owltools.cli
Class GafCommandRunner
java.lang.Object
owltools.cli.CommandRunner
owltools.cli.GafCommandRunner
- Direct Known Subclasses:
- TaxonCommandRunner
public class GafCommandRunner
- extends CommandRunner
GAF tools for command-line, includes validation of GAF files.
TODO implement a filtering mechanism for GAF files
Methods inherited from class owltools.cli.CommandRunner |
exit, help, helpFooter, parseArgString, resolveClass, resolveEntity, resolveEntity, resolveEntityList, resolveObjectProperty, run, run, summarizeOntology |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
gafdoc
public GafDocument gafdoc
GafCommandRunner
public GafCommandRunner()
gaf
public void gaf(CommandRunner.Opts opts)
throws Exception
- Used for loading GAFs into memory
- Parameters:
opts
-
- Throws:
Exception
gaf2Owl
public void gaf2Owl(CommandRunner.Opts opts)
throws org.semanticweb.owlapi.model.OWLException
- Throws:
org.semanticweb.owlapi.model.OWLException
gafXpPredict
public void gafXpPredict(CommandRunner.Opts opts)
gafTermCounts
public void gafTermCounts(CommandRunner.Opts opts)
gafQuery
public void gafQuery(CommandRunner.Opts opts)
runGAFChecks
public void runGAFChecks(CommandRunner.Opts opts)
throws AnnotationRulesEngine.AnnotationRuleCheckException,
IOException
- Throws:
AnnotationRulesEngine.AnnotationRuleCheckException
IOException
setGAFReportFile
public void setGAFReportFile(CommandRunner.Opts opts)
createRdfXml
public void createRdfXml(CommandRunner.Opts opts)
throws IOException
- Throws:
IOException
writeXgmml
public void writeXgmml(CommandRunner.Opts opts)
throws IOException
- Throws:
IOException
Copyright © 2010-2012. All Rights Reserved.