Package org.biojavax.bio.db.ncbi

Class GenbankRichSequenceDB

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojavax.bio.db.AbstractBioEntryDB

org.biojavax.bio.db.AbstractRichSequenceDB

org.biojavax.bio.db.ncbi.GenbankRichSequenceDB

All Implemented Interfaces:

SequenceDB, SequenceDBLite, Changeable, BioEntryDB, BioEntryDBLite, RichSequenceDB, RichSequenceDBLite

public class GenbankRichSequenceDB
extends AbstractRichSequenceDB
implements RichSequenceDBLite

This class contains functions accessing DNA sequences in Genbank format. It adds methods to return RichSequences instead of plain Sequences.

Since:

1.5

Author:

Lei Lai, Matthew Pocock, Laurent Jourdren, Shuvankar Mukherjee, Mark Schreiber, Richard Holland

Field Summary

Fields

Modifier and Type	Field	Description
protected static String	urlBatchSequences

Fields inherited from interface org.biojavax.bio.db.BioEntryDBLite

BIOENTRYS

Fields inherited from interface org.biojava.bio.seq.db.SequenceDBLite

SEQUENCES

Constructor Summary

Constructors

Constructor	Description
GenbankRichSequenceDB()	The default constructor delegates to the parent class.

Method Summary

Modifier and Type	Method	Description
protected URL	getAddress(String id)	Get the URL object for locating sequence object using eutils.
String	getEmail()	Get the email for Entrez.
RichSequenceBuilderFactory	getFactory()	Getter for property factory.
String	getName()	Get the name of this sequence database.
Namespace	getNamespace()	Getter for property namespace.
RichSequence	getRichSequence(String id)	Given the appropriate Genbank ID, return the matching RichSequence object.
RichSequence	getRichSequence(String id, Namespace nsp)	Given the appropriate Genbank ID, return the matching RichSequence object.
RichSequenceDB	getRichSequences(Set list)	Retrieve rich sequences from a Genbank
RichSequenceDB	getRichSequences(Set list, RichSequenceDB database)	Retrieve rich sequences from a Genbank
String	getTool()	Get the tool identifier for Entrez.
Set	ids()	Get an immutable set of all of the IDs in the database.
protected String	makeBatchRequest(URL url, Set list)	Create the Http Post Request to fetch (in batch mode) a list of sequence with Genbank.
void	setEmail(String email)	Set the email for Entrez.
void	setFactory(RichSequenceBuilderFactory factory)	Setter for property factory.
void	setNamespace(Namespace namespace)	Setter for property namespace.
void	setTool(String tool)	Set the tool identifier for Entrez.

Methods inherited from class org.biojavax.bio.db.AbstractRichSequenceDB

addBioEntry, addRichSequence, addSequence, filter, getBioEntry, getBioEntryIterator, getBioEntrys, getBioEntrys, getRichSequenceIterator, getSequence, removeBioEntry, removeRichSequence, removeSequence, sequenceIterator

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.biojavax.bio.db.BioEntryDBLite

addBioEntry, getBioEntry, getBioEntrys, getBioEntrys, removeBioEntry

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface org.biojavax.bio.db.RichSequenceDBLite

addRichSequence, removeRichSequence

Methods inherited from interface org.biojava.bio.seq.db.SequenceDBLite

addSequence, getSequence, removeSequence

Field Detail

urlBatchSequences

protected static final String urlBatchSequences

See Also:

Constant Field Values

Constructor Detail

GenbankRichSequenceDB

public GenbankRichSequenceDB()

The default constructor delegates to the parent class. The constructor refers to RichObjectFactory.getDefaultNamespace() so make sure your factory is initialised before calling this constructor. Sets the default factory to THRESHOLD.

Method Detail

getAddress

protected URL getAddress(String id)
                  throws MalformedURLException

Get the URL object for locating sequence object using eutils. The default value of the return format of the sequence object is text.

Throws:

MalformedURLException

makeBatchRequest

protected String makeBatchRequest(URL url,
                                  Set list)

Create the Http Post Request to fetch (in batch mode) a list of sequence with Genbank.

