Uses of Class
uk.ac.ebi.intenz.domain.exceptions.DomainException

Packages that use DomainException

uk.ac.ebi.intenz.domain.constants	The most commonly used constants are implemented as typesafe enums.
uk.ac.ebi.intenz.domain.exceptions
uk.ac.ebi.intenz.mapper	O/R mapping layer classes.
uk.ac.ebi.intenz.stats.db
uk.ac.ebi.intenz.tools.export
uk.ac.ebi.intenz.webapp.exceptions	All exceptions are located here.
uk.ac.ebi.intenz.webapp.utilities

Uses of DomainException in uk.ac.ebi.intenz.domain.constants

Methods in uk.ac.ebi.intenz.domain.constants that throw DomainException

static XrefDatabaseConstant

XrefDatabaseConstant.valueOf(String sourceCode)

Uses of DomainException in uk.ac.ebi.intenz.domain.exceptions

Subclasses of DomainException in uk.ac.ebi.intenz.domain.exceptions

class	EcException This exception is thrown when a EC number is not valid (e.g.
class	EnzymeNameException If an error regarding an enzyme name occurs this exception should be thrown.
class	EnzymeReactionException If an error regarding an enzyme reaction occurs this exception should be thrown.
class	EnzymeReferenceException If an error regarding an enzyme reference occurs this exception should be thrown.

Uses of DomainException in uk.ac.ebi.intenz.mapper

Methods in uk.ac.ebi.intenz.mapper that throw DomainException

List<EnzymeEntry>	EnzymeEntryMapper.exportAllEntries(Connection con) Exports every piece of data for publicly available entries.
List<EnzymeEntry>	EnzymeEntryMapper.exportApprovedSibEntries(Connection con) Tries to export all approved entries containing only ENZYME relevant information.
List<EnzymeLink>	EnzymeLinkMapper.exportSibLinks(Long enzymeId, Connection con) Exports all links which are displayed in the ENZYME view.
HistoryGraph	EnzymeHistoryMapper.find(EnzymeEntry enzymeEntry, Connection con)
HistoryGraph	EnzymeFutureMapper.find(EnzymeEntry enzymeEntry, Connection con)
EnzymeSubSubclass	EnzymeSubSubclassMapper.find(int ec1, int ec2, int ec3, Connection con) Tries to find Sub-subclass information about an enzyme.
List<EnzymeLink>	EnzymeLinkMapper.find(Long enzymeId, Connection con) Tries to find link information about an enzyme in tables LINKS and XREFS.
EnzymeClass	EnzymeClassMapper.find(String ec1, Connection con) Tries to find Class information about an enzyme.
EnzymeSubclass	EnzymeSubclassMapper.find(String ec1, String ec2, Connection con) Tries to find Subclass information about an enzyme.
List<EnzymeSubSubclass>	EnzymeSubSubclassMapper.findAll(Connection con)
List<EnzymeSubclass>	EnzymeSubclassMapper.findAll(Connection con)
List<EnzymeEntry>	EnzymeEntryMapper.findAll(Connection con) Tries to find all public entries but loads the entries only with minimum information.
List<EnzymeClass>	EnzymeClassMapper.findAll(Connection con)
List<EnzymeEntry>	EnzymeEntryMapper.findAllByEc(int ec1, int ec2, int ec3, int ec4, Boolean preliminary, Connection con)
List<EnzymeEntry>	EnzymeEntryMapper.findAllByEc(int ec1, int ec2, int ec3, int ec4, Connection con) Tries to find entry information about all enzymes specified by the given EC.
List<EnzymeEntry>	EnzymeEntryMapper.findAllSubSubclassEntriesByEc(int ec1, int ec2, int ec3, Connection con)
EnzymeEntry	EnzymeEntryMapper.findByEc(int ec1, int ec2, int ec3, int ec4, Status status, Connection con) Tries to find entry information about an enzyme.
EnzymeEntry	EnzymeEntryMapper.findByEc(String ecString, Status status, Connection con) Finds an enzyme by EC number (as String) and status.
EnzymeEntry	EnzymeEntryMapper.findById(long id, Connection con) Loads a complete version of the enzyme with the given ID.
EnzymeEntry	EnzymeEntryMapper.findById(Long id, Connection con, boolean ghost) Tries to find entry information about an enzyme.
List<EnzymeEntry>	EnzymeEntryMapper.findByStatus(Connection con, Status status) Retrieves the list of enzymes with a given status.
EnzymeCommissionNumber	EnzymeEntryMapper.findEC(String id, Connection con) Returns the EC number of the given enzyme ID.
List<EnzymeEntry>	EnzymeEntryMapper.findFullProposedList(Connection con) Tries to find all proposed entries with all information.
List<EnzymeEntry>	EnzymeEntryMapper.findFullSuggestedList(Connection con) Tries to find all suggested entries with all information.
EnzymeEntry	EnzymeEntryMapper.findGhostById(int id, Connection con) Loads a ghost version of the enzyme with the given ID.
List<EnzymeSubclass>	EnzymeSubclassMapper.findList(String ec1, Connection con) Tries to find all Subclasses requested.
List<EnzymeSubSubclass>	EnzymeSubSubclassMapper.findList(String ec1, String ec2, Connection con) Tries to find all Sub-subclasses requested.
List<EnzymeEntry>	EnzymeEntryMapper.findList(String ec1, String ec2, String ec3, Connection con) Tries to find all entries requested but loads the entries only with minimum information.
List<EnzymeEntry>	EnzymeEntryMapper.findPreliminaryEcsList(Connection con) Gets the list of preliminary EC numbers issued by UniProt.
List<EnzymeEntry>	EnzymeEntryMapper.findProposedList(Connection con) Tries to find all proposed entries but loads the entries only with minimum information.
List<EnzymeLink>	EnzymeLinkMapper.findSibXrefs(Long enzymeId, Connection con) Finds all xrefs which are displayed in the ENZYME view.
List<EnzymeEntry>	EnzymeEntryMapper.findSuggestedList(Connection con) Tries to find all suggested entries but loads the entries only with minimum information.
List<EnzymeLink>	EnzymeLinkMapper.findXrefs(Long enzymeId, Connection con) Tries to find SwissProt xref information about an enzyme.

