Package org.biojava.nbio.ws.alignment

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

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final long
    serialVersionUID
     

  • Method Summary

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

  • Field Details

  • Method Details

    • 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<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