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package edu.cmu.tetrad.algcomparison.algorithm.multi;

import edu.cmu.tetrad.algcomparison.algorithm.MultiDataSetAlgorithm;
import edu.cmu.tetrad.algcomparison.independence.IndependenceWrapper;
import edu.cmu.tetrad.algcomparison.score.ScoreWrapper;
import edu.cmu.tetrad.algcomparison.utils.HasKnowledge;
import edu.cmu.tetrad.algcomparison.utils.TakesIndependenceWrapper;
import edu.cmu.tetrad.annotation.Bootstrapping;
import edu.cmu.tetrad.data.*;
import edu.cmu.tetrad.graph.EdgeListGraph;
import edu.cmu.tetrad.graph.Graph;
import edu.cmu.tetrad.search.Fask;
import edu.cmu.tetrad.util.Parameters;
import edu.cmu.tetrad.util.Params;
import edu.pitt.dbmi.algo.resampling.GeneralResamplingTest;

import java.text.DecimalFormat;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;

/**
 * Wraps the IMaGES algorithm for continuous variables.
 * 
 * Requires that the parameter 'randomSelectionSize' be set to indicate how many datasets should be taken at a time
 * (randomly). This cannot given multiple values.
 *
 * @author josephramsey
 */
//@edu.cmu.tetrad.annotation.Algorithm(
//        name = "FASK Concatenated",
//        command = "fask-concatenated",
//        algoType = AlgType.forbid_latent_common_causes
//)
@Bootstrapping
public class FaskConcatenated implements MultiDataSetAlgorithm, HasKnowledge, TakesIndependenceWrapper {

    private static final long serialVersionUID = 23L;
    private IndependenceWrapper test;
    private ScoreWrapper score;
    private Knowledge knowledge = new Knowledge();

    public FaskConcatenated() {

    }

    public FaskConcatenated(ScoreWrapper score, IndependenceWrapper test) {
        this.score = score;
        this.test = test;
    }

    @Override
    public Graph search(List dataSets, Parameters parameters) {
        if (parameters.getInt(Params.NUMBER_RESAMPLING) < 1) {
            List centered = new ArrayList<>();

            for (DataModel dataSet : dataSets) {
                centered.add(DataTransforms.standardizeData((DataSet) dataSet));
            }

            DataSet dataSet = DataTransforms.concatenate(centered);

            dataSet.setNumberFormat(new DecimalFormat("0.000000000000000000"));

            Fask search = new Fask(dataSet,
                    this.score.getScore(dataSet, parameters),
                    this.test.getTest(dataSet, parameters));
            search.setDepth(parameters.getInt(Params.DEPTH));
            search.setSkewEdgeThreshold(parameters.getDouble(Params.SKEW_EDGE_THRESHOLD));
            search.setKnowledge(this.knowledge);

            return search.search();
        } else {
            FaskConcatenated algorithm = new FaskConcatenated(this.score, this.test);

            List datasets = new ArrayList<>();

            for (DataModel dataModel : dataSets) {
                datasets.add((DataSet) dataModel);
            }
            GeneralResamplingTest search = new GeneralResamplingTest(
                    datasets,
                    algorithm,
                    parameters.getInt(Params.NUMBER_RESAMPLING),
                    parameters.getDouble(Params.PERCENT_RESAMPLE_SIZE),
                    parameters.getBoolean(Params.RESAMPLING_WITH_REPLACEMENT), parameters.getInt(Params.RESAMPLING_ENSEMBLE), parameters.getBoolean(Params.ADD_ORIGINAL_DATASET));
            search.setKnowledge(this.knowledge);
            search.setScoreWrapper(score);

            search.setParameters(parameters);
            search.setVerbose(parameters.getBoolean(Params.VERBOSE));
            return search.search();
        }
    }

    @Override
    public void setScoreWrapper(ScoreWrapper score) {
        // Not used.
    }

    @Override
    public void setIndTestWrapper(IndependenceWrapper test) {
        // Not used.
    }

    @Override
    public Graph search(DataModel dataSet, Parameters parameters) {
        if (parameters.getInt(Params.NUMBER_RESAMPLING) < 1) {
            return search(Collections.singletonList(SimpleDataLoader.getContinuousDataSet(dataSet)), parameters);
        } else {
            FaskConcatenated algorithm = new FaskConcatenated(this.score, this.test);

            List dataSets = Collections.singletonList(SimpleDataLoader.getContinuousDataSet(dataSet));
            GeneralResamplingTest search = new GeneralResamplingTest(dataSets,
                    algorithm,
                    parameters.getInt(Params.NUMBER_RESAMPLING),
                    parameters.getDouble(Params.PERCENT_RESAMPLE_SIZE),
                    parameters.getBoolean(Params.RESAMPLING_WITH_REPLACEMENT), parameters.getInt(Params.RESAMPLING_ENSEMBLE), parameters.getBoolean(Params.ADD_ORIGINAL_DATASET));
            search.setKnowledge(this.knowledge);
            search.setScoreWrapper(score);

            search.setParameters(parameters);
            search.setVerbose(parameters.getBoolean(Params.VERBOSE));
            return search.search();
        }
    }

    @Override
    public Graph getComparisonGraph(Graph graph) {
        return new EdgeListGraph(graph);
    }

    @Override
    public String getDescription() {
        return "FASK Concatenated";
    }

    @Override
    public DataType getDataType() {
        return DataType.Continuous;
    }

    @Override
    public List getParameters() {
        List parameters = new ArrayList<>();
        parameters.add(Params.DEPTH);
        parameters.add(Params.TWO_CYCLE_ALPHA);
        parameters.add(Params.SKEW_EDGE_THRESHOLD);

        parameters.add(Params.NUM_RUNS);
        parameters.add(Params.RANDOM_SELECTION_SIZE);

        parameters.add(Params.VERBOSE);

        return parameters;
    }

    @Override
    public Knowledge getKnowledge() {
        return this.knowledge;
    }

    @Override
    public void setKnowledge(Knowledge knowledge) {
        this.knowledge = new Knowledge((Knowledge) knowledge);
    }

    @Override
    public IndependenceWrapper getIndependenceWrapper() {
        return this.test;
    }

    @Override
    public void setIndependenceWrapper(IndependenceWrapper independenceWrapper) {
        this.test = independenceWrapper;
    }
}