Class AbstractStructureAlignment

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static java.lang.String newline  
    • Method Summary

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      abstract AFPChain align​(Atom[] ca1, Atom[] ca2)
      Run an alignment while specifying the atoms to be aligned.
      abstract AFPChain align​(Atom[] ca1, Atom[] ca2, java.lang.Object params)
      run an alignment and also send a bean containing the parameters.
      abstract java.lang.String getAlgorithmName()
      Get the name of the Algorithm
      abstract ConfigStrucAligParams getParameters()
      Return the paramers for this algorithm.
      abstract java.lang.String getVersion()
      Get the Version information for this Algorithm.
      abstract void setParameters​(ConfigStrucAligParams parameters)
      Set the default parameters for this algorithm to use
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait