EnzymeEntryMapper (IntEnz mapper module 4.6.0 API)

java.lang.Object
- uk.ac.ebi.intenz.mapper.EnzymeEntryMapper

```
public class EnzymeEntryMapper
extends Object
```
Maps enzyme entry information to the corresponding database tables.
IMPORTANT: after using instances of this class, call the close() method, otherwise the underlying Rhea mapper objects will keep their statements open.

Version:

$Revision: 1.5 $ $Date: 2009/05/26 14:59:09 $

Author:

Michael Darsow

Constructor Summary

Constructors
Constructor and Description

EnzymeEntryMapper()

EnzymeEntryMapper(EnzymeReactionMapper enzymeReactionMapper)

Constructors
Constructor and Description
`EnzymeEntryMapper()`
`EnzymeEntryMapper(EnzymeReactionMapper enzymeReactionMapper)`

Method Summary

Methods
Modifier and Type	Method and Description
`boolean`	`cloneExists(Long id, Connection con)` Checks if a clone of an enzyme already exists.
`void`	`close()`
`static boolean`	`ecExists(uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber ec, Connection con)` Checks whether a given EC number already exists in the database.
`List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry>`	`exportAllEntries(Connection con)` Exports every piece of data for publicly available entries.
`List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry>`	`exportApprovedSibEntries(Connection con)` Tries to export all approved entries containing only ENZYME relevant information.
`protected void`	`finalize()`
`List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry>`	`findAll(Connection con)` Tries to find all public entries but loads the entries only with minimum information.
`List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry>`	`findAllByEc(int ec1, int ec2, int ec3, int ec4, Boolean preliminary, Connection con)`
`List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry>`	`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<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry>`	`findAllSubSubclassEntriesByEc(int ec1, int ec2, int ec3, Connection con)`
`uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry`	`findByEc(int ec1, int ec2, int ec3, int ec4, uk.ac.ebi.intenz.domain.constants.Status status, Connection con)` Tries to find entry information about an enzyme.
`uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry`	`findByEc(String ecString, uk.ac.ebi.intenz.domain.constants.Status status, Connection con)` Finds an enzyme by EC number (as String) and status.
`uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry`	`findById(long id, Connection con)` Loads a complete version of the enzyme with the given ID.
`uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry`	`findById(Long id, Connection con, boolean ghost)` Tries to find entry information about an enzyme.
`List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry>`	`findByStatus(Connection con, uk.ac.ebi.intenz.domain.constants.Status status)` Retrieves the list of enzymes with a given status.
`uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber`	`findEC(String id, Connection con)` Returns the EC number of the given enzyme ID.
`List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry>`	`findFullProposedList(Connection con)` Tries to find all proposed entries with all information.
`List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry>`	`findFullSuggestedList(Connection con)` Tries to find all suggested entries with all information.
`uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry`	`findGhostById(int id, Connection con)` Loads a ghost version of the enzyme with the given ID.
`String`	`findHistoryLine(Long id, Connection con)` Returns the history line of the enzyme with the given ID.
`Long`	`findIDInMappingTable(String ec, uk.ac.ebi.intenz.domain.constants.Status status, Connection con)`
`List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry>`	`findList(String ec1, String ec2, String ec3, Connection con)` Tries to find all entries requested but loads the entries only with minimum information.
`Long`	`findNextEnzymeId(Connection con)` Returns the next available enzyme ID.
`String`	`findNote(Long id, Connection con)` Returns the note of the enzyme with the given ID.
`List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry>`	`findPreliminaryEcsList(Connection con)` Gets the list of preliminary EC numbers issued by UniProt.
`List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry>`	`findProposedList(Connection con)` Tries to find all proposed entries but loads the entries only with minimum information.
`uk.ac.ebi.intenz.domain.stats.EnzymeStatistics`	`findStats(Connection con)`
`List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry>`	`findSuggestedList(Connection con)` Tries to find all suggested entries but loads the entries only with minimum information.
`void`	`insert(Long enzymeId, uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber ec, uk.ac.ebi.intenz.domain.constants.Status status, uk.ac.ebi.intenz.domain.constants.EnzymeSourceConstant source, String note, String historyLine, boolean isActive, Connection con)` Inserts the core data of a new enzyme entry.
`void`	`update(Long enzymeId, uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber ec, uk.ac.ebi.intenz.domain.constants.Status status, uk.ac.ebi.intenz.domain.constants.EnzymeSourceConstant source, String note, String historyLine, boolean active, Connection con)` Updates the core data of an enzyme stored in the table `ENZYMES`.
`void`	`updateEc(Long enzymeId, uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber newEc, Connection con)` Updates the EC of the given enzyme.
`void`	`updateHistoryLine(Long enzymeId, String historyLine, Connection con)` Updates the history line of the given enzyme.
`void`	`updateNote(Long enzymeId, String note, Connection con)` Updates the notes of the given enzyme.
`void`	`updateStatus(Long enzymeId, uk.ac.ebi.intenz.domain.constants.Status status, Connection con)` Updates the status of the given enzyme.

