--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/sketch/DisplayParams.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,1908 @@
+package sketch;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.Locale;
+import java.util.Map.Entry;
+
+import json.JsonObject;
+import shared.Colors;
+import shared.Parse;
+import shared.Tools;
+import structures.ByteBuilder;
+import tax.PrintTaxonomy;
+import tax.TaxFilter;
+import tax.TaxNode;
+import tax.TaxTree;
+
+public class DisplayParams implements Cloneable {
+	
+	@Override
+	public DisplayParams clone(){
+		try {
+			DisplayParams copy=(DisplayParams)super.clone();
+			if(taxFilterWhite!=null){
+				copy.taxFilterWhite=taxFilterWhite.deepCopy();
+			}
+			if(taxFilterBlack!=null){
+				copy.taxFilterBlack=taxFilterBlack.deepCopy();
+			}
+			copy.postParsed=false;
+			return copy;
+		} catch (CloneNotSupportedException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+			throw new RuntimeException();
+		}
+	}
+	
+	public DisplayParams parseDoubleHeader(String s){
+		if(!s.startsWith("##")){return this;}
+//		if(!s.startsWith("##")){return this.clone();}
+		StringBuilder sb=new StringBuilder();
+		for(int i=2; i<s.length(); i++){
+			char c=s.charAt(i);
+			if(c=='\n'){break;}
+			sb.append(c);
+		}
+		return parseDoubleHeaderLine(sb.toString());
+	}
+	
+	public DisplayParams parseDoubleHeaderLine(String line) {
+		if(line.startsWith("##")){line=line.substring(2);}
+		else{assert(!line.startsWith("#")) : line;}
+		if(line.length()<1){return this;}
+		
+		DisplayParams params=this.clone();
+		
+		String[] args=line.split(" ");
+		for(String arg : args){
+			String[] split=arg.split("=");
+			String a=split[0].toLowerCase();
+			String b=split.length>1 ? split[1] : null;
+			if(b==null || b.equalsIgnoreCase("null")){b=null;} //Normally handled by PreParser, but not in this case.
+			while(a.startsWith("-")){a=a.substring(1);} //Strip leading hyphens
+			
+			boolean x=params.parse(arg, a, b);
+//			assert(x) : "Unknown parameter "+arg+"\n"+line;
+			if(!x){System.err.println("Warning: Unknown parameter "+arg);}
+		}
+		if(SketchObject.verbose2){System.err.println("Made it to post-parse.  taxFilterWhite="+params.taxFilterWhite);}
+		params.postParse(true, true);
+		if(SketchObject.verbose2){System.err.println("Passed post-parse.  taxFilterWhite="+params.taxFilterWhite);}
+		
+		return params;
+	}
+	
+	public boolean parse(String arg, String a, String b){
+	
+		if(a.equals("chunk")){
+			chunkNum=Integer.parseInt(b);
+		}else if(a.equals("minhits")  || a.equals("hits")){
+			minHits=Integer.parseInt(b);
+		}else if(a.equalsIgnoreCase("minwkid") || a.equalsIgnoreCase("wkid")){
+			minWKID=Float.parseFloat(b);
+			if(minWKID>1){minWKID/=100;}
+			assert(minWKID<=1) : "minWKID should between 0 and 1";
+		}else if(a.equalsIgnoreCase("minid") || a.equalsIgnoreCase("id") || a.equalsIgnoreCase("minani") || a.equalsIgnoreCase("ani")){
+			minANI=Float.parseFloat(b);
+			if(minANI>1){minANI/=100;}
+			assert(minANI<=1) : "minANI should between 0 and 1";
+			if(minANI>0){
+				minWKID=(float)Tools.max(minWKID, Comparison.aniToWkid(minANI, 32));//Lowest possible minWKID for this ANI
+			}
+		}else if(a.equals("minbases")){
+			minBases=Integer.parseInt(b);
+		}else if(a.equals("minsizeratio")){
+			minSizeRatio=Float.parseFloat(b);
+//			assert(minSizeRatio>=0f && minSizeRatio<=1.0f) : "\nminSizeRatio must be between 0 and 1, inclusive.\n";
+			if(minSizeRatio>1){minSizeRatio=1f/minSizeRatio;}
+		}else if(a.equals("records") || a.equals("maxrecords") || a.equals("results")){
+			maxRecords=Integer.parseInt(b);
+			assert(maxRecords>=1) : "Max records must be at least 1.";
+		}else if(a.equals("recordsperlevel")){
+			recordsPerLevel=Integer.parseInt(b);
+		}else if(a.equals("format")){
+			assert(b!=null) : "Invalid format: "+arg;
+			if(b.equalsIgnoreCase("json")){
+				format=FORMAT_JSON;
+			}else if(b.equalsIgnoreCase("jsonarray")){
+				format=FORMAT_JSON;
+				jsonArray=true;
+			}else if(b.equalsIgnoreCase("d3")){
+				format=FORMAT_JSON;
+				printD3=true;
+			}else if(b.equalsIgnoreCase("constellation")){
+				format=FORMAT_CONSTELLATION;
+			}else if(b.equalsIgnoreCase("3column") || b.equalsIgnoreCase("queryrefani")){
+				format=FORMAT_QUERY_REF_ANI;
+			}else if(Tools.isDigit(b.charAt(0))){
+				format=Integer.parseInt(b);
+			}else{
+				assert(false) : "Invalid format: "+arg;
+			}
+		}else if(a.equalsIgnoreCase("json")){
+			if(Parse.parseBoolean(b)){
+				format=FORMAT_JSON;
+			}else{
+				if(format==FORMAT_JSON){format=default_format;}
+			}
+		}else if(a.equalsIgnoreCase("jsonarray") || a.equalsIgnoreCase("jsonarrays")){
+			if(Parse.parseBoolean(b)){
+				format=FORMAT_JSON;
+				jsonArray=true;
+			}else{
+				jsonArray=false;
+			}
+		}else if(a.equalsIgnoreCase("d3") || a.equalsIgnoreCase("printd3")){
+			if(Parse.parseBoolean(b)){
+				format=FORMAT_JSON;
+				printD3=true;
+			}else{
+				printD3=false;
+			}
+		}else if(a.equalsIgnoreCase("jsonarray") || a.equalsIgnoreCase("jsonarrays")){
+			if(Parse.parseBoolean(b)){
+				jsonArray=true;
+			}else{
+				jsonArray=false;
+			}
+		}else if(a.equalsIgnoreCase("d3levelnodes")){
+			D3LevelNodes=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("d3hitsize")){
+			if(Parse.parseBoolean(b)){D3sizeMode=D3_HIT_SIZE;}
+		}else if(a.equalsIgnoreCase("d3anisize")){
+			if(Parse.parseBoolean(b)){D3sizeMode=D3_ANI_SIZE;}
+		}else if(a.equalsIgnoreCase("d3wkidsize")){
+			if(Parse.parseBoolean(b)){D3sizeMode=D3_WKID_SIZE;}
+		}else if(a.equalsIgnoreCase("d3depthsize")){
+			if(Parse.parseBoolean(b)){
+				D3sizeMode=D3_DEPTH_SIZE;
+				printDepth=true;
+			}
+		}else if(a.equalsIgnoreCase("d3kidsize")){
+			if(Parse.parseBoolean(b)){D3sizeMode=D3_KID_SIZE;}
+		}else if(a.equalsIgnoreCase("D3sizeMode")){
+			D3sizeMode=Integer.parseInt(b);
+		}else if(a.equals("level") || a.equals("lv") || a.equals("taxlevel") || a.equals("tl") || a.equals("minlevel")){
+			taxLevel=TaxTree.parseLevel(b);//TODO: Change to extended
+		}
+		
+		else if(a.equalsIgnoreCase("requireSSU")){
+			requireSSU=Parse.parseBoolean(b);
+		}
+		
+		else if(a.equalsIgnoreCase("minRefSizeEstimate") || a.equalsIgnoreCase("minRefSize")){
+			minRefSizeEstimate=Long.parseLong(b);
+		}else if(a.equalsIgnoreCase("minRefSizeBases")){
+			minRefSizeBases=Long.parseLong(b);
+		}
+		
+		else if(a.equalsIgnoreCase("printtax") || a.equalsIgnoreCase("printtaxa")){
+			printTax=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printssu") || a.equalsIgnoreCase("print16s") || a.equalsIgnoreCase("ssu")){
+			printSSU=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printSSULen") || a.equalsIgnoreCase("print16slen") || a.equalsIgnoreCase("ssulen")){
+			printSSULen=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printssusequence") || a.equalsIgnoreCase("print16ssequence")){
+			printSSUSequence=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printqueryfilename") || a.equalsIgnoreCase("printqfname") || a.equalsIgnoreCase("printqfile") || a.equalsIgnoreCase("qfname")){
+			printQueryFileName=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printreffilename") || a.equalsIgnoreCase("printrfname") || a.equalsIgnoreCase("printrfile") || a.equalsIgnoreCase("rfname")){
+			printRefFileName=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printfilename") || a.equalsIgnoreCase("printfname") || a.equalsIgnoreCase("printfile")){
+			printQueryFileName=printRefFileName=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printoriginalname") || a.equalsIgnoreCase("printseqname") || a.equalsIgnoreCase("printname0") || a.equals("pn0")){
+			printOriginalName=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printimg")){
+			printImg=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printcompleteness") || a.equalsIgnoreCase("completeness") || a.equalsIgnoreCase("printcomplt")){
+			printCompleteness=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printani") || a.equalsIgnoreCase("ani")){
+			printAni=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printkid") || a.equalsIgnoreCase("kid")){
+			printKID=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printwkid") || a.equalsIgnoreCase("wkid")){
+			printWKID=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printscore") || a.equalsIgnoreCase("score")){
+			printScore=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printevalue") || a.equalsIgnoreCase("evalue")){
+			printEValue=Parse.parseBoolean(b);
+		}
+		
+		else if(a.equalsIgnoreCase("trackcounts")){
+			trackCounts=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printdepth") || a.equalsIgnoreCase("depth")){
+			printDepth=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printdepth2") || a.equalsIgnoreCase("depth2")){
+			printDepth2=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("actualdepth") || a.equalsIgnoreCase("printactualdepth")){
+			printActualDepth=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printvolume") || a.equalsIgnoreCase("volume")){
+			printVolume=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printavgrefhits") || a.equalsIgnoreCase("printrefhits") || a.equalsIgnoreCase("avgrefhits") || a.equalsIgnoreCase("refhits")){
+			printRefHits=Parse.parseBoolean(b);
+		}
+		
+		else if(a.equalsIgnoreCase("sortByDepth")){
+			boolean x=Parse.parseBoolean(b);
+			if(x){comparator=Comparison.depthComparator;}
+		}else if(a.equalsIgnoreCase("sortByDepth2")){
+			boolean x=Parse.parseBoolean(b);
