--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/sketch/SendSketch.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,806 @@
+package sketch;
+
+import java.io.File;
+import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.Collection;
+
+import fileIO.ByteFile;
+import fileIO.ByteStreamWriter;
+import fileIO.FileFormat;
+import fileIO.ReadWrite;
+import fileIO.TextStreamWriter;
+import kmer.AbstractKmerTableSet;
+import server.ServerTools;
+import shared.KillSwitch;
+import shared.Parse;
+import shared.Parser;
+import shared.PreParser;
+import shared.ReadStats;
+import shared.Shared;
+import shared.Timer;
+import shared.Tools;
+import structures.ByteBuilder;
+import structures.StringNum;
+import tax.TaxTree;
+
+/**
+ * Compares one or more input sketches to a set of reference sketches.
+ * 
+ * @author Brian Bushnell
+ * @date July 29, 2016
+ *
+ */
+public class SendSketch extends SketchObject {
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        Initialization        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/**
+	 * Code entrance from the command line.
+	 * @param args Command line arguments
+	 */
+	public static void main(String[] args){
+		//Start a timer immediately upon code entrance.
+		Timer t=new Timer();
+		
+		final boolean oldUnpigz=ReadWrite.USE_UNPIGZ;
+		final int oldBufLen=Shared.bufferLen();
+		
+		//Create an instance of this class
+		SendSketch x=new SendSketch(args);
+		
+		//Run the object
+		x.process(t);
+		
+		ReadWrite.USE_UNPIGZ=oldUnpigz;
+		Shared.setBufferLen(oldBufLen);
+		
+		//Close the print stream if it was redirected
+		Shared.closeStream(x.outstream);
+		
+		assert(!x.errorState) : "This program ended in an error state.";
+	}
+	
+	/**
+	 * Constructor.
+	 * @param args Command line arguments
+	 */
+	public SendSketch(String[] args){
+		
+		{//Preparse block for help, config files, and outstream
+			PreParser pp=new PreParser(args, null, false);
+			args=pp.args;
+			outstream=pp.outstream;
+			silent=PreParser.silent;
+			if(silent){AbstractKmerTableSet.DISPLAY_PROGRESS=false;}
+		}
+		
+		//Set shared static variables
+		ReadWrite.USE_UNPIGZ=true;
+		KILL_OK=true;
+		
+		//Create a parser object
+		Parser parser=new Parser();
+		parser.out1="stdout.txt";
+		
+		defaultParams.inputVersion=Shared.BBMAP_VERSION_STRING;
+		defaultParams.mode=PER_FILE;
+		boolean setBlacklist=false;
+		boolean setLocal=false;
+		boolean setPrintDepth=false;
+		
+		//Parse each argument
+		for(int i=0; i<args.length; i++){
+			String arg=args[i];
+			
+			//Break arguments into their constituent parts, in the form of "a=b"
+			String[] split=arg.split("=");
+			String a=split[0].toLowerCase();
+			String b=split.length>1 ? split[1] : null;
+			
+			if(a.equals("verbose")){
+				verbose=Parse.parseBoolean(b);
+			}else if(a.equals("in")){
+				addFiles(b, in);
+			}else if(a.equals("blacklist") || a.equalsIgnoreCase("bl")){
+				setBlacklist=true;
+				parseSketchFlags(arg, a, b);
+			}else if(parseSketchFlags(arg, a, b)){
+				//Do nothing
