--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/aligner/AllToAll.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,444 @@
+package aligner;
+
+import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.concurrent.atomic.AtomicInteger;
+
+import fileIO.ByteFile;
+import fileIO.ByteStreamWriter;
+import fileIO.FileFormat;
+import fileIO.ReadWrite;
+import shared.Parse;
+import shared.Parser;
+import shared.PreParser;
+import shared.ReadStats;
+import shared.Shared;
+import shared.Timer;
+import shared.Tools;
+import sketch.SketchObject;
+import stream.ConcurrentReadInputStream;
+import stream.FastaReadInputStream;
+import stream.Read;
+import template.Accumulator;
+import template.ThreadWaiter;
+
+/**
+ * Aligns all sequences to all sequences and produces an identity matrix.
+ * 
+ * @author Brian Bushnell
+ * @date January 27, 2020
+ *
+ */
+public class AllToAll implements Accumulator<AllToAll.ProcessThread> {
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        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();
+		
+		//Create an instance of this class
+		AllToAll x=new AllToAll(args);
+		
+		//Run the object
+		x.process(t);
+		
+		//Close the print stream if it was redirected
+		Shared.closeStream(x.outstream);
+	}
+	
+	/**
+	 * Constructor.
+	 * @param args Command line arguments
+	 */
+	public AllToAll(String[] args){
+		
+		{//Preparse block for help, config files, and outstream
+			PreParser pp=new PreParser(args, getClass(), false);
+			args=pp.args;
+			outstream=pp.outstream;
+		}
+		
+		//Set shared static variables prior to parsing
+		ReadWrite.USE_PIGZ=ReadWrite.USE_UNPIGZ=true;
+		ReadWrite.MAX_ZIP_THREADS=Shared.threads();
+		
+		{//Parse the arguments
+			final Parser parser=parse(args);
+			Parser.processQuality();
+			
+			maxReads=parser.maxReads;
+			overwrite=ReadStats.overwrite=parser.overwrite;
+			append=ReadStats.append=parser.append;
+			
+			in1=parser.in1;
+			qfin1=parser.qfin1;
+			extin=parser.extin;
+
+			out1=parser.out1;
+		}
+
+		validateParams();
+		fixExtensions(); //Add or remove .gz or .bz2 as needed
+		checkFileExistence(); //Ensure files can be read and written
+		checkStatics(); //Adjust file-related static fields as needed for this program 
+		
+		//Create output FileFormat objects
+		ffout1=FileFormat.testOutput(out1, FileFormat.TXT, null, true, overwrite, append, ordered);
+
+		//Create input FileFormat objects
+		ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true);
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------    Initialization Helpers    ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/** Parse arguments from the command line */
+	private Parser parse(String[] args){
+		
+		//Create a parser object
+		Parser parser=new Parser();
+		parser.out1="stdout.txt";
+		
+		//Set any necessary Parser defaults here
+		//parser.foo=bar;
+		
+		//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(b!=null && b.equalsIgnoreCase("null")){b=null;}
+			
+			if(a.equals("verbose")){
+				verbose=Parse.parseBoolean(b);
+			}else if(a.equals("ordered")){
+				ordered=Parse.parseBoolean(b);
+			}else if(a.equals("parse_flag_goes_here")){
+				long fake_variable=Parse.parseKMG(b);
+				//Set a variable here
+			}else if(parser.parse(arg, a, b)){//Parse standard flags in the parser
+				//do nothing
+			}else{
+				outstream.println("Unknown parameter "+args[i]);
+				assert(false) : "Unknown parameter "+args[i];
+			}
+		}
+		
+		return parser;
+	}
+	
+	/** Add or remove .gz or .bz2 as needed */
+	private void fixExtensions(){
+		in1=Tools.fixExtension(in1);
+		qfin1=Tools.fixExtension(qfin1);
+	}
+	
+	/** Ensure files can be read and written */
+	private void checkFileExistence(){
+		
+		//Ensure output files can be written
+		if(!Tools.testOutputFiles(overwrite, append, false, out1)){
+			outstream.println((out1==null)+", "+out1);
+			throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output file "+out1+"\n");
+		}
+		
+		//Ensure input files can be read
+		if(!Tools.testInputFiles(false, true, in1)){
+			throw new RuntimeException("\nCan't read some input files.\n");  
+		}