Methods inherited from class java.lang.Object
clone, equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

EnzymeEntryMapper
```
public EnzymeEntryMapper()
```

EnzymeEntryMapper

public EnzymeEntryMapper(EnzymeReactionMapper enzymeReactionMapper)

Method Detail

finalize

protected void finalize()
                 throws Throwable

Overrides:: finalize in class Object
Throws:: Throwable

close
```
public void close()
```

findByEc

public uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry findByEc(int ec1,
                                                  int ec2,
                                                  int ec3,
                                                  int ec4,
                                                  uk.ac.ebi.intenz.domain.constants.Status status,
                                                  Connection con)
                                                    throws SQLException,
                                                           uk.ac.ebi.intenz.domain.exceptions.DomainException,
                                                           uk.ac.ebi.rhea.mapper.MapperException

Tries to find entry information about an enzyme.

Parameters:: ec1 - Number of class to search for.; ec2 - Number of subclass to search for.; ec3 - Number of sub-subclass to search for.; ec4 - Number of entry to search for.; status - the status of the searched enzyme. If null, it defaults to Status.APPROVED.; con - The logical connection.
Returns:: an EnzymeEntry instance or null if nothing has been found.
Throws:: SQLException; uk.ac.ebi.intenz.domain.exceptions.DomainException; uk.ac.ebi.rhea.mapper.MapperException - in case of problem retrieving reaction/cofactor info.

findByEc

public uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry findByEc(String ecString,
                                                  uk.ac.ebi.intenz.domain.constants.Status status,
                                                  Connection con)
                                                    throws NumberFormatException,
                                                           SQLException,
                                                           uk.ac.ebi.intenz.domain.exceptions.DomainException,
                                                           uk.ac.ebi.rhea.mapper.MapperException

Finds an enzyme by EC number (as String) and status.

Parameters:: ecString - the EC number.; status - the enzyme status.; con - a database connection.
Returns:: an enzyme entry, or null if not found.
Throws:: NumberFormatException; SQLException; uk.ac.ebi.intenz.domain.exceptions.DomainException; uk.ac.ebi.rhea.mapper.MapperException

findAllByEc

public List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry> findAllByEc(int ec1,
                                                           int ec2,
                                                           int ec3,
                                                           int ec4,
                                                           Boolean preliminary,
                                                           Connection con)
                                                             throws SQLException,
                                                                    uk.ac.ebi.intenz.domain.exceptions.DomainException

Throws:: SQLException; uk.ac.ebi.intenz.domain.exceptions.DomainException

findAllByEc

public List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry> findAllByEc(int ec1,
                                                           int ec2,
                                                           int ec3,
                                                           int ec4,
                                                           Connection con)
                                                             throws SQLException,
                                                                    uk.ac.ebi.intenz.domain.exceptions.DomainException

Tries to find entry information about all enzymes specified by the given EC.

Parameters:: ec1 - Number of class to search for.; ec2 - Number of subclass to search for.; ec3 - Number of sub-subclass to search for.; ec4 - Number of entry to search for.; con - The logical connection.
Returns:: an EnzymeEntry instance or null if nothing has been found.
Throws:: NullPointerException - if parameter con is null.; SQLException - if a database error occurs.; uk.ac.ebi.intenz.domain.exceptions.DomainException - if any error related to domain information occurs.

findAllSubSubclassEntriesByEc

public List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry> findAllSubSubclassEntriesByEc(int ec1,
                                                                             int ec2,
                                                                             int ec3,
                                                                             Connection con)
                                                                               throws SQLException,
                                                                                      uk.ac.ebi.intenz.domain.exceptions.DomainException

Throws:: SQLException; uk.ac.ebi.intenz.domain.exceptions.DomainException

findById

public uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry findById(Long id,
                                                  Connection con,
                                                  boolean ghost)
                                                    throws SQLException,
                                                           uk.ac.ebi.intenz.domain.exceptions.DomainException,
                                                           uk.ac.ebi.rhea.mapper.MapperException

Tries to find entry information about an enzyme.

