jpayne@68: package sketch;
jpayne@68: 
jpayne@68: import java.util.ArrayList;
jpayne@68: import java.util.Collections;
jpayne@68: import java.util.Comparator;
jpayne@68: import java.util.Locale;
jpayne@68: import java.util.Map.Entry;
jpayne@68: 
jpayne@68: import json.JsonObject;
jpayne@68: import shared.Colors;
jpayne@68: import shared.Parse;
jpayne@68: import shared.Tools;
jpayne@68: import structures.ByteBuilder;
jpayne@68: import tax.PrintTaxonomy;
jpayne@68: import tax.TaxFilter;
jpayne@68: import tax.TaxNode;
jpayne@68: import tax.TaxTree;
jpayne@68: 
jpayne@68: public class DisplayParams implements Cloneable {
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public DisplayParams clone(){
jpayne@68: 		try {
jpayne@68: 			DisplayParams copy=(DisplayParams)super.clone();
jpayne@68: 			if(taxFilterWhite!=null){
jpayne@68: 				copy.taxFilterWhite=taxFilterWhite.deepCopy();
jpayne@68: 			}
jpayne@68: 			if(taxFilterBlack!=null){
jpayne@68: 				copy.taxFilterBlack=taxFilterBlack.deepCopy();
jpayne@68: 			}
jpayne@68: 			copy.postParsed=false;
jpayne@68: 			return copy;
jpayne@68: 		} catch (CloneNotSupportedException e) {
jpayne@68: 			// TODO Auto-generated catch block
jpayne@68: 			e.printStackTrace();
jpayne@68: 			throw new RuntimeException();
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public DisplayParams parseDoubleHeader(String s){
jpayne@68: 		if(!s.startsWith("##")){return this;}
jpayne@68: //		if(!s.startsWith("##")){return this.clone();}
jpayne@68: 		StringBuilder sb=new StringBuilder();
jpayne@68: 		for(int i=2; i<s.length(); i++){
jpayne@68: 			char c=s.charAt(i);
jpayne@68: 			if(c=='\n'){break;}
jpayne@68: 			sb.append(c);
jpayne@68: 		}
jpayne@68: 		return parseDoubleHeaderLine(sb.toString());
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public DisplayParams parseDoubleHeaderLine(String line) {
jpayne@68: 		if(line.startsWith("##")){line=line.substring(2);}
jpayne@68: 		else{assert(!line.startsWith("#")) : line;}
jpayne@68: 		if(line.length()<1){return this;}
jpayne@68: 		
jpayne@68: 		DisplayParams params=this.clone();
jpayne@68: 		
jpayne@68: 		String[] args=line.split(" ");
jpayne@68: 		for(String arg : args){
jpayne@68: 			String[] split=arg.split("=");
jpayne@68: 			String a=split[0].toLowerCase();
jpayne@68: 			String b=split.length>1 ? split[1] : null;
jpayne@68: 			if(b==null || b.equalsIgnoreCase("null")){b=null;} //Normally handled by PreParser, but not in this case.
jpayne@68: 			while(a.startsWith("-")){a=a.substring(1);} //Strip leading hyphens
jpayne@68: 			
jpayne@68: 			boolean x=params.parse(arg, a, b);
jpayne@68: //			assert(x) : "Unknown parameter "+arg+"\n"+line;
jpayne@68: 			if(!x){System.err.println("Warning: Unknown parameter "+arg);}
jpayne@68: 		}
jpayne@68: 		if(SketchObject.verbose2){System.err.println("Made it to post-parse.  taxFilterWhite="+params.taxFilterWhite);}
jpayne@68: 		params.postParse(true, true);
jpayne@68: 		if(SketchObject.verbose2){System.err.println("Passed post-parse.  taxFilterWhite="+params.taxFilterWhite);}
jpayne@68: 		
jpayne@68: 		return params;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public boolean parse(String arg, String a, String b){
jpayne@68: 	
jpayne@68: 		if(a.equals("chunk")){
jpayne@68: 			chunkNum=Integer.parseInt(b);
jpayne@68: 		}else if(a.equals("minhits")  || a.equals("hits")){
jpayne@68: 			minHits=Integer.parseInt(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("minwkid") || a.equalsIgnoreCase("wkid")){
jpayne@68: 			minWKID=Float.parseFloat(b);
jpayne@68: 			if(minWKID>1){minWKID/=100;}
jpayne@68: 			assert(minWKID<=1) : "minWKID should between 0 and 1";
jpayne@68: 		}else if(a.equalsIgnoreCase("minid") || a.equalsIgnoreCase("id") || a.equalsIgnoreCase("minani") || a.equalsIgnoreCase("ani")){
jpayne@68: 			minANI=Float.parseFloat(b);
jpayne@68: 			if(minANI>1){minANI/=100;}
jpayne@68: 			assert(minANI<=1) : "minANI should between 0 and 1";
jpayne@68: 			if(minANI>0){
jpayne@68: 				minWKID=(float)Tools.max(minWKID, Comparison.aniToWkid(minANI, 32));//Lowest possible minWKID for this ANI
jpayne@68: 			}
jpayne@68: 		}else if(a.equals("minbases")){
jpayne@68: 			minBases=Integer.parseInt(b);
jpayne@68: 		}else if(a.equals("minsizeratio")){
jpayne@68: 			minSizeRatio=Float.parseFloat(b);
jpayne@68: //			assert(minSizeRatio>=0f && minSizeRatio<=1.0f) : "\nminSizeRatio must be between 0 and 1, inclusive.\n";
jpayne@68: 			if(minSizeRatio>1){minSizeRatio=1f/minSizeRatio;}
jpayne@68: 		}else if(a.equals("records") || a.equals("maxrecords") || a.equals("results")){
jpayne@68: 			maxRecords=Integer.parseInt(b);
jpayne@68: 			assert(maxRecords>=1) : "Max records must be at least 1.";
jpayne@68: 		}else if(a.equals("recordsperlevel")){
jpayne@68: 			recordsPerLevel=Integer.parseInt(b);
jpayne@68: 		}else if(a.equals("format")){
jpayne@68: 			assert(b!=null) : "Invalid format: "+arg;
jpayne@68: 			if(b.equalsIgnoreCase("json")){
jpayne@68: 				format=FORMAT_JSON;
jpayne@68: 			}else if(b.equalsIgnoreCase("jsonarray")){
jpayne@68: 				format=FORMAT_JSON;
jpayne@68: 				jsonArray=true;
jpayne@68: 			}else if(b.equalsIgnoreCase("d3")){
jpayne@68: 				format=FORMAT_JSON;
jpayne@68: 				printD3=true;
jpayne@68: 			}else if(b.equalsIgnoreCase("constellation")){
jpayne@68: 				format=FORMAT_CONSTELLATION;
jpayne@68: 			}else if(b.equalsIgnoreCase("3column") || b.equalsIgnoreCase("queryrefani")){
jpayne@68: 				format=FORMAT_QUERY_REF_ANI;
jpayne@68: 			}else if(Tools.isDigit(b.charAt(0))){
jpayne@68: 				format=Integer.parseInt(b);
jpayne@68: 			}else{
jpayne@68: 				assert(false) : "Invalid format: "+arg;
jpayne@68: 			}
jpayne@68: 		}else if(a.equalsIgnoreCase("json")){
jpayne@68: 			if(Parse.parseBoolean(b)){
jpayne@68: 				format=FORMAT_JSON;
jpayne@68: 			}else{
jpayne@68: 				if(format==FORMAT_JSON){format=default_format;}
jpayne@68: 			}
jpayne@68: 		}else if(a.equalsIgnoreCase("jsonarray") || a.equalsIgnoreCase("jsonarrays")){
jpayne@68: 			if(Parse.parseBoolean(b)){
jpayne@68: 				format=FORMAT_JSON;
jpayne@68: 				jsonArray=true;
jpayne@68: 			}else{
jpayne@68: 				jsonArray=false;
jpayne@68: 			}
jpayne@68: 		}else if(a.equalsIgnoreCase("d3") || a.equalsIgnoreCase("printd3")){
jpayne@68: 			if(Parse.parseBoolean(b)){
jpayne@68: 				format=FORMAT_JSON;
jpayne@68: 				printD3=true;
jpayne@68: 			}else{
jpayne@68: 				printD3=false;
jpayne@68: 			}
jpayne@68: 		}else if(a.equalsIgnoreCase("jsonarray") || a.equalsIgnoreCase("jsonarrays")){
jpayne@68: 			if(Parse.parseBoolean(b)){
jpayne@68: 				jsonArray=true;
jpayne@68: 			}else{
jpayne@68: 				jsonArray=false;
jpayne@68: 			}
jpayne@68: 		}else if(a.equalsIgnoreCase("d3levelnodes")){
jpayne@68: 			D3LevelNodes=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("d3hitsize")){
jpayne@68: 			if(Parse.parseBoolean(b)){D3sizeMode=D3_HIT_SIZE;}
jpayne@68: 		}else if(a.equalsIgnoreCase("d3anisize")){
jpayne@68: 			if(Parse.parseBoolean(b)){D3sizeMode=D3_ANI_SIZE;}
jpayne@68: 		}else if(a.equalsIgnoreCase("d3wkidsize")){
jpayne@68: 			if(Parse.parseBoolean(b)){D3sizeMode=D3_WKID_SIZE;}
jpayne@68: 		}else if(a.equalsIgnoreCase("d3depthsize")){
jpayne@68: 			if(Parse.parseBoolean(b)){
jpayne@68: 				D3sizeMode=D3_DEPTH_SIZE;
jpayne@68: 				printDepth=true;
jpayne@68: 			}
jpayne@68: 		}else if(a.equalsIgnoreCase("d3kidsize")){
jpayne@68: 			if(Parse.parseBoolean(b)){D3sizeMode=D3_KID_SIZE;}
jpayne@68: 		}else if(a.equalsIgnoreCase("D3sizeMode")){
jpayne@68: 			D3sizeMode=Integer.parseInt(b);
jpayne@68: 		}else if(a.equals("level") || a.equals("lv") || a.equals("taxlevel") || a.equals("tl") || a.equals("minlevel")){
jpayne@68: 			taxLevel=TaxTree.parseLevel(b);//TODO: Change to extended
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		else if(a.equalsIgnoreCase("requireSSU")){
jpayne@68: 			requireSSU=Parse.parseBoolean(b);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		else if(a.equalsIgnoreCase("minRefSizeEstimate") || a.equalsIgnoreCase("minRefSize")){
jpayne@68: 			minRefSizeEstimate=Long.parseLong(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("minRefSizeBases")){
jpayne@68: 			minRefSizeBases=Long.parseLong(b);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		else if(a.equalsIgnoreCase("printtax") || a.equalsIgnoreCase("printtaxa")){
jpayne@68: 			printTax=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printssu") || a.equalsIgnoreCase("print16s") || a.equalsIgnoreCase("ssu")){
jpayne@68: 			printSSU=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printSSULen") || a.equalsIgnoreCase("print16slen") || a.equalsIgnoreCase("ssulen")){
jpayne@68: 			printSSULen=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printssusequence") || a.equalsIgnoreCase("print16ssequence")){
jpayne@68: 			printSSUSequence=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printqueryfilename") || a.equalsIgnoreCase("printqfname") || a.equalsIgnoreCase("printqfile") || a.equalsIgnoreCase("qfname")){
jpayne@68: 			printQueryFileName=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printreffilename") || a.equalsIgnoreCase("printrfname") || a.equalsIgnoreCase("printrfile") || a.equalsIgnoreCase("rfname")){
jpayne@68: 			printRefFileName=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printfilename") || a.equalsIgnoreCase("printfname") || a.equalsIgnoreCase("printfile")){
jpayne@68: 			printQueryFileName=printRefFileName=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printoriginalname") || a.equalsIgnoreCase("printseqname") || a.equalsIgnoreCase("printname0") || a.equals("pn0")){
jpayne@68: 			printOriginalName=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printimg")){
jpayne@68: 			printImg=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printcompleteness") || a.equalsIgnoreCase("completeness") || a.equalsIgnoreCase("printcomplt")){
jpayne@68: 			printCompleteness=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printani") || a.equalsIgnoreCase("ani")){
jpayne@68: 			printAni=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printkid") || a.equalsIgnoreCase("kid")){
jpayne@68: 			printKID=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printwkid") || a.equalsIgnoreCase("wkid")){
jpayne@68: 			printWKID=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printscore") || a.equalsIgnoreCase("score")){
jpayne@68: 			printScore=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printevalue") || a.equalsIgnoreCase("evalue")){
jpayne@68: 			printEValue=Parse.parseBoolean(b);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		else if(a.equalsIgnoreCase("trackcounts")){
jpayne@68: 			trackCounts=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printdepth") || a.equalsIgnoreCase("depth")){
jpayne@68: 			printDepth=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printdepth2") || a.equalsIgnoreCase("depth2")){
jpayne@68: 			printDepth2=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("actualdepth") || a.equalsIgnoreCase("printactualdepth")){
jpayne@68: 			printActualDepth=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printvolume") || a.equalsIgnoreCase("volume")){
jpayne@68: 			printVolume=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printavgrefhits") || a.equalsIgnoreCase("printrefhits") || a.equalsIgnoreCase("avgrefhits") || a.equalsIgnoreCase("refhits")){
jpayne@68: 			printRefHits=Parse.parseBoolean(b);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		else if(a.equalsIgnoreCase("sortByDepth")){
jpayne@68: 			boolean x=Parse.parseBoolean(b);
