owltools.web
Class OWLHandler

java.lang.Object
  extended by owltools.web.OWLHandler

public class OWLHandler
extends Object


Nested Class Summary
static class OWLHandler.Param
           
static class OWLHandler.ResultType
           
 
Constructor Summary
OWLHandler(OWLServer owlserver, OWLGraphWrapper graph, javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response)
           
 
Method Summary
 void aboutCommand()
          information about an ontology object (class, property, individual)
 void allSubClassOfCommand()
           
 String getCommandName()
           
 String getFormat()
           
 void getOutgoingEdgesCommand()
           
 void getSuperClassesCommand()
           
 void headerHTML()
           
 void headerImage(String fmt)
           
 void headerOWL()
           
 void headerText()
           
 void helpCommand()
           
 void info(String msg)
           
 void isClassApplicableForTaxonCommand()
          tests which of a set of input classes (specified using id) is applicable for a set of taxa (specified using taxid)
 void lcsExpressionCommand()
           
 void makeSubsetOntologyCommand()
          generates a sub-ontology consisting only of classes specified using the id param.
 void printCachedObjects()
           
 void qvizCommand()
          visualize using QuickGO graphdraw.
 void setCommandName(String commandName)
           
 void setFormat(String format)
           
 void topCommand()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

OWLHandler

public OWLHandler(OWLServer owlserver,
                  OWLGraphWrapper graph,
                  javax.servlet.http.HttpServletRequest request,
                  javax.servlet.http.HttpServletResponse response)
           throws IOException
Throws:
IOException
Method Detail

getFormat

public String getFormat()

setFormat

public void setFormat(String format)

getCommandName

public String getCommandName()

setCommandName

public void setCommandName(String commandName)

topCommand

public void topCommand()
                throws org.semanticweb.owlapi.model.OWLOntologyCreationException,
                       org.semanticweb.owlapi.model.OWLOntologyStorageException,
                       IOException
Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyStorageException
IOException

helpCommand

public void helpCommand()
                 throws IOException
Throws:
IOException

getSuperClassesCommand

public void getSuperClassesCommand()
                            throws org.semanticweb.owlapi.model.OWLOntologyCreationException,
                                   org.semanticweb.owlapi.model.OWLOntologyStorageException,
                                   IOException
Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyStorageException
IOException

allSubClassOfCommand

public void allSubClassOfCommand()
                          throws org.semanticweb.owlapi.model.OWLOntologyCreationException,
                                 org.semanticweb.owlapi.model.OWLOntologyStorageException,
                                 IOException
Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyStorageException
IOException

getOutgoingEdgesCommand

public void getOutgoingEdgesCommand()
                             throws IOException,
                                    org.semanticweb.owlapi.model.OWLOntologyCreationException,
                                    org.semanticweb.owlapi.model.OWLOntologyStorageException
Throws:
IOException
org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyStorageException

lcsExpressionCommand

public void lcsExpressionCommand()
                          throws IOException,
                                 org.semanticweb.owlapi.model.OWLOntologyCreationException,
                                 org.semanticweb.owlapi.model.OWLOntologyStorageException
Throws:
IOException
org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyStorageException
See Also:
SimEngine

aboutCommand

public void aboutCommand()
                  throws org.semanticweb.owlapi.model.OWLOntologyCreationException,
                         org.semanticweb.owlapi.model.OWLOntologyStorageException,
                         IOException
information about an ontology object (class, property, individual)

Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyStorageException
IOException

qvizCommand

public void qvizCommand()
                 throws org.semanticweb.owlapi.model.OWLOntologyCreationException,
                        org.semanticweb.owlapi.model.OWLOntologyStorageException,
                        IOException
visualize using QuickGO graphdraw.

Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyStorageException
IOException

makeSubsetOntologyCommand

public void makeSubsetOntologyCommand()
                               throws org.semanticweb.owlapi.model.OWLOntologyCreationException,
                                      org.semanticweb.owlapi.model.OWLOntologyStorageException,
                                      IOException
generates a sub-ontology consisting only of classes specified using the id param. If the include_ancestors param is true, then the transitive closure of the input classes is included. otherwise, intermediate classes are excluded and paths are filled.

Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyStorageException
IOException
See Also:
Mooncat.makeSubsetOntology(Set, IRI)

isClassApplicableForTaxonCommand

public void isClassApplicableForTaxonCommand()
                                      throws org.semanticweb.owlapi.model.OWLOntologyCreationException,
                                             org.semanticweb.owlapi.model.OWLOntologyStorageException,
                                             IOException
tests which of a set of input classes (specified using id) is applicable for a set of taxa (specified using taxid)

Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyStorageException
IOException

info

public void info(String msg)
          throws IOException
Throws:
IOException

headerHTML

public void headerHTML()

headerText

public void headerText()

headerImage

public void headerImage(String fmt)

headerOWL

public void headerOWL()

printCachedObjects

public void printCachedObjects()
                        throws org.semanticweb.owlapi.model.OWLOntologyCreationException,
                               org.semanticweb.owlapi.model.OWLOntologyStorageException,
                               IOException
Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyStorageException
IOException


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