Parameters:: id - The enzyme ID.; con - The logical connection.; ghost - return a ghost (minimal info)?
Returns:: an EnzymeEntry instance or null if nothing has been found.
Throws:: SQLException; uk.ac.ebi.intenz.domain.exceptions.DomainException; uk.ac.ebi.rhea.mapper.MapperException - in case of problem retrieving reaction/cofactor info for non-ghosts.

findById

public uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry findById(long id,
                                                  Connection con)
                                                    throws SQLException,
                                                           uk.ac.ebi.intenz.domain.exceptions.DomainException,
                                                           uk.ac.ebi.rhea.mapper.MapperException

Loads a complete version of the enzyme with the given ID.

Parameters:: id -; con -
Returns:: an EnzymeEntry instance or null if nothing has been found.
Throws:: SQLException; uk.ac.ebi.intenz.domain.exceptions.DomainException; uk.ac.ebi.rhea.mapper.MapperException - in case of problem retrieving reaction/cofactor info.

findGhostById

public uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry findGhostById(int id,
                                                       Connection con)
                                                         throws SQLException,
                                                                uk.ac.ebi.intenz.domain.exceptions.DomainException

Loads a ghost version of the enzyme with the given ID.

Parameters:: id - The enzyme ID.; con - The logical connection.
Returns:: an EnzymeEntry instance or null if nothing has been found.
Throws:: SQLException; uk.ac.ebi.intenz.domain.exceptions.DomainException

findIDInMappingTable

public Long findIDInMappingTable(String ec,
                        uk.ac.ebi.intenz.domain.constants.Status status,
                        Connection con)
                          throws SQLException

Throws:: SQLException

findAll
```
public List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry> findAll(Connection con)
                                                         throws SQLException,
                                                                uk.ac.ebi.intenz.domain.exceptions.DomainException
```
Tries to find all public entries but loads the entries only with minimum information.

Parameters:
con - The logical connection.

Returns:
a List of EnzymeEntry instances or null if nothing has been found.

Throws:

SQLException

uk.ac.ebi.intenz.domain.exceptions.DomainException

findList

public List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry> findList(String ec1,
                                                        String ec2,
                                                        String ec3,
                                                        Connection con)
                                                          throws SQLException,
                                                                 uk.ac.ebi.intenz.domain.exceptions.DomainException

Tries to find all entries requested but loads the entries only with minimum information.

Parameters:: ec1 - Number of class to search for.; ec2 - Number of subclass to search for.; ec3 - Number of sub-subclass to search for.; con - The logical connection.
Returns:: a List of EnzymeEntry instances or null if nothing has been found.
Throws:: SQLException; uk.ac.ebi.intenz.domain.exceptions.DomainException

findByStatus

public List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry> findByStatus(Connection con,
                                                            uk.ac.ebi.intenz.domain.constants.Status status)
                                                              throws SQLException,
                                                                     uk.ac.ebi.intenz.domain.exceptions.DomainException

Retrieves the list of enzymes with a given status.

Parameters:: con -; status -
Returns:: the list of enzymes with the given status.
Throws:: SQLException; uk.ac.ebi.intenz.domain.exceptions.DomainException

findProposedList
```
public List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry> findProposedList(Connection con)
                                                                  throws SQLException,
                                                                         uk.ac.ebi.intenz.domain.exceptions.DomainException
```
Tries to find all proposed entries but loads the entries only with minimum information.

Parameters:
con - The logical connection.

Returns:
a List of EnzymeEntry instances.

Throws:

SQLException - if a database error occurs.

uk.ac.ebi.intenz.domain.exceptions.DomainException - if a domain related error occurs.

findSuggestedList

public List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry> findSuggestedList(Connection con)
                                                                   throws SQLException,
                                                                          uk.ac.ebi.intenz.domain.exceptions.DomainException

Tries to find all suggested entries but loads the entries only with minimum information.

