--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/tax/ExplodeTree.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,360 @@
+package tax;
+
+import java.io.File;
+import java.io.PrintStream;
+import java.util.LinkedHashMap;
+import java.util.Locale;
+
+import fileIO.ByteFile;
+import fileIO.ByteStreamWriter;
+import fileIO.FileFormat;
+import fileIO.ReadWrite;
+import fileIO.TextStreamWriter;
+import shared.Parse;
+import shared.Parser;
+import shared.PreParser;
+import shared.Shared;
+import shared.Timer;
+import shared.Tools;
+import stream.FastaReadInputStream;
+
+/**
+ * Constructs a directory and file tree of sequences
+ * corresponding to a taxonomic tree.
+ * 
+ * @author Brian Bushnell
+ * @date December 12, 2017
+ *
+ */
+public class ExplodeTree {
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        Initialization        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/**
+	 * Code entrance from the command line.
+	 * @param args Command line arguments
+	 */
+	public static void main(String[] args){
+		Timer t=new Timer();
+		ExplodeTree x=new ExplodeTree(args);
+		x.process(t);
+		
+		//Close the print stream if it was redirected
+		Shared.closeStream(x.outstream);
+	}
+	
+	/**
+	 * Constructor.
+	 * @param args Command line arguments
+	 */
+	public ExplodeTree(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
+		ReadWrite.USE_PIGZ=ReadWrite.USE_UNPIGZ=true;
+		ReadWrite.MAX_ZIP_THREADS=Shared.threads();
+		
+		//Create a parser object
+		Parser parser=new Parser();
+		
+		//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("out") || a.equals("path") || a.equals("outpath")){
+				outPath=b;
+			}else if(a.equals("prefix")){
+				prefix=b;
+			}else if(a.equals("results") || a.equals("result")){
+				resultsFile=b;
+			}else if(a.equals("makedirectories") || a.equals("mkdirs") || a.equals("mkdir")){
+				makeDirectories=Parse.parseBoolean(b);
+			}else if(a.equals("tree") || a.equals("taxtree")){
+				taxTreeFile=b;
+			}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];
+				//				throw new RuntimeException("Unknown parameter "+args[i]);
+			}
+		}
+		if(prefix==null){prefix="";}
+		if("auto".equalsIgnoreCase(taxTreeFile)){taxTreeFile=TaxTree.defaultTreeFile();}
+		
+		{//Process parser fields
+			Parser.processQuality();
+			
+			maxReads=parser.maxReads;
+			
+			overwrite=parser.overwrite;
+			
+			in1=parser.in1;
+			
+			extin=parser.extin;
+		}
+		
+		if(outPath==null || outPath.trim().length()==0){outPath="";}
+		else{
+			outPath=outPath.trim().replace('\\', '/').replaceAll("/+", "/");
+			if(!outPath.endsWith("/")){outPath=outPath+"/";}
+		}
+		
+		assert(FastaReadInputStream.settingsOK());
+		
+		//Ensure there is an input file
+		if(in1==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;
+		}
+		
+		//Ensure output files can be written
+		if(!Tools.testOutputFiles(overwrite, false, false, resultsFile)){
+			outstream.println(resultsFile);
+			throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output files "+resultsFile+"\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, resultsFile)){
+			throw new RuntimeException("\nSome file names were specified multiple times.\n");
+		}
+
+		//Create input FileFormat objects
+		ffin1=FileFormat.testInput(in1, FileFormat.FASTA, extin, true, true);
+		
+		tree=TaxTree.loadTaxTree(taxTreeFile, outstream, true, false);
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Outer Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	public void makeDirectoryTree(String root, boolean writeNames){
+		for(TaxNode node : tree.nodes){
+			if(node!=null){
+				String dir=tree.toDir(node, root);
+				File df=new File(dir);
+				if(!df.exists()){df.mkdirs();}
+				if(writeNames){
+					try {
+						String fname=node.simpleName()+".name";
+						File nf=new File(fname);
+						if(!nf.exists()){
+							ReadWrite.writeString(node.name, dir+fname);
+						}
+					} catch (Exception e) {
+						// TODO Auto-generated catch block
+						e.printStackTrace();
+					}
+				}
+			}
+		}
+	}
+	
+	/** Create read streams and process all data */
+	public void process(Timer t){
+		
+		Timer t2=new Timer();
+		if(makeDirectories){
+			makeDirectoryTree(outPath, true);
+			t2.stop("Finished making directories. ");
+			t2.start();
+		}
+		processInner();
+		t2.stop();
+		t2.stop("Finished writing data. ");
+		
+		//Do anything necessary after processing
+		
+		if(resultsFile!=null){
+			TextStreamWriter tsw=new TextStreamWriter(resultsFile, overwrite, false, false);
+			tsw.start();
+			for(TaxNode tn : nodes.keySet()){
+				Long data=nodes.get(tn);
+				if(data==null){data=0L;}
