A B C D E F G H I L M N O P Q R S T U V W X 

A

AbstractJdbcQueryHandler - Class in uk.ac.ebi.ols.jdbc
Created by IntelliJ IDEA.
AbstractJdbcQueryHandler() - Constructor for class uk.ac.ebi.ols.jdbc.AbstractJdbcQueryHandler
 
AbstractParser - Class in uk.ac.ebi.ols.loader.parser
Abstract base class to interact with OBOEdit codebase and parse OBO files
AbstractParser() - Constructor for class uk.ac.ebi.ols.loader.parser.AbstractParser
 
AbstractQueryHandler - Class in uk.ac.ebi.ols.persistence.query
Base class for query handling.
AbstractQueryHandler() - Constructor for class uk.ac.ebi.ols.persistence.query.AbstractQueryHandler
 
AbstractQueryHandler(String) - Constructor for class uk.ac.ebi.ols.persistence.query.AbstractQueryHandler
 
AbstractTermLinker - Class in uk.ac.ebi.ols.model.ojb
relationship between controlled vocabulary / ontology term
AbstractTermLinker() - Constructor for class uk.ac.ebi.ols.model.ojb.AbstractTermLinker
 
ACRONYM - Static variable in class uk.ac.ebi.ols.loader.newt.SynHolder
 
addBatch() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
addBatch(String) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
addIsotope(String, String) - Method in class uk.ac.ebi.ols.loader.psiutils.Element
 
addLoadedOntology(String, long) - Method in class uk.ac.ebi.ols.model.ojb.LoaderRunBean
 
addProjectEntries(CVSEntryVector, CVSEntry) - Method in class uk.ac.ebi.ols.loader.cvsutils.CVSUpdater
 
ALT_ID - Variable in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
 
ALT_ID_SYNONYM_TYPE - Static variable in class uk.ac.ebi.ols.Constants
 
ANAMORPH - Static variable in class uk.ac.ebi.ols.loader.newt.SynHolder
 
Annotation - Interface in uk.ac.ebi.ols.model.interfaces
 
AnnotationBean - Class in uk.ac.ebi.ols.model.ojb
Implementation of Annotation interface
AnnotationBean() - Constructor for class uk.ac.ebi.ols.model.ojb.AnnotationBean
 
ANONYMOUS - Static variable in class uk.ac.ebi.ols.config.RepositoryConfigEntry
 

B

BaseOBO2AbstractLoader - Class in uk.ac.ebi.ols.loader.impl
Base class for all loaders.
BaseOBO2AbstractLoader() - Constructor for class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
 
BATCH_MODE - Static variable in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
batch mode will optimize inserts.
beginTransaction() - Method in class uk.ac.ebi.ols.persistence.query.AbstractQueryHandler
Begins a transaction on a non-null broker.
BLAST_NAME - Static variable in class uk.ac.ebi.ols.loader.newt.SynHolder
 
BROAD - Variable in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
 
BROAD_SYNONYM_TYPE - Static variable in class uk.ac.ebi.ols.Constants
 

C

cancel() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
checkCancelled() - Method in class uk.ac.ebi.ols.loader.svnutils.UpdateEventHandler
 
clearBatch() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
clearCache() - Method in class uk.ac.ebi.ols.persistence.query.AbstractQueryHandler
Clears the broker cache
clearParameters() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
clearWarnings() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
close() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
closeOnCompletion() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
 
collectionQuery(Query) - Method in class uk.ac.ebi.ols.persistence.query.AbstractQueryHandler
Performs a query and returns a collection of objects matching the criteria specified
commitTransaction() - Method in class uk.ac.ebi.ols.persistence.query.AbstractQueryHandler
Commits a transaction on a non-null broker.
COMMON_NAME - Static variable in class uk.ac.ebi.ols.loader.newt.SynHolder
 
compareTo(Object) - Method in class uk.ac.ebi.ols.loader.newt.SynHolder
 
computeChildPaths(int, Set, LinkedObject) - Method in interface uk.ac.ebi.ols.loader.interfaces.Parser
 
computeChildPaths(int, Set, LinkedObject) - Method in class uk.ac.ebi.ols.loader.parser.AbstractParser
Will compute all the term paths from a given term to all its children, irrespective of distance
computeChildPaths(int, Set, LinkedObject) - Method in class uk.ac.ebi.ols.loader.parser.OBO2FormatParser
Will compute all the term paths from a given term to all its children, irrespective of distance
config - Variable in class uk.ac.ebi.ols.loader.parser.AbstractParser
 
ConfigurableOBO2Loader - Class in uk.ac.ebi.ols.loader.impl
Primary loader for the OLS.
ConfigurableOBO2Loader() - Constructor for class uk.ac.ebi.ols.loader.impl.ConfigurableOBO2Loader
 
ConfigurationManager - Class in uk.ac.ebi.ols.config
User: Richard Cote Date: 17-Nov-2005 Time: 14:39:32
ConfigurationManager() - Constructor for class uk.ac.ebi.ols.config.ConfigurationManager
 
configure() - Method in class uk.ac.ebi.ols.loader.impl.NEWTOntologyLoader
 
configure(String, String) - Method in class uk.ac.ebi.ols.loader.parser.GOFormatParser
configure the parser
configure(Vector) - Method in class uk.ac.ebi.ols.loader.parser.OBOFormatParser
 
connectionProvider - Variable in class uk.ac.ebi.ols.jdbc.AbstractJdbcQueryHandler
 
ConnectionProvider - Interface in uk.ac.ebi.ols.jdbc.util
Created by IntelliJ IDEA.
Constants - Class in uk.ac.ebi.ols
User: Richard Cote Date: 21-Jul-2005 Time: 14:38:16
Constants() - Constructor for class uk.ac.ebi.ols.Constants
 
countQuery(Query) - Method in class uk.ac.ebi.ols.persistence.query.AbstractQueryHandler
Performs a query and returns the count of objects the criteria specified
createTermNameMapping(MultiMap<String, SynHolder>) - Static method in class uk.ac.ebi.ols.loader.newt.NEWTUtilities
This method will process the nameStorage multimap obtained from the parsing of the names.dat NEWT flatfile.
customizeQuery(Object, PersistenceBroker, CollectionDescriptor, QueryByCriteria) - Method in class uk.ac.ebi.ols.persistence.query.customizer.XrefQueryCustomizer
Overrides the inactive customizeQuery in the parent class (but makes use of its code for setting / retrieving parameter values from the XML file).
CVSException - Exception in uk.ac.ebi.ols.loader.cvsutils
Exception class that will be called on CVS Errors
CVSException(String) - Constructor for exception uk.ac.ebi.ols.loader.cvsutils.CVSException
 
CVSException(String, Throwable) - Constructor for exception uk.ac.ebi.ols.loader.cvsutils.CVSException
 
CVSUpdater - Class in uk.ac.ebi.ols.loader.cvsutils
Helper class to perform a CVS update on a given repository
CVSUpdater() - Constructor for class uk.ac.ebi.ols.loader.cvsutils.CVSUpdater
 

D

DbXref - Interface in uk.ac.ebi.ols.model.interfaces
 
DbXrefBean - Class in uk.ac.ebi.ols.model.ojb
DbXrefBean() - Constructor for class uk.ac.ebi.ols.model.ojb.DbXrefBean
 
DebuggableStatement - Class in uk.ac.ebi.ols.jdbc.util
PreparedStatements have no way to retrieve the statement that was executed on the database.
DebuggableStatement(Connection, String, SqlFormatter) - Constructor for class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Construct new DebugableStatement.
DEFAULT_SYNONYM_TYPE - Static variable in class uk.ac.ebi.ols.Constants
 
DefaultSqlFormatter - Class in uk.ac.ebi.ols.jdbc.util
 
DefaultSqlFormatter() - Constructor for class uk.ac.ebi.ols.jdbc.util.DefaultSqlFormatter
 
DEFINITION - Static variable in class uk.ac.ebi.ols.Constants
 
deleteCollection(Collection) - Method in class uk.ac.ebi.ols.persistence.query.AbstractQueryHandler
This method deletes all the Persistable objects in the Collection provided from the database.
deleteObject(Object) - Method in class uk.ac.ebi.ols.persistence.query.AbstractQueryHandler
This method deletes a Persistable from persistent store.
DEV_FROM_SET - Variable in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
 
DEVELOPS_FROM - Variable in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
 
DEVELOPS_FROM_RELATION_TYPE - Static variable in class uk.ac.ebi.ols.Constants
 
DEVELOPS_FROM_RELATION_TYPE_ID - Static variable in class uk.ac.ebi.ols.Constants
 
disableSSH() - Method in class uk.ac.ebi.ols.loader.cvsutils.CVSUpdater
if called, will disable CVS over SSH.
DOT_EXECUTABLE - Static variable in class uk.ac.ebi.ols.config.ConfigurationManager
 
DOT_FILEPATH - Static variable in class uk.ac.ebi.ols.config.ConfigurationManager
 
dumpOntology() - Method in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
for debugging
dumpOntologyStats() - Method in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
for debugging
dumpStats() - Method in class uk.ac.ebi.ols.loader.impl.NEWTOntologyLoader
 
dumpTerm(Term, String) - Method in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
for debugging

E

Element - Class in uk.ac.ebi.ols.loader.psiutils
Helper data class for ElementParser
Element() - Constructor for class uk.ac.ebi.ols.loader.psiutils.Element
 
ElementParser - Class in uk.ac.ebi.ols.loader.psiutils
Helper class that parses the atoms.dat file for PSI-MOD
enableSSH() - Method in class uk.ac.ebi.ols.loader.cvsutils.CVSUpdater
if called, will enable CVS over SSH.
equals(Object) - Method in class uk.ac.ebi.ols.config.RepositoryConfigEntry
 
equals(Object) - Method in class uk.ac.ebi.ols.loader.newt.SynHolder
 
equals(Object) - Method in class uk.ac.ebi.ols.model.ojb.AbstractTermLinker
 
equals(Object) - Method in class uk.ac.ebi.ols.model.ojb.AnnotationBean
 
equals(Object) - Method in class uk.ac.ebi.ols.model.ojb.DbXrefBean
 
equals(Object) - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
equals(Object) - Method in class uk.ac.ebi.ols.model.ojb.TermSynonymBean
 
EQUIVALENT_NAME - Static variable in class uk.ac.ebi.ols.loader.newt.SynHolder
 
errorsDetected() - Method in class uk.ac.ebi.ols.loader.cvsutils.CVSUpdater
Returns true if errors have been detected during update process, false if no errors detected.
EXACT - Variable in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
 
EXACT_SYNONYM_TYPE - Static variable in class uk.ac.ebi.ols.Constants
 
execute() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Executes query and Calculates query execution time
execute(String) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This method is only here for convenience.
execute(String, int) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This method is here to satisfy the PreparedStatement interface but is not implemented.
execute(String, int[]) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This method is here to satisfy the PreparedStatement interface but is not implemented.
execute(String, String[]) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This method is here to satisfy the PreparedStatement interface but is not implemented.
executeBatch() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Executes query and Calculates query execution time
executeQuery() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Executes query and Calculates query execution time
executeQuery(String) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This method is only here for convenience.
executeUpdate() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Executes query and Calculates query execution time
executeUpdate(String) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This method is only here for convenience.
executeUpdate(String, int) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This method is here to satisfy the PreparedStatement interface but is not implemented.
executeUpdate(String, int[]) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This method is here to satisfy the PreparedStatement interface but is not implemented.
executeUpdate(String, String[]) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This method is here to satisfy the PreparedStatement interface but is not implemented.

