jpayne@68: package sketch;
jpayne@68: 
jpayne@68: import java.io.PrintStream;
jpayne@68: import java.util.ArrayList;
jpayne@68: import java.util.Collections;
jpayne@68: import java.util.HashMap;
jpayne@68: import java.util.Map.Entry;
jpayne@68: import java.util.concurrent.atomic.AtomicInteger;
jpayne@68: 
jpayne@68: import fileIO.ByteFile;
jpayne@68: import fileIO.ByteStreamWriter;
jpayne@68: import fileIO.FileFormat;
jpayne@68: import fileIO.ReadWrite;
jpayne@68: import shared.Parse;
jpayne@68: import shared.Parser;
jpayne@68: import shared.PreParser;
jpayne@68: import shared.ReadStats;
jpayne@68: import shared.Shared;
jpayne@68: import shared.Timer;
jpayne@68: import shared.Tools;
jpayne@68: import stream.FASTQ;
jpayne@68: import stream.FastaReadInputStream;
jpayne@68: import stream.Read;
jpayne@68: import structures.ByteBuilder;
jpayne@68: import structures.FloatList;
jpayne@68: import tax.TaxNode;
jpayne@68: import tax.TaxTree;
jpayne@68: import template.Accumulator;
jpayne@68: import template.ThreadWaiter;
jpayne@68: 
jpayne@68: /**
jpayne@68:  * Compares SSUs, all-to-all or fractional matrix.
jpayne@68:  * 
jpayne@68:  * @author Brian Bushnell
jpayne@68:  * @date December 2, 2019
jpayne@68:  *
jpayne@68:  */
jpayne@68: public class CompareSSU implements Accumulator<CompareSSU.ProcessThread> {
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------        Initialization        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	/**
jpayne@68: 	 * Code entrance from the command line.
jpayne@68: 	 * @param args Command line arguments
jpayne@68: 	 */
jpayne@68: 	public static void main(String[] args){
jpayne@68: 		//Start a timer immediately upon code entrance.
jpayne@68: 		Timer t=new Timer();
jpayne@68: 		
jpayne@68: 		//Create an instance of this class
jpayne@68: 		CompareSSU x=new CompareSSU(args);
jpayne@68: 		
jpayne@68: 		//Run the object
jpayne@68: 		x.process(t);
jpayne@68: 		
jpayne@68: 		//Close the print stream if it was redirected
jpayne@68: 		Shared.closeStream(x.outstream);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/**
jpayne@68: 	 * Constructor.
jpayne@68: 	 * @param args Command line arguments
jpayne@68: 	 */
jpayne@68: 	public CompareSSU(String[] args){
jpayne@68: 		
jpayne@68: 		{//Preparse block for help, config files, and outstream
jpayne@68: 			PreParser pp=new PreParser(args, getClass(), false);
jpayne@68: 			args=pp.args;
jpayne@68: 			outstream=pp.outstream;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		//Set shared static variables prior to parsing
jpayne@68: 		ReadWrite.USE_PIGZ=ReadWrite.USE_UNPIGZ=true;
jpayne@68: 		ReadWrite.MAX_ZIP_THREADS=Shared.threads();
jpayne@68: 		
jpayne@68: 		{//Parse the arguments
jpayne@68: 			final Parser parser=parse(args);
jpayne@68: 			Parser.processQuality();
jpayne@68: 			
jpayne@68: 			maxReads=parser.maxReads;
jpayne@68: 			overwrite=ReadStats.overwrite=parser.overwrite;
jpayne@68: 			append=ReadStats.append=parser.append;
jpayne@68: 			
jpayne@68: 			in1=parser.in1;
jpayne@68: 
jpayne@68: 			out1=parser.out1;
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		validateParams();
jpayne@68: 		if(in1==null){throw new RuntimeException("Error - at least one input file is required.");}
jpayne@68: 		FASTQ.FORCE_INTERLEAVED=FASTQ.TEST_INTERLEAVED=false;
jpayne@68: 		checkFileExistence(); //Ensure files can be read and written
jpayne@68: 		checkStatics(); //Adjust file-related static fields as needed for this program 
jpayne@68: 		
jpayne@68: 		//Create output FileFormat objects
jpayne@68: 		ffout1=FileFormat.testOutput(out1, FileFormat.TXT, null, true, overwrite, append, ordered);
jpayne@68: 		
jpayne@68: 		tree=(treeFile==null) ? null : TaxTree.loadTaxTree(treeFile, outstream, true, false);
jpayne@68: 		
jpayne@68: 		SSUMap.r16SFile=in1;
jpayne@68: 		if(SSUMap.r16SFile!=null){
jpayne@68: 			SSUMap.load(outstream);
jpayne@68: 			HashMap<Integer, byte[]> ssuMap=SSUMap.r16SMap;
jpayne@68: 			ssuList=new ArrayList<Read>(ssuMap.size());
jpayne@68: 			for(Entry<Integer, byte[]> e : ssuMap.entrySet()){
jpayne@68: 				int id=e.getKey();
jpayne@68: 				byte[] value=e.getValue();
jpayne@68: 				if(value.length>=minlen && value.length<=maxlen){
jpayne@68: 					Read r=new Read(value, null, id);//Sets numeric ID to TaxID.