+			}else if(defaultParams.parse(arg, a, b)){
+				//Do nothing
+			}else if(a.equals("local")){
+				local=Parse.parseBoolean(b);
+				setLocal=true;
+			}else if(a.equals("refid") || a.equals("refids") || a.equals("refname") || a.equals("refnames")){
+				refNames=b;
+			}else if(a.equals("parse_flag_goes_here")){
+				long fake_variable=Parse.parseKMG(b);
+				//Set a variable here
+			}else if(a.equals("address")){
+				assert(b!=null) : "Bad parameter: "+arg;
+				address=b;
+			}
+//			else if(a.equals("alternateaddress") || a.equals("altaddress") || a.equalsIgnoreCase("vm")){
+//				boolean alt=Parse.parseBoolean(b);
+//				switchDefaultAddresses(alt);
+//			}
+			
+
+			else if(a.equalsIgnoreCase("nt") || a.equalsIgnoreCase("silva") || a.equalsIgnoreCase("ribo") || 
+					a.equalsIgnoreCase("refseq") || a.equalsIgnoreCase("img") || a.equalsIgnoreCase("nr") || 
+					a.equalsIgnoreCase("refseqprot") || a.equalsIgnoreCase("prokprot") || a.equalsIgnoreCase("protein") || 
+					a.equalsIgnoreCase("protien") || a.equalsIgnoreCase("prot") || a.equalsIgnoreCase("mito") || a.equalsIgnoreCase("fungi")){
+				address=a;
+				blacklist=a;
+			}
+			
+			else if(a.equals("taxtree") || a.equals("tree")){
+				taxTreeFile=b;
+			}
+			
+			else if(a.equals("name") || a.equals("taxname")){
+				outTaxName=b;
+			}else if(a.equals("name0")){
+				outName0=b;
+			}else if(a.equals("fname")){
+				outFname=b;
+			}else if(a.equals("taxid") || a.equals("tid")){
+				outTaxID=Integer.parseInt(b);
+			}else if(a.equals("spid")){
+				outSpid=Integer.parseInt(b);
+			}else if(a.equals("imgid")){
+				outImgID=Integer.parseInt(b);
+			}else if((a.startsWith("meta_") || a.startsWith("mt_")) && b!=null){
+				if(outMeta==null){outMeta=new ArrayList<String>();}
+				int underscore=a.indexOf('_', 0);
+				outMeta.add(a.substring(underscore+1)+":"+b);
+			}
+			
+			else if(a.equals("outsketch") || a.equals("outs") || a.equals("sketchout") || a.equals("sketch")){
+				outSketch=b;
+			}
+			
+			else if(parser.parse(arg, a, b)){//Parse standard flags in the parser
+				//do nothing
+			}
+			
+			else if(b==null && in.isEmpty() && new File(arg).exists()){
+				in.add(arg);
+			}
+			
+			else{
+				outstream.println("Unknown parameter "+args[i]);
+				assert(false) : "Unknown parameter "+args[i];
+			}
+		}
+		if("auto".equalsIgnoreCase(taxTreeFile)){taxTreeFile=TaxTree.defaultTreeFile();}
+		
+		address=toAddress(address);
+		outMeta=SketchObject.fixMeta(outMeta);
+		
+		if(address!=null && !SET_AUTOSIZE_FACTOR){
+			if(address.equals(refseqAddress())){
+				AUTOSIZE_FACTOR=2.0f;
+			}else if(address.equals(prokProtAddress())){
+				AUTOSIZE_FACTOR=3.0f;
+			}
+		}
+		
+		while(address!=null && address.endsWith("/")){
+			address=address.substring(0,  address.length()-1);
+		}
+		
+		setFromAddress(address, setBlacklist);
+		
+		if(local){blacklist=null;}
+		
+		postParse();
+		
+		{//Process parser fields
+			overwrite=ReadStats.overwrite=parser.overwrite;
+			append=ReadStats.append=parser.append;
+
+			out=parser.out1;
