Interface RemotePairwiseAlignmentProperties

  • All Superinterfaces:
    java.io.Serializable
    All Known Implementing Classes:
    NCBIQBlastAlignmentProperties

    public interface RemotePairwiseAlignmentProperties
    extends java.io.Serializable
    RemotePairwiseAlignmentProperties is a interface that contains the barest of methods for setting and getting Alignment properties. Ideally, one would extend this class if creating a service by creating wrapper methods that actually call either getAlignementOption or setAlignementOption with specific values for parameter names and checking values for options. For an example, go see NCBIQBlastProperties
    Since:
    Biojava 3
    Author:
    Sylvain Foisy, Diploide BioIT
    • Field Summary

      Fields 
      Modifier and Type Field Description
      static long serialVersionUID  
    • Method Summary

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      java.lang.String getAlignmentOption​(java.lang.String key)
      Method that returns the value associated with the key given in parameter.
      java.util.Set<java.lang.String> getAlignmentOptions()
      Method to get all keys to the information stored in this object.
      void setAlignementOption​(java.lang.String key, java.lang.String val)
      Method to set the value for a specific alignment parameter using a key to store in a map.
    • Method Detail

      • getAlignmentOption

        java.lang.String getAlignmentOption​(java.lang.String key)
                                     throws java.lang.Exception
        Method that returns the value associated with the key given in parameter.
        Parameters:
        key - :a String with the required key for this map.
        Returns:
        a String with the value associated with this key
        Throws:
        java.lang.Exception - if key is not in the map of output options.
      • setAlignementOption

        void setAlignementOption​(java.lang.String key,
                                 java.lang.String val)
        Method to set the value for a specific alignment parameter using a key to store in a map.
        Parameters:
        key - :the key use to designate the value to be stored
        val - :the actual value matched to key
      • getAlignmentOptions

        java.util.Set<java.lang.String> getAlignmentOptions()
        Method to get all keys to the information stored in this object.
        Returns:
        a Set with all keys held in this instance of the object