uk.ac.ebi.intenz.domain.constants
Class XrefDatabaseConstant

java.lang.Object
  uk.ac.ebi.intenz.domain.constants.XrefDatabaseConstant

All Implemented Interfaces:

Comparable<XrefDatabaseConstant>

public class XrefDatabaseConstant
extends Object
implements Comparable<XrefDatabaseConstant>

This class represents an enumeration of all supported link source types.

Instances of this class are immutable.

Version:

$Revision: 1.4 $ $Date: 2008/07/09 09:49:05 $

Author:

Michael Darsow

Field Summary

static XrefDatabaseConstant	BRENDA BRENDA collects functional data about enzymes.
static XrefDatabaseConstant	CAS CAS is commercial and cannot be linked to.
static XrefDatabaseConstant	CSA Catalytic Site Atlas provides catalytic residues details.
static XrefDatabaseConstant	DIAGRAM
static XrefDatabaseConstant	ENZYME ENZYME is the EXPASY version of the NC-IUBMB Nomenclature containing some additional information (cofactors, improved comments and additional links).
static XrefDatabaseConstant	ERGO ERGO is a not very reliable enzyme source ...
static XrefDatabaseConstant	GO GO is the Gene Ontology database.
static XrefDatabaseConstant	KEGG KEGG comprises several databases storing information especially related to enzymes (e.g.
static List<XrefDatabaseConstant>	LINK_SOURCE_CONSTANTS All link sources ordered alphabetically.
static XrefDatabaseConstant	MEROPS MEROPS is a resource for peptidases.
static XrefDatabaseConstant	METACYC
static XrefDatabaseConstant	MIM OMIM stores information about human genetic diseases.
static XrefDatabaseConstant	NC_IUBMB Gerry Moss' web pages (Nomenclature Comitee of the IUBMB).
static XrefDatabaseConstant	NIST74 NIST74 provides further information about the catalytic activity.
static XrefDatabaseConstant	PDB Link to the Protein Data Bank (PDB).
static XrefDatabaseConstant	PROSITE PROSITE is located at the SIB and contains information about protein families and domains.
static XrefDatabaseConstant	SWISSPROT Swiss-Prot is THE protein sequence database.
static XrefDatabaseConstant	UMBBD UM-BBD is a comprehensive resource about enzymes also containing enzymes which haven't got an EC number yet.
static XrefDatabaseConstant	UNDEF
static Set<XrefDatabaseConstant>	UNIQUE_LINK_SOURCES This set contains all link which can only occur once in an enzyme entry.
static XrefDatabaseConstant	WIT ERGO formerly WIT.

Method Summary

int	compareTo(XrefDatabaseConstant linkSourceConstant)
static boolean	contains(String sourceCode) Checks if the given link source code exists in this enumeration.
boolean	equals(Object o) Standard equals method.
String	getDatabaseCode()
static String	getDatabaseCodeOf(String databaseName)
String	getDisplayName()
static String	getDisplayNameOf(String sourceCode) Returns the display name of the source defined by databaseCode.
String	getUrl()
static String	getUrlOf(String sourceCode) Returns the URL of the given source code.
int	hashCode() Returns the hash code of this object.
static boolean	isUniqueXrefDatabaseCode(String databaseCode)
static boolean	isUniqueXrefDatabaseName(String databaseName)
boolean	isXref()
static boolean	isXref(String sourceCode) Returns true if this link belongs to the XREFS table.
String	toString() Returns the display name.
static XrefDatabaseConstant	valueOf(String sourceCode)

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

UNDEF

public static final XrefDatabaseConstant UNDEF

BRENDA

public static final XrefDatabaseConstant BRENDA

BRENDA collects functional data about enzymes. NOTE: this is now considered as xref, as the identifiers we are linking to are their preliminary EC numbers.

METACYC

public static final XrefDatabaseConstant METACYC

CAS

public static final XrefDatabaseConstant CAS

CAS is commercial and cannot be linked to.

ENZYME

public static final XrefDatabaseConstant ENZYME

ENZYME is the EXPASY version of the NC-IUBMB Nomenclature containing some additional information (cofactors, improved comments and additional links).

NC_IUBMB

public static final XrefDatabaseConstant NC_IUBMB

Gerry Moss' web pages (Nomenclature Comitee of the IUBMB).

GO

public static final XrefDatabaseConstant GO

GO is the Gene Ontology database.