+			if(x){comparator=Comparison.depth2Comparator;}
+		}else if(a.equalsIgnoreCase("sortByVolume")){
+			boolean x=Parse.parseBoolean(b);
+			if(x){comparator=Comparison.volumeComparator;}
+		}else if(a.equalsIgnoreCase("sortByScore")){
+			boolean x=Parse.parseBoolean(b);
+			if(x){comparator=Comparison.scoreComparator;}
+		}
+		else if(a.equalsIgnoreCase("sortByKID")){
+			boolean x=Parse.parseBoolean(b);
+			if(x){comparator=Comparison.KIDComparator;}
+		}else if(a.equalsIgnoreCase("sortByWKID") || a.equalsIgnoreCase("sortByANI")){
+			boolean x=Parse.parseBoolean(b);
+			if(x){comparator=Comparison.WKIDComparator;}
+		}else if(a.equalsIgnoreCase("sortBySSU") || a.equalsIgnoreCase("sortBy16S")){
+			boolean x=Parse.parseBoolean(b);
+			if(x){comparator=Comparison.SSUComparator;}
+		}else if(a.equalsIgnoreCase("sortByHits") || a.equalsIgnoreCase("sortByMatches")){
+			boolean x=Parse.parseBoolean(b);
+			if(x){comparator=Comparison.HitsComparator;}
+		}
+		
+		else if(a.equalsIgnoreCase("printUMatches") || a.equalsIgnoreCase("printUHits") || a.equalsIgnoreCase("printUnique")){
+			printUnique=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printUMatches2") || a.equalsIgnoreCase("printUnique2") || a.equalsIgnoreCase("unique2")){
+			printUnique2=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printUMatches3") || a.equalsIgnoreCase("printUnique3") || a.equalsIgnoreCase("unique3")){
+			printUnique3=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printUContam")){
+			printUContam=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printNoHit")){
+			printNoHit=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("contamhits") || a.equalsIgnoreCase("contam") || a.equalsIgnoreCase("printcontam")){
+			printContam=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("contamhits2") || a.equalsIgnoreCase("contam2") || a.equalsIgnoreCase("printcontam2")){
+			if(b==null || b.length()<1){
+				printContam2=true;
+			}else if(Tools.isDigit(b.charAt(0)) || b.charAt(0)=='-'){
+				contamLevel=Tools.max(0, TaxTree.levelToExtended(Integer.parseInt(b)));
+				printContam2=true;
+			}else if(TaxTree.levelMapExtendedContains(b)){
+				contamLevel=TaxTree.stringToLevelExtended(b);
+				printContam2=true;
+			}else{
+				printContam2=Parse.parseBoolean(b);
+			}
+		}else if(a.equalsIgnoreCase("contamLevel")){
+			if(Tools.isDigit(b.charAt(0)) || b.charAt(0)=='-'){
+				contamLevel=Tools.max(0, TaxTree.levelToExtended(Integer.parseInt(b)));
+				printContam2=true;
+			}else if(TaxTree.levelMapExtendedContains(b)){
+				contamLevel=TaxTree.stringToLevelExtended(b);
+				printContam2=true;
+			}
+		}
+		
+		else if(a.equalsIgnoreCase("reportAniOnly") || a.equalsIgnoreCase("AniOnly")){
+			reportAniOnly=Parse.parseBoolean(b);
+		}
+		
+		else if(a.equalsIgnoreCase("printMatches")){
+			printMatches=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printLength")){
+			printLength=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printTaxID")){
+			printTaxID=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printGSize")){
+			printGSize=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("gSizeKMG")){
+			gSizeKMG=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printGC")){
+			printGC=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printGKmers")){
+			printGKmers=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printCommonAncestor") || a.equalsIgnoreCase("printCA")){
+			printCommonAncestor=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printCommonAncestorLevel") || a.equalsIgnoreCase("printCAL")){
+			printCommonAncestorLevel=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printTaxName")){
+			printTaxName=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printGSeqs")){
+			printGSeqs=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printGBases")){
+			printGBases=Parse.parseBoolean(b);
+		}
+		
+		else if(a.equalsIgnoreCase("minEntropy") || a.equalsIgnoreCase("entropy") || a.equalsIgnoreCase("efilter")){
+			minEntropy=Float.parseFloat(b);
+		}else if(a.equalsIgnoreCase("minprob") || a.equalsIgnoreCase("pfilter")){
+			minProb=(float)Double.parseDouble(b);
+		}else if(a.equalsIgnoreCase("minQual") || a.equalsIgnoreCase("minq")){
+			minQual=Byte.parseByte(b);
+		}
+		
+		else if(a.equalsIgnoreCase("printColors") || a.equalsIgnoreCase("colors") || a.equalsIgnoreCase("color")){
+//			System.err.println("Parsing '"+arg+"'"); //123
+			if(b==null || b.length()<1){
+				printColors=true;
+			}else if(b.equalsIgnoreCase("t") || b.equalsIgnoreCase("true")){
+				printColors=true;
+			}else if(b.equalsIgnoreCase("f") || b.equalsIgnoreCase("false")){
+				printColors=false;
+			}else{
+				printColors=true;
+				if(Tools.isDigit(b.charAt(0)) || b.charAt(0)=='-'){
+					colorLevel=Tools.max(0, TaxTree.levelToExtended(Integer.parseInt(b)));
+				}else{
+					colorLevel=TaxTree.stringToLevelExtended(b);
+				}
+			}
+			setColors=true;
+//			System.err.println("Parsed "+arg); //123
+		}else if(a.equalsIgnoreCase("colorLevel")){
+//			System.err.println("Parsing '"+arg+"'"); //123
+			if(Tools.isDigit(b.charAt(0)) || b.charAt(0)=='-'){
+				colorLevel=Tools.max(0, TaxTree.levelToExtended(Integer.parseInt(b)));
+			}else{
+				colorLevel=TaxTree.stringToLevelExtended(b);
+			}
+//			System.err.println("Parsed "+arg); //123
+		}
+		
+		else if(a.equalsIgnoreCase("printRefDivisor") || a.equalsIgnoreCase("printRDiv")){
+			printRefDivisor=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printQueryDivisor") || a.equalsIgnoreCase("printQDiv")){
+			printQueryDivisor=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printRefSize") || a.equalsIgnoreCase("printRSize")){
+			printRefSize=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printQuerySize") || a.equalsIgnoreCase("printQSize")){
+			printQuerySize=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("printContamHits") || a.equalsIgnoreCase("printCHits")){
+			printContamHits=Parse.parseBoolean(b);
+		}
+		
+		else if(a.equalsIgnoreCase("printIntersection") || a.equalsIgnoreCase("intersection") || a.equalsIgnoreCase("intersect")){
+			printIntersection=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("mergePairs") || a.equalsIgnoreCase("merge")){
+			mergePairs=Parse.parseBoolean(b);
+		}
+		
+		else if(a.equalsIgnoreCase("printAll")){
+			if(Parse.parseBoolean(b)){
+				setPrintAll();
+			}
+		}
+		
+		else if(a.equals("samplerate")){
+			samplerate=Float.parseFloat(b);
+		}else if(a.equals("reads")){
+			maxReads=Parse.parseKMG(b);
+		}else if(a.equals("mode") || a.equalsIgnoreCase("single") || a.equalsIgnoreCase("singlesketch") || a.equalsIgnoreCase("onesketch")
+				|| a.equalsIgnoreCase("persequence") || a.equalsIgnoreCase("sequence") || a.equalsIgnoreCase("pertaxa") 
+				|| a.equalsIgnoreCase("perheader") || a.equalsIgnoreCase("perfile")){
+			mode=SketchObject.parseMode(arg, a, b);
+		}
+		
+		//For format 3
+		else if(a.equalsIgnoreCase("useTaxidName") || a.equalsIgnoreCase("useTaxidAsName")){
+			useTaxidName=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("useImgName") || a.equalsIgnoreCase("useImgAsName")){
+			useImgName=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("useTaxName") || a.equalsIgnoreCase("useTaxAsName")){
+			useTaxName=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("useFilePrefixName") || a.equalsIgnoreCase("useFilePrefixAsName")){
+			useFilePrefixName=Parse.parseBoolean(b);
+		}
+		
+		else if(a.equalsIgnoreCase("taxfilterincludelevel") || a.equalsIgnoreCase("includelevel") 
+				|| a.equalsIgnoreCase("taxlevelwhite") || a.equalsIgnoreCase("ilevel") || a.equalsIgnoreCase("whitelevel")){
+			taxLevelWhite=TaxTree.parseLevel(b);//TODO:  Change to extended
+		}else if(a.equalsIgnoreCase("taxfilterinclude") || a.equalsIgnoreCase("include") || a.equalsIgnoreCase("taxfilterwhitelist")){
+			taxFilterWhiteList=b;
+		}else if(a.equalsIgnoreCase("taxfilterincludestring") || a.equalsIgnoreCase("includestring")
+				|| a.equalsIgnoreCase("taxfilterwhitestring") || a.equalsIgnoreCase("istring")){
+			taxFilterWhiteString=b;
+		}else if(a.equalsIgnoreCase("banUnclassified") || a.equalsIgnoreCase("noUnclassified")){
+			banUnclassified=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("banVirus") || a.equalsIgnoreCase("noVirus") || a.equalsIgnoreCase("banViruses") || a.equalsIgnoreCase("noViruses")){
+			banVirus=Parse.parseBoolean(b);
+		}
+		
+		else if(a.equalsIgnoreCase("taxfilterexcludelevel") || a.equalsIgnoreCase("excludelevel") 
+				|| a.equalsIgnoreCase("taxlevelblack") || a.equalsIgnoreCase("elevel") || a.equalsIgnoreCase("blacklevel")){
+			taxLevelBlack=TaxTree.parseLevel(b);//TODO:  Change to extended
+		}else if(a.equalsIgnoreCase("taxfilterexclude") || a.equalsIgnoreCase("exclude") || a.equalsIgnoreCase("taxfilterblacklist")){
+			taxFilterBlackList=b;
+		}else if(a.equalsIgnoreCase("taxfilterexcludestring") || a.equalsIgnoreCase("excludestring")
+				|| a.equalsIgnoreCase("taxfilterblackstring") || a.equalsIgnoreCase("estring")){
+			taxFilterBlackString=b;
+		}
+		
+		else if(a.equalsIgnoreCase("minkmercount") || a.equalsIgnoreCase("minkeycount") || a.equalsIgnoreCase("mincount") || a.equalsIgnoreCase("minKeyOccuranceCount")){
+			minKeyOccuranceCount=Tools.max(1, Integer.parseInt(b));
+		}
+		
+		//TODO:  Eventually remove support for "amino" and "k" and just support "hamino" and "hk"
+		//This stands for "header amino" and "header k".