Parameters:: con - The logical connection.
Returns:: a Vector of EnzymeEntry instances or null if nothing has been found.
Throws:: SQLException; uk.ac.ebi.intenz.domain.exceptions.DomainException

findPreliminaryEcsList

public List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry> findPreliminaryEcsList(Connection con)
                                                                        throws SQLException,
                                                                               uk.ac.ebi.intenz.domain.exceptions.DomainException

Gets the list of preliminary EC numbers issued by UniProt.

Parameters:: con -
Returns:: A list of preliminary EC numbers issued by UniProt.
Throws:: SQLException; uk.ac.ebi.intenz.domain.exceptions.DomainException

exportAllEntries

public List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry> exportAllEntries(Connection con)
                                                                  throws SQLException,
                                                                         uk.ac.ebi.intenz.domain.exceptions.DomainException,
                                                                         uk.ac.ebi.rhea.mapper.MapperException

Exports every piece of data for publicly available entries.

Parameters:: con -
Returns:: A List of EnzymeEntrys
Throws:: SQLException; uk.ac.ebi.intenz.domain.exceptions.DomainException; uk.ac.ebi.rhea.mapper.MapperException - in case of problem retrieving reaction/cofactor info.

exportApprovedSibEntries

public List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry> exportApprovedSibEntries(Connection con)
                                                                          throws SQLException,
                                                                                 uk.ac.ebi.intenz.domain.exceptions.DomainException,
                                                                                 uk.ac.ebi.rhea.mapper.MapperException

Tries to export all approved entries containing only ENZYME relevant information.

Affected table rows will be locked.

Parameters:: con - The logical connection.
Returns:: an ArrayList of EnzymeEntry instances or null if nothing has been found.
Throws:: SQLException; uk.ac.ebi.intenz.domain.exceptions.DomainException; uk.ac.ebi.rhea.mapper.MapperException - in case of problem retrieving reaction/cofactor info.

findFullProposedList

public List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry> findFullProposedList(Connection con)
                                                                      throws SQLException,
                                                                             uk.ac.ebi.intenz.domain.exceptions.DomainException,
                                                                             uk.ac.ebi.rhea.mapper.MapperException

Tries to find all proposed entries with all information.

This feature is just needed to export a list of all proposed entries.

Parameters:: con - The logical connection.
Returns:: a Vector of EnzymeEntry instances or null if nothing has been found.
Throws:: SQLException; uk.ac.ebi.intenz.domain.exceptions.DomainException; uk.ac.ebi.rhea.mapper.MapperException - in case of problem retrieving reaction/cofactor info.

findFullSuggestedList

public List<uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry> findFullSuggestedList(Connection con)
                                                                       throws SQLException,
                                                                              uk.ac.ebi.intenz.domain.exceptions.DomainException,
                                                                              uk.ac.ebi.rhea.mapper.MapperException

Tries to find all suggested entries with all information.

This feature is just needed to export a list of all suggested entries.

Parameters:: con - The logical connection.
Returns:: a Vector of EnzymeEntry instances or null if nothing has been found.
Throws:: SQLException; uk.ac.ebi.intenz.domain.exceptions.DomainException; uk.ac.ebi.rhea.mapper.MapperException - in case of problem retrieving reaction/cofactor info.

findEC

public uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber findEC(String id,
                                                           Connection con)
                                                             throws SQLException,
                                                                    uk.ac.ebi.intenz.domain.exceptions.DomainException

Returns the EC number of the given enzyme ID.

Parameters:: id - The enzyme ID.; con - The logical connection.
Returns:: The EC, if found, otherwise null.
Throws:: SQLException; uk.ac.ebi.intenz.domain.exceptions.DomainException

ecExists
```
public static boolean ecExists(uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber ec,
               Connection con)
                        throws SQLException
```
Checks whether a given EC number already exists in the database.

Parameters:
ec - The EC number to be checked.
con - The database connection.

Returns:
true if the given EC number exists in the database.

Throws:

SQLException - if a database error occurs.

NullPointerException - if any of the parameters is null

findHistoryLine
```
public String findHistoryLine(Long id,
                     Connection con)
                       throws SQLException
```
Returns the history line of the enzyme with the given ID.