jpayne@68: 					if(maxns<0 || r.countNocalls()<=maxns){
jpayne@68: 						ssuList.add(r);
jpayne@68: 					}
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 			Collections.shuffle(ssuList);
jpayne@68: 		}
jpayne@68: 		for(int i=0; i<idLists.length; i++){
jpayne@68: 			idLists[i]=new FloatList();
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------    Initialization Helpers    ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	/** Parse arguments from the command line */
jpayne@68: 	private Parser parse(String[] args){
jpayne@68: 		
jpayne@68: 		//Create a parser object
jpayne@68: 		Parser parser=new Parser();
jpayne@68: 		
jpayne@68: 		//Set any necessary Parser defaults here
jpayne@68: 		//parser.foo=bar;
jpayne@68: 		
jpayne@68: 		//Parse each argument
jpayne@68: 		for(int i=0; i<args.length; i++){
jpayne@68: 			String arg=args[i];
jpayne@68: 			
jpayne@68: 			//Break arguments into their constituent parts, in the form of "a=b"
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;}
jpayne@68: 			
jpayne@68: 			if(a.equals("verbose")){
jpayne@68: 				verbose=Parse.parseBoolean(b);
jpayne@68: 			}else if(a.equals("tree")){
jpayne@68: 				treeFile=b;
jpayne@68: 			}else if(a.equals("ordered")){
jpayne@68: 				ordered=Parse.parseBoolean(b);
jpayne@68: 			}else if(a.equals("ata") || a.equals("alltoall")){
jpayne@68: 				allToAll=Parse.parseBoolean(b);
jpayne@68: 			}else if(a.equals("store") || a.equals("storeresults")){
jpayne@68: 				storeResults=Parse.parseBoolean(b);
jpayne@68: 			}else if(a.equals("minlen") || a.equals("maxlength")){
jpayne@68: 				minlen=Parse.parseIntKMG(b);
jpayne@68: 			}else if(a.equals("maxlen") || a.equals("maxlength")){
jpayne@68: 				maxlen=Parse.parseIntKMG(b);
jpayne@68: 			}else if(a.equalsIgnoreCase("maxns")){
jpayne@68: 				maxns=Parse.parseIntKMG(b);
jpayne@68: 			}else if(a.equals("parse_flag_goes_here")){
jpayne@68: 				long fake_variable=Parse.parseKMG(b);
jpayne@68: 				//Set a variable here
jpayne@68: 			}else if(parser.parse(arg, a, b)){//Parse standard flags in the parser
jpayne@68: 				//do nothing
jpayne@68: 			}else{
jpayne@68: 				outstream.println("Unknown parameter "+args[i]);
jpayne@68: 				assert(false) : "Unknown parameter "+args[i];
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		return parser;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Ensure files can be read and written */
jpayne@68: 	private void checkFileExistence(){
jpayne@68: 		//Ensure output files can be written
jpayne@68: 		if(!Tools.testOutputFiles(overwrite, append, false, out1)){
jpayne@68: 			outstream.println((out1==null)+", "+out1);
jpayne@68: 			throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output file "+out1+"\n");
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		//Ensure input files can be read
jpayne@68: 		if(!Tools.testInputFiles(false, true, in1)){
jpayne@68: 			throw new RuntimeException("\nCan't read some input files.\n");  
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		//Ensure that no file was specified multiple times
jpayne@68: 		if(!Tools.testForDuplicateFiles(true, in1, out1)){
jpayne@68: 			throw new RuntimeException("\nSome file names were specified multiple times.\n");
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Adjust file-related static fields as needed for this program */
jpayne@68: 	private static void checkStatics(){
jpayne@68: 		//Adjust the number of threads for input file reading
jpayne@68: 		if(!ByteFile.FORCE_MODE_BF1 && !ByteFile.FORCE_MODE_BF2 && Shared.threads()>2){
jpayne@68: 			ByteFile.FORCE_MODE_BF2=true;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		assert(FastaReadInputStream.settingsOK());
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Ensure parameter ranges are within bounds and required parameters are set */
jpayne@68: 	private boolean validateParams(){
jpayne@68: 		return true;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------         Outer Methods        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 
jpayne@68: 	/** Create read streams and process all data */
jpayne@68: 	void process(Timer t){
jpayne@68: 		
jpayne@68: 		ByteStreamWriter bsw=makeBSW(ffout1);
jpayne@68: 		if(bsw!=null){