+		}
+		
+		//Ensure there is an input file
+		if(in.isEmpty() && refNames==null){throw new RuntimeException("Error - at least one input file is required.");}
+		
+		//Adjust the number of threads for input file reading
+		if(!ByteFile.FORCE_MODE_BF1 && !ByteFile.FORCE_MODE_BF2 && Shared.threads()>2){
+			ByteFile.FORCE_MODE_BF2=true;
+		}
+		
+		ffout=FileFormat.testOutput(out, FileFormat.TEXT, null, false, overwrite, append, false);
+		if(!ffout.stdio() && !defaultParams.setColors){defaultParams.printColors=false;}
+		
+		//Ensure input files can be read
+		if(!Tools.testInputFiles(false, true, taxTreeFile)){
+			throw new RuntimeException("\nCan't read some input files.\n");  
+		}
+		
+		if(!local && refNames==null){
+			if(!Tools.testInputFiles(true, false, in.toArray(new String[0]))){
+				if(in.size()==1){
+					String s=in.get(0);
+					String s1=s.replaceFirst("#", "1"), s2=s.replaceFirst("#", "2");
+					Tools.testInputFiles(true, false, s1, s2);
+				}else{
+					throw new RuntimeException("\nCan't read some input files.\n");  
+				}
+			}
+		}
+		
+		if(!Tools.testOutputFiles(overwrite, append, false, out, outSketch)){
+			throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output files "+
+					out+", "+outSketch+"\n");
+		}
+		
+		//Ensure that no file was specified multiple times
+		if(!Tools.testForDuplicateFiles(true, in.toArray(new String[0]))){
+			throw new RuntimeException("\nSome file names were specified multiple times.\n");
+		}
+		
+		SSUMap.load(outstream);
+		tool=new SketchTool(targetSketchSize, defaultParams);
+		
+//		assert(false) : defaultParams.toString()+"\n"+k+", "+amino+", "+HASH_VERSION;
+		if(verbose){
+			if(local){outstream.println("Running in local mode.");}
+			if(useWhitelist){outstream.println("Using a whitelist.");}
+			if(blacklist!=null){outstream.println("Using a blacklist.");}
+		}
+		
+		if(taxTreeFile!=null){setTaxtree(taxTreeFile, silent ? null : outstream);}
+		defaultParams.postParse(false, false);
+		if(!defaultParams.printSSU){processSSU=false;}
+		allowMultithreadedFastq=(in.size()==1 && Shared.threads()>2);
+		if(!allowMultithreadedFastq){Shared.capBufferLen(40);}
+	}
+	
+	private void setFromAddress(String address, boolean setBlacklist){
+		if(address.equals(nrAddress())){
+			amino=true;
+			if(!setK){k=defaultKAmino; k2=defaultK2Amino;}
+//			defaultParams.dbName="nr";
+			assert(false) : "Need to set K.";
+		}else if(address.equals(prokProtAddress())){
+			translate=true;
+			if(!setK){k=defaultKAmino; k2=defaultK2Amino;}
+//			defaultParams.dbName="nr";
+			if(blacklist==null && !setBlacklist){blacklist=Blacklist.prokProtBlacklist();}
+		}else if(address.equals(ntAddress())){
+			if(!setK){k=defaultK; k2=defaultK2;}
+//			defaultParams.dbName="nt";
+			if(blacklist==null && !setBlacklist){blacklist=Blacklist.ntBlacklist();}
+		}else if(address.equals(refseqAddress())){
+			if(!setK){k=defaultK; k2=defaultK2;}
+//			defaultParams.dbName="RefSeq";
+			if(blacklist==null && !setBlacklist){blacklist=Blacklist.refseqBlacklist();}