+		
+		//Ensure that no file was specified multiple times
+		if(!Tools.testForDuplicateFiles(true, in1, out1)){
+			throw new RuntimeException("\nSome file names were specified multiple times.\n");
+		}
+	}
+	
+	/** Adjust file-related static fields as needed for this program */
+	private static void checkStatics(){
+		//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;
+		}
+		
+		assert(FastaReadInputStream.settingsOK());
+	}
+	
+	/** Ensure parameter ranges are within bounds and required parameters are set */
+	private boolean validateParams(){
+		//Ensure there is an input file
+		if(in1==null){throw new RuntimeException("Error - at least one input file is required.");}
+		return true;
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Outer Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+
+	/** Create read streams and process all reads */
+	void process(Timer t){
+		
+		//Turn off read validation in the input threads to increase speed
+		final boolean vic=Read.VALIDATE_IN_CONSTRUCTOR;
+		Read.VALIDATE_IN_CONSTRUCTOR=Shared.threads()<4;
+		
+		//Reset counters
+		readsProcessed=alignments=0;
+		basesProcessed=0;
+		
+		//Fetch data
+		reads=ConcurrentReadInputStream.getReads(maxReads, true, ffin1, null, qfin1, null); //TODO:  Note that this does not return the error state
+		results=new float[reads.size()][];
+		
+		outstream.println("Loaded "+reads.size()+" sequences.");
+		
+		//Process the reads in separate threads
+		spawnThreads();
+		mirrorMatrix(results);
+		if(verbose){outstream.println("Finished alignment.");}
+		
+		printResults();
+		
+		//Reset read validation
+		Read.VALIDATE_IN_CONSTRUCTOR=vic;
+		
+		//Report timing and results
+		t.stop();
+		outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8));
+		outstream.println(Tools.number("Alignments:", alignments, 8));
+		
+		//Throw an exception of there was an error in a thread
+		if(errorState){
+			throw new RuntimeException(getClass().getName()+" terminated in an error state; the output may be corrupt.");
+		}
+	}
+	
+	private static void mirrorMatrix(float[][] matrix){
+		for(int i=0; i<matrix.length; i++) {
+			for(int j=i; j<matrix.length; j++) {
+				assert(matrix[i][j]==0) : matrix[i][j];
+				matrix[i][j]=(i==j ? 1 : matrix[j][i]);
+			}
+		}
+	}
+	
+	private void printResults(){
+		if(ffout1==null){return;}
+		ByteStreamWriter bsw=new ByteStreamWriter(ffout1);
+		bsw.start();
+		final int max=reads.size();
+		bsw.print("Name");
+		for(int rnum=0; rnum<max; rnum++){
+			bsw.tab().print(reads.get(rnum).id);
+		}
+		bsw.println();
+		for(int qnum=0; qnum<max; qnum++){
+			bsw.print(reads.get(qnum).id);
+			final float[] scores=results[qnum];
+			for(int rnum=0; rnum<max; rnum++){
+				bsw.tab().print(100*scores[rnum], 2);
+			}
+			bsw.println();
+		}
+		bsw.poisonAndWait();
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------       Thread Management      ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/** Spawn process threads */
+	private void spawnThreads(){
+		
+		//Do anything necessary prior to processing
+		
+		//Determine how many threads may be used
+		final int threads=Shared.threads();
+		
+		AtomicInteger atom=new AtomicInteger(0);
+		
+		//Fill a list with ProcessThreads
+		ArrayList<ProcessThread> alpt=new ArrayList<ProcessThread>(threads);
+		for(int i=0; i<threads; i++){
+			alpt.add(new ProcessThread(reads, results, atom, i));
+		}
+		
+		//Start the threads and wait for them to finish
+		boolean success=ThreadWaiter.startAndWait(alpt, this);
+		errorState&=!success;
+		
+		//Do anything necessary after processing
+		
+	}
+	
+	@Override
+	public final void accumulate(ProcessThread pt){
+		readsProcessed+=pt.readsProcessedT;
+		basesProcessed+=pt.basesProcessedT;
+		alignments+=pt.alignmentsT;
+		errorState|=(!pt.success);
+	}
+	
+	@Override
+	public final boolean success(){return !errorState;}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Inner Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Inner Classes        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/** This class is static to prevent accidental writing to shared variables.
