package edu.mit.broad.picard.directed;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.BitSet;
import java.util.SortedMap;
import java.util.TreeMap;

/**
 * Utility class to store coordinates of interest in per-sequence bitmasks.
 */
public class GenomeMask {

    // if memory usage becomes a problem... this could be changed to a SparseBitSet
    // http://java.sun.com/developer/onlineTraining/collections/magercises/BitSet/index.html
    private SortedMap<Integer, BitSet> data = new TreeMap<Integer, BitSet>();


    public GenomeMask() {
    }

    public boolean get(int contig, int position) {
        BitSet bits = data.get(contig);
        return (bits != null) && bits.get(position);
    }

    public BitSet get(int contig) {
        return data.get(contig);
    }

    /**
     * Get an existing BitSet for the given contig, or create one if not already present.  This is
     * useful when initializing a GenomeMask from an external source.
     * @param contig which BitSet
     * @param numBits if there was not already a BitSet for this contig, one is created and initialized to this size.
     * @return the BitSet for the given contig, creating one if necessary
     */
    public BitSet getOrCreate(int contig, int numBits) {
        BitSet ret = data.get(contig);
        if (ret == null) {
            ret = new BitSet(numBits);
            data.put(contig, ret);
        }
        return ret;
    }

    public int getMaxContig() {
        return data.lastKey();
    }
}