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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/
 *
 * Created on May 21, 2006
 *
 */
package org.biojava.nbio.structure.align;

import org.biojava.nbio.structure.StructureTools;

/**
 * A class that contains all the parameters of the structure alignment algorithm.
 *
 * @author Andreas Prlic
 * @since 1.5
 * @version %I% %G%
 */
public class StrucAligParameters {


	int initialK;
	String[] usedAtomNames = { StructureTools.CA_ATOM_NAME, } ;

	// step 1

	int seedFragmentLength; // seed fragment length
	float seedRmsdCutoff;

	int fragmentLength;
	int diagonalDistance;
	int diagonalDistance2; // set to < 1 if not used.
	boolean reduceInitialFragments;

	// step 2
	float fragmentMiniDistance;
	float fragCompat;   // fragment compatibility cutoff
	int maxrefine;      // max number of JointFragments to be refined

	boolean joinPlo; // joining according to BioPython variant
	boolean joinFast; // apply a fast procedure for extending the alignments

	// joininf of fragments - checks
	boolean doAngleCheck  ;
	boolean doDistanceCheck;
	boolean doDensityCheck;
	boolean doRMSCheck;
	float densityCutoff;

	int angleDiff;      // directional difference
	double joinRMSCutoff; // rms cutoff to be applied during joining of fragments.

	// step 4
	float create_co; //  alignment generation cutoff
	int maxIter; //  # max number of iterations in refinement
	float gapOpen;// gap open penalty
	float gapExtension; // gap extensionpenalty
	int permutationSize; // minimal size for a permutated fragment ( -1 means no circular permutation search)
	float evalCutoff; //  alignment evaluation cutoff

	public StrucAligParameters() {
		super();
		setDefault();
	}

	public static StrucAligParameters getDefaultParameters(){
		StrucAligParameters n = new StrucAligParameters();
		return n;
	}

	private void setDefault() {
		initialK = 6;

		// step 1
		seedFragmentLength      = 8;
		seedRmsdCutoff          = 3.0f; // orig 2.0 - better?
		fragmentLength          = 10;
		diagonalDistance        = 3;
		diagonalDistance2       = 9; // this helps a lot in 1buz vs 1aua
		fragmentMiniDistance    = 3.5f; // orig 2
		angleDiff               = 10;
		fragCompat              = 6.0f; // orig 4.0
		maxrefine               = 20; // orig 20

		// step 2
		reduceInitialFragments  =  true; // if this is disabled, you might want to also disable doRMSCheck for large structures...
		joinRMSCutoff           = 5.0; // orig 4
		joinPlo                 = false;
		joinFast                = false;


		// 3 joint fragments
		doAngleCheck            = true;
		doDistanceCheck         = true;
		doRMSCheck              = true;

		doDensityCheck          = false; // hm this one needs improvements before being used
		densityCutoff           = 7.0f;

		//  step 3
		create_co           = 6.0f;
		maxIter             = 4;  // number of times dynamic programming is run. set to zero for quick search (but imprecise)
		gapOpen             = 20.0f;
		gapExtension        = 0.0f;
		permutationSize     = 20;
		evalCutoff          = 6.0f;
	}
	@Override
	public String toString() {
		StringBuffer buf = new StringBuffer();
		String t = " ";

		Object[] params = new Object[]{Integer.valueOf(initialK) ,Integer.valueOf(seedFragmentLength),
				Float.valueOf(seedRmsdCutoff),
				Integer.valueOf(fragmentLength),
				Integer.valueOf(diagonalDistance), Integer.valueOf(diagonalDistance2), Float.valueOf(fragmentMiniDistance),
				Integer.valueOf(angleDiff),
				Float.valueOf(fragCompat), Integer.valueOf(maxrefine),
				Boolean.valueOf(reduceInitialFragments), Double.valueOf(joinRMSCutoff), Boolean.valueOf(joinPlo),
				Boolean.valueOf(doAngleCheck), Boolean.valueOf(doDistanceCheck), Boolean.valueOf(doRMSCheck),
				Boolean.valueOf(doDensityCheck), Float.valueOf(densityCutoff), Float.valueOf(create_co), Integer.valueOf(maxIter),
				Float.valueOf(gapOpen), Float.valueOf(gapExtension), Integer.valueOf(permutationSize), Float.valueOf(evalCutoff)};

		for (int i=0 ; i< params.length ; i++){
			buf.append(params[i]);
			buf.append(t);
		}


		return buf.toString();

	}

	public static StrucAligParameters getDBSearchParameters(){
		StrucAligParameters params = new StrucAligParameters();

		params.setMaxIter(0); // not so nice alignments, but significant similarities should already be found,
		// one could do a second interation later over the top ranking hits and make a nicer alignment.