F

FAILOVER_DBALIAS - Static variable in class uk.ac.ebi.ols.config.ConfigurationManager
 
FAILOVER_USE - Static variable in class uk.ac.ebi.ols.config.ConfigurationManager
 
FlyweightOntology - Class in uk.ac.ebi.ols.loader.impl
class to hold basic data on ontologies
FlyweightOntology(String, String, String, String, String, String, String) - Constructor for class uk.ac.ebi.ols.loader.impl.FlyweightOntology
 
format(Object) - Method in class uk.ac.ebi.ols.jdbc.util.DefaultSqlFormatter
 
format(Object) - Method in class uk.ac.ebi.ols.jdbc.util.OracleSqlFormatter
Formats object to an Oracle specific formatted function.
format(Blob) - Method in class uk.ac.ebi.ols.jdbc.util.SqlFormatter
Formats a blob to the following String "''" This method's output will not translate directly into the database.
format(Clob) - Method in class uk.ac.ebi.ols.jdbc.util.SqlFormatter
Formats a clob to the following String "''" This method's output will not translate directly into the database.
format(Array) - Method in class uk.ac.ebi.ols.jdbc.util.SqlFormatter
Formats an Array to the following String "array.getBaseTypeName()" This method's output will not translate directly into the database.
format(Ref) - Method in class uk.ac.ebi.ols.jdbc.util.SqlFormatter
Formats a Ref to the following String "ref.getBaseTypeName()" This method's output will not translate directly into the database.
format(String) - Method in class uk.ac.ebi.ols.jdbc.util.SqlFormatter
Checks the String for null and returns "'" + string + "'".
format(Object) - Method in class uk.ac.ebi.ols.jdbc.util.SqlFormatter
If object is null, Blob, Clob, Array, Ref, or String this returns the value from the protected methods in this class that take those Classes.
FULL_NAME - Variable in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
 

G

GENBANK_ACRONYM - Static variable in class uk.ac.ebi.ols.loader.newt.SynHolder
 
GENBANK_ANAMORPH - Static variable in class uk.ac.ebi.ols.loader.newt.SynHolder
 
GENBANK_COMMON_NAME - Static variable in class uk.ac.ebi.ols.loader.newt.SynHolder
 
GENBANK_SYNONYM - Static variable in class uk.ac.ebi.ols.loader.newt.SynHolder
 
getAccession() - Method in interface uk.ac.ebi.ols.model.interfaces.DbXref
 
getAccession() - Method in class uk.ac.ebi.ols.model.ojb.DbXrefBean
 
getAllOBOFiles(String) - Method in class uk.ac.ebi.ols.loader.cvsutils.CVSUpdater
scans a CVS repository and returns a hashmap of all the files in it
getAllOntologies() - Method in class uk.ac.ebi.ols.persistence.query.OntologyQueryHandler
Queries the DB layer and returns a collection of fullyLoaded ontology objects
getAllowedPrefixes() - Method in class uk.ac.ebi.ols.loader.impl.FlyweightOntology
 
getAllTermReportFromOntology(String) - Method in class uk.ac.ebi.ols.persistence.query.OntologyQueryHandler
Queries the database and returns all the terms for a given ontology (assumes fully_loaded status = true)
getAllTermsFromOntology(String) - Method in class uk.ac.ebi.ols.jdbc.OntologyJdbcQueryHandler
returns a non-null map of all the terms in an ontology.
getAllTermsFromOntology(String) - Method in class uk.ac.ebi.ols.persistence.query.OntologyQueryHandler
Queries the database and returns all the terms for a given ontology (assumes fully_loaded status = true)
getAnnotationCompleteValue() - Method in interface uk.ac.ebi.ols.model.interfaces.Annotation
 
getAnnotationCompleteValue() - Method in class uk.ac.ebi.ols.model.ojb.AnnotationBean
returns "annotationStringValue, annotationNumberValue".
getAnnotationId() - Method in class uk.ac.ebi.ols.model.ojb.AnnotationBean
 
getAnnotationNumberValue() - Method in interface uk.ac.ebi.ols.model.interfaces.Annotation
 
getAnnotationNumberValue() - Method in class uk.ac.ebi.ols.model.ojb.AnnotationBean
 
getAnnotations() - Method in class uk.ac.ebi.ols.loader.newt.NEWTParser
 
getAnnotations() - Method in interface uk.ac.ebi.ols.model.interfaces.Term
Does ...
getAnnotations() - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
getAnnotationStringValue() - Method in interface uk.ac.ebi.ols.model.interfaces.Annotation
Does ...
getAnnotationStringValue() - Method in class uk.ac.ebi.ols.model.ojb.AnnotationBean
 
getAnnotationType() - Method in interface uk.ac.ebi.ols.model.interfaces.Annotation
Does ...
getAnnotationType() - Method in class uk.ac.ebi.ols.model.ojb.AnnotationBean
 
getAvgMass() - Method in class uk.ac.ebi.ols.loader.psiutils.Element
 
getBroker() - Method in class uk.ac.ebi.ols.persistence.query.AbstractQueryHandler
Returns the PersistenceBroker object, can be null
getChildrenFromRootTerm(String, String, Vector) - Method in class uk.ac.ebi.ols.jdbc.TermJdbcQueryHandler
Given two or more IDs, which are descendants of a given higher level ID?

0 / \ 1 2 / \ / \ 3 4 5

Given ID_3, ID_4 and ID_5, which are descendants(Children, grandchildren, great-grandchildren ...etc) of ID_1?

(Answer: ID_3 and ID_4)

getChildrenFromRootTerm(String, String, Collection) - Method in class uk.ac.ebi.ols.persistence.query.TermQueryHandler
Given two or more IDs, which are descendants of a given higher level ID?

0 / \ 1 2 / \ / \ 3 4 5

Given ID_3, ID_4 and ID_5, which are descendants(Children, grandchildren, great-grandchildren ...etc) of ID_1?

(Answer: ID_3 and ID_4)

getConflictFiles() - Method in class uk.ac.ebi.ols.loader.svnutils.UpdateEventHandler
 
getConnection() - Method in interface uk.ac.ebi.ols.jdbc.util.ConnectionProvider
 
getConnection() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
getConnection() - Method in class uk.ac.ebi.ols.jdbc.util.TomcatManagedConnectionProvider
 
getConnection() - Method in class uk.ac.ebi.ols.persistence.query.AbstractQueryHandler
returns a java.sql.Connection object from the current broker
getConnectionURL() - Method in class uk.ac.ebi.ols.persistence.query.AbstractQueryHandler
 
getCvsConfig() - Static method in class uk.ac.ebi.ols.config.ConfigurationManager
 
getDbName() - Method in interface uk.ac.ebi.ols.model.interfaces.DbXref
 
getDbName() - Method in class uk.ac.ebi.ols.model.ojb.DbXrefBean
 
getDbXrefId() - Method in class uk.ac.ebi.ols.model.ojb.DbXrefBean
 
getDefinition() - Method in class uk.ac.ebi.ols.loader.impl.FlyweightOntology
 
getDefinition() - Method in interface uk.ac.ebi.ols.model.interfaces.Ontology
 
getDefinition() - Method in interface uk.ac.ebi.ols.model.interfaces.Term
Does ...
getDefinition() - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
getDefinition() - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
getDescription() - Method in interface uk.ac.ebi.ols.model.interfaces.DbXref
 
getDescription() - Method in class uk.ac.ebi.ols.model.ojb.DbXrefBean
 
getDistance() - Method in interface uk.ac.ebi.ols.model.interfaces.TermPath
Does ...
getDistance() - Method in class uk.ac.ebi.ols.model.ojb.TermPathBean
 
getElements() - Method in class uk.ac.ebi.ols.loader.psiutils.ElementParser
 
getErrorMessage() - Method in class uk.ac.ebi.ols.loader.cvsutils.CVSUpdater
Returns the error message generated by the CVS request, if any
getFetchDirection() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
getFetchSize() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
getFileName() - Method in class uk.ac.ebi.ols.loader.impl.FlyweightOntology
 
getFullName() - Method in class uk.ac.ebi.ols.loader.impl.FlyweightOntology
 
getFullOntologyName() - Method in interface uk.ac.ebi.ols.model.interfaces.Ontology
 
getFullOntologyName() - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
getFullyLoaded() - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
getGeneratedKeys() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
getIdentifier() - Method in interface uk.ac.ebi.ols.model.interfaces.Term
Does ...
getIdentifier() - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
getIndexReader(String) - Method in class uk.ac.ebi.ols.loader.lucene.OntologyIndexer
returns a valid, opened IndexReader that points to the index for a given ontology or to the master index for all ontologies
getInstance() - Static method in class uk.ac.ebi.ols.jdbc.util.TomcatManagedConnectionProvider
 
getInstance() - Static method in class uk.ac.ebi.ols.loader.lucene.OntologyIndexer
 
getInstance(String) - Static method in class uk.ac.ebi.ols.loader.psiutils.ElementParser
 
getIsotopeMass(String) - Method in class uk.ac.ebi.ols.loader.psiutils.Element
 
getIsotopes() - Method in class uk.ac.ebi.ols.loader.psiutils.Element
 
getLoadDate() - Method in interface uk.ac.ebi.ols.model.interfaces.Ontology
 
getLoadDate() - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
getLoadedOntologies() - Method in interface uk.ac.ebi.ols.model.interfaces.LoaderRun
 
getLoadedOntologies() - Method in class uk.ac.ebi.ols.model.ojb.LoaderRunBean
 
getMaxFieldSize() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
getMaxRows() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
getMetaData() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
getMonoMass() - Method in class uk.ac.ebi.ols.loader.psiutils.Element
 