+		}else if(address.equals(silvaAddress())){
+			if(!setK){k=defaultK; k2=defaultK2;}
+//			defaultParams.dbName="Silva";
+			if(blacklist==null && !setBlacklist){blacklist=Blacklist.silvaBlacklist();}
+		}else if(address.equals(imgAddress())){
+			if(!setK){k=defaultK; k2=defaultK2;}
+//			defaultParams.dbName="IMG";
+			if(blacklist==null && !setBlacklist){blacklist=Blacklist.imgBlacklist();}
+		}else if(address.equals(mitoAddress())){
+			if(!setK){k=defaultK; k2=defaultK2;}
+			if(blacklist==null && !setBlacklist){blacklist=Blacklist.mitoBlacklist();}
+		}else if(address.equals(fungiAddress())){
+			if(!setK){k=defaultK; k2=defaultK2;}
+			if(blacklist==null && !setBlacklist){blacklist=Blacklist.fungiBlacklist();}
+		}
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Outer Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	public void process(Timer t){
+		if(local){processLocal(t);}
+		else if(refNames!=null){processRefMode(t);}
+		else{processRemote(t);}
+	}
+
+	@Deprecated
+	private void processRemote_old(Timer t){
+		Timer ttotal=new Timer();
+		
+		t.start();
+		inSketches=tool.loadSketches_MT(defaultParams, in);
+		final int numLoaded=(inSketches.size());
+		if(numLoaded>1 && defaultParams.mode==PER_FILE){
+			inSketches.sort(SketchIdComparator.comparator);//Otherwise they come out disordered
+		}
+		
+		t.stop();
+		if(!silent){outstream.println("Loaded "+numLoaded+" sketch"+(numLoaded==1 ? "" : "es")+" in "+t);}
+		assert(numLoaded<=MAX_ALLOWED_SKETCHES) : "\nSendSketch is configured to send at most "+MAX_ALLOWED_SKETCHES+" to prevent overwhelming the server.\n"
+				+ "If you need to compare more than that, please use CompareSketch locally instead.\n"
+				+ "References can be downloaded at http://portal.nersc.gov/dna/microbial/assembly/bushnell/\n";
+		t.start();
+//		outstream.println(inSketches.get(0));
+		
+		if(numLoaded>4000){
+			SEND_BUFFER_MAX_BYTES*=4;
+			SEND_BUFFER_MAX_SKETCHES*=4;
+		}else if(numLoaded>1000){
+			SEND_BUFFER_MAX_BYTES*=2;
+			SEND_BUFFER_MAX_SKETCHES*=2;
+		}
+		
+		if(ffout==null){return;}
+		TextStreamWriter tsw=new TextStreamWriter(ffout);
+		tsw.start();
+		if(defaultParams.format==DisplayParams.FORMAT_QUERY_REF_ANI || defaultParams.format==DisplayParams.FORMAT_CONSTELLATION){tsw.println(defaultParams.header());}
+		
+		ByteBuilder bb=new ByteBuilder();
+		
+		int cntr=0;
+		int chunks=0;
+		for(Sketch sk : inSketches){
+			
+			if(sk.taxID<1 || sk.taxID>=minFakeID || outTaxID>0){sk.taxID=outTaxID;}
+			if(defaultParams.printSSU()){sk.loadSSU();}
+			
+			if(outSpid>0){sk.spid=outSpid;}
+			if(outImgID>0){sk.imgID=outImgID;}
+			if(outTaxName!=null){sk.setTaxName(outTaxName);}
+			if(outFname!=null){sk.setFname(outFname);}
+			if(outName0!=null){sk.setName0(outName0);}
+			sk.setMeta(outMeta);
+			
+			if(bb.length==0){
+				bb.append(defaultParams.toString(chunks));
+				chunks++;
+			}
+			sk.toBytes(bb);
+			cntr++;
+			if(cntr>=SEND_BUFFER_MAX_SKETCHES || bb.length>SEND_BUFFER_MAX_BYTES){ //Don't allow too much data in a single transaction