jpayne@68: 			if(x){comparator=Comparison.depthComparator;}
jpayne@68: 		}else if(a.equalsIgnoreCase("sortByDepth2")){
jpayne@68: 			boolean x=Parse.parseBoolean(b);
jpayne@68: 			if(x){comparator=Comparison.depth2Comparator;}
jpayne@68: 		}else if(a.equalsIgnoreCase("sortByVolume")){
jpayne@68: 			boolean x=Parse.parseBoolean(b);
jpayne@68: 			if(x){comparator=Comparison.volumeComparator;}
jpayne@68: 		}else if(a.equalsIgnoreCase("sortByScore")){
jpayne@68: 			boolean x=Parse.parseBoolean(b);
jpayne@68: 			if(x){comparator=Comparison.scoreComparator;}
jpayne@68: 		}
jpayne@68: 		else if(a.equalsIgnoreCase("sortByKID")){
jpayne@68: 			boolean x=Parse.parseBoolean(b);
jpayne@68: 			if(x){comparator=Comparison.KIDComparator;}
jpayne@68: 		}else if(a.equalsIgnoreCase("sortByWKID") || a.equalsIgnoreCase("sortByANI")){
jpayne@68: 			boolean x=Parse.parseBoolean(b);
jpayne@68: 			if(x){comparator=Comparison.WKIDComparator;}
jpayne@68: 		}else if(a.equalsIgnoreCase("sortBySSU") || a.equalsIgnoreCase("sortBy16S")){
jpayne@68: 			boolean x=Parse.parseBoolean(b);
jpayne@68: 			if(x){comparator=Comparison.SSUComparator;}
jpayne@68: 		}else if(a.equalsIgnoreCase("sortByHits") || a.equalsIgnoreCase("sortByMatches")){
jpayne@68: 			boolean x=Parse.parseBoolean(b);
jpayne@68: 			if(x){comparator=Comparison.HitsComparator;}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		else if(a.equalsIgnoreCase("printUMatches") || a.equalsIgnoreCase("printUHits") || a.equalsIgnoreCase("printUnique")){
jpayne@68: 			printUnique=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printUMatches2") || a.equalsIgnoreCase("printUnique2") || a.equalsIgnoreCase("unique2")){
jpayne@68: 			printUnique2=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printUMatches3") || a.equalsIgnoreCase("printUnique3") || a.equalsIgnoreCase("unique3")){
jpayne@68: 			printUnique3=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printUContam")){
jpayne@68: 			printUContam=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printNoHit")){
jpayne@68: 			printNoHit=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("contamhits") || a.equalsIgnoreCase("contam") || a.equalsIgnoreCase("printcontam")){
jpayne@68: 			printContam=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("contamhits2") || a.equalsIgnoreCase("contam2") || a.equalsIgnoreCase("printcontam2")){
jpayne@68: 			if(b==null || b.length()<1){
jpayne@68: 				printContam2=true;
jpayne@68: 			}else if(Tools.isDigit(b.charAt(0)) || b.charAt(0)=='-'){
jpayne@68: 				contamLevel=Tools.max(0, TaxTree.levelToExtended(Integer.parseInt(b)));
jpayne@68: 				printContam2=true;
jpayne@68: 			}else if(TaxTree.levelMapExtendedContains(b)){
jpayne@68: 				contamLevel=TaxTree.stringToLevelExtended(b);
jpayne@68: 				printContam2=true;
jpayne@68: 			}else{
jpayne@68: 				printContam2=Parse.parseBoolean(b);
jpayne@68: 			}
jpayne@68: 		}else if(a.equalsIgnoreCase("contamLevel")){
jpayne@68: 			if(Tools.isDigit(b.charAt(0)) || b.charAt(0)=='-'){
jpayne@68: 				contamLevel=Tools.max(0, TaxTree.levelToExtended(Integer.parseInt(b)));
jpayne@68: 				printContam2=true;
jpayne@68: 			}else if(TaxTree.levelMapExtendedContains(b)){
jpayne@68: 				contamLevel=TaxTree.stringToLevelExtended(b);
jpayne@68: 				printContam2=true;
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		else if(a.equalsIgnoreCase("reportAniOnly") || a.equalsIgnoreCase("AniOnly")){
jpayne@68: 			reportAniOnly=Parse.parseBoolean(b);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		else if(a.equalsIgnoreCase("printMatches")){
jpayne@68: 			printMatches=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printLength")){
jpayne@68: 			printLength=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printTaxID")){
jpayne@68: 			printTaxID=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printGSize")){
jpayne@68: 			printGSize=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("gSizeKMG")){
jpayne@68: 			gSizeKMG=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printGC")){
jpayne@68: 			printGC=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printGKmers")){
jpayne@68: 			printGKmers=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printCommonAncestor") || a.equalsIgnoreCase("printCA")){
jpayne@68: 			printCommonAncestor=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printCommonAncestorLevel") || a.equalsIgnoreCase("printCAL")){
jpayne@68: 			printCommonAncestorLevel=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printTaxName")){
jpayne@68: 			printTaxName=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printGSeqs")){
jpayne@68: 			printGSeqs=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printGBases")){
jpayne@68: 			printGBases=Parse.parseBoolean(b);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		else if(a.equalsIgnoreCase("minEntropy") || a.equalsIgnoreCase("entropy") || a.equalsIgnoreCase("efilter")){
jpayne@68: 			minEntropy=Float.parseFloat(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("minprob") || a.equalsIgnoreCase("pfilter")){
jpayne@68: 			minProb=(float)Double.parseDouble(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("minQual") || a.equalsIgnoreCase("minq")){
jpayne@68: 			minQual=Byte.parseByte(b);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		else if(a.equalsIgnoreCase("printColors") || a.equalsIgnoreCase("colors") || a.equalsIgnoreCase("color")){
jpayne@68: //			System.err.println("Parsing '"+arg+"'"); //123
jpayne@68: 			if(b==null || b.length()<1){
jpayne@68: 				printColors=true;
jpayne@68: 			}else if(b.equalsIgnoreCase("t") || b.equalsIgnoreCase("true")){
jpayne@68: 				printColors=true;
jpayne@68: 			}else if(b.equalsIgnoreCase("f") || b.equalsIgnoreCase("false")){
jpayne@68: 				printColors=false;
jpayne@68: 			}else{
jpayne@68: 				printColors=true;
jpayne@68: 				if(Tools.isDigit(b.charAt(0)) || b.charAt(0)=='-'){
jpayne@68: 					colorLevel=Tools.max(0, TaxTree.levelToExtended(Integer.parseInt(b)));
jpayne@68: 				}else{
jpayne@68: 					colorLevel=TaxTree.stringToLevelExtended(b);
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 			setColors=true;
jpayne@68: //			System.err.println("Parsed "+arg); //123
jpayne@68: 		}else if(a.equalsIgnoreCase("colorLevel")){
jpayne@68: //			System.err.println("Parsing '"+arg+"'"); //123
jpayne@68: 			if(Tools.isDigit(b.charAt(0)) || b.charAt(0)=='-'){
jpayne@68: 				colorLevel=Tools.max(0, TaxTree.levelToExtended(Integer.parseInt(b)));
jpayne@68: 			}else{
jpayne@68: 				colorLevel=TaxTree.stringToLevelExtended(b);
jpayne@68: 			}
jpayne@68: //			System.err.println("Parsed "+arg); //123
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		else if(a.equalsIgnoreCase("printRefDivisor") || a.equalsIgnoreCase("printRDiv")){
jpayne@68: 			printRefDivisor=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printQueryDivisor") || a.equalsIgnoreCase("printQDiv")){
jpayne@68: 			printQueryDivisor=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printRefSize") || a.equalsIgnoreCase("printRSize")){
jpayne@68: 			printRefSize=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printQuerySize") || a.equalsIgnoreCase("printQSize")){
jpayne@68: 			printQuerySize=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("printContamHits") || a.equalsIgnoreCase("printCHits")){
jpayne@68: 			printContamHits=Parse.parseBoolean(b);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		else if(a.equalsIgnoreCase("printIntersection") || a.equalsIgnoreCase("intersection") || a.equalsIgnoreCase("intersect")){
jpayne@68: 			printIntersection=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("mergePairs") || a.equalsIgnoreCase("merge")){
jpayne@68: 			mergePairs=Parse.parseBoolean(b);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		else if(a.equalsIgnoreCase("printAll")){
jpayne@68: 			if(Parse.parseBoolean(b)){
jpayne@68: 				setPrintAll();
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		else if(a.equals("samplerate")){
jpayne@68: 			samplerate=Float.parseFloat(b);
jpayne@68: 		}else if(a.equals("reads")){
jpayne@68: 			maxReads=Parse.parseKMG(b);
jpayne@68: 		}else if(a.equals("mode") || a.equalsIgnoreCase("single") || a.equalsIgnoreCase("singlesketch") || a.equalsIgnoreCase("onesketch")
jpayne@68: 				|| a.equalsIgnoreCase("persequence") || a.equalsIgnoreCase("sequence") || a.equalsIgnoreCase("pertaxa") 
jpayne@68: 				|| a.equalsIgnoreCase("perheader") || a.equalsIgnoreCase("perfile")){
jpayne@68: 			mode=SketchObject.parseMode(arg, a, b);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		//For format 3
jpayne@68: 		else if(a.equalsIgnoreCase("useTaxidName") || a.equalsIgnoreCase("useTaxidAsName")){
jpayne@68: 			useTaxidName=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("useImgName") || a.equalsIgnoreCase("useImgAsName")){
jpayne@68: 			useImgName=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("useTaxName") || a.equalsIgnoreCase("useTaxAsName")){
jpayne@68: 			useTaxName=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("useFilePrefixName") || a.equalsIgnoreCase("useFilePrefixAsName")){
jpayne@68: 			useFilePrefixName=Parse.parseBoolean(b);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		else if(a.equalsIgnoreCase("taxfilterincludelevel") || a.equalsIgnoreCase("includelevel") 
jpayne@68: 				|| a.equalsIgnoreCase("taxlevelwhite") || a.equalsIgnoreCase("ilevel") || a.equalsIgnoreCase("whitelevel")){
jpayne@68: 			taxLevelWhite=TaxTree.parseLevel(b);//TODO:  Change to extended
jpayne@68: 		}else if(a.equalsIgnoreCase("taxfilterinclude") || a.equalsIgnoreCase("include") || a.equalsIgnoreCase("taxfilterwhitelist")){
jpayne@68: 			taxFilterWhiteList=b;
jpayne@68: 		}else if(a.equalsIgnoreCase("taxfilterincludestring") || a.equalsIgnoreCase("includestring")
jpayne@68: 				|| a.equalsIgnoreCase("taxfilterwhitestring") || a.equalsIgnoreCase("istring")){
jpayne@68: 			taxFilterWhiteString=b;
jpayne@68: 		}else if(a.equalsIgnoreCase("banUnclassified") || a.equalsIgnoreCase("noUnclassified")){
jpayne@68: 			banUnclassified=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("banVirus") || a.equalsIgnoreCase("noVirus") || a.equalsIgnoreCase("banViruses") || a.equalsIgnoreCase("noViruses")){
jpayne@68: 			banVirus=Parse.parseBoolean(b);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		else if(a.equalsIgnoreCase("taxfilterexcludelevel") || a.equalsIgnoreCase("excludelevel") 
jpayne@68: 				|| a.equalsIgnoreCase("taxlevelblack") || a.equalsIgnoreCase("elevel") || a.equalsIgnoreCase("blacklevel")){
jpayne@68: 			taxLevelBlack=TaxTree.parseLevel(b);//TODO:  Change to extended
jpayne@68: 		}else if(a.equalsIgnoreCase("taxfilterexclude") || a.equalsIgnoreCase("exclude") || a.equalsIgnoreCase("taxfilterblacklist")){
jpayne@68: 			taxFilterBlackList=b;
jpayne@68: 		}else if(a.equalsIgnoreCase("taxfilterexcludestring") || a.equalsIgnoreCase("excludestring")
jpayne@68: 				|| a.equalsIgnoreCase("taxfilterblackstring") || a.equalsIgnoreCase("estring")){
jpayne@68: 			taxFilterBlackString=b;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		else if(a.equalsIgnoreCase("minkmercount") || a.equalsIgnoreCase("minkeycount") || a.equalsIgnoreCase("mincount") || a.equalsIgnoreCase("minKeyOccuranceCount")){
jpayne@68: 			minKeyOccuranceCount=Tools.max(1, Integer.parseInt(b));
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		//TODO:  Eventually remove support for "amino" and "k" and just support "hamino" and "hk"
jpayne@68: 		//This stands for "header amino" and "header k".