getMonthyStats(int, int) - Method in class uk.ac.ebi.ols.jdbc.OntologyJdbcQueryHandler
 
getMonthyStats(int, int) - Method in class uk.ac.ebi.ols.persistence.query.OntologyQueryHandler
 
getMoreResults(int) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
getMoreResults() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
getName() - Method in interface uk.ac.ebi.ols.model.interfaces.LoadedOntology
 
getName() - Method in interface uk.ac.ebi.ols.model.interfaces.Term
Does ...
getName() - Method in class uk.ac.ebi.ols.model.ojb.LoadedOntologyBean
 
getName() - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
getNames() - Method in class uk.ac.ebi.ols.loader.newt.NEWTParser
 
getNamespace() - Method in class uk.ac.ebi.ols.loader.impl.FlyweightOntology
 
getNamespace() - Method in interface uk.ac.ebi.ols.model.interfaces.Term
Does ...
getNamespace() - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
getNodes() - Method in class uk.ac.ebi.ols.loader.newt.NEWTParser
 
getNumberOfTerms() - Method in interface uk.ac.ebi.ols.model.interfaces.LoadedOntology
 
getNumberOfTerms() - Method in class uk.ac.ebi.ols.model.ojb.LoadedOntologyBean
 
getObjectTerm() - Method in interface uk.ac.ebi.ols.model.interfaces.TermRelationship
Does ...
getObjectTerm() - Method in class uk.ac.ebi.ols.model.ojb.AbstractTermLinker
 
getObjectTermPk() - Method in class uk.ac.ebi.ols.model.ojb.AbstractTermLinker
 
getObsoleteTerms() - Method in class uk.ac.ebi.ols.loader.parser.AbstractParser
Gets a collection of all terms marked as obsolete
getOntologies() - Method in class uk.ac.ebi.ols.loader.impl.ConfigurableOBO2Loader
 
getOntology() - Method in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
returns the Ontology that has been loaded from file.
getOntology() - Method in interface uk.ac.ebi.ols.loader.interfaces.Loader
 
getOntology(String) - Method in class uk.ac.ebi.ols.persistence.query.OntologyQueryHandler
Will return an ontology whose shortName is an exact match to the name parameter (and whose fully_loaded state is true)
getOntologyId() - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
getOntologyName() - Method in class uk.ac.ebi.ols.loader.impl.NEWTOntologyLoader
 
getOntologyReport() - Method in class uk.ac.ebi.ols.jdbc.OntologyJdbcQueryHandler
 
getOntologyReport(String) - Method in class uk.ac.ebi.ols.jdbc.OntologyJdbcQueryHandler
 
getOntologyReport() - Method in class uk.ac.ebi.ols.persistence.query.OntologyQueryHandler
Performs a reportQuery and returns a collection of object arrays.
getOntologyReport(String, boolean) - Method in class uk.ac.ebi.ols.persistence.query.OntologyQueryHandler
Performs a reportQuery and returns a collection of object arrays.
getOntologyReport(String) - Method in class uk.ac.ebi.ols.persistence.query.OntologyQueryHandler
Performs a reportQuery and returns a collection of object arrays.
getOntologySize() - Method in class uk.ac.ebi.ols.loader.impl.NEWTOntologyLoader
 
getOntologyStatistics(long) - Method in class uk.ac.ebi.ols.persistence.query.OntologyQueryHandler
returns a map containing a breakdown of the number of terms, synonyms, termpaths, termrelations, annotations, dbxrefs for an ontologyId
getOntologyStatistics(OntologyBean) - Method in class uk.ac.ebi.ols.persistence.query.OntologyQueryHandler
returns a map containing a breakdown of the number of terms, synonyms, termpaths, termrelations, annotations, dbxrefs for a fully constructed ontology
getOntologyTermCount(String) - Method in class uk.ac.ebi.ols.jdbc.OntologyJdbcQueryHandler
 
getOntologyTermCount(String) - Method in class uk.ac.ebi.ols.persistence.query.OntologyQueryHandler
returns the number of terms present in a fully loaded ontology.
getParameterMetaData() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
getParentObjectPk() - Method in class uk.ac.ebi.ols.model.ojb.DbXrefBean
 
getParentOntology() - Method in interface uk.ac.ebi.ols.model.interfaces.Term
Does ...
getParentOntology() - Method in interface uk.ac.ebi.ols.model.interfaces.TermRelationship
Does ...
getParentOntology() - Method in class uk.ac.ebi.ols.model.ojb.AbstractTermLinker
 
getParentOntology() - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
getParentOntologyId() - Method in class uk.ac.ebi.ols.model.ojb.AbstractTermLinker
 
getParentOntologyId() - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
getParentOntologyReport(String) - Method in class uk.ac.ebi.ols.jdbc.OntologyJdbcQueryHandler
 
getParentRun() - Method in interface uk.ac.ebi.ols.model.interfaces.LoadedOntology
 
getParentRun() - Method in class uk.ac.ebi.ols.model.ojb.LoadedOntologyBean
 
getParentRunId() - Method in class uk.ac.ebi.ols.model.ojb.LoadedOntologyBean
 
getParentTerm() - Method in interface uk.ac.ebi.ols.model.interfaces.Annotation
Does ...
getParentTerm() - Method in interface uk.ac.ebi.ols.model.interfaces.TermSynonym
Does ...
getParentTerm() - Method in class uk.ac.ebi.ols.model.ojb.AnnotationBean
 
getParentTerm() - Method in class uk.ac.ebi.ols.model.ojb.TermSynonymBean
 
getParentTermPk() - Method in class uk.ac.ebi.ols.model.ojb.AnnotationBean
 
getParentTermPk() - Method in class uk.ac.ebi.ols.model.ojb.TermSynonymBean
 
getParentTermRelationships(String, String) - Method in class uk.ac.ebi.ols.jdbc.TermJdbcQueryHandler
 
getParentTermRelationships(String, String) - Method in class uk.ac.ebi.ols.persistence.query.TermQueryHandler
queries the database and returns all the term relationships for a given term in a given ontology
getPassword() - Method in class uk.ac.ebi.ols.config.RepositoryConfigEntry
 
getPaths() - Method in interface uk.ac.ebi.ols.model.interfaces.Term
Does ...
getPaths() - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
getPkId() - Method in class uk.ac.ebi.ols.model.ojb.LoadedOntologyBean
 
getPredicateTerm() - Method in interface uk.ac.ebi.ols.model.interfaces.TermRelationship
Does ...
getPredicateTerm() - Method in class uk.ac.ebi.ols.model.ojb.AbstractTermLinker
 
getPredicateTermPk() - Method in class uk.ac.ebi.ols.model.ojb.AbstractTermLinker
 
getProperties() - Static method in class uk.ac.ebi.ols.config.ConfigurationManager
 
getProperty(String) - Static method in class uk.ac.ebi.ols.config.ConfigurationManager
 
getQueryTimeout() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
getQueryURL() - Method in class uk.ac.ebi.ols.loader.impl.FlyweightOntology
 
getQueryURL() - Method in interface uk.ac.ebi.ols.model.interfaces.Ontology
 
getQueryURL() - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
getRelationships() - Method in interface uk.ac.ebi.ols.model.interfaces.Term
Does ...
getRelationships() - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
getRelationshipTypeId() - Method in interface uk.ac.ebi.ols.model.interfaces.TermPath
 
getRelationshipTypeId() - Method in class uk.ac.ebi.ols.model.ojb.TermPathBean
 
getRepository() - Method in class uk.ac.ebi.ols.config.RepositoryConfigEntry
 
getResultSet() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
getResultSetConcurrency() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
getResultSetHoldability() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
getResultSetType() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
getRootTerms(String) - Method in class uk.ac.ebi.ols.jdbc.TermJdbcQueryHandler
 
getRootTerms() - Method in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
will return a collection of TermBean accesssion strings that correspond to the root term
getRootTerms(boolean) - Method in interface uk.ac.ebi.ols.loader.interfaces.Parser
 
getRootTerms() - Method in class uk.ac.ebi.ols.loader.parser.AbstractParser
returns the root terms of an ontology
getRootTerms(boolean) - Method in class uk.ac.ebi.ols.loader.parser.OBO2FormatParser
returns the root terms of an ontology
getRootTerms() - Method in interface uk.ac.ebi.ols.model.interfaces.Ontology
 
getRootTerms() - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
getRootTerms(String) - Method in class uk.ac.ebi.ols.persistence.query.TermQueryHandler
returns a collection of root terms for an ontology
getRunDate() - Method in interface uk.ac.ebi.ols.model.interfaces.LoaderRun
 
getRunDate() - Method in class uk.ac.ebi.ols.model.ojb.LoaderRunBean
 
getRunId() - Method in interface uk.ac.ebi.ols.model.interfaces.LoaderRun
 
getRunId() - Method in class uk.ac.ebi.ols.model.ojb.LoaderRunBean
 
getSession() - Method in interface uk.ac.ebi.ols.loader.interfaces.Parser
 
getSession() - Method in class uk.ac.ebi.ols.loader.parser.AbstractParser
returns the OBOSession of the underlying parser
getSession() - Method in class uk.ac.ebi.ols.loader.parser.OBO2FormatParser
returns the OBOSession of the underlying parser
getShortOntologyName() - Method in interface uk.ac.ebi.ols.model.interfaces.Ontology
 
getShortOntologyName() - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
getSourceURL() - Method in class uk.ac.ebi.ols.loader.impl.FlyweightOntology
 
getSourceURL() - Method in interface uk.ac.ebi.ols.model.interfaces.Ontology
 
getSourceURL() - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
getStatement() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
getStatement(Connection, String) - Static method in class uk.ac.ebi.ols.jdbc.util.StatementFactory
Use this method if you want a class to override the global nature of a property file approach.
getSubjectTerm() - Method in interface uk.ac.ebi.ols.model.interfaces.TermRelationship
Does ...
getSubjectTerm() - Method in class uk.ac.ebi.ols.model.ojb.AbstractTermLinker
 
getSubjectTermPk() - Method in class uk.ac.ebi.ols.model.ojb.AbstractTermLinker
 
getSvnConfig() - Static method in class uk.ac.ebi.ols.config.ConfigurationManager
 
getSymbol() - Method in class uk.ac.ebi.ols.loader.psiutils.Element
 
getSynonym() - Method in interface uk.ac.ebi.ols.model.interfaces.TermSynonym
Does ...
getSynonym() - Method in class uk.ac.ebi.ols.model.ojb.TermSynonymBean
 
