org.biojavax.bio.alignment.blast

Class RemoteQBlastService

java.lang.Object

org.biojavax.bio.alignment.blast.RemoteQBlastService

All Implemented Interfaces:

RemotePairwiseAlignmentService

public class RemoteQBlastService
extends Object
implements RemotePairwiseAlignmentService

RemoteQBlastService - A simple way of submitting BLAST request to the QBlast service at NCBI.

NCBI provides a Blast server through a CGI-BIN interface. RemoteQBlastService simply encapsulates an access to it by giving users access to get/set methods to fix sequence, program and database as well as advanced options.

The philosophy behind RemoteQBlastService is to disconnect submission of Blast requests from collection of Blast results. This is done so to allow a user to submit multiple Blast requests while allowing recovery of the reports at a later time.

Presently, only blastall programs are accessible. blastpgp and megablast are high-priorities.

Since:

1.8

Author:

Sylvain Foisy, Diploide BioIT

Constructor Summary

Constructors

Constructor and Description
RemoteQBlastService() The constructor for a QBlast service request.

Method Summary

Methods

Modifier and Type	Method and Description
InputStream	getAlignmentResults(String id, RemotePairwiseAlignmentOutputProperties rb) This method extracts the actual Blast report for this request ID.
String	getEmail() Get the email for QBlast.
String	getTool() Get the tool identifier for QBlast.
boolean	isReady(String id, long present) This method is used only for the executeBlastSearch method to check for completion of request using the NCBI specified RTOE variable
void	printRemoteBlastInfo() A simple method to check the availability of the QBlast service
String	sendAlignmentRequest(int gid, RemotePairwiseAlignmentProperties rpa) This method is a wrapper that executes the Blast request via the Put command of the CGI-BIN interface with the specified parameters and a GenBank GID.
String	sendAlignmentRequest(RichSequence rs, RemotePairwiseAlignmentProperties rpa) This method is a wrapper that executes the Blast request via the Put command of the CGI-BIN interface with the specified parameters and a RichSequence.
String	sendAlignmentRequest(String str, RemotePairwiseAlignmentProperties rpa) This method is a wrapper that executes the Blast request via the Put command of the CGI-BIN interface with the specified parameters and a string representing the sequence.
void	setEmail(String email) Set the email for QBlast.
void	setTool(String tool) Set the tool identifier for QBlast.

Methods inherited from class java.lang.Object

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

Constructor Detail

RemoteQBlastService

public RemoteQBlastService()
                    throws BioException

The constructor for a QBlast service request.

Throws:

BioException - if the NCBI URL is unresponsive

Method Detail

sendAlignmentRequest

public String sendAlignmentRequest(String str,
                          RemotePairwiseAlignmentProperties rpa)
                            throws BioException

This method is a wrapper that executes the Blast request via the Put command of the CGI-BIN interface with the specified parameters and a string representing the sequence. It gets the estimated time of completion by capturing the value of the RTOE variable and sets a loop that will check for completion of analysis at intervals specified by RTOE.

It also capture the value for the RID variable, necessary for fetching the actual results after completion.

Specified by:

sendAlignmentRequest in interface RemotePairwiseAlignmentService

Parameters:

str - : a String with a sequence

rpa - : a RemotePairwiseAlignmentProperties object

Returns:

rid : a String with the request ID for this sequence

Throws:

BioException - if it is not possible to sent the BLAST command

sendAlignmentRequest

public String sendAlignmentRequest(RichSequence rs,
                          RemotePairwiseAlignmentProperties rpa)
                            throws BioException

This method is a wrapper that executes the Blast request via the Put command of the CGI-BIN interface with the specified parameters and a RichSequence. It gets the estimated time of completion by capturing the value of the RTOE variable and sets a loop that will check for completion of analysis at intervals specified by RTOE.

It also capture the value for the RID variable, necessary for fetching the actual results after completion.

Specified by:

sendAlignmentRequest in interface RemotePairwiseAlignmentService

Parameters:

rs - :a RichSequence object

rpa - :a RemotePairwiseAlignmentProperties object

Returns:

rid : a String with the request ID for this sequence

Throws:

BioException - if it is not possible to sent the BLAST command

sendAlignmentRequest

public String sendAlignmentRequest(int gid,
                          RemotePairwiseAlignmentProperties rpa)
                            throws BioException

This method is a wrapper that executes the Blast request via the Put command of the CGI-BIN interface with the specified parameters and a GenBank GID. It gets the estimated time of completion by capturing the value of the RTOE variable and sets a loop that will check for completion of analysis at intervals specified by RTOE.

It also capture the value for the RID variable, necessary for fetching the actual results after completion.

Parameters:

gid - :an integer with a Genbank GID

rpa - :a RemotePairwiseAlignmentProperties object

Returns:

rid : a String with the request ID for this sequence

Throws:

BioException - if it is not possible to sent the BLAST command

isReady

public boolean isReady(String id,
              long present)
                throws BioException

This method is used only for the executeBlastSearch method to check for completion of request using the NCBI specified RTOE variable

Specified by:

isReady in interface RemotePairwiseAlignmentService

Parameters:

id - : a valid request ID

present - : a representation of "now" using System.currentTimeMillis().

Returns:

a boolean value telling if the request has been completed or not.

Throws:

BioException - if the ID does not exist.

getAlignmentResults

public InputStream getAlignmentResults(String id,
                              RemotePairwiseAlignmentOutputProperties rb)
                                throws BioException

This method extracts the actual Blast report for this request ID. It uses an object implementing the RemotePairwiseAlignmentOutputProperties interface which will specify output formatting options.

Specified by:

getAlignmentResults in interface RemotePairwiseAlignmentService

Parameters:

id - :a valid request ID

rb - : a RemotePairwiseAlignmentOutputProperties that will specify specific output formatting commands

Returns:

an InputStream that can be use any way one might desire

Throws:

BioException - if it is not possible to recover the results.

printRemoteBlastInfo

public void printRemoteBlastInfo()
                          throws BioException

A simple method to check the availability of the QBlast service

Throws:

BioException - if unable to connect to the NCBI QBlast service

setTool

public void setTool(String tool)

Set the tool identifier for QBlast. Defaults to 'biojavax'.

Parameters:

tool - the new identifier.

getTool

public String getTool()

Get the tool identifier for QBlast. Defaults to 'biojavax'.

Returns:

the identifier.

setEmail

public void setEmail(String email)

Set the email for QBlast. Defaults to 'anonymous@biojava.org'.

Parameters:

email - the new email.

getEmail

public String getEmail()

Get the email for QBlast. Defaults to 'anonymous@biojava.org'.

Returns:

the email.