+		
+		//Parameters for compatibility verification
+		else if(a.equalsIgnoreCase("k") || a.equalsIgnoreCase("hk")){
+//			System.err.println("A: k="+k+", k2="+k2+", arg="+arg);
+			if(b.indexOf(',')>=0){
+				String[] split=b.split(",");
+				assert(split.length==2) : "\nBad argument "+arg+"\n"+b+"\n";
+				int x=Integer.parseInt(split[0]);
+				int y=Integer.parseInt(split[1]);
+				k=Tools.max(x, y);
+				k2=Tools.min(x, y);
+				if(k==k2){k2=0;}
+//				System.err.println("B: k="+k+", k2="+k2+", split="+Arrays.toString(split));
+			}else{
+				k=Integer.parseInt(b);
+//				System.err.println("C: k="+k+", k2="+k2);
+			}
+		}else if(a.equalsIgnoreCase("hashversion") || a.equalsIgnoreCase("hv")){
+			hashVersion=Integer.parseInt(b);
+		}else if(a.equalsIgnoreCase("amino") || a.equalsIgnoreCase("hamino")){
+			amino=Parse.parseBoolean(b);
+			if(amino){translate=false;}
+		}else if(a.equalsIgnoreCase("translate")){
+			translate=Parse.parseBoolean(b);
+			if(translate){amino=false;}
+		}else if(a.equalsIgnoreCase("sixframes")){
+			sixframes=Parse.parseBoolean(b);
+			if(sixframes){amino=false; translate=true;}
+		}
+		
+		else if(a.equalsIgnoreCase("requiredmeta") || a.equalsIgnoreCase("rmeta")){
+			if(b==null){requiredMeta=null;}
+			else{
+				String[] split2=b.split(",");
+				requiredMeta=new ArrayList<String>(split2.length);
+				for(String mt : split2){
+					assert(mt.indexOf(':')>=0) : "Metadata tags must contain ':' symbol: "+mt;
+					requiredMeta.add(mt);
+				}
+			}
+		}else if(a.equalsIgnoreCase("bannedmeta") || a.equalsIgnoreCase("bmeta")){
+			if(b==null){bannedMeta=null;}
+			else{
+				String[] split2=b.split(",");
+				bannedMeta=new ArrayList<String>(split2.length);
+				for(String mt : split2){
+					assert(mt.indexOf(':')>=0) : "Metadata tags must contain ':' symbol: "+mt;
+					bannedMeta.add(mt);
+				}
+			}
+		}
+		
+//		else if(a.equalsIgnoreCase("requiredtaxid") || a.equalsIgnoreCase("rtaxid")){
+//			if(b==null){requiredTaxid=null;}
+//			else{
+//				String[] split2=b.split(",");
+//				requiredTaxid=new IntList(split2.length);
+//				for(String mt : split2){
+//					requiredTaxid.add(Integer.parseInt(mt));
+//				}
+//				if(requiredTaxid.isEmpty()){requiredTaxid=null;}
+//			}
+//		}else if(a.equalsIgnoreCase("bannedtaxid") || a.equalsIgnoreCase("btaxid")){
+//			if(b==null){bannedTaxid=null;}
+//			else{
+//				String[] split2=b.split(",");
+//				bannedTaxid=new IntList(split2.length);
+//				for(String mt : split2){
+//					bannedTaxid.add(Integer.parseInt(mt));
+//				}
+//				if(bannedTaxid.isEmpty()){bannedTaxid=null;}
+//			}
+//		}
+		
+		else if(a.equalsIgnoreCase("requiredmetaand") || a.equalsIgnoreCase("rmetaand")){
+			requiredMetaAnd=Parse.parseBoolean(b);
+		}else if(a.equalsIgnoreCase("requiredmetaor") || a.equalsIgnoreCase("rmetaor")){
+			requiredMetaAnd=!Parse.parseBoolean(b);
+		}
+		
+		else if(a.equalsIgnoreCase("bbversion")){
+			inputVersion=b;
+		}
+		
+		else{
+			return false;
+		}
+		return true;
+	}
+	
+	public void postParse(boolean requireTree, boolean makeTaxFilters){
+		assert(!postParsed);
+		synchronized(this){
+			if(postParsed){return;}
+			
+			if(makeTaxFilters){
+				if(taxFilterWhiteList!=null || taxFilterWhiteString!=null){
+					taxFilterWhite=new TaxFilter(SketchObject.taxtree, true);
+					taxFilterWhite.setLevel(taxLevelWhite, false);
+					taxFilterWhite.makeSet();
+					taxFilterWhite.addNamesOrNumbers(taxFilterWhiteList, false);
+					taxFilterWhite.setContainsString(taxFilterWhiteString);
+					if(requireTree){
+						assert(SketchObject.taxtree!=null) : "No taxtree loaded.";
+						taxFilterWhite.setTree(SketchObject.taxtree);
+						taxFilterWhite.promote();
+					}
+				}
+				
+				if(taxFilterBlackList!=null || taxFilterBlackString!=null){
+					taxFilterBlack=new TaxFilter(SketchObject.taxtree, false);
+					taxFilterBlack.setLevel(taxLevelBlack, false);
+					taxFilterBlack.makeSet();
+					taxFilterBlack.addNamesOrNumbers(taxFilterBlackList, false);
+					taxFilterBlack.setContainsString(taxFilterBlackString);
+					if(requireTree){
+						assert(SketchObject.taxtree!=null) : "No taxtree loaded.";
+						taxFilterBlack.setTree(SketchObject.taxtree);
+						taxFilterBlack.promote();
+					}
+				}
+			}
+			
+			noFilters=(!hasMetaFilters() && !hasTaxFilters() && !requireSSU && minRefSizeEstimate<1 && minRefSizeBases<1);
+			postParsed=true;
+		}
+	}
+	
+	public boolean postParsed(){return postParsed;}
+	
+	@Override
+	public String toString(){
+		return toString(-1);
+	}
+	
+	public String toString(int chunkNum){
+		StringBuilder sb=new StringBuilder();
+		sb.append("##");
+		sb.append("hits=").append(minHits);
+		if(chunkNum>=0){sb.append(" chunk=").append(chunkNum);}
+		sb.append(" wkid=").append(String.format(Locale.ROOT, "%.5f",minWKID));
+		if(minANI>0){sb.append(" id=").append(String.format(Locale.ROOT, "%.5f",minANI));}
+		if(minBases>0){sb.append(" minbases=").append(minBases);}
+		if(minSizeRatio>0){sb.append(" minsizeratio=").append(String.format(Locale.ROOT, "%.5f",minSizeRatio));}
+		sb.append(" records=").append(maxRecords);
+		if(recordsPerLevel>0){sb.append(" recordsperlevel=").append(recordsPerLevel);}
+		sb.append(" format=").append(format);
+		sb.append(" level=").append(taxLevel);
+		if(inputVersion!=null){sb.append(" bbversion=").append(inputVersion);}
+		
+		if(k!=SketchObject.defaultK || k2!=0 || k!=SketchObject.k || k2!=SketchObject.k2){
+			assert(k>0 && k2>=0 && k2<k) : "Bad values for k: "+k+", "+k2+", "+SketchObject.k+", "+SketchObject.k2;
+			assert(SketchObject.k>0 && SketchObject.k2>=0 && SketchObject.k2<SketchObject.k) : "Bad values for k: "+k+", "+k2+", "+SketchObject.k+", "+SketchObject.k2;
+			sb.append(" hk=").append(SketchObject.k).append(',').append(SketchObject.k2);
+		}
+		if(SketchObject.amino){sb.append(" hamino=").append(SketchObject.amino);} //TODO: This conflicts with Parser flag
+		if(SketchObject.translate){sb.append(" translate=").append(SketchObject.translate);}
+		if(SketchObject.sixframes){sb.append(" sixframes=").append(SketchObject.sixframes);}
+		if(SketchObject.HASH_VERSION>1){sb.append(" hashversion=").append(SketchObject.HASH_VERSION);}
+
+		if(true){sb.append(" printSSU=").append(printSSU());}
+		if(requireSSU){sb.append(" requireSSU=").append(requireSSU);}
+		if(minRefSizeEstimate>0){sb.append(" minRefSizeEstimate=").append(minRefSizeEstimate);}
+		if(minRefSizeBases>0){sb.append(" minRefSizeBases=").append(minRefSizeBases);}
+		
+		if(json()){sb.append(" printSSUSequence=").append(printSSUSequence);}
+		if(printSSULen){sb.append(" printSSULen=").append(printSSULen);}
+		if(true || printTax!=default_printTax){sb.append(" printTax=").append(printTax);}
+//		if(true || printFileName!=default_printFileName){sb.append(" printfname=").append(printFileName);}
+		if(true || printQueryFileName!=default_printQueryFileName){sb.append(" printqfname=").append(printQueryFileName);}
+		if(true || printRefFileName!=default_printRefFileName){sb.append(" printrfname=").append(printRefFileName);}
+		if(true || printOriginalName!=default_printOriginalName){sb.append(" pn0=").append(printOriginalName);}
+		if(true || printImg!=default_printImg){sb.append(" printImg=").append(printImg);}
+		if(true || printAni!=default_printAni){sb.append(" printAni=").append(printAni);}
+		if(!printKID){sb.append(" printKID=").append(printKID);}
+		if(!printWKID){sb.append(" printWKID=").append(printWKID);}
+		if(true || printCompleteness!=default_printCompleteness){sb.append(" printCompleteness=").append(printCompleteness);}
+
+		if(true || printUnique!=default_printUnique){sb.append(" printUMatches=").append(printUnique);}
+		if(true || printUnique2!=default_printUnique2){sb.append(" printUnique2=").append(printUnique2);}
+		if(true || printUnique3!=default_printUnique3){sb.append(" printUnique3=").append(printUnique3);}
+		if(true || printUContam!=default_printUContam){sb.append(" printUContam=").append(printUContam);}
+		if(true || printNoHit!=default_printNoHit){sb.append(" printNoHit=").append(printNoHit);}
+		if(true || printContam!=default_printContam){sb.append(" contam=").append(printContam);}
+		if(true){sb.append(" contam2=").append(printContam2 ? TaxTree.extendedToLevel(contamLevel)+"" : "f");}
+
+		if(true || printScore!=default_printScore){sb.append(" printScore=").append(printScore);}
+		if(true || printEValue!=default_printEValue){sb.append(" printEValue=").append(printEValue);}
+		
+		if(true || printDepth!=default_printDepth){sb.append(" printDepth=").append(printDepth);}
+		if(true || printDepth2!=default_printDepth2){sb.append(" printDepth2=").append(printDepth2);}
+		if(true || printActualDepth!=default_printActualDepth){sb.append(" printActualDepth=").append(printActualDepth);}
+		if(true || printVolume!=default_printVolume){sb.append(" printVolume=").append(printVolume);}
+		if(true || printRefHits!=default_printRefHits){sb.append(" printRefHits=").append(printRefHits);}
+		
+		if(true || printMatches!=default_printMatches){sb.append(" printMatches=").append(printMatches);}
+		if(true || printLength!=default_printLength){sb.append(" printLength=").append(printLength);}
+		if(true || printTaxID!=default_printTaxID){sb.append(" printTaxID=").append(printTaxID);}
+		if(true || printGSize!=default_printGSize){sb.append(" printGSize=").append(printGSize);}