getSynonymPk() - Method in class uk.ac.ebi.ols.model.ojb.TermSynonymBean
 
getSynonyms() - Method in interface uk.ac.ebi.ols.model.interfaces.Term
Does ...
getSynonyms() - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
getSynonymType() - Method in interface uk.ac.ebi.ols.model.interfaces.TermSynonym
Does ...
getSynonymType() - Method in class uk.ac.ebi.ols.model.ojb.TermSynonymBean
 
getSynonymTypePk() - Method in class uk.ac.ebi.ols.model.ojb.TermSynonymBean
 
getSynonymXrefs() - Method in interface uk.ac.ebi.ols.model.interfaces.TermSynonym
Does ...
getSynonymXrefs() - Method in class uk.ac.ebi.ols.model.ojb.TermSynonymBean
 
getSynType() - Method in class uk.ac.ebi.ols.loader.newt.SynHolder
 
getSynValue() - Method in class uk.ac.ebi.ols.loader.newt.SynHolder
 
getTerm(String) - Method in class uk.ac.ebi.ols.loader.parser.AbstractParser
looks up a term from the session object based on the term id
getTermAnnotations(String) - Method in class uk.ac.ebi.ols.jdbc.TermJdbcQueryHandler
 
getTermAnnotations(String, String) - Method in class uk.ac.ebi.ols.persistence.query.TermQueryHandler
Given a term ID, will query the DB layer and return a collection of annotationBeans.
getTermAnnotations(String) - Method in class uk.ac.ebi.ols.persistence.query.TermQueryHandler
Given a term PK, will query the DB layer and return a collection of annotationBeans.
getTermById(String, String) - Method in class uk.ac.ebi.ols.jdbc.TermJdbcQueryHandler
queries the database and returns a term object from the specified termId.
getTermById(String, String) - Method in class uk.ac.ebi.ols.persistence.query.TermQueryHandler
Queries the database and returns a TermBean object from the specified termId.
getTermById(String) - Method in class uk.ac.ebi.ols.persistence.query.TermQueryHandler
Deprecated.
- this method will always return null. You should use getTermById(termId, null) instead.
getTermByPK(String) - Method in class uk.ac.ebi.ols.jdbc.TermJdbcQueryHandler
queries the database and returns a term object from the specified termPK.
getTermChildren(String, String, Integer, int[]) - Method in class uk.ac.ebi.ols.jdbc.TermJdbcQueryHandler
 
getTermChildren(String, String, Integer, int[]) - Method in class uk.ac.ebi.ols.persistence.query.TermQueryHandler
Given a term ID, will query the DB layer and return a collection of children terms.
getTermNameById(String, String) - Method in class uk.ac.ebi.ols.jdbc.TermJdbcQueryHandler
returns the preferred term name for a given term id or null if no term found.
getTermPathId() - Method in class uk.ac.ebi.ols.model.ojb.TermPathBean
 
getTermPaths() - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
getTermPk() - Method in interface uk.ac.ebi.ols.model.interfaces.Term
Does ...
getTermPk() - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
getTermRelationshipId() - Method in class uk.ac.ebi.ols.model.ojb.TermRelationshipBean
 
getTermRelationships(String, String) - Method in class uk.ac.ebi.ols.jdbc.TermJdbcQueryHandler
 
getTermRelationships(String, String, boolean) - Method in class uk.ac.ebi.ols.jdbc.TermJdbcQueryHandler
 
getTermRelationships() - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
getTermRelationships(String, String) - Method in class uk.ac.ebi.ols.persistence.query.TermQueryHandler
queries the database and returns all the term relationships for a given term in a given ontology
getTerms() - Method in interface uk.ac.ebi.ols.loader.interfaces.Parser
 
getTerms() - Method in class uk.ac.ebi.ols.loader.parser.AbstractParser
returns all the terms parsed from an ontology
getTerms() - Method in class uk.ac.ebi.ols.loader.parser.OBO2FormatParser
returns all the terms parsed from an ontology
getTerms() - Method in interface uk.ac.ebi.ols.model.interfaces.Ontology
 
getTerms() - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
getTermsByAnnotations(String, String, String, Double, Double) - Method in class uk.ac.ebi.ols.jdbc.TermJdbcQueryHandler
Will query the database and return term data based on search criteria.
getTermsByAnnotations(String, String, String, Double, Double) - Method in class uk.ac.ebi.ols.persistence.query.TermQueryHandler
Will query the database and return term data based on search criteria.
getTermsByName(String, String) - Method in class uk.ac.ebi.ols.jdbc.TermJdbcQueryHandler
 
getTermsByName(String, String, boolean, Integer, boolean, boolean) - Method in class uk.ac.ebi.ols.persistence.lucene.IndexedTermQueryHandler
Will query the database and return a map of terms that match a partial term name present in a specific ontology

getTermsByName(String) - Method in class uk.ac.ebi.ols.persistence.query.TermQueryHandler
Queries the database and returns a collection of TermBean object that exactly match the name.
getTermsByName(String, String, boolean, boolean) - Method in class uk.ac.ebi.ols.persistence.query.TermQueryHandler
Queries the database and returns a map of termId/termNames that exactly match the term name for a specific ontology.
getTermSynonyms(String) - Method in class uk.ac.ebi.ols.jdbc.TermJdbcQueryHandler
 
getTermXrefs(String, String) - Method in class uk.ac.ebi.ols.jdbc.TermJdbcQueryHandler
 
getTermXrefs(String) - Method in class uk.ac.ebi.ols.jdbc.TermJdbcQueryHandler
 
getTermXrefs(String, String) - Method in class uk.ac.ebi.ols.persistence.query.TermQueryHandler
Given a term ID, will query the DB layer and return a collection of DbXrefBean.
getTermXrefs(String) - Method in class uk.ac.ebi.ols.persistence.query.TermQueryHandler
Given a term PK, will query the DB layer and return a collection of DbXrefBean.
getUnknownRelationTermBean(String) - Method in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
helper method to create unknow relationship terms as they are required.
getUpdateCount() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
getUpdatedFiles() - Method in class uk.ac.ebi.ols.loader.svnutils.UpdateEventHandler
 
getUpdatedOBOFiles() - Method in class uk.ac.ebi.ols.loader.fileutils.ManualOBOFileUpdater
 
getUpdatedTerm(Term) - Method in class uk.ac.ebi.ols.persistence.query.TermQueryHandler
This method will return a term that should be used instead of a deprecated/obsoleted one.
getUserName() - Method in class uk.ac.ebi.ols.config.RepositoryConfigEntry
 
getVersion() - Method in interface uk.ac.ebi.ols.model.interfaces.Ontology
 
getVersion() - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
getWarnings() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
getXrefs() - Method in interface uk.ac.ebi.ols.model.interfaces.Term
Does ...
getXrefs() - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
getXrefType() - Method in interface uk.ac.ebi.ols.model.interfaces.DbXref
 
getXrefType() - Method in class uk.ac.ebi.ols.model.ojb.DbXrefBean
 
GOFormatParser - Class in uk.ac.ebi.ols.loader.parser
Go FlatFile Format parser that interacts with the OBOEdit codebase
GOFormatParser() - Constructor for class uk.ac.ebi.ols.loader.parser.GOFormatParser
 
GREEDY_ONTOLOGIES - Static variable in class uk.ac.ebi.ols.config.ConfigurationManager
 

H

handleEvent(SVNEvent, double) - Method in class uk.ac.ebi.ols.loader.svnutils.UpdateEventHandler
 
hashCode() - Method in class uk.ac.ebi.ols.config.RepositoryConfigEntry
 
hashCode() - Method in class uk.ac.ebi.ols.loader.newt.SynHolder
 
hashCode() - Method in class uk.ac.ebi.ols.model.ojb.AbstractTermLinker
 
hashCode() - Method in class uk.ac.ebi.ols.model.ojb.AnnotationBean
 
hashCode() - Method in class uk.ac.ebi.ols.model.ojb.TermSynonymBean
 

I

ignoreNonResolvingRelations - Variable in class uk.ac.ebi.ols.loader.impl.ResolvingOBO2AbstractLoader
to fix the problems of some ontologies where terms are not local and do not resolve if this is true, the offending relationships will be ignored
IN_PART - Static variable in class uk.ac.ebi.ols.loader.newt.SynHolder
 
INCLUDES - Static variable in class uk.ac.ebi.ols.loader.newt.SynHolder
 
INDEX_PATH - Static variable in class uk.ac.ebi.ols.config.ConfigurationManager
 
IndexedTermQueryHandler - Class in uk.ac.ebi.ols.persistence.lucene
Handler class to query lucene indexes for full-text term searches.
IndexedTermQueryHandler() - Constructor for class uk.ac.ebi.ols.persistence.lucene.IndexedTermQueryHandler
 
indexOntology(Ontology, File) - Method in class uk.ac.ebi.ols.loader.lucene.OntologyIndexer
 
initialize(Collection<String>, Parser.PARSER_TYPE) - Method in class uk.ac.ebi.ols.loader.impl.ConfigurableOBO2Loader
 
initializeBroker() - Method in class uk.ac.ebi.ols.persistence.query.AbstractQueryHandler
This method initializes the persistence broker framework.
initializeCommonObjects() - Method in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
inetrnal helper method to initialize and reset shared objects
initializePrefixMapping(MultiMap<String, FlyweightOntology>) - Method in class uk.ac.ebi.ols.loader.impl.ResolvingOBO2AbstractLoader
 
initializeTermBean(String, String, String) - Method in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
helper method to create a TermBean given a name, an accession and a definition.
IS_A - Variable in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
 
IS_A_RELATION_TYPE - Static variable in class uk.ac.ebi.ols.Constants
 
IS_A_RELATION_TYPE_ID - Static variable in class uk.ac.ebi.ols.Constants
 
IS_A_SET - Variable in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
 
isClosed() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
isCloseOnCompletion() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
 
isFullyLoaded() - Method in interface uk.ac.ebi.ols.model.interfaces.Ontology
 
isFullyLoaded() - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
isInstance() - Method in interface uk.ac.ebi.ols.model.interfaces.Term
Does ...
isInstance() - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
isLeaf() - Method in interface uk.ac.ebi.ols.model.interfaces.Term
Does ...
isLeaf() - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
isObsolete() - Method in interface uk.ac.ebi.ols.model.interfaces.Term
Does ...
isObsolete() - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
isPoolable() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
isResolveImports() - Method in class uk.ac.ebi.ols.loader.impl.ResolvingOBO2AbstractLoader
 
isRootTerm() - Method in interface uk.ac.ebi.ols.model.interfaces.Term
Does ...
isRootTerm() - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
isUsesImports() - Method in interface uk.ac.ebi.ols.model.interfaces.Ontology
 
isUsesImports() - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
isWrapperFor(Class<?>) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement

