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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
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
flexLoadOntologySolr(CommandRunner.Opts)
- Method in class owltools.cli.
SolrCommandRunner
TODO: Try 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
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.
loadOntologySolr(CommandRunner.Opts)
- Method in class owltools.cli.
SolrCommandRunner
Used for loading whatever ontology stuff we have into GOlr.
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
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
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
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
A
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