jpayne@68: package kmer;
jpayne@68: 
jpayne@68: import java.util.concurrent.atomic.AtomicLong;
jpayne@68: 
jpayne@68: import fileIO.ByteStreamWriter;
jpayne@68: import fileIO.TextStreamWriter;
jpayne@68: import structures.ByteBuilder;
jpayne@68: import structures.SuperLongList;
jpayne@68: 
jpayne@68: /**
jpayne@68:  * @author Brian Bushnell
jpayne@68:  * @date Nov 22, 2013
jpayne@68:  *
jpayne@68:  */
jpayne@68: public class HashBuffer extends AbstractKmerTable {
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------        Initialization        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	public HashBuffer(AbstractKmerTable[] tables_, int buflen_, int k_, boolean initValues, boolean setIfNotPresent_){
jpayne@68: 		tables=tables_;
jpayne@68: 		buflen=buflen_;
jpayne@68: 		halflen=(int)Math.ceil(buflen*0.5);
jpayne@68: 		ways=tables.length;
jpayne@68: 		buffers=new KmerBuffer[ways];
jpayne@68: 		setIfNotPresent=setIfNotPresent_;
jpayne@68: 		useValues=initValues;
jpayne@68: 		coreMask=(AbstractKmerTableSet.MASK_CORE ? ~(((-1L)<<(2*(k_-1)))|3) : -1L);
jpayne@68: 		for(int i=0; i<ways; i++){
jpayne@68: 			buffers[i]=new KmerBuffer(buflen, k_, useValues);
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------        Public Methods        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	public final int kmerToWay(final long kmer){
jpayne@68: 		final int way=(int)((kmer&coreMask)%ways);
jpayne@68: 		return way;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public int incrementAndReturnNumCreated(final long kmer, final int incr) {
jpayne@68: 		assert(incr==1); //I could just add the kmer multiple times if not true, with addMulti
jpayne@68: 		final int way=kmerToWay(kmer);
jpayne@68: 		KmerBuffer buffer=buffers[way];
jpayne@68: //		final int size=buffer.addMulti(kmer, incr);
jpayne@68: 		final int size=buffer.add(kmer);
jpayne@68: 		if(size>=halflen && (size>=buflen || (size&SIZEMASK)==0)){
jpayne@68: 			return dumpBuffer(way, size>=buflen);
jpayne@68: 		}
jpayne@68: 		return 0;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public final long flush(){
jpayne@68: 		long added=0;
jpayne@68: 		for(int i=0; i<ways; i++){added+=dumpBuffer(i, true);}
jpayne@68: 		return added;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public int set(long kmer, int value) {
jpayne@68: 		final int way=kmerToWay(kmer);
jpayne@68: 		KmerBuffer buffer=buffers[way];
jpayne@68: 		final int size=buffer.add(kmer, value);
jpayne@68: 		if(size>=halflen && (size>=buflen || (size&SIZEMASK)==0)){
jpayne@68: 			return dumpBuffer(way, size>=buflen);
jpayne@68: 		}
jpayne@68: 		return 0;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public int set(long kmer, int[] vals, int vlen) {
jpayne@68: 		throw new RuntimeException("Unimplemented method; this class lacks value buffers");
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public int setIfNotPresent(long kmer, int value) {
jpayne@68: 		throw new RuntimeException("Unimplemented method; this class lacks value buffers");
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public int getValue(long kmer) {
jpayne@68: 		final int way=kmerToWay(kmer);
jpayne@68: 		return tables[way].getValue(kmer);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public int[] getValues(long kmer, int[] singleton){
jpayne@68: 		final int way=kmerToWay(kmer);
jpayne@68: 		return tables[way].getValues(kmer, singleton);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public boolean contains(long kmer) {
jpayne@68: 		final int way=kmerToWay(kmer);
jpayne@68: 		return tables[way].contains(kmer);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------          Ownership           ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public final void initializeOwnership(){
