Package org.biojava.nbio.structure.align

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 Details

    • align

      MultipleAlignment align(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

      MultipleAlignment align(List<Atom[]> atomArrays, 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:

    • 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

      String getAlgorithmName()
      Get the name of this Algorithm.
      Returns:
      String name of the algorithm

    • getVersion

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