A B C D E F G H I L N P Q R S T U

A

analyseECType(String) - Method in class uk.ac.ebi.intenz.webapp.controller.SearchECCommand

Gets the type of the EC number.

B

BrowseResultCommand - Class in uk.ac.ebi.intenz.webapp.controller

This class ...

BrowseResultCommand() - Constructor for class uk.ac.ebi.intenz.webapp.controller.BrowseResultCommand

C

ChangeCharacterRepresentationCommand - Class in uk.ac.ebi.intenz.webapp.controller

This class provides methods to switch between a pure Unicode based special character representation and a browser dependent non-pure Unicode encoding.

ChangeCharacterRepresentationCommand() - Constructor for class uk.ac.ebi.intenz.webapp.controller.ChangeCharacterRepresentationCommand

cleanInternalLinks(String, boolean) - Static method in class uk.ac.ebi.intenz.webapp.IntEnzUtilities

Deprecated.

use IntEnzUtilities.cleanLinks(String) and IntEnzUtilities.firstLetterToUppercase(String)

cleanLinks(String) - Static method in class uk.ac.ebi.intenz.webapp.IntEnzUtilities

close() - Method in class uk.ac.ebi.intenz.webapp.controller.DatabaseCommand

closeConnection() - Method in class uk.ac.ebi.intenz.webapp.controller.DatabaseCommand

Closes the database connection or forwards to an error page if any error occured.

Command - Class in uk.ac.ebi.intenz.webapp.controller

This is the abstract base class of all commands.

Command() - Constructor for class uk.ac.ebi.intenz.webapp.controller.Command

con - Variable in class uk.ac.ebi.intenz.webapp.controller.DatabaseCommand

config - Variable in class uk.ac.ebi.intenz.webapp.controller.Command

context - Variable in class uk.ac.ebi.intenz.webapp.controller.DatabaseCommand

context - Variable in class uk.ac.ebi.intenz.webapp.controller.NonDatabaseCommand

D

DatabaseCommand - Class in uk.ac.ebi.intenz.webapp.controller

A database command always relies on a connection to the database.

DatabaseCommand() - Constructor for class uk.ac.ebi.intenz.webapp.controller.DatabaseCommand

databaseErrorMessage - Variable in class uk.ac.ebi.intenz.webapp.controller.DatabaseCommand

DatabaseException - Exception in uk.ac.ebi.intenz.webapp.exceptions

This exception is a wrapper around the SQLException.

DatabaseException(String, SQLException) - Constructor for exception uk.ac.ebi.intenz.webapp.exceptions.DatabaseException

Initialise this exception with a user friendly message and the SQLException object.

DatabaseException(String) - Constructor for exception uk.ac.ebi.intenz.webapp.exceptions.DatabaseException

DatabaseException(SQLException) - Constructor for exception uk.ac.ebi.intenz.webapp.exceptions.DatabaseException

Uses a standard message.

descriptionToHTML(EnzymeClass, SpecialCharacters, EncodingType) - Static method in class uk.ac.ebi.intenz.webapp.helper.EnzymeClassHelper

descriptionToHTML(EnzymeSubclass, SpecialCharacters, EncodingType) - Static method in class uk.ac.ebi.intenz.webapp.helper.EnzymeSubclassHelper

descriptionToHTML(EnzymeSubSubclass, SpecialCharacters, EncodingType) - Static method in class uk.ac.ebi.intenz.webapp.helper.EnzymeSubSubclassHelper

destroy() - Method in class uk.ac.ebi.intenz.webapp.controller.IntEnzHandlerServlet

doGet(HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intenz.webapp.controller.IntEnzContactServlet

doPost(HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intenz.webapp.controller.IntEnzContactServlet

E

EnzymeClassHelper - Class in uk.ac.ebi.intenz.webapp.helper

This class ...

EnzymeEntryHelper - Class in uk.ac.ebi.intenz.webapp.helper

Deprecated.

PLEASE PLEASE TAKE ALL THIS ******* HTML OUT OF HERE!

enzymeEntryMapper - Variable in class uk.ac.ebi.intenz.webapp.controller.DatabaseCommand

EnzymeLinkHelper - Class in uk.ac.ebi.intenz.webapp.helper

This class ...

EnzymeReactionHelper - Class in uk.ac.ebi.intenz.webapp.helper

Deprecated.

to hell with this and EnzymeEntryHelper

EnzymeSubclassHelper - Class in uk.ac.ebi.intenz.webapp.helper

This class ...

