Interface RemotePairwiseAlignmentProperties

  • All Superinterfaces:
    Serializable
    All Known Implementing Classes:
    NCBIQBlastAlignmentProperties

    public interface RemotePairwiseAlignmentProperties
    extends 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
    • Method Detail

      • getAlignmentOption

        String getAlignmentOption​(String key)
                           throws 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:
        Exception - if key is not in the map of output options.
      • setAlignementOption

        void setAlignementOption​(String key,
                                 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

        Set<StringgetAlignmentOptions()
        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