Class CallableStructureAlignment

  • All Implemented Interfaces:
    java.util.concurrent.Callable<AFPChain>

    public class CallableStructureAlignment
    extends java.lang.Object
    implements java.util.concurrent.Callable<AFPChain>
    • Constructor Detail

      • CallableStructureAlignment

        public CallableStructureAlignment()
        Default constructor. Used in DB search. Instantiates an empty object, everything has to be set independently.
      • CallableStructureAlignment

        public CallableStructureAlignment​(Atom[] ca1,
                                          Atom[] ca2,
                                          java.lang.String algorithmName,
                                          ConfigStrucAligParams params)
        Constructor for all-to-all alignment calculation. Used for MultipleMC seed alignment calculation, for example.
        Parameters:
        ca1 - Atoms to align of the first structure
        ca2 - Atoms to align of the second structure
        algorithmName - the pairwise aligner algorithm to use, a new instance will be created for each thread.
        params - parameter bean for the alignment.
    • Method Detail

      • call

        public AFPChain call()
                      throws java.lang.Exception
        Specified by:
        call in interface java.util.concurrent.Callable<AFPChain>
        Throws:
        java.lang.Exception
      • getPair

        public PdbPair getPair()
      • setPair

        public void setPair​(PdbPair pair)
      • setCache

        public void setCache​(AtomCache cache)
      • getCa1

        public Atom[] getCa1()
      • setCa1

        public void setCa1​(Atom[] ca1)
      • setOutputDir

        public void setOutputDir​(java.io.File outFileF)
      • setAlgorithmName

        public void setAlgorithmName​(java.lang.String algorithmName)