jpayne@68: package clump;
jpayne@68: 
jpayne@68: import java.util.ArrayList;
jpayne@68: 
jpayne@68: import bloom.KCountArray;
jpayne@68: import fileIO.ReadWrite;
jpayne@68: import shared.Shared;
jpayne@68: import stream.ConcurrentCollectionReadInputStream;
jpayne@68: import stream.Read;
jpayne@68: 
jpayne@68: /**
jpayne@68:  * @author Brian Bushnell
jpayne@68:  * @date Nov 12, 2015
jpayne@68:  *
jpayne@68:  */
jpayne@68: public class ClumpTools {
jpayne@68: 	
jpayne@68: 	public static KCountArray table(){
jpayne@68: 		return table;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static synchronized KCountArray getTable(ArrayList<Read> reads, int k, int minCount){
jpayne@68: 		fname1=fname2=null;
jpayne@68: 		table=null;
jpayne@68: 		ConcurrentCollectionReadInputStream cris=new ConcurrentCollectionReadInputStream(reads, null, -1);
jpayne@68: 		cris.start();
jpayne@68: 		table=PivotSet.makeKcaStatic(cris, k, minCount, Shared.AMINO_IN);
jpayne@68: 		ReadWrite.closeStream(cris);
jpayne@68: 		return table;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static synchronized KCountArray getTable(String fname1_, String fname2_, int k_, int minCount_){
jpayne@68: 		if(fname1==null || !fname1.equals(fname1_) || table==null){
jpayne@68: 			fname1=fname1_;
jpayne@68: 			fname2=fname2_;
jpayne@68: 			String[] args=new String[] {"in1="+fname1, "in2="+fname2, "k="+k_, "minCount="+minCount_};
jpayne@68: 			table=PivotSet.makeSet(args);
jpayne@68: 		}
jpayne@68: 		return table;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static synchronized void clearTable() {
jpayne@68: 		fname1=fname2=null;
jpayne@68: 		table=null;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private static String fname1=null, fname2=null;
jpayne@68: 	private static KCountArray table=null;
jpayne@68: 	
jpayne@68: }