EnzymeLink (IntEnz core module 4.3.3 API)

java.lang.Object
- uk.ac.ebi.intenz.domain.enzyme.EnzymeLink

All Implemented Interfaces:

Comparable<EnzymeLink>, Commented, Viewable
```
public class EnzymeLink
extends Object
implements Comparable<EnzymeLink>, Commented, Viewable
```
An enzyme link is used to store cross-reference information.
Most of the links use a static URL which differs only in the EC number used to identify the enzyme. These links can be obtained by accessing the class constants.
Other cross-references contain a static URL but need a different identifier. For example, a SwissProt cross-reference needs a protein accession number. These links are provided via the according factory methods. In case of SwissProt and MIM links it is also possible to provide a name for the protein or disease respectively.

The terms link and cross-reference are used synonymously.
Instances of this class are immutable.

Version:

$Revision: 1.2 $ $Date: 2008/01/28 12:33:00 $

Author:

Michael Darsow

Field Summary

Fields
Modifier and Type	Field and Description
`static EnzymeLink`	`BRENDA` Static link to the BRENDA database.
`static EnzymeLink`	`CSA` Static link to the CSA database.
`static EnzymeLink`	`ERGO` Deprecated. the ERGO website is not working any more.
`static EnzymeLink`	`EXPASY` Static link to the ENZYME database at expasy.org.
`static EnzymeLink`	`EXPLORENZ`
`static EnzymeLink`	`GO` Static link to the Gene Ontology database.
`static EnzymeLink`	`KEGG` Static link to the KEGG database.
`static EnzymeLink`	`METACYC` Link to MetaCyc.
`static EnzymeLink`	`NC_IUBMB` Static link to the GM pages (NC-IUBMB).
`static EnzymeLink`	`NIST74` Static link to the NIST 74 database.
`static EnzymeLink`	`PDB` Static link to the PDB database.
`static EnzymeLink`	`UMBBD` Static link to the UM-BBD database.
`static EnzymeLink`	`UNIPATHWAY`
`static EnzymeLink`	`WIT` Static link to the ERGO (formerly WIT) database.

Method Summary

Methods
Modifier and Type	Method and Description
`int`	`compareTo(EnzymeLink link)` Used for ordering links in a collection.
`boolean`	`equals(Object o)` Checks for equality.
`String`	`getAccession()`
`String`	`getDataComment()`
`String`	`getFullUrl(String ec)` Links with the EC number as identifier need to call this method to get the correct URL.
`String`	`getListOrderCriterion()` Creates a unique name for this link.
`String`	`getName()`
`EnzymeSourceConstant`	`getSource()`
`String`	`getSpecificUrl()`
`static EnzymeLink`	`getStaticLink(XrefDatabaseConstant databaseConstant)`
`EnzymeViewConstant`	`getView()`
`XrefDatabaseConstant`	`getXrefDatabaseConstant()`
`int`	`hashCode()` Generates a hash code for this object.
`static boolean`	`isStaticLink(XrefDatabaseConstant databaseConstant)` Checks if the given link is a static link.
`void`	`setDataComment(String comment)`
`String`	`toString()` Provides a string representation of an `EnzymeLink`.
`static EnzymeLink`	`valueOf(XrefDatabaseConstant xrefDatabaseConstant, String specificUrl, String accession, String name, EnzymeSourceConstant source, EnzymeViewConstant view)` Returns an `EnzymeLink` instance.
`static EnzymeLink`	`valueOf(XrefDatabaseConstant xrefDatabaseConstant, String specificUrl, String accession, String name, EnzymeSourceConstant source, EnzymeViewConstant view, String dataComment)` Returns a commented `EnzymeLink` instance.

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

- Field Detail
  - BRENDA
```
public static final EnzymeLink BRENDA
```
    Static link to the BRENDA database.
  - METACYC
```
public static final EnzymeLink METACYC
```
    Link to MetaCyc.
  - KEGG
```
public static final EnzymeLink KEGG
```
    Static link to the KEGG database.
  - EXPASY
```
public static final EnzymeLink EXPASY
```
    Static link to the ENZYME database at expasy.org.
  - NC_IUBMB
```
public static final EnzymeLink NC_IUBMB
```
    Static link to the GM pages (NC-IUBMB).
  - ERGO
```
@Deprecated
public static final EnzymeLink ERGO
```
    Deprecated. the ERGO website is not working any more.
    
