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package assemble;
import java.util.ArrayList;
import java.util.concurrent.atomic.AtomicInteger;
import shared.KillSwitch;
import structures.ByteBuilder;
/**
* Thread for exploring connectivity graph between contigs.
* @author Brian Bushnell
* @date July 12, 2018
*
*/
public abstract class AbstractProcessContigThread extends Thread {
AbstractProcessContigThread(ArrayList<Contig> contigs_, AtomicInteger next_){
contigs=contigs_;
next=next_;
}
@Override
public void run(){
processContigs(contigs);
}
public final void processContigs(ArrayList<Contig> contigs){
for(int cnum=next.getAndIncrement(); cnum<contigs.size(); cnum=next.getAndIncrement()){
Contig c=contigs.get(cnum);
processContigLeft(c, leftCounts, rightCounts, extraCounts, bb);
processContigRight(c, leftCounts, rightCounts, extraCounts, bb);
}
}
abstract void processContigLeft(Contig c, int[] leftCounts, int[] rightCounts, int[] extraCounts, ByteBuilder bb);
abstract void processContigRight(Contig c, int[] leftCounts, int[] rightCounts, int[] extraCounts, ByteBuilder bb);
final int[] leftCounts=KillSwitch.allocInt1D(4);
final int[] rightCounts=KillSwitch.allocInt1D(4);
final int[] extraCounts=KillSwitch.allocInt1D(4);
final ArrayList<Contig> contigs;
final AtomicInteger next;
int lastLength=-1;
int lastTarget=-1;
int lastExitCondition=-1;
int lastOrientation=-1;
ByteBuilder bb=new ByteBuilder();
long edgesMadeT=0;
}
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