+		if(true || gSizeKMG!=default_gSizeKMG){sb.append(" gSizeKMG=").append(gSizeKMG);}
+		if(true || printGC!=default_printGC){sb.append(" printGC=").append(printGC);}
+		if(true || printGKmers!=default_printGKmers){sb.append(" printGKmers=").append(printGKmers);}
+		
+		if(printCommonAncestor){sb.append(" printCommonAncestor=").append(printCommonAncestor);}
+		if(printCommonAncestorLevel){sb.append(" printCommonAncestorLevel=").append(printCommonAncestorLevel);}
+		
+		if(true || printTaxName!=default_printTaxName){sb.append(" printTaxName=").append(printTaxName);}
+		if(true || printGSeqs!=default_printGSeqs){sb.append(" printGSeqs=").append(printGSeqs);}
+		if(true || printGBases!=default_printGBases){sb.append(" printGBases=").append(printGBases);}
+		if(true || minEntropy!=default_minEntropy){sb.append(" minEntropy=").append(String.format(Locale.ROOT, "%.4f", minEntropy));}
+		if(true || minProb!=default_minProb){sb.append(" minProb=").append(String.format(Locale.ROOT, "%.4f", minProb));}
+		if(true || minQual!=default_minQual){sb.append(" minQual=").append((int)minQual);}
+		if(jsonArray!=default_jsonArray){sb.append(" jsonArray=").append(jsonArray);}
+		if(printD3!=default_printD3){sb.append(" d3=").append(printD3);}
+		if(printD3){
+			sb.append(" D3sizeMode=").append(D3sizeMode);
+			sb.append(" D3LevelNodes=").append(D3LevelNodes);
+		}
+		if(comparator!=Comparison.scoreComparator){sb.append(" ").append(comparator.toString());}
+		
+		if(taxFilterWhiteList!=null || taxFilterWhiteString!=null){
+			if(taxFilterWhiteList!=null){sb.append(" taxfilterwhitelist=").append(taxFilterWhiteList);}
+			if(taxFilterWhiteString!=null){sb.append(" taxfilterwhitestring=").append(taxFilterWhiteString);}
+			sb.append(" taxlevelwhite=").append(taxLevelWhite);
+		}
+		if(taxFilterBlackList!=null || taxFilterBlackString!=null){
+			if(taxFilterBlackList!=null){sb.append(" taxfilterblacklist=").append(taxFilterBlackList);}
+			if(taxFilterBlackString!=null){sb.append(" taxfilterblackstring=").append(taxFilterBlackString);}
+			sb.append(" taxlevelblack=").append(taxLevelBlack);
+		}
+		if(banUnclassified){sb.append(" banunclassified");}
+		if(banVirus){sb.append(" banvirus");}
+		
+		if(useTaxidName){sb.append(" useTaxidName=").append(useTaxidName);}
+		if(useImgName){sb.append(" useImgName=").append(useImgName);}
+		if(useTaxName){sb.append(" useTaxName=").append(useTaxName);}
+		
+		if(true){sb.append(" colors=").append(printColors ? TaxTree.extendedToLevel(colorLevel)+"" : "f");}
+		
+		if(minKeyOccuranceCount!=default_minKeyOccuranceCount){sb.append(" minKeyOccuranceCount=").append(minKeyOccuranceCount);}
+		
+//		if(printColors && colorLevel!=default_colorLevel){sb.append(" colorLevel=").append(TaxTree.extendedToLevel(colorLevel));}
+		
+
+		if(printRefDivisor){sb.append(" printRefDivisor=").append(printRefDivisor);}
+		if(printQueryDivisor){sb.append(" printQueryDivisor=").append(printQueryDivisor);}
+		if(printRefSize){sb.append(" printRefSize=").append(printRefSize);}
+		if(printQuerySize){sb.append(" printQuerySize=").append(printQuerySize);}
+		if(printContamHits){sb.append(" printContamHits=").append(printContamHits);}
+		if(printIntersection){sb.append(" printIntersection=").append(printIntersection);}
+		if(mergePairs){sb.append(" mergePairs=").append(mergePairs);}
+		
+		if(maxReads>-1){sb.append(" reads=").append(maxReads);}
+		if(mode!=default_mode){sb.append(" mode=").append(mode);}
+		if(samplerate!=default_samplerate){sb.append(" samplerate=").append(String.format(Locale.ROOT, "%.4f",samplerate));}
+
+		if(!requiredMetaAnd){sb.append(" requiredmetaand="+requiredMetaAnd);}
+		if(requiredMeta!=null && !requiredMeta.isEmpty()){
+			sb.append(" rmeta=");
+			for(String s : requiredMeta){
+				sb.append(s);
+				sb.append(',');
+			}
+			sb.setLength(sb.length()-1);
+		}
+		if(bannedMeta!=null && !bannedMeta.isEmpty()){
+			sb.append(" bmeta=");
+			for(String s : bannedMeta){
+				sb.append(s);
+				sb.append(',');
+			}
+			sb.setLength(sb.length()-1);
+		}
+//		if(requiredTaxid!=null && !requiredTaxid.isEmpty()){
+//			sb.append(" rtaxid=");
+//			for(int i=0; i<requiredTaxid.size; i++){
+//				sb.append(requiredTaxid.get(i));
+//				sb.append(',');
+//			}
+//			sb.setLength(sb.length()-1);
+//		}
+//		if(bannedTaxid!=null && !bannedTaxid.isEmpty()){
+//			sb.append(" btaxid=");
+//			for(int i=0; i<bannedTaxid.size; i++){
+//				sb.append(bannedTaxid.get(i));
+//				sb.append(',');
+//			}
+//			sb.setLength(sb.length()-1);
+//		}
+		
+		sb.append('\n');
+		return sb.toString();
+	}
+	
+	public boolean compatible(){
+		return SketchObject.k==k && SketchObject.k2==k2 && SketchObject.aminoOrTranslate()==aminoOrTranslate() && hashVersion==SketchObject.HASH_VERSION;
+	}
+	
+	public void setPrintAll(){
+		printSSU=true;
+		printSSULen=true;
+		printSSUSequence=true;
+		printTax=true;
+		printQueryFileName=true;
+		printRefFileName=true;
+		printOriginalName=true;
+		printImg=true;
+		printAni=true;
+		printKID=true;
+		printWKID=true;
+		printCompleteness=true;
+		printScore=true;
+		printEValue=true;
+		printDepth=true;
+		printDepth2=true;
+		printVolume=true;
+		printRefHits=true;
+		
+		printMatches=true;
+		printLength=true;
+		printTaxID=true;
+		printGSize=true;
+		printGC=true;
+		printGKmers=true;
+		printTaxName=true;
+		printGSeqs=true;
+		printGBases=true;
+		
+//		printColors=true;
+
+		printUnique=true;
+		printUnique2=true;
+		printUnique3=true;
+		printUContam=true;
+		printNoHit=true;
+		printContam=true;
+		printContam2=true;
+		
+		printRefDivisor=true;
+		printQueryDivisor=true;
+		printRefSize=true;
+		printQuerySize=true;
+		printContamHits=true;
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------             JSON             ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	public JsonObject toJson(SketchResults sr){
+		JsonObject j=toJson(sr.sketch);
+		if(sr.list!=null){
+			int i=0;
+			for(Comparison c : sr.list){
+				JsonObject jc=toJson(c);
+				j.add(c.name(), jc);
+				i++;
+				if(i>=maxRecords){break;}
+			}
+		}
+		
+		if(jsonArray){
+			toJsonArrayForm(j);
+		}
+		
+		if(printD3){
+			j.add("D3", toD3(sr));
+		}
+		
+		return j;
+	}
+	
+	public void toJsonArrayForm(JsonObject j0){
+		if(j0.jmapSize()<1){return;}
+		ArrayList<Object> list1=new ArrayList<Object>(j0.jmapSize());
+		Object[] keys=null;
+		for(Entry<String, JsonObject> e1 : j0.jmap.entrySet()){
+			JsonObject j1=e1.getValue();
+			ArrayList<Object> list2=new ArrayList<Object>(j1.omapSize());
+			for(Entry<String, Object> e2 : j1.omap.entrySet()){
+				Object o2=e2.getValue();
+				list2.add(o2);
+			}
+			list1.add(list2.toArray());
+			if(keys==null){
+				ArrayList<Object> keyList=new ArrayList<Object>(j1.omapSize());
+				for(Entry<String, Object> e2 : j1.omap.entrySet()){
+					Object o2=e2.getKey();
+					keyList.add(o2);
+				}
+				keys=keyList.toArray();
+			}
+		}
+
+		JsonObject title=new JsonObject();
+		for(Entry<String, Object> e : j0.omap.entrySet()){
+			title.add(e.getKey(), e.getValue());
+		}
+
+		j0.clearJson();
+		j0.clearOmap();
+
+		j0.add("title", title);
+		j0.add("header", keys);
+		j0.add("rows", list1.toArray());
+	}
+	
+	public JsonObject toJson(Sketch sk){
+		assert(format==FORMAT_JSON);
+		
+		JsonObject j=new JsonObject();
+		j.add("Name", sk.name());
+		if(dbName!=null){j.add("DB", dbName);}
+		j.add("SketchLen", sk.length());
+		
+		j.add("Seqs", sk.genomeSequences);
+		j.add("Bases", sk.genomeSizeBases);
+		j.add("gSize", sk.genomeSizeEstimate());
+		if(sk.baseCounts!=null){j.addLiteral("GC", sk.gc(), 3);}
+		if(sk.probCorrect<1 && sk.probCorrect>0){j.add("Quality", sk.probCorrect);}
+		if(sk.keyCounts!=null){
+			double d=Tools.averageDouble(sk.keyCounts);
+			j.add("AvgCount", d);
+			j.add("Depth", Tools.observedToActualCoverage(d));
+		}
+		
+		if(sk.imgID>0){j.add("IMG", sk.imgID);}
+		if(sk.spid>0){j.add("spid", sk.spid);}
+		if(sk.taxID>0 && sk.taxID<SketchObject.minFakeID){j.add("TaxID", sk.taxID);}
+
+		if((printRefFileName) && sk.fname()!=null){j.add("file", sk.fname());}
+		if(printOriginalName && sk.name0()!=null){j.add("SeqName", sk.name0());}
+		
+		if(sk.meta!=null){
+			for(String st : sk.meta){
+				int colon=st.indexOf(':');
+				j.add(st.substring(0,  colon), st.substring(colon+1));
+			}
+		}
+
+		if(printSSULen){
+			if(sk.r16SLen()>0){j.add("16SLen", sk.r16SLen());}
+			if(sk.r18SLen()>0){j.add("18SLen", sk.r18SLen());}
+		}
+		if(printSSUSequence){
+			if(sk.r16S()!=null){j.add("16SSequence", new String(sk.r16S()));}
+			if(sk.r18S()!=null){j.add("18SSequence", new String(sk.r18S()));}
+		}
+		
+		return j;
+	}
+	
+	public JsonObject toJson(Comparison c){
+		final int tid=c.taxID;
+		
+		JsonObject j=new JsonObject();
+		
+		//Text fields
+		if(printTaxName){j.add("taxName", c.taxName()==null ? "." : c.taxName());}
+		
+		if(printCommonAncestor){j.add("commonAncestor", c.commonAncestor());}
+		if(printCommonAncestorLevel){j.add("commonAncestorLevel", c.commonAncestorLevel());}
+		
+		if(printRefFileName){j.add("file", c.fname()==null ? "." : c.fname());}
+		if(printOriginalName){j.add("seqName", c.name0()==null ? "." : c.name0());}
+		if(printTax && SketchObject.taxtree!=null){
+			TaxNode tn=null;
+			if(tid>0 && tid<SketchObject.minFakeID){
+				tn=SketchObject.taxtree.getNode(tid);
+			}
+
+			if(tn!=null){