Uses of DomainException in uk.ac.ebi.intenz.stats.db

Methods in uk.ac.ebi.intenz.stats.db that throw DomainException

void	IntEnzDbStatistics.updateStatistics()

Constructors in uk.ac.ebi.intenz.stats.db that throw DomainException

IntEnzDbStatistics(Connection con)

Uses of DomainException in uk.ac.ebi.intenz.tools.export

Methods in uk.ac.ebi.intenz.tools.export that throw DomainException

static Map<String,Object>	ExporterApp.getDescriptions(Connection con) Builds a map of EC numbers (as String) to EnzymeClass, EnzymeSubClass or EnzymeSubSubClass objects from which to retrieve names and descriptions.
protected Collection<EnzymeEntry>	ExporterApp.getEnzymeList(String ecString) Gets the list of enzymes to be exported.
static void	ExporterApp.main(String[] args) Exports IntEnz data in the following formats: XML (both flavours ASCII and XCHARS), using the XmlExporter class. Site map XML file (sitemap.xml) to be used in Google sitemaps to make every IntEnz entry available to Google indexing.

Constructors in uk.ac.ebi.intenz.tools.export that throw DomainException

ExporterApp(String dbConfig)

Uses of DomainException in uk.ac.ebi.intenz.webapp.exceptions

Subclasses of DomainException in uk.ac.ebi.intenz.webapp.exceptions

class

DeregisterException This exception is the base exception for all domain exception and just acts as a wrapper.

Uses of DomainException in uk.ac.ebi.intenz.webapp.utilities

Methods in uk.ac.ebi.intenz.webapp.utilities that throw DomainException

void	UnitOfWork.commit(EnzymeDTO enzymeUnderDevelopment, Connection con) Compares the given enzyme entry to the copy stored in UnitOfWork.register(uk.ac.ebi.intenz.webapp.dtos.EnzymeDTO).
static void	PubMedAccessor.fetchPubMedJournal(List<ReferenceDTO> references, int index) Creates a Journal instance by using the PubMed ID of the reference.