Class RemoteQBlastOutputProperties

  • All Implemented Interfaces:
    java.io.Serializable, RemotePairwiseAlignmentOutputProperties

    public class RemoteQBlastOutputProperties
    extends java.lang.Object
    implements RemotePairwiseAlignmentOutputProperties
    The actual implementation of the RemotePairwiseAlignmentOutputProperties interface for the QBlast service. The constructor for this class builds an object with default format values. Any modification will either use the generic method setOutputOption method or use the wrapper methods that are actually build around the generic method.
    Since:
    1.8
    Author:
    Sylvain Foisy, Diploide BioIT
    See Also:
    Serialized Form
    • Constructor Summary

      Constructors 
      Constructor Description
      RemoteQBlastOutputProperties()
      This constructor build the parameters for the default output of the GET command sent to the QBlast service.
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      int getAlignmentNumber()
      A method that simply returns the number of alignments fetched with this RemoteQBlastOutputProperties object.
      java.lang.String getAlignmentOutputFormat()
      Method that returns the alignment output format for this actual RemoteQBlastOutputProperties object
      int getDescriptionNumber()
      A method that simply returns the number of descriptions fetched with this RemoteQBlastOutputProperties object.
      java.lang.String getOutputFormat()
      Simply returns stream output format for the actual RemoteQBlastOutputProperties object
      java.lang.String getOutputOption​(java.lang.String o)
      Method that returns any value associated to any key for this RemoteQBlastOutputProperties object.
      java.util.Set<java.lang.String> getOutputOptions()
      Method to get all keys to the information stored in this object.
      void setAlignmentNumber​(int i)
      A method to set the number of alignments to fetch to the GET command.
      void setAlignmentOutputFormat​(RemoteQBlastOutputFormat rf)
      This method is use to set the alignment output format to get from the QBlast service
      void setDescriptionNumber​(int i)
      A method to set the number of descriptions to fetch to the GET command.
      void setOutputFormat​(RemoteQBlastOutputFormat rf)
      This method is use to set the stream output format to get from the QBlast service
      void setOutputOption​(java.lang.String o, java.lang.String v)
      Method to set the value for a specific output parameter using a key to store in a map.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • RemoteQBlastOutputProperties

        public RemoteQBlastOutputProperties()
        This constructor build the parameters for the default output of the GET command sent to the QBlast service. Here are the default values: FORMAT_TYPE = Text; ALIGNMENT_VIEW = Pairwise DESCRIPTIONS = 100; ALIGNMENTS = 100;
    • Method Detail

      • getOutputFormat

        public java.lang.String getOutputFormat()
        Simply returns stream output format for the actual RemoteQBlastOutputProperties object
        Returns:
        a String with the value of key FORMAT_TYPE.
      • setOutputFormat

        public void setOutputFormat​(RemoteQBlastOutputFormat rf)
                             throws BioException
        This method is use to set the stream output format to get from the QBlast service
        Parameters:
        rf - :an enum from RemoteQBlastOutputFormat
        Throws:
        BioException - if the enum is neither of RemoteQBlastOutputFormat.TEXT/XML/HTML
      • getAlignmentOutputFormat

        public java.lang.String getAlignmentOutputFormat()
        Method that returns the alignment output format for this actual RemoteQBlastOutputProperties object
        Returns:
        a String with the value of key ALIGNMENT_VIEW
      • setAlignmentOutputFormat

        public void setAlignmentOutputFormat​(RemoteQBlastOutputFormat rf)
                                      throws BioException
        This method is use to set the alignment output format to get from the QBlast service
        Parameters:
        rf - :an enum from RemoteQBlastOutputFormat
        Throws:
        BioException - if the enum is neither of RemoteQBlastOutputFormat.PAIRWISE/QUERY_ANCHORED/QUERY_ANCHORED_NO_IDENTITIES/FLAT_QUERY_ANCHORED FLAT_QUERY_ANCHORED_NO_IDENTITIES/TABULAR
      • getDescriptionNumber

        public int getDescriptionNumber()
        A method that simply returns the number of descriptions fetched with this RemoteQBlastOutputProperties object.
        Returns:
        an int with the value of the key DESCRIPTIONS
      • setDescriptionNumber

        public void setDescriptionNumber​(int i)
        A method to set the number of descriptions to fetch to the GET command.
        Parameters:
        i - :an int with the required number of descriptions to fetch.
      • getAlignmentNumber

        public int getAlignmentNumber()
        A method that simply returns the number of alignments fetched with this RemoteQBlastOutputProperties object.
        Returns:
        an int with the value of the key ALIGNMENTS.
      • setAlignmentNumber

        public void setAlignmentNumber​(int i)
        A method to set the number of alignments to fetch to the GET command.
        Parameters:
        i - :an int with the required number of alignments to fetch.
      • getOutputOption

        public java.lang.String getOutputOption​(java.lang.String o)
                                         throws BioException
        Method that returns any value associated to any key for this RemoteQBlastOutputProperties object.
        Specified by:
        getOutputOption in interface RemotePairwiseAlignmentOutputProperties
        Parameters:
        o - :a String with the required key for this map.
        Returns:
        a String with the value associated with this key
        Throws:
        BioException - if key is not in the map of output options.