jpayne@68: 		
jpayne@68: 		//Parameters for compatibility verification
jpayne@68: 		else if(a.equalsIgnoreCase("k") || a.equalsIgnoreCase("hk")){
jpayne@68: //			System.err.println("A: k="+k+", k2="+k2+", arg="+arg);
jpayne@68: 			if(b.indexOf(',')>=0){
jpayne@68: 				String[] split=b.split(",");
jpayne@68: 				assert(split.length==2) : "\nBad argument "+arg+"\n"+b+"\n";
jpayne@68: 				int x=Integer.parseInt(split[0]);
jpayne@68: 				int y=Integer.parseInt(split[1]);
jpayne@68: 				k=Tools.max(x, y);
jpayne@68: 				k2=Tools.min(x, y);
jpayne@68: 				if(k==k2){k2=0;}
jpayne@68: //				System.err.println("B: k="+k+", k2="+k2+", split="+Arrays.toString(split));
jpayne@68: 			}else{
jpayne@68: 				k=Integer.parseInt(b);
jpayne@68: //				System.err.println("C: k="+k+", k2="+k2);
jpayne@68: 			}
jpayne@68: 		}else if(a.equalsIgnoreCase("hashversion") || a.equalsIgnoreCase("hv")){
jpayne@68: 			hashVersion=Integer.parseInt(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("amino") || a.equalsIgnoreCase("hamino")){
jpayne@68: 			amino=Parse.parseBoolean(b);
jpayne@68: 			if(amino){translate=false;}
jpayne@68: 		}else if(a.equalsIgnoreCase("translate")){
jpayne@68: 			translate=Parse.parseBoolean(b);
jpayne@68: 			if(translate){amino=false;}
jpayne@68: 		}else if(a.equalsIgnoreCase("sixframes")){
jpayne@68: 			sixframes=Parse.parseBoolean(b);
jpayne@68: 			if(sixframes){amino=false; translate=true;}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		else if(a.equalsIgnoreCase("requiredmeta") || a.equalsIgnoreCase("rmeta")){
jpayne@68: 			if(b==null){requiredMeta=null;}
jpayne@68: 			else{
jpayne@68: 				String[] split2=b.split(",");
jpayne@68: 				requiredMeta=new ArrayList<String>(split2.length);
jpayne@68: 				for(String mt : split2){
jpayne@68: 					assert(mt.indexOf(':')>=0) : "Metadata tags must contain ':' symbol: "+mt;
jpayne@68: 					requiredMeta.add(mt);
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 		}else if(a.equalsIgnoreCase("bannedmeta") || a.equalsIgnoreCase("bmeta")){
jpayne@68: 			if(b==null){bannedMeta=null;}
jpayne@68: 			else{
jpayne@68: 				String[] split2=b.split(",");
jpayne@68: 				bannedMeta=new ArrayList<String>(split2.length);
jpayne@68: 				for(String mt : split2){
jpayne@68: 					assert(mt.indexOf(':')>=0) : "Metadata tags must contain ':' symbol: "+mt;
jpayne@68: 					bannedMeta.add(mt);
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: //		else if(a.equalsIgnoreCase("requiredtaxid") || a.equalsIgnoreCase("rtaxid")){
jpayne@68: //			if(b==null){requiredTaxid=null;}
jpayne@68: //			else{
jpayne@68: //				String[] split2=b.split(",");
jpayne@68: //				requiredTaxid=new IntList(split2.length);
jpayne@68: //				for(String mt : split2){
jpayne@68: //					requiredTaxid.add(Integer.parseInt(mt));
jpayne@68: //				}
jpayne@68: //				if(requiredTaxid.isEmpty()){requiredTaxid=null;}
jpayne@68: //			}
jpayne@68: //		}else if(a.equalsIgnoreCase("bannedtaxid") || a.equalsIgnoreCase("btaxid")){
jpayne@68: //			if(b==null){bannedTaxid=null;}
jpayne@68: //			else{
jpayne@68: //				String[] split2=b.split(",");
jpayne@68: //				bannedTaxid=new IntList(split2.length);
jpayne@68: //				for(String mt : split2){
jpayne@68: //					bannedTaxid.add(Integer.parseInt(mt));
jpayne@68: //				}
jpayne@68: //				if(bannedTaxid.isEmpty()){bannedTaxid=null;}
jpayne@68: //			}
jpayne@68: //		}
jpayne@68: 		
jpayne@68: 		else if(a.equalsIgnoreCase("requiredmetaand") || a.equalsIgnoreCase("rmetaand")){
jpayne@68: 			requiredMetaAnd=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("requiredmetaor") || a.equalsIgnoreCase("rmetaor")){
jpayne@68: 			requiredMetaAnd=!Parse.parseBoolean(b);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		else if(a.equalsIgnoreCase("bbversion")){
jpayne@68: 			inputVersion=b;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		else{
jpayne@68: 			return false;
jpayne@68: 		}
jpayne@68: 		return true;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public void postParse(boolean requireTree, boolean makeTaxFilters){
jpayne@68: 		assert(!postParsed);
jpayne@68: 		synchronized(this){
jpayne@68: 			if(postParsed){return;}
jpayne@68: 			
jpayne@68: 			if(makeTaxFilters){
jpayne@68: 				if(taxFilterWhiteList!=null || taxFilterWhiteString!=null){
jpayne@68: 					taxFilterWhite=new TaxFilter(SketchObject.taxtree, true);
jpayne@68: 					taxFilterWhite.setLevel(taxLevelWhite, false);
jpayne@68: 					taxFilterWhite.makeSet();
jpayne@68: 					taxFilterWhite.addNamesOrNumbers(taxFilterWhiteList, false);
jpayne@68: 					taxFilterWhite.setContainsString(taxFilterWhiteString);
jpayne@68: 					if(requireTree){
jpayne@68: 						assert(SketchObject.taxtree!=null) : "No taxtree loaded.";
jpayne@68: 						taxFilterWhite.setTree(SketchObject.taxtree);
jpayne@68: 						taxFilterWhite.promote();
jpayne@68: 					}
jpayne@68: 				}
jpayne@68: 				
jpayne@68: 				if(taxFilterBlackList!=null || taxFilterBlackString!=null){
jpayne@68: 					taxFilterBlack=new TaxFilter(SketchObject.taxtree, false);
jpayne@68: 					taxFilterBlack.setLevel(taxLevelBlack, false);
jpayne@68: 					taxFilterBlack.makeSet();
jpayne@68: 					taxFilterBlack.addNamesOrNumbers(taxFilterBlackList, false);
jpayne@68: 					taxFilterBlack.setContainsString(taxFilterBlackString);
jpayne@68: 					if(requireTree){
jpayne@68: 						assert(SketchObject.taxtree!=null) : "No taxtree loaded.";
jpayne@68: 						taxFilterBlack.setTree(SketchObject.taxtree);
jpayne@68: 						taxFilterBlack.promote();
jpayne@68: 					}
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 			
jpayne@68: 			noFilters=(!hasMetaFilters() && !hasTaxFilters() && !requireSSU && minRefSizeEstimate<1 && minRefSizeBases<1);
jpayne@68: 			postParsed=true;
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public boolean postParsed(){return postParsed;}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public String toString(){
jpayne@68: 		return toString(-1);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public String toString(int chunkNum){
jpayne@68: 		StringBuilder sb=new StringBuilder();
jpayne@68: 		sb.append("##");
jpayne@68: 		sb.append("hits=").append(minHits);
jpayne@68: 		if(chunkNum>=0){sb.append(" chunk=").append(chunkNum);}
jpayne@68: 		sb.append(" wkid=").append(String.format(Locale.ROOT, "%.5f",minWKID));
jpayne@68: 		if(minANI>0){sb.append(" id=").append(String.format(Locale.ROOT, "%.5f",minANI));}
jpayne@68: 		if(minBases>0){sb.append(" minbases=").append(minBases);}
jpayne@68: 		if(minSizeRatio>0){sb.append(" minsizeratio=").append(String.format(Locale.ROOT, "%.5f",minSizeRatio));}
jpayne@68: 		sb.append(" records=").append(maxRecords);
jpayne@68: 		if(recordsPerLevel>0){sb.append(" recordsperlevel=").append(recordsPerLevel);}
jpayne@68: 		sb.append(" format=").append(format);
jpayne@68: 		sb.append(" level=").append(taxLevel);
jpayne@68: 		if(inputVersion!=null){sb.append(" bbversion=").append(inputVersion);}
jpayne@68: 		
jpayne@68: 		if(k!=SketchObject.defaultK || k2!=0 || k!=SketchObject.k || k2!=SketchObject.k2){
jpayne@68: 			assert(k>0 && k2>=0 && k2<k) : "Bad values for k: "+k+", "+k2+", "+SketchObject.k+", "+SketchObject.k2;
jpayne@68: 			assert(SketchObject.k>0 && SketchObject.k2>=0 && SketchObject.k2<SketchObject.k) : "Bad values for k: "+k+", "+k2+", "+SketchObject.k+", "+SketchObject.k2;
jpayne@68: 			sb.append(" hk=").append(SketchObject.k).append(',').append(SketchObject.k2);
jpayne@68: 		}
jpayne@68: 		if(SketchObject.amino){sb.append(" hamino=").append(SketchObject.amino);} //TODO: This conflicts with Parser flag
jpayne@68: 		if(SketchObject.translate){sb.append(" translate=").append(SketchObject.translate);}
jpayne@68: 		if(SketchObject.sixframes){sb.append(" sixframes=").append(SketchObject.sixframes);}
jpayne@68: 		if(SketchObject.HASH_VERSION>1){sb.append(" hashversion=").append(SketchObject.HASH_VERSION);}
jpayne@68: 
jpayne@68: 		if(true){sb.append(" printSSU=").append(printSSU());}
jpayne@68: 		if(requireSSU){sb.append(" requireSSU=").append(requireSSU);}
jpayne@68: 		if(minRefSizeEstimate>0){sb.append(" minRefSizeEstimate=").append(minRefSizeEstimate);}
jpayne@68: 		if(minRefSizeBases>0){sb.append(" minRefSizeBases=").append(minRefSizeBases);}
jpayne@68: 		
jpayne@68: 		if(json()){sb.append(" printSSUSequence=").append(printSSUSequence);}
jpayne@68: 		if(printSSULen){sb.append(" printSSULen=").append(printSSULen);}
jpayne@68: 		if(true || printTax!=default_printTax){sb.append(" printTax=").append(printTax);}
jpayne@68: //		if(true || printFileName!=default_printFileName){sb.append(" printfname=").append(printFileName);}
jpayne@68: 		if(true || printQueryFileName!=default_printQueryFileName){sb.append(" printqfname=").append(printQueryFileName);}
jpayne@68: 		if(true || printRefFileName!=default_printRefFileName){sb.append(" printrfname=").append(printRefFileName);}
jpayne@68: 		if(true || printOriginalName!=default_printOriginalName){sb.append(" pn0=").append(printOriginalName);}
jpayne@68: 		if(true || printImg!=default_printImg){sb.append(" printImg=").append(printImg);}
jpayne@68: 		if(true || printAni!=default_printAni){sb.append(" printAni=").append(printAni);}
jpayne@68: 		if(!printKID){sb.append(" printKID=").append(printKID);}
jpayne@68: 		if(!printWKID){sb.append(" printWKID=").append(printWKID);}
jpayne@68: 		if(true || printCompleteness!=default_printCompleteness){sb.append(" printCompleteness=").append(printCompleteness);}
jpayne@68: 
jpayne@68: 		if(true || printUnique!=default_printUnique){sb.append(" printUMatches=").append(printUnique);}
jpayne@68: 		if(true || printUnique2!=default_printUnique2){sb.append(" printUnique2=").append(printUnique2);}
jpayne@68: 		if(true || printUnique3!=default_printUnique3){sb.append(" printUnique3=").append(printUnique3);}
jpayne@68: 		if(true || printUContam!=default_printUContam){sb.append(" printUContam=").append(printUContam);}
jpayne@68: 		if(true || printNoHit!=default_printNoHit){sb.append(" printNoHit=").append(printNoHit);}
jpayne@68: 		if(true || printContam!=default_printContam){sb.append(" contam=").append(printContam);}
jpayne@68: 		if(true){sb.append(" contam2=").append(printContam2 ? TaxTree.extendedToLevel(contamLevel)+"" : "f");}
jpayne@68: 
jpayne@68: 		if(true || printScore!=default_printScore){sb.append(" printScore=").append(printScore);}
jpayne@68: 		if(true || printEValue!=default_printEValue){sb.append(" printEValue=").append(printEValue);}
jpayne@68: 		
jpayne@68: 		if(true || printDepth!=default_printDepth){sb.append(" printDepth=").append(printDepth);}
jpayne@68: 		if(true || printDepth2!=default_printDepth2){sb.append(" printDepth2=").append(printDepth2);}
jpayne@68: 		if(true || printActualDepth!=default_printActualDepth){sb.append(" printActualDepth=").append(printActualDepth);}
jpayne@68: 		if(true || printVolume!=default_printVolume){sb.append(" printVolume=").append(printVolume);}
jpayne@68: 		if(true || printRefHits!=default_printRefHits){sb.append(" printRefHits=").append(printRefHits);}
jpayne@68: 		
jpayne@68: 		if(true || printMatches!=default_printMatches){sb.append(" printMatches=").append(printMatches);}
jpayne@68: 		if(true || printLength!=default_printLength){sb.append(" printLength=").append(printLength);}
jpayne@68: 		if(true || printTaxID!=default_printTaxID){sb.append(" printTaxID=").append(printTaxID);}
jpayne@68: 		if(true || printGSize!=default_printGSize){sb.append(" printGSize=").append(printGSize);}
jpayne@68: 		if(true || gSizeKMG!=default_gSizeKMG){sb.append(" gSizeKMG=").append(gSizeKMG);}
jpayne@68: 		if(true || printGC!=default_printGC){sb.append(" printGC=").append(printGC);}
jpayne@68: 		if(true || printGKmers!=default_printGKmers){sb.append(" printGKmers=").append(printGKmers);}
jpayne@68: 		
jpayne@68: 		if(printCommonAncestor){sb.append(" printCommonAncestor=").append(printCommonAncestor);}
