/*
 *                    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.symmetry.internal;

import java.util.List;
import java.util.Random;

import org.biojava.nbio.structure.align.ce.CeParameters;

/**
 * Provides parameters to {@link CeSymm}.
 *
 * @author Spencer Bliven
 * @author Aleix Lafita
 * @since 4.1.1
 *
 */
public class CESymmParameters extends CeParameters {

        private int maxSymmOrder;
        private int userOrder;
        private SymmetryType symmType;
        private OrderDetectorMethod orderDetectorMethod;
        private RefineMethod refineMethod;
        private boolean optimization;
        private int rndSeed;
        private int symmLevels;
        private double unrefinedScoreThreshold;
        private double refinedScoreThreshold;
        private int sseThreshold;
        private int minCoreLength;
        private double distanceCutoff;
        private boolean gaps;
        private int optimizationSteps;

        public static enum OrderDetectorMethod {
                SEQUENCE_FUNCTION, GRAPH_COMPONENT, ANGLE, USER_INPUT;
                public static final OrderDetectorMethod DEFAULT = SEQUENCE_FUNCTION;
        }

        public static enum RefineMethod {
                NOT_REFINED, SEQUENCE_FUNCTION, GRAPH_COMPONENT;
                public static final RefineMethod DEFAULT = SEQUENCE_FUNCTION;
        }

        public static final double DEFAULT_SYMMETRY_THRESHOLD = 0.4;

        /**
         * The internal symmetry detection can be divided into two types: CLOSE:
         * includes the circular and dihedral symmetries, and OPEN: includes the
         * helical and protein repeats symmetries.
         * <p>
         * All internal symmetry cases share one property: all the repeats have the
         * same 3D transformation.
         * <p>
         * AUTO option automatically identifies the type. The criterion for
         * classification is that the CLOSE symmetry generates CeSymm alignments
         * with circular permutations (2 blocks in AFPChain), whereas the OPEN
         * symmetry generates alignments without a CP (only one block in AFPChain).
         */
        public enum SymmetryType {
                CLOSED, OPEN, AUTO;
                public static final SymmetryType DEFAULT = AUTO;
        }

        public CESymmParameters() {
                reset();
        }

        @Override
        public CESymmParameters clone() {
                return new CESymmParameters(this);
        }

        public CESymmParameters(CESymmParameters o) {
                this.maxSymmOrder = o.maxSymmOrder;
                this.symmType = o.symmType;
                this.orderDetectorMethod = o.orderDetectorMethod;
                this.userOrder = o.userOrder;
                this.refineMethod = o.refineMethod;
                this.optimization = o.optimization;
                this.rndSeed = o.rndSeed;
                this.symmLevels = o.symmLevels;
                this.unrefinedScoreThreshold = o.unrefinedScoreThreshold;
                this.refinedScoreThreshold = o.refinedScoreThreshold;
                this.sseThreshold = o.sseThreshold;
                this.minCoreLength = o.minCoreLength;
                this.distanceCutoff = o.distanceCutoff;
                this.gaps = o.gaps;
                this.optimizationSteps = o.optimizationSteps;

                this.winSize = o.winSize;
                this.rmsdThr = o.rmsdThr;
                this.rmsdThrJoin = o.rmsdThrJoin;
                this.scoringStrategy = o.scoringStrategy;
                this.maxGapSize = o.maxGapSize;
                this.showAFPRanges = o.showAFPRanges;
                this.maxOptRMSD = o.maxOptRMSD;
                this.gapOpen = o.gapOpen;
                this.gapExtension = o.gapExtension;
                this.distanceIncrement = o.distanceIncrement;
                this.oRmsdThr = o.oRmsdThr;
                this.maxNrIterationsForOptimization = o.maxNrIterationsForOptimization;
                this.seqWeight = o.seqWeight;
        }

        @Override
        public void reset() {
                super.reset();
                maxSymmOrder = 8;
                symmType = SymmetryType.DEFAULT;
                orderDetectorMethod = OrderDetectorMethod.DEFAULT;
                userOrder = 0;
                refineMethod = RefineMethod.DEFAULT;
                optimization = true;
                rndSeed = new Random().nextInt(10000);
                symmLevels = 0;
                unrefinedScoreThreshold = DEFAULT_SYMMETRY_THRESHOLD;
                refinedScoreThreshold = DEFAULT_SYMMETRY_THRESHOLD * 0.9;
                sseThreshold = 0;
                minCoreLength = 15;
                distanceCutoff = 7.0;
                gaps = true;
                optimizationSteps = 0;
        }

        @Override
        public List<String> getUserConfigHelp() {
                List<String> params = super.getUserConfigHelp();

                // maxSymmOrder help explanation
                params.add("Sets the maximum order of symmetry of the protein.");

