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package clump;
import java.util.ArrayList;
import bloom.KCountArray;
import fileIO.ReadWrite;
import shared.Shared;
import stream.ConcurrentCollectionReadInputStream;
import stream.Read;
/**
* @author Brian Bushnell
* @date Nov 12, 2015
*
*/
public class ClumpTools {
public static KCountArray table(){
return table;
}
public static synchronized KCountArray getTable(ArrayList<Read> reads, int k, int minCount){
fname1=fname2=null;
table=null;
ConcurrentCollectionReadInputStream cris=new ConcurrentCollectionReadInputStream(reads, null, -1);
cris.start();
table=PivotSet.makeKcaStatic(cris, k, minCount, Shared.AMINO_IN);
ReadWrite.closeStream(cris);
return table;
}
public static synchronized KCountArray getTable(String fname1_, String fname2_, int k_, int minCount_){
if(fname1==null || !fname1.equals(fname1_) || table==null){
fname1=fname1_;
fname2=fname2_;
String[] args=new String[] {"in1="+fname1, "in2="+fname2, "k="+k_, "minCount="+minCount_};
table=PivotSet.makeSet(args);
}
return table;
}
public static synchronized void clearTable() {
fname1=fname2=null;
table=null;
}
private static String fname1=null, fname2=null;
private static KCountArray table=null;
}
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