Trace.java

/*
 * Trace.java
 *
 * Copyright (c) 2002-2015 Alexei Drummond, Andrew Rambaut and Marc Suchard
 *
 * This file is part of BEAST.
 * See the NOTICE file distributed with this work for additional
 * information regarding copyright ownership and licensing.
 *
 * BEAST is free software; you can redistribute it and/or modify
 * it under the terms of the GNU Lesser General Public License as
 * published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 *  BEAST is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with BEAST; if not, write to the
 * Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
 * Boston, MA  02110-1301  USA
 */

package dr.inference.trace;

import java.util.*;

/**
 * A simple class that stores a trace for a single statistic
 *
 * @author Andrew Rambaut
 * @author Alexei Drummond
 * @version $Id: Trace.java,v 1.11 2005/07/11 14:07:26 rambaut Exp $
 */
public class Trace<T> { // TODO get rid of generic to make things easy

//    public static final int INITIAL_SIZE = 1000;
//    public static final int INCREMENT_SIZE = 1000;

    // use <Double> for integer, but traceType must = INTEGER, because of legacy issue at analyseCorrelationContinuous
    protected TraceType traceType = TraceType.REAL;
    protected List<T> values = new ArrayList<T>(); // TODO change to String only, and parse to double, int or string in getValues according to trace type
    //    protected int valueCount = 0;
    protected String name;

//    private Object[] range;

    public Trace(String name) { // traceType = TraceFactory.TraceType.DOUBLE; 
        this.name = name;
    }

    public Trace(String name, TraceType traceType) {
        this.name = name;
        setTraceType(traceType);
    }

//    public Trace(String name, T[] valuesArray) {
//        this(name);
////        List<T> newVL = Arrays.asList(valuesArray);
//        Collections.addAll(this.values, valuesArray);
//    }

    /**
     * @param value the valued to be added
     */
    public void add(T value) {
        values.add(value);
    }

    /**
     * @param valuesArray the values to be added
     */
    public void add(T[] valuesArray) {
        Collections.addAll(this.values, valuesArray);
    }

    public int getValueCount() {
        return values.size();
    }

    public int getUniqueVauleCount() {
        Set<T> uniqueValues = new HashSet<T>(values);
        return uniqueValues.size();
    }

    public T getValue(int index) {
        return values.get(index);
    }

    public double[] getRange() { // Double => bounds; Integer and String => unique values

        if (getValueCount() < 1) throw new IllegalArgumentException("Cannot find values in trace " + getName());

        if (getTraceType().isNumber()) {

            Double min = Double.MAX_VALUE;
            Double max = Double.MIN_VALUE;
            for (Object t : values) {
                if ((Double) t < min) {
                    min = (Double) t;
                } else if ((Double) t > max) {
                    max = (Double) t;
                }
            }
            return new double[] {min, max};
        } else {
            throw new UnsupportedOperationException("cannot call getRange for categorical data");
        }
    }

    public Set<String> getCategoricalValues() {
        return new TreeSet<String>((List<String>) values);
    }
    /**
     * @param fromIndex low endpoint (inclusive) of the subList.
     * @param toIndex   high endpoint (exclusive) of the subList.
     * @return The list of values (which are selected values if filter applied)
     */
    public List<T> getValues(int fromIndex, int toIndex) {
        return getValues(fromIndex, toIndex, null);
    }

    public List<T> getValues(int fromIndex, int toIndex, boolean[] filtered) {
        if (toIndex > getValueCount() || fromIndex > toIndex)
            throw new RuntimeException("Invalid index : fromIndex = " + fromIndex + "; toIndex = " + toIndex
                    + "; List size = " + getValueCount() + "; in Trace " + name);

        if (filtered == null || filtered.length < 1) {
            return values.subList(fromIndex, toIndex);
        } else {
            List<T> valuesList = new ArrayList<T>();
            for (int i = fromIndex; i < toIndex; i++) {
                if (!filtered[i])
                    valuesList.add(values.get(i));
            }
            if (valuesList.size() < 1)
                throw new RuntimeException("There is no value left after all filters are applied !");

            return valuesList;
        }
    }

    public String getName() {
        return name;
    }

    public void setName(String name) {
        this.name = name;
    }

//    public Class getTraceType() {
//        if (values.get(0) == null) {
//            return null;
//        }
//        return values.get(0).getClass();
//    }

    public TraceType getTraceType() {
        return traceType;
    }

    public void setTraceType(TraceType traceType) {
        this.traceType = traceType;
    }

    //******************** TraceCorrelation ****************************
    protected TraceCorrelation<T> traceStatistics;

    public TraceCorrelation getTraceStatistics() {
        return traceStatistics;
    }

    public void setTraceStatistics(TraceCorrelation traceStatistics) {
        this.traceStatistics = traceStatistics;
    }

    //******************** Filter ****************************
    protected Filter filter = null;

    public void setFilter(Filter filter) {
        this.filter = filter;
    }

    public Filter getFilter() {
        return filter;
    }
}