owltools.cli
Class SimCommandRunner

java.lang.Object
  extended by owltools.cli.CommandRunner
      extended by owltools.cli.GafCommandRunner
          extended by owltools.cli.TaxonCommandRunner
              extended by owltools.cli.SolrCommandRunner
                  extended by owltools.cli.SimCommandRunner
Direct Known Subclasses:
JsCommandRunner

public class SimCommandRunner
extends SolrCommandRunner

Semantic similarity and information content.

Author:
cjm

Nested Class Summary
 
Nested classes/interfaces inherited from class owltools.cli.CommandRunner
CommandRunner.OptionException, CommandRunner.Opts
 
Field Summary
 
Fields inherited from class owltools.cli.GafCommandRunner
gafdoc
 
Fields inherited from class owltools.cli.CommandRunner
exitOnException, g, owlObjectCachedSet, owlpp, pw, queryOntology, reasoner, reasonerName
 
Constructor Summary
SimCommandRunner()
           
 
Method Summary
 void allClassIC(CommandRunner.Opts opts)
           
 void getAncestorsWithIC(CommandRunner.Opts opts)
           
 void getIC(CommandRunner.Opts opts)
           
 void lcsx(CommandRunner.Opts opts)
           
 void lcsxAll(CommandRunner.Opts opts)
           
 void mergeSim(CommandRunner.Opts opts)
           
 void saveSim(CommandRunner.Opts opts)
           
 void setSimMethod(CommandRunner.Opts opts)
           
 void sim(CommandRunner.Opts opts)
           
 void simAll(CommandRunner.Opts opts)
           
 
Methods inherited from class owltools.cli.SolrCommandRunner
configRead, dumpShuntGraphs, flexDumpOntologySolr, flexLoadOntologySolr, loadGafSolr, loadGafsSolr, loadGPADsSolr, loadOntologySolr, purgeSolr, setSolrUrl, solrSchemaDump
 
Methods inherited from class owltools.cli.TaxonCommandRunner
makeClassTaxonMatrix, makeTaxonSet
 
Methods inherited from class owltools.cli.GafCommandRunner
createRdfXml, gaf, gaf2Owl, gafQuery, gafTermCounts, gafXpPredict, runGAFChecks, setGAFReportFile, writeXgmml
 
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
 

Constructor Detail

SimCommandRunner

public SimCommandRunner()
Method Detail

setSimMethod

public void setSimMethod(CommandRunner.Opts opts)

simAll

public void simAll(CommandRunner.Opts opts)
            throws SimEngine.SimilarityAlgorithmException
Throws:
SimEngine.SimilarityAlgorithmException

saveSim

public void saveSim(CommandRunner.Opts opts)
             throws Exception
Throws:
Exception

mergeSim

public void mergeSim(CommandRunner.Opts opts)
              throws Exception
Throws:
Exception

sim

public void sim(CommandRunner.Opts opts)
         throws Exception
Throws:
Exception

lcsx

public void lcsx(CommandRunner.Opts opts)

lcsxAll

public void lcsxAll(CommandRunner.Opts opts)
             throws Exception
Throws:
Exception

getIC

public void getIC(CommandRunner.Opts opts)

getAncestorsWithIC

public void getAncestorsWithIC(CommandRunner.Opts opts)

allClassIC

public void allClassIC(CommandRunner.Opts opts)
                throws Exception
Throws:
Exception


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