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73 lines (64 loc) · 2.04 KB
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/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.structure.align;
import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.align.ce.ConfigStrucAligParams;
import org.biojava.nbio.structure.align.model.AFPChain;
public interface StructureAlignment {
/** Run an alignment while specifying the atoms to be aligned. Will used default parameters for the algorithm.
*
* @param ca1
* @param ca2
* @return the afpChain object that contains the alignment.
* @throws StructureException
*/
public AFPChain align(Atom[] ca1, Atom[] ca2) throws StructureException;
/** run an alignment and also send a bean containing the parameters.
*
* @param ca1
* @param ca2
* @param params
* @return the afpChain object that contains the alignment.
* @throws StructureException
*/
public AFPChain align(Atom[] ca1, Atom[] ca2, Object params) throws StructureException;
/** Return the paramers for this algorithm.
*
* @return The returned object will be a Java bean.
*/
public ConfigStrucAligParams getParameters();
/** Set the default parameters for this algorithm to use
*
* @param parameters
*/
public void setParameters(ConfigStrucAligParams parameters);
/** Get the name of the Algorithm
*
* @return the name of the algorithm
*/
public String getAlgorithmName();
/** Get the Version information for this Algorithm.
*
* @return the version of the algorithm
*/
public String getVersion();
}