// Path: biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/ProfilePair.java
// public interface ProfilePair<S extends Sequence<C>, C extends Compound> extends Profile<S, C> {
// 
// 	/**
// 	 * Returns the first {@link Profile} of the pair.
// 	 *
// 	 * @return the first {@link Profile} of the pair
// 	 */
// 	Profile<S, C> getQuery();
// 
// 	/**
// 	 * Returns the second {@link Profile} of the pair.
// 	 *
// 	 * @return the second {@link Profile} of the pair
// 	 */
// 	Profile<S, C> getTarget();
// 
// }


import org.biojava.nbio.core.alignment.template.ProfilePair;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;
/*
 *                    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/
 *
 * Created on June 7, 2010
 * Author: Mark Chapman
 */

package org.biojava.nbio.alignment.template;


/**
 * Defines an {@link Aligner} for a pair of {@link Profile}s.
 *
 * @author Mark Chapman
 * @param <S> each {@link Sequence} in the pair of alignment {@link Profile}s is of type S
 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
 */
public interface ProfileProfileAligner<S extends Sequence<C>, C extends Compound> extends Aligner<S, C>,
		ProfileProfileScorer<S, C> {

	/**
	 * Returns alignment profile pair.
	 *
	 * @return alignment profile pair
	 */
// Path: biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/ProfilePair.java
// public interface ProfilePair<S extends Sequence<C>, C extends Compound> extends Profile<S, C> {
// 
// 	/**
// 	 * Returns the first {@link Profile} of the pair.
// 	 *
// 	 * @return the first {@link Profile} of the pair
// 	 */
// 	Profile<S, C> getQuery();
// 
// 	/**
// 	 * Returns the second {@link Profile} of the pair.
// 	 *
// 	 * @return the second {@link Profile} of the pair
// 	 */
// 	Profile<S, C> getTarget();
// 
// }


// Path: biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java
import org.biojava.nbio.core.alignment.template.ProfilePair;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;

/*
 *                    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/
 *
 * Created on June 7, 2010
 * Author: Mark Chapman
 */

package org.biojava.nbio.alignment.template;


/**
 * Defines an {@link Aligner} for a pair of {@link Profile}s.
 *
 * @author Mark Chapman
 * @param <S> each {@link Sequence} in the pair of alignment {@link Profile}s is of type S
 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
 */
public interface ProfileProfileAligner<S extends Sequence<C>, C extends Compound> extends Aligner<S, C>,
		ProfileProfileScorer<S, C> {

	/**
	 * Returns alignment profile pair.
	 *
	 * @return alignment profile pair
	 */
	ProfilePair<S, C> getPair();