		return params;
	}

	public float getDensityCutoff() {
		return densityCutoff;
	}

	public void setDensityCutoff(float densityCutoff) {
		this.densityCutoff = densityCutoff;
	}

	public int getInitialK() {
		return initialK;
	}

	public void setInitialK(int initialK) {
		this.initialK = initialK;
	}

	public int getSeedFragmentLength() {
		return seedFragmentLength;
	}

	public boolean isJoinFast(){
	   return joinFast;
	}

	public void setJoinFast(boolean fastJoin){
	   joinFast = fastJoin;
	}

	public boolean isJoinPlo() {
		return joinPlo;
	}

	public void setJoinPlo(boolean joinPlo) {
		this.joinPlo = joinPlo;
	}

	public void setSeedFragmentLength(int seedFragmentLength) {
		this.seedFragmentLength = seedFragmentLength;
	}



	public float getSeedRmsdCutoff() {
		return seedRmsdCutoff;
	}



	public void setSeedRmsdCutoff(float seedRmsdCutoff) {
		this.seedRmsdCutoff = seedRmsdCutoff;
	}



	public boolean isDoAngleCheck() {
		return doAngleCheck;
	}

	public void setDoAngleCheck(boolean doAngleCheck) {
		this.doAngleCheck = doAngleCheck;
	}

	public boolean isDoDensityCheck() {
		return doDensityCheck;
	}

	public void setDoDensityCheck(boolean doDensityCheck) {
		this.doDensityCheck = doDensityCheck;
	}

	public boolean isDoDistanceCheck() {
		return doDistanceCheck;
	}

	public void setDoDistanceCheck(boolean doDistanceCheck) {
		this.doDistanceCheck = doDistanceCheck;
	}

	public boolean isDoRMSCheck() {
		return doRMSCheck;
	}

	public void setDoRMSCheck(boolean doRMSCheck) {
		this.doRMSCheck = doRMSCheck;
	}

	public double getJoinRMSCutoff() {
		return joinRMSCutoff;
	}



	public void setJoinRMSCutoff(double joinRMSCutoff) {
		this.joinRMSCutoff = joinRMSCutoff;
	}



	public float getEvalCutoff() {
		return evalCutoff;
	}

	public void setEvalCutoff(float evalCutoff) {
		this.evalCutoff = evalCutoff;
	}




	public int getPermutationSize() {
		return permutationSize;
	}

	public void setPermutationSize(int permutationSize) {
		this.permutationSize = permutationSize;
	}

	public float getGapExtension() {
		return gapExtension;
	}

	public void setGapExtension(float gapExtension) {
		this.gapExtension = gapExtension;
	}

	public float getGapOpen() {
		return gapOpen;
	}

	public void setGapOpen(float gapOpen) {
		this.gapOpen = gapOpen;
	}

	public int getMaxIter() {
		return maxIter;
	}

	public void setMaxIter(int maxIter) {
		this.maxIter = maxIter;
	}

	public float getCreate_co() {
		return create_co;
	}

	public void setCreate_co(float create_co) {
		this.create_co = create_co;
	}

	/**
	 * if this is set to false, the time spent to joint the initial fragments (step 2)
	 * is increased. - particular for large structures this increases calc. time a lot.
	 * advantage: more combinations of fragments are used.
	 *
	 * @return a flag if the inital fragments should be reduced
	 */
	public boolean reduceInitialFragments() {
		return reduceInitialFragments;
	}

	public void setReduceInitialFragments(boolean reduceInitialFragments) {
		this.reduceInitialFragments = reduceInitialFragments;
	}

	public int getAngleDiff() {
		return angleDiff;
	}

	public void setAngleDiff(int angleDiff) {
		this.angleDiff = angleDiff;
	}

	public float getFragCompat() {
		return fragCompat;
	}

	public void setFragCompat(float fragCompat) {
		this.fragCompat = fragCompat;
	}

	public int getMaxrefine() {
		return maxrefine;
	}

	public void setMaxrefine(int maxrefine) {
		this.maxrefine = maxrefine;
	}

	public String[] getUsedAtomNames() {
		return usedAtomNames;
	}

	public void setUsedAtomNames(String[] usedAtomNames) {
		this.usedAtomNames = usedAtomNames;
	}

	public int getFragmentLength() {
		return fragmentLength;
	}

	public void setFragmentLength(int fragmentLength) {
		this.fragmentLength = fragmentLength;
	}

	public int getDiagonalDistance() {
		return diagonalDistance;
	}

	public void setDiagonalDistance(int diagonalDistance) {
		this.diagonalDistance = diagonalDistance;
	}



	public int getDiagonalDistance2() {
		return diagonalDistance2;
	}

	public void setDiagonalDistance2(int diagonalDistance2) {
		this.diagonalDistance2 = diagonalDistance2;
	}

	public float getFragmentMiniDistance() {
		return fragmentMiniDistance;
	}

	public void setFragmentMiniDistance(float fragmentMiniDistance) {
		this.fragmentMiniDistance = fragmentMiniDistance;
	}




}