owltools.cli
Class GafCommandRunner

java.lang.Object
  extended by owltools.cli.CommandRunner
      extended by 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


Nested Class Summary
 
Nested classes/interfaces inherited from class owltools.cli.CommandRunner
CommandRunner.OptionException, CommandRunner.Opts
 
Field Summary
 GafDocument gafdoc
           
 
Fields inherited from class owltools.cli.CommandRunner
exitOnException, g, owlpp, pw, queryOntology, reasoner, reasonerName
 
Constructor Summary
GafCommandRunner()
           
 
Method Summary
 void gaf(CommandRunner.Opts opts)
          Used for loading GAFs into memory
 void gaf2Owl(CommandRunner.Opts opts)
           
 void gafQuery(CommandRunner.Opts opts)
           
 void gafTermCounts(CommandRunner.Opts opts)
           
 void gafXpPredict(CommandRunner.Opts opts)
           
 void runGAFChecks(CommandRunner.Opts opts)
           
 void setGAFReportFile(CommandRunner.Opts opts)
           
 
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
 

Field Detail

gafdoc

public GafDocument gafdoc
Constructor Detail

GafCommandRunner

public GafCommandRunner()
Method Detail

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)


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