+				if(verbose){outstream.println("Sending:\n"+bb);}
+//				outstream.println(cntr+", "+bb.length);
+				
+				byte[] message=bb.toBytes();
+				bb.clear();
+				try {
+//					outstream.println("Sending to "+address+"\n"+message+"\n"); //123
+					StringNum result=ServerTools.sendAndReceive(message, address);
+					if(!ServerTools.suppressErrors && (result.n<200 || result.n>299)){
+						System.err.println("ERROR: Server returned code "+result.n+" and this message:\n"+result.s);
+						KillSwitch.kill();
+					}
+					errorState|=checkForError(result.s);
+					tsw.print(result.s);
+				} catch (Exception e) {
+					// TODO Auto-generated catch block
+					e.printStackTrace();
+				}
+				cntr=0;
+			}
+		}
+		
+		if(bb.length>0){
+			if(verbose){outstream.println("Sending:\n"+bb);}
+			byte[] message=bb.toBytes();
+			bb.clear();
+			try {
+				StringNum result=ServerTools.sendAndReceive(message, address);
+				if(!ServerTools.suppressErrors && (result.n<200 || result.n>299)){
+					System.err.println("ERROR: Server returned code "+result.n+" and this message:\n"+result.s);
+					KillSwitch.kill();
+				}
+				errorState|=checkForError(result.s);
+				tsw.print(result.s);
+			} catch (Exception e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			}
+		}
+		if(!silent){tsw.println();}
+		tsw.poison();
+		
+//		outstream.println("sending "+bb.toString());
+		
+		if(outSketch!=null){
+			ByteStreamWriter bsw=new ByteStreamWriter(outSketch, overwrite, append, true, FileFormat.SKETCH);
+			bsw.start();
+			for(Sketch sk : inSketches){
+				sk.toBytes(bb);
+				bsw.print(bb);
+				bb.clear();
+			}
+			bsw.poisonAndWait();
+			errorState|=bsw.errorState;
+		}
+		
+		tsw.waitForFinish();
+		errorState|=tsw.errorState;
+		
+		t.stop();
+//		outstream.println("\nRan "+(inSketches.size()*refSketches.size())+" comparisons in \t"+t);
+		ttotal.stop();
+		if(!silent){outstream.println("Total Time: \t"+ttotal);}
+	}
+	
+
+	private void processRemote(Timer t){
+		Timer ttotal=new Timer();
+		
+		t.start();
+		inSketches=tool.loadSketches_MT(defaultParams, in);
+		final int numLoaded=(inSketches.size());
+		if(numLoaded>1 && defaultParams.mode==PER_FILE){
+			inSketches.sort(SketchIdComparator.comparator);//Otherwise they come out disordered
+		}
+		
+		t.stop();
+		if(!silent){outstream.println("Loaded "+numLoaded+" sketch"+(numLoaded==1 ? "" : "es")+" in "+t);}
+		assert(numLoaded<=MAX_ALLOWED_SKETCHES) : "\nSendSketch is configured to send at most "+MAX_ALLOWED_SKETCHES+" to prevent overwhelming the server.\n"
+				+ "If you need to compare more than that, please use CompareSketch locally instead.\n"
+				+ "References can be downloaded at http://portal.nersc.gov/dna/microbial/assembly/bushnell/\n";
+		t.start();
+//		outstream.println(inSketches.get(0));
+		
+		if(numLoaded>4000){
+			SEND_BUFFER_MAX_BYTES*=4;
+			SEND_BUFFER_MAX_SKETCHES*=4;
+		}else if(numLoaded>1000){
+			SEND_BUFFER_MAX_BYTES*=2;
+			SEND_BUFFER_MAX_SKETCHES*=2;
+		}
+//		SEND_BUFFER_MAX_SKETCHES=1;//This is for testing json array format.
