org.biojava.bio.program.das.dasalignment

Class DASAlignmentCall

java.lang.Object

org.biojava.bio.program.das.dasalignment.DASAlignmentCall

public class DASAlignmentCall
extends java.lang.Object

takes care of the communication with a DAS Alignment service.

Since:

1.4

Version:

%I% %G%

Author:

Andreas Prlic

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
Alignment[]	getAlignments() connect to a DAS alignment service and retreive alignments.
Alignment[]	getAlignments(java.lang.String query) connect to a DAS alignment service and retreive data.
java.lang.String	getServerurl() get url of alignment service.
Alignment[]	parseDASResponse(java.io.InputStream inStream) parse the Response of a DAS ALignment service and return a biojava Alignment object.
void	setServerurl(java.lang.String s) set url of aligmnent service.

Methods inherited from class java.lang.Object

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

Constructor Detail

DASAlignmentCall

public DASAlignmentCall()

Constructs a DASAlignmentCall object.

DASAlignmentCall

public DASAlignmentCall(java.lang.String url)

Constructs a DASAlignmentCall object.

Parameters:

url - a String ...

Method Detail

setServerurl

public void setServerurl(java.lang.String s)

set url of aligmnent service.

Parameters:

s - a String specifying the serverurl value

See Also:

getServerurl()

getServerurl

public java.lang.String getServerurl()

get url of alignment service.

Returns:

a String representing the serverurl value

See Also:

setServerurl(java.lang.String)

getAlignments

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

connect to a DAS alignment service and retreive alignments. return Alignment objects. uses the serverurl specified in the constructore to create http request

Returns:

an array of Alignment objects

Throws:

java.io.IOException - ...

getAlignments

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

connect to a DAS alignment service and retreive data. return a biojava Alignment object.

Parameters:

query - a String

Returns:

an array of Alignment objects

Throws:

java.io.IOException - ...

parseDASResponse

public Alignment[] parseDASResponse(java.io.InputStream inStream)
                             throws java.io.IOException,
                                    org.xml.sax.SAXException

parse the Response of a DAS ALignment service and return a biojava Alignment object.

Throws:

java.io.IOException

org.xml.sax.SAXException