A C D E F G H I J L M N O P Q R S T W

A

allClassIC(CommandRunner.Opts) - Method in class owltools.cli.SimCommandRunner
 

C

CLIMethod - Annotation Type in owltools.cli.tools
Annotation indicating, that this method can be called from the command line interface.
CommandLineInterface - Class in owltools.cli
Wrapper class to provide a stable class name for the main method.
CommandLineInterface() - Constructor for class owltools.cli.CommandLineInterface
 
CommandRunner - Class in owltools.cli
An instance of this class can execute owltools commands in sequence.
CommandRunner() - Constructor for class owltools.cli.CommandRunner
 
CommandRunner.OptionException - Exception in owltools.cli
 
CommandRunner.OptionException(String) - Constructor for exception owltools.cli.CommandRunner.OptionException
 
CommandRunner.Opts - Class in owltools.cli
 
CommandRunner.Opts(String[]) - Constructor for class owltools.cli.CommandRunner.Opts
 
CommandRunner.Opts(List<String>) - Constructor for class owltools.cli.CommandRunner.Opts
 
configRead(CommandRunner.Opts) - Method in class owltools.cli.SolrCommandRunner
Output (STDOUT) a XML segment to put into the Solr schema file after reading the YAML file.
createRdfXml(CommandRunner.Opts) - Method in class owltools.cli.GafCommandRunner
 

D

dumpShuntGraphs(CommandRunner.Opts) - Method in class owltools.cli.SolrCommandRunner
Used for generating output for units tests in other languages.

E

exit(int) - Method in class owltools.cli.CommandRunner
 
exitOnException - Variable in class owltools.cli.CommandRunner
 

F

fail() - Method in class owltools.cli.CommandRunner.Opts
 
flexDumpOntologySolr(CommandRunner.Opts) - Method in class owltools.cli.SolrCommandRunner
Dump experimental flexible loader output to JSON(?) blob.
flexLoadOntologySolr(CommandRunner.Opts) - Method in class owltools.cli.SolrCommandRunner
Experimental flexible loader.

G

g - Variable in class owltools.cli.CommandRunner
 
gaf(CommandRunner.Opts) - Method in class owltools.cli.GafCommandRunner
Used for loading GAFs into memory
gaf2Owl(CommandRunner.Opts) - Method in class owltools.cli.GafCommandRunner
 
GafCommandRunner - Class in owltools.cli
GAF tools for command-line, includes validation of GAF files.
GafCommandRunner() - Constructor for class owltools.cli.GafCommandRunner
 
gafdoc - Variable in class owltools.cli.GafCommandRunner
 
gafQuery(CommandRunner.Opts) - Method in class owltools.cli.GafCommandRunner
 
gafTermCounts(CommandRunner.Opts) - Method in class owltools.cli.GafCommandRunner
 
gafXpPredict(CommandRunner.Opts) - Method in class owltools.cli.GafCommandRunner
 
getAncestorsWithIC(CommandRunner.Opts) - Method in class owltools.cli.SimCommandRunner
 
getIC(CommandRunner.Opts) - Method in class owltools.cli.SimCommandRunner
 

H

hasArgs() - Method in class owltools.cli.CommandRunner.Opts
 
hasOpt(String) - Method in class owltools.cli.CommandRunner.Opts
 
hasOpts() - Method in class owltools.cli.CommandRunner.Opts
 
help() - Method in class owltools.cli.CommandRunner
 
helpFooter() - Method in class owltools.cli.CommandRunner
 

I

info(String, String) - Method in class owltools.cli.CommandRunner.Opts
 

J

JsCommandRunner - Class in owltools.cli
Provide a JavaScript interpreter for OWLTools.
JsCommandRunner() - Constructor for class owltools.cli.JsCommandRunner
 

L

lcsx(CommandRunner.Opts) - Method in class owltools.cli.SimCommandRunner
 
lcsxAll(CommandRunner.Opts) - Method in class owltools.cli.SimCommandRunner
 
loadGafSolr(CommandRunner.Opts) - Method in class owltools.cli.SolrCommandRunner
Requires the --gaf argument (or something else that fills the gafdoc object).
loadGafsSolr(CommandRunner.Opts) - Method in class owltools.cli.SolrCommandRunner
Used for loading a list of GAFs into GOlr.
loadGPADsSolr(CommandRunner.Opts) - Method in class owltools.cli.SolrCommandRunner
Used for loading a list of GPAD pairs into GOlr.
loadOntologySolr(CommandRunner.Opts) - Method in class owltools.cli.SolrCommandRunner
Deprecated. 