+		
+		if(ffout==null){return;}
+		TextStreamWriter tsw=new TextStreamWriter(ffout);
+		tsw.start();
+		if(defaultParams.format==DisplayParams.FORMAT_QUERY_REF_ANI || defaultParams.format==DisplayParams.FORMAT_CONSTELLATION){tsw.println(defaultParams.header());}
+		
+		ByteBuilder bb=new ByteBuilder();
+		
+		int cntr=0;
+		int chunks=0;
+		boolean firstBlock=true; //Set to false after printing has started
+		final Sketch lastSketch=Tools.getLast(inSketches); //Last input sketch to process
+		for(Sketch sk : inSketches){
+			
+			if(sk.taxID<1 || sk.taxID>=minFakeID || outTaxID>0){sk.taxID=outTaxID;}
+			if(defaultParams.printSSU()){sk.loadSSU();}
+			
+			if(outSpid>0){sk.spid=outSpid;}
+			if(outImgID>0){sk.imgID=outImgID;}
+			if(outTaxName!=null){sk.setTaxName(outTaxName);}
+			if(outFname!=null){sk.setFname(outFname);}
+			if(outName0!=null){sk.setName0(outName0);}
+			sk.setMeta(outMeta);
+			
+			if(bb.length==0){
+				bb.append(defaultParams.toString(chunks));
+				chunks++;
+			}
+			sk.toBytes(bb);
+			cntr++;
+			if(cntr>=SEND_BUFFER_MAX_SKETCHES || bb.length>SEND_BUFFER_MAX_BYTES || sk==lastSketch){ //Don't allow too much data in a single transaction
+				if(verbose){outstream.println("Sending:\n"+bb);}
+//				outstream.println(cntr+", "+bb.length);
+				
+				byte[] message=bb.toBytes();
+				bb.clear();
+				try {
+//					outstream.println("Sending to "+address+"\n"+message+"\n"); //123
+					StringNum result=ServerTools.sendAndReceive(message, address);
+					if(!ServerTools.suppressErrors && (result.n<200 || result.n>299)){
+						System.err.println("ERROR: Server returned code "+result.n+" and this message:\n"+result.s);
+						KillSwitch.kill();
+					}
+					errorState|=checkForError(result.s);
+					if(!defaultParams.json()){
+						tsw.print(result.s);
+					}else{
+						String s=result.s;
+						
+						{//Fixes rare case of multiple sketches broken into single sketches per block
+							if(!firstBlock || sk!=lastSketch){
+								if(s.charAt(0)!='['){s="["+s;}
+								if(!s.endsWith("]")){;s=s+"]";}
+							}
+						}
+						
+						{//Case where there are more than one block of sketches, breaking JSON array format
+							if(!firstBlock){
+								s=","+s.substring(1);
+							}
+							if(sk!=lastSketch){
+								s=s.substring(0, s.length()-1);
+							}
+						}
+						
+						tsw.print(s);
+						firstBlock=false;
+					}
+				} catch (Exception e) {
+					// TODO Auto-generated catch block
+					e.printStackTrace();
+				}
+				cntr=0;
+			}
+		}
+		
+		if(bb.length>0){//This should no longer trigger unless there are no sketches since it's handled above.
+			if(verbose){outstream.println("Sending:\n"+bb);}
+			byte[] message=bb.toBytes();
+			bb.clear();
+			try {
+				StringNum result=ServerTools.sendAndReceive(message, address);
+				if(!ServerTools.suppressErrors && (result.n<200 || result.n>299)){
+					System.err.println("ERROR: Server returned code "+result.n+" and this message:\n"+result.s);
+					KillSwitch.kill();
+				}
+				errorState|=checkForError(result.s);
+				tsw.print(result.s);
+			} catch (Exception e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			}
+		}
+		if(!silent){tsw.println();}
+		tsw.poison();
+		
+//		outstream.println("sending "+bb.toString());
+		
+		if(outSketch!=null){
+			ByteStreamWriter bsw=new ByteStreamWriter(outSketch, overwrite, append, true, FileFormat.SKETCH);
+			bsw.start();
+			for(Sketch sk : inSketches){
+				sk.toBytes(bb);
+				bsw.print(bb);
+				bb.clear();
+			}
+			bsw.poisonAndWait();
+			errorState|=bsw.errorState;
+		}
+		
+		tsw.waitForFinish();
+		errorState|=tsw.errorState;
+		
+		t.stop();
+//		outstream.println("\nRan "+(inSketches.size()*refSketches.size())+" comparisons in \t"+t);
+		ttotal.stop();
