Field Detail

• algorithmName

  public static final java.lang.String algorithmName

  See Also:

  Constant Field Values

Constructor Detail

• BioJavaStructureAlignment

  public BioJavaStructureAlignment()

Method Detail

• getAlgorithmName

  public java.lang.String getAlgorithmName()

  Description copied from interface: StructureAlignment
  Get the name of the Algorithm

  Specified by:

  getAlgorithmName in interface StructureAlignment

  Returns:

  the name of the algorithm

• getParameters

  public ConfigStrucAligParams getParameters()

  Description copied from interface: StructureAlignment
  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)

  Description copied from interface: StructureAlignment
  Set the default parameters for this algorithm to use

  Specified by:

  setParameters in interface StructureAlignment

• getVersion

  public java.lang.String getVersion()

  Description copied from interface: StructureAlignment
  Get the Version information for this Algorithm.

  Specified by:

  getVersion in interface StructureAlignment

  Returns:

  the version of the algorithm

• printHelp

  public java.lang.String printHelp()

• align

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

  Description copied from interface: StructureAlignment
  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,
                        java.lang.Object params)
                 throws StructureException

  Description copied from interface: StructureAlignment
  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