DataSource (BridgeDb 3.0.3 API)

java.lang.Object
- org.bridgedb.DataSource

```
public final class DataSource
extends Object
```
Contains information about a certain DataSource. This includes:
- Its full name ("Ensembl")
- Its system code ("En")
- Its main url ("http://www.ensembl.org")
- Id-specific url's ("http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=" + id)
The DataSource class uses the extensible enum pattern. You cannot instantiate DataSources directly, instead you have to use one of the constants from the org.bridgedb.bio module such as BioDataSource.ENSEMBL, or the getBySystemcode or "getByFullname" methods. These methods return a predefined DataSource object if it exists. If a predefined DataSource for a requested SystemCode doesn't exists, a new one springs to life automatically. This can be used when the user requests new, unknown data sources. If you call getBySystemCode twice with the same argument, it is guaranteed that you get the same return object. However, there is no way to combine a new DataSource with a new FullName unless you use the "register" method.
This way any number of pre-defined DataSources can be used, but plugins can define new ones and you can handle unknown data sources in the same way as predefined ones.
Definitions for common DataSources can be found in org.bridgedb.bio.BioDataSource.

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class DataSource.Builder
Uses builder pattern to set optional attributes for a DataSource.

Nested Classes
Modifier and Type	Class and Description
`static class`	`DataSource.Builder` Uses builder pattern to set optional attributes for a DataSource.

Field Summary

Fields
Modifier and Type Field and Description

static String UNKOWN

Fields
Modifier and Type	Field and Description
`static String`	`UNKOWN`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static boolean`	`fullNameExists(String fullName)` Check if a DataSoucre with this sfullName has been registered
`String`	`getAlternative()` Retrieves any saved alternative name.
`static DataSource`	`getByAlias(String alias)`
`static DataSource`	`getByIdentiferOrgBase(String base)` Since version 2.0 this method will return null if no DataSource is known
`static DataSource`	`getByMiriamBase(String base)` Since version 2.0 this method will return null if no DataSource is known
`String`	`getCompactIdentifier(String id)` Creates a compact identifier.
`static Set<DataSource>`	`getDataSources()` get all registered datasoures as a set.
`String`	`getDescription()` Retrieves any saved description.
`Xref`	`getExample()`
`static DataSource`	`getExistingByFullName(String fullName)` returns pre-existing DataSource object
`static DataSource`	`getExistingBySystemCode(String systemCode)`
`static Set<DataSource>`	`getFilteredSet(Boolean primary, Boolean metabolite, Object o)` returns a filtered subset of available datasources.
`String`	`getFullName()` returns full name of DataSource e.g.
`static List<String>`	`getFullNames()` Get a list of all non-null full names.
`String`	`getIdentifiersOrgUri(String id)`
`String`	`getKnownUrl(String id)` Turn id into url pointing to info page on the web, e.g.
`String`	`getMainUrl()` Return the main Url for this datasource, that can be used to refer to the datasource in general.
`String`	`getMiriamURN(String id)` Creates a global identifier.
`Object`	`getOrganism()`
`String`	`getSystemCode()` returns GenMAPP SystemCode, e.g.
`String`	`getType()`
`boolean`	`isDeprecated()` A DataSource is deprecated if it is replaced by another data source which should be used instead.
`DataSource`	`isDeprecatedBy()` Returns the DataSource that should be used instead if this DataSource is deprecated.
`boolean`	`isMetabolite()`
`boolean`	`isPrimary()`
`static DataSource.Builder`	`register(String sysCode, String fullName)` Register a new DataSource with (optional) detailed information.
`void`	`registerAlias(String alias)`
`static boolean`	`systemCodeExists(String systemCode)` Check if a DataSoucre with this systemCode has been registered
`String`	`toString()` The string representation of a DataSource is equal to it's full name.
`boolean`	`urlPatternKnown()` Check if a Url pattern is know for this DataSource.

