org.biojava.bio.structure.io
Class PDBMSDReader

java.lang.Object
  extended by org.biojava.bio.structure.io.PDBMSDReader
All Implemented Interfaces:
StructureIO

public class PDBMSDReader
extends java.lang.Object
implements StructureIO

retreive a structure from an installation of the MSD - search database ( http://www.ebi.ac.uk/msd/index.html , http://www.ebi.ac.uk/msd-srv/docs/dbdoc/ )


Field Summary
protected  javax.sql.DataSource dataSource
           
 
Constructor Summary
PDBMSDReader()
           
 
Method Summary
 Structure getStructureById(java.lang.String pdbId)
          Get a structure by providing a PDB code.
 void setDBConnection(java.lang.String dbDriver, java.lang.String dbUrl, java.lang.String dbUsername, java.lang.String dbPassword)
          open a database conenction to the MSD search database
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

dataSource

protected javax.sql.DataSource dataSource
Constructor Detail

PDBMSDReader

public PDBMSDReader()
Method Detail

setDBConnection

public void setDBConnection(java.lang.String dbDriver,
                            java.lang.String dbUrl,
                            java.lang.String dbUsername,
                            java.lang.String dbPassword)
                     throws java.sql.SQLException
open a database conenction to the MSD search database

Parameters:
dbDriver - specified which JDBC driver to use e.g.
dbUrl - connection string
dbUsername - the username in the db
dbPassword - password to use
Throws:
java.sql.SQLException

getStructureById

public Structure getStructureById(java.lang.String pdbId)
                           throws java.io.IOException
Get a structure by providing a PDB code. expects connections parameters to be set a system properties.

Specified by:
getStructureById in interface StructureIO
Parameters:
pdbId - a String specifying the id value (PDB code)
Returns:
a Structure object, or null if no structure with matching PDB code has been found
Throws:
java.io.IOException - ...