L

load() - Method in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
will use OJB to store ontology to db
load(boolean) - Method in class uk.ac.ebi.ols.loader.impl.ConfigurableOBO2Loader
will use OJB to store ontology to db
load(boolean) - Method in class uk.ac.ebi.ols.loader.impl.NEWTOntologyLoader
will use OJB to store ontology to db
loadAndIndex(boolean, Set<String>, Set<String>) - Method in class uk.ac.ebi.ols.loader.impl.ConfigurableOBO2Loader
main I/O and indexing function.
LoadedOntology - Interface in uk.ac.ebi.ols.model.interfaces
User: Richard Cote Date: 09-Jan-2006 Time: 11:44:54
LoadedOntologyBean - Class in uk.ac.ebi.ols.model.ojb
User: Richard Cote Date: 09-Jan-2006 Time: 11:46:17
LoadedOntologyBean() - Constructor for class uk.ac.ebi.ols.model.ojb.LoadedOntologyBean
 
LoadedOntologyBean(String, long) - Constructor for class uk.ac.ebi.ols.model.ojb.LoadedOntologyBean
 
Loader - Interface in uk.ac.ebi.ols.loader.interfaces
Constants for the loader package and all loaded ontolgies#
LOADER_DATA_PATH - Static variable in class uk.ac.ebi.ols.config.ConfigurationManager
 
LOADER_PASSWORD - Static variable in class uk.ac.ebi.ols.config.ConfigurationManager
 
LOADER_USERNAME - Static variable in class uk.ac.ebi.ols.config.ConfigurationManager
 
LoaderRun - Interface in uk.ac.ebi.ols.model.interfaces
User: Richard Cote Date: 09-Jan-2006 Time: 11:40:32
LoaderRunBean - Class in uk.ac.ebi.ols.model.ojb
User: Richard Cote Date: 09-Jan-2006 Time: 11:43:16
LoaderRunBean() - Constructor for class uk.ac.ebi.ols.model.ojb.LoaderRunBean
 
loadFromOBOFile(String, String, String, String) - Static method in class uk.ac.ebi.ols.model.ojb.OntologyBean
Facade method to simplify most of the Loader package code for user who simply want to obtain a fully-constructed ontology object from a single OBO source file.
loadFromOBOFile(URL, String, String, String) - Static method in class uk.ac.ebi.ols.model.ojb.OntologyBean
Facade method to simplify most of the Loader package code for user who simply want to obtain a fully-constructed ontology object from a single OBO source file that is accessed via an URL.
loadFromOBOFile(File, String, String, String) - Static method in class uk.ac.ebi.ols.model.ojb.OntologyBean
Facade method to simplify most of the Loader package code for user who simply want to obtain a fully-constructed ontology object from a single OBO source file.
logger - Static variable in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
 
logger - Static variable in class uk.ac.ebi.ols.loader.impl.ResolvingOBO2AbstractLoader
 

M

main(String[]) - Static method in class uk.ac.ebi.ols.loader.impl.ConfigurableOBO2Loader
 
main(String[]) - Static method in class uk.ac.ebi.ols.loader.impl.NEWTOntologyLoader
 
main(String[]) - Static method in class uk.ac.ebi.ols.loader.impl.OntologyUnloader
Usage: OntologyUnloader methodToUse ontologiesToUnload
main(String[]) - Static method in class uk.ac.ebi.ols.loader.impl.SimpleOntologyLoader
 
main(String[]) - Static method in class uk.ac.ebi.ols.loader.lucene.OntologyIndexer
 
main(String[]) - Static method in class uk.ac.ebi.ols.loader.psiutils.ElementParser
 
main(String[]) - Static method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
ManualOBOFileUpdater - Class in uk.ac.ebi.ols.loader.fileutils
User: rcote Date: 26-Aug-2009 Time: 14:25:11

This class will check for the existence of a file created by an external shell script.

ManualOBOFileUpdater() - Constructor for class uk.ac.ebi.ols.loader.fileutils.ManualOBOFileUpdater
 
mergeAllIndexes(File) - Method in class uk.ac.ebi.ols.loader.lucene.OntologyIndexer
 
MISNOMER - Static variable in class uk.ac.ebi.ols.loader.newt.SynHolder
 
MISSPELLING - Static variable in class uk.ac.ebi.ols.loader.newt.SynHolder
 

N

NARROW - Variable in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
 
NARROW_SYNONYM_TYPE - Static variable in class uk.ac.ebi.ols.Constants
 
NEWTOntologyLoader - Class in uk.ac.ebi.ols.loader.impl
User: Richard Cote Date: 08-Jun-2005 Time: 13:26:00
NEWTOntologyLoader() - Constructor for class uk.ac.ebi.ols.loader.impl.NEWTOntologyLoader
 
NEWTParser - Class in uk.ac.ebi.ols.loader.newt
User: Richard Cote Date: 22-Sep-2005 Time: 11:49:57
NEWTParser(String, String) - Constructor for class uk.ac.ebi.ols.loader.newt.NEWTParser
 
NEWTUtilities - Class in uk.ac.ebi.ols.loader.newt
User: Richard Cote Date: 22-Sep-2005 Time: 15:37:53
NEWTUtilities() - Constructor for class uk.ac.ebi.ols.loader.newt.NEWTUtilities
 
NO_DISTANCE_CONSTRAINT - Static variable in class uk.ac.ebi.ols.Constants
 
NORESOLVE_ONTOLOGIES - Static variable in class uk.ac.ebi.ols.config.ConfigurationManager
 
NULL_CHAR - Static variable in class uk.ac.ebi.ols.loader.newt.NEWTParser
 

O

objectQuery(Query) - Method in class uk.ac.ebi.ols.persistence.query.AbstractQueryHandler
Performs a query and returns an object matching the criteria specified
OBO2FormatParser - Class in uk.ac.ebi.ols.loader.parser
Abstract base class to interact with OBOEdit codebase and parse OBO files
OBO2FormatParser(String) - Constructor for class uk.ac.ebi.ols.loader.parser.OBO2FormatParser
 
OBO2FormatParser(Collection<String>) - Constructor for class uk.ac.ebi.ols.loader.parser.OBO2FormatParser
 
OBO_COMMENT - Static variable in interface uk.ac.ebi.ols.model.interfaces.Annotation
 
OBO_CONSIDER_REPLACEMENT - Static variable in interface uk.ac.ebi.ols.model.interfaces.Annotation
 
OBO_DBXREF_ANALOG - Static variable in interface uk.ac.ebi.ols.model.interfaces.DbXref
 
OBO_DBXREF_ANALOG_STRING - Static variable in interface uk.ac.ebi.ols.model.interfaces.DbXref
 
OBO_DBXREF_ANATOMICAL - Static variable in interface uk.ac.ebi.ols.model.interfaces.DbXref
 
OBO_DBXREF_ANATOMICAL_STRING - Static variable in interface uk.ac.ebi.ols.model.interfaces.DbXref
 
OBO_DBXREF_DEFINITION - Static variable in interface uk.ac.ebi.ols.model.interfaces.DbXref
 
OBO_DBXREF_DEFINITION_STRING - Static variable in interface uk.ac.ebi.ols.model.interfaces.DbXref
 
OBO_DBXREF_SYNONYM - Static variable in interface uk.ac.ebi.ols.model.interfaces.DbXref
 
OBO_DBXREF_SYNONYM_STRING - Static variable in interface uk.ac.ebi.ols.model.interfaces.DbXref
 
OBO_DBXREF_UNKNOWN - Static variable in interface uk.ac.ebi.ols.model.interfaces.DbXref
 
OBO_DBXREF_UNKNOWN_STRING - Static variable in interface uk.ac.ebi.ols.model.interfaces.DbXref
 
OBO_REPLACED_BY - Static variable in interface uk.ac.ebi.ols.model.interfaces.Annotation
 
OBOFormatParser - Class in uk.ac.ebi.ols.loader.parser
OBO Format parser/writer that interacts with the OBOEdit codebase
OBOFormatParser() - Constructor for class uk.ac.ebi.ols.loader.parser.OBOFormatParser
 
OJB__SYNONYM_XREF - Static variable in class uk.ac.ebi.ols.model.ojb.DbXrefBean
 
OJB__TERM_XREF - Static variable in class uk.ac.ebi.ols.model.ojb.DbXrefBean
 
OLS_BUILD_DATE - Static variable in class uk.ac.ebi.ols.config.ConfigurationManager
 
OLS_BUILD_PROFILES - Static variable in class uk.ac.ebi.ols.config.ConfigurationManager
 
OLS_BUILD_USER - Static variable in class uk.ac.ebi.ols.config.ConfigurationManager
 
OLS_CONFIG_FILE - Static variable in class uk.ac.ebi.ols.Constants
 
OLS_DBALIAS - Static variable in class uk.ac.ebi.ols.config.ConfigurationManager
 
OLS_DBALIAS - Static variable in class uk.ac.ebi.ols.Constants
 
OLS_FAILOVER_DBALIAS - Static variable in class uk.ac.ebi.ols.Constants
 
OLS_VERSION - Static variable in class uk.ac.ebi.ols.config.ConfigurationManager
 
ontBean - Variable in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
 
Ontology - Interface in uk.ac.ebi.ols.model.interfaces
 
ONTOLOGY_DEFINITION - Variable in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
 
ONTOLOGY_NAME - Static variable in class uk.ac.ebi.ols.loader.lucene.OntologyIndexer
 
ONTOLOGY_NAME_ATTRIBUTE - Static variable in class uk.ac.ebi.ols.Constants
 
OntologyBean - Class in uk.ac.ebi.ols.model.ojb
 
OntologyBean() - Constructor for class uk.ac.ebi.ols.model.ojb.OntologyBean
 
OntologyIndexer - Class in uk.ac.ebi.ols.loader.lucene
User: Richard Cote Date: 16-Nov-2005 Time: 14:28:45
OntologyJdbcQueryHandler - Class in uk.ac.ebi.ols.jdbc
User: rcote Date: 10-Aug-2009 Time: 16:17:38
OntologyJdbcQueryHandler(ConnectionProvider) - Constructor for class uk.ac.ebi.ols.jdbc.OntologyJdbcQueryHandler
 
OntologyQueryHandler - Class in uk.ac.ebi.ols.persistence.query
Handler class for ontology-related queries
OntologyQueryHandler(String) - Constructor for class uk.ac.ebi.ols.persistence.query.OntologyQueryHandler
 
