--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/clump/ClumpTools.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,50 @@
+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;
+	
+}