Parameters:
id - The enzyme ID.
con - The logical connection.

Returns:
The history line, if found, otherwise null.

Throws:

SQLException

findNote
```
public String findNote(Long id,
              Connection con)
                throws SQLException
```
Returns the note of the enzyme with the given ID.

Parameters:
id - The enzyme ID.
con - The logical connection.

Returns:
The note, if found, otherwise null.

Throws:

SQLException

findStats

public uk.ac.ebi.intenz.domain.stats.EnzymeStatistics findStats(Connection con)
                                                         throws SQLException

Parameters:: con - The logical connection.
Returns:
Throws:: SQLException

insert

public void insert(Long enzymeId,
          uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber ec,
          uk.ac.ebi.intenz.domain.constants.Status status,
          uk.ac.ebi.intenz.domain.constants.EnzymeSourceConstant source,
          String note,
          String historyLine,
          boolean isActive,
          Connection con)
            throws SQLException

Inserts the core data of a new enzyme entry.

A new enzyme ID must already be available. It can be obtained via findNextEnzymeId(java.sql.Connection)

Parameters:: enzymeId -; ec -; status -; source -; isActive -; note -; historyLine -; con -
Throws:: SQLException

update
```
public void update(Long enzymeId,
          uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber ec,
          uk.ac.ebi.intenz.domain.constants.Status status,
          uk.ac.ebi.intenz.domain.constants.EnzymeSourceConstant source,
          String note,
          String historyLine,
          boolean active,
          Connection con)
            throws SQLException
```
Updates the core data of an enzyme stored in the table ENZYMES.
NOTE: The ACTIVE column of this table is cannot be updated using this method since this column is managed by the event package.

Parameters:
enzymeId - The enzyme's ID.
ec - The EC number.
status - The current status of the enzyme.
source - The source of this enzyme.
note - A note the curator might have added.
historyLine - The enzyme's history line.
active - The enzyme's active status.
con - A database connection.

Throws:

SQLException

updateEc

public void updateEc(Long enzymeId,
            uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber newEc,
            Connection con)
              throws SQLException

Updates the EC of the given enzyme.

Parameters:: enzymeId - The enzyme's ID.; newEc - The new EC.; con - The logical connection.
Throws:: SQLException

updateNote

public void updateNote(Long enzymeId,
              String note,
              Connection con)
                throws SQLException

Updates the notes of the given enzyme.

Parameters:: enzymeId - The enzyme's ID.; note - The note.; con - The logical connection.
Throws:: SQLException

updateStatus

public void updateStatus(Long enzymeId,
                uk.ac.ebi.intenz.domain.constants.Status status,
                Connection con)
                  throws SQLException

Updates the status of the given enzyme.

Parameters:: enzymeId - The enzyme's ID.; status - The status.; con - The logical connection.
Throws:: SQLException

updateHistoryLine

public void updateHistoryLine(Long enzymeId,
                     String historyLine,
                     Connection con)
                       throws SQLException

Updates the history line of the given enzyme.

Parameters:: enzymeId - The enzyme's ID.; historyLine - The new history line.; con - The logical connection.
Throws:: SQLException

cloneExists
```
public boolean cloneExists(Long id,
                  Connection con)
                    throws SQLException
```
Checks if a clone of an enzyme already exists.

Parameters:
id - The enzyme ID.
con - The logical connection.

Returns:
true, if a clone already exists.

Throws:

SQLException

findNextEnzymeId
```
public Long findNextEnzymeId(Connection con)
                      throws SQLException
```
Returns the next available enzyme ID.

Parameters:
con - The connection.

Returns:
The next enzyme ID.

Throws:

SQLException

Class EnzymeEntryMapper

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

EnzymeEntryMapper

EnzymeEntryMapper

Method Detail

finalize

close

findByEc

findByEc

findAllByEc

findAllByEc

findAllSubSubclassEntriesByEc

findById

findById

findGhostById

findIDInMappingTable

findAll

findList

findByStatus

findProposedList

findSuggestedList

findPreliminaryEcsList

exportAllEntries

exportApprovedSibEntries

findFullProposedList

findFullSuggestedList

findEC

ecExists

findHistoryLine

findNote

findStats

insert

update

updateEc

updateNote

updateStatus

updateHistoryLine

cloneExists

findNextEnzymeId