jpayne@68: 			bsw.forcePrint("#Level\tIdentity\tQueryID\tRefID\n");
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		//Reset counters
jpayne@68: 		queriesProcessed=0;
jpayne@68: 		comparisons=0;
jpayne@68: 		
jpayne@68: 		//Process the reads in separate threads
jpayne@68: 		spawnThreads(bsw);
jpayne@68: 		
jpayne@68: 		if(verbose){outstream.println("Finished; closing streams.");}
jpayne@68: 		
jpayne@68: 		//Close the read streams
jpayne@68: 		if(bsw!=null){errorState|=bsw.poisonAndWait();}
jpayne@68: 		
jpayne@68: 		{
jpayne@68: 			ByteBuilder bb=new ByteBuilder();
jpayne@68: 			bb.append("\nLevel       \tCount\tMean"+(storeResults ? "\tMedian\t90%ile\t10%ile\tSTDev" : "")+"\n");
jpayne@68: 			outstream.print(bb);
jpayne@68: 			final int minlen="superkingdom".length();
jpayne@68: 			for(int level=0; level<taxLevels; level++){
jpayne@68: 				if(counts[level]>0){
jpayne@68: 					bb.clear();
jpayne@68: 					bb.append(TaxTree.levelToStringExtended(level));
jpayne@68: 					while(bb.length()<minlen){bb.space();}
jpayne@68: 					bb.tab().append(counts[level]).tab();
jpayne@68: 					bb.append(sums[level]/counts[level]*100, 3);
jpayne@68: 					if(storeResults){
jpayne@68: 						FloatList list=idLists[level];
jpayne@68: 						list.sort();
jpayne@68: 						double stdev=list.stdev();
jpayne@68: 						double median=list.median();
jpayne@68: //						double mode=list.mode();
jpayne@68: 						double percent90=list.percentile(0.9f);
jpayne@68: 						double percent10=list.percentile(0.1f);
jpayne@68: 						bb.tab().append(median*100, 3).tab().append(percent90*100, 3).tab().append(percent10*100, 3).tab().append(stdev*100, 3);
jpayne@68: 					}
jpayne@68: 					bb.nl();
jpayne@68: 					outstream.print(bb);
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		//Report timing and results
jpayne@68: 		t.stop();
jpayne@68: 		outstream.println();
jpayne@68: 		outstream.println(Tools.timeQueriesComparisonsProcessed(t, queriesProcessed, comparisons, 8));
jpayne@68: 		
jpayne@68: 		//Throw an exception of there was an error in a thread
jpayne@68: 		if(errorState){
jpayne@68: 			throw new RuntimeException(getClass().getName()+" terminated in an error state; the output may be corrupt.");
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------       Thread Management      ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	/** Spawn process threads */
jpayne@68: 	private void spawnThreads(ByteStreamWriter bsw){
jpayne@68: 		
jpayne@68: 		//Do anything necessary prior to processing
jpayne@68: 		
jpayne@68: 		//Determine how many threads may be used
jpayne@68: 		final int threads=Shared.threads();
jpayne@68: 		
jpayne@68: 		//Fill a list with ProcessThreads
jpayne@68: 		ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads);
jpayne@68: 		for(int i=0; i<threads; i++){
jpayne@68: 			alpt.add(new ProcessThread(bsw, i, threads));
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		//Start the threads and wait for them to finish
jpayne@68: 		boolean success=ThreadWaiter.startAndWait(alpt, this);
jpayne@68: 		errorState&=!success;
jpayne@68: 		
jpayne@68: 		//Do anything necessary after processing
jpayne@68: 		
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public final void accumulate(ProcessThread pt){
jpayne@68: 		queriesProcessed+=pt.querysProcessedT;
jpayne@68: 		comparisons+=pt.comparisonsT;
jpayne@68: 		errorState|=(!pt.success);
jpayne@68: 
jpayne@68: 		for(int i=0; i<taxLevels; i++){
jpayne@68: 			idLists[i].addAll(pt.idListsT[i]);
jpayne@68: 			counts[i]+=pt.countsT[i];
jpayne@68: 			sums[i]+=pt.sumsT[i];
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public final boolean success(){return !errorState;}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------         Inner Methods        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	private static ByteStreamWriter makeBSW(FileFormat ff){
jpayne@68: 		if(ff==null){return null;}
jpayne@68: 		ByteStreamWriter bsw=new ByteStreamWriter(ff);
jpayne@68: 		bsw.start();
jpayne@68: 		return bsw;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------         Inner Classes        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	/** This class is static to prevent accidental writing to shared variables.
