ubic.basecode.ontology.search

Class OntologySearch

java.lang.Object

ubic.basecode.ontology.search.OntologySearch

public class OntologySearch
extends Object

Author:

pavlidis

Constructor Summary

Constructors

Constructor and Description
OntologySearch()

Method Summary

Modifier and Type	Method and Description
static Collection<OntologyTerm>	matchClasses(com.hp.hpl.jena.ontology.OntModel model, SearchIndex index, String queryString) Find classes that match the query string.
static Collection<OntologyIndividual>	matchIndividuals(com.hp.hpl.jena.ontology.OntModel model, SearchIndex index, String queryString) Find individuals that match the query string
static Collection<OntologyResource>	matchResources(com.hp.hpl.jena.ontology.OntModel model, SearchIndex index, String queryString) Find OntologyIndividuals and OntologyTerms that match the query string.
static String	stripInvalidCharacters(String toStrip) Will remove characters that jena is unable to parse.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

OntologySearch

public OntologySearch()

Method Detail

matchClasses

public static Collection<OntologyTerm> matchClasses(com.hp.hpl.jena.ontology.OntModel model,
                                                    SearchIndex index,
                                                    String queryString)
                                             throws OntologySearchException

Find classes that match the query string. Obsolete terms are not returned.

Parameters:

model - that goes with the index

index - to search

queryString -

Returns:

Collection of OntologyTerm objects

Throws:

OntologySearchException

matchIndividuals

public static Collection<OntologyIndividual> matchIndividuals(com.hp.hpl.jena.ontology.OntModel model,
                                                              SearchIndex index,
                                                              String queryString)
                                                       throws OntologySearchException

Find individuals that match the query string

Parameters:

model - that goes with the index

index - to search

queryString -

Returns:

Collection of OntologyTerm objects

Throws:

OntologySearchException

matchResources

public static Collection<OntologyResource> matchResources(com.hp.hpl.jena.ontology.OntModel model,
                                                          SearchIndex index,
                                                          String queryString)
                                                   throws OntologySearchException

Find OntologyIndividuals and OntologyTerms that match the query string. Search with a wildcard is attempted whenever possible.

Parameters:

model - that goes with the index

index - to search

queryString -

Returns:

Collection of OntologyResource objects

Throws:

OntologySearchException

stripInvalidCharacters

public static String stripInvalidCharacters(String toStrip)

Will remove characters that jena is unable to parse. Will also escape and remove leading and trailing white space (which also causes jena to die)

Parameters:

toStrip - the string to clean

Returns: