XrefDatabaseConstant (IntEnz core module 4.3.3 API)

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

Fields
Modifier and Type	Field and Description
`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` Deprecated. This website does not work any more (if it ever did).
`static XrefDatabaseConstant`	`EXPLORENZ` Link to ExplorEnz (Dublin's MySQL implementation of NC-IUBMB).
`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 XrefDatabaseConstant`	`UNIPATHWAY`
`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

Methods
Modifier and Type	Method and Description
`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
```
@Deprecated
public static final XrefDatabaseConstant ERGO
```
    Deprecated. This website does not work any more (if it ever did).
    
    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).
  - EXPLORENZ
```
public static final XrefDatabaseConstant EXPLORENZ
```
    Link to ExplorEnz (Dublin's MySQL implementation of NC-IUBMB).
  - UNIPATHWAY
```
public static final XrefDatabaseConstant UNIPATHWAY
```
  - 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()
```

Class XrefDatabaseConstant

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

UNDEF

BRENDA

METACYC

CAS

ENZYME

NC_IUBMB

GO

CSA

NIST74

KEGG

MEROPS

MIM

PROSITE

SWISSPROT

UMBBD

DIAGRAM

ERGO

WIT

PDB

EXPLORENZ

UNIPATHWAY

LINK_SOURCE_CONSTANTS

UNIQUE_LINK_SOURCES

Method Detail

valueOf

compareTo

contains

isUniqueXrefDatabaseName

isUniqueXrefDatabaseCode

isXref

equals

hashCode

toString

getUrlOf

getDisplayNameOf

getDatabaseCodeOf

getDatabaseCode

getDisplayName

getUrl

isXref