+				tsw.println(tn.id+"\t"+data+"\t"+tn.levelStringExtended(false)+"\t"+tn.name);
+			}
+			errorState|=tsw.poisonAndWait();
+		}
+		
+		//Report timing and results
+		{
+			t.stop();
+			
+			//Calculate units per nanosecond
+			double rpnano=readsProcessed/(double)(t.elapsed);
+			double lpnano=linesProcessed/(double)(t.elapsed);
+			double bpnano=basesProcessed/(double)(t.elapsed);
+			
+			//Add "k" and "m" for large numbers
+			String rpstring=Tools.padKM(readsProcessed, 8);
+			String lpstring=Tools.padKM(linesProcessed, 8);
+			String bpstring=Tools.padKM(basesProcessed, 8);
+
+			String li="Lines In:               \t"+linesProcessed+" lines";
+			String lo="Lines Out:              \t"+linesOut+" lines";
+			while(lo.length()<li.length()){lo=lo+" ";}
+
+			String ri="Reads In:               \t"+readsProcessed+" reads";
+			String ro="Reads Out:              \t"+readsOut+" reads";
+			while(ro.length()<ri.length()){ro=ro+" ";}
+
+			outstream.println(ri+"\t"+basesProcessed+" bases");
+			outstream.println(ro+"\t"+basesOut+" bases");
+			outstream.println(li);
+			outstream.println(lo);
+			outstream.println();
+			
+			outstream.println("Time:                         \t"+t);
+			outstream.println("Reads Processed:    "+rpstring+" \t"+String.format(Locale.ROOT, "%.2fk reads/sec", rpnano*1000000));
+			outstream.println("Lines Processed:    "+lpstring+" \t"+String.format(Locale.ROOT, "%.2fk reads/sec", lpnano*1000000));
+			outstream.println("Bases Processed:    "+bpstring+" \t"+String.format(Locale.ROOT, "%.2fm bases/sec", bpnano*1000));
+		}
+		
+		//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.");
+		}
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Inner Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/** Iterate through the reads */
+	void processInner(){
+		ByteFile bf=ByteFile.makeByteFile(ffin1);
+		TaxNode currentNode=null;
+		long currentSize=0;
+		ByteStreamWriter bsw=null;
+		for(byte[] line=bf.nextLine(); line!=null; line=bf.nextLine()){
+			linesProcessed++;
+			if(line.length>0){
+				final boolean header=(line[0]=='>');
+				if(header){
+					if(maxReads>0 && readsProcessed>=maxReads){break;}
+					readsProcessed++;
+					if(currentNode!=null){nodes.put(currentNode, nodes.get(currentNode)+currentSize);}
+					
+					final TaxNode tn=tree.parseNodeFromHeader(new String(line, 1, line.length-1), false);
+					
+					if(tn==null || tn!=currentNode){
+						if(bsw!=null){errorState=bsw.poisonAndWait()|errorState; bsw=null;}
+					}
+					if(tn!=null && tn!=currentNode){
+						String dir=tree.toDir(tn, outPath);
+						final boolean found=nodes.containsKey(tn);
+						if(!found){nodes.put(tn, 0L);}
+						FileFormat ff=FileFormat.testOutput(dir+prefix+tn.id+".fa.gz", FileFormat.FASTA, null, true, overwrite && !found, found, false);
+						bsw=new ByteStreamWriter(ff);
+						bsw.start();
+					}
+					
+					currentNode=tn;
+					currentSize=0;
+					if(bsw!=null){readsOut++;}
+				}else{
+					basesProcessed+=line.length;
+					currentSize+=line.length;
+				}
+				if(bsw!=null){
+					linesOut++;
+					if(!header){basesOut+=line.length;}
+					bsw.println(line);
+				}
+			}
+		}
+		if(bsw!=null){
+			errorState=bsw.poisonAndWait()|errorState; bsw=null;
+			if(currentNode!=null){nodes.put(currentNode, nodes.get(currentNode)+currentSize);}
+		}
+		bf.close();
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------            Fields            ----------------*/
+	/*--------------------------------------------------------------*/
+
+	/** Primary input file path */
+	private String in1=null;
+
+	/** Primary output file path */
+	private String outPath=null;
+	
+	private String prefix;
+	
+	/** Override input file extension */
+	private String extin=null;
+	
+	/** For listing what is present in the output */
+	public String resultsFile=null;
+	
+	public String taxTreeFile=null;
+	
+	public boolean makeDirectories=true;
+	
+	public LinkedHashMap<TaxNode, Long> nodes=new LinkedHashMap<TaxNode, Long>();
+	
+	/*--------------------------------------------------------------*/
+
+	/** Number of reads processed */
+	protected long readsProcessed=0;
+	/** Number of lines processed */
+	protected long linesProcessed=0;
+	/** Number of bases processed */
+	protected long basesProcessed=0;
+
+	/** Number of reads out */
+	public long readsOut=0;
+	/** Number of lines out */
+	public long linesOut=0;
+	/** Number of bases out */
+	public long basesOut=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;
+	
+	private final TaxTree tree;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        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=true;
+	
+}