jpayne@68: 		if(printCommonAncestorLevel){sb.append(" printCommonAncestorLevel=").append(printCommonAncestorLevel);}
jpayne@68: 		
jpayne@68: 		if(true || printTaxName!=default_printTaxName){sb.append(" printTaxName=").append(printTaxName);}
jpayne@68: 		if(true || printGSeqs!=default_printGSeqs){sb.append(" printGSeqs=").append(printGSeqs);}
jpayne@68: 		if(true || printGBases!=default_printGBases){sb.append(" printGBases=").append(printGBases);}
jpayne@68: 		if(true || minEntropy!=default_minEntropy){sb.append(" minEntropy=").append(String.format(Locale.ROOT, "%.4f", minEntropy));}
jpayne@68: 		if(true || minProb!=default_minProb){sb.append(" minProb=").append(String.format(Locale.ROOT, "%.4f", minProb));}
jpayne@68: 		if(true || minQual!=default_minQual){sb.append(" minQual=").append((int)minQual);}
jpayne@68: 		if(jsonArray!=default_jsonArray){sb.append(" jsonArray=").append(jsonArray);}
jpayne@68: 		if(printD3!=default_printD3){sb.append(" d3=").append(printD3);}
jpayne@68: 		if(printD3){
jpayne@68: 			sb.append(" D3sizeMode=").append(D3sizeMode);
jpayne@68: 			sb.append(" D3LevelNodes=").append(D3LevelNodes);
jpayne@68: 		}
jpayne@68: 		if(comparator!=Comparison.scoreComparator){sb.append(" ").append(comparator.toString());}
jpayne@68: 		
jpayne@68: 		if(taxFilterWhiteList!=null || taxFilterWhiteString!=null){
jpayne@68: 			if(taxFilterWhiteList!=null){sb.append(" taxfilterwhitelist=").append(taxFilterWhiteList);}
jpayne@68: 			if(taxFilterWhiteString!=null){sb.append(" taxfilterwhitestring=").append(taxFilterWhiteString);}
jpayne@68: 			sb.append(" taxlevelwhite=").append(taxLevelWhite);
jpayne@68: 		}
jpayne@68: 		if(taxFilterBlackList!=null || taxFilterBlackString!=null){
jpayne@68: 			if(taxFilterBlackList!=null){sb.append(" taxfilterblacklist=").append(taxFilterBlackList);}
jpayne@68: 			if(taxFilterBlackString!=null){sb.append(" taxfilterblackstring=").append(taxFilterBlackString);}
jpayne@68: 			sb.append(" taxlevelblack=").append(taxLevelBlack);
jpayne@68: 		}
jpayne@68: 		if(banUnclassified){sb.append(" banunclassified");}
jpayne@68: 		if(banVirus){sb.append(" banvirus");}
jpayne@68: 		
jpayne@68: 		if(useTaxidName){sb.append(" useTaxidName=").append(useTaxidName);}
jpayne@68: 		if(useImgName){sb.append(" useImgName=").append(useImgName);}
jpayne@68: 		if(useTaxName){sb.append(" useTaxName=").append(useTaxName);}
jpayne@68: 		
jpayne@68: 		if(true){sb.append(" colors=").append(printColors ? TaxTree.extendedToLevel(colorLevel)+"" : "f");}
jpayne@68: 		
jpayne@68: 		if(minKeyOccuranceCount!=default_minKeyOccuranceCount){sb.append(" minKeyOccuranceCount=").append(minKeyOccuranceCount);}
jpayne@68: 		
jpayne@68: //		if(printColors && colorLevel!=default_colorLevel){sb.append(" colorLevel=").append(TaxTree.extendedToLevel(colorLevel));}
jpayne@68: 		
jpayne@68: 
jpayne@68: 		if(printRefDivisor){sb.append(" printRefDivisor=").append(printRefDivisor);}
jpayne@68: 		if(printQueryDivisor){sb.append(" printQueryDivisor=").append(printQueryDivisor);}
jpayne@68: 		if(printRefSize){sb.append(" printRefSize=").append(printRefSize);}
jpayne@68: 		if(printQuerySize){sb.append(" printQuerySize=").append(printQuerySize);}
jpayne@68: 		if(printContamHits){sb.append(" printContamHits=").append(printContamHits);}
jpayne@68: 		if(printIntersection){sb.append(" printIntersection=").append(printIntersection);}
jpayne@68: 		if(mergePairs){sb.append(" mergePairs=").append(mergePairs);}
jpayne@68: 		
jpayne@68: 		if(maxReads>-1){sb.append(" reads=").append(maxReads);}
jpayne@68: 		if(mode!=default_mode){sb.append(" mode=").append(mode);}
jpayne@68: 		if(samplerate!=default_samplerate){sb.append(" samplerate=").append(String.format(Locale.ROOT, "%.4f",samplerate));}
jpayne@68: 
jpayne@68: 		if(!requiredMetaAnd){sb.append(" requiredmetaand="+requiredMetaAnd);}
jpayne@68: 		if(requiredMeta!=null && !requiredMeta.isEmpty()){
jpayne@68: 			sb.append(" rmeta=");
jpayne@68: 			for(String s : requiredMeta){
jpayne@68: 				sb.append(s);
jpayne@68: 				sb.append(',');
jpayne@68: 			}
jpayne@68: 			sb.setLength(sb.length()-1);
jpayne@68: 		}
jpayne@68: 		if(bannedMeta!=null && !bannedMeta.isEmpty()){
jpayne@68: 			sb.append(" bmeta=");
jpayne@68: 			for(String s : bannedMeta){
jpayne@68: 				sb.append(s);
jpayne@68: 				sb.append(',');
jpayne@68: 			}
jpayne@68: 			sb.setLength(sb.length()-1);
jpayne@68: 		}
jpayne@68: //		if(requiredTaxid!=null && !requiredTaxid.isEmpty()){
jpayne@68: //			sb.append(" rtaxid=");
jpayne@68: //			for(int i=0; i<requiredTaxid.size; i++){
jpayne@68: //				sb.append(requiredTaxid.get(i));
jpayne@68: //				sb.append(',');
jpayne@68: //			}
jpayne@68: //			sb.setLength(sb.length()-1);
jpayne@68: //		}
jpayne@68: //		if(bannedTaxid!=null && !bannedTaxid.isEmpty()){
jpayne@68: //			sb.append(" btaxid=");
jpayne@68: //			for(int i=0; i<bannedTaxid.size; i++){
jpayne@68: //				sb.append(bannedTaxid.get(i));
jpayne@68: //				sb.append(',');
jpayne@68: //			}
jpayne@68: //			sb.setLength(sb.length()-1);
jpayne@68: //		}
jpayne@68: 		
jpayne@68: 		sb.append('\n');
jpayne@68: 		return sb.toString();
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public boolean compatible(){
jpayne@68: 		return SketchObject.k==k && SketchObject.k2==k2 && SketchObject.aminoOrTranslate()==aminoOrTranslate() && hashVersion==SketchObject.HASH_VERSION;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public void setPrintAll(){
jpayne@68: 		printSSU=true;
jpayne@68: 		printSSULen=true;
jpayne@68: 		printSSUSequence=true;
jpayne@68: 		printTax=true;
jpayne@68: 		printQueryFileName=true;
jpayne@68: 		printRefFileName=true;
jpayne@68: 		printOriginalName=true;
jpayne@68: 		printImg=true;
jpayne@68: 		printAni=true;
jpayne@68: 		printKID=true;
jpayne@68: 		printWKID=true;
jpayne@68: 		printCompleteness=true;
jpayne@68: 		printScore=true;
jpayne@68: 		printEValue=true;
jpayne@68: 		printDepth=true;
jpayne@68: 		printDepth2=true;
jpayne@68: 		printVolume=true;
jpayne@68: 		printRefHits=true;
jpayne@68: 		
jpayne@68: 		printMatches=true;
jpayne@68: 		printLength=true;
jpayne@68: 		printTaxID=true;
jpayne@68: 		printGSize=true;
jpayne@68: 		printGC=true;
jpayne@68: 		printGKmers=true;
jpayne@68: 		printTaxName=true;
jpayne@68: 		printGSeqs=true;
jpayne@68: 		printGBases=true;
jpayne@68: 		
jpayne@68: //		printColors=true;
jpayne@68: 
jpayne@68: 		printUnique=true;
jpayne@68: 		printUnique2=true;
jpayne@68: 		printUnique3=true;
jpayne@68: 		printUContam=true;
jpayne@68: 		printNoHit=true;
jpayne@68: 		printContam=true;
jpayne@68: 		printContam2=true;
jpayne@68: 		
jpayne@68: 		printRefDivisor=true;
jpayne@68: 		printQueryDivisor=true;
jpayne@68: 		printRefSize=true;
jpayne@68: 		printQuerySize=true;
jpayne@68: 		printContamHits=true;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------             JSON             ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	public JsonObject toJson(SketchResults sr){
jpayne@68: 		JsonObject j=toJson(sr.sketch);
jpayne@68: 		if(sr.list!=null){
jpayne@68: 			int i=0;
jpayne@68: 			for(Comparison c : sr.list){
jpayne@68: 				JsonObject jc=toJson(c);
jpayne@68: 				j.add(c.name(), jc);
jpayne@68: 				i++;
jpayne@68: 				if(i>=maxRecords){break;}
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		if(jsonArray){
jpayne@68: 			toJsonArrayForm(j);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		if(printD3){
jpayne@68: 			j.add("D3", toD3(sr));
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		return j;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public void toJsonArrayForm(JsonObject j0){
jpayne@68: 		if(j0.jmapSize()<1){return;}
jpayne@68: 		ArrayList<Object> list1=new ArrayList<Object>(j0.jmapSize());
jpayne@68: 		Object[] keys=null;
jpayne@68: 		for(Entry<String, JsonObject> e1 : j0.jmap.entrySet()){
jpayne@68: 			JsonObject j1=e1.getValue();
jpayne@68: 			ArrayList<Object> list2=new ArrayList<Object>(j1.omapSize());
jpayne@68: 			for(Entry<String, Object> e2 : j1.omap.entrySet()){
jpayne@68: 				Object o2=e2.getValue();
jpayne@68: 				list2.add(o2);
jpayne@68: 			}
jpayne@68: 			list1.add(list2.toArray());
jpayne@68: 			if(keys==null){
jpayne@68: 				ArrayList<Object> keyList=new ArrayList<Object>(j1.omapSize());
jpayne@68: 				for(Entry<String, Object> e2 : j1.omap.entrySet()){
jpayne@68: 					Object o2=e2.getKey();
jpayne@68: 					keyList.add(o2);
jpayne@68: 				}
jpayne@68: 				keys=keyList.toArray();
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		JsonObject title=new JsonObject();
jpayne@68: 		for(Entry<String, Object> e : j0.omap.entrySet()){
jpayne@68: 			title.add(e.getKey(), e.getValue());
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		j0.clearJson();
jpayne@68: 		j0.clearOmap();
jpayne@68: 
jpayne@68: 		j0.add("title", title);
jpayne@68: 		j0.add("header", keys);
jpayne@68: 		j0.add("rows", list1.toArray());
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public JsonObject toJson(Sketch sk){
jpayne@68: 		assert(format==FORMAT_JSON);
jpayne@68: 		
jpayne@68: 		JsonObject j=new JsonObject();
jpayne@68: 		j.add("Name", sk.name());
jpayne@68: 		if(dbName!=null){j.add("DB", dbName);}
jpayne@68: 		j.add("SketchLen", sk.length());
jpayne@68: 		
jpayne@68: 		j.add("Seqs", sk.genomeSequences);
jpayne@68: 		j.add("Bases", sk.genomeSizeBases);
jpayne@68: 		j.add("gSize", sk.genomeSizeEstimate());
jpayne@68: 		if(sk.baseCounts!=null){j.addLiteral("GC", sk.gc(), 3);}
jpayne@68: 		if(sk.probCorrect<1 && sk.probCorrect>0){j.add("Quality", sk.probCorrect);}
jpayne@68: 		if(sk.keyCounts!=null){
jpayne@68: 			double d=Tools.averageDouble(sk.keyCounts);
jpayne@68: 			j.add("AvgCount", d);
jpayne@68: 			j.add("Depth", Tools.observedToActualCoverage(d));
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		if(sk.imgID>0){j.add("IMG", sk.imgID);}
jpayne@68: 		if(sk.spid>0){j.add("spid", sk.spid);}
jpayne@68: 		if(sk.taxID>0 && sk.taxID<SketchObject.minFakeID){j.add("TaxID", sk.taxID);}
jpayne@68: 
jpayne@68: 		if((printRefFileName) && sk.fname()!=null){j.add("file", sk.fname());}
jpayne@68: 		if(printOriginalName && sk.name0()!=null){j.add("SeqName", sk.name0());}
jpayne@68: 		
jpayne@68: 		if(sk.meta!=null){
jpayne@68: 			for(String st : sk.meta){
jpayne@68: 				int colon=st.indexOf(':');
jpayne@68: 				j.add(st.substring(0,  colon), st.substring(colon+1));
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		if(printSSULen){
jpayne@68: 			if(sk.r16SLen()>0){j.add("16SLen", sk.r16SLen());}
jpayne@68: 			if(sk.r18SLen()>0){j.add("18SLen", sk.r18SLen());}
jpayne@68: 		}
jpayne@68: 		if(printSSUSequence){
jpayne@68: 			if(sk.r16S()!=null){j.add("16SSequence", new String(sk.r16S()));}
jpayne@68: 			if(sk.r18S()!=null){j.add("18SSequence", new String(sk.r18S()));}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		return j;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public JsonObject toJson(Comparison c){
jpayne@68: 		final int tid=c.taxID;
jpayne@68: 		
jpayne@68: 		JsonObject j=new JsonObject();
jpayne@68: 		
jpayne@68: 		//Text fields
jpayne@68: 		if(printTaxName){j.add("taxName", c.taxName()==null ? "." : c.taxName());}
jpayne@68: 		
jpayne@68: 		if(printCommonAncestor){j.add("commonAncestor", c.commonAncestor());}
jpayne@68: 		if(printCommonAncestorLevel){j.add("commonAncestorLevel", c.commonAncestorLevel());}
jpayne@68: 		
jpayne@68: 		if(printRefFileName){j.add("file", c.fname()==null ? "." : c.fname());}
jpayne@68: 		if(printOriginalName){j.add("seqName", c.name0()==null ? "." : c.name0());}
jpayne@68: 		if(printTax && SketchObject.taxtree!=null){
jpayne@68: 			TaxNode tn=null;
jpayne@68: 			if(tid>0 && tid<SketchObject.minFakeID){
jpayne@68: 				tn=SketchObject.taxtree.getNode(tid);
jpayne@68: 			}
jpayne@68: 
jpayne@68: 			if(tn!=null){
jpayne@68: 				j.add("taxonomy", SketchObject.taxtree.toSemicolon(tn, SketchObject.skipNonCanonical, false));
jpayne@68: 			}else{
