org.biojava.bio.seq.db

Class NCBISequenceDB

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.seq.db.WebSequenceDB

org.biojava.bio.seq.db.NCBISequenceDB

All Implemented Interfaces:

SequenceDBLite, Changeable

public class NCBISequenceDB
extends WebSequenceDB

Author:

Matthew Pocock, Mark Schreiber

Field Summary

Fields

Modifier and Type	Field and Description
static String	DB_NUCLEOTIDE
static String	DB_PROTEIN

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

SEQUENCES

Constructor Summary

Constructors

Constructor and Description
NCBISequenceDB() Default constructor, querys the Genbank nucleotide database on "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi" and retrieves sequences in FastaFormat.
NCBISequenceDB(String database, SequenceFormat format) Parameterized constructor
NCBISequenceDB(String server, String CGI, String database, SequenceFormat format) Parameterized constructor

Method Summary

Modifier and Type	Method and Description
protected URL	getAddress(String uid)
protected Alphabet	getAlphabet()
String	getDataBase()
String	getName() Get the name of this sequence database.
SequenceFormat	getSequenceFormat()
void	setDatabase(String dataBase)
void	setSequenceFormat(SequenceFormat format)

Methods inherited from class org.biojava.bio.seq.db.WebSequenceDB

addSequence, getSequence, removeSequence

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.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

DB_NUCLEOTIDE

public static final String DB_NUCLEOTIDE

See Also:

Constant Field Values

DB_PROTEIN

public static final String DB_PROTEIN

See Also:

Constant Field Values

Constructor Detail

NCBISequenceDB

public NCBISequenceDB()

Default constructor, querys the Genbank nucleotide database on "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi" and retrieves sequences in FastaFormat.

NCBISequenceDB

public NCBISequenceDB(String database,
                      SequenceFormat format)

Parameterized constructor

Parameters:

database - must be one of "nucleotide" or "protein" (use the static DB fields)

format - must be one of GenbankFormat or FastaFormat

Throws:

BioRuntimeException - if the database or format is invalid

NCBISequenceDB

public NCBISequenceDB(String server,
                      String CGI,
                      String database,
                      SequenceFormat format)
               throws BioRuntimeException

Parameterized constructor

Parameters:

server - eg "http://www.ncbi.nlm.nih.gov/"

CGI - eg "entrez/query.fcgi"

database - must be one of "nucleotide" or "protein" (use the static DB fields)

format - must be one of GenbankFormat or FastaFormat

Throws:

BioRuntimeException - if the database or format is invalid

Method Detail

getDataBase

public String getDataBase()

setDatabase

public void setDatabase(String dataBase)
                 throws BioException

Parameters:

dataBase - must be one of "nucleotide" or "protein" (use the static DB fields)

Throws:

BioException - if an unknown database name is used.

getSequenceFormat

public SequenceFormat getSequenceFormat()

Specified by:

getSequenceFormat in class WebSequenceDB

setSequenceFormat

public void setSequenceFormat(SequenceFormat format)
                       throws BioException

Parameters:

format - must be one of FastaFormat or GenbankFormat

Throws:

BioException - if an unknown SequenceFormat is used

getAlphabet

protected Alphabet getAlphabet()

Specified by:

getAlphabet in class WebSequenceDB

getAddress

protected URL getAddress(String uid)
                  throws MalformedURLException

Specified by:

getAddress in class WebSequenceDB

Throws:

MalformedURLException

getName

public String getName()

Description copied from interface: SequenceDBLite

Get the name of this sequence database.

Returns:

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