public class GafCommandRunner extends CommandRunner
CommandRunner.OptionException
Modifier and Type | Field and Description |
---|---|
BioentityDocument |
bioentityDocument |
TraversingEcoMapper |
eco |
GafDocument |
gafdoc |
exitOnException, g, isDisposeReasonerOnExit, owlObjectCachedSet, pw, queryOntology, reasoner, reasonerName
Constructor and Description |
---|
GafCommandRunner() |
Modifier and Type | Method and Description |
---|---|
void |
createExperimentalPredictions(Opts opts) |
void |
createRdfXml(Opts opts) |
void |
extractOntologySubsetByGaf(Opts opts) |
void |
fetchCandidateProcess(Opts opts) |
void |
foldGafExtensions(Opts opts) |
void |
gaCalculateSpecificity(Opts opts) |
void |
gaf(Opts opts)
Used for loading GAFs into memory
|
void |
gaf2Lego(Opts opts) |
void |
gaf2LegoIndivduals(Opts opts)
Translate the GeneAnnotations into a lego all individual OWL representation.
|
void |
gaf2oa(Opts opts) |
void |
gaf2Owl(Opts opts) |
void |
gaf2OwlSimple(Opts opts)
Created to mimic the translation to OWL for GAF checks
|
void |
gafCompareBasic(Opts opts) |
void |
gafFoldInferences(Opts opts) |
void |
gafQuery(Opts opts) |
void |
gafRemoveRedundant(Opts opts) |
void |
gafTermCounts(Opts opts) |
void |
gafTermICValues(Opts opts) |
void |
gafXpPredict(Opts opts) |
void |
generateJsonGafStatistics(Opts opts) |
void |
generateMolecularModel(Opts opts) |
void |
goMultiEnrichment(Opts opts) |
void |
legoToAnnotations(Opts opts) |
void |
loadGpadGpi(Opts opts) |
void |
mapToSlim(Opts opts) |
protected int |
preCheckOntology(String inConsistentMsg,
String unsatisfiableMsg) |
void |
runGAFChecks(Opts opts) |
void |
runOntologyPreCheck(Opts opts)
Similar method to '--run-reasoner', but not only checks for unsatisfiable
classes, but also checks first for a consistent ontology.
|
void |
setExperimentalGAFPredictionFile(Opts opts) |
void |
setExperimentalGAFPredictionReportFile(Opts opts) |
void |
setGAFPredictionFile(Opts opts) |
void |
setGAFPredictionReportFile(Opts opts) |
void |
setGAFReportFile(Opts opts) |
void |
setGAFReportSummaryFile(Opts opts) |
void |
setGAFTaxonModule(Opts opts) |
void |
unfoldGafExtensions(Opts opts) |
void |
visualizeLego(Opts opts)
Deprecated.
|
void |
writeGaf(Opts opts) |
void |
writeGpad(Opts opts) |
void |
writeGpi(Opts opts) |
void |
writeLego(org.semanticweb.owlapi.model.OWLOntology ontology,
String output,
String name)
Deprecated.
|
void |
writeXgmml(Opts opts) |
assertAboxInferences, assertInferredSubClassAxioms, createBioChebi, createExternalMappings, createPartOfLinks, createSlim, createSubsetTags, exit, extractAnnotationValue, extractExtensionFile, filterExtensionFile, getPrettyPrinter, handlePrettyPrinter, help, helpFooter, jsonLdToRdf, parseArgString, rdfToJsonLd, removeRedundantInferredSuperClassAxioms, removeSubsetEntities, resolveClass, resolveClassList, resolveEntity, resolveEntity, resolveEntityList, resolveObjectProperty, resolveObjectPropertyList, resolveObjectPropertyListAsList, run, run, runDAGCheck, runSingleIteration, runSingleIteration, summarizeOntology, verifyChanges
public GafDocument gafdoc
public BioentityDocument bioentityDocument
public TraversingEcoMapper eco
public void gaf(Opts opts) throws Exception
opts
- Exception
public void gaf2OwlSimple(Opts opts) throws Exception
opts
- Exception
public void gaf2Owl(Opts opts) throws org.semanticweb.owlapi.model.OWLException
org.semanticweb.owlapi.model.OWLException
public void gafXpPredict(Opts opts)
public void gafTermICValues(Opts opts)
public void gaCalculateSpecificity(Opts opts)
public void gafTermCounts(Opts opts)
public void gafQuery(Opts opts)
public void extractOntologySubsetByGaf(Opts opts) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyCreationException
public void mapToSlim(Opts opts) throws org.semanticweb.owlapi.model.OWLOntologyCreationException, IOException
org.semanticweb.owlapi.model.OWLOntologyCreationException
IOException
public void runOntologyPreCheck(Opts opts) throws Exception
opts
- Exception
public void setGAFReportFile(Opts opts)
public void setGAFReportSummaryFile(Opts opts)
public void setGAFPredictionFile(Opts opts)
public void setGAFPredictionReportFile(Opts opts)
public void setGAFTaxonModule(Opts opts)
public void setExperimentalGAFPredictionFile(Opts opts)
public void setExperimentalGAFPredictionReportFile(Opts opts)
public void createExperimentalPredictions(Opts opts) throws Exception
Exception
public void writeXgmml(Opts opts) throws IOException
IOException
public void gaf2LegoIndivduals(Opts opts) throws Exception
opts
- Exception
public void generateMolecularModel(Opts opts) throws Exception
Exception
public void fetchCandidateProcess(Opts opts) throws Exception
Exception
@Deprecated public void visualizeLego(Opts opts) throws Exception
Exception
@Deprecated public void writeLego(org.semanticweb.owlapi.model.OWLOntology ontology, String output, String name) throws Exception
Exception
public void generateJsonGafStatistics(Opts opts) throws Exception
Exception
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