+		if(!silent){outstream.println("Total Time: \t"+ttotal);}
+	}
+	
+	/** For programmatic use */
+	public static String sendSketch(Sketch sk, String address, int format, int chunkNum){
+		address=toAddress(address);
+		ByteBuilder bb=new ByteBuilder();
+
+		DisplayParams params=defaultParams;
+		if(format>=0){
+			new DisplayParams();
+			params.format=format;
+		}
+		if(bb.length==0){bb.append(params.toString(chunkNum));}
+		sk.toBytes(bb);
+
+		byte[] message=bb.toBytes();
+		try {
+//			System.err.println("Sending to "+address+"\n"+new String(message)+"\n"); //123
+			StringNum result=ServerTools.sendAndReceive(message, address);
+			if(!ServerTools.suppressErrors && (result.n<200 || result.n>299)){
+				System.err.println("ERROR: Server returned code "+result.n+" and this message:\n"+result.s);
+				KillSwitch.kill();
+			}
+			return result.s;
+		} catch (Exception e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		return null;
+	}
+	
+	private static boolean checkForError(String s){
+		if(s==null){return false;}
+		return s.contains("java.io.IOException: Server returned HTTP response code:");
+	}
+	
+	private void processLocal(Timer t){
+		Timer ttotal=new Timer();
+		
+		t.start();
+		
+		if(ffout==null){return;}
+		TextStreamWriter tsw=new TextStreamWriter(ffout);
+		tsw.start();
+		
+		final String message=defaultParams.toString(0);
+		for(String fname : in){
+			String address2=address+"/file/"+new File(fname).getAbsolutePath();
+			
+			if(verbose){outstream.println("Sending:\n"+message+"\nto "+address2);}
+			try {
+//				outstream.println("Sending to "+address2+"\n"+message+"\n"); //123
+				StringNum result=ServerTools.sendAndReceive(message.getBytes(), address2);
+				if(!ServerTools.suppressErrors && (result.n<200 || result.n>299)){
+					System.err.println("ERROR: Server returned code "+result.n+" and this message:\n"+result.s);
+					KillSwitch.kill();
+				}
+				tsw.print(result.s);
+			} catch (Exception e) {
+				// TODO Auto-generated catch block
+				if(!suppressErrors){e.printStackTrace();}
+			}
+		}
+		tsw.println();
+		
+//		outstream.println("sending "+bb.toString());
+		
+		tsw.poisonAndWait();
+		errorState|=tsw.errorState;
+		
+		t.stop();
+//		outstream.println("\nRan "+(inSketches.size()*refSketches.size())+" comparisons in \t"+t);
+		ttotal.stop();
+		outstream.println("Total Time: \t"+ttotal);
+	}
+	
+	private void processRefMode(Timer t){
+		Timer ttotal=new Timer();
+		
+		t.start();
+		
+		if(ffout==null){return;}
+		TextStreamWriter tsw=new TextStreamWriter(ffout);
+		tsw.start();
+		
+		final String message=defaultParams.toString(0);
+		{
+			String address2=address+"/ref/"+refNames;
+			
+			if(verbose){outstream.println("Sending:\n"+message+"\nto "+address2);}
+			try {
+//				outstream.println("Sending to "+address2+"\n"+message+"\n"); //123
+				StringNum result=ServerTools.sendAndReceive(message.getBytes(), address2);
+				if(!ServerTools.suppressErrors && (result.n<200 || result.n>299)){
+					System.err.println("ERROR: Server returned code "+result.n+" and this message:\n"+result.s);
+					KillSwitch.kill();
+				}
+				tsw.print(result.s);
+			} catch (Exception e) {
+				// TODO Auto-generated catch block
+				if(!suppressErrors){e.printStackTrace();}
+			}
+		}	
+		tsw.println();
+		
+//		outstream.println("sending "+bb.toString());
+		
+		tsw.poisonAndWait();
+		errorState|=tsw.errorState;
+		
+		t.stop();
+//		outstream.println("\nRan "+(inSketches.size()*refSketches.size())+" comparisons in \t"+t);
+		ttotal.stop();
+		outstream.println("Total Time: \t"+ttotal);
+	}
+	
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Inner Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	private static boolean addFiles(String a, Collection<String> list){