                // userOrder help explanation
                params.add("Order of symmetry determined by the user. "
                                + "Use it with the USER_INPUT order option. Imposes an order"
                                + " of symmetry to the alignment. If 0 the order is set "
                                + "automatically.");

                StringBuilder symmTypes = new StringBuilder("Type of Symmetry: ");
                SymmetryType[] vals = SymmetryType.values();
                if (vals.length == 1) {
                        symmTypes.append(vals[0].name());
                } else if (vals.length > 1) {
                        for (int i = 0; i < vals.length - 1; i++) {
                                symmTypes.append(vals[i].name());
                                symmTypes.append(", ");
                        }
                        symmTypes.append("or ");
                        symmTypes.append(vals[vals.length - 1].name());
                }
                params.add(symmTypes.toString());

                StringBuilder orderTypes = new StringBuilder("Order Detection Method: ");
                OrderDetectorMethod[] vals2 = OrderDetectorMethod.values();
                if (vals2.length == 1) {
                        orderTypes.append(vals2[0].name());
                } else if (vals2.length > 1) {
                        for (int i = 0; i < vals2.length - 1; i++) {
                                orderTypes.append(vals2[i].name());
                                orderTypes.append(", ");
                        }
                        orderTypes.append("or ");
                        orderTypes.append(vals[vals.length - 1].name());
                }
                params.add(orderTypes.toString());

                StringBuilder refineTypes = new StringBuilder("Refinement Method: ");
                RefineMethod[] values = RefineMethod.values();
                if (values.length == 1) {
                        refineTypes.append(values[0].name());
                } else if (values.length > 1) {
                        for (int i = 0; i < values.length - 1; i++) {
                                refineTypes.append(values[i].name());
                                refineTypes.append(", ");
                        }
                        refineTypes.append("or ");
                        refineTypes.append(values[values.length - 1].name());
                }
                params.add(refineTypes.toString());

                // optimization help explanation
                params.add("Optimize the refined alignment if true.");
                // seed help explanation
                params.add("Random seed for the Monte Carlo optimization, "
                                + "for reproducibility of results.");
                // symmetry levels
                params.add("Specify the maximum number of symmetry levels to explore "
                                + "recursively. If equal to 1, only C and H symmetries can be "
                                + "found. If equal to 2, D and two-level hierarchical C and H "
                                + "can be found, etc. If equal to 0, the number of recursive "
                                + "iterations is unbounded (until thresholds reached).");
                // unrefined score threshold
                params.add("Unrefined score threshold: TM-score values for the optimal"
                                + " self-alignment, before refinement, below the "
                                + "threshold will be considered asymmetric.");
                // refined score threshold
                params.add("Refined score threshold: TM-score values for the refined "
                                + "multiple alignment of repeats below the "
                                + "threshold will be considered asymmetric.");
                // SSE threshold
                params.add("SSE threshold: The minimum number of secondary structure "
                                + "elements (strands or helices) in each symmetrical repeat. "
                                + "If the repeats do not have enough SSE, the structure will "
                                + "be considered asymmetric. 0 means no restriction.");
                // min core repeat length
                params.add("Minimum core length: the minimum number of non-gapped "
                                + "residues in every symmetric repeat.");
                // distance cutoff
                params.add("Distance Cutoff: the maximum allowed distance (in A) "
                                + "between two aligned residues.");

                // gaps
                params.add("Internal Gaps: allow up to 50% of repeats to have gaps in "
                                + "the multiple alignment if true, "
                                + "otherwise all repeats must be aligned at each position.");

                // optimization steps
                params.add("Optimization Steps: maximum number of optimization steps:"
                                + " 0 means calculated automatically with the alignment length.");

                return params;
        }

        @Override
        public List<String> getUserConfigParameters() {
                List<String> params = super.getUserConfigParameters();
                params.add("MaxSymmOrder");
                params.add("UserOrder");
                params.add("SymmType");
                params.add("OrderDetectorMethod");
                params.add("RefineMethod");
                params.add("Optimization");
                params.add("RndSeed");
                params.add("SymmLevels");
                params.add("UnrefinedScoreThreshold");
                params.add("RefinedScoreThreshold");
                params.add("SSEThreshold");
                params.add("MinCoreLength");
                params.add("DistanceCutoff");
                params.add("Gaps");
                params.add("OptimizationSteps");
                return params;
        }

        @Override
        public List<String> getUserConfigParameterNames() {
                List<String> params = super.getUserConfigParameterNames();
                params.add("Maximum Order of Symmetry");
                params.add("User Input Order");
                params.add("Type of Symmetry");
                params.add("Order Detection Method");
                params.add("Refinement Method");
                params.add("Optimization");
                params.add("Random Seed");
                params.add("Symmetry Levels");
                params.add("Unrefined Score Threshold");
                params.add("Refined Score Threshold");
                params.add("SSE Threshold");
                params.add("Minimum Core Length");
                params.add("Distance Cutoff");
                params.add("Internal Gaps");
                params.add("Optimization Steps");
                return params;
        }