OntologyQueryHandler() - Constructor for class uk.ac.ebi.ols.persistence.query.OntologyQueryHandler
 
ontologyTerms - Variable in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
 
OntologyUnloader - Class in uk.ac.ebi.ols.loader.impl
Helper class to unload an ontology from the database
OntologyUnloader() - Constructor for class uk.ac.ebi.ols.loader.impl.OntologyUnloader
 
OracleSqlFormatter - Class in uk.ac.ebi.ols.jdbc.util
OracleSqlFormatter formats Oracle specific types.
OracleSqlFormatter() - Constructor for class uk.ac.ebi.ols.jdbc.util.OracleSqlFormatter
 
OTHER_RELATION_TYPE_ID - Static variable in class uk.ac.ebi.ols.Constants
 

P

ParameterIndexOutOfBoundsException - Exception in uk.ac.ebi.ols.jdbc.util
 
ParameterIndexOutOfBoundsException() - Constructor for exception uk.ac.ebi.ols.jdbc.util.ParameterIndexOutOfBoundsException
 
ParameterIndexOutOfBoundsException(String) - Constructor for exception uk.ac.ebi.ols.jdbc.util.ParameterIndexOutOfBoundsException
 
parse(Object) - Method in class uk.ac.ebi.ols.loader.impl.NEWTOntologyLoader
 
parse() - Method in class uk.ac.ebi.ols.loader.newt.NEWTParser
 
parseFile() - Method in class uk.ac.ebi.ols.loader.parser.AbstractParser
 
parseFile() - Method in class uk.ac.ebi.ols.loader.parser.GOFormatParser
Parses the file
parseFile() - Method in class uk.ac.ebi.ols.loader.parser.OBOFormatParser
Parses an OBO formatted file
parseIRI(String) - Method in class uk.ac.ebi.ols.jdbc.TermJdbcQueryHandler
This checks if the termId is a URI/IRI.
parser - Variable in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
 
Parser - Interface in uk.ac.ebi.ols.loader.interfaces
Created by IntelliJ IDEA.
Parser.PARSER_TYPE - Enum in uk.ac.ebi.ols.loader.interfaces
 
PART_OF - Variable in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
 
PART_OF_RELATION_TYPE - Static variable in class uk.ac.ebi.ols.Constants
 
PART_OF_RELATION_TYPE_ID - Static variable in class uk.ac.ebi.ols.Constants
 
PART_OF_SET - Variable in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
 
Persistable - Interface in uk.ac.ebi.ols.persistence.interfaces
Interface for all model implementation classes as an OJB sanity check
persistCollection(Collection) - Method in class uk.ac.ebi.ols.persistence.query.AbstractQueryHandler
This method deletes all the Persistable objects in the Collection provided from the database.
PersistenceException - Class in uk.ac.ebi.ols.persistence.exceptions
Exception for the persistence package - placeholder for unexpected events that don't fall under other exceptions
PersistenceException(String) - Constructor for class uk.ac.ebi.ols.persistence.exceptions.PersistenceException
 
PersistenceException(String, Throwable) - Constructor for class uk.ac.ebi.ols.persistence.exceptions.PersistenceException
 
persistObject(Object) - Method in class uk.ac.ebi.ols.persistence.query.AbstractQueryHandler
Method to persist a new Person record to the database, either as part of or outside an existing transaction.
postScanEntries(CVSEntry) - Method in class uk.ac.ebi.ols.loader.cvsutils.CVSUpdater
 
PREFERRED_NAME - Static variable in class uk.ac.ebi.ols.Constants
 
printUsage() - Method in class uk.ac.ebi.ols.loader.impl.ConfigurableOBO2Loader
definition of the abstract printUsage method
printUsage() - Method in class uk.ac.ebi.ols.loader.impl.NEWTOntologyLoader
 
process() - Method in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
Will iterate through all parsed terms and generate memory structure suitable for loading to db
process() - Method in class uk.ac.ebi.ols.loader.impl.NEWTOntologyLoader
 
process() - Method in class uk.ac.ebi.ols.loader.impl.ResolvingOBO2AbstractLoader
overrides the default behaviour of process defined in BaseAbstractLoader.
processTerm(OBOObject) - Method in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
This method will convert an OBOEdit model term into a valid TermBean, while creating synonyms, xrefs and annotations.

Q

QUERY_URL - Variable in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
 

R

rawSQLDeleteOntology(long) - Method in class uk.ac.ebi.ols.persistence.query.OntologyQueryHandler
deletes an ontology from the db layer using direct SQL.
REFRESH_URL - Static variable in class uk.ac.ebi.ols.config.ConfigurationManager
 
RELATED - Variable in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
 
RELATED_SYNONYM_TYPE - Static variable in class uk.ac.ebi.ols.Constants
 
RELATION_TYPE - Static variable in interface uk.ac.ebi.ols.loader.interfaces.Loader
 
RELATIONSHIPS_TO_IGNORE - Static variable in class uk.ac.ebi.ols.Constants
 
releaseBroker() - Method in class uk.ac.ebi.ols.persistence.query.AbstractQueryHandler
Releases the broker to the connection pool
reportQuery(Query) - Method in class uk.ac.ebi.ols.persistence.query.AbstractQueryHandler
Performs a report query and returns an iterator on the report
RepositoryConfigEntry - Class in uk.ac.ebi.ols.config
User: Richard Cote Date: 17-Nov-2006 Time: 10:59:02
RepositoryConfigEntry() - Constructor for class uk.ac.ebi.ols.config.RepositoryConfigEntry
 
RepositoryConfigurationException - Exception in uk.ac.ebi.ols.config
User: Richard Cote Date: 17-Nov-2006 Time: 10:56:20
RepositoryConfigurationException(String) - Constructor for exception uk.ac.ebi.ols.config.RepositoryConfigurationException
Constructs a new runtime exception with the specified detail message.
RESID_FILE - Static variable in class uk.ac.ebi.ols.config.ConfigurationManager
 
ResolvingOBO2AbstractLoader - Class in uk.ac.ebi.ols.loader.impl
 
ResolvingOBO2AbstractLoader() - Constructor for class uk.ac.ebi.ols.loader.impl.ResolvingOBO2AbstractLoader
 
RETURN_VALUE_CVS_ERROR - Static variable in class uk.ac.ebi.ols.Constants
 
RETURN_VALUE_ERROR - Static variable in class uk.ac.ebi.ols.Constants
 
RETURN_VALUE_OK - Static variable in class uk.ac.ebi.ols.Constants
 
RETURN_VALUE_OK_NO_ONTOLOGIES_LOADED - Static variable in class uk.ac.ebi.ols.Constants
 
rollbackTransaction() - Method in class uk.ac.ebi.ols.persistence.query.AbstractQueryHandler
Aborts transaction on a non-null broker in transaction.

S

safeTrim(String, boolean) - Method in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
takes a string and trims whitespace.
safeTrim(String) - Method in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
takes a string and trims whitespace.
SCIENTIFIC_NAME - Static variable in class uk.ac.ebi.ols.loader.newt.SynHolder
 
session - Variable in class uk.ac.ebi.ols.loader.parser.AbstractParser
 
setAccession(String) - Method in class uk.ac.ebi.ols.model.ojb.DbXrefBean
 
setAllowCircular(boolean) - Method in class uk.ac.ebi.ols.loader.parser.GOFormatParser
allow circular references in DAG file
setAllowDangling(boolean) - Method in class uk.ac.ebi.ols.loader.parser.GOFormatParser
allow dandling references in DAG file
setAnnotationDoubleValue(String) - Method in class uk.ac.ebi.ols.model.ojb.AnnotationBean
 
setAnnotationId(long) - Method in class uk.ac.ebi.ols.model.ojb.AnnotationBean
 
setAnnotationNumberValue(Double) - Method in class uk.ac.ebi.ols.model.ojb.AnnotationBean
 
setAnnotations(Collection<Annotation>) - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
setAnnotationStringValue(String) - Method in class uk.ac.ebi.ols.model.ojb.AnnotationBean
 
setAnnotationType(String) - Method in class uk.ac.ebi.ols.model.ojb.AnnotationBean
 
setArray(int, Array) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Adds name of the Array's internal class type(by using x.getBaseTypeName()) to the debug String.
setAsciiStream(int, InputStream, int) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Debug string prints NULL if InputStream is null, or adds "stream length = " + length
setAsciiStream(int, InputStream, long) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This method is here to satisfy the PreparedStatement interface but is not implemented.
setAsciiStream(int, InputStream) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This method is here to satisfy the PreparedStatement interface but is not implemented.
setAvgMass(double) - Method in class uk.ac.ebi.ols.loader.psiutils.Element
 
setAvgMass(String) - Method in class uk.ac.ebi.ols.loader.psiutils.Element
 
setBatchMode(boolean) - Method in class uk.ac.ebi.ols.persistence.query.AbstractQueryHandler
 
setBigDecimal(int, BigDecimal) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Adds BigDecimal to debug string in parameterIndex position.
setBinaryStream(int, InputStream, int) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Debug string prints NULL if InputStream is null, or adds "stream length= " + length.
setBinaryStream(int, InputStream, long) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This method is here to satisfy the PreparedStatement interface but is not implemented.
setBinaryStream(int, InputStream) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This method is here to satisfy the PreparedStatement interface but is not implemented.
setBlob(int, Blob) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Adds name of the object's class type(Blob) to the debug String.
setBlob(int, InputStream) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This method is here to satisfy the PreparedStatement interface but is not implemented.
setBlob(int, InputStream, long) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This method is here to satisfy the PreparedStatement interface but is not implemented.
setBoolean(int, boolean) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Adds boolean to debug string in parameterIndex position.
setByte(int, byte) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Adds byte to debug string in parameterIndex position.
setBytes(int, byte[]) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Adds byte[] to debug string in parameterIndex position.
setCharacterStream(int, Reader, int) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Debug string prints NULL if reader is null, or adds "stream length= " + length.
setCharacterStream(int, Reader, long) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This method is here to satisfy the PreparedStatement interface but is not implemented.
setCharacterStream(int, Reader) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This method is here to satisfy the PreparedStatement interface but is not implemented.
setClob(int, Clob) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Adds name of the object's class type(Clob) to the debug String.
setClob(int, Reader) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This method is here to satisfy the PreparedStatement interface but is not implemented.
setClob(int, Reader, long) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This method is here to satisfy the PreparedStatement interface but is not implemented.
setConnectionProvider(ConnectionProvider) - Method in class uk.ac.ebi.ols.jdbc.AbstractJdbcQueryHandler
 
setCursorName(String) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
 
setDate(int, Date) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Debug string displays date in YYYY-MM-DD HH24:MI:SS.# format.
setDate(int, Date, Calendar) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
this implementation assumes that the Date has the date, and the calendar has the local info.
setDbName(String) - Method in class uk.ac.ebi.ols.model.ojb.DbXrefBean
 