+				j.add("taxonomy", SketchObject.taxtree.toSemicolon(tn, SketchObject.skipNonCanonical, false));
+			}else{
+				j.add("taxonomy", (Object)null);
+			}
+		}
+		
+		if(printWKID){j.addLiteral("WKID", 100*c.wkid(), 4);}
+		if(printKID){j.addLiteral("KID", 100*c.kid(), 4);}
+//		if(printSSU() && c.ssuIdentity()>0){j.addLiteral("SSU", 100*c.ssuIdentity(), 3);} //Old
+		if(printSSU() && c.ssuIdentity()>0){
+			j.addLiteral(c.ssuType()==18 ? "18S" : "16S", 100*c.ssuIdentity(), 3);
+		}
+		
+		//Primary fields
+		if(printAni){j.addLiteral((aminoOrTranslate() ? "AAI" : "ANI"), 100*c.ani(), 3);}
+		if(printCompleteness){j.addLiteral("Complt", 100*c.completeness(), 3);}
+		if(printContam){j.addLiteral("Contam", 100*c.contamFraction(), 3);}
+		if(printContam2){j.addLiteral("Contam2", 100*c.contam2Fraction(), 3);}
+		if(printUContam){j.addLiteral("uContam", 100*c.uContamFraction(), 3);}
+		if(printScore){j.add("Score", c.score());}
+		if(printEValue){j.add("E-Val", String.format(Locale.ROOT, "%5.2e", c.eValue()));}
+		
+		if(printDepth){j.add("Depth", c.depth(printActualDepth));}
+		if(printDepth2){j.add("Depth2", c.depth2(printActualDepth));}
+		if(printVolume){j.add("Volume", c.volume()+0.001);}
+		if(printRefHits){j.add("RefHits", c.avgRefHits());}
+		
+		if(printMatches){j.add("Matches", c.hits());}
+		if(printUnique){j.add("Unique", c.uHits());}
+		if(printUnique2){j.add("Unique2", c.unique2());}
+		if(printUnique3){j.add("Unique3", c.unique3());}
+		if(printNoHit){j.add("noHit", c.noHits());}
+		if(printLength){j.add("Length", c.maxDivisor());}
+		if(printTaxID){j.add("TaxID", tid>=SketchObject.minFakeID ? -1 : tid);}
+		if(printImg){j.add("ImgID", c.imgID());}
+		if(printGBases){j.add("gBases", c.genomeSizeBases());}
+		if(printGKmers){j.add("gKmers", c.genomeSizeKmers());}
+		if(printGSize){j.add("gSize", c.genomeSizeEstimate());}
+		if(printGSeqs){j.add("gSeqs", c.genomeSequences());}
+		if(c.hasGC()){j.addLiteral("GC", c.gc(), 3);}
+		
+		//Raw fields
+		if(printRefDivisor){j.add("rDiv", c.refDivisor());}
+		if(printQueryDivisor){j.add("qDiv", c.queryDivisor());}
+		if(printRefSize){j.add("rSize", c.refSize());}
+		if(printQuerySize){j.add("qSize", c.querySize());}
+		if(printContamHits){j.add("cHits", c.contamHits());}
+		
+
+
+		if(printSSULen){
+			if(c.has18S()){j.add("18SLen", c.b.r18SLen());}
+			/*else*/ if(c.has16S()){j.add("16SLen", c.b.r16SLen());}
+		}
+		if(printSSUSequence){
+			if(c.has18S()){j.add("18SSequence", new String(c.b.r18S()));}
+			/*else*/ if(c.has16S()){j.add("16SSequence", new String(c.b.r16S()));}
+		}
+		
+		if(printIntersection){
+			Sketch intersection=Sketch.intersection(c.a, c.b);
+			j.add("intersection", intersection.toString());
+		}
+		
+		return j;
+	}
+
+	public boolean json(){return format==FORMAT_JSON;}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------              D3              ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	public JsonObject toD3(SketchResults sr){
+		if(sr==null || sr.isEmpty()){return new JsonObject("name", "no hits");}
+		JsonObject root=new JsonObject("name", "life");
+		root.add("level", TaxTree.LIFE_E);
+		if(sr.list!=null){
+			int i=0;
+			for(Comparison c : sr.list){
+				ArrayList<JsonObject> tax=toD3List(c);
+				addToLevel(root, tax, 0);
+				i++;
+				if(i>=maxRecords){break;}
+			}
+		}
+		if(D3LevelNodes){
+			root=converToD3ArrayFormat_LevelNode(root);
+		}else{
+			root=converToD3ArrayFormat_SingleNodeRoot(root);
+		}
+		return root;
+	}
+	
+	private JsonObject converToD3ArrayFormat_SingleNodeRoot(JsonObject root){
+		JsonObject children=root.removeJson("children");
+		if(children==null){return root;}
+		Object[] array=children.toJmapArray();
+		root=(JsonObject)array[0];//Life node
+		
+		assert(root.getString("name").equalsIgnoreCase("Life")) : root;
+		return converToD3ArrayFormat_SingleNode(root);
+	}
+	
+	private JsonObject converToD3ArrayFormat_SingleNode(JsonObject nameNode){
+		Object[] levelNodes=nameNode.toJmapArray();
+		if(levelNodes==null){return nameNode;}
+		nameNode.clearJson();
+		
+		ArrayList<JsonObject> fixed=new ArrayList<JsonObject>();
+		for(Object o : levelNodes){
+			JsonObject levelNode=(JsonObject)o;
+			String level=levelNode.getString("name");
+			JsonObject children=levelNode.removeJson("children");
+			if(children!=null){
+				Object[] childArray=children.toJmapArray();
+				for(Object o2 : childArray){
+					JsonObject child=(JsonObject)o2;//Now a name node
+					String name=(String)child.removeObject("name");
+					child.add("name", level+": "+name);
+					converToD3ArrayFormat_SingleNode(child);
+					fixed.add(child);
+				}
+			}
+		}
+		Object[] children=fixed.toArray();
+		nameNode.add("children", children);
+		return nameNode;
+	}
+	
+	private JsonObject converToD3ArrayFormat_LevelNode(JsonObject levelNode){
+		JsonObject children=levelNode.removeJson("children");
+		if(children==null){return levelNode;}
+		
+		Object[] array=children.toJmapArray();
+		levelNode.add("children", array);
+		for(Object o : array){
+			converToD3ArrayFormat_NameNode((JsonObject)o);
+		}
+		return levelNode;
+	}
+	
+	private JsonObject converToD3ArrayFormat_NameNode(JsonObject nameNode){
+		Object[] array=nameNode.toJmapArray();
+		if(array==null){return nameNode;}
+		
+		nameNode.clearJson();
+		nameNode.add("children", array);
+		for(Object o : array){
+			converToD3ArrayFormat_LevelNode((JsonObject)o);
+		}
+		return nameNode;
+	}
+	
+	void addToLevel(JsonObject levelNode, ArrayList<JsonObject> list, int pos){
+		JsonObject jo=list.get(pos);
+		int rootLevel=levelNode.getInt("level");
+		int joLevel=jo.getInt("level");
+		if(rootLevel==joLevel){
+			assert(levelNode.getString("name").equalsIgnoreCase(jo.getString("levelname"))) : levelNode+"\n"+jo;
+			addAsChild(levelNode, list, pos);
+		}else{
+			assert(joLevel<rootLevel) : levelNode+"\n"+jo;
+			assert(false) : levelNode+"\n"+jo;
+		}
+	}
+		
+	void addAsChild(JsonObject levelNode, ArrayList<JsonObject> list, int pos){
+		JsonObject children=levelNode.getJson("children");
+		if(children==null){
+			children=new JsonObject();
+			levelNode.add("children", children);
+		}
+		JsonObject jo=list.get(pos);
+		String taxName=jo.getString("name");
+		JsonObject nameNode=children.getJson(taxName);
+		if(nameNode==null){
+			nameNode=new JsonObject("name", taxName);
+			children.add(taxName, nameNode);
+		}
+		Number size=jo.getNumber("size");
+		Number oldSize=nameNode.getNumber("size");
+		if(size!=null && (oldSize==null || oldSize.doubleValue()<size.doubleValue())){
+			nameNode.add("size", jo.getNumber("size"));
+			nameNode.add("kid", jo.getNumber("kid"));
+			nameNode.add("wkid", jo.getNumber("wkid"));
+			nameNode.add("ani", jo.getNumber("ani"));
+			nameNode.add("hits", jo.getNumber("hits"));
+			nameNode.add("depth", jo.getNumber("depth"));
+		}
+
+		if(pos<list.size()-1){//recur
+			jo=list.get(pos+1);
+			String levelName=jo.getString("levelname");
+			int level=jo.getInt("level");
+			JsonObject nextLevelNode=nameNode.getJson(levelName);
+			if(nextLevelNode==null){
+				nextLevelNode=new JsonObject("name", levelName);
+				nextLevelNode.add("level", level);
+				nameNode.add(levelName, nextLevelNode);
+			}
+			addAsChild(nextLevelNode, list, pos+1);
+		}
+	}
+	
+	int promote(int levelE) {
+		if(levelE<0){return levelE;}
+		while(!TaxTree.isSimple2(levelE) && levelE<TaxTree.LIFE){
+			levelE++;
+		}
+		return levelE;
+	}
+	
+	public ArrayList<JsonObject> toD3List(Comparison c){
+		final ArrayList<TaxNode> nodes=toTNList(c.taxID);
+		ArrayList<JsonObject> list=new ArrayList<JsonObject>(nodes.size());
+		for(TaxNode tn : nodes){
+			JsonObject jo=new JsonObject("name", tn.name);
+			int levelE=promote(tn.levelExtended);
+			jo.add("level", levelE);
+			jo.add("levelname", TaxTree.levelToStringExtended(levelE));
+			list.add(jo);
+		}
+		if(list.size()>0){
+			JsonObject tail=list.get(list.size()-1);
+			tail.add("size", toD3Size(c));
+			tail.add("kid", c.kid());
+			tail.add("wkid", c.wkid());
+			tail.add("ani", c.ani());
+			tail.add("hits", c.hits());
+			tail.add("depth", c.depth(printActualDepth));
+		}
+		return list;
+	}
+	
+	private Number toD3Size(Comparison c){
+		if(D3sizeMode==D3_ANI_SIZE){
+			return c.ani();
+		}else if(D3sizeMode==D3_KID_SIZE){
+			return c.kid();
+		}else if(D3sizeMode==D3_WKID_SIZE){
+			return c.wkid();
+		}else if(D3sizeMode==D3_HIT_SIZE){
+			return c.hits();
+		}else if(D3sizeMode==D3_DEPTH_SIZE){
+			return c.depth(printActualDepth);
+		}
+		assert(false) : "Invalid D3sizeMode "+D3sizeMode;
+		return c.hits();
+	}
+	
+	public ArrayList<TaxNode> toTNList(final int tid){
+		final TaxTree tree=TaxTree.getTree();
+		
+		final ArrayList<TaxNode> list=new ArrayList<TaxNode>();
+		int nulls=0;
+		{
+			TaxNode tn=tree.getNode(tid);
+			if(tn.isRanked() && !tn.cellularOrganisms()){list.add(tn);}
+			while(tn.pid!=tn.id){
+				tn=tree.getNode(tn.pid);
+				if(tn.isRanked() && !tn.cellularOrganisms()){list.add(tn);}
+			}
+		}
+		Collections.reverse(list);
+		int prevLevelE=TaxTree.LIFE;
+		for(int i=0; i<list.size(); i++){
+			TaxNode tn=list.get(i);
+			int levelE=promote(tn.levelExtended);
+			
+			if(!TaxTree.isSimple2(levelE) || (i>0 && levelE>=prevLevelE)){
+				list.set(i, null);
+				nulls++;
+			}else{prevLevelE=levelE;}
+		}
+		if(nulls>0){Tools.condenseStrict(list);}
+		return list;
