--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/sketch/SketchResults.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,202 @@
+package sketch;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Map.Entry;
+import java.util.concurrent.ConcurrentHashMap;
+
+import fileIO.TextStreamWriter;
+import json.JsonObject;
+import shared.Shared;
+import shared.Tools;
+import structures.ByteBuilder;
+import structures.IntHashMap;
+import tax.TaxTree;
+
+public class SketchResults extends SketchObject {
+	
+	SketchResults(Sketch s){
+		sketch=s;
+	}
+	
+	SketchResults(Sketch s, ArrayList<Sketch> sketchList_, int[][] taxHits_){
+		sketch=s;
+		refSketchList=sketchList_;
+		taxHits=taxHits_;
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------            Methods           ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	public void addMap(ConcurrentHashMap<Integer, Comparison> map, DisplayParams params, CompareBuffer buffer) {
+
+		if(map.isEmpty()){return;}
+		list=addToList(map, params, list);
+		
+		if((true || params.needContamCounts())){
+			recompare(buffer, params);
+		}
+	}
+	
+	public void recompare(CompareBuffer buffer, DisplayParams params){
+//		assert(makeIndex || !AUTOSIZE);
+		
+		assert(!sketch.merged());
+		sketch.mergeBitSets();
+		
+//		System.err.println(sketch.compareBitSet());
+//		assert(false) : sketch.compareBitSet().getClass();
+		
+		for(Comparison c : list){
+			c.recompare(buffer, taxHits, params.contamLevel());
+		}
+		Collections.sort(list, params.comparator);
+		Collections.reverse(list);
+	}
+	
+	private static ArrayList<Comparison> addToList(ConcurrentHashMap<Integer, Comparison> map, DisplayParams params, ArrayList<Comparison> old){
+		
+//		System.err.println(map.size());
+//		System.err.println(map.keySet());
+
+//		final TaxFilter white=params.taxFilterWhite;
+//		final TaxFilter black=params.taxFilterBlack;
+//		final boolean noFilter=(white==null && black==null);
+		final int size=map.size();
+		ArrayList<Comparison> al=(old==null ? new ArrayList<Comparison>(size) : old);
+		for(Entry<Integer, Comparison> e : map.entrySet()){
+			final Comparison c=e.getValue();
+			al.add(c);
+//			if(noFilter || c.passesFilter(white, black)){
+//				al.add(c);
+//			}
+		}
+		Shared.sort(al, params.comparator);
+		Collections.reverse(al);
+		
+		//Apply records per level filter
+		if(params.recordsPerLevel>0 && al.size()>params.recordsPerLevel && al.get(0).hasQueryTaxID()){
+			int[] count=new int[TaxTree.numTaxLevelNamesExtended];
+			int removed=0;
+			for(int i=0; i<al.size(); i++){
+				Comparison c=al.get(i);
+				int calevel=c.commonAncestorLevelInt();
+				count[calevel]++;
+				if(count[calevel]>params.recordsPerLevel){
+					al.set(i, null);
+					removed++;
+				}
+			}
+			if(removed>0){Tools.condenseStrict(al);}
+		}
+		
+		final long limit=(params.maxRecords*2+5);
+		while(al.size()>limit){
+			al.remove(al.size()-1);
+		}
+		return al;
+	}
+	
+	public boolean isEmpty(){
+		return list==null || list.isEmpty();
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------          Tax Methods         ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	public int primaryTax(int level){
+		//I have no idea how to implement this...
+		IntHashMap map=new IntHashMap();
+		assert(false);
+		return -1;
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Print Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	private static String recordBreak="\n"; //"\n\n"
+	
+	void writeResults(DisplayParams params, TextStreamWriter tsw){
+		ByteBuilder sb=toText(params);
+		tsw.print(sb);
+	}
+	
+	public ByteBuilder toText(DisplayParams params){
+		assert(params.postParsed);
+		if(sketch.hasSSU()){
+			if(params.comparator==Comparison.SSUComparator){
+				alignSSUs(params.maxRecords*4);//This should be enough...
+				list.sort(params.comparator);
+				Collections.reverse(list);
+			}else if(params.printSSU()){
+				alignSSUs(params.maxRecords);
+			}
+		}
+		if(params.json()){
+			JsonObject j=params.toJson(this);
+			return j.toText();
+		}
+		final ByteBuilder sb=params.queryHeader(sketch);
+		if(params.format==DisplayParams.FORMAT_QUERY_REF_ANI || params.format==DisplayParams.FORMAT_CONSTELLATION){
+			if(list==null || list.isEmpty()){return sb;}
+			int idx=0;
+			int prevTaxID=0;
+			for(Comparison c : list){
+				assert(!params.printSSU() || !c.needsAlignment());
+				params.formatComparison(c, sb, prevTaxID);
+				prevTaxID=c.taxID();
+				idx++;
+				if(idx>=params.maxRecords){break;}
+			}
+		}else{
+			sb.append(recordBreak);
+
+			if(list==null || list.isEmpty()){
+				sb.append("No hits.\n");
+			}else{
+				if(params.format==DisplayParams.FORMAT_MULTICOLUMN){sb.append(params.header()).append('\n');}
+				int idx=0;
+				int prevTaxID=0;
+				for(Comparison c : list){
+					params.formatComparison(c, sb, prevTaxID);
+					prevTaxID=c.taxID();
+					idx++;
+					if(idx>=params.maxRecords){break;}
+				}
+			}
+		}
+		return sb;
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------          Alignment           ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	void alignSSUs(int maxRecords){
+		if(!sketch.hasSSU()){return;}
+//		if(list!=null && list.size()>0){
+//			int idx=0;
+//			for(Comparison c : list){
+//				c.ssuIdentity();
+//				idx++;
+//				if(idx>=maxRecords){break;}
+//			}
+//		}
+		assert(alignerPool!=null);
+		alignerPool.addJobs(list, maxRecords);
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------            Fields            ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	public final Sketch sketch;
+	public ArrayList<Sketch> refSketchList;
+	public int[][] taxHits;
+	public ArrayList<Comparison> list;
+	public int totalRecords=0;
+	
+}