uk.ac.ebi.intenz.webapp.controller
Class SearchECCommand

java.lang.Object
  uk.ac.ebi.intenz.webapp.controller.Command
      uk.ac.ebi.intenz.webapp.controller.DatabaseCommand
          uk.ac.ebi.intenz.webapp.controller.SearchECCommand

public class SearchECCommand
extends DatabaseCommand

This command processes all inquiries about EC numbers.

Version:

0.9 - 21-July-2003

Author:

Michael Darsow

Nested Class Summary

protected static class

SearchECCommand.EnzymeEntryCacheKey

Field Summary

static org.apache.log4j.Logger

LOGGER

Fields inherited from class uk.ac.ebi.intenz.webapp.controller.DatabaseCommand

con, context, databaseErrorMessage, enzymeEntryMapper, request, response

Constructor Summary

SearchECCommand()

Method Summary

protected int	analyseECType(String ec) Gets the type of the EC number.
protected EnzymeClass	findEnzymeClass(EnzymeCommissionNumber ec) Calls the according find() method and handles empty results and SQL exceptions.
protected EnzymeEntry	findEnzymeEntry(EnzymeCommissionNumber ec, Status status) Calls the according find() method and handles empty results and SQL exceptions.
protected EnzymeSubclass	findEnzymeSubclass(EnzymeCommissionNumber ec) Calls the according find() method and handles empty results and SQL exceptions.
protected EnzymeSubSubclass	findEnzymeSubSubclass(EnzymeCommissionNumber ec) Calls the according find() method and handles empty results and SQL exceptions.
void	process() This is unique to each command and has to be implemented by the inherting subclass.

Methods inherited from class uk.ac.ebi.intenz.webapp.controller.DatabaseCommand

close, closeConnection, finalize, forward, init

Methods inherited from class java.lang.Object

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

Field Detail

LOGGER

public static final org.apache.log4j.Logger LOGGER

Constructor Detail

SearchECCommand

public SearchECCommand()

Method Detail

process

public void process()
             throws javax.servlet.ServletException,
                    IOException

Description copied from class: Command

This is unique to each command and has to be implemented by the inherting subclass.

Specified by:

process in class Command

Throws:

javax.servlet.ServletException

IOException

uk.ac.ebi.rhea.mapper.MapperException

findEnzymeClass

protected EnzymeClass findEnzymeClass(EnzymeCommissionNumber ec)

Calls the according find() method and handles empty results and SQL exceptions.

Parameters:

ec - Number of enzyme class to search for.

Returns:

An EnzymeClass instance or null.

findEnzymeSubclass

protected EnzymeSubclass findEnzymeSubclass(EnzymeCommissionNumber ec)

Calls the according find() method and handles empty results and SQL exceptions.

Parameters:

ec - Number of enzyme class to search for.

Returns:

An EnzymeClass instance or null.

Throws:

NullPointerException - if any of the parameters is null.

findEnzymeSubSubclass

protected EnzymeSubSubclass findEnzymeSubSubclass(EnzymeCommissionNumber ec)

Calls the according find() method and handles empty results and SQL exceptions.

Parameters:

ec - Number of enzyme class to search for.

Returns:

An EnzymeClass instance or null.

Throws:

NullPointerException - if any of the parameters is null.

analyseECType

protected int analyseECType(String ec)

Gets the type of the EC number.

The following types are possible (in [] the value returned by this method):

• Class EC (e.g. EC 1) [1]
• Subclass EC (e.g. EC 1.1) [2]
• Sub-subclass EC (e.g. EC 1.1.1) [3]
• Entry EC (e.g. EC 1.1.1.1) [4]

Parameters:

ec - The EC string.

Returns:

Integer code for the type.

findEnzymeEntry

protected EnzymeEntry findEnzymeEntry(EnzymeCommissionNumber ec,
                                      Status status)

Calls the according find() method and handles empty results and SQL exceptions.

Parameters:

ec - EC number of enzyme to search for.

status - the enzyme status.

Returns:

An EnzymeEntry instance or null.

Throws:

NullPointerException - if any of the parameters is null.