Parameters:

url - URL of the request

list - List of sequence identifier

Returns:

The Post request.

getRichSequence

public RichSequence getRichSequence(String id)
                             throws BioException,
                                    IllegalIDException

Given the appropriate Genbank ID, return the matching RichSequence object.

Specified by:

getRichSequence in interface RichSequenceDBLite

Parameters:

id - the Genbank ID to retrieve.

Returns:

the matching RichSequence object, or null if not found.

Throws:

Exception - if the sequence could not be retrieved for reasons other than the identifier not being found.

IllegalIDException - if the database doesn't know about the id

BioException

getRichSequence

public RichSequence getRichSequence(String id,
                                    Namespace nsp)
                             throws BioException,
                                    IllegalIDException

Given the appropriate Genbank ID, return the matching RichSequence object. Additionally define a new Namespace for the received RichSequence object.

Parameters:

id - the Genbank ID to retrieve.

nsp - the Namespace to define.

Returns:

the matching RichSequence object, or null if not found.

Throws:

Exception - if the sequence could not be retrieved for reasons other than the identifier not being found.

BioException

IllegalIDException

getRichSequences

public RichSequenceDB getRichSequences(Set list)
                                throws BioException,
                                       IllegalIDException

Retrieve rich sequences from a Genbank

Specified by:

getRichSequences in interface RichSequenceDBLite

Parameters:

list - List of NCBI sequence number (GI), accession, accession.version, fasta or seqid.

Returns:

The rich database object (HashSequenceDB) with downloaded rich sequences. You will need to cast the sequences you get from this database object into RichSequence objects if you want to access their full features.

Throws:

IllegalIDException - if the database doesn't know about the id

BioException

getRichSequences

public RichSequenceDB getRichSequences(Set list,
                                       RichSequenceDB database)
                                throws BioException,
                                       IllegalIDException

Retrieve rich sequences from a Genbank

Specified by:

getRichSequences in interface RichSequenceDBLite

Parameters:

list - List of NCBI sequence number (GI), accession, accession.version, fasta or seqid.

database - Where to store rich sequences. If database is null, use an HashSequenceDB Object.

Returns:

The database object with downloaded rich sequences. You will need to cast the sequences you get from this database object into RichSequence objects if you want to access their full features.

Throws:

IllegalIDException - if the database doesn't know about the id

BioException

getName

public String getName()

Description copied from interface: BioEntryDBLite

Get the name of this sequence database.

Specified by:

getName in interface BioEntryDBLite

Specified by:

getName in interface SequenceDBLite

Returns:

the name of the sequence database, which may be null.

ids

public Set ids()

Description copied from interface: SequenceDB

Get an immutable set of all of the IDs in the database. The ids are legal arguments to getSequence.

Specified by:

ids in interface BioEntryDB

Specified by:

ids in interface SequenceDB

Returns:

a Set of ids - at the moment, strings

getFactory

public RichSequenceBuilderFactory getFactory()

Getter for property factory.

Returns:

Value of property factory.

setFactory

public void setFactory(RichSequenceBuilderFactory factory)

Setter for property factory.

Parameters:

factory - New value of property factory.

getNamespace

public Namespace getNamespace()

Getter for property namespace.

Returns:

Value of property namespace.

setNamespace

public void setNamespace(Namespace namespace)

Setter for property namespace.

Parameters:

namespace - New value of property namespace.

setTool

public void setTool(String tool)

Set the tool identifier for Entrez. Defaults to 'biojavax'.

Parameters:

tool - the new identifier.

getTool

public String getTool()

Get the tool identifier for Entrez. Defaults to 'biojavax'.

Returns:

the identifier.

setEmail

public void setEmail(String email)

Set the email for Entrez. Defaults to 'anonymous@biojava.org'.

Parameters:

email - the new email.

getEmail

public String getEmail()

Get the email for Entrez. Defaults to 'anonymous@biojava.org'.

Returns:

the email.