EnzymeSubSubclassHelper - Class in uk.ac.ebi.intenz.webapp.helper

This class ...

equals(Object) - Method in class uk.ac.ebi.intenz.webapp.controller.SearchECCommand.EnzymeEntryCacheKey

F

finalize() - Method in class uk.ac.ebi.intenz.webapp.controller.DatabaseCommand

findEnzymeClass(EnzymeCommissionNumber) - Method in class uk.ac.ebi.intenz.webapp.controller.SearchECCommand

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

findEnzymeEntry(EnzymeCommissionNumber, Status) - Method in class uk.ac.ebi.intenz.webapp.controller.SearchECCommand

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

findEnzymeEntry(Long) - Method in class uk.ac.ebi.intenz.webapp.controller.SearchIDCommand

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

findEnzymeSubclass(EnzymeCommissionNumber) - Method in class uk.ac.ebi.intenz.webapp.controller.SearchECCommand

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

findEnzymeSubSubclass(EnzymeCommissionNumber) - Method in class uk.ac.ebi.intenz.webapp.controller.SearchECCommand

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

firstLetterToUppercase(String) - Static method in class uk.ac.ebi.intenz.webapp.IntEnzUtilities

Deprecated.

use JSTL's fn:toUpperCase and fn:substring instead

forward(String) - Method in class uk.ac.ebi.intenz.webapp.controller.DatabaseCommand

Forwards to the given target.

forward(String) - Method in class uk.ac.ebi.intenz.webapp.controller.NonDatabaseCommand

Forwards to the given target.

G

getCofactorObjectLinks(Object, SpecialCharacters, EncodingType, boolean) - Static method in class uk.ac.ebi.intenz.webapp.helper.EnzymeEntryHelper

Deprecated.

getCofactorSetLinks(OperatorSet, SpecialCharacters, EncodingType, boolean) - Static method in class uk.ac.ebi.intenz.webapp.helper.EnzymeEntryHelper

Deprecated.

getCommonName() - Method in class uk.ac.ebi.intenz.webapp.controller.SearchCommand.Result

getCompoundLink(Compound, SpecialCharacters, EncodingType) - Static method in class uk.ac.ebi.intenz.webapp.helper.EnzymeEntryHelper

Deprecated.

getEc() - Method in class uk.ac.ebi.intenz.webapp.controller.SearchCommand.Result

getId() - Method in class uk.ac.ebi.intenz.webapp.controller.SearchCommand.Result

getIntEnzCofactor(Set<Object>, SpecialCharacters, EncodingType) - Static method in class uk.ac.ebi.intenz.webapp.helper.EnzymeEntryHelper

Deprecated.

getLinkedFlatFile(String) - Static method in class uk.ac.ebi.intenz.webapp.IntEnzUtilities

Create hyperlinks for all cross-references (xrefs) in a flat file.

getSibView(EnzymeEntry, SpecialCharacters, EncodingType) - Static method in class uk.ac.ebi.intenz.webapp.helper.EnzymeEntryHelper

Deprecated.

getSqlExceptionMessage() - Method in exception uk.ac.ebi.intenz.webapp.exceptions.DatabaseException

Return the details about this exception.

getStatus() - Method in class uk.ac.ebi.intenz.webapp.controller.SearchCommand.Result

H

hashCode() - Method in class uk.ac.ebi.intenz.webapp.controller.SearchECCommand.EnzymeEntryCacheKey

I

init(ServletContext, HttpServletRequest, HttpServletResponse, Connection) - Method in class uk.ac.ebi.intenz.webapp.controller.DatabaseCommand

Initialises the attributes which will be used to extract information for the command execution.

init() - Method in class uk.ac.ebi.intenz.webapp.controller.IntEnzContactServlet

init(ServletConfig) - Method in class uk.ac.ebi.intenz.webapp.controller.IntEnzHandlerServlet

init(ServletContext, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intenz.webapp.controller.NonDatabaseCommand

Initialises the attributes which will be used to extract information for the command execution.

IntEnzContactServlet - Class in uk.ac.ebi.intenz.webapp.controller

IntEnzContactServlet() - Constructor for class uk.ac.ebi.intenz.webapp.controller.IntEnzContactServlet

IntEnzHandlerServlet - Class in uk.ac.ebi.intenz.webapp.controller

This servlet acts as a handler of the front controller.

IntEnzHandlerServlet() - Constructor for class uk.ac.ebi.intenz.webapp.controller.IntEnzHandlerServlet

IntEnzMessenger - Class in uk.ac.ebi.intenz.webapp.utilities

This class ...

IntEnzMessenger() - Constructor for class uk.ac.ebi.intenz.webapp.utilities.IntEnzMessenger

IntEnzUtilities - Class in uk.ac.ebi.intenz.webapp

Provides utility classes, which are used throughout the whole project.

IntEnzUtilities() - Constructor for class uk.ac.ebi.intenz.webapp.IntEnzUtilities

InvalidECException - Exception in uk.ac.ebi.intenz.webapp.exceptions

This exception is thrown when a EC number is not valid (e.g.