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------          Formatting          ----------------*/
+	/*--------------------------------------------------------------*/
+
+	ByteBuilder queryHeader(Sketch sk){
+		ByteBuilder bb=new ByteBuilder();
+		if(format>2){return bb;}
+		
+		String color=toColor(sk.taxID);
+		if(color!=null){bb.append(color);}
+		
+		bb.append("\nQuery: ").append(sk.name()==null ? "." : sk.name());
+		if(dbName!=null){bb.append("\tDB: ").append(dbName);}
+		bb.append("\tSketchLen: ").append(sk.length());
+		bb.append("\tSeqs: ").append(sk.genomeSequences).append(' ');
+		bb.append("\t"+(aminoOrTranslate() ? "SeqLen" : "Bases")+": ").append(sk.genomeSizeBases);
+		bb.append("\tgSize: ").append(sk.genomeSizeEstimate());
+		if(sk.baseCounts!=null){bb.append("\tGC: ").append(sk.gc(), 3);}
+		if(sk.probCorrect<1 && sk.probCorrect>0){bb.append("\tQuality: ").append(sk.probCorrect, 4);}
+		if(sk.keyCounts!=null){
+			double d=Tools.averageDouble(sk.keyCounts);
+			bb.append("\tAvgCount: ").append(d, 3);
+			bb.append("\tDepth: ").append(Tools.observedToActualCoverage(d), 3);
+		}
+
+		if(sk.imgID>0){bb.append("\tIMG: ").append(sk.imgID);}
+		if(sk.spid>0){bb.append("\tspid: ").append(sk.spid);}
+		if(sk.taxID>0 && sk.taxID<SketchObject.minFakeID){bb.append("\tTaxID: ").append(sk.taxID);}
+
+		if(printQueryFileName && sk.fname()!=null){bb.append("\tFile: "+sk.fname());}
+		if(printOriginalName && sk.name0()!=null && !sk.name0().equals(sk.name())){bb.append("\tSeqName: "+sk.name0());}
+		
+		if(sk.meta!=null){
+			for(String st : sk.meta){
+				bb.append("\t").append(st.replaceFirst(":", ": "));
+			}
+		}
+		
+		if(color!=null){bb.append(Colors.RESET);}
+		
+		return bb;
+	}
+	
+	int toColorTid(final int taxID){
+		if(!printColors || SketchObject.taxtree==null || taxID<=0 || taxID>=SketchObject.minFakeID){return 0;}
+		TaxNode tn=SketchObject.taxtree.getNode(taxID);
+		while(tn!=null && tn.id!=tn.pid && tn.levelExtended<colorLevel){
+			tn=SketchObject.taxtree.getNode(tn.pid);
+//			System.err.println(tn);
+		}
+		return tn==null || tn.levelExtended>=TaxTree.LIFE_E || (tn.levelExtended>colorLevel && tn.levelExtended>TaxTree.PHYLUM_E) ? 0 : tn.id;
+	}
+	
+	String toColor(final int taxID){
+		if(!printColors || SketchObject.taxtree==null || taxID<=0 || taxID>=SketchObject.minFakeID){return null;}
+		TaxNode tn=SketchObject.taxtree.getNode(taxID);
+		while(tn!=null && tn.id!=tn.pid && tn.levelExtended<colorLevel){
+			tn=SketchObject.taxtree.getNode(tn.pid);
+//			System.err.println(tn);
+		}
+		if(tn==null){
+			return null;
+		}else{
+			if(tn.levelExtended>=TaxTree.LIFE_E || (tn.levelExtended>colorLevel && tn.levelExtended>TaxTree.PHYLUM_E)){return Colors.WHITE;}
+			else{
+//				System.err.println("*"+tn.id+", "+tn.id%Colors.colorArray.length);
+				return Colors.colorArray[tn.id%Colors.colorArray.length];
+			}
+		}
+	}
+	
+	String header(){
+		if(format==FORMAT_JSON){return null;}
+		final String ani=(aminoOrTranslate() ? "AAI" : "ANI");
+		if(format==FORMAT_QUERY_REF_ANI || format==FORMAT_CONSTELLATION){
+			if(reportAniOnly){return "#Query\tRef\t"+ani;}
+			if(format==FORMAT_QUERY_REF_ANI){
+				return "#Query\tRef\t"+ani+
+				"\tQSize\tRefSize\tQBases\tRBases"+
+				(printTaxID ? "\tQTaxID\tRTaxID" : "")+(printKID ? "\tKID" : "")+(printWKID ? "\tWKID" : "")+
+				(printSSU() ? "\tSSU" : "")+(printCommonAncestorLevel ? "\tCALevel" : "");
+			}
+			if(format==FORMAT_CONSTELLATION){return "#Query\tRef\tKID\tWKID\t"+ani+"\tCmplt\tQSize\tRefSize\tQBases\tRefBases";}
+		}
+		return columnwiseHeader();
+	}
+	
+	String columnwiseHeader(){
+		final String ani=(aminoOrTranslate() ? "AAI" : "ANI");
+		
+		StringBuilder sb=new StringBuilder();
+		
+		//Numeric fields
+		if(printKID){sb.append("WKID\t");}
+		if(printWKID){sb.append("KID\t");}
+		if(printAni){sb.append(ani+"\t");}
+		if(printSSU()){sb.append("SSU\t");}
+		if(printSSULen){sb.append("SSULen\t");}
+		if(printCompleteness){sb.append("Complt\t");}
+		if(printContam){sb.append("Contam\t");}
+		if(printContam2){sb.append("Contam2\t");}
+		if(printUContam){sb.append("uContam\t");}
+		if(printScore){sb.append("Score\t");}
+		if(printEValue){sb.append("E-Val\t");}
+		
+		if(printDepth){sb.append("Depth\t");}
+		if(printDepth2){sb.append("Depth2\t");}
+		if(printVolume){sb.append("Volume\t");}
+		if(printRefHits){sb.append("RefHits\t");}
+		if(printMatches){sb.append("Matches\t");}
+		if(printUnique){sb.append("Unique\t");}
+		if(printUnique2){sb.append("Unique2\t");}
+		if(printUnique3){sb.append("Unique3\t");}
+		if(printNoHit){sb.append("noHit\t");}
+		if(printLength){sb.append("Length\t");}
+		if(printTaxID){sb.append("TaxID\t");}
+		if(printImg){sb.append("ImgID    \t");}
+		if(printGBases){sb.append("gBases\t");}
+		if(printGKmers){sb.append("gKmers\t");}
+		if(printGSize){sb.append("gSize\t");}
+		if(printGSeqs){sb.append("gSeqs\t");}
+		if(printGC){sb.append("GC\t");}
+		
+		
+		//Raw fields
+		if(printRefDivisor){sb.append("rDiv\t");}
+		if(printQueryDivisor){sb.append("qDiv\t");}
+		if(printRefSize){sb.append("rSize\t");}
+		if(printQuerySize){sb.append("qSize\t");}
+		if(printContamHits){sb.append("cHits\t");}
+		
+		//Text fields
+		if(printCommonAncestor){sb.append("CA\t");}
+		if(printCommonAncestorLevel){sb.append("CALevel\t");}
+		if(printTaxName){sb.append("taxName\t");}
+		if(printRefFileName){sb.append("file\t");}
+		if(printOriginalName){sb.append("seqName\t");}
+		if(printTax && SketchObject.taxtree!=null){sb.append("taxonomy\t");}
+		
+		if(sb.length()>1){sb.setLength(sb.length()-1);}//trim trailing tab
+		
+		return sb.toString();
+	}
+	
+	void formatComparisonColumnwise(Comparison c, ByteBuilder bb, int prevTid){
+		final int tid=c.taxID;
+		boolean reset=false;
+		
+		if(printColors){
+			final int ctid=toColorTid(tid);
+			final int prevCtid=toColorTid(prevTid);
+
+			final int cnum=ctid%Colors.colorArray.length;
+			final int prevCnum=prevCtid%Colors.colorArray.length;
+
+			String color=toColor(tid);
+			String underline=(printColors && cnum==prevCnum && ctid!=prevCtid && (ctid>1 && prevCtid>1) ? Colors.UNDERLINE : null);
+
+			if(color!=null){bb.append(color);}
+			if(underline!=null){bb.append(underline);}
+			reset=(color!=null || underline!=null);
+			
+//			System.err.println((color==null ? "" : color)+(underline==null ? "" : underline)+
+//					tid+", "+prevTid+";     \t"+ctid+", "+prevCtid+";     \t"+cnum+", "+prevCnum+"; \t"+((underline!=null)+"")+Colors.RESET);
+//			System.err.println(color==null ? "null" : color.substring(1));
+		}
+		
+//		sb.append(String.format(Locale.ROOT, "%.2f%%\t%.2f%%", 100*c.idMinDivisor(), 100*c.idMaxDivisor()));
+		if(printWKID){bb.append(100*c.wkid(), 2).append('%').tab();}
+		if(printKID){bb.append(100*c.kid(), 2).append('%');}
+		
+//		if(printAni){sb.append(String.format(Locale.ROOT, "\t%.2f%%", 100*c.ani()));}
+//		if(printCompleteness){sb.append(String.format(Locale.ROOT, "\t%.2f%%", 100*c.completeness()));}
+//		if(printContam){sb.append(String.format(Locale.ROOT, "\t%.2f%%", 100*c.contamFraction()));}
+//		if(printContam2){sb.append(String.format(Locale.ROOT, "\t%.2f%%", 100*c.contam2Fraction()));}
+//		if(printUContam){sb.append(String.format(Locale.ROOT, "\t%.2f%%", 100*c.uContamFraction()));}
+		
+		if(printAni){bb.tab().append(100*c.ani(), 2).append('%');}
+		if(printSSU()){
+			float id=100*c.ssuIdentity();
+			if(id>0){
+				bb.tab().append(id, 2).append(c.ssuType()==16 ? '%' : '*'); //This is where 16S and 18S are differentiated
+			}else{
+				bb.tab().append('.');
+			}
+		}
+		if(printSSULen){
+			bb.tab().append(c.ssuLen());
+		}
+		if(printCompleteness){bb.tab().append(100*c.completeness(), 2).append('%');}
+		if(printContam){bb.tab().append(100*c.contamFraction(), 2).append('%');}
+		if(printContam2){bb.tab().append(100*c.contam2Fraction(), 2).append('%');}
+		if(printUContam){bb.tab().append(100*c.uContamFraction(), 2).append('%');}
+		if(printScore){bb.tab().append(c.scoreS());}
+		if(printEValue){bb.tab().append(String.format(Locale.ROOT, "%5.2e", c.eValue()));}
+		
+		if(printDepth){bb.tab().append(c.depthS(printActualDepth));}
+		if(printDepth2){bb.tab().append(c.depth2S(printActualDepth));}
+		if(printVolume){bb.tab().append(c.volumeS());}
+		if(printRefHits){bb.tab().append(c.avgRefHitsS());}
+		
+		if(printMatches){bb.tab().append(c.hits());}
+		if(printUnique){bb.tab().append(c.uHits());}
+		if(printUnique2){bb.tab().append(c.unique2());}
+		if(printUnique3){bb.tab().append(c.unique3());}
+		if(printNoHit){bb.tab().append(c.noHits());}
+		if(printLength){bb.tab().append( c.maxDivisor());}
+		if(printTaxID){bb.tab().append(tid>=SketchObject.minFakeID ? -1 : tid);}
+		if(printImg){bb.tab().append(c.imgID());}
+		if(printGBases){appendKMG(c.genomeSizeBases(), bb);}
+		if(printGKmers){appendKMG(c.genomeSizeKmers(), bb);}
+		if(printGSize){appendKMG(c.genomeSizeEstimate(), bb);}
+		if(printGSeqs){appendKMG(c.genomeSequences(), bb);}
+		if(printGC){bb.tab().append(c.gc(),3);}
+		
+		//Raw fields
+		if(printRefDivisor){bb.tab().append(c.refDivisor());}
+		if(printQueryDivisor){bb.tab().append(c.queryDivisor());}
+		if(printRefSize){bb.tab().append(c.refSize());}
+		if(printQuerySize){bb.tab().append(c.querySize());}
+		if(printContamHits){bb.tab().append(c.contamHits());}
+		
+		//Text fields
+		if(printCommonAncestor){bb.tab().append(c.commonAncestor());}
