Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/clump/ClumpTools.java @ 68:5028fdace37b

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
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67:0e9998148a16 68:5028fdace37b
1 package clump;
2
3 import java.util.ArrayList;
4
5 import bloom.KCountArray;
6 import fileIO.ReadWrite;
7 import shared.Shared;
8 import stream.ConcurrentCollectionReadInputStream;
9 import stream.Read;
10
11 /**
12 * @author Brian Bushnell
13 * @date Nov 12, 2015
14 *
15 */
16 public class ClumpTools {
17
18 public static KCountArray table(){
19 return table;
20 }
21
22 public static synchronized KCountArray getTable(ArrayList<Read> reads, int k, int minCount){
23 fname1=fname2=null;
24 table=null;
25 ConcurrentCollectionReadInputStream cris=new ConcurrentCollectionReadInputStream(reads, null, -1);
26 cris.start();
27 table=PivotSet.makeKcaStatic(cris, k, minCount, Shared.AMINO_IN);
28 ReadWrite.closeStream(cris);
29 return table;
30 }
31
32 public static synchronized KCountArray getTable(String fname1_, String fname2_, int k_, int minCount_){
33 if(fname1==null || !fname1.equals(fname1_) || table==null){
34 fname1=fname1_;
35 fname2=fname2_;
36 String[] args=new String[] {"in1="+fname1, "in2="+fname2, "k="+k_, "minCount="+minCount_};
37 table=PivotSet.makeSet(args);
38 }
39 return table;
40 }
41
42 public static synchronized void clearTable() {
43 fname1=fname2=null;
44 table=null;
45 }
46
47 private static String fname1=null, fname2=null;
48 private static KCountArray table=null;
49
50 }