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

- Field Detail
  - UNKOWN
```
public static final String UNKOWN
```
    See Also:
    
    Constant Field Values
- Method Detail
  - getKnownUrl
```
public String getKnownUrl(String id)
```
    Turn id into url pointing to info page on the web, e.g. "http://www.ensembl.org/get?id=ENSG..." Since version 2 this will return null if no pattern has been set.
    
    Parameters:
    
    id - identifier to use in url
    
    Returns:
    
    Url
  - urlPatternKnown
```
public boolean urlPatternKnown()
```
    Check if a Url pattern is know for this DataSource.
    
    Returns:
    
    True if and only if a Url pattern is known/ has been registered
  - getFullName
```
public String getFullName()
```
    returns full name of DataSource e.g. "Ensembl". May return null if only the system code is known. Also used as identifier in GPML
    
    Returns:
    
    full name of DataSource
  - getSystemCode
```
public String getSystemCode()
```
    returns GenMAPP SystemCode, e.g. "En". May return null, if only the full name is known. Also used as identifier in
    1. Gdb databases,
    2. Gex databases.
    3. Imported data
    4. the Mapp format.
    We should try not to use the system code anywhere outside these 4 uses.
    Returns:
    
    systemcode, a short unique code.
  - getMainUrl
```
public String getMainUrl()
```
    Return the main Url for this datasource, that can be used to refer to the datasource in general. (e.g. http://www.ensembl.org/) May return null in case the main url is unknown.
    
    Returns:
    
    main url
  - getType
```
public String getType()
```
    Returns:
    
    type of entity that this DataSource describes, for example "metabolite", "gene", "protein", "interaction" or "probe"
  - getMiriamURN
```
public String getMiriamURN(String id)
```
    Creates a global identifier. It uses the MIRIAM data type list to create a MIRIAM URI like "urn:miriam:uniprot:P12345", or if this DataSource is not included in the MIRIAM data types list, a bridgedb URI.
    
    Parameters:
    
    id - Id to generate URN from.
    
    Returns:
    
    the URN.
    
    Since:
    
    Version 2.0.0
  - getCompactIdentifier
```
public String getCompactIdentifier(String id)
```
    Creates a compact identifier. It uses the MIRIAM data type list to create a compact identifier like "uniprot:P12345".
    
    Parameters:
    
    id - identifier to generate compact identifier from.
    
    Returns:
    
    the compact identifier.
    
    Since:
    
    Version 3.0.0
  - getIdentifiersOrgUri
```
public String getIdentifiersOrgUri(String id)
```
  - getAlternative
```
public String getAlternative()
```
    Retrieves any saved alternative name.
    
    Returns:
    
    Saved alternative name or null if none is known
    
    Since:
    
    version 2.0.0
  - getDescription
```
public String getDescription()
```
    Retrieves any saved description.
    
    Returns:
    
    Saved description or null if none is known
    
    Since:
    
    version 2.0.0
  - register
```
public static DataSource.Builder register(String sysCode,
                                          String fullName)
```
    Register a new DataSource with (optional) detailed information. This can be used by other modules to define new DataSources. Note: Since version 2 this method is stricter. It will no longer allow an existing dataSource to have either its full name of sysCode changed.
    
    Parameters:
    
    sysCode - short unique code between 1-4 letters, originally used by GenMAPP
    
    fullName - full name used in GPML.
    
    Returns:
    
    Builder that can be used for adding detailed information.
  - registerAlias
```
public void registerAlias(String alias)
```
  - getExistingBySystemCode
```
public static DataSource getExistingBySystemCode(String systemCode)
```
    Parameters:
    
    systemCode - short unique code to query for
    
    Returns:
    
    pre-existing DataSource object by system code if it exists
    
    Throws:
    
    IllegalArgumentException - if no DataSource is known with this systemCode
  - systemCodeExists
```
public static boolean systemCodeExists(String systemCode)
```
    Check if a DataSoucre with this systemCode has been registered
    
    Parameters:
    
    systemCode - to check
    
    Returns:
    
    True if and only if a DataSource has been registered with this systemCode.
  - getExistingByFullName
```
public static DataSource getExistingByFullName(String fullName)
```
    returns pre-existing DataSource object
    
