Package org.biojava.bio.program.das.dasalignment

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

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method 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 - ...