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package assemble;
import java.io.PrintStream;
import java.util.ArrayList;
import java.util.concurrent.atomic.AtomicInteger;
import kmer.AbstractKmerTableSet;
import kmer.HashArray1D;
import kmer.KmerNode;
import kmer.KmerTableSet;
import shared.Timer;
import ukmer.HashArrayU1D;
import ukmer.KmerNodeU;
import ukmer.KmerTableSetU;
/**
* Removes kmers with counts outside a certain range.
* @author Brian Bushnell
* @date Jul 20, 2015
*/
public abstract class AbstractRemoveThread extends Thread{
/**
* Constructor
*/
public AbstractRemoveThread(int id_, int min_, int max_, AtomicInteger nextTable_){
id=id_;
min=min_;
max=max_;
nextTable=nextTable_;
assert(nextTable.get()==0);
}
@Override
public final void run(){
while(processNextTable()){}
}
abstract boolean processNextTable();
/*--------------------------------------------------------------*/
public static long process(final int threads, final int min, final int max, AbstractKmerTableSet tables, boolean print){
Timer t=new Timer();
final AtomicInteger nextTable=new AtomicInteger(0);
long kmersRemoved=0;
/* Create Removethreads */
ArrayList<AbstractRemoveThread> alpt=new ArrayList<AbstractRemoveThread>(threads);
for(int i=0; i<threads; i++){
final AbstractRemoveThread art;
if(tables.getClass()==KmerTableSet.class){
art=new RemoveThread1(i, min, max, nextTable, (KmerTableSet)tables);
}else{
art=new RemoveThread2(i, min, max, nextTable, (KmerTableSetU)tables);
}
alpt.add(art);
}
for(AbstractRemoveThread pt : alpt){pt.start();}
for(AbstractRemoveThread pt : alpt){
while(pt.getState()!=Thread.State.TERMINATED){
try {
pt.join();
} catch (InterruptedException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
kmersRemoved+=pt.kmersRemovedT;
}
t.stop();
if(print){
outstream.println("Removed "+kmersRemoved+" kmers.");
outstream.println("Remove time: "+t);
}
return kmersRemoved;
}
/*--------------------------------------------------------------*/
private static class RemoveThread1 extends AbstractRemoveThread{
/**
* Constructor
*/
public RemoveThread1(int id_, int min_, int max_, AtomicInteger nextTable_, KmerTableSet tables_){
super(id_, min_, max_, nextTable_);
tables=tables_;
}
@Override
boolean processNextTable(){
final int tnum=nextTable.getAndAdd(1);
if(tnum>=tables.ways){return false;}
final HashArray1D table=tables.getTable(tnum);
final int[] values=table.values();
final int lim=table.arrayLength();
for(int cell=0; cell<lim; cell++){
final int value=values[cell];
if(value<min || value>max){values[cell]=0;}
}
for(KmerNode kn : table.victims().array()){
if(kn!=null){traverseKmerNode(kn);}
}
table.clearOwnership();
kmersRemovedT+=table.regenerate(0);
return true;
}
private void traverseKmerNode(KmerNode kn){
if(kn==null){return;}
final int value=kn.count();
if(value<min || value>max){kn.set(0);}
traverseKmerNode(kn.left());
traverseKmerNode(kn.right());
}
private final KmerTableSet tables;
}
/*--------------------------------------------------------------*/
private static class RemoveThread2 extends AbstractRemoveThread{
/**
* Constructor
*/
public RemoveThread2(int id_, int min_, int max_, AtomicInteger nextTable_, KmerTableSetU tables_){
super(id_, min_, max_, nextTable_);
tables=tables_;
}
@Override
boolean processNextTable(){
final int tnum=nextTable.getAndAdd(1);
if(tnum>=tables.ways){return false;}
final HashArrayU1D table=tables.getTable(tnum);
final int[] values=table.values();
final int lim=table.arrayLength();
for(int cell=0; cell<lim; cell++){
final int value=values[cell];
if(value<min || value>max){values[cell]=0;}
}
for(KmerNodeU kn : table.victims().array()){
if(kn!=null){traverseKmerNode(kn);}
}
table.clearOwnership();
kmersRemovedT+=table.regenerate(0);
return true;
}
private void traverseKmerNode(KmerNodeU kn){
if(kn==null){return;}
final int value=kn.count();
if(value<min || value>max){kn.set(0);}
traverseKmerNode(kn.left());
traverseKmerNode(kn.right());
}
private final KmerTableSetU tables;
}
/*--------------------------------------------------------------*/
long kmersRemovedT=0;
final int id;
final int min;
final int max;
final AtomicInteger nextTable;
/** Print messages to this stream */
static PrintStream outstream=System.err;
}
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