import jalview.io.FormatAdapter;
import jalview.util.MessageManager;
import jalview.ws.ebi.EBIFetchClient;
-import jalview.ws.seqfetcher.DbSourceProxy;
import java.util.ArrayList;
import java.util.List;
* @author JimP
*
*/
-public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
+public class Pdb extends EbiFileRetrievedProxy
{
public Pdb()
{
super();
- addDbSourceProperty(DBRefSource.PROTSEQDB);
}
/*
*
* @see jalview.ws.DbSourceProxy#getAccessionSeparator()
*/
+ @Override
public String getAccessionSeparator()
{
// TODO Auto-generated method stub
*
* @see jalview.ws.DbSourceProxy#getAccessionValidator()
*/
+ @Override
public Regex getAccessionValidator()
{
return new Regex("([1-9][0-9A-Za-z]{3}):?([ _A-Za-z0-9]?)");
*
* @see jalview.ws.DbSourceProxy#getDbSource()
*/
+ @Override
public String getDbSource()
{
return DBRefSource.PDB;
*
* @see jalview.ws.DbSourceProxy#getDbVersion()
*/
+ @Override
public String getDbVersion()
{
return "0";
*
* @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
*/
+ @Override
public AlignmentI getSequenceRecords(String queries) throws Exception
{
AlignmentI pdbAlignment = null;
*
* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
*/
+ @Override
public boolean isValidReference(String accession)
{
Regex r = getAccessionValidator();
/**
* obtain human glyoxalase chain A sequence
*/
+ @Override
public String getTestQuery()
{
return "1QIPA";
}
+ @Override
public String getDbName()
{
return "PDB"; // getDbSource();