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package assemble;
import shared.KillSwitch;
import structures.ByteBuilder;
import ukmer.Kmer;
/**
* Searches for dead ends.
* @author Brian Bushnell
* @date Jul 20, 2015
*
*/
abstract class AbstractExploreThread extends ShaveObject implements Runnable {
/**
* Constructor
*/
public AbstractExploreThread(int id_, int kbig_){
id=id_;
myKmer=new Kmer(kbig_);
myKmer2=new Kmer(kbig_);
thread=new Thread(this);
}
@Override
public final void run(){
//TODO:
//With processNextVictims enabled, the number of dead ends found drops from the first pass to the next, then stabilizes.
//So, they are not being reset correctly.
//Also, the number found - even with one thread - is nondeterministic if both are enabled.
//Unstable whether or not processNextVictims is disabled. But that's probably to be expected as the count is not exact.
//What should be exact is the number of kmers removed for being dead ends.
//The number is lower than expected. 65k for 600k reads with errors. Most are bubbles, but 40% should be dead ends, or 240k.
while(processNextTable(myKmer, myKmer2)){}
while(processNextVictims(myKmer, myKmer2)){}
for(int i=0; i<removeMatrixT.length; i++){
for(int j=0; j<removeMatrixT.length; j++){
if((i==F_BRANCH || i==B_BRANCH) && (j==F_BRANCH || j==B_BRANCH)){
bubblesFoundT+=removeMatrixT[i][j];
}
}
}
}
boolean processNextTable(){return processNextTable(myKmer, myKmer2);}
abstract boolean processNextTable(final Kmer kmer, Kmer temp);
boolean processNextVictims(){return processNextVictims(myKmer, myKmer);}
abstract boolean processNextVictims(final Kmer kmer, Kmer temp);
/*--------------------------------------------------------------*/
public final void start(){thread.start();}
public final Thread.State getState(){return thread.getState();}
public final void join() throws InterruptedException{thread.join();}
/*--------------------------------------------------------------*/
long kmersTestedT=0;
long deadEndsFoundT=0;
long bubblesFoundT=0;
final int id;
final Kmer myKmer, myKmer2;
final int[] leftCounts=KillSwitch.allocInt1D(4);
final int[] rightCounts=KillSwitch.allocInt1D(4);
final ByteBuilder builderT=new ByteBuilder();
long[][] countMatrixT=new long[MAX_CODE+1][MAX_CODE+1];
long[][] removeMatrixT=new long[MAX_CODE+1][MAX_CODE+1];
public final Thread thread;
}
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