- saveSim(Opts) - Method in class owltools.cli.Sim2CommandRunner
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- saveSim(Opts) - Method in class owltools.cli.SimCommandRunner
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- setExperimentalGAFPredictionFile(Opts) - Method in class owltools.cli.GafCommandRunner
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- setExperimentalGAFPredictionReportFile(Opts) - Method in class owltools.cli.GafCommandRunner
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- setGAFPredictionFile(Opts) - Method in class owltools.cli.GafCommandRunner
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- setGAFPredictionReportFile(Opts) - Method in class owltools.cli.GafCommandRunner
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- setGAFReportFile(Opts) - Method in class owltools.cli.GafCommandRunner
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- setGAFReportSummaryFile(Opts) - Method in class owltools.cli.GafCommandRunner
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- setGAFTaxonModule(Opts) - Method in class owltools.cli.GafCommandRunner
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- setOwlSimFactory(OwlSimFactory) - Method in class owltools.cli.Sim2CommandRunner
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- setSimMethod(Opts) - Method in class owltools.cli.SimCommandRunner
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- setSimProperty(Opts) - Method in class owltools.cli.Sim2CommandRunner
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- setSolrLogFile(Opts) - Method in class owltools.cli.SolrCommandRunner
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Set an optional file to use for logging load data (can be consumed by AmiGO 2).
- setSolrUrl(Opts) - Method in class owltools.cli.SolrCommandRunner
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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
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- showAttributeGroupingsAsList(Opts) - Method in class owltools.cli.Sim2CommandRunner
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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
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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
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- sim(Opts) - Method in class owltools.cli.SimCommandRunner
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- Sim2CommandRunner - Class in owltools.cli
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Semantic similarity and information content.
- Sim2CommandRunner() - Constructor for class owltools.cli.Sim2CommandRunner
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- simAll(Opts) - Method in class owltools.cli.SimCommandRunner
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- simAttMatchOld(Opts) - Method in class owltools.cli.Sim2CommandRunner
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Deprecated.
- simBasic(Opts) - Method in class owltools.cli.Sim2CommandRunner
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Deprecated.
- simBasic(Opts) - Method in class owltools.cli.SimCommandRunner
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- simBasicStats(Opts) - Method in class owltools.cli.Sim2CommandRunner
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This method will report to the user some metadata about the previous similarity
run.
- SimCommandRunner - Class in owltools.cli
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Semantic similarity and information content.
- SimCommandRunner() - Constructor for class owltools.cli.SimCommandRunner
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- simDlQuery(Opts) - Method in class owltools.cli.Sim2CommandRunner
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- simLCS(Opts) - Method in class owltools.cli.Sim2CommandRunner
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- simLoadICCache(Opts) - Method in class owltools.cli.Sim2CommandRunner
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- simLoadLCSCache(Opts) - Method in class owltools.cli.Sim2CommandRunner
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- simPairwiseAttMatch(Opts) - Method in class owltools.cli.Sim2CommandRunner
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- simResume(Opts) - Method in class owltools.cli.SimCommandRunner
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- simSaveICCache(Opts) - Method in class owltools.cli.Sim2CommandRunner
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- simSaveLCSCache(Opts) - Method in class owltools.cli.Sim2CommandRunner
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- simSavePhenodigmClassScores(Opts) - Method in class owltools.cli.Sim2CommandRunner
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- simSaveState(Opts) - Method in class owltools.cli.Sim2CommandRunner
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- simTest(Opts) - Method in class owltools.cli.Sim2CommandRunner
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- SolrCommandRunner - Class in owltools.cli
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Solr/GOlr loading.
- SolrCommandRunner() - Constructor for class owltools.cli.SolrCommandRunner
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- solrEcoSubsetName(Opts) - Method in class owltools.cli.SolrCommandRunner
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- solrSchemaDump(Opts) - Method in class owltools.cli.SolrCommandRunner
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Output (STDOUT) XML segment to put into the Solr schema file after reading the YAML configuration file(s).
- solrTaxonSubsetName(Opts) - Method in class owltools.cli.SolrCommandRunner
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- startSimServer(Opts) - Method in class owltools.cli.Sim2CommandRunner
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- summarizeOntology(OWLOntology) - Method in class owltools.cli.CommandRunnerBase
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