Package org.biojava.nbio.core.sequence

Class AccessionID

java.lang.Object

org.biojava.nbio.core.sequence.AccessionID

public class AccessionID
extends Object

Used in Sequences as the unique identifier. If possible, set the DataSource to know the source of the id. This allows a SequenceProxy to gather features or related sequences Protein->Gene as an example. When parsing a Blast file it is also possible to identify the type of ID

Author:

Scooter Willis, Jacek Grzebyta

Constructor Summary

Constructors

Constructor	Description
AccessionID()	Default constructor sets id t empty string
AccessionID(String id)	Creates an id with default DataSource.LOCAL source
AccessionID(String id, DataSource source)
AccessionID(String id, DataSource source, Integer version, String identifier)

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object o)
DataSource	getDataSource()
String	getID()
String	getIdentifier()	In case if getID() is not unique, keeps the alternative id, e.g.
Integer	getVersion()	In case if the getID() is not unique keeps the id version.
int	hashCode()
void	setIdentifier(String identifier)
void	setVersion(Integer version)
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Details

AccessionID

public AccessionID()

Default constructor sets id t empty string

AccessionID

public AccessionID(String id)

Creates an id with default DataSource.LOCAL source

Parameters:

id - non-null

AccessionID

public AccessionID(String id,
 DataSource source)

Parameters:

id -

source -

AccessionID

public AccessionID(String id,
 DataSource source,
 Integer version,
 String identifier)

Method Details

getID

public String getID()

Returns:

the id

getDataSource

public DataSource getDataSource()

Returns:

the source

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

getVersion

public Integer getVersion()

In case if the getID() is not unique keeps the id version.

Returns:

the version

setVersion

public void setVersion(Integer version)

getIdentifier

public String getIdentifier()

In case if getID() is not unique, keeps the alternative id, e.g. NCBI GI number. This may be null.

Returns:

setIdentifier

public void setIdentifier(String identifier)

toString

public String toString()

Overrides:

toString in class Object