org.biojava.bio.program.das.dasalignment

Class DASAlignmentClient

java.lang.Object

org.biojava.bio.program.das.dasalignment.DASAlignmentClient

public class DASAlignmentClient
extends java.lang.Object

A DAS client that connects to a DAS aligmnent service and returns a Biojava Alignment object.

Constructor Summary

Constructors

Constructor and Description
DASAlignmentClient() Constructs a DASAlignmentClient object.
DASAlignmentClient(java.lang.String url) Constructs a DASAlignmentClient object.

Method Summary

Modifier and Type	Method and Description
Alignment[]	getAlignments() Returns the alignments.
Alignment[]	getAlignments(java.lang.String query_) Returns the alignments.
java.lang.String	getQuery() Returns the query.
void	setQuery(java.lang.String q) Specifies the query.

Methods inherited from class java.lang.Object

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

Constructor Detail

DASAlignmentClient

public DASAlignmentClient()

Constructs a DASAlignmentClient object.

DASAlignmentClient

public DASAlignmentClient(java.lang.String url)

Constructs a DASAlignmentClient object.

Parameters:

url - a String ...

Method Detail

setQuery

public void setQuery(java.lang.String q)

Specifies the query.

Parameters:

q - a String specifying the query value

See Also:

getQuery()

getQuery

public java.lang.String getQuery()

Returns the query.

Returns:

a String representing the query value

See Also:

setQuery(java.lang.String)

getAlignments

public Alignment[] getAlignments(java.lang.String query_)
                          throws java.io.IOException

Returns the alignments.

Parameters:

query_ - a String

Returns:

an array of Alignment objects

Throws:

java.io.IOException - ...

getAlignments

public Alignment[] getAlignments()
                          throws java.io.IOException

Returns the alignments.

Returns:

an array of Alignment objects

Throws:

java.io.IOException - ...