Package org.biojava.bio.seq.db

Class GenbankSequenceDB

java.lang.Object

org.biojava.bio.seq.db.GenbankSequenceDB

public class GenbankSequenceDB
extends Object

This class contains functions accessing DNA sequences in Genbank format.

Author:

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

Field Summary

Fields

Modifier and Type	Field	Description
protected boolean	ExceptionFound
protected boolean	IOExceptionFound
protected static String	urlBatchSequences

Constructor Summary

Constructors

Constructor	Description
GenbankSequenceDB()

Method Summary

Modifier and Type	Method	Description
boolean	checkException()
boolean	checkIOException()
protected URL	getAddress(String id)	Get the URL object for locating sequence object using eutils.
protected URL	getAddress(String id, String format)	Get the URL object for locating sequence object using eutils.
protected Alphabet	getAlphabet()
String	getName()
Sequence	getSequence(String id)
protected SequenceFormat	getSequenceFormat()
SequenceDB	getSequences(Set list)	Retrieve sequences from a Genbank
SequenceDB	getSequences(Set list, SequenceDB database)	Retrieve sequences from a Genbank
protected String	makeBatchRequest(URL url, Set list)	Create the Http Post Request to fetch (in batch mode) a list of sequence with Genbank.

Methods inherited from class java.lang.Object

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

Field Detail

IOExceptionFound

protected boolean IOExceptionFound

ExceptionFound

protected boolean ExceptionFound

urlBatchSequences

protected static final String urlBatchSequences

See Also:

Constant Field Values

Constructor Detail

GenbankSequenceDB

public GenbankSequenceDB()

Method Detail

getSequenceFormat

protected SequenceFormat getSequenceFormat()

getAlphabet

protected Alphabet getAlphabet()

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

getAddress

protected URL getAddress(String id,
                         String format)
                  throws MalformedURLException

Get the URL object for locating sequence object using eutils. User could specify the return format of the sequence object.

Throws:

MalformedURLException

getName

public String getName()

getSequence

public Sequence getSequence(String id)
                     throws Exception

Throws:

Exception

checkIOException

public boolean checkIOException()

checkException

public boolean checkException()

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.

getSequences

public SequenceDB getSequences(Set list)
                        throws BioException

Retrieve sequences from a Genbank

Parameters:

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

Returns:

The database object (HashSequenceDB) with downloaded sequences.

Throws:

BioException

getSequences

public SequenceDB getSequences(Set list,
                               SequenceDB database)
                        throws BioException

Retrieve sequences from a Genbank

Parameters:

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

database - Where to store sequences. if database is null, use an HashSequenceDB Objet.

Returns:

The database object with downloaded sequences.

Throws:

BioException