Class PairedKeysBloomFilter

src/rnabloom/bloom/PairedKeysBloomFilter.java:40–231

@author Ka Ming Nip

 * @author Ka Ming Nip
 */
public class PairedKeysBloomFilter {
    
    protected AbstractLargeBitBuffer bitArrayPair;
    protected int numHash;
    protected long size;
    protected HashFunction hashFunction;
    protected long popcount = -1;
    
    public PairedKeysBloomFilter(long size, int numHash, HashFunction hashFunction) {
        this.size = size;
        try {
            this.bitArrayPair = new UnsafeBitBuffer(size);
        }
        catch(NoSuchFieldException | IllegalArgumentException | IllegalAccessException e) {
            this.bitArrayPair = 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 PairedKeysBloomFilter(File desc, File pairBits, 
            HashFunction hashFunction) 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.bitArrayPair = new UnsafeBitBuffer(size);
        }
        catch(NoSuchFieldException | IllegalArgumentException | IllegalAccessException e) {
            this.bitArrayPair = new LargeBitBuffer(size);
        }
        
        FileInputStream fin = new FileInputStream(pairBits);
        this.bitArrayPair.read(fin);
        fin.close();