jpayne@68: 		for(AbstractKmerTable t : tables){t.initializeOwnership();}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public final void clearOwnership(){
jpayne@68: 		for(AbstractKmerTable t : tables){t.clearOwnership();}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public final int setOwner(final long kmer, final int newOwner){
jpayne@68: 		final int way=kmerToWay(kmer);
jpayne@68: 		return tables[way].setOwner(kmer, newOwner);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public final boolean clearOwner(final long kmer, final int owner){
jpayne@68: 		final int way=kmerToWay(kmer);
jpayne@68: 		return tables[way].clearOwner(kmer, owner);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public final int getOwner(final long kmer){
jpayne@68: 		final int way=kmerToWay(kmer);
jpayne@68: 		return tables[way].getOwner(kmer);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------      Nonpublic Methods       ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	Object get(long kmer) {
jpayne@68: 		final int way=kmerToWay(kmer);
jpayne@68: 		return tables[way].get(kmer);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------       Private Methods        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	private int dumpBuffer(final int way, boolean force){
jpayne@68: 		final KmerBuffer buffer=buffers[way];
jpayne@68: 		final AbstractKmerTable table=tables[way];
jpayne@68: 		final int lim=buffer.size();
jpayne@68: 		if(lim<0){return 0;}
jpayne@68: 		
jpayne@68: 		if(force){table.lock();}
jpayne@68: 		else if(!table.tryLock()){return 0;}
jpayne@68: 		
jpayne@68: 		if(SORT_BUFFERS && buffer.values==null){//Can go before or after lock; neither helps much
jpayne@68: 			buffer.kmers.sortSerial();
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		final int x=dumpBuffer_inner(way);
jpayne@68: 		table.unlock();
jpayne@68: 		return x;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private int dumpBuffer_inner(final int way){
jpayne@68: 		if(verbose){System.err.println("Dumping buffer for way "+way+" of "+ways);}
jpayne@68: 		final KmerBuffer buffer=buffers[way];
jpayne@68: 		final int lim=buffer.size();
jpayne@68: 		if(lim<1){return 0;}
jpayne@68: 		final long[] kmers=buffer.kmers.array;
jpayne@68: 		final int[] values=(buffer.values==null ? null : buffer.values.array);
jpayne@68: 		if(lim<1){return 0;}
jpayne@68: 		int added=0;
jpayne@68: 		final AbstractKmerTable table=tables[way];
jpayne@68: //		synchronized(table){
jpayne@68: 			if(values==null){
jpayne@68: //				Arrays.sort(kmers, 0, lim); //Makes it slower
jpayne@68: 				if(SORT_BUFFERS){
jpayne@68: 					long prev=-1;
jpayne@68: 					int sum=0;
jpayne@68: 					for(int i=0; i<lim; i++){
jpayne@68: 						final long kmer=kmers[i];
jpayne@68: 						if(kmer==prev){
jpayne@68: 							sum++;
jpayne@68: 						}else{
jpayne@68: 							if(sum>0){added+=table.incrementAndReturnNumCreated(prev, sum);}
jpayne@68: 							prev=kmer;
jpayne@68: 							sum=1;
jpayne@68: 						}
jpayne@68: 					}
jpayne@68: 					if(sum>0){added+=table.incrementAndReturnNumCreated(prev, sum);}
jpayne@68: 				}else{
jpayne@68: 					for(int i=0; i<lim; i++){
jpayne@68: 						final long kmer=kmers[i];
jpayne@68: 						added+=table.incrementAndReturnNumCreated(kmer, 1);
jpayne@68: 					}
jpayne@68: 				}
jpayne@68: 			}else{
jpayne@68: 				if(setIfNotPresent){
jpayne@68: 					for(int i=0; i<lim; i++){
jpayne@68: 						final long kmer=kmers[i];
jpayne@68: 						final int value=values[i];
jpayne@68: 						added+=table.setIfNotPresent(kmer, value);
jpayne@68: 					}
jpayne@68: 				}else{
jpayne@68: 					for(int i=0; i<lim; i++){
jpayne@68: 						final long kmer=kmers[i];
jpayne@68: 						final int value=values[i];
jpayne@68: 						added+=table.set(kmer, value);
jpayne@68: //						System.err.println("B: "+kmer+", "+Arrays.toString(((HashArrayHybrid)table).getValues(kmer, new int[1])));
jpayne@68: 					}