        @Override
        @SuppressWarnings("rawtypes")
        public List<Class> getUserConfigTypes() {
                List<Class> params = super.getUserConfigTypes();
                params.add(Integer.class);
                params.add(Integer.class);
                params.add(SymmetryType.class);
                params.add(OrderDetectorMethod.class);
                params.add(RefineMethod.class);
                params.add(Boolean.class);
                params.add(Integer.class);
                params.add(Integer.class);
                params.add(Double.class);
                params.add(Double.class);
                params.add(Integer.class);
                params.add(Integer.class);
                params.add(Double.class);
                params.add(Boolean.class);
                params.add(Integer.class);
                return params;
        }

        public RefineMethod getRefineMethod() {
                return refineMethod;
        }

        public void setRefineMethod(RefineMethod refineMethod) {
                this.refineMethod = refineMethod;
        }

        @Deprecated
        public void setRefineResult(boolean doRefine) {
                if (!doRefine) {
                        refineMethod = RefineMethod.NOT_REFINED;
                } else {
                        refineMethod = RefineMethod.DEFAULT;
                }
        }

        public OrderDetectorMethod getOrderDetectorMethod() {
                return orderDetectorMethod;
        }

        public void setOrderDetectorMethod(OrderDetectorMethod orderDetectorMethod) {
                this.orderDetectorMethod = orderDetectorMethod;
        }

        public void setUserOrder(Integer userOrder) {
                this.userOrder = userOrder;
        }

        public int getUserOrder() {
                return userOrder;
        }

        public void setMaxSymmOrder(Integer maxSymmOrder) {
                this.maxSymmOrder = maxSymmOrder;
        }

        public int getMaxSymmOrder() {
                return maxSymmOrder;
        }

        public SymmetryType getSymmType() {
                return symmType;
        }

        public void setSymmType(SymmetryType type) {
                this.symmType = type;
        }

        public boolean getOptimization() {
                return optimization;
        }

        public void setOptimization(Boolean optimization) {
                this.optimization = optimization;
        }

        public int getRndSeed() {
                return rndSeed;
        }

        public void setRndSeed(Integer seed) {
                this.rndSeed = seed;
        }

        public int getSymmLevels() {
                return symmLevels;
        }

        public void setSymmLevels(Integer symmLevels) {
                this.symmLevels = symmLevels;
        }

        public double getUnrefinedScoreThreshold() {
                return unrefinedScoreThreshold;
        }

        public void setUnrefinedScoreThreshold(Double unrefinedScoreThreshold) {
                this.unrefinedScoreThreshold = unrefinedScoreThreshold;
        }

        public double getRefinedScoreThreshold() {
                return refinedScoreThreshold;
        }

        public void setRefinedScoreThreshold(Double refinedScoreThreshold) {
                this.refinedScoreThreshold = refinedScoreThreshold;
        }

        public int getSSEThreshold() {
                return sseThreshold;
        }

        public void setSSEThreshold(Integer sseThreshold) {
                this.sseThreshold = sseThreshold;
        }

        public int getMinCoreLength() {
                return minCoreLength;
        }

        public void setMinCoreLength(Integer minCoreLength) {
                this.minCoreLength = minCoreLength;
        }

        public double getDistanceCutoff() {
                return distanceCutoff;
        }

        public void setDistanceCutoff(Double distanceCutoff) {
                this.distanceCutoff = distanceCutoff;
        }

        public boolean isGaps() {
                return gaps;
        }

        public void setGaps(Boolean gaps) {
                this.gaps = gaps;
        }

        public int getOptimizationSteps() {
                return optimizationSteps;
        }

        public void setOptimizationSteps(Integer optimizationSteps) {
                this.optimizationSteps = optimizationSteps;
        }

        @Override
        public String toString() {
                return "CESymmParameters [maxSymmOrder=" + maxSymmOrder
                                + ", userOrder=" + userOrder + ", symmType=" + symmType
                                + ", orderDetectorMethod=" + orderDetectorMethod
                                + ", refineMethod=" + refineMethod + ", optimization="
                                + optimization + ", rndSeed=" + rndSeed + ", symmLevels="
                                + symmLevels + ", unrefinedScoreThreshold="
                                + unrefinedScoreThreshold + ", refinedScoreThreshold="
                                + refinedScoreThreshold + ", sseThreshold=" + sseThreshold
                                + ", minCoreLength=" + minCoreLength + ", distanceCutoff="
                                + distanceCutoff + ", gaps=" + gaps + ", optimizationSteps="
                                + optimizationSteps + "]";
        }

}