+	 * It is safe to remove the static modifier. */
+	static class ProcessThread extends Thread {
+		
+		//Constructor
+		ProcessThread(final ArrayList<Read> reads_, float[][] results_, final AtomicInteger atom_, final int tid_){
+			reads=reads_;
+			results=results_;
+			atom=atom_;
+			tid=tid_;
+		}
+		
+		//Called by start()
+		@Override
+		public void run(){
+			//Do anything necessary prior to processing
+			
+			//Process the reads
+			processInner();
+			
+			//Do anything necessary after processing
+			
+			//Indicate successful exit status
+			success=true;
+		}
+		
+		/** Iterate through the reads */
+		void processInner(){
+			
+			for(int next=atom.getAndIncrement(); next<reads.size(); next=atom.getAndIncrement()){
+				processQuery(next);
+			}
+			
+		}
+		
+		void processQuery(final int qnum){
+			final Read query=reads.get(qnum);
+			final float[] scores=new float[reads.size()];
+			readsProcessedT++;
+			basesProcessedT+=query.length();
+			for(int rnum=0; rnum<qnum; rnum++){
+				final Read ref=reads.get(rnum);
+				float identity=SketchObject.align(query.bases, ref.bases);
+				scores[rnum]=identity;
+				alignmentsT++;
+			}
+			synchronized(results){
+				results[qnum]=scores;
+			}
+		}
+		
+		/**
+		 * Process a read or a read pair.
+		 * @param r1 Read 1
+		 * @param r2 Read 2 (may be null)
+		 * @return True if the reads should be kept, false if they should be discarded.
+		 */
+		boolean processReadPair(final Read r1, final Read r2){
+			throw new RuntimeException("TODO: Implement this method."); //TODO
+//			return true;
+		}
+
+		/** Number of reads processed by this thread */
+		protected long readsProcessedT=0;
+		/** Number of bases processed by this thread */
+		protected long basesProcessedT=0;
+		
+		/** Number of reads retained by this thread */
+		protected long alignmentsT=0;
+		/** Number of bases retained by this thread */
+		protected long basesOutT=0;
+		
+		/** True only if this thread has completed successfully */
+		boolean success=false;
+		
+		/** Thread ID */
+		final int tid;
+		
+		final ArrayList<Read> reads;
+		final float[][] results;
+		final AtomicInteger atom;
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------            Fields            ----------------*/
+	/*--------------------------------------------------------------*/
+
+	/** Primary input file path */
+	private String in1=null;
+	
+	private String qfin1=null;
+
+	/** Primary output file path */
+	private String out1=null;
+	
+	/** Override input file extension */
+	private String extin=null;
+	
+	/*--------------------------------------------------------------*/
+
+	ArrayList<Read> reads;
+	float[][] results;
+	
+	/** Number of reads processed */
+	protected long readsProcessed=0;
+	/** Number of bases processed */
+	protected long basesProcessed=0;
+
+	/** Number of reads retained */
+	protected long alignments=0;
+
+	/** Quit after processing this many input reads; -1 means no limit */
+	private long maxReads=-1;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Final Fields         ----------------*/
+	/*--------------------------------------------------------------*/
+
+	/** Primary input file */
+	private final FileFormat ffin1;
+	
+	/** Primary output file */
+	private final FileFormat ffout1;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        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;
+	/** Reads are output in input order */
+	private boolean ordered=false;
+	
+}