jpayne@68: package kmer;
jpayne@68: 
jpayne@68: import java.util.concurrent.atomic.AtomicLong;
jpayne@68: 
jpayne@68: import fileIO.ByteStreamWriter;
jpayne@68: import structures.ByteBuilder;
jpayne@68: 
jpayne@68: /**
jpayne@68:  * @author Brian Bushnell
jpayne@68:  * @date Oct 22, 2013
jpayne@68:  *
jpayne@68:  */
jpayne@68: public class KmerNode1D extends KmerNode {
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------        Initialization        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	public KmerNode1D(long pivot_){
jpayne@68: 		super(pivot_);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public KmerNode1D(long pivot_, int value_){
jpayne@68: 		super(pivot_);
jpayne@68: 		value=value_;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public final KmerNode makeNode(long pivot_, int value_){
jpayne@68: 		return new KmerNode1D(pivot_, value_);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public final KmerNode makeNode(long pivot_, int[] values_, int vlen){
jpayne@68: 		throw new RuntimeException("Unimplemented");
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------        Public Methods        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public final int set(long kmer, int[] vals, int vlen) {
jpayne@68: 		throw new RuntimeException("Unimplemented.");
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------      Nonpublic Methods       ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public int value(){return value;}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	protected int[] values(int[] singleton){
jpayne@68: 		assert(singleton.length==1);
jpayne@68: 		singleton[0]=value;
jpayne@68: 		return singleton;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public int set(int value_){return value=value_;}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	protected int set(int[] values_, int vlen){
jpayne@68: 		throw new RuntimeException("Unimplemented");
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	int numValues(){return value<1 ? 0 : 1;}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------       Private Methods        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------   Resizing and Rebalancing   ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	boolean canResize() {
jpayne@68: 		return false;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public boolean canRebalance() {
jpayne@68: 		return true;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Deprecated
jpayne@68: 	@Override
jpayne@68: 	public int arrayLength() {
jpayne@68: 		throw new RuntimeException("Unsupported.");
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Deprecated
jpayne@68: 	@Override
jpayne@68: 	void resize() {
jpayne@68: 		throw new RuntimeException("Unsupported.");
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Deprecated
jpayne@68: 	@Override
jpayne@68: 	public void rebalance() {
jpayne@68: 		throw new RuntimeException("Please call rebalance(ArrayList<KmerNode>) instead, with an empty list.");
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------         Info Dumping         ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public final boolean dumpKmersAsBytes(ByteStreamWriter bsw, int k, int mincount, int maxcount, AtomicLong remaining){
jpayne@68: 		if(value<1){return true;}
jpayne@68: 		if(value>=mincount){
jpayne@68: 			if(remaining!=null && remaining.decrementAndGet()<0){return true;}
jpayne@68: 			bsw.printlnKmer(pivot, value, k);
jpayne@68: 		}
jpayne@68: 		if(left!=null){left.dumpKmersAsBytes(bsw, k, mincount, maxcount, remaining);}
jpayne@68: 		if(right!=null){right.dumpKmersAsBytes(bsw, k, mincount, maxcount, remaining);}
jpayne@68: 		return true;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public final boolean dumpKmersAsBytes_MT(final ByteStreamWriter bsw, final ByteBuilder bb, final int k, final int mincount, int maxcount, AtomicLong remaining){
jpayne@68: 		if(value<1){return true;}
jpayne@68: 		if(value>=mincount){
jpayne@68: 			if(remaining!=null && remaining.decrementAndGet()<0){return true;}
jpayne@68: 			toBytes(pivot, value, k, bb);
jpayne@68: 			bb.nl();
jpayne@68: 			if(bb.length()>=16000){
jpayne@68: 				ByteBuilder bb2=new ByteBuilder(bb);
jpayne@68: 				synchronized(bsw){bsw.addJob(bb2);}
jpayne@68: 				bb.clear();
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		if(left!=null){left.dumpKmersAsBytes_MT(bsw, bb, k, mincount, maxcount, remaining);}
jpayne@68: 		if(right!=null){right.dumpKmersAsBytes_MT(bsw, bb, k, mincount, maxcount, remaining);}
jpayne@68: 		return true;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	protected final StringBuilder dumpKmersAsText(StringBuilder sb, int k, int mincount, int maxcount){
jpayne@68: 		if(value<1){return sb;}
jpayne@68: 		if(sb==null){sb=new StringBuilder(32);}
jpayne@68: 		if(value>=mincount){sb.append(AbstractKmerTable.toText(pivot, value, k)).append('\n');}
jpayne@68: 		if(left!=null){left.dumpKmersAsText(sb, k, mincount, maxcount);}
jpayne@68: 		if(right!=null){right.dumpKmersAsText(sb, k, mincount, maxcount);}
jpayne@68: 		return sb;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	protected final ByteBuilder dumpKmersAsText(ByteBuilder bb, int k, int mincount, int maxcount){
jpayne@68: 		if(value<1){return bb;}
jpayne@68: 		if(bb==null){bb=new ByteBuilder(32);}
jpayne@68: 		if(value>=mincount){bb.append(AbstractKmerTable.toBytes(pivot, value, k)).append('\n');}
jpayne@68: 		if(left!=null){left.dumpKmersAsText(bb, k, mincount, maxcount);}
jpayne@68: 		if(right!=null){right.dumpKmersAsText(bb, k, mincount, maxcount);}
jpayne@68: 		return bb;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	final boolean TWOD(){return false;}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------       Invalid Methods        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------            Fields            ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	int value;
jpayne@68: 	
jpayne@68: }