setDbXrefId(long) - Method in class uk.ac.ebi.ols.model.ojb.DbXrefBean
 
setDefinition(String) - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
setDefinition(String) - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
setDescription(String) - Method in class uk.ac.ebi.ols.model.ojb.DbXrefBean
 
setDistance(int) - Method in class uk.ac.ebi.ols.model.ojb.TermPathBean
 
setDouble(int, double) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Adds double to debug string in parameterIndex position.
setEscapeProcessing(boolean) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
setFetchDirection(int) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
setFetchSize(int) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
setFloat(int, float) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Adds float to debug string in parameterIndex position.
setFormatter(SqlFormatter) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
setFullOntologyName(String) - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
setFullyLoaded(boolean) - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
setIdentifier(String) - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
setIgnoreNonResolvingRelations(boolean) - Method in class uk.ac.ebi.ols.loader.impl.ResolvingOBO2AbstractLoader
 
setInstance(boolean) - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
setInt(int, int) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Adds int to debug string in parameterIndex position.
setIsotopes(HashMap) - Method in class uk.ac.ebi.ols.loader.psiutils.Element
 
setLeaf(boolean) - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
setLoadData(Date) - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
setLoadDate(Date) - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
setLoadedOntologies(Collection<LoadedOntology>) - Method in class uk.ac.ebi.ols.model.ojb.LoaderRunBean
 
setLocalTermPrefixes(HashSet<String>) - Method in class uk.ac.ebi.ols.loader.impl.ResolvingOBO2AbstractLoader
 
setLoggerLevel(Level) - Method in interface uk.ac.ebi.ols.loader.interfaces.Parser
 
setLoggerLevel(Level) - Method in class uk.ac.ebi.ols.loader.parser.AbstractParser
manipulate the logging level at runtime.
setLoggerLevel(Level) - Method in class uk.ac.ebi.ols.loader.parser.OBO2FormatParser
manipulate the logging level at runtime.
setLong(int, long) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Adds long to debug string in parameterIndex position.
setMaxFieldSize(int) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
setMaxRows(int) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
setMonoMass(double) - Method in class uk.ac.ebi.ols.loader.psiutils.Element
 
setMonoMass(String) - Method in class uk.ac.ebi.ols.loader.psiutils.Element
 
setName(String) - Method in class uk.ac.ebi.ols.model.ojb.LoadedOntologyBean
 
setName(String) - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
setNamespace(String) - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
setNCharacterStream(int, Reader) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This method is here to satisfy the PreparedStatement interface but is not implemented.
setNCharacterStream(int, Reader, long) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This method is here to satisfy the PreparedStatement interface but is not implemented.
setNClob(int, Reader) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This method is here to satisfy the PreparedStatement interface but is not implemented.
setNClob(int, NClob) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This method is here to satisfy the PreparedStatement interface but is not implemented.
setNClob(int, Reader, long) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This method is here to satisfy the PreparedStatement interface but is not implemented.
setNString(int, String) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This method is here to satisfy the PreparedStatement interface but is not implemented.
setNull(int, int) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Adds a NULL to the debug String.
setNull(int, int, String) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Adds a NULL to the debug String.
setNumberOfTerms(long) - Method in class uk.ac.ebi.ols.model.ojb.LoadedOntologyBean
 
setObject(int, Object) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Adds name of the object's class type to the debug String.
setObject(int, Object, int) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Adds name of the object's class type to the debug String.
setObject(int, Object, int, int) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Adds name of the object's class type to the debug String.
setObjectTerm(Term) - Method in class uk.ac.ebi.ols.model.ojb.AbstractTermLinker
 
setObjectTermPk(String) - Method in class uk.ac.ebi.ols.model.ojb.AbstractTermLinker
 
setObsolete(boolean) - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
setOntologyId(long) - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
setParentObjectPk(String) - Method in class uk.ac.ebi.ols.model.ojb.DbXrefBean
 
setParentOntology(Ontology) - Method in class uk.ac.ebi.ols.model.ojb.AbstractTermLinker
 
setParentOntology(Ontology) - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
setParentOntologyId(long) - Method in class uk.ac.ebi.ols.model.ojb.AbstractTermLinker
 
setParentOntologyId(long) - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
setParentRun(LoaderRun) - Method in class uk.ac.ebi.ols.model.ojb.LoadedOntologyBean
 
setParentRunId(long) - Method in class uk.ac.ebi.ols.model.ojb.LoadedOntologyBean
 
setParentTerm(Term) - Method in class uk.ac.ebi.ols.model.ojb.AnnotationBean
 
setParentTerm(Term) - Method in class uk.ac.ebi.ols.model.ojb.TermSynonymBean
 
setParentTermPk(String) - Method in class uk.ac.ebi.ols.model.ojb.AnnotationBean
 
setParentTermPk(String) - Method in class uk.ac.ebi.ols.model.ojb.TermSynonymBean
 
setParser(Parser) - Method in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
 
setPassword(String) - Method in class uk.ac.ebi.ols.config.RepositoryConfigEntry
 
setPaths(Collection<TermPath>) - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
setPkId(long) - Method in class uk.ac.ebi.ols.model.ojb.LoadedOntologyBean
 
setPoolable(boolean) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
setPredicateTerm(Term) - Method in class uk.ac.ebi.ols.model.ojb.AbstractTermLinker
 
setPredicateTermPk(String) - Method in class uk.ac.ebi.ols.model.ojb.AbstractTermLinker
 
setQueryTimeout(int) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
setQueryURL(String) - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
setQueryXrefType(long) - Method in class uk.ac.ebi.ols.model.ojb.DbXrefBean
 
setRef(int, Ref) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
From the javadocs: A reference to an SQL structured type value in the database.
setRelationships(Collection<TermRelationship>) - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
setRelationshipTypeId(long) - Method in class uk.ac.ebi.ols.model.ojb.TermPathBean
 
setRepository(String) - Method in class uk.ac.ebi.ols.config.RepositoryConfigEntry
 
setResolveImports(boolean) - Method in class uk.ac.ebi.ols.loader.impl.ResolvingOBO2AbstractLoader
 
setRootTerm(boolean) - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
setRootTerms(Collection<Term>) - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
setRowId(int, RowId) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This method is here to satisfy the PreparedStatement interface but is not implemented.
setRunDate(Date) - Method in class uk.ac.ebi.ols.model.ojb.LoaderRunBean
 
setRunId(long) - Method in class uk.ac.ebi.ols.model.ojb.LoaderRunBean
 
setShort(int, short) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Adds short to debug string in parameterIndex position.
setShortOntologyName(String) - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
setSourceURL(String) - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
setSQLXML(int, SQLXML) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This method is here to satisfy the PreparedStatement interface but is not implemented.
setString(int, String) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Adds String to debug string in parameterIndex position.
setSubjectTerm(Term) - Method in class uk.ac.ebi.ols.model.ojb.AbstractTermLinker
 
setSubjectTermPk(String) - Method in class uk.ac.ebi.ols.model.ojb.AbstractTermLinker
 
setSymbol(String) - Method in class uk.ac.ebi.ols.loader.psiutils.Element
 
setSynonym(String) - Method in class uk.ac.ebi.ols.model.ojb.TermSynonymBean
 
setSynonymPk(String) - Method in class uk.ac.ebi.ols.model.ojb.TermSynonymBean
 
setSynonyms(Collection<TermSynonym>) - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
setSynonymType(Term) - Method in class uk.ac.ebi.ols.model.ojb.TermSynonymBean
 
setSynonymTypePk(String) - Method in class uk.ac.ebi.ols.model.ojb.TermSynonymBean
 
setSynonymXrefs(Collection<DbXref>) - Method in class uk.ac.ebi.ols.model.ojb.TermSynonymBean
 
setTermPathId(long) - Method in class uk.ac.ebi.ols.model.ojb.TermPathBean
 
setTermPaths(Collection<TermPath>) - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
setTermPk(String) - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
setTermRelationshipId(long) - Method in class uk.ac.ebi.ols.model.ojb.TermRelationshipBean
 
setTermRelationships(Collection<TermRelationship>) - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
setTerms(Collection<Term>) - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
setTime(int, Time) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Debug string displays Time in HH24:MI:SS.# format.
setTime(int, Time, Calendar) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This implementation assumes that the Time object has the time and Calendar has the locale info.
setTimestamp(int, Timestamp) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Debug string displays timestamp in YYYY-MM-DD HH24:MI:SS.# format.
setTimestamp(int, Timestamp, Calendar) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This implementation assumes that the Timestamp has the date/time and Calendar has the locale info.
setUnicodeStream(int, InputStream, int) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Deprecated. 
setURL(int, URL) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
This method is here to satisfy the PreparedStatement interface but is not implemented.
setUseAnonymous(boolean) - Method in class uk.ac.ebi.ols.config.RepositoryConfigEntry
 
setUseAnonymous(String) - Method in class uk.ac.ebi.ols.config.RepositoryConfigEntry
 
setUseGreedy(boolean) - Method in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
 
setUserName(String) - Method in class uk.ac.ebi.ols.config.RepositoryConfigEntry
 
setUsesImports(boolean) - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
setUseSSH(boolean) - Method in class uk.ac.ebi.ols.config.RepositoryConfigEntry
 
setUseSSH(String) - Method in class uk.ac.ebi.ols.config.RepositoryConfigEntry
 
setVersion(String) - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
setXrefs(Collection<DbXref>) - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
setXrefType(int) - Method in class uk.ac.ebi.ols.model.ojb.DbXrefBean
 
SHORT_NAME - Variable in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
 
SimpleOntologyLoader - Class in uk.ac.ebi.ols.loader.impl
 
SimpleOntologyLoader() - Constructor for class uk.ac.ebi.ols.loader.impl.SimpleOntologyLoader
 
SOURCE_URL - Variable in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
 
SPTR_COMMON_NAME - Static variable in class uk.ac.ebi.ols.loader.newt.SynHolder
 
SPTR_FULL_NAME - Static variable in class uk.ac.ebi.ols.loader.newt.SynHolder
 
SPTR_MNEMONIC - Static variable in class uk.ac.ebi.ols.loader.newt.SynHolder
 
SPTR_SCIENTIFIC_NAME - Static variable in class uk.ac.ebi.ols.loader.newt.SynHolder
 
SPTR_SYNONYM - Static variable in class uk.ac.ebi.ols.loader.newt.SynHolder
 
SqlFormatter - Class in uk.ac.ebi.ols.jdbc.util
Base class for all database Formatters such as OracleFormatter.
SqlFormatter() - Constructor for class uk.ac.ebi.ols.jdbc.util.SqlFormatter
 
