommandRunner.mergeSim(Opts opts) |
void |
SolrCommandRunner.optimizeSolr(Opts opts)
Requires the --solr-url argument.
|
void |
SimCommandRunner.owlsimEnrichmentAnalysis(Opts opts) |
void |
Sim2CommandRunner.owlsimEnrichmentAnalysis(Opts opts) |
void |
Sim2CommandRunner.owlsimEnrichmentAnalysisAllByAll(Opts opts) |
void |
SimCommandRunner.phenoSim(Opts opts) |
void |
SolrCommandRunner.processCAFiles(Opts opts)
Used for reading the lego files to be used for loading complex annotations.
|
void |
SolrCommandRunner.processLegoCatalogs(Opts opts)
Used for reading the ontology catalogs to be used for loading complex annotations.
|
void |
SolrCommandRunner.processLegoFiles(Opts opts)
Used for reading the lego files to be used for loading complex annotations.
|
void |
SolrCommandRunner.processPantherTrees(Opts opts)
Used for applying the panther trees to the currently data run.
|
void |
SolrCommandRunner.purgeSolr(Opts opts)
Manually purge the index to try again.
|
void |
CommandRunner.rdfToJsonLd(Opts opts) |
void |
Sim2CommandRunner.removeDangningAnnotations(Opts opts) |
void |
CommandRunner.removeRedundantInferredSuperClassAxioms(Opts opts) |
void |
CommandRunner.removeSubsetEntities(Opts opts) |
void |
CommandRunner.runDAGCheck(Opts opts) |
void |
GafCommandRunner.runGAFChecks(Opts opts) |
void |
JsCommandRunner.runJavaScript(Opts opts)
Run the given js with the current graph (and reasoner).
|
void |
GafCommandRunner.runOntologyPreCheck(Opts opts)
Similar method to '--run-reasoner', but not only checks for unsatisfiable
classes, but also checks first for a consistent ontology.
|
void |
SimCommandRunner.saveSim(Opts opts) |
void |
Sim2CommandRunner.saveSim(Opts opts) |
void |
GafCommandRunner.setExperimentalGAFPredictionFile(Opts opts) |
void |
GafCommandRunner.setExperimentalGAFPredictionReportFile(Opts opts) |
void |
GafCommandRunner.setGAFPredictionFile(Opts opts) |
void |
GafCommandRunner.setGAFPredictionReportFile(Opts opts) |
void |
GafCommandRunner.setGAFReportFile(Opts opts) |
void |
GafCommandRunner.setGAFReportSummaryFile(Opts opts) |
void |
GafCommandRunner.setGAFTaxonModule(Opts opts) |
void |
SimCommandRunner.setSimMethod(Opts opts) |
void |
Sim2CommandRunner.setSimProperty(Opts opts) |
void |
SolrCommandRunner.setSolrLogFile(Opts opts)
Set an optional file to use for logging load data (can be consumed by AmiGO 2).
|
void |
SolrCommandRunner.setSolrUrl(Opts opts)
Set an optional Solr URL to use with Solr options so they don't have to
be specified separately for every option.
|
void |
Sim2CommandRunner.showAttributeGroupings(Opts opts) |
void |
Sim2CommandRunner.showAttributeGroupingsAsList(Opts opts)
Given a set of classes, will print the grouping class(es) for each
annotation in a comma-separated list.
|
void |
Sim2CommandRunner.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 |
Sim2CommandRunner.showSimProperties(Opts opts) |
void |
SimCommandRunner.sim(Opts opts) |
void |
SimCommandRunner.simAll(Opts opts) |
void |
Sim2CommandRunner.simAttMatchOld(Opts opts)
Deprecated.
|
void |
SimCommandRunner.simBasic(Opts opts) |
void |
Sim2CommandRunner.simBasic(Opts opts)
Deprecated.
|
void |
Sim2CommandRunner.simBasicStats(Opts opts)
This method will report to the user some metadata about the previous similarity
run.
|
void |
Sim2CommandRunner.simDlQuery(Opts opts) |
void |
Sim2CommandRunner.simLCS(Opts opts) |
void |
Sim2CommandRunner.simLoadICCache(Opts opts) |
void |
Sim2CommandRunner.simLoadLCSCache(Opts opts) |
void |
Sim2CommandRunner.simPairwiseAttMatch(Opts opts) |
void |
SimCommandRunner.simResume(Opts opts) |
void |
Sim2CommandRunner.simSaveICCache(Opts opts) |
void |
Sim2CommandRunner.simSaveLCSCache(Opts opts) |
void |
Sim2CommandRunner.simSavePhenodigmClassScores(Opts opts) |
void |
Sim2CommandRunner.simSaveState(Opts opts) |
void |
Sim2CommandRunner.simTest(Opts opts) |
void |
SolrCommandRunner.solrSchemaDump(Opts opts)
Output (STDOUT) XML segment to put into the Solr schema file after reading the YAML configuration file(s).
|
void |
Sim2CommandRunner.startSimServer(Opts opts) |
void |
GafCommandRunner.unfoldGafExtensions(Opts opts) |
void |
Sim2CommandRunner.useFastOwlSim(Opts opts) |
void |
Sim2CommandRunner.useSimpleOwlSim(Opts opts) |
void |
CommandRunner.verifyChanges(Opts opts) |
void |
GafCommandRunner.visualizeLego(Opts opts)
Deprecated.
|
void |
GafCommandRunner.writeGaf(Opts opts) |
void |
GafCommandRunner.writeGpad(Opts opts) |
void |
GafCommandRunner.writeGpi(Opts opts) |
void |
GafCommandRunner.writeXgmml(Opts opts) |
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