    Static link to the ERGO database.
  - WIT
```
public static final EnzymeLink WIT
```
    Static link to the ERGO (formerly WIT) database.
  - GO
```
public static final EnzymeLink GO
```
    Static link to the Gene Ontology database.
  - NIST74
```
public static final EnzymeLink NIST74
```
    Static link to the NIST 74 database.
  - UMBBD
```
public static final EnzymeLink UMBBD
```
    Static link to the UM-BBD database.
  - PDB
```
public static final EnzymeLink PDB
```
    Static link to the PDB database.
  - CSA
```
public static final EnzymeLink CSA
```
    Static link to the CSA database.
  - EXPLORENZ
```
public static final EnzymeLink EXPLORENZ
```
  - UNIPATHWAY
```
public static final EnzymeLink UNIPATHWAY
```
- Method Detail
  - valueOf
```
public static EnzymeLink valueOf(XrefDatabaseConstant xrefDatabaseConstant,
                 String specificUrl,
                 String accession,
                 String name,
                 EnzymeSourceConstant source,
                 EnzymeViewConstant view)
```
    Returns an EnzymeLink instance.
    
    Parameters:
    xrefDatabaseConstant - The link's xrefDatabaseConstant.
    specificUrl - The link's URL.
    accession - The accession of this link.
    name - The name of this link.
    
    Returns:
    the EnzymeLink instance.
    
    Throws:
    
    NullPointerException - if xrefDatabaseConstant is null.
    
    IllegalArgumentException - if the arguments are not sufficient to create a link.
  - valueOf
```
public static EnzymeLink valueOf(XrefDatabaseConstant xrefDatabaseConstant,
                 String specificUrl,
                 String accession,
                 String name,
                 EnzymeSourceConstant source,
                 EnzymeViewConstant view,
                 String dataComment)
```
    Returns a commented EnzymeLink instance.
    
    Parameters:
    xrefDatabaseConstant -
    specificUrl -
    accession -
    name -
    source -
    view -
    dataComment -
    
    Returns:
  - isStaticLink
```
public static boolean isStaticLink(XrefDatabaseConstant databaseConstant)
```
    Checks if the given link is a static link.
    
    Parameters:
    databaseConstant - The database constant to be checked.
    
    Returns:
    true if the link is a static link.
    
    Throws:
    
    NullPointerException - if link is null.
  - getStaticLink
```
public static EnzymeLink getStaticLink(XrefDatabaseConstant databaseConstant)
```
  - compareTo
```
public int compareTo(EnzymeLink link)
```
    Used for ordering links in a collection.
    Static and other links are ordered by their xrefDatabaseConstant name, SwissProt and MIM cross-references by their name and PROSITE links by their accession. Other links are ordered by their specific URL if the xrefDatabaseConstant name is the same. Noted: Changed so that only SwissProt compares on the basis of name and OMIM compares on the basis of accession like PROSITE.
    
    Specified by:
    
    compareTo in interface Comparable<EnzymeLink>
    
    Parameters:
    link - The object to be compared to this.
    
    Returns:
    neg, 0 or pos. value to indicate the order of these two objects.
    
    Throws:
    
    NullPointerException - if o is null.
  - equals
```
public boolean equals(Object o)
```
    Checks for equality.
    
    Overrides:
    
    equals in class Object
    
    Parameters:
    o - The object to be compared to this.
    
    Returns:
    true if o is equal this object.
  - hashCode
```
public int hashCode()
```
    Generates a hash code for this object.
    
    Overrides:
    
    hashCode in class Object
    
    Returns:
    the hash code.
  - toString
```
public String toString()
```
    Provides a string representation of an EnzymeLink.
    
    Overrides:
    
    toString in class Object
    
    Returns:
    the string representation.
  - getListOrderCriterion
```
public String getListOrderCriterion()
```
    Creates a unique name for this link.
    This method will be used to populate lists (esp. combo box content).
    
    Returns:
    the unique name.
  - getFullUrl
```
public String getFullUrl(String ec)
```
    Links with the EC number as identifier need to call this method to get the correct URL.
    
    Parameters:
    ec - The EC number.
    
    Returns:
    the full URL.
    
    Throws:
    
    NullPointerException - if ec is null.
  - getXrefDatabaseConstant
```
public XrefDatabaseConstant getXrefDatabaseConstant()
```
  - getSpecificUrl
```
public String getSpecificUrl()
```
  - getAccession
```
public String getAccession()
```
  - getName
```
public String getName()
```
  - getView
```
public EnzymeViewConstant getView()
```
    Specified by:
    
    getView in interface Viewable
  - getSource
```
public EnzymeSourceConstant getSource()
```
  - getDataComment
```
public String getDataComment()
```
    Specified by:
    
    getDataComment in interface Commented
  - setDataComment
```
public void setDataComment(String comment)
```
    Specified by:
    
    setDataComment in interface Commented

Class EnzymeLink

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

BRENDA

METACYC

KEGG

EXPASY

NC_IUBMB

ERGO

WIT

GO

NIST74

UMBBD

PDB

CSA

EXPLORENZ

UNIPATHWAY

Method Detail

valueOf

valueOf

isStaticLink

getStaticLink

compareTo

equals

hashCode

toString

getListOrderCriterion

getFullUrl

getXrefDatabaseConstant

getSpecificUrl

getAccession

getName

getView

getSource

getDataComment

setDataComment