jpayne@68: 	 * It is safe to remove the static modifier. */
jpayne@68: 	class ProcessThread extends Thread {
jpayne@68: 		
jpayne@68: 		//Constructor
jpayne@68: 		ProcessThread(ByteStreamWriter bsw_, final int tid_, final int threads_){
jpayne@68: 			bsw=bsw_;
jpayne@68: 			threadID=tid_;
jpayne@68: 			threads=threads_;
jpayne@68: 			listCopy=new ArrayList<Read>(ssuList.size());
jpayne@68: 			listCopy.addAll(ssuList);
jpayne@68: 			for(int i=0; i<idListsT.length; i++){
jpayne@68: 				idListsT[i]=new FloatList();
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		//Called by start()
jpayne@68: 		@Override
jpayne@68: 		public void run(){
jpayne@68: 			//Do anything necessary prior to processing
jpayne@68: 			
jpayne@68: 			//Process the reads
jpayne@68: 			processInner();
jpayne@68: 			
jpayne@68: 			//Do anything necessary after processing
jpayne@68: 			
jpayne@68: 			//Indicate successful exit status
jpayne@68: 			success=true;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		/** Iterate through the reads */
jpayne@68: 		void processInner(){
jpayne@68: 			final long limit=Tools.min(ssuList.size(), (maxReads>0 ? maxReads : Integer.MAX_VALUE));
jpayne@68: 			
jpayne@68: 			for(int num=next.getAndIncrement(); num<limit; num=next.getAndIncrement()){
jpayne@68: 				Read r=ssuList.get(num);
jpayne@68: 				processRead(r);
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		void processRead(Read query){
jpayne@68: 			if(query.numericID<1){return;}//invalid TID
jpayne@68: 			final int qid=(int)query.numericID;
jpayne@68: 			if(tree.getNode(qid)==null) {return;}
jpayne@68: 			if(querysProcessedT%5==0) {
jpayne@68: 				Collections.shuffle(listCopy);
jpayne@68: 			}
jpayne@68: 			querysProcessedT++;
jpayne@68: 			
jpayne@68: 			ByteBuilder bb=new ByteBuilder();
jpayne@68: 			
jpayne@68: 			long seen=0;
jpayne@68: 			for(Read ref :listCopy){
jpayne@68: 				int rid=(int)ref.numericID;
jpayne@68: 				if(rid!=qid && rid>0 && tree.getNode(rid)!=null){
jpayne@68: 					int aid=tree.commonAncestor(qid, rid);
jpayne@68: 					if(aid>0){
jpayne@68: 						TaxNode tn=tree.getNode(aid);
jpayne@68: 						if(tn.isRanked()){
jpayne@68: 							int level=tn.levelExtended;
jpayne@68: 							long mask=1L<<level;
jpayne@68: 							if(allToAll || ((mask&printLevels)!=0 && (mask&seen)==0)){
jpayne@68: 								seen|=mask;
jpayne@68: 								float identity=compare(query, ref, level);
jpayne@68: 								bb.append(TaxTree.levelToStringExtended(level)).tab().append(identity, 6);
jpayne@68: 								bb.tab().append(qid).tab().append(rid).nl();
jpayne@68: 							}
jpayne@68: 						}
jpayne@68: 					}
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 			if(bsw!=null){
jpayne@68: 				bsw.addJob(bb);
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		float compare(Read query, Read ref, int level){
jpayne@68: 			comparisonsT++;
jpayne@68: 			float identity=SketchObject.align(query.bases, ref.bases);
jpayne@68: 			if(storeResults){idListsT[level].add(identity);}
jpayne@68: 			countsT[level]++;
jpayne@68: 			sumsT[level]+=identity;
jpayne@68: 			return identity;
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		/** Number of reads processed by this thread */
jpayne@68: 		protected long querysProcessedT=0;
jpayne@68: 		/** Number of bases processed by this thread */
jpayne@68: 		protected long comparisonsT=0;
jpayne@68: 		
jpayne@68: 		/** True only if this thread has completed successfully */