InvalidECException() - Constructor for exception uk.ac.ebi.intenz.webapp.exceptions.InvalidECException

InvalidECException(String) - Constructor for exception uk.ac.ebi.intenz.webapp.exceptions.InvalidECException

InvalidLinkNameException - Exception in uk.ac.ebi.intenz.webapp.exceptions

This exception is thrown when a link was requested but the given name is not supported.

InvalidLinkNameException() - Constructor for exception uk.ac.ebi.intenz.webapp.exceptions.InvalidLinkNameException

InvalidLinkNameException(String) - Constructor for exception uk.ac.ebi.intenz.webapp.exceptions.InvalidLinkNameException

isActive() - Method in class uk.ac.ebi.intenz.webapp.controller.SearchCommand.Result

L

link2carb(String) - Static method in class uk.ac.ebi.intenz.webapp.IntEnzUtilities

Generates links to IUPAC carbohydrate nomenclature pages wherever it finds a 2-Carb- prefixed word.

linkEcNumber(String, boolean) - Static method in class uk.ac.ebi.intenz.webapp.IntEnzUtilities

Deprecated.

use IntEnzUtilities.linkEcNumbers(String) instead and - if needed - IntEnzUtilities.firstLetterToUppercase(String)

linkEcNumbers(String) - Static method in class uk.ac.ebi.intenz.webapp.IntEnzUtilities

linkMerops(String) - Static method in class uk.ac.ebi.intenz.webapp.IntEnzUtilities

Generates a hypertext link to MEROPS.

LOGGER - Static variable in class uk.ac.ebi.intenz.webapp.controller.IntEnzContactServlet

LOGGER - Static variable in class uk.ac.ebi.intenz.webapp.controller.SearchCommand

LOGGER - Static variable in class uk.ac.ebi.intenz.webapp.controller.SearchECCommand

LOGGER - Static variable in class uk.ac.ebi.intenz.webapp.controller.SearchIDCommand

LOGGER - Static variable in class uk.ac.ebi.intenz.webapp.controller.SearchPreliminaryCommand

LOGGER - Static variable in class uk.ac.ebi.intenz.webapp.controller.SearchProposedCommand

LOGGER - Static variable in class uk.ac.ebi.intenz.webapp.utilities.IntEnzMessenger

N

NonDatabaseCommand - Class in uk.ac.ebi.intenz.webapp.controller

All commands of this type do not need a connection to the database.

NonDatabaseCommand() - Constructor for class uk.ac.ebi.intenz.webapp.controller.NonDatabaseCommand

P

process() - Method in class uk.ac.ebi.intenz.webapp.controller.BrowseResultCommand

Provides functionality to browse through search results.

process() - Method in class uk.ac.ebi.intenz.webapp.controller.ChangeCharacterRepresentationCommand

Depending on the given parameter this method switches between a Unicode representation for some very special characters (scissile, activated, ...) and a browser-dependent encoding.

process() - Method in class uk.ac.ebi.intenz.webapp.controller.Command

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

process() - Method in class uk.ac.ebi.intenz.webapp.controller.SearchCommand

Processes the full text query.

process() - Method in class uk.ac.ebi.intenz.webapp.controller.SearchECCommand

process() - Method in class uk.ac.ebi.intenz.webapp.controller.SearchIDCommand

TBD

process() - Method in class uk.ac.ebi.intenz.webapp.controller.SearchPreliminaryCommand

process() - Method in class uk.ac.ebi.intenz.webapp.controller.SearchProposedCommand

TBD

process() - Method in class uk.ac.ebi.intenz.webapp.controller.UnknownDatabaseCommand

Just forwards to a notification page.

propertyChange(PropertyChangeEvent) - Method in class uk.ac.ebi.intenz.webapp.controller.IntEnzHandlerServlet

Q

QueryException - Exception in uk.ac.ebi.intenz.webapp.exceptions

If a query is invalid this exception will be thrown.

QueryException() - Constructor for exception uk.ac.ebi.intenz.webapp.exceptions.QueryException

QueryException(String) - Constructor for exception uk.ac.ebi.intenz.webapp.exceptions.QueryException

R

renderIubmbLinks(SortedSet, String) - Static method in class uk.ac.ebi.intenz.webapp.helper.EnzymeLinkHelper

renderLinks(SortedSet, String) - Static method in class uk.ac.ebi.intenz.webapp.helper.EnzymeLinkHelper

renderUniprotLinks(SortedSet, String) - Static method in class uk.ac.ebi.intenz.webapp.helper.EnzymeLinkHelper

request - Variable in class uk.ac.ebi.intenz.webapp.controller.DatabaseCommand

request - Variable in class uk.ac.ebi.intenz.webapp.controller.NonDatabaseCommand

response - Variable in class uk.ac.ebi.intenz.webapp.controller.DatabaseCommand

response - Variable in class uk.ac.ebi.intenz.webapp.controller.NonDatabaseCommand

S

SearchCommand - Class in uk.ac.ebi.intenz.webapp.controller

This class processes all full text queries.