jpayne@68: 				j.add("taxonomy", (Object)null);
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		if(printWKID){j.addLiteral("WKID", 100*c.wkid(), 4);}
jpayne@68: 		if(printKID){j.addLiteral("KID", 100*c.kid(), 4);}
jpayne@68: //		if(printSSU() && c.ssuIdentity()>0){j.addLiteral("SSU", 100*c.ssuIdentity(), 3);} //Old
jpayne@68: 		if(printSSU() && c.ssuIdentity()>0){
jpayne@68: 			j.addLiteral(c.ssuType()==18 ? "18S" : "16S", 100*c.ssuIdentity(), 3);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		//Primary fields
jpayne@68: 		if(printAni){j.addLiteral((aminoOrTranslate() ? "AAI" : "ANI"), 100*c.ani(), 3);}
jpayne@68: 		if(printCompleteness){j.addLiteral("Complt", 100*c.completeness(), 3);}
jpayne@68: 		if(printContam){j.addLiteral("Contam", 100*c.contamFraction(), 3);}
jpayne@68: 		if(printContam2){j.addLiteral("Contam2", 100*c.contam2Fraction(), 3);}
jpayne@68: 		if(printUContam){j.addLiteral("uContam", 100*c.uContamFraction(), 3);}
jpayne@68: 		if(printScore){j.add("Score", c.score());}
jpayne@68: 		if(printEValue){j.add("E-Val", String.format(Locale.ROOT, "%5.2e", c.eValue()));}
jpayne@68: 		
jpayne@68: 		if(printDepth){j.add("Depth", c.depth(printActualDepth));}
jpayne@68: 		if(printDepth2){j.add("Depth2", c.depth2(printActualDepth));}
jpayne@68: 		if(printVolume){j.add("Volume", c.volume()+0.001);}
jpayne@68: 		if(printRefHits){j.add("RefHits", c.avgRefHits());}
jpayne@68: 		
jpayne@68: 		if(printMatches){j.add("Matches", c.hits());}
jpayne@68: 		if(printUnique){j.add("Unique", c.uHits());}
jpayne@68: 		if(printUnique2){j.add("Unique2", c.unique2());}
jpayne@68: 		if(printUnique3){j.add("Unique3", c.unique3());}
jpayne@68: 		if(printNoHit){j.add("noHit", c.noHits());}
jpayne@68: 		if(printLength){j.add("Length", c.maxDivisor());}
jpayne@68: 		if(printTaxID){j.add("TaxID", tid>=SketchObject.minFakeID ? -1 : tid);}
jpayne@68: 		if(printImg){j.add("ImgID", c.imgID());}
jpayne@68: 		if(printGBases){j.add("gBases", c.genomeSizeBases());}
jpayne@68: 		if(printGKmers){j.add("gKmers", c.genomeSizeKmers());}
jpayne@68: 		if(printGSize){j.add("gSize", c.genomeSizeEstimate());}
jpayne@68: 		if(printGSeqs){j.add("gSeqs", c.genomeSequences());}
jpayne@68: 		if(c.hasGC()){j.addLiteral("GC", c.gc(), 3);}
jpayne@68: 		
jpayne@68: 		//Raw fields
jpayne@68: 		if(printRefDivisor){j.add("rDiv", c.refDivisor());}
jpayne@68: 		if(printQueryDivisor){j.add("qDiv", c.queryDivisor());}
jpayne@68: 		if(printRefSize){j.add("rSize", c.refSize());}
jpayne@68: 		if(printQuerySize){j.add("qSize", c.querySize());}
jpayne@68: 		if(printContamHits){j.add("cHits", c.contamHits());}
jpayne@68: 		
jpayne@68: 
jpayne@68: 
jpayne@68: 		if(printSSULen){
jpayne@68: 			if(c.has18S()){j.add("18SLen", c.b.r18SLen());}
jpayne@68: 			/*else*/ if(c.has16S()){j.add("16SLen", c.b.r16SLen());}
jpayne@68: 		}
jpayne@68: 		if(printSSUSequence){
jpayne@68: 			if(c.has18S()){j.add("18SSequence", new String(c.b.r18S()));}
jpayne@68: 			/*else*/ if(c.has16S()){j.add("16SSequence", new String(c.b.r16S()));}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		if(printIntersection){
jpayne@68: 			Sketch intersection=Sketch.intersection(c.a, c.b);
jpayne@68: 			j.add("intersection", intersection.toString());
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		return j;
jpayne@68: 	}
jpayne@68: 
jpayne@68: 	public boolean json(){return format==FORMAT_JSON;}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------              D3              ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	public JsonObject toD3(SketchResults sr){
jpayne@68: 		if(sr==null || sr.isEmpty()){return new JsonObject("name", "no hits");}
jpayne@68: 		JsonObject root=new JsonObject("name", "life");
jpayne@68: 		root.add("level", TaxTree.LIFE_E);
jpayne@68: 		if(sr.list!=null){
jpayne@68: 			int i=0;
jpayne@68: 			for(Comparison c : sr.list){
jpayne@68: 				ArrayList<JsonObject> tax=toD3List(c);
jpayne@68: 				addToLevel(root, tax, 0);
jpayne@68: 				i++;
jpayne@68: 				if(i>=maxRecords){break;}
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		if(D3LevelNodes){
jpayne@68: 			root=converToD3ArrayFormat_LevelNode(root);
jpayne@68: 		}else{
jpayne@68: 			root=converToD3ArrayFormat_SingleNodeRoot(root);
jpayne@68: 		}
jpayne@68: 		return root;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private JsonObject converToD3ArrayFormat_SingleNodeRoot(JsonObject root){
jpayne@68: 		JsonObject children=root.removeJson("children");
jpayne@68: 		if(children==null){return root;}
jpayne@68: 		Object[] array=children.toJmapArray();
jpayne@68: 		root=(JsonObject)array[0];//Life node
jpayne@68: 		
jpayne@68: 		assert(root.getString("name").equalsIgnoreCase("Life")) : root;
jpayne@68: 		return converToD3ArrayFormat_SingleNode(root);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private JsonObject converToD3ArrayFormat_SingleNode(JsonObject nameNode){
jpayne@68: 		Object[] levelNodes=nameNode.toJmapArray();
jpayne@68: 		if(levelNodes==null){return nameNode;}
jpayne@68: 		nameNode.clearJson();
jpayne@68: 		
jpayne@68: 		ArrayList<JsonObject> fixed=new ArrayList<JsonObject>();
jpayne@68: 		for(Object o : levelNodes){
jpayne@68: 			JsonObject levelNode=(JsonObject)o;
jpayne@68: 			String level=levelNode.getString("name");
jpayne@68: 			JsonObject children=levelNode.removeJson("children");
jpayne@68: 			if(children!=null){
jpayne@68: 				Object[] childArray=children.toJmapArray();
jpayne@68: 				for(Object o2 : childArray){
jpayne@68: 					JsonObject child=(JsonObject)o2;//Now a name node
jpayne@68: 					String name=(String)child.removeObject("name");
jpayne@68: 					child.add("name", level+": "+name);
jpayne@68: 					converToD3ArrayFormat_SingleNode(child);
jpayne@68: 					fixed.add(child);
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		Object[] children=fixed.toArray();
jpayne@68: 		nameNode.add("children", children);
jpayne@68: 		return nameNode;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private JsonObject converToD3ArrayFormat_LevelNode(JsonObject levelNode){
jpayne@68: 		JsonObject children=levelNode.removeJson("children");
jpayne@68: 		if(children==null){return levelNode;}
jpayne@68: 		
jpayne@68: 		Object[] array=children.toJmapArray();
jpayne@68: 		levelNode.add("children", array);
jpayne@68: 		for(Object o : array){
jpayne@68: 			converToD3ArrayFormat_NameNode((JsonObject)o);
jpayne@68: 		}
jpayne@68: 		return levelNode;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private JsonObject converToD3ArrayFormat_NameNode(JsonObject nameNode){
jpayne@68: 		Object[] array=nameNode.toJmapArray();
jpayne@68: 		if(array==null){return nameNode;}
jpayne@68: 		
jpayne@68: 		nameNode.clearJson();
jpayne@68: 		nameNode.add("children", array);
jpayne@68: 		for(Object o : array){
jpayne@68: 			converToD3ArrayFormat_LevelNode((JsonObject)o);
jpayne@68: 		}
jpayne@68: 		return nameNode;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	void addToLevel(JsonObject levelNode, ArrayList<JsonObject> list, int pos){
jpayne@68: 		JsonObject jo=list.get(pos);
jpayne@68: 		int rootLevel=levelNode.getInt("level");
jpayne@68: 		int joLevel=jo.getInt("level");
jpayne@68: 		if(rootLevel==joLevel){
jpayne@68: 			assert(levelNode.getString("name").equalsIgnoreCase(jo.getString("levelname"))) : levelNode+"\n"+jo;
jpayne@68: 			addAsChild(levelNode, list, pos);
jpayne@68: 		}else{
jpayne@68: 			assert(joLevel<rootLevel) : levelNode+"\n"+jo;
jpayne@68: 			assert(false) : levelNode+"\n"+jo;
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 		
jpayne@68: 	void addAsChild(JsonObject levelNode, ArrayList<JsonObject> list, int pos){
jpayne@68: 		JsonObject children=levelNode.getJson("children");
jpayne@68: 		if(children==null){
jpayne@68: 			children=new JsonObject();
jpayne@68: 			levelNode.add("children", children);
jpayne@68: 		}
jpayne@68: 		JsonObject jo=list.get(pos);
jpayne@68: 		String taxName=jo.getString("name");
jpayne@68: 		JsonObject nameNode=children.getJson(taxName);
jpayne@68: 		if(nameNode==null){
jpayne@68: 			nameNode=new JsonObject("name", taxName);
jpayne@68: 			children.add(taxName, nameNode);
jpayne@68: 		}
jpayne@68: 		Number size=jo.getNumber("size");
jpayne@68: 		Number oldSize=nameNode.getNumber("size");
jpayne@68: 		if(size!=null && (oldSize==null || oldSize.doubleValue()<size.doubleValue())){
jpayne@68: 			nameNode.add("size", jo.getNumber("size"));
jpayne@68: 			nameNode.add("kid", jo.getNumber("kid"));
jpayne@68: 			nameNode.add("wkid", jo.getNumber("wkid"));
jpayne@68: 			nameNode.add("ani", jo.getNumber("ani"));
jpayne@68: 			nameNode.add("hits", jo.getNumber("hits"));
jpayne@68: 			nameNode.add("depth", jo.getNumber("depth"));
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		if(pos<list.size()-1){//recur
jpayne@68: 			jo=list.get(pos+1);
jpayne@68: 			String levelName=jo.getString("levelname");
jpayne@68: 			int level=jo.getInt("level");
jpayne@68: 			JsonObject nextLevelNode=nameNode.getJson(levelName);
jpayne@68: 			if(nextLevelNode==null){
jpayne@68: 				nextLevelNode=new JsonObject("name", levelName);
jpayne@68: 				nextLevelNode.add("level", level);
jpayne@68: 				nameNode.add(levelName, nextLevelNode);
jpayne@68: 			}
jpayne@68: 			addAsChild(nextLevelNode, list, pos+1);
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	int promote(int levelE) {
jpayne@68: 		if(levelE<0){return levelE;}
jpayne@68: 		while(!TaxTree.isSimple2(levelE) && levelE<TaxTree.LIFE){
jpayne@68: 			levelE++;
jpayne@68: 		}
jpayne@68: 		return levelE;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public ArrayList<JsonObject> toD3List(Comparison c){
jpayne@68: 		final ArrayList<TaxNode> nodes=toTNList(c.taxID);
jpayne@68: 		ArrayList<JsonObject> list=new ArrayList<JsonObject>(nodes.size());
jpayne@68: 		for(TaxNode tn : nodes){
jpayne@68: 			JsonObject jo=new JsonObject("name", tn.name);
jpayne@68: 			int levelE=promote(tn.levelExtended);
jpayne@68: 			jo.add("level", levelE);
jpayne@68: 			jo.add("levelname", TaxTree.levelToStringExtended(levelE));
jpayne@68: 			list.add(jo);
jpayne@68: 		}
jpayne@68: 		if(list.size()>0){
jpayne@68: 			JsonObject tail=list.get(list.size()-1);
jpayne@68: 			tail.add("size", toD3Size(c));
jpayne@68: 			tail.add("kid", c.kid());
jpayne@68: 			tail.add("wkid", c.wkid());
jpayne@68: 			tail.add("ani", c.ani());
jpayne@68: 			tail.add("hits", c.hits());
jpayne@68: 			tail.add("depth", c.depth(printActualDepth));
jpayne@68: 		}
jpayne@68: 		return list;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private Number toD3Size(Comparison c){
jpayne@68: 		if(D3sizeMode==D3_ANI_SIZE){
jpayne@68: 			return c.ani();
jpayne@68: 		}else if(D3sizeMode==D3_KID_SIZE){
jpayne@68: 			return c.kid();
jpayne@68: 		}else if(D3sizeMode==D3_WKID_SIZE){
jpayne@68: 			return c.wkid();
jpayne@68: 		}else if(D3sizeMode==D3_HIT_SIZE){
jpayne@68: 			return c.hits();
jpayne@68: 		}else if(D3sizeMode==D3_DEPTH_SIZE){
jpayne@68: 			return c.depth(printActualDepth);
jpayne@68: 		}
jpayne@68: 		assert(false) : "Invalid D3sizeMode "+D3sizeMode;
jpayne@68: 		return c.hits();
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public ArrayList<TaxNode> toTNList(final int tid){
jpayne@68: 		final TaxTree tree=TaxTree.getTree();
jpayne@68: 		
jpayne@68: 		final ArrayList<TaxNode> list=new ArrayList<TaxNode>();
jpayne@68: 		int nulls=0;
jpayne@68: 		{
jpayne@68: 			TaxNode tn=tree.getNode(tid);
jpayne@68: 			if(tn.isRanked() && !tn.cellularOrganisms()){list.add(tn);}
jpayne@68: 			while(tn.pid!=tn.id){
jpayne@68: 				tn=tree.getNode(tn.pid);
jpayne@68: 				if(tn.isRanked() && !tn.cellularOrganisms()){list.add(tn);}
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		Collections.reverse(list);
jpayne@68: 		int prevLevelE=TaxTree.LIFE;
jpayne@68: 		for(int i=0; i<list.size(); i++){
jpayne@68: 			TaxNode tn=list.get(i);
jpayne@68: 			int levelE=promote(tn.levelExtended);