jpayne@68: 		boolean success=false;
jpayne@68: 		
jpayne@68: 		/** Shared output stream */
jpayne@68: 		private final ByteStreamWriter bsw;
jpayne@68: 		/** Thread ID */
jpayne@68: 		final int threadID;
jpayne@68: 		
jpayne@68: 		final int threads;
jpayne@68: 		
jpayne@68: 		ArrayList<Read> listCopy;
jpayne@68: 		
jpayne@68: 		final FloatList[] idListsT=new FloatList[taxLevels];
jpayne@68: 		long[] countsT=new long[taxLevels];
jpayne@68: 		double[] sumsT=new double[taxLevels];
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------            Fields            ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 
jpayne@68: 	/** Primary input file path */
jpayne@68: 	private String in1=null;
jpayne@68: 	
jpayne@68: 	private String treeFile="auto";
jpayne@68: 
jpayne@68: 	/** Primary output file path */
jpayne@68: 	private String out1=null;
jpayne@68: 	
jpayne@68: 	public static ArrayList<Read> ssuList=null;
jpayne@68: 
jpayne@68: 	final static int taxLevels=TaxTree.numTaxLevelNamesExtended;
jpayne@68: 	static final String[] printLevelsArray=new String[] {"strain", "species", "genus", "family", "order", "class", "phylum", "superkingdom", "life"};
jpayne@68: 	static final long printLevels=makePrintLevels(printLevelsArray);
jpayne@68: 	
jpayne@68: 	private final TaxTree tree;
jpayne@68: 	
jpayne@68: 	private static final long makePrintLevels(String[] names){
jpayne@68: 		long mask=0;
jpayne@68: 		for(String s : names){
jpayne@68: 			int level=TaxTree.stringToLevelExtended(s);
jpayne@68: 			mask|=(1L<<level);
jpayne@68: 		}
jpayne@68: 		return mask;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private FloatList[] idLists=new FloatList[taxLevels];
jpayne@68: 	private long[] counts=new long[taxLevels];
jpayne@68: 	private double[] sums=new double[taxLevels];
jpayne@68: 	
jpayne@68: 	private int minlen=0;
jpayne@68: 	private int maxlen=Integer.MAX_VALUE;
jpayne@68: 	private int maxns=-1;
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 
jpayne@68: 	/** Number of reads processed */
jpayne@68: 	protected long queriesProcessed=0;
jpayne@68: 	/** Number of bases processed */
jpayne@68: 	protected long comparisons=0;
jpayne@68: 
jpayne@68: 	/** Quit after processing this many input reads; -1 means no limit */
jpayne@68: 	private long maxReads=-1;
jpayne@68: 	
jpayne@68: 	private AtomicInteger next=new AtomicInteger(0);
jpayne@68: 
jpayne@68: 	private boolean allToAll=false;
jpayne@68: 	private boolean storeResults=false;
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------         Final Fields         ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	/** Primary output file */
jpayne@68: 	private final FileFormat ffout1;
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------        Common Fields         ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	/** Print status messages to this output stream */
jpayne@68: 	private PrintStream outstream=System.err;
jpayne@68: 	/** Print verbose messages */
jpayne@68: 	public static boolean verbose=false;
jpayne@68: 	/** True if an error was encountered */
jpayne@68: 	public boolean errorState=false;
jpayne@68: 	/** Overwrite existing output files */
jpayne@68: 	private boolean overwrite=false;
jpayne@68: 	/** Append to existing output files */
jpayne@68: 	private boolean append=false;
jpayne@68: 	/** Reads are output in input order */
jpayne@68: 	private boolean ordered=false;
jpayne@68: 	
jpayne@68: }