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The protein structure modules of BioJava.
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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.ce;

import java.util.List;

/**
 * Provides parameters to {@link CeCPMain}
 *
 * @author Spencer Bliven
 *
 */
public class CECPParameters extends CeParameters {

	public static final int DEFAULT_MIN_CP_LENGTH = 5; //The minimum block length for CPs. Blocks shorter than this will be ignored.

	public static enum DuplicationHint {
		SHORTER("Shorter of the two"),
		LEFT("Left"),
		RIGHT("Right");


		private String name;
		private DuplicationHint(String name) {
			this.name = name;
		}
		@Override
		public String toString() {
			return name;
		}
	}

	protected DuplicationHint duplicationHint;
	protected Integer minCPLength;

	public CECPParameters() {
		super();
		// super calls reset();
	}

	@Override
	public String toString() {
		return "CECPParameters [scoringStrategy=" + scoringStrategy
		+ ", maxGapSize=" + maxGapSize
		+ ", rmsdThr=" + rmsdThr
		+ ", rmsdThrJoin="+ rmsdThrJoin
		+ ", winSize=" + winSize
		+ ", showAFPRanges=" + showAFPRanges
		+ ", maxOptRMSD=" + maxOptRMSD
		+ ", seqWeight=" + seqWeight
		+ ", duplicationHint=" + duplicationHint
		+ ", minCPLength=" + minCPLength
		+ "]";
	}


	@Override
	public void reset(){
		super.reset();
		duplicationHint = DuplicationHint.SHORTER;
		minCPLength = DEFAULT_MIN_CP_LENGTH;
		setMaxGapSize(0);
	}


	@Override
	public List getUserConfigHelp() {
		List params = super.getUserConfigHelp();
		params.add("Direction to duplicate: SHORTER, LEFT, or RIGHT");
		params.add("Minimum length of a CP block to consider");
		return params;
	}

	@Override
	public List getUserConfigParameters() {
		List params = super.getUserConfigParameters();
		params.add("DuplicationHint");
		params.add("MinCPLength");
		return params;
	}

	@Override
	public List getUserConfigParameterNames(){
		List params = super.getUserConfigParameterNames();

		params.add("Which to duplicate");
		params.add("Min CP Length");
		return params;
	}

	@Override
	@SuppressWarnings("rawtypes")
	public List getUserConfigTypes() {
		List params = super.getUserConfigTypes();
		params.add(DuplicationHint.class);
		params.add(Integer.class);
		return params;
	}

	public DuplicationHint getDuplicationHint() {
		return duplicationHint;
	}

	public void setDuplicationHint(DuplicationHint duplicationHint) {
		this.duplicationHint = duplicationHint;
	}


	public Integer getMinCPLength() {
		return minCPLength;
	}


	public void setMinCPLength(Integer minCPLength) {
		this.minCPLength = minCPLength;
	}
}