+		if(printCommonAncestorLevel){bb.tab().append(c.commonAncestorLevel());}
+		if(printTaxName){bb.tab().append(c.taxName()==null ? "." : c.taxName());}
+		if(printRefFileName){bb.tab().append(c.fname()==null ? "." : c.fname());}
+		if(printOriginalName){bb.tab().append(c.name0()==null ? "." : c.name0());}
+		if(printTax && SketchObject.taxtree!=null){
+			bb.tab();
+			TaxNode tn=null;
+			if(tid>0 && tid<SketchObject.minFakeID){
+				tn=SketchObject.taxtree.getNode(tid);
+			}
+
+			if(tn!=null){
+				bb.append(SketchObject.taxtree.toSemicolon(tn, SketchObject.skipNonCanonical, false));
+			}else{
+				bb.append('.');
+			}
+		}
+		if(printTaxName && !printOriginalName && !printRefFileName && c.taxName()==null && c.name0()!=null){bb.tab().append(c.name0());} //Extra column
+		
+		if(reset){bb.append(Colors.RESET);}
+		
+		bb.append('\n');
+		
+		if(printIntersection){
+			Sketch intersection=Sketch.intersection(c.a, c.b);
+			bb.append(intersection.toString());
+			bb.append('\n');
+		}
+		
+	}
+	
+	void appendKMG(long value, ByteBuilder bb){
+		if(gSizeKMG){
+			bb.tab().append(toKMG(value));
+		}else{
+			bb.tab().append(value);
+		}
+	}
+	
+	String toKMG(long value){
+		if(value<10000000L){return Long.toString(value);}
+		value+=5;
+		if(value<1000000000L){return value/1000L+"K";}
+		if(value<1000000000000L){return value/1000000L+"M";}
+		if(value<1000000000000000L){return value/1000000000L+"G";}
+		return value/1000000000000L+"T";
+	}
+	
+	void formatComparison3Column(Comparison c, ByteBuilder sb, int prevTid){
+		Sketch query=c.a;
+		final long sea=Tools.max(1, c.a.genomeSizeEstimate());
+		final long seb=Tools.max(1, c.b.genomeSizeEstimate());
+		final long ba=Tools.max(1, c.a.genomeSizeBases);
+		final long bb=Tools.max(1, c.b.genomeSizeBases);
+		final String qName=format==FORMAT_CONSTELLATION ? (useFilePrefixName ? query.filePrefix() : ""+query.sketchID) : useTaxidName ? ""+query.taxID :
+			useImgName ?  ""+query.imgID : useTaxName ? query.taxName() : query.name();
+		final String rName=format==FORMAT_CONSTELLATION ? (useFilePrefixName ? c.b.filePrefix() : ""+c.b.sketchID) : useTaxidName ? ""+c.taxID() :
+			useImgName ?  ""+c.imgID() : useTaxName ? c.taxName() : c.name();
+		final int tid=c.taxID;
+		boolean reset=false;
+		
+		sb.append(qName).append('\t');
+		if(printColors){
+			final int ctid=toColorTid(tid);
+			final int prevCtid=toColorTid(prevTid);
+
+			final int cnum=ctid%Colors.colorArray.length;
+			final int prevCnum=prevCtid%Colors.colorArray.length;
+
+			String color=toColor(tid);
+			String underline=(printColors && cnum==prevCnum && ctid!=prevCtid && (ctid>1 && prevCtid>1) ? Colors.UNDERLINE : null);
+
+			if(color!=null){sb.append(color);}
+			if(underline!=null){sb.append(underline);}
+			reset=(color!=null || underline!=null);
+			
+//			System.err.println((color==null ? "" : color)+(underline==null ? "" : underline)+
+//					tid+", "+prevTid+";     \t"+ctid+", "+prevCtid+";     \t"+cnum+", "+prevCnum+"; \t"+((underline!=null)+"")+Colors.RESET);
+//			System.err.println(color==null ? "null" : color.substring(1));
+		}
+
+//		sb.append(rName).append(String.format(Locale.ROOT, "\t%.2f\t%.3f", 100*c.ani(), sea/(float)seb));
+//		sb.append(rName).append(String.format(Locale.ROOT, "\t%.2f\t%d\t%d\t%d", 100*c.ani(), sea, seb, ba));
+		
+		//"#Query\tRef\tKID\tWKID\tANI\tCmplt\tQSize\tRefSize\tQBases\tRefBases";
+
+		float kid=100*c.kid();
+		float wkid=100*c.wkid();
+		float ani=100*c.ani();
+		float complt=100*c.completeness();
+		float ssu=printSSU() ? 100*c.ssuIdentity() : 0;
+		
+		sb.append(rName).append('\t');
+		if(reportAniOnly){
+			sb.append(ani, 3).append('\t');
+		}else if(format==FORMAT_CONSTELLATION){
+			sb.append(kid, 3).append('\t');
+			sb.append(wkid, 3).append('\t');
+			sb.append(ani, 3).append('\t');
+			sb.append(complt, 3).append('\t');
+			sb.append(sea).append('\t');
+			sb.append(seb).append('\t');
+//			sb.append(ba).append('\t');
+//			sb.append(bb).append('\t');
+		}else{
+			sb.append(ani, 3).append('\t');
+			sb.append(sea).append('\t');
+			sb.append(seb).append('\t');
+			sb.append(ba).append('\t');
+			sb.append(bb).append('\t');
+			if(printTaxID){sb.append(c.a.taxID).append('\t');}
+			if(printTaxID){sb.append(c.b.taxID).append('\t');}
+			if(printKID){sb.append(kid, 3).append('\t');}
+			if(printWKID){sb.append(wkid, 3).append('\t');}
+			if(printSSU()){
+				if(ssu>0){
+					sb.append(ssu, 3).append('\t');
+				}else{
+					sb.append('.').append('\t');
+				}
+			}
+			if(printCommonAncestorLevel){sb.append(c.commonAncestorLevel()).append('\t');}
+		}
+		sb.setLength(sb.length()-1);
+		if(reset){sb.append(Colors.RESET);}
+		
+		sb.append('\n');
+		
+//		System.err.println(sb);
+	}
+	
+	void formatComparison(Comparison c, ByteBuilder sb, int prevTaxID){
+		if(format==FORMAT_MULTICOLUMN){
+			formatComparisonColumnwise(c, sb, prevTaxID);
+			return;
+		}else if(format==FORMAT_QUERY_REF_ANI || format==FORMAT_CONSTELLATION){
+			formatComparison3Column(c, sb, prevTaxID);
+			return;
+		}
+		String complt=(printCompleteness ? String.format(Locale.ROOT, "\tcomplt %.2f%%%%", 100*c.completeness()) : "");
+		String contam=(printContam ? String.format(Locale.ROOT, "\tcontam %.2f%%%%", 100*c.contamFraction()) : "");
+//		String score=(printScore ? String.format(Locale.ROOT, "\tscore %.2f", c.score2()) : "");
+		String score=(printScore ? "\tscore "+c.scoreS() : "");
+		String depth=(printDepth ? "\tdepth "+c.depthS(printActualDepth) : "");
+		String depth2=(printDepth2 ? "\tdepth2 "+c.depth2S(printActualDepth) : "");
+		String volume=(printVolume ? "\tvolume "+c.volumeS() : "");
+		String ccs=complt+contam+score;
+		
+		if(format==FORMAT_OLD){
+			sb.append(String.format(Locale.ROOT, "WKID %.2f%%\tKID %.2f%%"+ccs+"\tmatches %d\tcompared %d",
+					100*c.wkid(), 100*c.kid(), c.hits(), c.minDivisor())+"\ttaxID "+c.taxID()+
+					(printImg ? "\timgID "+c.imgID() : "")+"\tgKmers "+c.genomeSizeKmers()+"\t"+
+					(c.taxName()==null ? "." : c.taxName())+
+					((printOriginalName || (c.taxName()==null && c.name0()!=null)) ? "\t"+(c.name0()==null ? "." : c.name0()) : "")+"\n");
+			if(printTax && SketchObject.taxtree!=null){
+				if(c.taxID()>=0 && c.taxID()<SketchObject.minFakeID){
+					TaxNode tn=SketchObject.taxtree.getNode(c.taxID());
+					if(tn!=null){
+						PrintTaxonomy.printTaxonomy(tn, sb, SketchObject.taxtree, TaxTree.DOMAIN, SketchObject.skipNonCanonical);
+					}
+				}
+				sb.append('\n');
+			}
+		}else{
+			ArrayList<TaxNode> tnl=new ArrayList<TaxNode>();
+			if(SketchObject.taxtree!=null && c.taxID()>=0 && c.taxID()<SketchObject.minFakeID){
+				TaxNode tn=SketchObject.taxtree.getNode(c.taxID());
+				while(tn!=null && tn.pid!=tn.id && tn.level<=TaxTree.DOMAIN){
+					tnl.add(tn);
+					tn=SketchObject.taxtree.getNode(tn.pid);
+				}
+			}
+			
+			sb.append(String.format(Locale.ROOT, "WKID %.2f%%\tKID %.2f%%"+ccs+"\tmatches %d\tcompared %d\t",
+					100*c.wkid(), 100*c.kid(), c.hits(), c.minDivisor()));
+			sb.append("\ttaxID ").append(c.taxID()).append('\t');
+			if(printImg){sb.append("\timgID ").append(c.imgID()).append('\t');}
+			sb.append(c.taxName()).append('\t');
+			if(printRefFileName){sb.append(c.fname()).append('\t');}
+			if(printOriginalName || (c.taxName()==null && c.name0()!=null && !printRefFileName)){sb.append(c.name0()).append('\t');}
+			
+			if(printTax){
+				for(int i=tnl.size()-1; i>=0; i--){
+					TaxNode tn=tnl.get(i);
+					sb.append(tn.name);
+					if(i>0){sb.append(';');}
+				}
+			}
+			sb.append('\n');
+			
+			tnl.clear();
+		}
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------           Filtering          ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	public boolean passesFilter(Sketch sk){
+		assert(postParsed);
+		if(noFilters){return true;}
+		return passesSSUFilter(sk) && passesSizeFilter(sk) && passesTaxFilter(sk) && passesMetaFilter(sk);
+	}
+	
+	private boolean passesTaxFilter(Sketch sk){
+		if(taxFilterWhite==null && taxFilterBlack==null){return true;}
+		int id=sk.taxID;
+		if(id>0){
+			if(banUnclassified && SketchObject.taxtree.isUnclassified(id)){return false;}
+			if(banVirus && SketchObject.taxtree.isVirus(id)){return false;}
+		}
+		String s=sk.name();
+		return passesTaxFilter(taxFilterWhite, id, s) && passesTaxFilter(taxFilterBlack, id, s);
+	}
+	
+	private boolean passesTaxFilter(TaxFilter filter, int id, String s){
+		if(filter==null){return true;}
+		if(id>0 && !filter.passesFilter(id)){return false;}
+//		if(id>0 && !filter.passesFilterFast(id)){return false;}
+		if(s!=null && !filter.passesFilterByNameOnly(s)){return false;}
+		return true;
+	}
+	
+	private boolean passesMetaFilter(Sketch sk){
+		if(requiredMeta==null && bannedMeta==null){return true;}
+		return sk.passesMeta(requiredMeta, bannedMeta, requiredMetaAnd);
+	}
+	
+	private boolean passesSSUFilter(Sketch sk){
+		return !requireSSU || sk.hasSSU();
+	}
+	
+	private boolean passesSizeFilter(Sketch sk){
+		if(minRefSizeEstimate>0 && sk.genomeSizeEstimate()<minRefSizeEstimate){return false;}
+		return sk.genomeSizeBases>=minRefSizeBases;
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------            Fields            ----------------*/
+	/*--------------------------------------------------------------*/
+
+	//These are shared with SketchObject
+	//They do not affect anything and are just for the server to validate remote settings.
