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package ukmer;
import java.util.concurrent.atomic.AtomicLong;
import fileIO.ByteStreamWriter;
import structures.ByteBuilder;
/**
* @author Brian Bushnell
* @date Oct 22, 2013
*
*/
public class KmerNodeU1D extends KmerNodeU {
/*--------------------------------------------------------------*/
/*---------------- Initialization ----------------*/
/*--------------------------------------------------------------*/
public KmerNodeU1D(long[] pivot_){
super(pivot_);
}
public KmerNodeU1D(long[] pivot_, int value_){
super(pivot_);
value=value_;
}
@Override
public final KmerNodeU makeNode(long[] pivot_, int value_){
return new KmerNodeU1D(pivot_, value_);
}
@Override
public final KmerNodeU makeNode(long[] pivot_, int[] values_){
throw new RuntimeException("Unimplemented");
}
/*--------------------------------------------------------------*/
/*---------------- Public Methods ----------------*/
/*--------------------------------------------------------------*/
@Override
public final int set(long[] kmer, int[] vals) {
throw new RuntimeException("Unimplemented.");
}
/*--------------------------------------------------------------*/
/*---------------- Nonpublic Methods ----------------*/
/*--------------------------------------------------------------*/
@Override
public int value(){return value;}
@Override
protected int[] values(int[] singleton){
assert(singleton.length==1);
singleton[0]=value;
return singleton;
}
@Override
public int set(int value_){return value=value_;}
@Override
protected int set(int[] values_){
throw new RuntimeException("Unimplemented");
}
@Override
int numValues(){return value<1 ? 0 : 1;}
/*--------------------------------------------------------------*/
/*---------------- Private Methods ----------------*/
/*--------------------------------------------------------------*/
/*--------------------------------------------------------------*/
/*---------------- Resizing and Rebalancing ----------------*/
/*--------------------------------------------------------------*/
@Override
boolean canResize() {
return false;
}
@Override
public boolean canRebalance() {
return true;
}
@Deprecated
@Override
public int arrayLength() {
throw new RuntimeException("Unsupported.");
}
@Deprecated
@Override
void resize() {
throw new RuntimeException("Unsupported.");
}
@Deprecated
@Override
public void rebalance() {
throw new RuntimeException("Please call rebalance(ArrayList<KmerNode>) instead, with an empty list.");
}
/*--------------------------------------------------------------*/
/*---------------- Info Dumping ----------------*/
/*--------------------------------------------------------------*/
@Override
public final boolean dumpKmersAsBytes(ByteStreamWriter bsw, int k, int mincount, int maxcount, AtomicLong remaining){
if(value<1){return true;}
if(value>=mincount){
if(remaining!=null && remaining.decrementAndGet()<0){return true;}
bsw.printlnKmer(pivot, value, k);
}
if(left!=null){left.dumpKmersAsBytes(bsw, k, mincount, maxcount, remaining);}
if(right!=null){right.dumpKmersAsBytes(bsw, k, mincount, maxcount, remaining);}
return true;
}
@Override
public final boolean dumpKmersAsBytes_MT(final ByteStreamWriter bsw, final ByteBuilder bb, final int k, final int mincount, int maxcount, AtomicLong remaining){
if(value<1){return true;}
if(value>=mincount){
if(remaining!=null && remaining.decrementAndGet()<0){return true;}
toBytes(pivot, value, k, bb);
bb.nl();
if(bb.length()>=16000){
ByteBuilder bb2=new ByteBuilder(bb);
synchronized(bsw){bsw.addJob(bb2);}
bb.clear();
}
}
if(left!=null){left.dumpKmersAsBytes_MT(bsw, bb, k, mincount, maxcount, remaining);}
if(right!=null){right.dumpKmersAsBytes_MT(bsw, bb, k, mincount, maxcount, remaining);}
return true;
}
@Override
protected final StringBuilder dumpKmersAsText(StringBuilder sb, int k, int mincount, int maxcount){
if(value<1){return sb;}
if(sb==null){sb=new StringBuilder(32);}
if(value>=mincount){sb.append(AbstractKmerTableU.toText(pivot, value, k)).append('\n');}
if(left!=null){left.dumpKmersAsText(sb, k, mincount, maxcount);}
if(right!=null){right.dumpKmersAsText(sb, k, mincount, maxcount);}
return sb;
}
@Override
protected final ByteBuilder dumpKmersAsText(ByteBuilder bb, int k, int mincount, int maxcount){
if(value<1){return bb;}
if(bb==null){bb=new ByteBuilder(32);}
if(value>=mincount){bb.append(AbstractKmerTableU.toBytes(pivot, value, k)).append('\n');}
if(left!=null){left.dumpKmersAsText(bb, k, mincount, maxcount);}
if(right!=null){right.dumpKmersAsText(bb, k, mincount, maxcount);}
return bb;
}
@Override
final boolean TWOD(){return false;}
/*--------------------------------------------------------------*/
/*---------------- Invalid Methods ----------------*/
/*--------------------------------------------------------------*/
/*--------------------------------------------------------------*/
/*---------------- Fields ----------------*/
/*--------------------------------------------------------------*/
int value;
}
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