    Parameters:
    
    fullName - full name to query for
    
    Returns:
    
    DataSource
    
    Throws:
    
    IllegalArgumentException - if no DataSource is known with this systemCode
  - fullNameExists
```
public static boolean fullNameExists(String fullName)
```
    Check if a DataSoucre with this sfullName has been registered
    
    Parameters:
    
    fullName - to check
    
    Returns:
    
    True if and only if a DataSource has been registered with this systemCode.
  - getByAlias
```
public static DataSource getByAlias(String alias)
```
  - getDataSources
```
public static Set<DataSource> getDataSources()
```
    get all registered datasoures as a set.
    
    Returns:
    
    set of all registered DataSources
  - getFilteredSet
```
public static Set<DataSource> getFilteredSet(Boolean primary,
                                             Boolean metabolite,
                                             Object o)
```
    returns a filtered subset of available datasources.
    
    Parameters:
    
    primary - Filter for specified primary-ness. If null, don't filter on primary-ness.
    
    metabolite - Filter for specified metabolite-ness. If null, don't filter on metabolite-ness.
    
    o - Filter for specified organism. If null, don't filter on organism.
    
    Returns:
    
    filtered set.
  - getFullNames
```
public static List<String> getFullNames()
```
    Get a list of all non-null full names.
    Warning: the ordering of this list is undefined. Two subsequent calls may give different results.
    
    Returns:
    
    List of full names
  - toString
```
public String toString()
```
    The string representation of a DataSource is equal to it's full name. (e.g. "Ensembl")
    
    Overrides:
    
    toString in class Object
    
    Returns:
    
    String representation
  - getExample
```
public Xref getExample()
```
    Returns:
    
    example Xref, mostly for testing purposes
  - isPrimary
```
public boolean isPrimary()
```
    Returns:
    
    if this is a primary DataSource or not. Primary DataSources are preferred when annotating models. A DataSource is primary if it is not of type probe, so that means e.g. Affymetrix or Agilent probes are not primary. All gene, protein and metabolite identifiers are primary.
  - isDeprecated
```
public boolean isDeprecated()
```
    A DataSource is deprecated if it is replaced by another data source which should be used instead. Even if this DataSource is deprecated, it does not imply it says what it is deprecated by.
    
    Returns:
    
    true if this DataSource is deprecated
  - isDeprecatedBy
```
public DataSource isDeprecatedBy()
```
    Returns the DataSource that should be used instead if this DataSource is deprecated. This method may return null even if this DataSource is deprecated.
    
    Returns:
    
    if defined, the DataSource that should be used instead of this one
  - isMetabolite
```
public boolean isMetabolite()
```
    Returns:
    
    if this DataSource describes metabolites or not.
  - getOrganism
```
public Object getOrganism()
```
    Returns:
    
    Organism that this DataSource describes, or null if multiple / not applicable.
  - getByMiriamBase
```
public static DataSource getByMiriamBase(String base)
```
    Since version 2.0 this method will return null if no DataSource is known
    
    Parameters:
    
    base - the base urn, which must start with "urn:miriam:". It it isn't, null is returned.
  - getByIdentiferOrgBase
```
public static DataSource getByIdentiferOrgBase(String base)
```
    Since version 2.0 this method will return null if no DataSource is known
    
    Parameters:
    
    base - the base urn, which must start with "http://identifiers.org/". It it isn't, null is returned.

Class DataSource

Nested Class Summary

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

UNKOWN

Method Detail

getKnownUrl

urlPatternKnown

getFullName

getSystemCode

getMainUrl

getType

getMiriamURN

getCompactIdentifier

getIdentifiersOrgUri

getAlternative

getDescription

register

registerAlias

getExistingBySystemCode

systemCodeExists

getExistingByFullName

fullNameExists

getByAlias

getDataSources

getFilteredSet

getFullNames

toString

getExample

isPrimary

isDeprecated

isDeprecatedBy

isMetabolite

getOrganism

getByMiriamBase

getByIdentiferOrgBase