M

main(String[]) - Static method in class owltools.cli.CommandLineInterface
 
makeClassTaxonMatrix(CommandRunner.Opts) - Method in class owltools.cli.TaxonCommandRunner
 
makeTaxonSet(CommandRunner.Opts) - Method in class owltools.cli.TaxonCommandRunner
 
mergeSim(CommandRunner.Opts) - Method in class owltools.cli.SimCommandRunner
 

N

nextArgIsHelp() - Method in class owltools.cli.CommandRunner.Opts
 
nextEq(String) - Method in class owltools.cli.CommandRunner.Opts
 
nextEq(Collection<String>) - Method in class owltools.cli.CommandRunner.Opts
 
nextList() - Method in class owltools.cli.CommandRunner.Opts
 
nextOpt() - Method in class owltools.cli.CommandRunner.Opts
 

O

owlObjectCachedSet - Variable in class owltools.cli.CommandRunner
 
owlpp - Variable in class owltools.cli.CommandRunner
 
owltools.cli - package owltools.cli
CLI - Command Line Interface
owltools.cli.tools - package owltools.cli.tools
 

P

parseArgString(String) - Method in class owltools.cli.CommandRunner
 
peekArg() - Method in class owltools.cli.CommandRunner.Opts
 
purgeSolr(CommandRunner.Opts) - Method in class owltools.cli.SolrCommandRunner
Manually purge the index to try again.
pw - Variable in class owltools.cli.CommandRunner
 

Q

queryOntology - Variable in class owltools.cli.CommandRunner
 

R

reasoner - Variable in class owltools.cli.CommandRunner
 
reasonerName - Variable in class owltools.cli.CommandRunner
 
resolveClass(String) - Method in class owltools.cli.CommandRunner
 
resolveEntity(CommandRunner.Opts) - Method in class owltools.cli.CommandRunner
 
resolveEntity(String) - Method in class owltools.cli.CommandRunner
 
resolveEntityList(CommandRunner.Opts) - Method in class owltools.cli.CommandRunner
 
resolveObjectProperty(String) - Method in class owltools.cli.CommandRunner
 
run(String[]) - Method in class owltools.cli.CommandRunner
 
run(CommandRunner.Opts) - Method in class owltools.cli.CommandRunner
 
runGAFChecks(CommandRunner.Opts) - Method in class owltools.cli.GafCommandRunner
 
runJavaScript(CommandRunner.Opts) - Method in class owltools.cli.JsCommandRunner
Run the given js with the current graph (and reasoner).

S

saveSim(CommandRunner.Opts) - Method in class owltools.cli.SimCommandRunner
 
setGAFReportFile(CommandRunner.Opts) - Method in class owltools.cli.GafCommandRunner
 
setSimMethod(CommandRunner.Opts) - Method in class owltools.cli.SimCommandRunner
 
setSolrUrl(CommandRunner.Opts) - Method in class owltools.cli.SolrCommandRunner
Set an optional Solr URL to use with Solr options so they don't have to be specified separately for every option.
sim(CommandRunner.Opts) - Method in class owltools.cli.SimCommandRunner
 
simAll(CommandRunner.Opts) - Method in class owltools.cli.SimCommandRunner
 
SimCommandRunner - Class in owltools.cli
Semantic similarity and information content.
SimCommandRunner() - Constructor for class owltools.cli.SimCommandRunner
 
SolrCommandRunner - Class in owltools.cli
Solr/GOlr loading.
SolrCommandRunner() - Constructor for class owltools.cli.SolrCommandRunner
 
solrSchemaDump(CommandRunner.Opts) - Method in class owltools.cli.SolrCommandRunner
Output (STDOUT) XML segment to put into the Solr schema file after reading the YAML configuration file(s).
summarizeOntology(OWLOntology) - Method in class owltools.cli.CommandRunner
 

T

TaxonCommandRunner - Class in owltools.cli
Command-line module for taxon constraints.
TaxonCommandRunner() - Constructor for class owltools.cli.TaxonCommandRunner
 

W

writeXgmml(CommandRunner.Opts) - Method in class owltools.cli.GafCommandRunner
 

A C D E F G H I J L M N O P Q R S T W

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