CSA

public static final XrefDatabaseConstant CSA

Catalytic Site Atlas provides catalytic residues details.

NIST74

public static final XrefDatabaseConstant NIST74

NIST74 provides further information about the catalytic activity.

KEGG

public static final XrefDatabaseConstant KEGG

KEGG comprises several databases storing information especially related to enzymes (e.g. LIGAND, REACTION) and genes and genomes in general.

MEROPS

public static final XrefDatabaseConstant MEROPS

MEROPS is a resource for peptidases.

MIM

public static final XrefDatabaseConstant MIM

OMIM stores information about human genetic diseases.

PROSITE

public static final XrefDatabaseConstant PROSITE

PROSITE is located at the SIB and contains information about protein families and domains.

SWISSPROT

public static final XrefDatabaseConstant SWISSPROT

Swiss-Prot is THE protein sequence database.

UMBBD

public static final XrefDatabaseConstant UMBBD

UM-BBD is a comprehensive resource about enzymes also containing enzymes which haven't got an EC number yet.

UM-BBD links can be static (using EC number) or non-static (using UM-BBD identifier). Therefore a UM-BBD link will not be part of the list of static links.

DIAGRAM

public static final XrefDatabaseConstant DIAGRAM

ERGO

public static final XrefDatabaseConstant ERGO

ERGO is a not very reliable enzyme source ... (I couldn't get any information about it because the server was down).

WIT

public static final XrefDatabaseConstant WIT

ERGO formerly WIT.

PDB

public static final XrefDatabaseConstant PDB

Link to the Protein Data Bank (PDB).

LINK_SOURCE_CONSTANTS

public static final List<XrefDatabaseConstant> LINK_SOURCE_CONSTANTS

All link sources ordered alphabetically. This set is immutable.

UNIQUE_LINK_SOURCES

public static final Set<XrefDatabaseConstant> UNIQUE_LINK_SOURCES

This set contains all link which can only occur once in an enzyme entry.

Method Detail

valueOf

public static XrefDatabaseConstant valueOf(String sourceCode)
                                    throws DomainException

Throws:

DomainException

compareTo

public int compareTo(XrefDatabaseConstant linkSourceConstant)

Specified by:

compareTo in interface Comparable<XrefDatabaseConstant>

contains

public static boolean contains(String sourceCode)

Checks if the given link source code exists in this enumeration.

Parameters:

sourceCode - The source code of the link.

Returns:

true if the source code exists.

Throws:

NullPointerException - if databaseCode is null.

isUniqueXrefDatabaseName

public static boolean isUniqueXrefDatabaseName(String databaseName)

isUniqueXrefDatabaseCode

public static boolean isUniqueXrefDatabaseCode(String databaseCode)

isXref

public static boolean isXref(String sourceCode)

Returns true if this link belongs to the XREFS table.

If the source code is not a valid source code an exception is thrown (see below).

Parameters:

sourceCode - The source code of this link constant.

Returns:

true if this link belongs to the XREFS table.

Throws:

NullPointerException - if databaseCode is null.

IllegalArgumentException - if databaseCode is invalid.

equals

public boolean equals(Object o)

Standard equals method.

Overrides:

equals in class Object

Parameters:

o - Object to be compared to this one.

Returns:

true if the objects are equal.

hashCode

public int hashCode()

Returns the hash code of this object.

Overrides:

hashCode in class Object

Returns:

the hash code of this object.

toString

public String toString()

Returns the display name.

Overrides:

toString in class Object

Returns:

the display name.

getUrlOf

public static String getUrlOf(String sourceCode)

Returns the URL of the given source code.

If the source code is not a valid source code an exception is thrown (see below).

Parameters:

sourceCode - The source code of this link constant.

Returns:

the URL.

Throws:

NullPointerException - if databaseCode is null.

IllegalArgumentException - if databaseCode is invalid.

getDisplayNameOf

public static String getDisplayNameOf(String sourceCode)

Returns the display name of the source defined by databaseCode.

Parameters:

sourceCode - The source's code.

Returns:

the display name.

Throws:

NullPointerException - if databaseCode is null.

getDatabaseCodeOf

public static String getDatabaseCodeOf(String databaseName)

getDatabaseCode

public String getDatabaseCode()

getDisplayName

public String getDisplayName()

getUrl

public String getUrl()

isXref

public boolean isXref()