StatementFactory - Class in uk.ac.ebi.ols.jdbc.util
 
StatementFactory() - Constructor for class uk.ac.ebi.ols.jdbc.util.StatementFactory
StatementFactory returns either a regular PreparedStatement or a DebuggableStatement class depending on the Level of the Log4J Logger.
storeOntology(Ontology, boolean) - Method in class uk.ac.ebi.ols.persistence.query.OntologyQueryHandler
Stores an ontology object to the DB layer and flushes the cache to remove stale data
storeStats(LoaderRunBean) - Method in class uk.ac.ebi.ols.persistence.query.OntologyQueryHandler
Stores statistics on a loader run to the db
strictObjectQuery(Query) - Method in class uk.ac.ebi.ols.persistence.query.AbstractQueryHandler
Performs a query and returns an object matching the criteria specified.
SUBSET - Static variable in interface uk.ac.ebi.ols.model.interfaces.Annotation
 
SVNUpdater - Class in uk.ac.ebi.ols.loader.svnutils
 
SVNUpdater() - Constructor for class uk.ac.ebi.ols.loader.svnutils.SVNUpdater
 
switchLoadedFlag(String) - Method in class uk.ac.ebi.ols.persistence.query.OntologyQueryHandler
switches the fully_loaded flag for all ontologies of a given name
SynHolder - Class in uk.ac.ebi.ols.loader.newt
User: Richard Cote Date: 22-Sep-2005 Time: 11:51:34
SynHolder(int, String) - Constructor for class uk.ac.ebi.ols.loader.newt.SynHolder
 
SYNONYM - Variable in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
 
SYNONYM - Static variable in class uk.ac.ebi.ols.loader.newt.SynHolder
 
SYNONYM_TYPE - Static variable in interface uk.ac.ebi.ols.loader.interfaces.Loader
 

T

TELEOMORPH - Static variable in class uk.ac.ebi.ols.loader.newt.SynHolder
 
Term - Interface in uk.ac.ebi.ols.model.interfaces
 
TERM_ACCESSION - Static variable in class uk.ac.ebi.ols.loader.lucene.OntologyIndexer
 
TERM_ID - Static variable in class uk.ac.ebi.ols.loader.lucene.OntologyIndexer
 
TERM_IS_OBSOLETE - Static variable in class uk.ac.ebi.ols.loader.lucene.OntologyIndexer
 
TERM_IS_SYNONYM - Static variable in class uk.ac.ebi.ols.loader.lucene.OntologyIndexer
 
TERM_NAME - Static variable in class uk.ac.ebi.ols.loader.lucene.OntologyIndexer
 
TERM_NAME_LENGTH - Static variable in class uk.ac.ebi.ols.loader.lucene.OntologyIndexer
 
TermBean - Class in uk.ac.ebi.ols.model.ojb
 
TermBean() - Constructor for class uk.ac.ebi.ols.model.ojb.TermBean
 
TermJdbcQueryHandler - Class in uk.ac.ebi.ols.jdbc
Created by IntelliJ IDEA.
TermJdbcQueryHandler(ConnectionProvider) - Constructor for class uk.ac.ebi.ols.jdbc.TermJdbcQueryHandler
 
TermPath - Interface in uk.ac.ebi.ols.model.interfaces
 
TermPathBean - Class in uk.ac.ebi.ols.model.ojb
 
TermPathBean() - Constructor for class uk.ac.ebi.ols.model.ojb.TermPathBean
 
TermQueryHandler - Class in uk.ac.ebi.ols.persistence.query
Handler class for Term-related queries
TermQueryHandler() - Constructor for class uk.ac.ebi.ols.persistence.query.TermQueryHandler
 
TermQueryHandler(String) - Constructor for class uk.ac.ebi.ols.persistence.query.TermQueryHandler
 
TermRelationship - Interface in uk.ac.ebi.ols.model.interfaces
 
TermRelationshipBean - Class in uk.ac.ebi.ols.model.ojb
 
TermRelationshipBean() - Constructor for class uk.ac.ebi.ols.model.ojb.TermRelationshipBean
 
TermSynonym - Interface in uk.ac.ebi.ols.model.interfaces
 
TermSynonymBean - Class in uk.ac.ebi.ols.model.ojb
 
TermSynonymBean() - Constructor for class uk.ac.ebi.ols.model.ojb.TermSynonymBean
 
toFile(String) - Method in class uk.ac.ebi.ols.loader.psiutils.ElementParser
 
TomcatManagedConnectionProvider - Class in uk.ac.ebi.ols.jdbc.util
Created by IntelliJ IDEA.
toString() - Method in class uk.ac.ebi.ols.config.RepositoryConfigEntry
 
toString() - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
this toString is overidden to return a String representation of the sql statement being sent to the database.
toString() - Method in class uk.ac.ebi.ols.loader.impl.FlyweightOntology
 
toString() - Method in class uk.ac.ebi.ols.loader.newt.SynHolder
 
toString() - Method in class uk.ac.ebi.ols.model.ojb.AbstractTermLinker
 
toString() - Method in class uk.ac.ebi.ols.model.ojb.AnnotationBean
 
toString() - Method in class uk.ac.ebi.ols.model.ojb.DbXrefBean
 
toString() - Method in class uk.ac.ebi.ols.model.ojb.LoadedOntologyBean
 
toString() - Method in class uk.ac.ebi.ols.model.ojb.LoaderRunBean
 
toString() - Method in class uk.ac.ebi.ols.model.ojb.OntologyBean
 
toString() - Method in class uk.ac.ebi.ols.model.ojb.TermBean
 
toString() - Method in class uk.ac.ebi.ols.model.ojb.TermSynonymBean
 

U

uk.ac.ebi.ols - package uk.ac.ebi.ols
 
uk.ac.ebi.ols.config - package uk.ac.ebi.ols.config
Configuration Helper/Manager Classes
uk.ac.ebi.ols.jdbc - package uk.ac.ebi.ols.jdbc
 
uk.ac.ebi.ols.jdbc.util - package uk.ac.ebi.ols.jdbc.util
 
uk.ac.ebi.ols.loader.cvsutils - package uk.ac.ebi.ols.loader.cvsutils
CVS Helper classes
uk.ac.ebi.ols.loader.fileutils - package uk.ac.ebi.ols.loader.fileutils
 
uk.ac.ebi.ols.loader.impl - package uk.ac.ebi.ols.loader.impl
Implementation classes for loaders, parsers and indexers
uk.ac.ebi.ols.loader.interfaces - package uk.ac.ebi.ols.loader.interfaces
Loader interface
uk.ac.ebi.ols.loader.lucene - package uk.ac.ebi.ols.loader.lucene
Lucene Indexer classes
uk.ac.ebi.ols.loader.newt - package uk.ac.ebi.ols.loader.newt
NEWT taxonomy helper classes
uk.ac.ebi.ols.loader.parser - package uk.ac.ebi.ols.loader.parser
OBO and GO flat-file parser classes
uk.ac.ebi.ols.loader.psiutils - package uk.ac.ebi.ols.loader.psiutils
PSI-MOD pre- and post-processing helper classes
uk.ac.ebi.ols.loader.svnutils - package uk.ac.ebi.ols.loader.svnutils
 
uk.ac.ebi.ols.model.interfaces - package uk.ac.ebi.ols.model.interfaces
OLS Model Interfaces
uk.ac.ebi.ols.model.ojb - package uk.ac.ebi.ols.model.ojb
OLS implementation classes
uk.ac.ebi.ols.persistence.exceptions - package uk.ac.ebi.ols.persistence.exceptions
Exception handler
uk.ac.ebi.ols.persistence.interfaces - package uk.ac.ebi.ols.persistence.interfaces
Persistable sanity-check interface
uk.ac.ebi.ols.persistence.lucene - package uk.ac.ebi.ols.persistence.lucene
Lucene index query handler
uk.ac.ebi.ols.persistence.query - package uk.ac.ebi.ols.persistence.query
Query handlers that return OLS model objects
uk.ac.ebi.ols.persistence.query.customizer - package uk.ac.ebi.ols.persistence.query.customizer
 
unload() - Method in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
will use OJB to store delete old ontology from db
unload(boolean) - Method in class uk.ac.ebi.ols.loader.impl.ConfigurableOBO2Loader
will use OJB to store delete old ontology from db
unload(boolean) - Method in class uk.ac.ebi.ols.loader.impl.NEWTOntologyLoader
will use OJB to store delete old ontology from db
unwrap(Class<T>) - Method in class uk.ac.ebi.ols.jdbc.util.DebuggableStatement
Facade for PreparedStatement
updateBeanFieldsOnly(Persistable) - Method in class uk.ac.ebi.ols.persistence.query.AbstractQueryHandler
Use With Care! This method updates a persistable bean to the database without updating any referenced objects, ie.
UpdateEventHandler - Class in uk.ac.ebi.ols.loader.svnutils
User: rcote Date: 15-Apr-2008 Time: 15:17:25 $Id: UpdateEventHandler.java,v 1.1 2008/04/16 13:49:44 rglcote Exp $
UpdateEventHandler(HashSet<String>, HashSet<String>) - Constructor for class uk.ac.ebi.ols.loader.svnutils.UpdateEventHandler
 
updateOBOFiles(String, String, String) - Method in class uk.ac.ebi.ols.loader.cvsutils.CVSUpdater
performs a CVS update on a repository using the given credentials and returns a hashmap of all updated files
updateOBOFiles(String, String, String) - Method in class uk.ac.ebi.ols.loader.svnutils.SVNUpdater
performs a SVN update on a repository using the given credentials and returns a hashset of all updated files names.
useAnonymous() - Method in class uk.ac.ebi.ols.config.RepositoryConfigEntry
 
useGreedy - Variable in class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
determine which root detection algorithm will be used
useSSH() - Method in class uk.ac.ebi.ols.config.RepositoryConfigEntry
 

V

valueOf(String) - Static method in enum uk.ac.ebi.ols.loader.interfaces.Parser.PARSER_TYPE
Returns the enum constant of this type with the specified name.
values() - Static method in enum uk.ac.ebi.ols.loader.interfaces.Parser.PARSER_TYPE
Returns an array containing the constants of this enum type, in the order they are declared.

W

writeFile(String) - Method in class uk.ac.ebi.ols.loader.parser.OBOFormatParser
Writes an OBO formatted file

X

XrefQueryCustomizer - Class in uk.ac.ebi.ols.persistence.query.customizer
 
XrefQueryCustomizer() - Constructor for class uk.ac.ebi.ols.persistence.query.customizer.XrefQueryCustomizer
 
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