Class 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 Description
      DASAlignmentCall()
      Constructs a DASAlignmentCall object.
      DASAlignmentCall​(java.lang.String url)
      Constructs a DASAlignmentCall object.
    • 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.
      • 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