jpayne@68: 			
jpayne@68: 			if(!TaxTree.isSimple2(levelE) || (i>0 && levelE>=prevLevelE)){
jpayne@68: 				list.set(i, null);
jpayne@68: 				nulls++;
jpayne@68: 			}else{prevLevelE=levelE;}
jpayne@68: 		}
jpayne@68: 		if(nulls>0){Tools.condenseStrict(list);}
jpayne@68: 		return list;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------          Formatting          ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 
jpayne@68: 	ByteBuilder queryHeader(Sketch sk){
jpayne@68: 		ByteBuilder bb=new ByteBuilder();
jpayne@68: 		if(format>2){return bb;}
jpayne@68: 		
jpayne@68: 		String color=toColor(sk.taxID);
jpayne@68: 		if(color!=null){bb.append(color);}
jpayne@68: 		
jpayne@68: 		bb.append("\nQuery: ").append(sk.name()==null ? "." : sk.name());
jpayne@68: 		if(dbName!=null){bb.append("\tDB: ").append(dbName);}
jpayne@68: 		bb.append("\tSketchLen: ").append(sk.length());
jpayne@68: 		bb.append("\tSeqs: ").append(sk.genomeSequences).append(' ');
jpayne@68: 		bb.append("\t"+(aminoOrTranslate() ? "SeqLen" : "Bases")+": ").append(sk.genomeSizeBases);
jpayne@68: 		bb.append("\tgSize: ").append(sk.genomeSizeEstimate());
jpayne@68: 		if(sk.baseCounts!=null){bb.append("\tGC: ").append(sk.gc(), 3);}
jpayne@68: 		if(sk.probCorrect<1 && sk.probCorrect>0){bb.append("\tQuality: ").append(sk.probCorrect, 4);}
jpayne@68: 		if(sk.keyCounts!=null){
jpayne@68: 			double d=Tools.averageDouble(sk.keyCounts);
jpayne@68: 			bb.append("\tAvgCount: ").append(d, 3);
jpayne@68: 			bb.append("\tDepth: ").append(Tools.observedToActualCoverage(d), 3);
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		if(sk.imgID>0){bb.append("\tIMG: ").append(sk.imgID);}
jpayne@68: 		if(sk.spid>0){bb.append("\tspid: ").append(sk.spid);}
jpayne@68: 		if(sk.taxID>0 && sk.taxID<SketchObject.minFakeID){bb.append("\tTaxID: ").append(sk.taxID);}
jpayne@68: 
jpayne@68: 		if(printQueryFileName && sk.fname()!=null){bb.append("\tFile: "+sk.fname());}
jpayne@68: 		if(printOriginalName && sk.name0()!=null && !sk.name0().equals(sk.name())){bb.append("\tSeqName: "+sk.name0());}
jpayne@68: 		
jpayne@68: 		if(sk.meta!=null){
jpayne@68: 			for(String st : sk.meta){
jpayne@68: 				bb.append("\t").append(st.replaceFirst(":", ": "));
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		if(color!=null){bb.append(Colors.RESET);}
jpayne@68: 		
jpayne@68: 		return bb;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	int toColorTid(final int taxID){
jpayne@68: 		if(!printColors || SketchObject.taxtree==null || taxID<=0 || taxID>=SketchObject.minFakeID){return 0;}
jpayne@68: 		TaxNode tn=SketchObject.taxtree.getNode(taxID);
jpayne@68: 		while(tn!=null && tn.id!=tn.pid && tn.levelExtended<colorLevel){
jpayne@68: 			tn=SketchObject.taxtree.getNode(tn.pid);
jpayne@68: //			System.err.println(tn);
jpayne@68: 		}
jpayne@68: 		return tn==null || tn.levelExtended>=TaxTree.LIFE_E || (tn.levelExtended>colorLevel && tn.levelExtended>TaxTree.PHYLUM_E) ? 0 : tn.id;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	String toColor(final int taxID){
jpayne@68: 		if(!printColors || SketchObject.taxtree==null || taxID<=0 || taxID>=SketchObject.minFakeID){return null;}
jpayne@68: 		TaxNode tn=SketchObject.taxtree.getNode(taxID);
jpayne@68: 		while(tn!=null && tn.id!=tn.pid && tn.levelExtended<colorLevel){
jpayne@68: 			tn=SketchObject.taxtree.getNode(tn.pid);
jpayne@68: //			System.err.println(tn);
jpayne@68: 		}
jpayne@68: 		if(tn==null){
jpayne@68: 			return null;
jpayne@68: 		}else{
jpayne@68: 			if(tn.levelExtended>=TaxTree.LIFE_E || (tn.levelExtended>colorLevel && tn.levelExtended>TaxTree.PHYLUM_E)){return Colors.WHITE;}
jpayne@68: 			else{
jpayne@68: //				System.err.println("*"+tn.id+", "+tn.id%Colors.colorArray.length);
jpayne@68: 				return Colors.colorArray[tn.id%Colors.colorArray.length];
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	String header(){
jpayne@68: 		if(format==FORMAT_JSON){return null;}
jpayne@68: 		final String ani=(aminoOrTranslate() ? "AAI" : "ANI");
jpayne@68: 		if(format==FORMAT_QUERY_REF_ANI || format==FORMAT_CONSTELLATION){
jpayne@68: 			if(reportAniOnly){return "#Query\tRef\t"+ani;}
jpayne@68: 			if(format==FORMAT_QUERY_REF_ANI){
jpayne@68: 				return "#Query\tRef\t"+ani+
jpayne@68: 				"\tQSize\tRefSize\tQBases\tRBases"+
jpayne@68: 				(printTaxID ? "\tQTaxID\tRTaxID" : "")+(printKID ? "\tKID" : "")+(printWKID ? "\tWKID" : "")+
jpayne@68: 				(printSSU() ? "\tSSU" : "")+(printCommonAncestorLevel ? "\tCALevel" : "");
jpayne@68: 			}
jpayne@68: 			if(format==FORMAT_CONSTELLATION){return "#Query\tRef\tKID\tWKID\t"+ani+"\tCmplt\tQSize\tRefSize\tQBases\tRefBases";}
jpayne@68: 		}
jpayne@68: 		return columnwiseHeader();
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	String columnwiseHeader(){
jpayne@68: 		final String ani=(aminoOrTranslate() ? "AAI" : "ANI");
jpayne@68: 		
jpayne@68: 		StringBuilder sb=new StringBuilder();
jpayne@68: 		
jpayne@68: 		//Numeric fields
jpayne@68: 		if(printKID){sb.append("WKID\t");}
jpayne@68: 		if(printWKID){sb.append("KID\t");}
jpayne@68: 		if(printAni){sb.append(ani+"\t");}
jpayne@68: 		if(printSSU()){sb.append("SSU\t");}
jpayne@68: 		if(printSSULen){sb.append("SSULen\t");}
jpayne@68: 		if(printCompleteness){sb.append("Complt\t");}
jpayne@68: 		if(printContam){sb.append("Contam\t");}
jpayne@68: 		if(printContam2){sb.append("Contam2\t");}
jpayne@68: 		if(printUContam){sb.append("uContam\t");}
jpayne@68: 		if(printScore){sb.append("Score\t");}
jpayne@68: 		if(printEValue){sb.append("E-Val\t");}
jpayne@68: 		
jpayne@68: 		if(printDepth){sb.append("Depth\t");}
jpayne@68: 		if(printDepth2){sb.append("Depth2\t");}
jpayne@68: 		if(printVolume){sb.append("Volume\t");}
jpayne@68: 		if(printRefHits){sb.append("RefHits\t");}
jpayne@68: 		if(printMatches){sb.append("Matches\t");}
jpayne@68: 		if(printUnique){sb.append("Unique\t");}
jpayne@68: 		if(printUnique2){sb.append("Unique2\t");}
jpayne@68: 		if(printUnique3){sb.append("Unique3\t");}
jpayne@68: 		if(printNoHit){sb.append("noHit\t");}
jpayne@68: 		if(printLength){sb.append("Length\t");}
jpayne@68: 		if(printTaxID){sb.append("TaxID\t");}
jpayne@68: 		if(printImg){sb.append("ImgID    \t");}
jpayne@68: 		if(printGBases){sb.append("gBases\t");}
jpayne@68: 		if(printGKmers){sb.append("gKmers\t");}
jpayne@68: 		if(printGSize){sb.append("gSize\t");}
jpayne@68: 		if(printGSeqs){sb.append("gSeqs\t");}
jpayne@68: 		if(printGC){sb.append("GC\t");}
jpayne@68: 		
jpayne@68: 		
jpayne@68: 		//Raw fields
jpayne@68: 		if(printRefDivisor){sb.append("rDiv\t");}
jpayne@68: 		if(printQueryDivisor){sb.append("qDiv\t");}
jpayne@68: 		if(printRefSize){sb.append("rSize\t");}
jpayne@68: 		if(printQuerySize){sb.append("qSize\t");}
jpayne@68: 		if(printContamHits){sb.append("cHits\t");}
jpayne@68: 		
jpayne@68: 		//Text fields
jpayne@68: 		if(printCommonAncestor){sb.append("CA\t");}
jpayne@68: 		if(printCommonAncestorLevel){sb.append("CALevel\t");}
jpayne@68: 		if(printTaxName){sb.append("taxName\t");}
jpayne@68: 		if(printRefFileName){sb.append("file\t");}
jpayne@68: 		if(printOriginalName){sb.append("seqName\t");}
jpayne@68: 		if(printTax && SketchObject.taxtree!=null){sb.append("taxonomy\t");}
jpayne@68: 		
jpayne@68: 		if(sb.length()>1){sb.setLength(sb.length()-1);}//trim trailing tab
jpayne@68: 		
jpayne@68: 		return sb.toString();
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	void formatComparisonColumnwise(Comparison c, ByteBuilder bb, int prevTid){
jpayne@68: 		final int tid=c.taxID;
jpayne@68: 		boolean reset=false;
jpayne@68: 		
jpayne@68: 		if(printColors){
jpayne@68: 			final int ctid=toColorTid(tid);
jpayne@68: 			final int prevCtid=toColorTid(prevTid);
jpayne@68: 
jpayne@68: 			final int cnum=ctid%Colors.colorArray.length;
jpayne@68: 			final int prevCnum=prevCtid%Colors.colorArray.length;
jpayne@68: 
jpayne@68: 			String color=toColor(tid);
jpayne@68: 			String underline=(printColors && cnum==prevCnum && ctid!=prevCtid && (ctid>1 && prevCtid>1) ? Colors.UNDERLINE : null);
jpayne@68: 
jpayne@68: 			if(color!=null){bb.append(color);}
jpayne@68: 			if(underline!=null){bb.append(underline);}
jpayne@68: 			reset=(color!=null || underline!=null);
jpayne@68: 			
jpayne@68: //			System.err.println((color==null ? "" : color)+(underline==null ? "" : underline)+
jpayne@68: //					tid+", "+prevTid+";     \t"+ctid+", "+prevCtid+";     \t"+cnum+", "+prevCnum+"; \t"+((underline!=null)+"")+Colors.RESET);
jpayne@68: //			System.err.println(color==null ? "null" : color.substring(1));
jpayne@68: 		}
jpayne@68: 		
jpayne@68: //		sb.append(String.format(Locale.ROOT, "%.2f%%\t%.2f%%", 100*c.idMinDivisor(), 100*c.idMaxDivisor()));
jpayne@68: 		if(printWKID){bb.append(100*c.wkid(), 2).append('%').tab();}
jpayne@68: 		if(printKID){bb.append(100*c.kid(), 2).append('%');}
jpayne@68: 		
jpayne@68: //		if(printAni){sb.append(String.format(Locale.ROOT, "\t%.2f%%", 100*c.ani()));}
jpayne@68: //		if(printCompleteness){sb.append(String.format(Locale.ROOT, "\t%.2f%%", 100*c.completeness()));}
jpayne@68: //		if(printContam){sb.append(String.format(Locale.ROOT, "\t%.2f%%", 100*c.contamFraction()));}
jpayne@68: //		if(printContam2){sb.append(String.format(Locale.ROOT, "\t%.2f%%", 100*c.contam2Fraction()));}
jpayne@68: //		if(printUContam){sb.append(String.format(Locale.ROOT, "\t%.2f%%", 100*c.uContamFraction()));}
jpayne@68: 		
jpayne@68: 		if(printAni){bb.tab().append(100*c.ani(), 2).append('%');}
jpayne@68: 		if(printSSU()){
jpayne@68: 			float id=100*c.ssuIdentity();
jpayne@68: 			if(id>0){
jpayne@68: 				bb.tab().append(id, 2).append(c.ssuType()==16 ? '%' : '*'); //This is where 16S and 18S are differentiated
jpayne@68: 			}else{
jpayne@68: 				bb.tab().append('.');
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		if(printSSULen){
jpayne@68: 			bb.tab().append(c.ssuLen());
jpayne@68: 		}
jpayne@68: 		if(printCompleteness){bb.tab().append(100*c.completeness(), 2).append('%');}
jpayne@68: 		if(printContam){bb.tab().append(100*c.contamFraction(), 2).append('%');}
jpayne@68: 		if(printContam2){bb.tab().append(100*c.contam2Fraction(), 2).append('%');}
jpayne@68: 		if(printUContam){bb.tab().append(100*c.uContamFraction(), 2).append('%');}
jpayne@68: 		if(printScore){bb.tab().append(c.scoreS());}
jpayne@68: 		if(printEValue){bb.tab().append(String.format(Locale.ROOT, "%5.2e", c.eValue()));}
jpayne@68: 		
jpayne@68: 		if(printDepth){bb.tab().append(c.depthS(printActualDepth));}
jpayne@68: 		if(printDepth2){bb.tab().append(c.depth2S(printActualDepth));}
jpayne@68: 		if(printVolume){bb.tab().append(c.volumeS());}
jpayne@68: 		if(printRefHits){bb.tab().append(c.avgRefHitsS());}
jpayne@68: 		
jpayne@68: 		if(printMatches){bb.tab().append(c.hits());}
jpayne@68: 		if(printUnique){bb.tab().append(c.uHits());}
jpayne@68: 		if(printUnique2){bb.tab().append(c.unique2());}
jpayne@68: 		if(printUnique3){bb.tab().append(c.unique3());}
jpayne@68: 		if(printNoHit){bb.tab().append(c.noHits());}
jpayne@68: 		if(printLength){bb.tab().append( c.maxDivisor());}
jpayne@68: 		if(printTaxID){bb.tab().append(tid>=SketchObject.minFakeID ? -1 : tid);}
jpayne@68: 		if(printImg){bb.tab().append(c.imgID());}
jpayne@68: 		if(printGBases){appendKMG(c.genomeSizeBases(), bb);}
jpayne@68: 		if(printGKmers){appendKMG(c.genomeSizeKmers(), bb);}
jpayne@68: 		if(printGSize){appendKMG(c.genomeSizeEstimate(), bb);}
jpayne@68: 		if(printGSeqs){appendKMG(c.genomeSequences(), bb);}
jpayne@68: 		if(printGC){bb.tab().append(c.gc(),3);}
jpayne@68: 		
jpayne@68: 		//Raw fields
jpayne@68: 		if(printRefDivisor){bb.tab().append(c.refDivisor());}
jpayne@68: 		if(printQueryDivisor){bb.tab().append(c.queryDivisor());}
jpayne@68: 		if(printRefSize){bb.tab().append(c.refSize());}
jpayne@68: 		if(printQuerySize){bb.tab().append(c.querySize());}
jpayne@68: 		if(printContamHits){bb.tab().append(c.contamHits());}
jpayne@68: 		
jpayne@68: 		//Text fields
