Interface MultipleStructureAligner

  • All Known Implementing Classes:
    MultipleMcMain

    public interface MultipleStructureAligner
    Interface for the Multiple Structure Alignment Algorithms. The Pairwise Alignment Algorithms can also implement this class to be able to return MultipleAlignment Objects.
    Author:
    Aleix Lafita
    • Method Detail

      • align

        MultipleAlignment align​(java.util.List<Atom[]> atomArrays)
                         throws StructureException
        Run an alignment while specifying the atoms to be aligned. The default parameters for the algorithm are used.
        Parameters:
        atomArrays - List of Atoms of all the structures
        Returns:
        MultipleAlignment object that contains the alignment.
        Throws:
        StructureException
        See Also:
        align(List,Object)
      • align

        MultipleAlignment align​(java.util.List<Atom[]> atomArrays,
                                java.lang.Object params)
                         throws StructureException
        Run an alignment and also send a bean containing the parameters.
        Parameters:
        atomArrays - List of Atoms of all the structures
        Returns:
        MultipleAlignment object that contains the alignment.
        Throws:
        StructureException
        See Also:
        align(List)
      • getParameters

        ConfigStrucAligParams getParameters()
        Return the parameters of this algorithm instance.
        Returns:
        The returned Object will be a Java bean.
      • setParameters

        void setParameters​(ConfigStrucAligParams parameters)
        Set the parameters for this algorithm to use.
        Parameters:
        parameters -
      • getAlgorithmName

        java.lang.String getAlgorithmName()
        Get the name of this Algorithm.
        Returns:
        String name of the algorithm
      • getVersion

        java.lang.String getVersion()
        Get the Version information for this Algorithm.
        Returns:
        String version of the algorithm