Class BloomFilter

src/rnabloom/bloom/BloomFilter.java:40–258

@author Ka Ming Nip

 * @author Ka Ming Nip
 */
public class BloomFilter implements BloomFilterInterface {    
    protected AbstractLargeBitBuffer bitArray;
    protected int numHash;
    protected long size;
    protected HashFunction hashFunction;
    protected long popcount = -1;
        
    public BloomFilter(long size, int numHash, HashFunction hashFunction) {
        
        this.size = size;
        try {
            //System.out.println("unsafe");
            this.bitArray = new UnsafeBitBuffer(size);
        }
        catch(NoSuchFieldException | IllegalArgumentException | IllegalAccessException e) {
            this.bitArray = new LargeBitBuffer(size);
        }
        this.numHash = numHash;
        this.hashFunction = hashFunction;
    }
    
    private static final String LABEL_SEPARATOR = ":";
    private static final String LABEL_SIZE = "size";
    private static final String LABEL_NUM_HASH = "numhash";
    private static final String LABEL_FPR = "fpr";
    
    public BloomFilter(File desc, File bits, HashFunction hashFunction) throws FileNotFoundException, IOException {
        this(desc, bits, hashFunction, true);
    }
    
    public BloomFilter(File desc, File bits, HashFunction hashFunction, boolean loadBits) throws FileNotFoundException, IOException {
        
        BufferedReader br = new BufferedReader(new FileReader(desc));
        String line;
        while ((line = br.readLine()) != null) {
            String[] entry = line.split(LABEL_SEPARATOR);
            String key = entry[0];
            String val = entry[1];
            switch(key) {
                case LABEL_SIZE:
                    size = Long.parseLong(val);
                    break;
                case LABEL_NUM_HASH:
                    numHash = Integer.parseInt(val);
                    break;
            }
        }
        br.close();
        
        this.hashFunction = hashFunction;
        
        try {
            //System.out.println("unsafe");
            this.bitArray = new UnsafeBitBuffer(size);
        }
        catch(NoSuchFieldException | IllegalArgumentException | IllegalAccessException e) {
            this.bitArray = new LargeBitBuffer(size);
        }