jpayne@68: 		if(printCommonAncestor){bb.tab().append(c.commonAncestor());}
jpayne@68: 		if(printCommonAncestorLevel){bb.tab().append(c.commonAncestorLevel());}
jpayne@68: 		if(printTaxName){bb.tab().append(c.taxName()==null ? "." : c.taxName());}
jpayne@68: 		if(printRefFileName){bb.tab().append(c.fname()==null ? "." : c.fname());}
jpayne@68: 		if(printOriginalName){bb.tab().append(c.name0()==null ? "." : c.name0());}
jpayne@68: 		if(printTax && SketchObject.taxtree!=null){
jpayne@68: 			bb.tab();
jpayne@68: 			TaxNode tn=null;
jpayne@68: 			if(tid>0 && tid<SketchObject.minFakeID){
jpayne@68: 				tn=SketchObject.taxtree.getNode(tid);
jpayne@68: 			}
jpayne@68: 
jpayne@68: 			if(tn!=null){
jpayne@68: 				bb.append(SketchObject.taxtree.toSemicolon(tn, SketchObject.skipNonCanonical, false));
jpayne@68: 			}else{
jpayne@68: 				bb.append('.');
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		if(printTaxName && !printOriginalName && !printRefFileName && c.taxName()==null && c.name0()!=null){bb.tab().append(c.name0());} //Extra column
jpayne@68: 		
jpayne@68: 		if(reset){bb.append(Colors.RESET);}
jpayne@68: 		
jpayne@68: 		bb.append('\n');
jpayne@68: 		
jpayne@68: 		if(printIntersection){
jpayne@68: 			Sketch intersection=Sketch.intersection(c.a, c.b);
jpayne@68: 			bb.append(intersection.toString());
jpayne@68: 			bb.append('\n');
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	void appendKMG(long value, ByteBuilder bb){
jpayne@68: 		if(gSizeKMG){
jpayne@68: 			bb.tab().append(toKMG(value));
jpayne@68: 		}else{
jpayne@68: 			bb.tab().append(value);
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	String toKMG(long value){
jpayne@68: 		if(value<10000000L){return Long.toString(value);}
jpayne@68: 		value+=5;
jpayne@68: 		if(value<1000000000L){return value/1000L+"K";}
jpayne@68: 		if(value<1000000000000L){return value/1000000L+"M";}
jpayne@68: 		if(value<1000000000000000L){return value/1000000000L+"G";}
jpayne@68: 		return value/1000000000000L+"T";
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	void formatComparison3Column(Comparison c, ByteBuilder sb, int prevTid){
jpayne@68: 		Sketch query=c.a;
jpayne@68: 		final long sea=Tools.max(1, c.a.genomeSizeEstimate());
jpayne@68: 		final long seb=Tools.max(1, c.b.genomeSizeEstimate());
jpayne@68: 		final long ba=Tools.max(1, c.a.genomeSizeBases);
jpayne@68: 		final long bb=Tools.max(1, c.b.genomeSizeBases);
jpayne@68: 		final String qName=format==FORMAT_CONSTELLATION ? (useFilePrefixName ? query.filePrefix() : ""+query.sketchID) : useTaxidName ? ""+query.taxID :
jpayne@68: 			useImgName ?  ""+query.imgID : useTaxName ? query.taxName() : query.name();
jpayne@68: 		final String rName=format==FORMAT_CONSTELLATION ? (useFilePrefixName ? c.b.filePrefix() : ""+c.b.sketchID) : useTaxidName ? ""+c.taxID() :
jpayne@68: 			useImgName ?  ""+c.imgID() : useTaxName ? c.taxName() : c.name();
jpayne@68: 		final int tid=c.taxID;
jpayne@68: 		boolean reset=false;
jpayne@68: 		
jpayne@68: 		sb.append(qName).append('\t');
jpayne@68: 		if(printColors){
jpayne@68: 			final int ctid=toColorTid(tid);
jpayne@68: 			final int prevCtid=toColorTid(prevTid);
jpayne@68: 
jpayne@68: 			final int cnum=ctid%Colors.colorArray.length;
jpayne@68: 			final int prevCnum=prevCtid%Colors.colorArray.length;
jpayne@68: 
jpayne@68: 			String color=toColor(tid);
jpayne@68: 			String underline=(printColors && cnum==prevCnum && ctid!=prevCtid && (ctid>1 && prevCtid>1) ? Colors.UNDERLINE : null);
jpayne@68: 
jpayne@68: 			if(color!=null){sb.append(color);}
jpayne@68: 			if(underline!=null){sb.append(underline);}
jpayne@68: 			reset=(color!=null || underline!=null);
jpayne@68: 			
jpayne@68: //			System.err.println((color==null ? "" : color)+(underline==null ? "" : underline)+
jpayne@68: //					tid+", "+prevTid+";     \t"+ctid+", "+prevCtid+";     \t"+cnum+", "+prevCnum+"; \t"+((underline!=null)+"")+Colors.RESET);
jpayne@68: //			System.err.println(color==null ? "null" : color.substring(1));
jpayne@68: 		}
jpayne@68: 
jpayne@68: //		sb.append(rName).append(String.format(Locale.ROOT, "\t%.2f\t%.3f", 100*c.ani(), sea/(float)seb));
jpayne@68: //		sb.append(rName).append(String.format(Locale.ROOT, "\t%.2f\t%d\t%d\t%d", 100*c.ani(), sea, seb, ba));
jpayne@68: 		
jpayne@68: 		//"#Query\tRef\tKID\tWKID\tANI\tCmplt\tQSize\tRefSize\tQBases\tRefBases";
jpayne@68: 
jpayne@68: 		float kid=100*c.kid();
jpayne@68: 		float wkid=100*c.wkid();
jpayne@68: 		float ani=100*c.ani();
jpayne@68: 		float complt=100*c.completeness();
jpayne@68: 		float ssu=printSSU() ? 100*c.ssuIdentity() : 0;
jpayne@68: 		
jpayne@68: 		sb.append(rName).append('\t');
jpayne@68: 		if(reportAniOnly){
jpayne@68: 			sb.append(ani, 3).append('\t');
jpayne@68: 		}else if(format==FORMAT_CONSTELLATION){
jpayne@68: 			sb.append(kid, 3).append('\t');
jpayne@68: 			sb.append(wkid, 3).append('\t');
jpayne@68: 			sb.append(ani, 3).append('\t');
jpayne@68: 			sb.append(complt, 3).append('\t');
jpayne@68: 			sb.append(sea).append('\t');
jpayne@68: 			sb.append(seb).append('\t');
jpayne@68: //			sb.append(ba).append('\t');
jpayne@68: //			sb.append(bb).append('\t');
jpayne@68: 		}else{
jpayne@68: 			sb.append(ani, 3).append('\t');
jpayne@68: 			sb.append(sea).append('\t');
jpayne@68: 			sb.append(seb).append('\t');
jpayne@68: 			sb.append(ba).append('\t');
jpayne@68: 			sb.append(bb).append('\t');
jpayne@68: 			if(printTaxID){sb.append(c.a.taxID).append('\t');}
jpayne@68: 			if(printTaxID){sb.append(c.b.taxID).append('\t');}
jpayne@68: 			if(printKID){sb.append(kid, 3).append('\t');}
jpayne@68: 			if(printWKID){sb.append(wkid, 3).append('\t');}
jpayne@68: 			if(printSSU()){
jpayne@68: 				if(ssu>0){
jpayne@68: 					sb.append(ssu, 3).append('\t');
jpayne@68: 				}else{
jpayne@68: 					sb.append('.').append('\t');
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 			if(printCommonAncestorLevel){sb.append(c.commonAncestorLevel()).append('\t');}
jpayne@68: 		}
jpayne@68: 		sb.setLength(sb.length()-1);
jpayne@68: 		if(reset){sb.append(Colors.RESET);}
jpayne@68: 		
jpayne@68: 		sb.append('\n');
jpayne@68: 		
jpayne@68: //		System.err.println(sb);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	void formatComparison(Comparison c, ByteBuilder sb, int prevTaxID){
jpayne@68: 		if(format==FORMAT_MULTICOLUMN){
jpayne@68: 			formatComparisonColumnwise(c, sb, prevTaxID);
jpayne@68: 			return;
jpayne@68: 		}else if(format==FORMAT_QUERY_REF_ANI || format==FORMAT_CONSTELLATION){
jpayne@68: 			formatComparison3Column(c, sb, prevTaxID);
jpayne@68: 			return;
jpayne@68: 		}
jpayne@68: 		String complt=(printCompleteness ? String.format(Locale.ROOT, "\tcomplt %.2f%%%%", 100*c.completeness()) : "");
jpayne@68: 		String contam=(printContam ? String.format(Locale.ROOT, "\tcontam %.2f%%%%", 100*c.contamFraction()) : "");
jpayne@68: //		String score=(printScore ? String.format(Locale.ROOT, "\tscore %.2f", c.score2()) : "");
jpayne@68: 		String score=(printScore ? "\tscore "+c.scoreS() : "");
jpayne@68: 		String depth=(printDepth ? "\tdepth "+c.depthS(printActualDepth) : "");
jpayne@68: 		String depth2=(printDepth2 ? "\tdepth2 "+c.depth2S(printActualDepth) : "");
jpayne@68: 		String volume=(printVolume ? "\tvolume "+c.volumeS() : "");
jpayne@68: 		String ccs=complt+contam+score;
jpayne@68: 		
jpayne@68: 		if(format==FORMAT_OLD){
jpayne@68: 			sb.append(String.format(Locale.ROOT, "WKID %.2f%%\tKID %.2f%%"+ccs+"\tmatches %d\tcompared %d",
jpayne@68: 					100*c.wkid(), 100*c.kid(), c.hits(), c.minDivisor())+"\ttaxID "+c.taxID()+
jpayne@68: 					(printImg ? "\timgID "+c.imgID() : "")+"\tgKmers "+c.genomeSizeKmers()+"\t"+
jpayne@68: 					(c.taxName()==null ? "." : c.taxName())+
jpayne@68: 					((printOriginalName || (c.taxName()==null && c.name0()!=null)) ? "\t"+(c.name0()==null ? "." : c.name0()) : "")+"\n");
jpayne@68: 			if(printTax && SketchObject.taxtree!=null){
jpayne@68: 				if(c.taxID()>=0 && c.taxID()<SketchObject.minFakeID){
jpayne@68: 					TaxNode tn=SketchObject.taxtree.getNode(c.taxID());
jpayne@68: 					if(tn!=null){
jpayne@68: 						PrintTaxonomy.printTaxonomy(tn, sb, SketchObject.taxtree, TaxTree.DOMAIN, SketchObject.skipNonCanonical);
jpayne@68: 					}
jpayne@68: 				}
jpayne@68: 				sb.append('\n');
jpayne@68: 			}
jpayne@68: 		}else{
jpayne@68: 			ArrayList<TaxNode> tnl=new ArrayList<TaxNode>();
jpayne@68: 			if(SketchObject.taxtree!=null && c.taxID()>=0 && c.taxID()<SketchObject.minFakeID){
jpayne@68: 				TaxNode tn=SketchObject.taxtree.getNode(c.taxID());
jpayne@68: 				while(tn!=null && tn.pid!=tn.id && tn.level<=TaxTree.DOMAIN){
jpayne@68: 					tnl.add(tn);
jpayne@68: 					tn=SketchObject.taxtree.getNode(tn.pid);
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 			
jpayne@68: 			sb.append(String.format(Locale.ROOT, "WKID %.2f%%\tKID %.2f%%"+ccs+"\tmatches %d\tcompared %d\t",
jpayne@68: 					100*c.wkid(), 100*c.kid(), c.hits(), c.minDivisor()));
jpayne@68: 			sb.append("\ttaxID ").append(c.taxID()).append('\t');
jpayne@68: 			if(printImg){sb.append("\timgID ").append(c.imgID()).append('\t');}
jpayne@68: 			sb.append(c.taxName()).append('\t');
jpayne@68: 			if(printRefFileName){sb.append(c.fname()).append('\t');}
jpayne@68: 			if(printOriginalName || (c.taxName()==null && c.name0()!=null && !printRefFileName)){sb.append(c.name0()).append('\t');}
jpayne@68: 			
jpayne@68: 			if(printTax){
jpayne@68: 				for(int i=tnl.size()-1; i>=0; i--){
jpayne@68: 					TaxNode tn=tnl.get(i);
jpayne@68: 					sb.append(tn.name);
jpayne@68: 					if(i>0){sb.append(';');}
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 			sb.append('\n');
jpayne@68: 			
jpayne@68: 			tnl.clear();
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------           Filtering          ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	public boolean passesFilter(Sketch sk){
jpayne@68: 		assert(postParsed);
jpayne@68: 		if(noFilters){return true;}
jpayne@68: 		return passesSSUFilter(sk) && passesSizeFilter(sk) && passesTaxFilter(sk) && passesMetaFilter(sk);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private boolean passesTaxFilter(Sketch sk){
jpayne@68: 		if(taxFilterWhite==null && taxFilterBlack==null){return true;}
jpayne@68: 		int id=sk.taxID;
jpayne@68: 		if(id>0){
jpayne@68: 			if(banUnclassified && SketchObject.taxtree.isUnclassified(id)){return false;}
jpayne@68: 			if(banVirus && SketchObject.taxtree.isVirus(id)){return false;}
jpayne@68: 		}
jpayne@68: 		String s=sk.name();
jpayne@68: 		return passesTaxFilter(taxFilterWhite, id, s) && passesTaxFilter(taxFilterBlack, id, s);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private boolean passesTaxFilter(TaxFilter filter, int id, String s){
jpayne@68: 		if(filter==null){return true;}
jpayne@68: 		if(id>0 && !filter.passesFilter(id)){return false;}
jpayne@68: //		if(id>0 && !filter.passesFilterFast(id)){return false;}
jpayne@68: 		if(s!=null && !filter.passesFilterByNameOnly(s)){return false;}
jpayne@68: 		return true;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private boolean passesMetaFilter(Sketch sk){
jpayne@68: 		if(requiredMeta==null && bannedMeta==null){return true;}
jpayne@68: 		return sk.passesMeta(requiredMeta, bannedMeta, requiredMetaAnd);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private boolean passesSSUFilter(Sketch sk){
jpayne@68: 		return !requireSSU || sk.hasSSU();
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private boolean passesSizeFilter(Sketch sk){
jpayne@68: 		if(minRefSizeEstimate>0 && sk.genomeSizeEstimate()<minRefSizeEstimate){return false;}
jpayne@68: 		return sk.genomeSizeBases>=minRefSizeBases;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------            Fields            ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 
jpayne@68: 	//These are shared with SketchObject
jpayne@68: 	//They do not affect anything and are just for the server to validate remote settings.
