DataSource.Builder (BridgeDb 3.0.3 API)

java.lang.Object
- org.bridgedb.DataSource.Builder

Enclosing class:: DataSource

public static final class DataSource.Builder
extends Object

Uses builder pattern to set optional attributes for a DataSource. For example, this allows you to use the following code:

 DataSource.register("X", "Affymetrix")
     .mainUrl("http://www.affymetrix.com")
     .type("probe")
     .primary(false);

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`DataSource.Builder`	`alternative(String alternative)` Allow the setting but not changing of an alternative name
`DataSource`	`asDataSource()`
`DataSource.Builder`	`deprecated(boolean isDeprecated)`
`DataSource.Builder`	`deprecatedBy(DataSource sourceToUseInstead)` Sets the DataSource which should be used instead of this deprecated one.
`DataSource.Builder`	`description(String description)` Allow the setting but not changing of a description
`DataSource.Builder`	`identifiersOrgBase(String base)` Note: Since version 2 The base must start with urn:miriam:.
`DataSource.Builder`	`idExample(String idExample)` Note: Unlike most builder methods this one does allow the idExample to be change even if already set.
`DataSource.Builder`	`mainUrl(String mainUrl)` Note: Since version 2 this method no longer allows changing a mainUrl once set.
`DataSource.Builder`	`organism(Object organism)` Since version 2 This method no longer allows you to change the Organism of a DataSource once set.
`DataSource.Builder`	`primary(boolean isPrimary)` Note: Unlike most builder methods this one does allow the idPrimary to be change even if already set.
`DataSource.Builder`	`type(String type)` Since version 2 This method no longer allow changing the type of a DataSource once set.
`DataSource.Builder`	`urlPattern(String urlPattern)`
`DataSource.Builder`	`urnBase(String base)` This adds a miriam base to the DataSource.

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

- Method Detail
  - asDataSource
```
public DataSource asDataSource()
```
    Returns:
    
    the DataSource under construction
  - urlPattern
```
public DataSource.Builder urlPattern(String urlPattern)
```
    Parameters:
    
    urlPattern - is a template for generating valid URL's for identifiers. The pattern should contain the substring "$ID", which will be replaced by the actual identifier. Since version 2.0.0 it is no longer allowed to change the urlPattern once set.
    
    Returns:
    
    the same Builder object so you can chain setters
  - mainUrl
```
public DataSource.Builder mainUrl(String mainUrl)
```
    Note: Since version 2 this method no longer allows changing a mainUrl once set.
    
    Parameters:
    
    mainUrl - url of homepage
    
    Returns:
    
    the same Builder object so you can chain setters
    
    Throws:
    
    IllegalArgumentException - is a none null mainUrl is changed to a different value.
  - idExample
```
public DataSource.Builder idExample(String idExample)
```
    Note: Unlike most builder methods this one does allow the idExample to be change even if already set. There may be good reasons why a specific example works better in a specific case then the original one set. However there is no known case that replies on this flexibility to change.
    
    Parameters:
    
    idExample - an example id from this system
    
    Returns:
    
    the same Builder object so you can chain setters
  - primary
```
public DataSource.Builder primary(boolean isPrimary)
```
    Note: Unlike most builder methods this one does allow the idPrimary to be change even if already set. There may be good reasons why a specific DataSource's primary status is different in different applications. However there is no known case that replies this on flexibility to change.
    
    Parameters:
    
    isPrimary - secondary id's such as EC numbers, Gene Ontology or vendor-specific systems occur in data or linkouts, but their use in pathways is discouraged
    
    Returns:
    
    the same Builder object so you can chain setters
  - deprecated
```
public DataSource.Builder deprecated(boolean isDeprecated)
```
    Parameters:
    
    isDeprecated - a boolean indicating this DataSource should no longer be used
    
    Returns:
    
    the same Builder object so you can chain setters
  - deprecatedBy
```
public DataSource.Builder deprecatedBy(DataSource sourceToUseInstead)
```
    Sets the DataSource which should be used instead of this deprecated one. It automatically sets isDeprecated to true.
    
    Parameters:
    
    sourceToUseInstead - the DataSource that should be used instead of this deprecated one
    
    Returns:
    
    the same Builder object so you can chain setters
  - type
```
public DataSource.Builder type(String type)
```
    Since version 2 This method no longer allow changing the type of a DataSource once set.
    
    Parameters:
    
    type - the type of datasource, for example "protein", "gene", "metabolite"
    
    Returns:
    
    the same Builder object so you can chain setters
  - organism
```
public DataSource.Builder organism(Object organism)
```
    Since version 2 This method no longer allows you to change the Organism of a DataSource once set.
    
    Parameters:
    
    organism - organism for which this system code is suitable, or null for any / not applicable
    
    Returns:
    
    the same Builder object so you can chain setters
  - urnBase
```
public DataSource.Builder urnBase(String base)
```
    This adds a miriam base to the DataSource. Note: Since version 2 The base must start with urn:miriam:. The urnBase and identifiersOrgBase methods share the same miriam base. If the SystemCode is used as the urnBase this is just ignored! (As the default to use the sysCode as the urnbase)
    
    Parameters:
    
    base - for urn generation, for example "urn:miriam:uniprot"
    
    Returns:
    
    the same Builder object so you can chain setters
  - identifiersOrgBase
```
public DataSource.Builder identifiersOrgBase(String base)
```
    Note: Since version 2 The base must start with urn:miriam:. The urnBase and identifiersOrgBase methods share the same miriam basee. It is no longer allowed to change a none null miriam Base
    
    Parameters:
    
    base - for identifiersOrg generation, for example "http://www.identifiers.org/uniprot" It will also accept an identifiersOrg Pattern such as "http://www.identifiers.org/uniprot/$id"
    
    Returns:
    
    the same Builder object so you can chain setters
  - alternative
```
public DataSource.Builder alternative(String alternative)
```
    Allow the setting but not changing of an alternative name
    
    Parameters:
    
    alternative -
    
    Returns:
    
    the same Builder object so you can chain setters
    
    Since:
    
    version 2.0.0
  - description
```
public DataSource.Builder description(String description)
```
    Allow the setting but not changing of a description
    
    Parameters:
    
    alternative -
    
    Returns:
    
    the same Builder object so you can chain setters
    
    Since:
    
    version 2.0.0

Class DataSource.Builder

Method Summary

Methods inherited from class java.lang.Object

Method Detail

asDataSource

urlPattern

mainUrl

idExample

primary

deprecated

deprecatedBy

type

organism

urnBase

identifiersOrgBase

alternative

description