+		int initial=list.size();
+		if(a==null){return false;}
+		File f=null;
+		if(a.indexOf(',')>=0){f=new File(a);}
+		if(f==null || f.exists()){
+			list.add(a);
+		}else{
+			for(String s : a.split(",")){
+				list.add(s);
+			}
+		}
+		return list.size()>initial;
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------            Fields            ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	private ArrayList<String> in=new ArrayList<String>();
+	
+	private String out="stdout.txt";
+	private String outSketch=null;
+	
+	private String taxTreeFile=null;
+	
+	private final SketchTool tool;
+	
+	private ArrayList<Sketch> inSketches;
+
+	private String address=null;
+	private boolean local=false;
+	/** List of reference names or TaxIDs to use as queries */
+	private String refNames=null;
+	
+	/*Override metadata */
+	private String outTaxName=null;
+	private String outFname=null;
+	private String outName0=null;
+	private int outTaxID=-1;
+	private long outSpid=-1;
+	private long outImgID=-1;
+	private ArrayList<String> outMeta=null;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Final Fields         ----------------*/
+	/*--------------------------------------------------------------*/
+
+	/** Primary output file */
+	private final FileFormat ffout;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        Common Fields         ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/** Print status messages to this output stream */
+	private PrintStream outstream=System.err;
+	/** Print verbose messages */
+	public static boolean verbose=false;
+	/** True if an error was encountered */
+	public boolean errorState=false;
+	/** Overwrite existing output files */
+	private boolean overwrite=false;
+	/** Append to existing output files */
+	private boolean append=false;
+	
+	private boolean silent=false;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        Static Fields         ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	public static final String toAddress(String b){
+		String address=b;
+		if(b==null){
+			address=refseqAddress();//default
+		}else if(b.equalsIgnoreCase("nt")){
+			address=ntAddress();
+		}else if(b.equalsIgnoreCase("refseq")){
+			address=refseqAddress();
+		}else if(b.equalsIgnoreCase("silva") || b.equalsIgnoreCase("ribo")){
+			address=silvaAddress();
+		}else if(b.equalsIgnoreCase("img")){
+			address=imgAddress();
+		}else if(b.equalsIgnoreCase("refseqprot") || b.equalsIgnoreCase("prokprot") 
+				|| b.equalsIgnoreCase("protein") || b.equalsIgnoreCase("protien") || b.equalsIgnoreCase("prot")){
+			address=prokProtAddress();
+		}else if(b.equalsIgnoreCase("refseqmito") || b.equalsIgnoreCase("mito")){
+			address=mitoAddress();
+		}else if(b.equalsIgnoreCase("refseqfungi") || b.equalsIgnoreCase("fungi")){
+			address=fungiAddress();
+		}
+		return address;
+	}
+	
+	public int SEND_BUFFER_MAX_BYTES=8000000;
+	public int SEND_BUFFER_MAX_SKETCHES=400;
+	private static final int MAX_ALLOWED_SKETCHES=100000;
+	
+	/** Don't print caught exceptions */
+	public static boolean suppressErrors=false;
+	
+	private static String ntAddress(){return Shared.ntSketchServer()+"sketch";}
+	private static String refseqAddress(){return Shared.refseqSketchServer()+"sketch";}
+	private static String silvaAddress(){return Shared.riboSketchServer()+"sketch";}
+	private static String imgAddress(){return null;}//Shared.SketchServer()+"sketch";
+	private static String nrAddress(){return null;}//Shared.SketchServer()+"sketch";
+	private static String prokProtAddress(){return Shared.proteinSketchServer()+"sketch";}
+	private static String mitoAddress(){return null;}//Shared.SketchServer()+"sketch";
+	private static String fungiAddress(){return null;}//Shared.SketchServer()+"sketch";
+	
+}