jpayne@68: 	private int hashVersion=SketchObject.HASH_VERSION;
jpayne@68: 	private int k=SketchObject.k;
jpayne@68: 	private int k2=SketchObject.k2;
jpayne@68: 	boolean amino=SketchObject.amino;
jpayne@68: 	boolean translate=SketchObject.translate;
jpayne@68: 	boolean sixframes=SketchObject.sixframes;
jpayne@68: 	private boolean aminoOrTranslate(){return amino | translate;}
jpayne@68: 	
jpayne@68: 	boolean noFilters=false;
jpayne@68: 	boolean postParsed=false;
jpayne@68: 	
jpayne@68: 	boolean amino(){return amino;}
jpayne@68: 	
jpayne@68: 	//These are unique
jpayne@68: 	public int maxRecords=default_maxRecords;
jpayne@68: 	public int recordsPerLevel=0;
jpayne@68: 	public float minANI=0;
jpayne@68: 	public int minBases=0;
jpayne@68: 	public float minSizeRatio=0;
jpayne@68: 	public float minWKID=default_minWKID;
jpayne@68: 	public int format=default_format;
jpayne@68: 	
jpayne@68: 	/** For tracking unique SendSketch queries */
jpayne@68: 	public int chunkNum=-1;
jpayne@68: 	public int minHits=default_minHits;
jpayne@68: 	public int taxLevel=default_taxLevel;
jpayne@68: 	public int mode=default_mode;
jpayne@68: 	public float samplerate=default_samplerate;
jpayne@68: 	public long maxReads=default_maxReads;
jpayne@68: 	public int minKeyOccuranceCount=default_minKeyOccuranceCount;
jpayne@68: 	public String inputVersion=null;
jpayne@68: 	
jpayne@68: 	public String dbName=null;
jpayne@68: 
jpayne@68: 	boolean hasMetaFilters(){return requiredMeta!=null || bannedMeta!=null/* || requiredTaxid!=null || bannedTaxid!=null*/;}
jpayne@68: 	boolean hasTaxFilters(){return taxFilterWhite!=null || taxFilterBlack!=null || banUnclassified || banVirus;}
jpayne@68: 	boolean requireSSU=false;
jpayne@68: 	long minRefSizeEstimate=-1;
jpayne@68: 	long minRefSizeBases=-1;
jpayne@68: 	
jpayne@68: 	boolean requiredMetaAnd=true;
jpayne@68: 	ArrayList<String> requiredMeta=null;
jpayne@68: 	ArrayList<String> bannedMeta=null;
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------         Print Columns        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 
jpayne@68: 	public boolean printKID=true;
jpayne@68: 	public boolean printWKID=true;
jpayne@68: 	public boolean printSSU=true;
jpayne@68: 	public boolean printSSULen=false;
jpayne@68: 	public boolean printSSU(){return SketchObject.processSSU && printSSU;}
jpayne@68: 	public boolean printSSUSequence=default_printSSUSequence;
jpayne@68: 	
jpayne@68: 	//For format 2
jpayne@68: 	public boolean printTax=default_printTax;
jpayne@68: 	public boolean printOriginalName=default_printOriginalName;
jpayne@68: 	public boolean printQueryFileName=default_printQueryFileName;
jpayne@68: 	public boolean printRefFileName=default_printRefFileName;
jpayne@68: 	public boolean printImg=default_printImg;
jpayne@68: 	public boolean printAni=default_printAni;
jpayne@68: 	public boolean printCompleteness=default_printCompleteness;
jpayne@68: 	public boolean printScore=default_printScore;
jpayne@68: 	public boolean printEValue=default_printEValue;
jpayne@68: 
jpayne@68: 	private boolean trackCounts=default_trackCounts;
jpayne@68: 	public boolean printDepth=default_printDepth;
jpayne@68: 	public boolean printDepth2=default_printDepth2;
jpayne@68: 	public boolean printActualDepth=default_printActualDepth;
jpayne@68: 	public boolean printVolume=default_printVolume;
jpayne@68: 	public boolean printRefHits=default_printRefHits;
jpayne@68: 	
jpayne@68: 	public boolean printLength=default_printLength;
jpayne@68: 	public boolean printTaxID=default_printTaxID;
jpayne@68: 	public boolean printGSize=default_printGSize;
jpayne@68: 	public boolean printGC=default_printGC;
jpayne@68: 	public boolean gSizeKMG=default_gSizeKMG;
jpayne@68: 	public boolean printGKmers=default_printGKmers;
jpayne@68: 	public boolean printCommonAncestor=default_printCommonAncestor;
jpayne@68: 	public boolean printCommonAncestorLevel=default_printCommonAncestorLevel;
jpayne@68: 	public boolean printTaxName=default_printTaxName;
jpayne@68: 	public boolean printGSeqs=default_printGSeqs;
jpayne@68: 	public boolean printGBases=default_printGBases;
jpayne@68: 	
jpayne@68: 	public boolean jsonArray=default_jsonArray;
jpayne@68: 	public boolean printD3=default_printD3;
jpayne@68: 	public boolean D3LevelNodes=false;
jpayne@68: 	public int D3sizeMode=D3_HIT_SIZE;
jpayne@68: 	public static final int D3_HIT_SIZE=0, D3_ANI_SIZE=1, D3_KID_SIZE=2, D3_WKID_SIZE=3, D3_DEPTH_SIZE=4;
jpayne@68: 	
jpayne@68: 	public float minEntropy=default_minEntropy;
jpayne@68: 	
jpayne@68: 	//For k=32:
jpayne@68: 	//0.000095f is >=Q6 (75%); 0.0008 is >=Q7 (80%); 0.0039 is >=Q8 (84%).
jpayne@68: 	//0.002f is >=Q7.53 (82.3%)
jpayne@68: 	//0.0017f is >=Q7.44 (82.0%)
jpayne@68: 	//0.6f works better for Illumina reads but this is more robust for PacBio. 
jpayne@68: 	public float minProb=0.0008f;
jpayne@68: 	public byte minQual=0;
jpayne@68: 
jpayne@68: 	public boolean printUnique=default_printUnique;
jpayne@68: 	public boolean printUnique2=default_printUnique2;
jpayne@68: 	public boolean printUnique3=default_printUnique3;
jpayne@68: 	public boolean printUContam=default_printUContam;
jpayne@68: 	public boolean printNoHit=default_printNoHit;
jpayne@68: 
jpayne@68: 	public boolean printColors=default_printColors;
jpayne@68: 	public boolean setColors=false;
jpayne@68: 	public int colorLevel=default_colorLevel;
jpayne@68: 	
jpayne@68: 	/** TODO: Note this is conflated between printing %contam and calculating things based on contam hits. */
jpayne@68: 	public boolean printContam=default_printContam;
jpayne@68: 	public boolean printContam2=default_printContam2;
jpayne@68: 	private int contamLevel=default_contamLevel;
jpayne@68: 	
jpayne@68: 	/** Raw fields */
jpayne@68: 	public boolean printMatches=default_printMatches;
jpayne@68: 	
jpayne@68: 	public boolean printRefDivisor=false;
jpayne@68: 	public boolean printQueryDivisor=false;
jpayne@68: 	public boolean printRefSize=false;
jpayne@68: 	public boolean printQuerySize=false;
jpayne@68: 	public boolean printContamHits=false;
jpayne@68: 	
jpayne@68: 	public boolean mergePairs=false;
jpayne@68: 	public boolean printIntersection=false;
jpayne@68: 	
jpayne@68: 	//For format 3 or 5
jpayne@68: 	public boolean useTaxidName=false;
jpayne@68: 	public boolean useImgName=false;
jpayne@68: 	public boolean useTaxName=false;
jpayne@68: 	public boolean useFilePrefixName=false;
jpayne@68: 	public boolean reportAniOnly=false;
jpayne@68: 
jpayne@68: 	public int taxLevelWhite=0;
jpayne@68: 	public int taxLevelBlack=0;
jpayne@68: 
jpayne@68: 	public String taxFilterWhiteList=null;
jpayne@68: 	public String taxFilterBlackList=null;
jpayne@68: 
jpayne@68: 	public String taxFilterWhiteString=null;
jpayne@68: 	public String taxFilterBlackString=null;
jpayne@68: 	
jpayne@68: 	public TaxFilter taxFilterWhite=null;
jpayne@68: 	public TaxFilter taxFilterBlack=null;
jpayne@68: 
jpayne@68: 	public boolean banUnclassified=false;
jpayne@68: 	public boolean banVirus=false;
jpayne@68: 
jpayne@68: 	/** Make sure the settings are consistent, for CompareSketch.
jpayne@68: 	 * This is not yet complete. */
jpayne@68: 	public boolean checkValid(){
jpayne@68: 		if(printUnique2 || printUnique3){
jpayne@68: 			assert(contamLevel()>=TaxTree.SUBSPECIES_E);
jpayne@68: 			assert(needContamCounts());
jpayne@68: 			assert(SketchObject.makeIndex);
jpayne@68: 			assert(SketchObject.taxtree!=null);
jpayne@68: 		}
jpayne@68: 		if(printContam2){
jpayne@68: 			assert(contamLevel()>=TaxTree.SUBSPECIES_E);
jpayne@68: 			assert(needContamCounts());
jpayne@68: 			assert(SketchObject.makeIndex);
jpayne@68: 			assert(SketchObject.taxtree!=null);
jpayne@68: 		}
jpayne@68: 		return true;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public boolean trackCounts() {
jpayne@68: 		return trackCounts || printDepth || printDepth2 || printVolume 
jpayne@68: 				|| comparator!=Comparison.scoreComparator || printD3; //|| minKeyOccuranceCount>1;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public boolean needContamCounts() {
jpayne@68: 		return printContam || printContam2 || printContamHits || printUnique || printUnique2 || printUnique3 || printUContam || printNoHit; // || true
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public boolean needIndex(){
jpayne@68: 		return printContam2 || printUnique2 || printUnique3;
jpayne@68: 	}
jpayne@68: 
jpayne@68: 	public int contamLevel() {
jpayne@68: 		return needIndex() ? contamLevel : -1;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public int compare(Comparison a, Comparison b){
jpayne@68: 		return comparator.compare(a, b);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public Comparator<Comparison> comparator=Comparison.scoreComparator;
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------          Constants           ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	public static final int FORMAT_OLD=0, FORMAT_MULTICOLUMN=2, FORMAT_QUERY_REF_ANI=3, FORMAT_JSON=4, FORMAT_CONSTELLATION=5;
jpayne@68: 	public static final boolean default_printD3=false;
jpayne@68: 	public static final boolean default_jsonArray=false;
jpayne@68: 	
jpayne@68: 	public static final int default_maxRecords=20;
jpayne@68: 	public static final float default_minWKID=0.0001f;
jpayne@68: 	public static final int default_format=FORMAT_MULTICOLUMN;
jpayne@68: 	public static final boolean default_printSSUSequence=false;
jpayne@68: 	public static final boolean default_printTax=false;
jpayne@68: 	public static final boolean default_printOriginalName=false;
jpayne@68: 	public static final boolean default_printQueryFileName=true;
jpayne@68: 	public static final boolean default_printRefFileName=false;
jpayne@68: 	public static final boolean default_printImg=false;
jpayne@68: 	public static final boolean default_printAni=true;
jpayne@68: 	public static final boolean default_printCompleteness=true;
jpayne@68: 	public static final boolean default_printScore=false;
jpayne@68: 	public static final boolean default_printEValue=false;
jpayne@68: 	
jpayne@68: 	public static final boolean default_trackCounts=false;
jpayne@68: 	public static final boolean default_printDepth=false;
jpayne@68: 	public static final boolean default_printDepth2=false;
jpayne@68: 	public static final boolean default_printActualDepth=true;
jpayne@68: 	public static final boolean default_printVolume=false;
jpayne@68: 	public static final boolean default_printRefHits=false;
jpayne@68: 
jpayne@68: 	public static final boolean default_printContam=true;
jpayne@68: 	public static final boolean default_printContam2=false;
jpayne@68: 	
jpayne@68: 	public static final boolean default_printMatches=true;
jpayne@68: 	public static final boolean default_printLength=false;
jpayne@68: 	public static final boolean default_printTaxID=true;
jpayne@68: 	public static final boolean default_printGSize=true;
jpayne@68: 	public static final boolean default_printGC=false;
jpayne@68: 	public static final boolean default_gSizeKMG=true;
jpayne@68: 	public static final boolean default_printGKmers=false;
jpayne@68: 	public static final boolean default_printCommonAncestor=false;
jpayne@68: 	public static final boolean default_printCommonAncestorLevel=false;
jpayne@68: 	public static final boolean default_printTaxName=true;
jpayne@68: 	public static final boolean default_printGSeqs=true;
jpayne@68: 	public static final boolean default_printGBases=false;
jpayne@68: 
jpayne@68: 	public static final float default_minEntropy=0.66f;
jpayne@68: 	public static final float default_minEntropy_amino=0.70f;
jpayne@68: 	public static final float default_minProb=0.0008f;
jpayne@68: 	public static final byte default_minQual=0;
jpayne@68: 
jpayne@68: 	public static final boolean default_printUnique=true;
jpayne@68: 	public static final boolean default_printUnique2=false;
jpayne@68: 	public static final boolean default_printUnique3=false;
jpayne@68: 	public static final boolean default_printUContam=false;
jpayne@68: 	public static final boolean default_printNoHit=false;
jpayne@68: 
jpayne@68: 	public static final boolean default_printColors=true;
jpayne@68: 	public static final int default_colorLevel=TaxTree.FAMILY_E;
jpayne@68: 
jpayne@68: 	public static final int default_taxLevel=TaxTree.SPECIES;
jpayne@68: 	public static final int default_contamLevel=TaxTree.GENUS_E;
jpayne@68: 	
jpayne@68: 	public static final int default_mode=SketchObject.ONE_SKETCH;
jpayne@68: 	
jpayne@68: 	public static final int default_minHits=3;
jpayne@68: 	public static final float default_samplerate=1;
jpayne@68: 	public static final long default_maxReads=-1;
jpayne@68: 	public static final int default_minKeyOccuranceCount=1;
jpayne@68: 	
jpayne@68: }