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: //		}
jpayne@68: 		buffer.clear();
jpayne@68: 		uniqueAdded+=added;
jpayne@68: 		return added;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------   Resizing and Rebalancing   ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	final boolean canResize() {return false;}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public final boolean canRebalance() {return false;}
jpayne@68: 	
jpayne@68: 	@Deprecated
jpayne@68: 	@Override
jpayne@68: 	public long size() {
jpayne@68: 		throw new RuntimeException("Unimplemented.");
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Deprecated
jpayne@68: 	@Override
jpayne@68: 	public int arrayLength() {
jpayne@68: 		throw new RuntimeException("Unimplemented.");
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Deprecated
jpayne@68: 	@Override
jpayne@68: 	void resize() {
jpayne@68: 		throw new RuntimeException("Unimplemented.");
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Deprecated
jpayne@68: 	@Override
jpayne@68: 	public void rebalance() {
jpayne@68: 		throw new RuntimeException("Unimplemented.");
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public long regenerate(final int limit){
jpayne@68: 		long sum=0;
jpayne@68: 		for(AbstractKmerTable table : tables){
jpayne@68: 			sum+=table.regenerate(limit);
jpayne@68: 		}
jpayne@68: 		return sum;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------         Info Dumping         ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public boolean dumpKmersAsText(TextStreamWriter tsw, int k, int mincount, int maxcount){
jpayne@68: 		for(AbstractKmerTable table : tables){
jpayne@68: 			table.dumpKmersAsText(tsw, k, mincount, maxcount);
jpayne@68: 		}
jpayne@68: 		return true;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public boolean dumpKmersAsBytes(ByteStreamWriter bsw, int k, int mincount, int maxcount, AtomicLong remaining){
jpayne@68: 		for(AbstractKmerTable table : tables){
jpayne@68: 			table.dumpKmersAsBytes(bsw, k, mincount, maxcount, remaining);
jpayne@68: 		}
jpayne@68: 		return true;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	@Deprecated
jpayne@68: 	public boolean dumpKmersAsBytes_MT(final ByteStreamWriter bsw, final ByteBuilder bb, final int k, final int mincount, int maxcount, AtomicLong remaining){
jpayne@68: 		throw new RuntimeException("Unsupported.");
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	@Deprecated
jpayne@68: 	public void fillHistogram(long[] ca, int max){
jpayne@68: 		throw new RuntimeException("Unsupported.");
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	@Deprecated
jpayne@68: 	public void fillHistogram(SuperLongList sll){
jpayne@68: 		throw new RuntimeException("Unsupported.");
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public void countGC(long[] gcCounts, int max){
jpayne@68: 		for(AbstractKmerTable table : tables){
jpayne@68: 			table.countGC(gcCounts, max);
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------       Invalid Methods        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public int increment(final long kmer, final int incr) {
jpayne@68: 		throw new RuntimeException("Unsupported");
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------            Fields            ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	private final AbstractKmerTable[] tables;
jpayne@68: 	private final int buflen;
jpayne@68: 	private final int halflen;
jpayne@68: 	private final int ways;
jpayne@68: 	private final boolean useValues;
jpayne@68: 	private final KmerBuffer[] buffers;
jpayne@68: 	private final long coreMask;
jpayne@68: 	public long uniqueAdded=0;
jpayne@68: 	
jpayne@68: 	private static final int SIZEMASK=15;
jpayne@68: 	private final boolean setIfNotPresent;
jpayne@68: 	
jpayne@68: 	public static boolean SORT_BUFFERS=false;
jpayne@68: 
jpayne@68: }