SearchCommand() - Constructor for class uk.ac.ebi.intenz.webapp.controller.SearchCommand

SearchCommand.Result - Class in uk.ac.ebi.intenz.webapp.controller

SearchCommand.Result() - Constructor for class uk.ac.ebi.intenz.webapp.controller.SearchCommand.Result

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

This command processes all inquiries about EC numbers.

SearchECCommand() - Constructor for class uk.ac.ebi.intenz.webapp.controller.SearchECCommand

SearchECCommand.EnzymeEntryCacheKey - Class in uk.ac.ebi.intenz.webapp.controller

SearchECCommand.EnzymeEntryCacheKey(EnzymeCommissionNumber, Status) - Constructor for class uk.ac.ebi.intenz.webapp.controller.SearchECCommand.EnzymeEntryCacheKey

SearchIDCommand - Class in uk.ac.ebi.intenz.webapp.controller

This command handles enzyme ID requests.

SearchIDCommand() - Constructor for class uk.ac.ebi.intenz.webapp.controller.SearchIDCommand

SearchPreliminaryCommand - Class in uk.ac.ebi.intenz.webapp.controller

SearchPreliminaryCommand() - Constructor for class uk.ac.ebi.intenz.webapp.controller.SearchPreliminaryCommand

SearchProposedCommand - Class in uk.ac.ebi.intenz.webapp.controller

This command handles requests about proposed entries.

SearchProposedCommand() - Constructor for class uk.ac.ebi.intenz.webapp.controller.SearchProposedCommand

sendError(String, String, String) - Static method in class uk.ac.ebi.intenz.webapp.utilities.IntEnzMessenger

service(HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intenz.webapp.controller.IntEnzHandlerServlet

service(HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intenz.webapp.controller.SitemapServlet

setConfig(IntEnzConfig) - Method in class uk.ac.ebi.intenz.webapp.controller.Command

setIntenzConfig(IntEnzConfig) - Static method in class uk.ac.ebi.intenz.webapp.utilities.IntEnzMessenger

SitemapServlet - Class in uk.ac.ebi.intenz.webapp.controller

Simple servlet which reads an external sitemap file and writes it as is to the response.

SitemapServlet() - Constructor for class uk.ac.ebi.intenz.webapp.controller.SitemapServlet

T

textualRepresentationToHTML(Reaction, SpecialCharacters, EncodingType) - Static method in class uk.ac.ebi.intenz.webapp.helper.EnzymeReactionHelper

Deprecated.

toHTML(EnzymeEntry, SpecialCharacters, EncodingType, EnzymeViewConstant) - Static method in class uk.ac.ebi.intenz.webapp.helper.EnzymeEntryHelper

Deprecated.

toHTML(EnzymeSubclass, SpecialCharacters, EncodingType) - Static method in class uk.ac.ebi.intenz.webapp.helper.EnzymeSubclassHelper

toHTML(EnzymeSubSubclass, SpecialCharacters, EncodingType) - Static method in class uk.ac.ebi.intenz.webapp.helper.EnzymeSubSubclassHelper

toPrinterFriendlyHTML(EnzymeClass, SpecialCharacters, EncodingType) - Static method in class uk.ac.ebi.intenz.webapp.helper.EnzymeClassHelper

toString() - Method in class uk.ac.ebi.intenz.webapp.controller.SearchECCommand.EnzymeEntryCacheKey

transformQuery(String, SearchCommand.QueryType, boolean) - Method in class uk.ac.ebi.intenz.webapp.controller.SearchCommand

U

uk.ac.ebi.intenz.webapp - package uk.ac.ebi.intenz.webapp

This package contains packages and classes used for the public read-only IntEnz web application.

uk.ac.ebi.intenz.webapp.controller - package uk.ac.ebi.intenz.webapp.controller

All front controller related classes are stored here.

uk.ac.ebi.intenz.webapp.exceptions - package uk.ac.ebi.intenz.webapp.exceptions

All exceptions are located here.

uk.ac.ebi.intenz.webapp.helper - package uk.ac.ebi.intenz.webapp.helper

uk.ac.ebi.intenz.webapp.utilities - package uk.ac.ebi.intenz.webapp.utilities

UnknownDatabaseCommand - Class in uk.ac.ebi.intenz.webapp.controller

This class is used if the parsed URL provides a wrong class name parameter.

UnknownDatabaseCommand() - Constructor for class uk.ac.ebi.intenz.webapp.controller.UnknownDatabaseCommand

A B C D E F G H I L N P Q R S T U