Class DASAlignmentCall
- java.lang.Object
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- org.biojava.bio.program.das.dasalignment.DASAlignmentCall
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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
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Constructor Summary
Constructors Constructor Description DASAlignmentCall()
Constructs a DASAlignmentCall object.DASAlignmentCall(java.lang.String url)
Constructs a DASAlignmentCall object.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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.
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Method Detail
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setServerurl
public void setServerurl(java.lang.String s)
set url of aligmnent service.- Parameters:
s
- a String specifying the serverurl value- See Also:
getServerurl()
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getServerurl
public java.lang.String getServerurl()
get url of alignment service.- Returns:
- a String representing the serverurl value
- See Also:
setServerurl(java.lang.String)
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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
- ...
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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
- ...
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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
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