+	private int hashVersion=SketchObject.HASH_VERSION;
+	private int k=SketchObject.k;
+	private int k2=SketchObject.k2;
+	boolean amino=SketchObject.amino;
+	boolean translate=SketchObject.translate;
+	boolean sixframes=SketchObject.sixframes;
+	private boolean aminoOrTranslate(){return amino | translate;}
+	
+	boolean noFilters=false;
+	boolean postParsed=false;
+	
+	boolean amino(){return amino;}
+	
+	//These are unique
+	public int maxRecords=default_maxRecords;
+	public int recordsPerLevel=0;
+	public float minANI=0;
+	public int minBases=0;
+	public float minSizeRatio=0;
+	public float minWKID=default_minWKID;
+	public int format=default_format;
+	
+	/** For tracking unique SendSketch queries */
+	public int chunkNum=-1;
+	public int minHits=default_minHits;
+	public int taxLevel=default_taxLevel;
+	public int mode=default_mode;
+	public float samplerate=default_samplerate;
+	public long maxReads=default_maxReads;
+	public int minKeyOccuranceCount=default_minKeyOccuranceCount;
+	public String inputVersion=null;
+	
+	public String dbName=null;
+
+	boolean hasMetaFilters(){return requiredMeta!=null || bannedMeta!=null/* || requiredTaxid!=null || bannedTaxid!=null*/;}
+	boolean hasTaxFilters(){return taxFilterWhite!=null || taxFilterBlack!=null || banUnclassified || banVirus;}
+	boolean requireSSU=false;
+	long minRefSizeEstimate=-1;
+	long minRefSizeBases=-1;
+	
+	boolean requiredMetaAnd=true;
+	ArrayList<String> requiredMeta=null;
+	ArrayList<String> bannedMeta=null;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Print Columns        ----------------*/
+	/*--------------------------------------------------------------*/
+
+	public boolean printKID=true;
+	public boolean printWKID=true;
+	public boolean printSSU=true;
+	public boolean printSSULen=false;
+	public boolean printSSU(){return SketchObject.processSSU && printSSU;}
+	public boolean printSSUSequence=default_printSSUSequence;
+	
+	//For format 2
+	public boolean printTax=default_printTax;
+	public boolean printOriginalName=default_printOriginalName;
+	public boolean printQueryFileName=default_printQueryFileName;
+	public boolean printRefFileName=default_printRefFileName;
+	public boolean printImg=default_printImg;
+	public boolean printAni=default_printAni;
+	public boolean printCompleteness=default_printCompleteness;
+	public boolean printScore=default_printScore;
+	public boolean printEValue=default_printEValue;
+
+	private boolean trackCounts=default_trackCounts;
+	public boolean printDepth=default_printDepth;
+	public boolean printDepth2=default_printDepth2;
+	public boolean printActualDepth=default_printActualDepth;
+	public boolean printVolume=default_printVolume;
+	public boolean printRefHits=default_printRefHits;
+	
+	public boolean printLength=default_printLength;
+	public boolean printTaxID=default_printTaxID;
+	public boolean printGSize=default_printGSize;
+	public boolean printGC=default_printGC;
+	public boolean gSizeKMG=default_gSizeKMG;
+	public boolean printGKmers=default_printGKmers;
+	public boolean printCommonAncestor=default_printCommonAncestor;
+	public boolean printCommonAncestorLevel=default_printCommonAncestorLevel;
+	public boolean printTaxName=default_printTaxName;
+	public boolean printGSeqs=default_printGSeqs;
+	public boolean printGBases=default_printGBases;
+	
+	public boolean jsonArray=default_jsonArray;
+	public boolean printD3=default_printD3;
+	public boolean D3LevelNodes=false;
+	public int D3sizeMode=D3_HIT_SIZE;
+	public static final int D3_HIT_SIZE=0, D3_ANI_SIZE=1, D3_KID_SIZE=2, D3_WKID_SIZE=3, D3_DEPTH_SIZE=4;
+	
+	public float minEntropy=default_minEntropy;
+	
+	//For k=32:
+	//0.000095f is >=Q6 (75%); 0.0008 is >=Q7 (80%); 0.0039 is >=Q8 (84%).
+	//0.002f is >=Q7.53 (82.3%)
+	//0.0017f is >=Q7.44 (82.0%)
+	//0.6f works better for Illumina reads but this is more robust for PacBio. 
+	public float minProb=0.0008f;
+	public byte minQual=0;
+
+	public boolean printUnique=default_printUnique;
+	public boolean printUnique2=default_printUnique2;
+	public boolean printUnique3=default_printUnique3;
+	public boolean printUContam=default_printUContam;
+	public boolean printNoHit=default_printNoHit;
+
+	public boolean printColors=default_printColors;
+	public boolean setColors=false;
+	public int colorLevel=default_colorLevel;
+	
+	/** TODO: Note this is conflated between printing %contam and calculating things based on contam hits. */
+	public boolean printContam=default_printContam;
+	public boolean printContam2=default_printContam2;
+	private int contamLevel=default_contamLevel;
+	
+	/** Raw fields */
+	public boolean printMatches=default_printMatches;
+	
+	public boolean printRefDivisor=false;
+	public boolean printQueryDivisor=false;
+	public boolean printRefSize=false;
+	public boolean printQuerySize=false;
+	public boolean printContamHits=false;
+	
+	public boolean mergePairs=false;
+	public boolean printIntersection=false;
+	
+	//For format 3 or 5
+	public boolean useTaxidName=false;
+	public boolean useImgName=false;
+	public boolean useTaxName=false;
+	public boolean useFilePrefixName=false;
+	public boolean reportAniOnly=false;
+
+	public int taxLevelWhite=0;
+	public int taxLevelBlack=0;
+
+	public String taxFilterWhiteList=null;
+	public String taxFilterBlackList=null;
+
+	public String taxFilterWhiteString=null;
+	public String taxFilterBlackString=null;
+	
+	public TaxFilter taxFilterWhite=null;
+	public TaxFilter taxFilterBlack=null;
+
+	public boolean banUnclassified=false;
+	public boolean banVirus=false;
+
+	/** Make sure the settings are consistent, for CompareSketch.
+	 * This is not yet complete. */
+	public boolean checkValid(){
+		if(printUnique2 || printUnique3){
+			assert(contamLevel()>=TaxTree.SUBSPECIES_E);
+			assert(needContamCounts());
+			assert(SketchObject.makeIndex);
+			assert(SketchObject.taxtree!=null);
+		}
+		if(printContam2){
+			assert(contamLevel()>=TaxTree.SUBSPECIES_E);
+			assert(needContamCounts());
+			assert(SketchObject.makeIndex);
+			assert(SketchObject.taxtree!=null);
+		}
+		return true;
+	}
+	
+	public boolean trackCounts() {
+		return trackCounts || printDepth || printDepth2 || printVolume 
+				|| comparator!=Comparison.scoreComparator || printD3; //|| minKeyOccuranceCount>1;
+	}
+	
+	public boolean needContamCounts() {
+		return printContam || printContam2 || printContamHits || printUnique || printUnique2 || printUnique3 || printUContam || printNoHit; // || true
+	}
+	
+	public boolean needIndex(){
+		return printContam2 || printUnique2 || printUnique3;
+	}
+
+	public int contamLevel() {
+		return needIndex() ? contamLevel : -1;
+	}
+	
+	public int compare(Comparison a, Comparison b){
+		return comparator.compare(a, b);
+	}
+	
+	public Comparator<Comparison> comparator=Comparison.scoreComparator;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------          Constants           ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	public static final int FORMAT_OLD=0, FORMAT_MULTICOLUMN=2, FORMAT_QUERY_REF_ANI=3, FORMAT_JSON=4, FORMAT_CONSTELLATION=5;
+	public static final boolean default_printD3=false;
+	public static final boolean default_jsonArray=false;
+	
+	public static final int default_maxRecords=20;
+	public static final float default_minWKID=0.0001f;
+	public static final int default_format=FORMAT_MULTICOLUMN;
+	public static final boolean default_printSSUSequence=false;
+	public static final boolean default_printTax=false;
+	public static final boolean default_printOriginalName=false;
+	public static final boolean default_printQueryFileName=true;
+	public static final boolean default_printRefFileName=false;
+	public static final boolean default_printImg=false;
+	public static final boolean default_printAni=true;
+	public static final boolean default_printCompleteness=true;
+	public static final boolean default_printScore=false;
+	public static final boolean default_printEValue=false;
+	
+	public static final boolean default_trackCounts=false;
+	public static final boolean default_printDepth=false;
+	public static final boolean default_printDepth2=false;
+	public static final boolean default_printActualDepth=true;
+	public static final boolean default_printVolume=false;
+	public static final boolean default_printRefHits=false;
+
+	public static final boolean default_printContam=true;
+	public static final boolean default_printContam2=false;
+	
+	public static final boolean default_printMatches=true;
+	public static final boolean default_printLength=false;
+	public static final boolean default_printTaxID=true;
+	public static final boolean default_printGSize=true;
+	public static final boolean default_printGC=false;
+	public static final boolean default_gSizeKMG=true;
+	public static final boolean default_printGKmers=false;
+	public static final boolean default_printCommonAncestor=false;
+	public static final boolean default_printCommonAncestorLevel=false;
+	public static final boolean default_printTaxName=true;
+	public static final boolean default_printGSeqs=true;
+	public static final boolean default_printGBases=false;
+
+	public static final float default_minEntropy=0.66f;
+	public static final float default_minEntropy_amino=0.70f;
+	public static final float default_minProb=0.0008f;
+	public static final byte default_minQual=0;
+
+	public static final boolean default_printUnique=true;
+	public static final boolean default_printUnique2=false;
+	public static final boolean default_printUnique3=false;
+	public static final boolean default_printUContam=false;
+	public static final boolean default_printNoHit=false;
+
+	public static final boolean default_printColors=true;
+	public static final int default_colorLevel=TaxTree.FAMILY_E;
+
+	public static final int default_taxLevel=TaxTree.SPECIES;
+	public static final int default_contamLevel=TaxTree.GENUS_E;
+	
+	public static final int default_mode=SketchObject.ONE_SKETCH;
+	
+	public static final int default_minHits=3;
+	public static final float default_samplerate=1;
+	public static final long default_maxReads=-1;
+	public static final int default_minKeyOccuranceCount=1;
+	
+}