owltools.gaf.eco
Class TraversingEcoMapperImpl

java.lang.Object
  extended by owltools.gaf.eco.EcoMapperImpl
      extended by owltools.gaf.eco.TraversingEcoMapperImpl
All Implemented Interfaces:
EcoMapper, TraversingEcoMapper

public class TraversingEcoMapperImpl
extends EcoMapperImpl
implements TraversingEcoMapper


Field Summary
 
Fields inherited from interface owltools.gaf.eco.EcoMapper
ECO_MAPPING_PURL, ECO_PURL, ECO_PURL_IRI
 
Method Summary
 void dispose()
          Dispose this instance
 Set<String> getAllValidEvidenceIds(Set<String> codes, boolean includeChildren)
          Get all strings which are valid identifiers for the given evidence codes.
 Set<String> getAllValidEvidenceIds(String code, boolean includeChildren)
          Get all strings which are valid identifiers for a given evidence code.
 Set<org.semanticweb.owlapi.model.OWLClass> getAncestors(org.semanticweb.owlapi.model.OWLClass source, boolean reflexive)
          Traversing method for the ECO ontology.
 Set<org.semanticweb.owlapi.model.OWLClass> getAncestors(Set<org.semanticweb.owlapi.model.OWLClass> sources, boolean reflexive)
          Traversing method for the ECO ontology.
 Set<org.semanticweb.owlapi.model.OWLClass> getDescendents(org.semanticweb.owlapi.model.OWLClass source, boolean reflexive)
          Traversing method for the ECO ontology.
 Set<org.semanticweb.owlapi.model.OWLClass> getDescendents(Set<org.semanticweb.owlapi.model.OWLClass> sources, boolean reflexive)
          Traversing method for the ECO ontology.
 
Methods inherited from class owltools.gaf.eco.EcoMapperImpl
getAllEcoClassesForCode, getEcoClassForCode, getEcoClassForCode, isGoEvidenceCode
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface owltools.gaf.eco.EcoMapper
getAllEcoClassesForCode, getEcoClassForCode, getEcoClassForCode, isGoEvidenceCode
 

Method Detail

getAncestors

public Set<org.semanticweb.owlapi.model.OWLClass> getAncestors(Set<org.semanticweb.owlapi.model.OWLClass> sources,
                                                               boolean reflexive)
Description copied from interface: TraversingEcoMapper
Traversing method for the ECO ontology.

Specified by:
getAncestors in interface TraversingEcoMapper
Returns:
set of super classes

getAncestors

public Set<org.semanticweb.owlapi.model.OWLClass> getAncestors(org.semanticweb.owlapi.model.OWLClass source,
                                                               boolean reflexive)
Description copied from interface: TraversingEcoMapper
Traversing method for the ECO ontology.

Specified by:
getAncestors in interface TraversingEcoMapper
Returns:
set of super classes

getDescendents

public Set<org.semanticweb.owlapi.model.OWLClass> getDescendents(Set<org.semanticweb.owlapi.model.OWLClass> sources,
                                                                 boolean reflexive)
Description copied from interface: TraversingEcoMapper
Traversing method for the ECO ontology.

Specified by:
getDescendents in interface TraversingEcoMapper
Returns:
set of sub classes

getDescendents

public Set<org.semanticweb.owlapi.model.OWLClass> getDescendents(org.semanticweb.owlapi.model.OWLClass source,
                                                                 boolean reflexive)
Description copied from interface: TraversingEcoMapper
Traversing method for the ECO ontology.

Specified by:
getDescendents in interface TraversingEcoMapper
Returns:
set of sub classes

getAllValidEvidenceIds

public Set<String> getAllValidEvidenceIds(String code,
                                          boolean includeChildren)
Description copied from interface: TraversingEcoMapper
Get all strings which are valid identifiers for a given evidence code. This includes, the the codes itself and valid OBO-style identifier from ECO.

Specified by:
getAllValidEvidenceIds in interface TraversingEcoMapper
Returns:
set of ids

getAllValidEvidenceIds

public Set<String> getAllValidEvidenceIds(Set<String> codes,
                                          boolean includeChildren)
Description copied from interface: TraversingEcoMapper
Get all strings which are valid identifiers for the given evidence codes. This includes, the the codes itself and valid OBO-style identifier from ECO.

Specified by:
getAllValidEvidenceIds in interface TraversingEcoMapper
Returns:
set of ids

dispose

public void dispose()
Description copied from interface: TraversingEcoMapper
Dispose this instance

Specified by:
dispose in interface TraversingEcoMapper


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