Package org.biojavax.bio.alignment

Interface RemotePairwiseAlignmentProperties

  • All Superinterfaces:
    Serializable
    All Known Implementing Classes:
    RemoteQBlastAlignmentProperties
    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 RemoteQBlastProperties
    Since:
    1.8
    Author:
    Sylvain Foisy, Diploide BioIT

    • Method Detail

      • getAlignmentOption

        String getAlignmentOption​(String key)
                   throws BioException
        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:
        BioException - 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<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