Class RemoteQBlastOutputProperties

java.lang.Object
org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties
All Implemented Interfaces:
Serializable, 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:
  • Constructor Details

    • 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 Details

    • getOutputFormat

      Simply returns stream output format for the actual RemoteQBlastOutputProperties object
      Returns:
      a String with the value of key FORMAT_TYPE.
    • setOutputFormat

      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

      Method that returns the alignment output format for this actual RemoteQBlastOutputProperties object
      Returns:
      a String with the value of key ALIGNMENT_VIEW
    • setAlignmentOutputFormat

      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

      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.
    • setOutputOption

      public void setOutputOption(String o, String v)
      Description copied from interface: RemotePairwiseAlignmentOutputProperties
      Method to set the value for a specific output parameter using a key to store in a map.
      Specified by:
      setOutputOption in interface RemotePairwiseAlignmentOutputProperties
      Parameters:
      o - :the key use to designate the value to be stored
      v - :the actual value matched to key
    • getOutputOptions

      Description copied from interface: RemotePairwiseAlignmentOutputProperties
      Method to get all keys to the information stored in this object.
      Specified by:
      getOutputOptions in interface RemotePairwiseAlignmentOutputProperties
      Returns:
      a Set with all keys held in this instance of the object