/*
 *                    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.survival.cox;

import java.util.ArrayList;
import java.util.LinkedHashMap;

/**
 * Data class to represent a single sample where time and event/censor status is required
 * Additionally each variable and data associated with that variable.
 * The code handles figuring out if a variables is continuous or categorical. If categorical will
 * convert to numerical values.
 *
 * @author Scooter Willis <willishf at gmail dot com>
 */
public class SurvivalInfo implements Comparable<SurvivalInfo> {

        private String id = "";
        private double time;
        private int status;
        private int order = 0; //not really used but included to keep track of original position if sorting.
        private double offset = 0; //offsets for linear predictor ????
        private double weight = 1; //used to set weight of survivor for over sampling.
        private int strata = 0; // this should be a boolean but leaving as an int
        private double score = 0.0;
        private double linearPredictor = 0.0;
        private double residual = 0.0;
        private String clusterValue = "";

        LinkedHashMap<String,Double> residualVariableMap = new LinkedHashMap<String,Double>();

        LinkedHashMap<String, Double> data = new LinkedHashMap<String, Double>();
        //    LinkedHashMap<String, Double> discreteData = new LinkedHashMap<String, Double>();
        LinkedHashMap<String, String> unknownDataType = new LinkedHashMap<String, String>();
        LinkedHashMap<String, String> originalMetaData = new LinkedHashMap<String,String>();

        /**
         *
         * @param t
         * @param e
         */
        public SurvivalInfo(double t, int e) {
                time = t;
                status = e;

        }

        /**
         *
         * @param t
         * @param e
         * @param d
         */
        public SurvivalInfo(double t, int e, LinkedHashMap<String, Double> d) {
                time = t;
                status = e;

                data = d;
                for(String key : d.keySet()){
                        Double value = d.get(key);
                        originalMetaData.put(key, value + "");
                }
        }

        /**
         *
         * @param t
         * @param e
         * @param variable
         * @param d
         */
        public SurvivalInfo(double t, int e, String variable, double d) {
                time = t;
                status = e;

                data.put(variable, d);
                originalMetaData.put(variable, String.valueOf(d));
        }


        /**
         * Set the residual value for the variable for this sample. Called from CoxScore.java
         * @param variable
         * @param value
         */
        public void setResidualVariable(String variable, Double value){
                residualVariableMap.put(variable, value);
        }

        /**
         *
         * @param variable
         * @return
         */
        public Double getResidualVariable(String variable){
                return residualVariableMap.get(variable);

        }

        /**
         *
         * @param variable
         * @return
         */
        public String getUnknownDataTypeVariable(String variable){
                return unknownDataType.get(variable);
        }

        /**
         *
         * @param variable
         * @return
         */
        public String getOriginalMetaData(String variable){
                return originalMetaData.get(variable);
        }

        /**
         *
         * @param variable
         * @param value
         */
        public void addUnknownDataTypeVariable(String variable, String value) {
                originalMetaData.put(variable, value);
                unknownDataType.put(variable, value);
        }

        /**
         *
         * @param variable
         * @param value
         */
        public void updateContinousVariable(String variable, Double value){
                data.put(variable, value);
        }

        /**
         *
         * @param variable
         * @param value
         */
        public void addContinuousVariable(String variable, Double value) {
                originalMetaData.put(variable, value + "");
                data.put(variable, value);
        }

        /**
         *
         * @param variable
         * @return
         */
        public Double getContinuousVariable(String variable) {
                return data.get(variable);
        }

        /**
         *
         * @param groupName
         * @return
         */
        public ArrayList<String> getGroupCategories(String groupName) {
                ArrayList<String> groupNameList = new ArrayList<String>();
                for (String key : data.keySet()) {
                        if (key.startsWith(groupName + "_")) {
                                groupNameList.add(key);
                        }
                }
                return groupNameList;
        }

//    public void addDiscreteVariable(String variable, double value) {
//        discreteData.put(variable, value);
//    }

//    public Double getDiscreteVariable(String variable) {
//        return discreteData.get(variable);
//    }

        /**
         *
         * @return
         */
        public ArrayList<String> getDataVariables(){
                ArrayList<String> v = new ArrayList<String>();
                v.addAll(data.keySet());
                v.addAll(unknownDataType.keySet());

                return v;
        }

        /**
         *
         * @return
         */
        public int getNumberVariables(){
                return data.size();
        }

        /**
         *
         * @param variable
         * @return
         */
        public Double getVariable(String variable) {
                Double value = data.get(variable);

                return value;
        }

        @Override
        public String toString() {
                return "t=" + time + " e=" + status + " o=" + order;
        }
        //    double CompNum4Sort(double[] a, double[] b) {
        //(time - time - (status -status) /1024)
        //    return (a[0] - b[0] - (a[1] - b[1]) / 1024);
        // }

        @Override
        public int compareTo(SurvivalInfo o) {
                //    return (int) (this.time - o.time - (this.status - o.status) / 1024);
                if (time < o.time) {
                        return -1;
                } else if (time > o.time) {
                        return 1;
                } else {
                        if (this.status == o.status) {
                                return 0;
                        } else if (status == 1) {
                                return -1;
                        } else {
                                return 1;
                        }
                }

        }

        /**
         * @return the offset
         */
        public double getOffset() {
                return offset;
        }

        /**
         * @param offset the offset to set
         */
        public void setOffset(double offset) {
                this.offset = offset;
        }

        /**
         * @return the weight
         */
        public double getWeight() {
                return weight;
        }

        /**
         * @param weight the weight to set
         */
        public void setWeight(double weight) {
                this.weight = weight;
        }

        /**
         * @return the strata
         */
        public int getStrata() {
                return strata;
        }

        /**
         * @param strata the strata to set
         */
        public void setStrata(int strata) {
                this.strata = strata;
        }

        /**
         * @return the score
         */
        public double getScore() {
                return score;
        }

        /**
         * @param score the score to set
         */
        public void setScore(double score) {
                this.score = score;
        }

        /**
         * @return the linearPredictor
         */
        public double getLinearPredictor() {
                return linearPredictor;
        }

        /**
         * @param linearPredictor the linearPredictor to set
         */
        public void setLinearPredictor(double linearPredictor) {
                this.linearPredictor = linearPredictor;
        }

        /**
         * @return the residual
         */
        public double getResidual() {
                return residual;
        }

        /**
         * @param residual the residual to set
         */
        public void setResidual(double residual) {
                this.residual = residual;
        }

        /**
         * @return the clusterValue
         */
        public String getClusterValue() {
                return clusterValue;
        }

        /**
         * @param clusterValue the clusterValue to set
         */
        public void setClusterValue(String clusterValue) {
                this.clusterValue = clusterValue;
        }

        /**
         * @return the id
         */
        public String getId() {
                return id;
        }

        /**
         * @param id the id to set
         */
        public void setId(String id) {
                this.id = id;
        }

        /**
         * @return the order
         */
        public int getOrder() {
                return order;
        }

        /**
         * @param order the order to set
         */
        public void setOrder(int order) {
                this.order = order;
        }

        /**
         * @return the time
         */
        public double getTime() {
                return time;
        }

        /**
         * @param time the time to set
         */
        public void setTime(double time) {
                this.time = time;
        }

        /**
         * @return the status
         */
        public int getStatus() {
                return status;
        }

        /**
         * @param status the status to set
         */
        public void setStatus(int status) {
                this.status = status;
        }
}