org.biojava.bio.seq.db
Class NCBISequenceDB

java.lang.Object
  extended byorg.biojava.utils.AbstractChangeable
      extended byorg.biojava.bio.seq.db.WebSequenceDB
          extended byorg.biojava.bio.seq.db.NCBISequenceDB
All Implemented Interfaces:
Changeable, SequenceDBLite

public class NCBISequenceDB
extends WebSequenceDB

Author:
Matthew Pocock, Mark Schreiber

Field Summary
static java.lang.String DB_NUCLEOTIDE
           
static java.lang.String DB_PROTEIN
           
 
Fields inherited from interface org.biojava.bio.seq.db.SequenceDBLite
SEQUENCES
 
Constructor Summary
NCBISequenceDB()
          Default constructor, querys the Genbank nucleotide database on "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi" and retrieves sequences in FastaFormat.
NCBISequenceDB(java.lang.String database, SequenceFormat format)
          Parameterized constructor
NCBISequenceDB(java.lang.String server, java.lang.String CGI, java.lang.String database, SequenceFormat format)
          Parameterized constructor
 
Method Summary
protected  java.net.URL getAddress(java.lang.String uid)
           
protected  Alphabet getAlphabet()
           
 java.lang.String getDataBase()
           
 java.lang.String getName()
          Get the name of this sequence database.
 SequenceFormat getSequenceFormat()
           
 void setDatabase(java.lang.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, 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 java.lang.String DB_NUCLEOTIDE
See Also:
Constant Field Values

DB_PROTEIN

public static final java.lang.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(java.lang.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(java.lang.String server,
                      java.lang.String CGI,
                      java.lang.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 java.lang.String getDataBase()

setDatabase

public void setDatabase(java.lang.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 java.net.URL getAddress(java.lang.String uid)
                           throws java.net.MalformedURLException
Specified by:
getAddress in class WebSequenceDB
Throws:
java.net.MalformedURLException

getName

public java.lang.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.