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

java.lang.Object
  extended by 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
DASAlignmentCall()
          Constructs a DASAlignmentCall object.
DASAlignmentCall(java.lang.String url)
          Constructs a DASAlignmentCall object.
 
Method Summary
 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