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BioJavaStructureAlignment (biojava 5.2.0 API)

  • java.lang.Object
    • org.biojava.nbio.structure.align.BioJavaStructureAlignment
  • All Implemented Interfaces:
    StructureAlignment
    public class BioJavaStructureAlignment
extends Object
implements StructureAlignment

    Wrapper for the BioJava Structure Alignment Implementation

    Author:
    Andreas Prlic

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static String algorithmName  

    • Constructor Summary

      Constructors 
      Constructor Description
      BioJavaStructureAlignment()  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      AFPChain align​(Atom[] ca1, Atom[] ca2)

      Run an alignment while specifying the atoms to be aligned.
      AFPChain align​(Atom[] ca1, Atom[] ca2, Object params)

      run an alignment and also send a bean containing the parameters.
      String getAlgorithmName()

      Get the name of the Algorithm
      ConfigStrucAligParams getParameters()

      Return the paramers for this algorithm.
      String getVersion()

      Get the Version information for this Algorithm.
      String printHelp()  
      void setParameters​(ConfigStrucAligParams o)

      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

    • Field Detail

      • algorithmName

        public static final String algorithmName
        See Also:
        Constant Field Values

    • Constructor Detail

      • BioJavaStructureAlignment

        public BioJavaStructureAlignment()

    • Method Detail

      • getAlgorithmName

        public String getAlgorithmName()

        Get the name of the Algorithm

        Specified by:
        getAlgorithmName in interface StructureAlignment
        Returns:
        the name of the algorithm

      • getParameters

        public ConfigStrucAligParams getParameters()

        Return the paramers for this algorithm.

        Specified by:
        getParameters in interface StructureAlignment
        Returns:
        The returned object will be a Java bean.

      • setParameters

        public void setParameters​(ConfigStrucAligParams o)

        Set the default parameters for this algorithm to use

        Specified by:
        setParameters in interface StructureAlignment

      • getVersion

        public String getVersion()

        Get the Version information for this Algorithm.

        Specified by:
        getVersion in interface StructureAlignment
        Returns:
        the version of the algorithm

      • printHelp

        public String printHelp()

      • align

        public AFPChain align​(Atom[] ca1,
                      Atom[] ca2)
               throws StructureException

        Run an alignment while specifying the atoms to be aligned. Will used default parameters for the algorithm.

        Specified by:
        align in interface StructureAlignment
        Returns:
        the afpChain object that contains the alignment.
        Throws:
        StructureException

      • align

        public AFPChain align​(Atom[] ca1,
                      Atom[] ca2,
                      Object params)
               throws StructureException

        run an alignment and also send a bean containing the parameters.

        Specified by:
        align in interface StructureAlignment
        Returns:
        the afpChain object that contains the alignment.
        Throws:
        StructureException